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Silva FLD, de Medeiros BAS, Farrell BD. Once upon a fly: The biogeographical odyssey of Labrundinia (Chironomidae, Tanypodinae), an aquatic non-biting midge towards diversification. Mol Phylogenet Evol 2024; 194:108025. [PMID: 38342160 DOI: 10.1016/j.ympev.2024.108025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2023] [Revised: 01/17/2024] [Accepted: 02/04/2024] [Indexed: 02/13/2024]
Abstract
Labrundinia is a highly recognizable lineage in the Pentaneurini tribe (Diptera, Chironomidae). The distinct predatory free-swimming larvae of this genus are typically present in unpolluted aquatic environments, such as small streams, ponds, lakes, and bays. They can be found on the bottom mud, clinging to rocks and wood, and dwelling among aquatic vegetation. Labrundinia has been extensively studied in ecological research and comprises 39 species, all but one of which has been described from regions outside the Palearctic. Earlier phylogenetic studies have suggested that the initial diversification of the genus likely occurred in the Neotropical Region, with its current presence in the Nearctic Region and southern South America being the result of subsequent dispersal events. Through the integration of molecular and morphological data in a calibrated phylogeny, we reveal a complex and nuanced evolutionary history for Labrundinia, providing insights into its biogeographical and diversification patterns. In this comprehensive study, we analyze a dataset containing 46 Labrundinia species, totaling 10,662 characters, consisting of 10,616 nucleotide sites and 46 morphological characters. The molecular data was generated mainly by anchored enrichment hybrid methods. Using this comprehensive dataset, we inferred the phylogeny of the group based on a total evidence matrix. Subsequently, we employed the generated tree for time calibration and further analysis of biogeography and diversification patterns. Our findings reveal multiple dispersal events out of the Neotropics, where the group originated in the late Cretaceous approximately 72 million years ago (69-78 Ma). We further reveal that the genus experienced an early burst of diversification rates during the Paleocene, which gradually decelerated towards the present-day. We also find that the Neotropics have played a pivotal role in the evolution of Labrundinia by serving as both a cradle and a museum. By "cradle," we mean that the region has been a hotspot for the origin and diversification of new Labrundinia lineages, while "museum" refers to the region's ability to preserve ancestral lineages over extended periods. In summary, our findings indicate that the Neotropics have been a key source of genetic diversity for Labrundinia, resulting in the development of distinctive adaptations and characteristics within the genus. This evidence highlights the crucial role that these regions have played in shaping the evolutionary trajectory of Labrundinia.
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Affiliation(s)
- Fabio Laurindo da Silva
- Laboratory of Aquatic Insect Biodiversity and Ecology, Department of Zoology, Institute of Biosciences, University of São Paulo, São Paulo, Brazil; Museum of Comparative Zoology, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, USA.
| | - Bruno A S de Medeiros
- Field Museum of Natural History, Negaunee Integrative Research Center, Chicago, USA; Museum of Comparative Zoology, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, USA
| | - Brian D Farrell
- Museum of Comparative Zoology, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, USA
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Villalobos R, Aylagas E, Pearman JK, Curdia J, Coker D, Bell AC, Brown SD, Rowe K, Lozano-Cortés D, Rabaoui LJ, Marshell A, Qurban M, Jones B, Berumen ML, Carvalho S. Biodiversity patterns of the coral reef cryptobiota around the Arabian Peninsula. Sci Rep 2024; 14:9532. [PMID: 38664507 DOI: 10.1038/s41598-024-60336-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2024] [Accepted: 04/22/2024] [Indexed: 04/28/2024] Open
Abstract
The Arabian Peninsula accounts for approximately 6% of the world's coral reefs. Some thrive in extreme environments of temperature and salinity. Using 51 Autonomous Reef Monitoring Structure (ARMS), a standardized non-destructive monitoring device, we investigated the spatial patterns of coral reef cryptobenthic diversity in four ecoregions around the Arabian Peninsula and analyzed how geographical and/or environmental drivers shape those patterns. The mitochondrial cytochrome c oxidase subunit I (COI) gene was used to identify Amplicon Sequence Variants and assign taxonomy of the cryptobenthic organisms collected from the sessile and mobile fractions of each ARMS. Cryptobenthic communities sampled from the two ecoregions in the Red Sea showed to be more diverse than those inhabiting the Arabian (Persian) Gulf and the Gulf of Oman. Geographic distance revealed a stronger relationship with beta diversity in the Mantel partial correlation than environmental distance. However, the two mobile fractions (106-500 µm and 500-2000 µm) also had a significant correlation between environmental distance and beta diversity. In our study, dispersal limitations explained the beta diversity patterns in the selected reefs, supporting the neutral theory of ecology. Still, increasing differences in environmental variables (environmental filtering) also had an effect on the distribution patterns of assemblages inhabiting reefs within short geographic distances. The influence of geographical distance in the cryptofauna assemblages makes these relevant, yet usually ignored, communities in reef functioning vulnerable to large scale coastal development and should be considered in ecosystem management of such projects.
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Affiliation(s)
- Rodrigo Villalobos
- King Abdullah University of Science and Technology (KAUST), Red Sea Research Center, 23955-6900, Thuwal, Kingdom of Saudi Arabia
| | - Eva Aylagas
- King Abdullah University of Science and Technology (KAUST), Red Sea Research Center, 23955-6900, Thuwal, Kingdom of Saudi Arabia
| | - John K Pearman
- King Abdullah University of Science and Technology (KAUST), Red Sea Research Center, 23955-6900, Thuwal, Kingdom of Saudi Arabia
- Coastal and Freshwater Group, Cawthron Institute, Nelson, New Zealand
| | - Joao Curdia
- King Abdullah University of Science and Technology (KAUST), Red Sea Research Center, 23955-6900, Thuwal, Kingdom of Saudi Arabia
| | - Darren Coker
- King Abdullah University of Science and Technology (KAUST), Red Sea Research Center, 23955-6900, Thuwal, Kingdom of Saudi Arabia
| | - Alyssa Clothilde Bell
- King Abdullah University of Science and Technology (KAUST), Red Sea Research Center, 23955-6900, Thuwal, Kingdom of Saudi Arabia
- Department of Biology, University of Konstanz, Konstanz, Germany
| | - Shannon D Brown
- King Abdullah University of Science and Technology (KAUST), Red Sea Research Center, 23955-6900, Thuwal, Kingdom of Saudi Arabia
- Cooperative Institute for Climate, Ocean, and Ecosystem Studies, University of Washington, Seattle, WA, USA
| | - Katherine Rowe
- King Abdullah University of Science and Technology (KAUST), Red Sea Research Center, 23955-6900, Thuwal, Kingdom of Saudi Arabia
- School of Science, The University of Waikato, Hamilton, New Zealand
| | | | - Lotfi J Rabaoui
- Center for Environment & Marine Studies, Research Institute, King Fahd University of Petroleum and Minerals, 31261, Dhahran, Eastern Province, Kingdom of Saudi Arabia
- National Center for Wildlife, Riyadh, Saudi Arabia
| | - Alyssa Marshell
- Sultan Qaboos University, Al Seeb Al Khoudh SQU SEPS, 123, Muscat, Oman
- Institute for Marine and Antarctic Studies, University of Tasmania, Hobart, TAS, 7053, Australia
| | - Mohammad Qurban
- Center for Environment & Marine Studies, Research Institute, King Fahd University of Petroleum and Minerals, 31261, Dhahran, Eastern Province, Kingdom of Saudi Arabia
- Ministry of Environment, Water and Agriculture, Riyadh, Saudi Arabia
| | - Burton Jones
- King Abdullah University of Science and Technology (KAUST), Red Sea Research Center, 23955-6900, Thuwal, Kingdom of Saudi Arabia
| | - Michael Lee Berumen
- King Abdullah University of Science and Technology (KAUST), Red Sea Research Center, 23955-6900, Thuwal, Kingdom of Saudi Arabia
| | - Susana Carvalho
- King Abdullah University of Science and Technology (KAUST), Red Sea Research Center, 23955-6900, Thuwal, Kingdom of Saudi Arabia.
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Almeida-Silva D, Servino LM, Pontes-Nogueira M, Sawaya RJ. Marine introgressions and Andean uplift have driven diversification in neotropical Monkey tree frogs (Anura, Phyllomedusinae). PeerJ 2024; 12:e17232. [PMID: 38646479 PMCID: PMC11027904 DOI: 10.7717/peerj.17232] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Accepted: 03/21/2024] [Indexed: 04/23/2024] Open
Abstract
The species richness in the Neotropics has been linked to environmental heterogeneity and a complex geological history. We evaluated which biogeographic processes were associated with the diversification of Monkey tree frogs, an endemic clade from the Neotropics. We tested two competing hypotheses: the diversification of Phyllomedusinae occurred either in a "south-north" or a "north-south" direction in the Neotropics. We also hypothesized that marine introgressions and Andean uplift had a crucial role in promoting their diversification. We used 13 molecular markers in a Bayesian analysis to infer phylogenetic relationships among 57 species of Phyllomedusinae and to estimate their divergence times. We estimated ancestral ranges based on 12 biogeographic units considering the landscape modifications of the Neotropical region. We found that the Phyllomedusinae hypothetical ancestor range was probably widespread throughout South America, from Western Amazon to Southern Atlantic Forest, at 29.5 Mya. The Phyllomedusines' ancestor must have initially diverged through vicariance, generally followed by jump-dispersals and sympatric speciation. Dispersal among areas occurred mostly from Western Amazonia towards Northern Andes and the South American diagonal of dry landscapes, a divergent pattern from both "south-north" and "north-south" diversification hypotheses. Our results revealed a complex diversification process of Monkey tree frogs, occurring simultaneously with the orogeny of Northern Andes and the South American marine introgressions in the last 30 million years.
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Affiliation(s)
- Diego Almeida-Silva
- Centro de Ciências Naturais e Humanas, Universidade Federal do ABC, São Bernardo do Campo, São Paulo, Brazil
- Miguel Lillo, Unidad Ejecutora Lillo, San Miguel de Tucumán, Tucumán, Argentina
| | - Leonardo Matheus Servino
- Centro de Ciências Naturais e Humanas, Universidade Federal do ABC, São Bernardo do Campo, São Paulo, Brazil
- Instituto de Biociências, Universidade de São Paulo, São Paulo, São Paulo, Brazil
| | - Matheus Pontes-Nogueira
- Centro de Ciências Naturais e Humanas, Universidade Federal do ABC, São Bernardo do Campo, São Paulo, Brazil
| | - Ricardo J. Sawaya
- Centro de Ciências Naturais e Humanas, Universidade Federal do ABC, São Bernardo do Campo, São Paulo, Brazil
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Maslin M, Paix B, van der Windt N, Ambo-Rappe R, Debitus C, Gaertner-Mazouni N, Ho R, de Voogd NJ. Prokaryotic communities of the French Polynesian sponge Dactylospongia metachromia display a site-specific and stable diversity during an aquaculture trial. Antonie Van Leeuwenhoek 2024; 117:65. [PMID: 38602593 PMCID: PMC11008079 DOI: 10.1007/s10482-024-01962-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2024] [Accepted: 03/28/2024] [Indexed: 04/12/2024]
Abstract
Dynamics of microbiomes through time are fundamental regarding survival and resilience of their hosts when facing environmental alterations. As for marine species with commercial applications, such as marine sponges, assessing the temporal change of prokaryotic communities allows us to better consider the adaptation of sponges to aquaculture designs. The present study aims to investigate the factors shaping the microbiome of the sponge Dactylospongia metachromia, in a context of aquaculture development in French Polynesia, Rangiroa, Tuamotu archipelago. A temporal approach targeting explants collected during farming trials revealed a relative high stability of the prokaryotic diversity, meanwhile a complementary biogeographical study confirmed a spatial specificity amongst samples at different longitudinal scales. Results from this additional spatial analysis confirmed that differences in prokaryotic communities might first be explained by environmental changes (mainly temperature and salinity), while no significant effect of the host phylogeny was observed. The core community of D. metachromia is thus characterized by a high spatiotemporal constancy, which is a good prospect for the sustainable exploitation of this species towards drug development. Indeed, a microbiome stability across locations and throughout the farming process, as evidenced by our results, should go against a negative influence of sponge translocation during in situ aquaculture.
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Affiliation(s)
- Mathilde Maslin
- Univ Polynesie Française, Ifremer, ILM, IRD, EIO UMR 241, Tahiti, French Polynesia
| | - Benoît Paix
- Naturalis Biodiversity Center, PO Box 9517, 2300 RA, Leiden, the Netherlands.
| | - Niels van der Windt
- Naturalis Biodiversity Center, PO Box 9517, 2300 RA, Leiden, the Netherlands
- Institute of Environmental Sciences (CML), Leiden University, PO Box 9518, 2300 RA, Leiden, the Netherlands
| | - Rohani Ambo-Rappe
- Faculty of Marine Science and Fisheries, Department of Marine Science, Hasanuddin University, Makassar, Indonesia
| | - Cécile Debitus
- IRD, Univ Brest, CNRS, Ifremer, LEMAR, 29280, Plouzané, France
| | | | - Raimana Ho
- Univ Polynesie Française, Ifremer, ILM, IRD, EIO UMR 241, Tahiti, French Polynesia
| | - Nicole J de Voogd
- Naturalis Biodiversity Center, PO Box 9517, 2300 RA, Leiden, the Netherlands.
- Institute of Biology (IBL), Leiden University, 2333 BE, PO Box 9505, Leiden, the Netherlands.
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Wang Z, Liu X, Wang X, Wang H, Sun Y, Zhang J, Li H. Contrasting benthic bacterial and fungal communities in two temperate coastal areas affected by different levels of anthropogenic pressure. Mar Environ Res 2024; 198:106501. [PMID: 38615486 DOI: 10.1016/j.marenvres.2024.106501] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2023] [Revised: 03/19/2024] [Accepted: 04/08/2024] [Indexed: 04/16/2024]
Abstract
Benthic microbial communities play a crucial role in maintaining the stability and function of estuarine ecosystems. However, their organization and response to multiple stresses in severely disturbed coastal areas remains to be elucidated. In this study, we revealed the presence of contrasting benthic bacterial and fungal communities in the Liaohe (LH) and Yalujiang (YLJ) estuaries, which are located at similar latitudes and are characterized by similar climates but are subjected to different levels of anthropogenic pressure. The results showed that Firmicutes and Chloroflexi were more abundant in LH, which reflected the influence of anthropogenic pressure in this area. Functional analyses indicated that the functional genes involved in the generation of precursor metabolites and energy pathways were more enriched in the LH community, while genes regulating degradation/utilization/assimilation processes were more enriched in the YLJ community. Distance-dependent similarity analysis showed that the bacterial community in LH was more affected by environmental changes, while that in YLJ was more influenced by geographic dispersion. In contrast, no significant distance-dependent similarity was found for the fungal communities in the two areas. In addition, the network analysis showed that the bacterial-fungal network in YLJ was more complex and stable than that in the LH. Our results highlight the important roles of environmental heterogeneity in controlling microbial community composition, biogeographic patterns, and co-occurrence networks. These findings fill knowledge gaps in the understanding of the different response patterns of benthic communities under varying anthropogenic pressures.
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Affiliation(s)
- Zhen Wang
- College of Marine Technology and Environment, Dalian Ocean University, Dalian, 116023, China; State Environmental Protection Key Laboratory of Coastal Ecosystem, National Marine Environmental Monitoring Center, Dalian, 116023, China
| | - Xiaohan Liu
- State Environmental Protection Key Laboratory of Coastal Ecosystem, National Marine Environmental Monitoring Center, Dalian, 116023, China
| | - Xiaocheng Wang
- State Environmental Protection Key Laboratory of Coastal Ecosystem, National Marine Environmental Monitoring Center, Dalian, 116023, China
| | - Haining Wang
- State Environmental Protection Key Laboratory of Coastal Ecosystem, National Marine Environmental Monitoring Center, Dalian, 116023, China
| | - Yi Sun
- State Environmental Protection Key Laboratory of Coastal Ecosystem, National Marine Environmental Monitoring Center, Dalian, 116023, China
| | - Jinyong Zhang
- State Environmental Protection Key Laboratory of Coastal Ecosystem, National Marine Environmental Monitoring Center, Dalian, 116023, China
| | - Hongjun Li
- State Environmental Protection Key Laboratory of Coastal Ecosystem, National Marine Environmental Monitoring Center, Dalian, 116023, China.
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Sato S, Derkarabetian S, Valdez-Mondragón A, Pérez-González A, Benavides LR, Daniels SR, Giribet G. Under the hood: Phylogenomics of hooded tick spiders (Arachnida, Ricinulei) uncovers discordance between morphology and molecules. Mol Phylogenet Evol 2024; 193:108026. [PMID: 38341007 DOI: 10.1016/j.ympev.2024.108026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Revised: 11/14/2023] [Accepted: 02/04/2024] [Indexed: 02/12/2024]
Abstract
Ricinulei or hooded tick-spiders are a cryptic and ancient group of arachnids. The order consists of around 100 highly endemic extant species restricted to the Afrotropics and the Neotropics along with 22 fossil species. Their antiquity and low vagility make them an excellent group with which to interrogate biogeographic questions. To date, only four molecular analyses have been conducted on the group and they failed to resolve the relationships of the main lineages and even recovering the non-monophyly of the three genera. These studies were limited to a few Sanger loci or phylogenomic analyses with at most seven ingroup samples. To increase phylogenetic resolution in this little-understood and poorly studied group, we present the most comprehensive phylogenomic study of Ricinulei to date leveraging the Arachnida ultra-conserved element probe set. With a data set of 473 loci across 96 ingroup samples, analyses resolved a monophyletic Neotropical clade consisting of four main lineages. Two of them correspond to the current genera Cryptocellus and Pseudocellus while topology testing revealed one lineage to likely be a phylogenetic reconstruction artefact. The fourth lineage, restricted to Northwestern, Andean South America, is consistent with the Cryptocellus magnus group, likely corresponding to the historical genus Heteroricinoides. Since we did not sample the type species for this old genus, we do not formally re-erect Heteroricinoides but our data suggest the need for a thorough morphological re-examination of Neotropical Ricinulei.
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Affiliation(s)
- Shoyo Sato
- Museum of Comparative Zoology, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA.
| | - Shahan Derkarabetian
- Museum of Comparative Zoology, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA
| | - Alejandro Valdez-Mondragón
- Collection of Arachnology (CARCIB), Programa Académico de Planeación Ambiental y Conservación (PLAYCO), Centro de Investigaciones Biológicas del Noroeste (CIBNOR), S.C., La Paz, Baja California Sur, Mexico
| | - Abel Pérez-González
- Museo Argentino de Ciencias Naturales "Bernardino Rivadavia", Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - Ligia R Benavides
- Museum of Comparative Zoology, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA
| | - Savel R Daniels
- Department of Botany and Zoology, Private Bag X1, Stellenbosch University, Matieland, Stellenbosch, South Africa
| | - Gonzalo Giribet
- Museum of Comparative Zoology, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA
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Wang B, Ma B, Zhang Y, Stirling E, Yan Q, He Z, Liu Z, Yuan X, Zhang H. Global diversity, coexistence and consequences of resistome in inland waters. Water Res 2024; 253:121253. [PMID: 38350193 DOI: 10.1016/j.watres.2024.121253] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Revised: 01/04/2024] [Accepted: 02/01/2024] [Indexed: 02/15/2024]
Abstract
Human activities have long impacted the health of Earth's rivers and lakes. These inland waters, crucial for our survival and productivity, have suffered from contamination which allows the formation and spread of antibiotic-resistant genes (ARGs) and consequently, ARG-carrying pathogens (APs). Yet, our global understanding of waterborne pathogen antibiotic resistance remains in its infancy. To shed light on this, our study examined 1240 metagenomic samples from both open and closed inland waters. We identified 22 types of ARGs, 19 types of mobile genetic elements (MGEs), and 14 types of virulence factors (VFs). Our findings showed that open waters have a higher average abundance and richness of ARGs, MGEs, and VFs, with more robust co-occurrence network compared to closed waters. Out of the samples studied, 321 APs were detected, representing a 43 % detection rate. Of these, the resistance gene 'bacA' was the most predominant. Notably, AP hotspots were identified in regions including East Asia, India, Western Europe, the eastern United States, and Brazil. Our research underscores how human activities profoundly influence the diversity and spread of resistome. It also emphasizes that both abiotic and biotic factors play pivotal roles in the emergence of ARG-carrying pathogens.
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Affiliation(s)
- Binhao Wang
- School of Engineering, Hangzhou Normal University, Hangzhou 310018, PR China
| | - Bin Ma
- Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, PR China; Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou 310058, PR China
| | - Yinan Zhang
- School of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 310036, PR China
| | - Erinne Stirling
- Agriculture and Food, Commonwealth Scientific and Industrial Research Organisation, Adelaide 5064, Australia; School of Biological Sciences, The University of Adelaide, Adelaide 5005, Australia
| | - Qingyun Yan
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai 519080, PR China
| | - Zhili He
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai 519080, PR China
| | - Zhiquan Liu
- School of Engineering, Hangzhou Normal University, Hangzhou 310018, PR China
| | - Xia Yuan
- School of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 310036, PR China
| | - Hangjun Zhang
- School of Engineering, Hangzhou Normal University, Hangzhou 310018, PR China; Hangzhou International Urbanology Research Center and Center for Zhejiang Urban Governance Studies, Hangzhou, 311121, PR China.
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Farmer TA, Jansen RK. Out of Place: Phylogenomics resolves the placement of Eurasian taxa and sheds light on origin of Thermopsideae in North America. Mol Phylogenet Evol 2024; 193:108024. [PMID: 38341005 DOI: 10.1016/j.ympev.2024.108024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Revised: 01/16/2024] [Accepted: 02/01/2024] [Indexed: 02/12/2024]
Abstract
The North American Thermopsideae (Fabaceae: Papilionoideae), a monophyletic group comprising the North American endemic genus Baptisia, and the paraphyletic Eurasian-North American disjunct Thermopsis, is nested within the tribe Sophoreae. Previous phylogenetic studies have identified two East Asian taxa within the North American Thermopsideae, suggesting two independent dispersal events between North America-East Asia. More recent studies have also placed a third taxon, Vuralia turcica, an endemic species from Turkey, among the North American Thermopsideae. The presence of three geographically distant Eurasian taxa within a relatively young clade of North American origin is unprecedented among papilionoid legumes, and the biogeographic implications of this observation are not clear. To investigate this matter, 1540 low-copy nuclear genes and complete plastomes were obtained from 36 taxa across the core genistoids, including 26 newly sequenced taxa. Nuclear and plastome based maximum likelihood (ML) and ASTRAL analyses were conducted based on varying degrees of taxon coverage and read mapping consensus threshold values. Additional analyses were performed to estimate divergence times and to reconstruct biogeographic history. The results strongly support a previously undetected Old World clade, presently composed of V. turcica and T. chinensis, which diverged from the ancestor of the North American lineage during the mid to late Miocene. A single and recent North America-East Asia dispersal involving T. lupinoides is reported. Furthermore, the traditional inclusion of the genus Ammopiptanthus among Thermopsideae is not supported, and the monotypic generic status of Vuralia is called into question. A relatively high degree of cytonuclear discordance is reported within each sub-clade of the North American Thermopsideae. This finding is likely attributable to the high degree of interspecific hybridization reported within these groups and raises the need for more rigorous genome-scale testing to better delimit species within each of the reticulating subclades. Subjects: Biodiversity, Biogeography, Evolutionary Studies, Genetics, Plant Science.
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Affiliation(s)
- Todd A Farmer
- University of Texas at Austin, Department of Integrative Biology, Austin, TX, USA.
| | - Robert K Jansen
- University of Texas at Austin, Department of Integrative Biology, Austin, TX, USA
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9
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Amir Afzali Y, Naderloo R, Keikhosravi A, Klaus S. Phylogeography of the freshwater crab Potamon persicum (Decapoda: Potamidae): an ancestral ring species? J Hered 2024:esae016. [PMID: 38501510 DOI: 10.1093/jhered/esae016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2023] [Indexed: 03/20/2024] Open
Abstract
The Zagros Mountains, characterized by complex topography and three large drainage systems, harbor the endemic freshwater crab Potamon persicum in Iran. Our study delves into the evolutionary history of P. persicum, utilizing two mitochondrial and one nuclear marker. We collected 214 specimens from 24 localities, identifying 21 haplotypes grouped into two major evolutionary lineages. Substantial differentiation exists between drainage systems and lineages. Historical demographic analysis revealed a significant decrease in population size during the late-Holocene, accompanied by a recent population bottleneck. Species distribution modelling has revealed eastward shifts in suitable habitats between the last glacial maximum and the present day. Following the last glacial maximum, habitat fragmentation occurred, resulting in the establishment of small populations. These smaller populations are more vulnerable to climatic and geological events, thereby limiting gene flow and accelerating genetic differentiation within species. Historical biogeographic analysis traced the origin of P. persicum to the western Zagros Mountains, with major genetic divergence occurring during the Pleistocene. Our genetic analyses suggest that P. persicum may have shown a genetic pattern similar to a classical ring species before the Pleistocene. The Namak Lake sub-basin could have served as a contact zone where populations did not interbreed but were connected through gene flow in a geographic ring. Currently genetic separation is evident between basins, indicating that P. persicum in the Zagros Mountains is not a contemporary ring species. Also, our biogeographical analysis estimated that range evolution may have been driven initially by dispersal, and only during the late Pleistocene by vicariance.
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Affiliation(s)
- Yaser Amir Afzali
- School of Biology, College of Science, University of Tehran, Tehran, 1417935840, Iran
| | - Reza Naderloo
- School of Biology, College of Science, University of Tehran, Tehran, 1417935840, Iran
| | - Alireza Keikhosravi
- Department of Biology, Hakim Sabzevari University, Sabzevar, 9617976487, Iran
| | - Sebastian Klaus
- Environmental Resources Management, ERM GmbH, Neu-Isenburg, Siemensstr. 9 · 63263, Germany
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Chavez DE, Hains T, Espinoza S, Wayne RK, Chaves J. Whole-genome analysis reveals the diversification of Galapagos rail (Aves: Rallidae) and confirms the success of goat eradication programs. J Hered 2024:esae017. [PMID: 38498380 DOI: 10.1093/jhered/esae017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Indexed: 03/20/2024] Open
Abstract
Similar to other insular birds around the world, the Galapagos rail (Laterallus spilonota Gould, 1841) exhibits reduced flight capacity following its colonization of the archipelago ~1.2 mya. Despite their short evolutionary history, rails have colonized seven different islands spanning the entire width of the archipelago. Galapagos rails were once common on islands with sufficiently high altitudes to support shrubs in humid habitats. After humans introduced goats, this habitat was severely reduced due to overgrazing. Habitat loss devastated some rail populations, with less than 50 individuals surviving, rendering the genetic diversity of Galapagos rail a pressing conservation concern. Additionally, one enigma is the reappearance of rails on the island of Pinta after they were considered extirpated. Our approach was to investigate the evolutionary history and geographic distribution of Galapagos rails as well as examine the genome-wide effects of historical population bottlenecks using 39 whole genomes across different island populations. We recovered an early divergence of rail ancestors leading to the isolated populations on Pinta and a second clade comprising the rest of the islands, historically forming a single landmass. Subsequently, the separation of the landmass ~900 kya may have led to the isolation of the Isabela population with more panmictic populations found on Santa Cruz and Santiago islands. We found that rails genomes contain long runs of homozygosity (>2Mb) that could be related to the introduction of goats. Finally, our findings show that the modern eradication of goats was critical to avoiding episodes of inbreeding in most populations.
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Affiliation(s)
- Daniel E Chavez
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, Los Angeles, California 90095, USA
- School of Biology. Pontifical Catholic University of Ecuador, Av. 12 de Octubre, Quito 170901, Ecuador
- Arizona Cancer Evolution Center, The Biodesign Institute, Arizona State University, Tempe, AZ School of Life Sciences, Arizona State University, Tempe, AZ
| | - Taylor Hains
- Committee on Evolutionary Biology, University of Chicago, Illinois, Chicago 60637, USA
- Negaunee Integrative Research Center, The Field Museum, Illinois, Chicago, 60605, USA
- Grainger Bioinformatics Center, The Field Museum, Chicago, Illinois, Chicago, 60605, USA
| | - Sebastian Espinoza
- School of Medicine. Pontifical Catholic University of Ecuador, Av. 12 de Octubre, Quito 170901, Ecuador
| | - Robert K Wayne
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, Los Angeles, California 90095, USA
| | - Jaime Chaves
- Department of Biology, San Francisco State University, San Francisco, CA 94132-1722, USA
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11
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Lavery TH, DeRaad DA, Holland PS, Olson KV, DeCicco LH, Seddon JM, Leung LKP, Moyle RG. Parallel evolution in an island archipelago revealed by genomic sequencing of Hipposideros leaf-nosed bats. Evolution 2024:qpae039. [PMID: 38457362 DOI: 10.1093/evolut/qpae039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2023] [Indexed: 03/10/2024]
Abstract
Body size is a key morphological attribute, often used to delimit species boundaries among closely related taxa. But body size can evolve in parallel, reaching similar final states despite independent evolutionary and geographic origins, leading to faulty assumptions of evolutionary history. Here we document parallel evolution in body size in the widely distributed leaf-nosed bat genus Hipposideros, which has misled both taxonomic and evolutionary inference. We sequenced reduced representation genomic loci and measured external morphological characters from three closely related species from the Solomon Islands archipelago, delimited by body size. Species tree reconstruction confirms the paraphyly of two morphologically designated species. The non-sister relationship between large-bodied H. dinops lineages found on different islands indicates large-bodied ecomorphs have evolved independently at least twice in the history of this radiation. A lack of evidence for gene flow between sympatric, closely related taxa suggests the rapid evolution of strong reproductive isolating barriers between morphologically distinct populations. Our results position Solomon Islands Hipposideros as a novel vertebrate system for studying the repeatability of parallel evolution under natural conditions. We conclude by offering testable hypotheses for how geography and ecology could be mediating the repeated evolution of large-bodied Hipposideros lineages in the Solomon Islands.
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Affiliation(s)
- Tyrone H Lavery
- School of BioSciences, The University of Melbourne, Melbourne, VIC 3010, Australia
- Biodiversity Institute and Department of Ecology and Evolutionary Biology, The University of Kansas, Lawrence, KS 66045, USA
| | - Devon A DeRaad
- Biodiversity Institute and Department of Ecology and Evolutionary Biology, The University of Kansas, Lawrence, KS 66045, USA
| | - Piokera S Holland
- Ecological Solutions Solomon Islands, Gizo, Western Province, Solomon Islands
| | - Karen V Olson
- Biodiversity Institute and Department of Ecology and Evolutionary Biology, The University of Kansas, Lawrence, KS 66045, USA
- Department of Earth and Environmental Sciences, Rutgers University, Newark, USA
| | - Lucas H DeCicco
- Biodiversity Institute and Department of Ecology and Evolutionary Biology, The University of Kansas, Lawrence, KS 66045, USA
| | - Jennifer M Seddon
- Research Division, James Cook University, Townsville, QLD 4811, Australia
| | | | - Robert G Moyle
- Biodiversity Institute and Department of Ecology and Evolutionary Biology, The University of Kansas, Lawrence, KS 66045, USA
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12
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Csordas M, Starko S, Neufeld CJ, Thompson SA, Baum JK. Multiscale stability of an intertidal kelp (Postelsia palmaeformis) near its northern range edge through a period of prolonged heatwaves. Ann Bot 2024; 133:61-72. [PMID: 37878014 PMCID: PMC10921842 DOI: 10.1093/aob/mcad148] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Accepted: 10/06/2023] [Indexed: 10/26/2023]
Abstract
BACKGROUND AND AIMS Climate change, including gradual changes and extreme weather events, is driving widespread species losses and range shifts. These climatic changes are felt acutely in intertidal ecosystems, where many organisms live close to their thermal limits and experience the extremes of both marine and terrestrial environments. A recent series of multiyear heatwaves in the northeast Pacific Ocean might have impacted species even towards their cooler, northern range edges. Among them, the high intertidal kelp Postelsia palmaeformis has traits that could make it particularly vulnerable to climate change, but it is critically understudied. METHODS In 2021 and 2022, we replicated in situ and aerial P. palmaeformis surveys that were conducted originally in 2006 and 2007, in order to assess the state of northern populations following recent heatwaves. Changes in P. palmaeformis distribution, extent, density and morphometrics were assessed between these two time points over three spatial scales, ranging from 250 m grid cells across the entire 167 km study region, to within grid cells and the individual patch. KEY RESULTS We found evidence consistent with population stability at all three scales: P. palmaeformis remained present in all 250 m grid cells in the study region where it was previously found, and neither the extent within cells nor the patch density changed significantly between time points. However, there was evidence of slight distributional expansion, increased blade lengths and a shift to earlier reproductive timing. CONCLUSIONS We suggest that apparent long-term stability of P. palmaeformis might be attributable to thermal buffering near its northern range edge and from the wave-exposed coastlines it inhabits, which may have decreased the impacts of heatwaves. Our results highlight the importance of multiscale assessments when examining changes within species and populations, in addition to the importance of dispersal capability and local conditions in regulating the responses of species to climate change.
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Affiliation(s)
- Matthew Csordas
- Department of Biology, University of Victoria, Victoria, BC, V8W 2Y2, Canada
| | - Samuel Starko
- Department of Biology, University of Victoria, Victoria, BC, V8W 2Y2, Canada
- UWA Oceans Institute and School of Biological Sciences, University of Western Australia, Crawley, WA 6009, Australia
| | - Christopher J Neufeld
- Department of Biology, University of Victoria, Victoria, BC, V8W 2Y2, Canada
- The Kelp Rescue Initiative, Bamfield Marine Sciences Centre, Bamfield, BC, V0R 1B0, Canada
- Department of Biology, University of British Columbia Okanogan, Kelowna, BC, V1V 1V7, Canada
| | | | - Julia K Baum
- Department of Biology, University of Victoria, Victoria, BC, V8W 2Y2, Canada
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13
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Vacher JP, Kok PJR, Rodrigues MT, Lima A, Hrbek T, Werneck FP, Manzi S, Thébaud C, Fouquet A. Diversification of the terrestrial frog genus Anomaloglossus (Anura, Aromobatidae) in the Guiana Shield proceeded from highlands to lowlands, with successive loss and reacquisition of endotrophy. Mol Phylogenet Evol 2024; 192:108008. [PMID: 38181828 DOI: 10.1016/j.ympev.2023.108008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2022] [Revised: 09/23/2023] [Accepted: 12/30/2023] [Indexed: 01/07/2024]
Abstract
Two main landscapes emerge from the Guiana Shield: the highlands to the west called the Pantepui region and the Amazonian lowlands to the east, both harbouring numerous endemic species. With 32 currently recognized species, the genus Anomaloglossus stands out among Neotropical frogs as one that diversified only within the Guiana Shield both in the highlands and the lowlands. We present a time-calibrated phylogeny obtained by using combined mitogenomic and nuclear DNA, which suggests that the genus originates from Pantepui where extant lineages started diversifying around 21 Ma, and subsequently (ca. 17 Ma) dispersed during the Miocene Climatic Optimum to the lowlands of the eastern Guiana Shield where the ability to produce endotrophic tadpoles evolved. Further diversification within the lowlands in the A. stepheni group notably led to an evolutionary reversal toward exotrophy in one species group during the late Miocene, followed by reacquisition of endotrophy during the Pleistocene. These successive shifts of reproductive mode seem to have accompanied climatic oscillations. Long dry periods might have triggered evolution of exotrophy, whereas wetter climates favoured endotrophic forms, enabling colonization of terrestrial habitats distant from water. Acquisition, loss, and reacquisition of endotrophy makes Anomaloglossus unique among frogs and may largely explain the current species diversity. The micro evolutionary processes involved in these rapid shifts of reproductive mode remain to be revealed.
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Affiliation(s)
- Jean-Pierre Vacher
- Centre de Recherche sur la Biodiversité et l'Environnement (CRBE), UMR 5300 CNRS-IRD-TINP-UPS3, Université Paul Sabatier, Toulouse, France.
| | - Philippe J R Kok
- Department of Ecology and Vertebrate Zoology, Faculty of Biology and Environmental Protection, University of Łódź, 12/16 Banacha Str, Łódź 90-237, Poland; Department of Life Sciences, The Natural History Museum, Cromwell Road, London SW7 5BD, United Kingdom
| | - Miguel Trefaut Rodrigues
- Universidade de São Paulo, Instituto de Biociências, Departamento de Zoologia, Caixa Postal 11.461, CEP 05508-090 São Paulo, Brazil
| | - Albertina Lima
- Instituto Nacional de Pesquisas da Amazônia, Coordenação de Biodiversidade, Avenida André Araújo 2936, 69080-971 Manaus, AM, Brazil
| | - Tomas Hrbek
- Departamento de Biologia, Instituto de Ciências Biológicas, Universidade Federal do Amazonas, 69080-900 Manaus, AM, Brazil
| | - Fernanda P Werneck
- Instituto Nacional de Pesquisas da Amazônia, Coordenação de Biodiversidade, Avenida André Araújo 2936, 69080-971 Manaus, AM, Brazil
| | - Sophie Manzi
- Centre de Recherche sur la Biodiversité et l'Environnement (CRBE), UMR 5300 CNRS-IRD-TINP-UPS3, Université Paul Sabatier, Toulouse, France
| | - Christophe Thébaud
- Centre de Recherche sur la Biodiversité et l'Environnement (CRBE), UMR 5300 CNRS-IRD-TINP-UPS3, Université Paul Sabatier, Toulouse, France
| | - Antoine Fouquet
- Centre de Recherche sur la Biodiversité et l'Environnement (CRBE), UMR 5300 CNRS-IRD-TINP-UPS3, Université Paul Sabatier, Toulouse, France
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14
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Ren P, Sun A, Jiao X, Chen QL, Li F, He JZ, Hu HW. National-scale investigation reveals the dominant role of phyllosphere fungal pathogens in sorghum yield loss. Environ Int 2024; 185:108511. [PMID: 38382404 DOI: 10.1016/j.envint.2024.108511] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Revised: 02/06/2024] [Accepted: 02/16/2024] [Indexed: 02/23/2024]
Abstract
Fungal plant pathogens threaten crop production and sustainable agricultural development. However, the environmental factors driving their diversity and nationwide biogeographic model remain elusive, impacting our capacity to predict their changes under future climate scenarios. Here, we analyzed potential fungal plant pathogens from 563 samples collected from 57 agricultural fields across China. Over 28.0% of fungal taxa in the phyllosphere were identified as potential plant pathogens, compared to 22.3% in the rhizosphere. Dominant fungal plant pathogen groups were Cladosporium (in the phyllosphere) and Fusarium (in the rhizosphere), with higher diversity observed in the phyllosphere than in rhizosphere soil. Deterministic processes played an important role in shaping the potential fungal plant pathogen community assembly in both habitats. Mean annual precipitation and temperature were the most important factor influencing phyllosphere fungal plant pathogen richness. Significantly negative relationships were found between fungal pathogen diversity and sorghum yield. Notably, compared to the rhizosphere, the phyllosphere fungal plant pathogen diversity played a more crucial role in sorghum yield. Together, our work provides novel insights into the factors governing the spatial patterns of fungal plant pathogens in the crop microbiome, and highlights the potential significance of aboveground phyllosphere fungal plant pathogens in crop productivity.
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Affiliation(s)
- Peixin Ren
- Key Laboratory for Humid Subtropical Eco-geographical Processes of the Ministry of Education, School of Geographical Sciences, Fujian Normal University, Fuzhou 350007, China
| | - Anqi Sun
- Key Laboratory of Urban Environment and Health, Ningbo Observation and Research Station, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; Zhejiang Key Laboratory of Urban Environmental Processes and Pollution Control, CAS Haixi Industrial Technology Innovation Center in Beilun, Ningbo 315830, China
| | - Xiaoyan Jiao
- College of Resource and Environment, Shanxi Agricultural University, Taiyuan 030031, China
| | - Qing-Lin Chen
- Key Laboratory of Urban Environment and Health, Ningbo Observation and Research Station, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; Zhejiang Key Laboratory of Urban Environmental Processes and Pollution Control, CAS Haixi Industrial Technology Innovation Center in Beilun, Ningbo 315830, China
| | - Fangfang Li
- Key Laboratory for Humid Subtropical Eco-geographical Processes of the Ministry of Education, School of Geographical Sciences, Fujian Normal University, Fuzhou 350007, China
| | - Ji-Zheng He
- School of Agriculture, Food and Ecosystem Sciences, Faculty of Science, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Hang-Wei Hu
- School of Agriculture, Food and Ecosystem Sciences, Faculty of Science, The University of Melbourne, Parkville, Victoria 3010, Australia.
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15
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Chang SC, Ahyong ST, Tsang LM. Molecular phylogeny of deep-sea blind lobsters of the family Polychelidae (Decapoda: Polychelida), with implications for the origin and evolution of these "living fossils". Mol Phylogenet Evol 2024; 192:107998. [PMID: 38142793 DOI: 10.1016/j.ympev.2023.107998] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Revised: 12/14/2023] [Accepted: 12/20/2023] [Indexed: 12/26/2023]
Abstract
A comprehensive molecular analysis of the deep-sea blind lobsters of the family Polychelidae, often referred to as "living fossils", is conducted based on all six modern genera and 27 of the 38 extant species. Using six genetic markers from both mitochondrial and nuclear genomes, the molecular phylogenetic results differ considerably from previous morphological analyses and reveal the genera Polycheles and Pentacheles to be para- or polyphyletic. As the splitting of Polycheles has strong support from both molecular and morphological data, two new genera, Dianecheles and Neopolycheles, are erected for those species excluded from the clade containing the type species of Polycheles. The pattern of polyphyly of Pentacheles, however, is not robustly resolved, so it is retained as a single genus. Fossil evidence suggests that fossil polychelids inhabited deep-sea environments as early as the Early to Middle Jurassic, demonstrating the enduring adaptation of extant polychelid species to the deep-sea. Time-calibrated phylogeny suggested that modern polychelids probably had an Atlantic origin during the Jurassic period. Since their emergence, this ancient lobster group has continued to diversify, particularly in the West Pacific, and has colonized the abyssal zone, with the deepest genus, Willemoesia, representing the more 'derived' members among extant polychelids. Differences in eye reduction among extant polychelid genera highlight the necessity for ongoing investigations to ascertain the relative degree of functionality of their eyes, if they indeed retain any function.
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Affiliation(s)
- Su-Ching Chang
- Department of Biological Resources, National Chiayi University, Chiayi 600355, Taiwan, ROC
| | - Shane T Ahyong
- Australian Museum, 1 William St, Sydney, NSW 2010, Australia; School of Biological, Earth & Environmental Sciences, University of New South Wales, Kensington, NSW 2052, Australia
| | - Ling-Ming Tsang
- Simon F. S. Li Marine Science Laboratory, School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong, China.
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16
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Shi Z, Meng Q, Luo Y, Zhang M, Han W. Broadleaf trees switch from phosphorus to nitrogen limitation at lower latitudes than conifers. Sci Total Environ 2024; 914:169924. [PMID: 38199381 DOI: 10.1016/j.scitotenv.2024.169924] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Revised: 12/13/2023] [Accepted: 01/03/2024] [Indexed: 01/12/2024]
Abstract
Nitrogen (N) and phosphorus (P) are common limiting elements for terrestrial ecosystem productivity. Understanding N-P nutrient limitations patterns is crucial for comprehending variations in productivity within terrestrial ecosystems. However, the global nutrient limitation patterns of woody plants, that dominate forests, especially across different functional types, remain unclear. Here, we compiled a global dataset of leaf N and P concentrations and resorption efficiency (NRE and PRE) to explore latitudinal nutrient limitation patterns in natural woody plants and their environmental drivers. Based on published fertilization experiments, we compiled another global woody plant nutrient database to validate such identified patterns. The results showed that with increasing latitude, the relative P vs N resorption efficiency (PRE minus NRE) and the N and P ratio decreased in woody plant leaves, suggesting that the nutrient status of woody plants shifts from P to N limitation as latitude increases, with a switching point of N-P balance occurring at mid-latitudes (42.9°-43.6°). Different functional types exhibited similar trends, but with different switching latitudes of N vs P limitation. Due to the lower N uptake capacity of broadleaves than conifers, broadleaves reached N-P balance at lower latitudes (39.6°-43.3°) than conifers (57.1°-59.1°) in both hemispheres. Data from fertilization experiments successfully identified 81 % of the N limitation cases and 91 % of the P limitation cases identified using the first database. N and P limitation cases for conifers and broadleaves were also well identified separately. The latitudinal nutrient limitations in global woody plants are primarily shaped by climate and soil. Our study demonstrates the switching latitudes of N vs P limitation which varies between broadleaves and conifers. These findings enhance our understanding of plant nutrient dynamics in global climate change and aid in refining forest management.
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Affiliation(s)
- Zhijuan Shi
- Key Laboratory of Plant-Soil Interactions, Ministry of Education, College of Resources and Environmental Sciences, China Agricultural University, Beijing 100193, China
| | - Qingquan Meng
- Key Laboratory of Plant-Soil Interactions, Ministry of Education, College of Resources and Environmental Sciences, China Agricultural University, Beijing 100193, China
| | - Yan Luo
- Key Laboratory of Oasis Ecology of Education Ministry, College of Ecology and Environment, Xinjiang University, Urumqi 830017, China
| | - Meixia Zhang
- Key Laboratory of Plant-Soil Interactions, Ministry of Education, College of Resources and Environmental Sciences, China Agricultural University, Beijing 100193, China
| | - Wenxuan Han
- Key Laboratory of Plant-Soil Interactions, Ministry of Education, College of Resources and Environmental Sciences, China Agricultural University, Beijing 100193, China.
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17
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Victor BC, Frable BW, Ludt WB. Halichoeres sanchezi n. sp., a new wrasse from the Revillagigedo Archipelago of Mexico, tropical eastern Pacific Ocean (Teleostei: Labridae). PeerJ 2024; 12:e16828. [PMID: 38436023 PMCID: PMC10908266 DOI: 10.7717/peerj.16828] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Accepted: 01/04/2024] [Indexed: 03/05/2024] Open
Abstract
A new labrid fish species, Halichoeres sanchezi n. sp., is described from eight specimens collected in the Revillagigedo Archipelago in the tropical eastern Pacific Ocean, off the coast of Mexico. The new species belongs to the Halichoeres melanotis species complex that is found throughout the region, differing by 2.4% in the mtDNA cytochrome c oxidase I sequence from its nearest relative, H. melanotis from Panama, and 2.9% from Halichoeres salmofasciatus from Cocos Island, off Costa Rica. The complex is distinguished from others in the region by having a black spot on the opercular flap and a prominent black area on the caudal fin of males. The juveniles and initial phase of the new species closely resemble those of H. salmofasciatus and Halichoeres malpelo from Malpelo Island of Colombia, differing in having an oblong black spot with a yellow dorsal margin on the mid-dorsal fin of initial-phase adults as well as on juveniles. In contrast, the terminal-phase male color pattern is distinct from other relatives, being vermilion to orangish brown with dark scale outlines, a white patch on the upper abdomen, and a prominent black band covering the posterior caudal peduncle and base of the caudal fin. The new species adds to the list of endemic fish species for the isolated archipelago and is an interesting case of island endemism in the region. The discovery was made during the joint 2022 collecting expedition to the archipelago, which featured a pioneering collaborative approach to an inventory of an island ichthyofauna, specifically including expert underwater photographers systematically documenting specimens in situ, before hand-collection, and then photographed fresh, tissue-sampled, and subsequently vouchered in museum collections.
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Affiliation(s)
- Benjamin C. Victor
- Guy Harvey Research Institute, Nova Southeastern University, Dania Beach, Florida, United States
- Marine Biology, Ocean Science Foundation, Irvine, California, United States
| | - Benjamin W. Frable
- Marine Vertebrate Collection, Scripps Institution of Oceanography, La Jolla, California, United States
| | - William B. Ludt
- Ichthyology, Natural History Museum of Los Angeles County, Los Angeles, California, United States
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18
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Boonmachai T, Bergey EA, Wongsawad C, Nantarat N. Influence of limestone and anthropogenic activities on land snail communities in Satun Province, Thailand. Sci Total Environ 2024; 912:169372. [PMID: 38104843 DOI: 10.1016/j.scitotenv.2023.169372] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/05/2023] [Revised: 12/11/2023] [Accepted: 12/12/2023] [Indexed: 12/19/2023]
Abstract
Southeast Asia is renowned for its rich biodiversity and serves as a global hotspot for organisms. Satun Province, located in southern Thailand, represents a significant biogeographic and biodiversity region situated in the transition zone between the Indochinese and Sundaland hotspots. Thus, Satun Province has high diversity and abundance of organisms, especially land snails. However, Satun Province has been largely understudied for both diversity and biogeography. Our study aimed to investigate land snail communities, emphasizing comparisons between the mainland and island sites, and the influence of limestone and other rock types in Satun Province. Our exploration efforts identified a diverse land snail community comprising 17 families, which updated the total reported species in the province from 22 to 58 species. The results showed that islands had significantly greater land snail species richness and abundance, and larger Shannon index values in comparison to the mainland. Anthropogenic activities on the mainland led to habitat transformation and had detrimental impacts on native land snail diversity while promoting the spread of invasive species. In contrast, the presence of little-disturbed limestone habitats on some of the islands contributed to higher richness of land snails, as limestone areas are known for their high diversity and endemism. Snail communities varied along site characteristics; especially, limestone versus non-limestone areas and human activity levels (which were associated with national park protection), with limestone and protected areas having the highest diversity. Our study illustrates the value of protected areas as potential hotspots of biodiversity, especially for islands that are little disturbed by human activities and that have habitats that support high diversity, such as limestone outcrops. This study provides valuable insights into the biogeography of land snails in Satun Province and Southeast Asia and contributes to our understanding of the factors influencing land snail diversity.
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Affiliation(s)
- Tuangthong Boonmachai
- Ph.D. Degree Program in Biology (International Program), Faculty of Science, Chiang Mai University, Chiang Mai 50200, Thailand; Department of Biology, Faculty of Science, Chiang Mai University, 50200, Thailand; Oklahoma Biological Survey, University of Oklahoma, Norman, OK 73019, United States of America
| | - Elizabeth A Bergey
- Department of Biology, Faculty of Science, Chiang Mai University, 50200, Thailand; Oklahoma Biological Survey, University of Oklahoma, Norman, OK 73019, United States of America
| | - Chalobol Wongsawad
- Department of Biology, Faculty of Science, Chiang Mai University, 50200, Thailand
| | - Nattawadee Nantarat
- Department of Biology, Faculty of Science, Chiang Mai University, 50200, Thailand; Environmental Science Research Center, Faculty of Science, Chiang Mai University, Chiang Mai 50200, Thailand; Science and Technology Research Institute, Chiang Mai University, Chiang Mai 50200, Thailand.
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19
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Liu Z, Fang J, He Y, Bending GD, Song B, Guo Y, Wang X, Fang Z, Adams JM. Distinct biogeographic patterns in Glomeromycotinian and Mucoromycotinian arbuscular mycorrhizal fungi across China: A meta-analysis. Sci Total Environ 2024; 912:168907. [PMID: 38061652 DOI: 10.1016/j.scitotenv.2023.168907] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Revised: 11/20/2023] [Accepted: 11/24/2023] [Indexed: 01/18/2024]
Abstract
Fine root endophytes, recently reclassified as Mucoromycotinian arbuscular mycorrhizal fungi (M-AMF), are now recognized as functionally important as Glomeromycotinian AMF (G-AMF). However, little is known about the biogeography and ecology of M-AMF and G-AMF communities, particularly on a large scale, preventing a systematic assessment of ecosystem diversity and functioning. Here, we investigated the biogeographic assemblies and ecological diversity patterns of both G-AMF and M-AMF, using published 18S rDNA amplicon datasets and associated metadata from 575 soil samples in six ecosystems across China. Contrasting with G-AMF, putative M-AMF were rare in natural/semi-natural sites, where their communities were a subset of those in agricultural sites characterized by intensive disturbances, suggesting different ecological niches that they could occupy. Spatial and environmental factors (e.g., vegetation type) significantly influenced both fungal communities, with soil total‑nitrogen and mean-annual-precipitation being the strongest predictors for G-AMF and M-AMF richness, respectively. Both groups exhibited a strong spatial distance-decay relationship, shaped more by environmental filtering than spatial effects for M-AMF, and the opposite for G-AMF, presumably because stochasticity (e.g., drift) dominantly structured G-AMF communities; while the narrower niche breadth (at community-level) of M-AMF compared to G-AMF suggested its more susceptibility to environmental differences. Furthermore, co-occurrence network links between G-AMF and M-AMF were prevalent across ecosystems, and were predicted to play a key role in stabilizing overall communities harboring both fungi. Based on the macroecological spatial scale datasets, this study provides solid evidence that the two AMF groups have distinct ecological preferences at the continental scale in China, and also highlights the potential impacts of anthropogenic activities on distributions of AMF. These results advance our knowledge of the ecological differences between the two fungal groups in terrestrial ecosystems, suggesting the need for further field-based investigation that may lead to a more sophisticated understanding of ecosystem function and sustainable management.
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Affiliation(s)
- Zihao Liu
- School of Geography and Ocean Science, Nanjing University, Nanjing 210008, China
| | - Jie Fang
- School of Geography and Ocean Science, Nanjing University, Nanjing 210008, China
| | - Yucheng He
- School of Geography and Ocean Science, Nanjing University, Nanjing 210008, China
| | - Gary D Bending
- School of Life Sciences, University of Warwick, Coventry CV4 7AL, UK
| | - Bin Song
- School of Geography and Ocean Science, Nanjing University, Nanjing 210008, China; Department of Forest Sciences, University of Helsinki, PO Box 27, Latokartanonkaari 7, FI-00014 Helsinki, Finland.
| | - Yaping Guo
- School of Geography and Ocean Science, Nanjing University, Nanjing 210008, China
| | - Xiaojie Wang
- School of Life Sciences, Anhui University, Hefei 230601, China
| | - Zemin Fang
- School of Life Sciences, Anhui University, Hefei 230601, China
| | - Jonathan M Adams
- School of Geography and Ocean Science, Nanjing University, Nanjing 210008, China.
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20
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Karin BR, Lough-Stevens M, Lin TE, Reilly SB, Barley AJ, Das I, Iskandar DT, Arida E, Jackman TR, McGuire JA, Bauer AM. The natural and human-mediated expansion of a human-commensal lizard into the fringes of Southeast Asia. BMC Ecol Evol 2024; 24:25. [PMID: 38378475 PMCID: PMC10880348 DOI: 10.1186/s12862-024-02212-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Accepted: 02/09/2024] [Indexed: 02/22/2024] Open
Abstract
BACKGROUND Human-commensal species often display deep ancestral genetic structure within their native range and founder-effects and/or evidence of multiple introductions and admixture in newly established areas. We investigated the phylogeography of Eutropis multifasciata, an abundant human-commensal scincid lizard that occurs across Southeast Asia, to determine the extent of its native range and to assess the sources and signatures of human introduction outside of the native range. We sequenced over 350 samples of E. multifasciata for the mitochondrial ND2 gene and reanalyzed a previous RADseq population genetic dataset in a phylogenetic framework. RESULTS Nuclear and mitochondrial trees are concordant and show that E. multifasciata has retained high levels of genetic structure across Southeast Asia despite being frequently moved by humans. Lineage boundaries in the native range roughly correspond to several major biogeographic barriers, including Wallace's Line and the Isthmus of Kra. Islands at the outer fringe of the range show evidence of founder-effects and multiple introductions. CONCLUSIONS Most of enormous range of E. multifasciata across Southeast Asia is native and it only displays signs of human-introduction or recent expansion along the eastern and northern fringe of its range. There were at least three events of human-introductions to Taiwan and offshore islands, and several oceanic islands in eastern Indonesia show a similar pattern. In Myanmar and Hainan, there is a founder-effect consistent with post-warming expansion after the last glacial maxima or human introduction.
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Affiliation(s)
- Benjamin R Karin
- Museum of Vertebrate Zoology and Department of Integrative Biology, University of California, Berkeley, CA, 94720, USA.
- Department of Biology, Villanova University, Villanova, PA, 19085, USA.
| | - Michael Lough-Stevens
- Department of Biology, Villanova University, Villanova, PA, 19085, USA
- Molecular and Computational Biology, University of Southern California, Los Angeles, CA, USA
| | - Te-En Lin
- Endemic Species Research Institute, 1, Minsheng E Rd., Jiji Township, Nantou County, 55244, Taiwan
| | - Sean B Reilly
- Museum of Vertebrate Zoology and Department of Integrative Biology, University of California, Berkeley, CA, 94720, USA
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, CA, 95060, USA
| | - Anthony J Barley
- Department of Evolution and Ecology, University of California, 2320 Storer Hall, Davis, CA, 95616, USA
| | - Indraneil Das
- Institute of Biodiversity and Environmental Conservation, Universiti Malaysia Sarawak, 94300, Kota Samarahan, Sarawak, Malaysia
| | - Djoko T Iskandar
- School of Life Sciences and Technology, Bandung Institute of Technology, 10 Jalan Ganesa, Bandung, 40132, Indonesia
- Basic Sciences Commission, Indonesian Academy of Sciences, 11 Jalan Medan Merdeka Selatan, Jakarta, 10110, Indonesia
| | - Evy Arida
- Research Center for Ecology and Ethnobiology, Badan Riset dan Inovasi Nasional (BRIN), Cibinong Science Center, Jalan Raya Jakarta-Bogor km 46, Cibinong, 16911, Indonesia
| | - Todd R Jackman
- Department of Biology, Villanova University, Villanova, PA, 19085, USA
| | - Jimmy A McGuire
- Museum of Vertebrate Zoology and Department of Integrative Biology, University of California, Berkeley, CA, 94720, USA
| | - Aaron M Bauer
- Department of Biology, Villanova University, Villanova, PA, 19085, USA
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21
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Chen C, Jamieson JW, Tunnicliffe V. Hydrothermal vent fauna of the Galápagos Rift: updated species list with new records. Mar Biodivers 2024; 54:16. [PMID: 38371229 PMCID: PMC10869388 DOI: 10.1007/s12526-024-01408-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Revised: 01/09/2024] [Accepted: 01/18/2024] [Indexed: 02/20/2024]
Abstract
The sighting of giant bivalves and tubeworms at the Rose Garden vent field on the Galápagos Rift in 1977 marked the discovery of hydrothermal vents, a turning point for modern biology. The following decade saw a flurry of taxonomic descriptions of vent endemic species from the first vents. With the finding of high-temperature "black smokers" on the East Pacific Rise, exploration shifted away from Galápagos. A faunal list of Galápagos vents with 65 species was published in 1991, then updated to 74 species in 2006. Since then, few expeditions returned to the Galápagos Rift. Here, we revisited several Galápagos vents including recently confirmed high-temperature sites and inactive sulfide mounds. From our collecting efforts and observations, as well as revisions from the literature, we update the faunal list to 92 species including 15 new records, restricted to obvious vent associates. Accurate regional faunal lists are important for understanding the biogeography of vent fauna, and our list will also be valuable for setting management strategies.
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Affiliation(s)
- Chong Chen
- X-STAR, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2-15 Natsushima-cho, Yokosuka, Kanagawa 237-0061 Japan
| | - John W. Jamieson
- Department of Earth Sciences, Memorial University of Newfoundland, St. John’s, Newfoundland A1B 3X5 Canada
| | - Verena Tunnicliffe
- Department of Biology and School of Earth/Ocean Sciences, University of Victoria, Victoria, British Columbia V8P 3E6 Canada
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22
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Mbanyana N, Blaimer BB, Le Roux JJ, van Noort S, Brady SG, Wossler TC. Out of the desert: Paleoclimatic changes drove the diversification of arid-adapted Ocymyrmex ants in southern Africa. Mol Phylogenet Evol 2024; 191:107977. [PMID: 38008369 DOI: 10.1016/j.ympev.2023.107977] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Revised: 11/06/2023] [Accepted: 11/23/2023] [Indexed: 11/28/2023]
Abstract
A highly endemic ant fauna is found in the arid regions of southern Africa, including species in the genus Ocymyrmex. This genus of ants has higher species richness in the western arid regions of southern Africa compared to tropical and subtropical parts of the continent. The processes that have produced these patterns of diversity and distribution of arid adapted ants in southern Africa have never been investigated. The diversification of many other taxa in the region has been associated with past climate fluctuations that occurred during the Miocene epoch. In this study, the nature and timing of historical processes that may have led to the diversification within Ocymyrmex were assessed. We hypothesized that past climate oscillations, characterized by long periods of aridification, have driven the current distribution of Ocymyrmex species that resulted in the highest species richness of the genus in the Deserts & xeric shrublands biome in southern Africa. Ninety-four Ocymyrmex worker specimens from Botswana, Kenya, Namibia, South Africa, Tanzania and Zimbabwe, representing 21 currently described species and six morphospecies, were included in a phylogenomic analysis. Phylogenies for the genus, based on next generation sequencing data from ultraconserved elements, were inferred using Maximum Likelihood, and a dating analysis was performed using secondary age estimates as calibration points. A distribution database of Ocymyrmex records was used to assign species ranges, which were then coded according to major biomes in southern Africa and used as input for biogeographical analysis. We explored the phylogenomic relationships of Ocymyrmex and analysed these within a biogeographical and paleoclimatic framework to disentangle the potential processes responsible for diversification in this group. Dating analyses estimated that the crown age of Ocymyrmex dates to the Oligocene, around 32 Ma. Diversification within this group occurred between the mid-Miocene (∼12.5 Ma) and Pleistocene (∼2 Ma). Our biogeographic analyses suggest that Ocymyrmex species originated in the south-western region of southern Africa, which is now part of the Deserts & xeric shrublands biome and diversified into eastern subtropical areas during the Pliocene. Paleoclimatic changes resulting in increased aridity during the Miocene likely drove the diversification of the genus Ocymyrmex. It is most likely that the diversification of grasslands, because of historical climate change, facilitated the diversification of these ants to the eastern parts of southern Africa when open grasslands replaced forests during the early Miocene.
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Affiliation(s)
- Nokuthula Mbanyana
- Research and Exhibitions Department, South African Museum, Iziko Museums of South Africa, P.O. Box 61, Cape Town, 8000, South Africa; Department of Botany and Zoology, Stellenbosch University, Stellenbosch, 7602, South Africa.
| | - Bonnie B Blaimer
- Museum für Naturkunde, Leibniz-Institute for Evolution and Biodiversity Science, Center for Integrative Biodiversity Discovery, Invalidenstr. 43, Berlin, 10115, Germany
| | - Johannes J Le Roux
- School of Natural Sciences, Macquarie University, Sydney, 2113, New South Wales, Australia
| | - Simon van Noort
- Research and Exhibitions Department, South African Museum, Iziko Museums of South Africa, P.O. Box 61, Cape Town, 8000, South Africa; Department of Biological Sciences, University of Cape Town, Private Bag, Rondebosch, 7701, South Africa
| | - Seán G Brady
- Department of Entomology, National Museum of Natural History, Smithsonian Institution, Washington, DC 20560, USA
| | - Theresa C Wossler
- Department of Botany and Zoology, Stellenbosch University, Stellenbosch, 7602, South Africa
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23
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Fouquet A, Kok PJR, Recoder RS, Prates I, Camacho A, Marques-Souza S, Ghellere JM, McDiarmid RW, Rodrigues MT. Relicts in the mist: Two new frog families, genera and species highlight the role of Pantepui as a biodiversity museum throughout the Cenozoic. Mol Phylogenet Evol 2024; 191:107971. [PMID: 38000706 DOI: 10.1016/j.ympev.2023.107971] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Revised: 11/21/2023] [Accepted: 11/21/2023] [Indexed: 11/26/2023]
Abstract
The iconic mountains of the Pantepui biogeographical region host many early-diverging endemic animal and plant lineages, concurring with Conan Doyle's novel about an ancient "Lost World". While this is the case of several frog lineages, others appear to have more recent origins, adding to the controversy around the diversification processes in this region. Due to its remoteness, Pantepui is challenging for biological surveys, and only a glimpse of its biodiversity has been described, which hampers comprehensive evolutionary studies in many groups. During a recent expedition to the Neblina massif on the Brazil-Venezuela border, we sampled two new frog species that could not be assigned to any known genus. Here, we perform phylogenetic analyses of mitogenomic and nuclear loci to infer the evolutionary relationships of the new taxa and support their description. We find that both species represent single lineages deeply nested within Brachycephaloidea, a major Neotropical clade of direct-developing frogs. Both species diverged >45 Ma from their closest relatives: the first is sister to all other Brachycephaloidea except for Ceuthomantis, another Pantepui endemic, and the second is sister to Brachycephalidae, endemic to the Brazilian Atlantic Forest. In addition to these considerable phylogenetic and biogeographic divergences, external morphology and osteological features support the proposition of two new family and genus-level taxa to accommodate these new branches of the amphibian tree of life. These findings add to other recently described ancient vertebrate lineages from the Neblina massif, providing a bewildering reminder that our perception of the Pantepui's biodiversity remains vastly incomplete. It also provides insights into how these mountains acted as "museums" during the diversification of Brachycephaloidea and of Neotropical biotas more broadly, in line with the influential "Plateau theory". Finally, these discoveries point at the yet unknown branches of the tree of life that may go extinct, due to global climate change and zoonotic diseases, before we even learn about their existence, amphibians living at higher elevations being particularly at risk.
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Affiliation(s)
- Antoine Fouquet
- Laboratoire Évolution et Diversité Biologique, UMR 5174, CNRS, IRD, Université Paul Sabatier, Bâtiment 4R1 31062 cedex 9, 118 Route de Narbonne, 31077 Toulouse, France.
| | - Philippe J R Kok
- Department of Ecology and Vertebrate Zoology, Faculty of Biology and Environmental Protection, University of Łódź, 12/16 Banacha Str., Łódź 90-237, Poland; Life Sciences, The Natural History Museum, Cromwell Road, London SW7 5BD, United Kingdom.
| | - Renato Sousa Recoder
- Universidade de São Paulo, Instituto de Biociências, Departamento de Zoologia, São Paulo, SP, Brazil.
| | - Ivan Prates
- Department of Ecology and Evolutionary Biology and Museum of Zoology, University of Michigan, Ann Arbor, MI, USA
| | - Agustin Camacho
- Universidade de São Paulo, Instituto de Biociências, Departamento de Zoologia, São Paulo, SP, Brazil
| | - Sergio Marques-Souza
- Universidade de São Paulo, Instituto de Biociências, Departamento de Zoologia, São Paulo, SP, Brazil
| | - José Mario Ghellere
- Universidade de São Paulo, Instituto de Biociências, Departamento de Zoologia, São Paulo, SP, Brazil
| | - Roy W McDiarmid
- Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, PO Box 37012, Washington, DC 20013, USA
| | - Miguel Trefaut Rodrigues
- Universidade de São Paulo, Instituto de Biociências, Departamento de Zoologia, São Paulo, SP, Brazil
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24
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Kulkarni SS, Yamasaki T, Thi Hong Phung L, Karuaera N, Daniels SR, Gavish-Regev E, Sharma PP. Phylogenomic data reveal three new families of poorly studied Solifugae (camel spiders). Mol Phylogenet Evol 2024; 191:107989. [PMID: 38072141 DOI: 10.1016/j.ympev.2023.107989] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Revised: 11/16/2023] [Accepted: 12/07/2023] [Indexed: 12/18/2023]
Abstract
The systematics of the arachnid order Solifugae have been an enigma, owing to challenges in interpreting morphology, a paucity of molecular phylogenetic studies sampling across the group, and a dearth of taxonomic attention for many lineages. Recent work has suggested that solifuge families largely exhibit contiguous distributions and reflect patterns of vicariance, with the exception of three families: Melanoblossidae, Daesiidae and Gylippidae. Morphological studies have cast doubt on their existing circumscriptions and the present composition of these taxa renders their distributions as disjunct. We leveraged ultraconserved elements (UCEs) to test the phylogenetic placement of three key lineages of Solifugae that cause these anomalous distributions: Dinorhax rostrumpsittaci (putative melanoblossid), Namibesia (putative daesiid), and Trichotoma (putative gylippid). Phylogenetic placement of these three genera based on UCEs rendered the families that harbor them as para- or polyphyletic, recovering instead relationships that better accord with a biogeographic history driven by vicariance. Toward a stable and phylogenetically informed classification of Solifugae, we establish three new families, Dinorhaxidae new rank, Namibesiidae new rank and Lipophagidae new rank.
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Affiliation(s)
- Siddharth S Kulkarni
- Department of Integrative Biology, University of Wisconsin-Madison, Madison, WI 53706, USA.
| | - Takeshi Yamasaki
- Institute of Natural and Environmental Sciences, University of Hyogo, Yayoigaoka 6, Sanda-shi, Hyogo 669-1546, Japan; Museum of Nature and Human Activities, Hyogo, Yayoigaoka 6, Sanda-shi, Hyogo 669-1546, Japan
| | - Luong Thi Hong Phung
- Institute of Ecology and Biological Resources, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet Road, Cau Giay District, Hanoi, Viet Nam
| | - Nanguei Karuaera
- Department of Arachnology & Myriapodology & Ichthyology Natural Science, The National Museum of Namibia, 59 Robert Mugabe Ave, Windhoek, Namibia
| | - Savel R Daniels
- Department of Botany and Zoology, University of Stellenbosch, Private Bag X1, Matieland 7602, South Africa
| | - Efrat Gavish-Regev
- The National Natural History Collections, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Giv'at Ram, Jerusalem 9190401, Israel
| | - Prashant P Sharma
- Department of Integrative Biology, University of Wisconsin-Madison, Madison, WI 53706, USA; Zoology Museum, University of Wisconsin-Madison, Madison, WI 53706, USA
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25
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Varliero G, Lebre PH, Adams B, Chown SL, Convey P, Dennis PG, Fan D, Ferrari B, Frey B, Hogg ID, Hopkins DW, Kong W, Makhalanyane T, Matcher G, Newsham KK, Stevens MI, Weigh KV, Cowan DA. Biogeographic survey of soil bacterial communities across Antarctica. Microbiome 2024; 12:9. [PMID: 38212738 PMCID: PMC10785390 DOI: 10.1186/s40168-023-01719-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Accepted: 11/11/2023] [Indexed: 01/13/2024]
Abstract
BACKGROUND Antarctica and its unique biodiversity are increasingly at risk from the effects of global climate change and other human influences. A significant recent element underpinning strategies for Antarctic conservation has been the development of a system of Antarctic Conservation Biogeographic Regions (ACBRs). The datasets supporting this classification are, however, dominated by eukaryotic taxa, with contributions from the bacterial domain restricted to Actinomycetota and Cyanobacteriota. Nevertheless, the ice-free areas of the Antarctic continent and the sub-Antarctic islands are dominated in terms of diversity by bacteria. Our study aims to generate a comprehensive phylogenetic dataset of Antarctic bacteria with wide geographical coverage on the continent and sub-Antarctic islands, to investigate whether bacterial diversity and distribution is reflected in the current ACBRs. RESULTS Soil bacterial diversity and community composition did not fully conform with the ACBR classification. Although 19% of the variability was explained by this classification, the largest differences in bacterial community composition were between the broader continental and maritime Antarctic regions, where a degree of structural overlapping within continental and maritime bacterial communities was apparent, not fully reflecting the division into separate ACBRs. Strong divergence in soil bacterial community composition was also apparent between the Antarctic/sub-Antarctic islands and the Antarctic mainland. Bacterial communities were partially shaped by bioclimatic conditions, with 28% of dominant genera showing habitat preferences connected to at least one of the bioclimatic variables included in our analyses. These genera were also reported as indicator taxa for the ACBRs. CONCLUSIONS Overall, our data indicate that the current ACBR subdivision of the Antarctic continent does not fully reflect bacterial distribution and diversity in Antarctica. We observed considerable overlap in the structure of soil bacterial communities within the maritime Antarctic region and within the continental Antarctic region. Our results also suggest that bacterial communities might be impacted by regional climatic and other environmental changes. The dataset developed in this study provides a comprehensive baseline that will provide a valuable tool for biodiversity conservation efforts on the continent. Further studies are clearly required, and we emphasize the need for more extensive campaigns to systematically sample and characterize Antarctic and sub-Antarctic soil microbial communities. Video Abstract.
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Affiliation(s)
- Gilda Varliero
- Department of Biochemistry, Genetics and Microbiology, Centre for Microbial Ecology and Genomics, University of Pretoria, Pretoria, 0002, South Africa
- Rhizosphere Processes Group, Swiss Federal Research Institute WSL, 8903, Birmensdorf, Switzerland
| | - Pedro H Lebre
- Department of Biochemistry, Genetics and Microbiology, Centre for Microbial Ecology and Genomics, University of Pretoria, Pretoria, 0002, South Africa
| | - Byron Adams
- Department of Biology, Brigham Young University, Provo, UT, 84602, USA
- Monte L. Bean Life Science Museum, Brigham Young University, Provo, UT, 84602, USA
| | - Steven L Chown
- Securing Antarctica's Environmental Future, School of Biological Sciences, Monash University, Clayton, VA, 3800, Australia
| | - Peter Convey
- British Antarctic Survey, Natural Environment Research Council, High Cross, Madingley Road, Cambridge, CB3 0ET, UK
- Department of Zoology, University of Johannesburg, PO Box 524, Auckland Park, 2006, South Africa
- Biodiversity of Antarctic and Sub-Antarctic Ecosystems (BASE), Santiago, Chile
| | - Paul G Dennis
- School of the Environment, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Dandan Fan
- State Key Laboratory of Tibetan Plateau Earth System, Environment and Resources (TPESER), Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing, 100101, China
| | - Belinda Ferrari
- School of Biotechnology and Biomolecular Sciences, University of NSW, Sydney, NSW, 2052, Australia
| | - Beat Frey
- Rhizosphere Processes Group, Swiss Federal Research Institute WSL, 8903, Birmensdorf, Switzerland
| | - Ian D Hogg
- School of Science, University of Waikato, Hamilton, New Zealand
- Canadian High Arctic Research Station, Polar Knowledge Canada, Cambridge Bay, NU, Canada
| | - David W Hopkins
- SRUC - Scotland's Rural College, West Mains Road, Edinburgh, EH9 3JG, Scotland, UK
| | - Weidong Kong
- State Key Laboratory of Tibetan Plateau Earth System, Environment and Resources (TPESER), Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing, 100101, China
| | - Thulani Makhalanyane
- Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, 0002, South Africa
| | - Gwynneth Matcher
- Department of Biochemistry and Microbiology, Rhodes University, Makhanda, South Africa
| | - Kevin K Newsham
- British Antarctic Survey, Natural Environment Research Council, High Cross, Madingley Road, Cambridge, CB3 0ET, UK
| | - Mark I Stevens
- Securing Antarctica's Environmental Future, Earth and Biological Sciences, South Australian Museum, Adelaide, SA, 5000, Australia
- School of Biological Sciences, University of Adelaide, Adelaide, SA, 5005, Australia
| | - Katherine V Weigh
- School of the Environment, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Don A Cowan
- Department of Biochemistry, Genetics and Microbiology, Centre for Microbial Ecology and Genomics, University of Pretoria, Pretoria, 0002, South Africa.
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26
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Liu L, Wang H, Luo Z, Chen J. Biogeographic patterns of micro-eukaryotic generalists and specialists and their effects on regional α-diversity at inter-oceanic scale. Mar Environ Res 2024; 193:106261. [PMID: 37981448 DOI: 10.1016/j.marenvres.2023.106261] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Revised: 10/31/2023] [Accepted: 11/09/2023] [Indexed: 11/21/2023]
Abstract
Inter-oceanic scale studies allow us to understand the global spread of micro-organisms in marine ecosystems. In this study, micro-eukaryotic communities in marine surface sediment were collected from tropical to Arctic sites. We found that micro-eukaryotic generalists had much higher intraspecific variation than specialists which allow them to distribute more widely through higher spatiotemporal asynchrony and complementary niche preferences among conspecific taxa. Moreover, comparing to the host-associated protozoa and small metazoa, the algae and free-living protozoa with higher intraspecific variation allow them to have wider distribution ranges. Species abundance also played an important role in driving the distribution ranges of generalists and specialists. The generalists had important effects on regional α-diversity even at an inter-oceanic scale which led to the micro-eukaryotic species richness in polar sites to be mainly influenced by the regional generalists but not the local specialists. In particular, more than 97% of algal species in polar sites were shared with the tropical and subtropical sites (including toxic dinoflagellate). Overall, our study suggests that the effects of global change and human activities on the vulnerable high latitude habitats may lead to biotic homogenization for the whole microbial community (not only the dispersal of some harmful algae) through the potential long-distance spread of generalists.
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Affiliation(s)
- Lemian Liu
- College of Biological Science and Engineering, Fuzhou University, Fuzhou 350108, China; Marine Engineering Research and Development Center of Jinjiang Science and Education Park, Fuzhou University, Fuzhou 350108, China.
| | - Hongwei Wang
- College of Biological Science and Engineering, Fuzhou University, Fuzhou 350108, China; Marine Engineering Research and Development Center of Jinjiang Science and Education Park, Fuzhou University, Fuzhou 350108, China
| | - Zhaohe Luo
- Third Institute of Oceanography, Ministry of Natural Resources, Xiamen 361005, China; Key Laboratory of Marine Ecological Conservation and Restoration, Ministry of Natural Resources, Xiamen 361005, China.
| | - Jianfeng Chen
- College of Biological Science and Engineering, Fuzhou University, Fuzhou 350108, China; Marine Engineering Research and Development Center of Jinjiang Science and Education Park, Fuzhou University, Fuzhou 350108, China
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27
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Mujic AB, Elliott TF, Stephens RB, Trappe JM, Kristol R, Sublett D, Smith ME. Rare but widespread: A systematic revision of the truffle-forming genera Destuntzia and Kjeldsenia and the formation of a new genus, Hosakaea. Mycologia 2024; 116:148-169. [PMID: 38064355 DOI: 10.1080/00275514.2023.2259786] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Accepted: 09/13/2023] [Indexed: 01/23/2024]
Abstract
Here we present the results of taxonomic and systematic study of the rare truffle-forming genera Destuntzia and Kjeldsenia. Truffle-forming fungi are difficult to study due to their reduced morphological features and their cryptic, hypogeous fruiting habits. The rare occurrence of Destuntzia and Kjeldsenia further compounds these difficulties due to the lack of adequate material for study. Recent forays in North Carolina and Tennessee recovered new specimens of another rarely collected fungus, Octaviania purpurea. Morphological and phylogenetic analysis revealed that Octaviania purpurea is a member of the genus Destuntzia, and this led us to reevaluate the taxonomic status and systematic relationships of other Destuntzia species. We performed a multilocus phylogenetic analysis of Destuntzia specimens deposited in public fungaria, including all available type material, and environmental sequences from animal scat and soil. Our analyses indicate that Destuntzia is a member of the family Claustulaceae within the order Phallales and is a close relative of Kjeldsenia. Results of our phylogenetic analysis infer that three species originally described in the genus Destuntzia are members of the genus Kjeldsenia. We propose three new combinations in Kjeldsenia to accommodate these species as well as a new combination in Destuntzia to accommodate Octaviania purpurea. We also describe a new genus in Claustulaceae, Hosakaea, to accommodate a closely affiliated species, Octaviania violascens. Finally, we transfer the genus Destunzia into the family Claustulaceae and emend the description of the family. The newly proposed combinations in Destuntzia and Kjeldsenia significantly expand the known geographic ranges of both genera. The data from metabarcode analysis of scat and soil also reveal several additional undescribed species that expand these ranges well beyond those suggested by basidiomata collections. Systematic placement of Destuntzia in the saprotrophic order Phallales suggests that this genus is not ectomycorrhizal, and the ecological implications of this systematic revision are discussed.
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Affiliation(s)
- Alija B Mujic
- Department of Biology, California State University, Fresno, California 93740
| | - Todd F Elliott
- Ecosystem Management, University of New England, Armidale, New South Wales 2351, Australia
| | - Ryan B Stephens
- Department of Biological Sciences, East Tennessee State University, Johnson City, Tennessee 37614
| | - James M Trappe
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon 97331
| | - Rebecca Kristol
- Department of Plant Pathology, University of Florida, Fifield Hall, Gainesville, Florida 32611
| | - Danielle Sublett
- Department of Biology, California State University, Fresno, California 93740
| | - Matthew E Smith
- Department of Plant Pathology, University of Florida, Fifield Hall, Gainesville, Florida 32611
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Cozzolino L, Nicastro KR, Hubbard PC, Seuront L, McQuaid CD, Zardi GI. Intraspecific genetic lineages of a marine mussel show behavioural divergence when exposed to microplastic leachates. Environ Pollut 2024; 340:122779. [PMID: 37863252 DOI: 10.1016/j.envpol.2023.122779] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Revised: 10/02/2023] [Accepted: 10/17/2023] [Indexed: 10/22/2023]
Abstract
Worldwide, microplastic pollution has numerous negative implications for marine biota, exacerbating the effects of other forms of global anthropogenic disturbance. Mounting evidence shows that microplastics (MPs) not only cause physical damage through their ingestion, but also act as vectors for hazardous compounds by leaching absorbed and adsorbed chemicals. Research on the effects of plastic pollution has, however, largely assumed that species respond uniformly, while ignoring intraspecific diversity (i.e., variation within a single species). We investigated the effects of plastic leachates derived from factory-fresh (virgin) and beached microplastics on the behavioural responses of two genetic lineages of the Mediterranean mussel Mytilus galloprovincialis. Through laboratory behavioural experiments, we found that during exposure to leachates from beached microplastics (beached MPLs), Atlantic specimens moved significantly less than Mediterranean individuals in terms of both (i) proportion of individuals responding through movement and (ii) net and gross distances crawled. In contrast, no significant intraspecific differences were observed in the behaviour of either adults or recruits when exposed to MPLs from virgin microplastics (virgin MPLs). Additionally, the reception of cues from three amino acids (L-cysteine, proline and L-leucine) at increasing concentrations (10-5 M to 10-3 M in charcoal-filtered seawater) was tested by electrophysiological analysis using mussels exposed to beached MPLs or control seawater. We found significant intraspecific differences in response to 10-3 M L-cysteine (regardless of treatment) and 10-4 M L-cysteine (in mussels exposed to beached MPLs) and to 10-3 M proline (in mussels exposed to beached MPLs) and 10-5 M L-leucine. Our study suggests that intraspecific variation in a marine mussel may prompt different responses to plastic pollution, potentially triggered by local adaptation and physiological variability between lineages. Our work highlights the importance of assessing the effects of intraspecific variation, especially in environmental sentinel species as this level of diversity could modulate responses to plastic pollution.
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Affiliation(s)
- Lorenzo Cozzolino
- CCMAR-Centro de Ciências do Mar, CIMAR Laboratório Associado, Universidade do Algarve, Campus de Gambelas, Faro, 8005-139, Portugal.
| | - Katy R Nicastro
- CCMAR-Centro de Ciências do Mar, CIMAR Laboratório Associado, Universidade do Algarve, Campus de Gambelas, Faro, 8005-139, Portugal; Univ. Lille, CNRS, Univ. Littoral Côte d'Opale, IRD, UMR 8187 - LOG - Laboratoire d'Océanologie et de Géosciences, F-59000, Lille, France; Department of Zoology and Entomology, Rhodes University, Grahamstown, 6140, South Africa
| | - Peter C Hubbard
- CCMAR-Centro de Ciências do Mar, CIMAR Laboratório Associado, Universidade do Algarve, Campus de Gambelas, Faro, 8005-139, Portugal
| | - Laurent Seuront
- Univ. Lille, CNRS, Univ. Littoral Côte d'Opale, IRD, UMR 8187 - LOG - Laboratoire d'Océanologie et de Géosciences, F-59000, Lille, France; Department of Zoology and Entomology, Rhodes University, Grahamstown, 6140, South Africa; Department of Marine Resources and Energy, Tokyo University of Marine Science and Technology, 4-5-7 Konan, Minato-ku, Tokyo, 108- 8477, Japan
| | - Christopher D McQuaid
- Department of Zoology and Entomology, Rhodes University, Grahamstown, 6140, South Africa
| | - Gerardo I Zardi
- CCMAR-Centro de Ciências do Mar, CIMAR Laboratório Associado, Universidade do Algarve, Campus de Gambelas, Faro, 8005-139, Portugal; Department of Zoology and Entomology, Rhodes University, Grahamstown, 6140, South Africa; Normandie Université, UNICAEN, Laboratoire Biologie des Organismes et Ecosystèmes Aquatiques, UMR 8067 BOREA (CNRS, MNHN, UPMC, UCBN, IRD-207), CS 14032, 14000, Caen, France
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Shi BY, Pan D, Zhang KQ, Gu TY, Yeo DCJ, Ng PKL, Cumberlidge N, Sun HY. Diversification of freshwater crabs on the sky islands in the Hengduan Mountains Region, China. Mol Phylogenet Evol 2024; 190:107955. [PMID: 37898294 DOI: 10.1016/j.ympev.2023.107955] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Revised: 10/23/2023] [Accepted: 10/25/2023] [Indexed: 10/30/2023]
Abstract
The numerous naturally-fragmented sky islands (SIs) in the Hengduan Mountains Region (HMR) of southwestern China constitute discontinuous landscapes where montane habitats are isolated by dry-hot valleys which have fostered exceptional species diversification and endemicity. However, studies documenting the crucial role of SI on the speciation dynamics of native freshwater organisms are scarce. Here we used a novel set of comprehensive genetic markers (24 nuclear DNA sequences and complete mitogenomes), morphological characters, and biogeographical information to reveal the evolutionary history and speciation mechanisms of a group of small-bodied montane potamids in the genus Tenuipotamon. Our results provide a robustly supported phylogeny, and suggest that the vicariance events of these montane crabs correlate well with the emergence of SIs due to the uplift of the HMR during the Late Oligocene. Furthermore, ancestrally, mountain ridges provided corridors for the dispersal of these montane crabs that led to the colonization of moist montane-specific habitats, aided by past climatic conditions that were the crucial determinants of their evolutionary history. The present results illustrated that the mechanisms isolating SIs are reinforced by the harsh-dry isolating climatic features of dry-hot valleys separating SIs and continue to affect local diversification. This offers insights into the causes of the high biodiversity and endemism shown by the freshwater crabs of the HMR-SIs in southwestern China.
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Affiliation(s)
- Bo-Yang Shi
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing 210023, China
| | - Da Pan
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing 210023, China.
| | - Kang-Qin Zhang
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing 210023, China
| | - Tian-Yu Gu
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing 210023, China
| | - Darren C J Yeo
- Department of Biological Sciences, National University of Singapore, 16 Science Drive 4, Singapore 117558, Republic of Singapore; Lee Kong Chian Natural History Museum, National University of Singapore, 2 Conservatory Drive, Singapore 117377, Republic of Singapore
| | - Peter K L Ng
- Lee Kong Chian Natural History Museum, National University of Singapore, 2 Conservatory Drive, Singapore 117377, Republic of Singapore
| | - Neil Cumberlidge
- Department of Biology, Northern Michigan University, Marquette, MI 49855, USA
| | - Hong-Ying Sun
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing 210023, China.
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Wood HM, Wunderlich J. Burma Terrane Amber Fauna Shows Connections to Gondwana and Transported Gondwanan Lineages to the Northern Hemisphere (Araneae: Palpimanoidea). Syst Biol 2023; 72:1233-1246. [PMID: 37527553 DOI: 10.1093/sysbio/syad047] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Revised: 07/24/2023] [Accepted: 07/31/2023] [Indexed: 08/03/2023] Open
Abstract
Burmese amber is a significant source of fossils that documents the mid-Cretaceous biota. This deposit was formed around 99 Ma on the Burma Terrane, which broke away from Gondwana and later collided with Asia, although the timing is disputed. Palpimanoidea is a dispersal-limited group that was a dominant element of the Mesozoic spider fauna, and has an extensive fossil record, particularly from Burmese amber. Using morphological and molecular data, evolutionary relationships of living and fossil Palpimanoidea are examined. Divergence dating with fossils as terminal tips shows timing of diversification is contemporaneous with continental breakup.Ancestral range estimations show widespread ancestral ranges that divide into lineages that inherit different Pangean fragments, consistent with vicariance. Our results suggest that the Burmese amber fauna has ties to Gondwana due to a historical connection in the Early Cretaceous, and that the Burma Terrane facilitated biotic exchange by transporting lineages from Gondwana into the Holarctic in the Cretaceous.
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Affiliation(s)
- Hannah M Wood
- Department of Entomology, National Museum of Natural History, Smithsonian Institution, 10th & Constitution Ave. NW, Washington, DC 20560, USA
| | - Jörg Wunderlich
- Oberer Häuselbergweg 24, 69493 Hirschberg an der Bergstraße, Germany
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Csősz S, Seifert B, László M, Yusupov ZM, Herczeg G. Broadly sympatric occurrence of two thief ant species Solenopsisfugax (Latreille, 1798) and S.juliae (Arakelian, 1991) in the East European Pontic-Caspian region (Hymenoptera, Formicidae) is disclosed. Zookeys 2023; 1187:189-222. [PMID: 38161709 PMCID: PMC10756144 DOI: 10.3897/zookeys.1187.105866] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Accepted: 09/19/2023] [Indexed: 01/03/2024] Open
Abstract
This paper presents numeric morphology-based evidence on the broadly overlapping distribution of two thief ant species Solenopsisfugax (Latreille, 1798) and S.juliae (Arakelian, 1991) in the East European Pontic-Caspian region. The paper integrates two autonomous data collections and independent analyses performed by different researchers, using different equipment, considering different character combinations, and evaluating partially different samples. Five type series, the neotype series of Solenopsisfugax (Latreille 1798) and the type series of S.flavidula (Nylander, 1849), S. (Diplorhoptrum) fugax var. furtiva Santschi, 1934, S. (Diplorhoptrum) fugax var. pontica Santschi, 1934, S. (Diplorhoptrum) fugax var. scytica Santschi, 1934 were nested in one cluster and we propose the junior synonymy of the latter four taxa names with S.fugax. The other cluster contained only one type specimen of Solenopsisnitida (Dlussky & Radchenko, 1994) measured from AntWeb images. The naming of this cluster was based on both verbal statements and measurements of gynes given in the original description of Solenopsisjuliae (Arakelian, 1991), which represents the oldest available name for this cluster. Hence, S.nitida is proposed as junior synonym of S.juliae. Solenopsiscypridis Santschi, 1934 is raised to species rank based on investigation of worker and gyne type specimens.
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Affiliation(s)
- Sándor Csősz
- HUN-REN-ELTE-MTM Integrative Ecology Research Group, Pázmány Péter ave 1/C, Budapest 1117, HungaryELTE-Eötvös Loránd UniversityBudapestHungary
- Department of Systematic Zoology and Ecology, Institute of Biology, ELTE-Eötvös Loránd University, Pázmány Péter ave 1/C, Budapest 1117, HungaryHUN-REN-ELTE-MTM Integrative Ecology Research GroupBudapestHungary
| | - Bernhard Seifert
- Department of Entomology, Senckenberg Museum of Natural History Görlitz, Am Museum 1, 02826 Görlitz, GermanySenckenberg Museum of Natural History GörlitzGörlitzGermany
| | - Márk László
- Department of Systematic Zoology and Ecology, Institute of Biology, ELTE-Eötvös Loránd University, Pázmány Péter ave 1/C, Budapest 1117, HungaryHUN-REN-ELTE-MTM Integrative Ecology Research GroupBudapestHungary
| | - Zalimkhan M. Yusupov
- Tembotov Institute of Ecology of Mountain Territories of RAS, Nalchik, 360051, RussiaTembotov Institute of Ecology of Mountain Territories of RASNalchikRussia
| | - Gábor Herczeg
- HUN-REN-ELTE-MTM Integrative Ecology Research Group, Pázmány Péter ave 1/C, Budapest 1117, HungaryELTE-Eötvös Loránd UniversityBudapestHungary
- Department of Systematic Zoology and Ecology, Institute of Biology, ELTE-Eötvös Loránd University, Pázmány Péter ave 1/C, Budapest 1117, HungaryHUN-REN-ELTE-MTM Integrative Ecology Research GroupBudapestHungary
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Wen Y, Zhang G, Zhang W, Liu G. Distribution patterns and functional characteristics of soil bacterial communities in desert ecosystems of northern China. Sci Total Environ 2023; 905:167081. [PMID: 37714348 DOI: 10.1016/j.scitotenv.2023.167081] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2023] [Revised: 09/04/2023] [Accepted: 09/12/2023] [Indexed: 09/17/2023]
Abstract
Deserts are extremely arid environments where life is exposed to multiple environmental stresses, including low water availability, high temperatures, intense radiation environments and soil carbon and nitrogen limitation. Microorganisms have enormous potential applications due to their unique physiological adaptation mechanisms, extensive involvement in geochemical cycles and production of new antibiotics, among many other characteristics. With the increasing amount of open data provides unprecedented opportunities to further reveal bacterial biodiversity and its global role in ecosystem function. Through the collection of published high-quality sequencing data supplemented with experimental findings, we investigated the distribution characteristics and functional properties of bacteria in desert ecosystems in northern China. We show that there are significant differences in bacterial diversity among different sandy areas, and that soil properties and climatic factors are the main factors affecting bacterial diversity in desert ecosystems. The mean annual precipitation in growing season, soil organic carbon, total nitrogen and total phosphorus had significant effects on the diversity of desert bacteria and main bacteria. Desert bacteria primarily participate in the macromolecular decomposition, phototrophy, and geochemical cycling of nitrogen. These findings deepen our understanding of the regional-scale soil microbial diversity patterns in Chinese desert ecosystems and broaden our understanding of the ecological functions carried out by bacteria in these environments.
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Affiliation(s)
- Ying Wen
- Key Laboratory of Extreme Environmental Microbial Resources and Engineering of Gansu Province, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou 730000, China; Key Laboratory of Desert and Desertification, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou 730000, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Gaosen Zhang
- Key Laboratory of Extreme Environmental Microbial Resources and Engineering of Gansu Province, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou 730000, China; Key Laboratory of Desert and Desertification, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou 730000, China
| | - Wei Zhang
- Key Laboratory of Extreme Environmental Microbial Resources and Engineering of Gansu Province, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou 730000, China; Key Laboratory of Desert and Desertification, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou 730000, China
| | - Guangxiu Liu
- Key Laboratory of Extreme Environmental Microbial Resources and Engineering of Gansu Province, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou 730000, China; Key Laboratory of Desert and Desertification, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou 730000, China.
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Santamaria CA, Griffiths CL. Cryptic diversity and phylogeographic patterns of Deto echinata (Isopoda: Detonidae) in southern Africa. PeerJ 2023; 11:e16529. [PMID: 38077409 PMCID: PMC10702337 DOI: 10.7717/peerj.16529] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Accepted: 11/06/2023] [Indexed: 12/18/2023] Open
Abstract
Recent phylogeographic studies of poorly-dispersing coastal invertebrates in highly biodiverse regions have led to the discovery of high levels of cryptic diversity and complex phylogeographic patterns that suggest isolation, geological, and ecological processes have shaped their biodiversity. Studies of southern African coastal invertebrates have uncovered cryptic diversity for various taxa and phylogeographic patterns that, although sharing some similarities across taxa, do differ. These findings underscore the need for additional studies to better understand the biodiversity levels, distributional patterns, and processes responsible for producing coastal biodiversity in that region. The coastal isopod Deto echinata is of particular interest, as its complex taxonomic history, poor dispersal capabilities, and broad geographic distribution suggest the potential for cryptic diversity. We use mitochondrial and nuclear sequences to characterize D. echinata individuals from localities ranging from northern Namibia to Glentana, about 2,500 km along the coastline on the south coast of South Africa. These are used to assess whether D. echinata harbors cryptic genetic diversity and whether phylogeographic distributional patterns correlate with those previously documented for other coastal isopods in the region. Analysis of mitochondrial and nuclear sequences revealed two deeply-divergent lineages that exhibit a distributional break in the Cape Peninsula region. These findings suggest D. echinata is a cryptic species complex in need of taxonomic revision and highlight the need for further taxonomic and phylogeographic studies of similarly poorly-dispersing coastal invertebrates in southern Africa.
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Affiliation(s)
- Carlos A. Santamaria
- Department of Biology, The University of Tampa, Tampa, FL, United States of America
| | - Charles L. Griffiths
- Department of Biological Sciences and Marine Research Institute, University of Cape Town, Rondebosch, South Africa
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De León LF, Arias CF, Sharpe DMT, Bravo V, González R, Krahe R, Aguilar C. Unraveling the complex phylogeographic history of freshwater fishes in Lower Central America: A study of the electric fish Brachyhypopomus occidentalis. Mol Phylogenet Evol 2023; 189:107941. [PMID: 37804958 DOI: 10.1016/j.ympev.2023.107941] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Revised: 10/03/2023] [Accepted: 10/04/2023] [Indexed: 10/09/2023]
Abstract
Lower Central America (LCA) has a complex biogeographic history shaped by the rise of the Isthmus of Panama and the global climatic oscillations of the Pleistocene. These events have been crucial in structuring biodiversity in LCA, but their consequences for the distribution and partitions of genetic diversity across the region remain to be elucidated. We combined complete mitochondrial genomes and nuclear ultraconserved elements (UCEs) to study the phylogeographic history and population genetic structure of the electric fish Brachyhypopomus occidentalis in LCA. Our results are consistent with the known phylogeographic history of B. occidentalis in LCA, but we update this history in several important ways that help illuminate the phylogeographic history of freshwater fishes in the region. We provide: i) support for three waves of colonization, two of which occurred prior to the final closure of the Panama Isthmus; ii) a more precise understanding of each colonization event, with evidence for a larger footprint of the first event, as well as genetic exchange across the continental divide in subsequent events; and iii) evidence for high levels of previously unrecognized population genetic structure across LCA. This updated model of colonization and diversification of B. occidentalis consists of three waves of dispersal and colonization, which triggered the evolution of geographic breaks in both nuclear and mitochondrial genomes across LCA. These processes are tightly linked to the dynamic uplift of the Isthmus, recent volcanic activity in the region, and the sea-level oscillations of the Pleistocene. These results improve previous phylogeographic inferences regarding the distribution and diversification of freshwater fishes in LCA, and generate testable hypotheses to guide future research exploring the factors shaping biodiversity in the region.
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Affiliation(s)
- Luis F De León
- Department of Biology, University of Massachusetts Boston, Boston, MA, USA; Centro de Biodiversidad y Descubrimiento de Drogas, Instituto de Investigaciones Científicas y Servicios de Alta Tecnología (INDICASAT AIP), P. O. Box 0843-01103, Panamá, Panama; Smithsonian Tropical Research Institute, P.O. Box 0843-03092, Balboa Ancón, Panamá, Panama.
| | - Carlos F Arias
- Smithsonian Tropical Research Institute, P.O. Box 0843-03092, Balboa Ancón, Panamá, Panama; Data Science Lab, Office of the Chief Information Officer, Smithsonian Institution, Washington DC, USA
| | - Diana M T Sharpe
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA
| | - Víctor Bravo
- Department of Biology, University of Massachusetts Boston, Boston, MA, USA
| | - Rigoberto González
- Smithsonian Tropical Research Institute, P.O. Box 0843-03092, Balboa Ancón, Panamá, Panama
| | - Rüdiger Krahe
- Institute of Biology, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Celestino Aguilar
- Centro de Biodiversidad y Descubrimiento de Drogas, Instituto de Investigaciones Científicas y Servicios de Alta Tecnología (INDICASAT AIP), P. O. Box 0843-01103, Panamá, Panama; Smithsonian Tropical Research Institute, P.O. Box 0843-03092, Balboa Ancón, Panamá, Panama
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Carter JE, Sporre MA, Eytan RI. Phylogenetic review of the comb-tooth blenny genus Hypleurochilus in the northwest Atlantic and Gulf of Mexico. Mol Phylogenet Evol 2023; 189:107933. [PMID: 37769827 DOI: 10.1016/j.ympev.2023.107933] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Revised: 09/25/2023] [Accepted: 09/25/2023] [Indexed: 10/03/2023]
Abstract
As some of the smallest vertebrates, yet largest producers of consumed reef biomass, cryptobenthic reef fishes serve a disproportionate role in reef ecosystems and are one of the most poorly understood groups of fish. The blenny genera Hypleurochilus and Parablennius are currently considered paraphyletic and the interrelationships of Parablennius have been the focus of recent phylogenetic studies. However, the interrelationships of Hypleurochilus remain understudied. This genus is transatlantically distributed and comprises 11 species with a convoluted taxonomic history. In this study, relationships for ten Hypleurochilus species are resolved using multi-locus nuclear and mtDNA sequence data, morphological data, and mined COI barcode data. Mitochondrial and nuclear sequence data from 61 individuals collected from the western Atlantic and northern Gulf of Mexico (N. GoM) delimit seven species into a temperate clade, a tropical clade, and a third distinct lineage. This lineage, herein referred to as H. cf. aequipinnis, may represent a species of Hypleurochilus whose range has expanded into the N. GoM. Inclusion of publicly available COI sequence for an additional three species provides further phylogenetic resolution. H. bananensis forms a new eastern Atlantic clade with H. cf. aequipinnis, providing further evidence for a western Atlantic range expansion. Single marker COI delimitation was unable to elucidate the relationships between H. springeri/H. pseudoaequipinnis and between H. multifilis/H. caudovittatus due to incomplete lineage sorting. Mitochondrial data are also unable to accurately resolve the placement of H. bermudensis. However, a comprehensive approach using multi-locus phylogenetic and species delimitation methods was able to resolve these relationships. While mining publicly available sequence data allowed for the inclusion of an increased number of species in the analysis and a more comprehensive phylogeny, it was not without drawbacks, as a handful of sequences are potentially mis-identified. Overall, we find that the recent divergence of some species within this genus and potential introgression events confound the results of single locus delimitation methods, yet a combination of single and multi-locus analyses has allowed for insights into the biogeography of this genus and uncovered a potential transatlantic range expansion.
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Affiliation(s)
- Joshua E Carter
- Department of Marine Biology, Texas A&M University at Galveston, 1001 Texas Clipper Road, Galveston, TX 77554, United States.
| | - Megan A Sporre
- Department of Marine Biology, Texas A&M University at Galveston, 1001 Texas Clipper Road, Galveston, TX 77554, United States
| | - Ron I Eytan
- Department of Marine Biology, Texas A&M University at Galveston, 1001 Texas Clipper Road, Galveston, TX 77554, United States
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Rodero Madrid J, Olmo JL, Esteban GF. First record of Colpodidium caudatum (Ciliophora, Colpodidiidae) in Europe. Protist 2023; 174:125995. [PMID: 37995544 DOI: 10.1016/j.protis.2023.125995] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2023] [Revised: 10/17/2023] [Accepted: 10/31/2023] [Indexed: 11/25/2023]
Abstract
The present study documents the discovery of the first European population of Colpodidium caudatum (Ciliophora, Colpodidiidae) in a water drain in a school playground in Manzanares (Ciudad Real, Spain). This species has been documented on every continent except Antarctica and Europe, until now. The ciliate was isolated from wet run-off soil collected from the water drain and was grown in semi-permanent cultures in the laboratory. The infraciliature of the ciliate was revealed using silver carbonate impregnation and cell measurements were taken from living and silver-impregnated specimens. A comparative analysis of published data from various populations of C. caudatum across the globe showed high intraspecific morphological variability in this species. To differentiate between species within the Colpodidium genus, a dichotomous key is presented. This investigation shows that C. caudatum is a ciliate that is found all over the world and is particularly associated with terrestrial habitats that are periodically flooded.
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Affiliation(s)
- Juan Rodero Madrid
- ISE Azuer, Carretera de La Solana 77, 13200 Manzanares, Ciudad Real, Spain
| | - José Luis Olmo
- ISE Azuer, Carretera de La Solana 77, 13200 Manzanares, Ciudad Real, Spain.
| | - Genoveva F Esteban
- Bournemouth University, Department of Life and Environmental Sciences, Poole, Dorset BH12 5BB, UK.
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Johansson US, Irestedt M, Ericson PGP. Patterns of phylogenetic diversification in the Dollarbird (Eurystomus orientalis) and Azure Roller (Eurystomus azureus) complex. Mol Phylogenet Evol 2023; 189:107909. [PMID: 37611647 DOI: 10.1016/j.ympev.2023.107909] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Revised: 08/17/2023] [Accepted: 08/20/2023] [Indexed: 08/25/2023]
Abstract
Genetic isolation and morphological differentiation are two important factors in the speciation process that not always act in concert. A rapid morphological change in a lineage can hide its close relationship to another lineage, while slight morphological differentiation between two taxa can give the appearance of a closer relationship than is actually the case. The Dollarbird (Eurystomus orientalis) and the Azure Roller (Eurystomus azureus) is such an example. Today the Dollarbird and the Azure Roller are unanimously considered to constitute two distinct species, but in a recent genetic study it has been shown that the latter taxon, despite being larger and having a distinctly different coloration, is phylogenetically nested within the former. Its precise placement within this complex has not been determined, however. In this study, we investigate the phylogenetic relationships within the Dollarbird/Azure Roller complex. We estimate divergence times and infer phylogenetic relationships using sequence data from 6,475 genome-wide intronic regions, as well as complete mitochondrial genomes, using both concatenation and multispecies coalescence approaches. We find that within the Dollarbird/Azure Roller complex there are several examples of discrepancies between genetic and morphological differentiation. The Dollarbird is currently divided into between nine to twelve subspecies. Some of these subspecies are poorly differentiated, whereas others are morphologically more clearly discernable. Our data suggest that the complex consist of at least seven distinct genetic lineages that do not entirely match the morphological variation within the group. For instance, our results show that the subspecies solomonensis from the Solomon Islands, despite being morphologically very similar to its geographically closest neighbors, in fact is a highly distinct lineage that became isolated more than 700,000 years ago. In contrast, the morphologically distinct Azure Roller, which is currently treated as a distinct species, is nested within the Dollarbird and forms a slightly younger lineage than solomonensis and is the sister group to a clade with Australian and New Guinean Dollarbirds. Our results also show a deep genetic split within the Dollarbirds on the Asian mainland. This stands in contrast to the apparent clinal morphological variation reported for the birds on the Asian mainland. We also find support for the presence of a genetically distinct clade in the Wallacea region. The birds from the Wallacea region has previously been recognized as a distinct subspecies, connectens, but is currently placed in synonymy of other subspecies. Our results are thus at odds with the current division of the Dollarbird/Azure Roller complex into two species. Given that the species status of azureus is undisputed, the apparent genetic isolation of solomonensis and its clear separation from the other lineages suggests that this taxon also warrants species status. Based on the genetic and morphological variation observed within the Dollarbird/Azure Roller complex there is little doubt that even more taxa should regarded as species, but this require further examination.
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Affiliation(s)
- Ulf S Johansson
- Department of Zoology, Swedish Museum of Natural History, Box 50007, SE-104 05 Stockholm, Sweden.
| | - Martin Irestedt
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Box 50007, SE-104 05 Stockholm, Sweden
| | - Per G P Ericson
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Box 50007, SE-104 05 Stockholm, Sweden
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Hunt EP, Willis SC, Conway KW, Portnoy DS. Interrelationships and biogeography of the New World pufferfish genus Sphoeroides (Tetraodontiformes: Tetraodontidae) inferred using ultra-conserved DNA elements. Mol Phylogenet Evol 2023; 189:107935. [PMID: 37778529 DOI: 10.1016/j.ympev.2023.107935] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Revised: 09/27/2023] [Accepted: 09/28/2023] [Indexed: 10/03/2023]
Abstract
Colonization of the New World by marine taxa has been hypothesized to have occurred through the Tethys Sea or by crossing the East Pacific Barrier. To better understand patterns and timing of diversification, geological events can be coupled with time calibrated phylogenetic hypotheses to infer major drivers of diversification. Phylogenetic relationships among members of Sphoeroides, a genus of four toothed pufferfishes (Tetraodontiformes: Tetraodontidae) which are found nearly exclusively in the New World (eastern Pacific and western Atlantic), were reconstructed using sequences from ultra-conserved DNA elements, nuclear markers with clear homology among many vertebrate taxa. Hypotheses derived from concatenated maximum-likelihood and species tree summary methods support a paraphyletic Sphoeroides, with Colomesus deeply nested within the genus. Analyses also revealed S. pachygaster, a pelagic species with a cosmopolitan distribution, as the sister taxon to the remainder of Sphoeroides and recovered distinct lineages within S. pachygaster, indicating that this cosmopolitan species may represent a species complex. Ancestral range reconstruction may suggest the genus colonized the New World through the eastern Pacific before diversifying in the western Atlantic, though date estimates for these events are uncertain due to the lack of reliable fossil record for the genus.
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Affiliation(s)
- Elizabeth P Hunt
- Department of Life Sciences, Texas A&M University - Corpus Christi, 6300 Ocean Dr., Corpus Christi, TX 78412, USA.
| | - Stuart C Willis
- Department of Life Sciences, Texas A&M University - Corpus Christi, 6300 Ocean Dr., Corpus Christi, TX 78412, USA; Columbia River Inter-Tribal Fish Commission - Hagerman Genetics Lab, 3059-F National Fish Hatchery Road, Hagerman, ID 83332, USA
| | - Kevin W Conway
- Department of Ecology and Conservation Biology and Biodiversity Research and Teaching Collections, Texas A&M University, 534 John Kimbrough Blvd., College Station, TX 77843, USA
| | - David S Portnoy
- Department of Life Sciences, Texas A&M University - Corpus Christi, 6300 Ocean Dr., Corpus Christi, TX 78412, USA
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García-Carrasco JM, Muñoz AR, Olivero J, Figuerola J, Fa JE, Real R. Gone (and spread) with the birds: Can chorotype analysis highlight the spread of West Nile virus within the Afro-Palaearctic flyway? One Health 2023; 17:100585. [PMID: 37359749 PMCID: PMC10285635 DOI: 10.1016/j.onehlt.2023.100585] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Revised: 06/13/2023] [Accepted: 06/13/2023] [Indexed: 06/28/2023] Open
Abstract
West Nile virus (WNV) is a globally significant vector-borne disease that is primarily transmitted between birds and mosquitoes. Recently, there has been an increase in WNV in southern Europe, with new cases reported in more northern regions. Bird migration plays a crucial role in the introduction of WNV in distant areas. To better understand and address this complex issue, we adopted a One Health approach, integrating clinical, zoological, and ecological data. We analyzed the role of migratory birds in the Palaearctic-African region in the spread of WNV across Africa and Europe. We categorized bird species into breeding and wintering chorotypes based on their distribution during the breeding season in the Western Palaearctic and the wintering season in the Afrotropical region, respectively. By linking these chorotypes to the occurrence of WNV outbreaks in both continents throughout the annual bird migration cycle, we investigated the relationship between migratory patterns and virus spread. We demonstrate that WNV-risk areas are interconnected through the migration of birds. We identified a total of 61 species that potentially contribute to the intercontinental spread of the virus or its variants, as well as pinpointed high-risk areas for future outbreaks. This interdisciplinary approach, which considers the interconnectedness of animals, humans, and ecosystems, represents a pioneering effort to establish connections between zoonotic diseases across continents. The findings of our study can aid in anticipating the arrival of new WNV strains and predicting the occurrence of other re-emerging diseases. By incorporating various disciplines, we can enhance our understanding of these complex dynamics and provide valuable insights for proactive and comprehensive disease management strategies.
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Affiliation(s)
- José-María García-Carrasco
- Biogeography, Diversity and Conservation Lab, Department of Animal Biology, Faculty of Sciences, University of Málaga, Málaga, Spain
| | - Antonio-Román Muñoz
- Biogeography, Diversity and Conservation Lab, Department of Animal Biology, Faculty of Sciences, University of Málaga, Málaga, Spain
| | - Jesús Olivero
- Biogeography, Diversity and Conservation Lab, Department of Animal Biology, Faculty of Sciences, University of Málaga, Málaga, Spain
- Instituto IBYDA, Centro de Experimentación Grice-Hutchinson, Malaga, Spain
| | - Jordi Figuerola
- Estación Biológica de Doñana – CSIC, Avda. Américo Vespucio 26, 41092 Sevilla, Spain
- CIBER de Epidemiología y Salud Pública (CIBERESP), Spain
| | - Julia E. Fa
- Department of Natural Sciences, School of Science and the Environment, Manchester Metropolitan University, Manchester, UK
- Center for International Forestry Research (CIFOR), CIFOR Headquarters, Bogor, Indonesia
| | - Raimundo Real
- Biogeography, Diversity and Conservation Lab, Department of Animal Biology, Faculty of Sciences, University of Málaga, Málaga, Spain
- Instituto IBYDA, Centro de Experimentación Grice-Hutchinson, Malaga, Spain
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Herrando-Moraira S, Roquet C, Calleja JA, Chen YS, Fujikawa K, Galbany-Casals M, Garcia-Jacas N, Liu JQ, López-Alvarado J, López-Pujol J, Mandel JR, Mehregan I, Sáez L, Sennikov AN, Susanna A, Vilatersana R, Xu LS. Impact of the climatic changes in the Pliocene-Pleistocene transition on Irano-Turanian species. The radiation of genus Jurinea (Compositae). Mol Phylogenet Evol 2023; 189:107928. [PMID: 37714444 DOI: 10.1016/j.ympev.2023.107928] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Revised: 09/07/2023] [Accepted: 09/12/2023] [Indexed: 09/17/2023]
Abstract
The Irano-Turanian region is one of the world's richest floristic regions and the centre of diversity for numerous xerophytic plant lineages. However, we still have limited knowledge on the timing of evolution and biogeographic history of its flora, and potential drivers of diversification remain underexplored. To fill this knowledge gap, we focus on the Eurasian genus Jurinea (ca. 200 species), one of the largest plant radiations that diversified in the region. We applied a macroevolutionary integrative approach to explicitly test diversification hypotheses and investigate the relative roles of geography vs. ecology and niche conservatism vs. niche lability in speciation processes. To do so, we gathered a sample comprising 77% of total genus richness and obtained data about (1) its phylogenetic history, recovering 502 nuclear loci sequences; (2) growth forms; (3) ecological niche, compiling data of 21 variables for more than 2500 occurrences; and (4) paleoclimatic conditions, to estimate climatic stability. Our results revealed that climate was a key factor in the evolutionary dynamics of Jurinea. The main diversification and biogeographic events that occurred during past climate changes, which led to colder and drier conditions, are the following: (1) the origin of the genus (10.7 Ma); (2) long-distance dispersals from the Iranian Plateau to adjacent regions (∼7-4 Ma); and (3) the diversification shift during Pliocene-Pleistocene Transition (ca. 3 Ma), when net diversification rate almost doubled. Our results supported the pre-adaptation hypothesis, i.e., the evolutionary success of Jurinea was linked to the retention of the ancestral niche adapted to aridity. Interestingly, the paleoclimatic analyses revealed that in the Iranian Plateau long-term climatic stability favoured old-lineage persistence, resulting in current high species richness of semi-arid and cold adapted clades; whereas moderate climate oscillations stimulated allopatric diversification in the lineages distributed in the Circumboreal region. In contrast, growth form lability and high niche disparity among closely related species in the Central Asian clade suggest adaptive radiation to mountain habitats. In sum, the radiation of Jurinea is the result of both adaptive and non-adaptive processes influenced by climatic, orogenic and ecological factors.
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Affiliation(s)
- Sonia Herrando-Moraira
- Botanic Institute of Barcelona (IBB, CSIC-Ajuntament de Barcelona), Pg. del Migdia, s.n., 08038 Barcelona, Spain
| | - Cristina Roquet
- Systematics and Evolution of Vascular Plants (UAB) - Associated Unit to CSIC, Departament de Biologia Animal, Biologia Vegetal i Ecologia, Facultat de Biociències, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain.
| | - Juan-Antonio Calleja
- Departament of Biology (Botany), Faculty of Sciences, Research Centre on Biodiversity and Global Change (CIBC-UAM), 28049 Madrid, Spain
| | - You-Sheng Chen
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
| | - Kazumi Fujikawa
- Kochi Prefectural Makino Botanical Garden, 4200-6, Godaisan, Kochi 781-8125, Japan
| | - Mercè Galbany-Casals
- Systematics and Evolution of Vascular Plants (UAB) - Associated Unit to CSIC, Departament de Biologia Animal, Biologia Vegetal i Ecologia, Facultat de Biociències, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain
| | - Núria Garcia-Jacas
- Botanic Institute of Barcelona (IBB, CSIC-Ajuntament de Barcelona), Pg. del Migdia, s.n., 08038 Barcelona, Spain
| | - Jian-Quan Liu
- Key Laboratory for Bio-Resources and Eco-Environment, College of Life Sciences, Sichuan University, Chengdu, China
| | - Javier López-Alvarado
- Systematics and Evolution of Vascular Plants (UAB) - Associated Unit to CSIC, Departament de Biologia Animal, Biologia Vegetal i Ecologia, Facultat de Biociències, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain
| | - Jordi López-Pujol
- Botanic Institute of Barcelona (IBB, CSIC-Ajuntament de Barcelona), Pg. del Migdia, s.n., 08038 Barcelona, Spain; Escuela de Ciencias Ambientales, Universidad Espíritu Santo (UEES), Samborondón 091650, Ecuador
| | - Jennifer R Mandel
- Department of Biological Sciences, Center for Biodiversity, University of Memphis, Memphis, TN 38152, USA
| | - Iraj Mehregan
- Department of Biology, Science and Research Branch, Islamic Azad University, Tehran, Iran
| | - Llorenç Sáez
- Systematics and Evolution of Vascular Plants (UAB) - Associated Unit to CSIC, Departament de Biologia Animal, Biologia Vegetal i Ecologia, Facultat de Biociències, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain
| | - Alexander N Sennikov
- Botanical Museum, Finnish Museum of Natural History, P.O. Box 7, 00014 University of Helsinki, Finland
| | - Alfonso Susanna
- Botanic Institute of Barcelona (IBB, CSIC-Ajuntament de Barcelona), Pg. del Migdia, s.n., 08038 Barcelona, Spain
| | - Roser Vilatersana
- Botanic Institute of Barcelona (IBB, CSIC-Ajuntament de Barcelona), Pg. del Migdia, s.n., 08038 Barcelona, Spain
| | - Lian-Sheng Xu
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
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Golikov AV, Gudmundsson G, Blicher ME, Jørgensen LL, Korneeva EI, Olafsdottir SH, Shagimardanova EI, Shigapova LH, Zakharov DV, Zimina OL, Sabirov RM. A review of the genus Muusoctopus (Cephalopoda: Octopoda) from Arctic waters. Zoological Lett 2023; 9:21. [PMID: 37974237 PMCID: PMC10655294 DOI: 10.1186/s40851-023-00220-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/26/2022] [Accepted: 09/20/2023] [Indexed: 11/19/2023]
Abstract
We report two Arctic species of incirrate octopods new to science. One is formally described here as Muusoctopus aegir Golikov, Gudmundsson & Sabirov sp. nov. while the other, Muusoctopus sp. 1, is not formally described due to a limited number of samples (all are immature individuals). These two species differ from each other, and from other Muusoctopus, especially in: 1) absence of stylets (in M. aegir sp. nov.); 2) proportions of mantle and head; 3) funnel organ morphology (W-shaped with medial and marginal limbs of equal length in M. aegir sp. nov., or medial are slightly longer; V V-shaped with medial limbs slightly longer and broader than marginal in Muusoctopus sp. 1); 4) sucker and gill lamellae counts; 5) relative arm length and sucker diameter; and 6) male reproductive system relative size and morphology. Species of Muusoctopus now comprise four of 12 known Arctic cephalopods. Additionally, this study provides: a) new data on the morphology and reproductive biology of M. johnsonianus and M. sibiricus, and a diagnosis of M. sibiricus; b) the equations to estimate mantle length and body mass from beak measurements of M. aegir sp. nov. and M. johnsonianus; c) a cytochrome c oxidase subunit I gene barcode for M. sibiricus; d) new data on the ecology and distribution of all studied species; and e) a data table for the identification of northern North Atlantic and Arctic species of Muusoctopus.
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Affiliation(s)
- Alexey V Golikov
- GEOMAR Helmholtz Centre for Ocean Research Kiel, Dusternbrooker Weg 20, 24105, Kiel, Germany.
| | - Gudmundur Gudmundsson
- Collections and Systematics Department, Icelandic Institute of Natural History, Urriðaholtsstræti 6-8, 210, Gardabaer, Iceland
| | - Martin E Blicher
- NIRAS A/S, Ceres Allé 3, 8000, Aarhus, Denmark
- Greenland Institute of Natural Resources, Greenland Climate Research Centre, Kivioq 2, 3900, Nuuk, Greenland
| | - Lis L Jørgensen
- Institute of Marine Research, Tromsø Department, P.O. Box 6606 Langnes, 9294, Tromsø, Norway
| | - Ekaterina I Korneeva
- Department of Zoology, Kazan Federal University, Kremlyovskaya Str. 18, 420008, Kazan, Russia
| | - Steinunn H Olafsdottir
- Marine and Freshwater Research Institute, Demersal Division, Fornubúðir 5, 220, Hafnarfjordur, Iceland
| | - Elena I Shagimardanova
- Kazan Federal University, Extreme Biology Laboratory, Volkova Str. 18, 420021, Kazan, Russia
| | - Leyla H Shigapova
- Kazan Federal University, Extreme Biology Laboratory, Volkova Str. 18, 420021, Kazan, Russia
| | - Denis V Zakharov
- Zoological Institute of Russian Academy of Sciences, Laboratory of Marine Research, Universitetskaya Nab. 1, 199034, Sankt-Petersburg, Russia
| | - Olga L Zimina
- Zoological Institute of Russian Academy of Sciences, Laboratory of Marine Research, Universitetskaya Nab. 1, 199034, Sankt-Petersburg, Russia
- Murmansk Marine Biological Institute, Laboratory of Zoobenthos, Vladimirskaya Str. 17, 183010, Murmansk, Russia
| | - Rushan M Sabirov
- Department of Zoology, Kazan Federal University, Kremlyovskaya Str. 18, 420008, Kazan, Russia
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Hakobyan A, Velte S, Sickel W, Quandt D, Stoll A, Knief C. Tillandsia landbeckii phyllosphere and laimosphere as refugia for bacterial life in a hyperarid desert environment. Microbiome 2023; 11:246. [PMID: 37936139 PMCID: PMC10631034 DOI: 10.1186/s40168-023-01684-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Accepted: 09/28/2023] [Indexed: 11/09/2023]
Abstract
BACKGROUND The lack of water is a major constraint for microbial life in hyperarid deserts. Consequently, the abundance and diversity of microorganisms in common habitats such as soil are strongly reduced, and colonization occurs primarily by specifically adapted microorganisms that thrive in particular refugia to escape the harsh conditions that prevail in these deserts. We suggest that plants provide another refugium for microbial life in hyperarid deserts. We studied the bacterial colonization of Tillandsia landbeckii (Bromeliaceae) plants, which occur in the hyperarid regions of the Atacama Desert in Chile, one of the driest and oldest deserts on Earth. RESULTS We detected clear differences between the bacterial communities being plant associated to those of the bare soil surface (PERMANOVA, R2 = 0.187, p = 0.001), indicating that Tillandsia plants host a specific bacterial community, not only dust-deposited cells. Moreover, the bacterial communities in the phyllosphere were distinct from those in the laimosphere, i.e., on buried shoots (R2 = 0.108, p = 0.001), indicating further habitat differentiation within plant individuals. The bacterial taxa detected in the phyllosphere are partly well-known phyllosphere colonizers, but in addition, some rather unusual taxa (subgroup2 Acidobacteriae, Acidiphilum) and insect endosymbionts (Wolbachia, "Candidatus Uzinura") were found. The laimosphere hosted phyllosphere-associated as well as soil-derived taxa. The phyllosphere bacterial communities showed biogeographic patterns across the desert (R2 = 0.331, p = 0.001). These patterns were different and even more pronounced in the laimosphere (R2 = 0.467, p = 0.001), indicating that different factors determine community assembly in the two plant compartments. Furthermore, the phyllosphere microbiota underwent temporal changes (R2 = 0.064, p = 0.001). CONCLUSIONS Our data demonstrate that T. landbeckii plants host specific bacterial communities in the phyllosphere as well as in the laimosphere. Therewith, these plants provide compartment-specific refugia for microbial life in hyperarid desert environments. The bacterial communities show biogeographic patterns and temporal variation, as known from other plant microbiomes, demonstrating environmental responsiveness and suggesting that bacteria inhabit these plants as viable microorganisms. Video Abstract.
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Affiliation(s)
- Anna Hakobyan
- Molecular Biology of the Rhizosphere, Institute for Crop Science and Resource Conservation (INRES), University of Bonn, 53115, Bonn, Germany
| | - Stefanie Velte
- Molecular Biology of the Rhizosphere, Institute for Crop Science and Resource Conservation (INRES), University of Bonn, 53115, Bonn, Germany
| | - Wiebke Sickel
- Molecular Biology of the Rhizosphere, Institute for Crop Science and Resource Conservation (INRES), University of Bonn, 53115, Bonn, Germany
- Institute of Biodiversity, Johann Heinrich Von Thünen Institute, Brunswick, Germany
| | - Dietmar Quandt
- Nees Institute for Biodiversity of Plants, University of Bonn, Bonn, Germany
| | - Alexandra Stoll
- Centro de Estudios Avanzados en Zonas Áridas Ceaza, La Serena, Chile
- Instituto de Investigación Multidisciplinar en Ciencia y Tecnología, Universidad de La Serena, La Serena, Chile
| | - Claudia Knief
- Molecular Biology of the Rhizosphere, Institute for Crop Science and Resource Conservation (INRES), University of Bonn, 53115, Bonn, Germany.
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Wei N, Tan J. Environment and Host Genetics Influence the Biogeography of Plant Microbiome Structure. Microb Ecol 2023; 86:2858-2868. [PMID: 37610498 DOI: 10.1007/s00248-023-02288-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Accepted: 08/14/2023] [Indexed: 08/24/2023]
Abstract
To understand how microbiota influence plant populations in nature, it is important to examine the biogeographic distribution of plant-associated microbiomes and the underlying mechanisms. However, we currently lack a fundamental understanding of the biogeography of plant microbiomes across populations and the environmental and host genetic factors that shape their distribution. Leveraging the broad distribution and extensive genetic variation in duckweeds (the Lemna species complex), we identified key factors that governed plant microbiome diversity and compositional variation geographically. In line with the microbial biogeography of free-living microbiomes, we observed higher bacterial richness in temperate regions relative to lower latitudes in duckweed microbiomes (with 10% higher in temperate populations). Our analyses revealed that higher temperature and sodium concentration in aquatic environments showed a negative impact on duckweed bacterial richness, whereas temperature, precipitation, pH, and concentrations of phosphorus and calcium, along with duckweed genetic variation, influenced the biogeographic variation of duckweed bacterial community composition. Analyses of plant microbiome assembly processes further revealed that niche-based selection played an important role (26%) in driving the biogeographic variation of duckweed bacterial communities, alongside the contributions of dispersal limitation (33%) and drift (39%). These findings add significantly to our understanding of host-associated microbial biogeography and provide important insights for predicting plant microbiome vulnerability and resilience under changing climates and intensifying anthropogenic activities.
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Affiliation(s)
- Na Wei
- The Holden Arboretum, Kirtland, OH, 44094, USA.
| | - Jiaqi Tan
- Department of Biological Sciences, Louisianan State University, Baton Rouge, LA, 70803, USA.
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Huang S, Lentendu G, Fujinuma J, Shiono T, Kubota Y, Mitchell EAD. Soil Micro-eukaryotic Diversity Patterns Along Elevation Gradient Are Best Estimated by Increasing the Number of Elevation Steps Rather than Within Elevation Band Replication. Microb Ecol 2023; 86:2606-2617. [PMID: 37458790 PMCID: PMC10640418 DOI: 10.1007/s00248-023-02259-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Accepted: 06/21/2023] [Indexed: 11/12/2023]
Abstract
The development of high-throughput sequencing (HTS) of environmental DNA (eDNA) has stimulated the study of soil microbial diversity patterns and drivers at all scales. However, given the heterogeneity of soils, a challenge is to define effective and efficient sampling protocols that allow sound comparison with other records, especially vegetation. In studies of elevational diversity pattern, a trade-off is choosing between replication within elevation bands vs. sampling more elevation bands. We addressed this question for soil protists along an elevation gradient on Mt. Asahi, Hokkaido, Japan. We compared two sampling approaches: (1) the replicate strategy (five replicates at six elevational bands, total = 30) and (2) the transect strategy (one sample in each of 16 different elevational bands). Despite a nearly twofold lower sampling effort, the transect strategy yielded congruent results compared to the replicate strategy for the estimation of elevational alpha diversity pattern: the regression coefficients between diversity indices and elevation did not differ between the two options. Furthermore, for a given total number of samples, gamma diversity estimated across the entire transect was higher when sampling more elevational bands as compared to replication from fewer elevational bands. Beta diversity (community composition turnover) was lower within a given elevational band than between adjacent bands and increased with elevation distance. In redundancy analyses, soil organic matter-related variable (the first principal component of soil organic matter, water content, total organic carbon, and nitrogen by whom were highly correlated) and elevation best explained elevational beta diversity pattern for both sampling approaches. Taken together, our results suggest that sampling a single plot per elevation band will be sufficient to obtain a good estimate of soil micro-eukaryotic diversity patterns along elevation gradients. This study demonstrated the effectiveness of the transect strategy in estimating diversity patterns along elevation gradients which is instructive for future environmental or even experimental studies. While not advocating for completely replacing replication-based sampling practices, it is important to note that both replicate and transect strategies have their merits and can be employed based on specific research goals and resource limitations.
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Affiliation(s)
- Shuyin Huang
- Laboratory of Biodiversity and Conservation Biogeography, University of the Ryukyus, Okinawa, Japan.
| | - Guillaume Lentendu
- Laboratory of Soil Biodiversity, University of Neuchâtel, Neuchâtel, Switzerland.
| | - Junichi Fujinuma
- Laboratory of Biodiversity and Conservation Biogeography, University of the Ryukyus, Okinawa, Japan
- Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Estonia
| | - Takayuki Shiono
- Laboratory of Biodiversity and Conservation Biogeography, University of the Ryukyus, Okinawa, Japan
| | - Yasuhiro Kubota
- Laboratory of Biodiversity and Conservation Biogeography, University of the Ryukyus, Okinawa, Japan
| | - Edward A D Mitchell
- Laboratory of Soil Biodiversity, University of Neuchâtel, Neuchâtel, Switzerland
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Fan X, Ji M, Mu D, Zeng X, Tian Z, Sun K, Gao R, Liu Y, He X, Wu L, Li Q. Global diversity and biogeography of DNA viral communities in activated sludge systems. Microbiome 2023; 11:234. [PMID: 37865788 PMCID: PMC10589946 DOI: 10.1186/s40168-023-01672-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Accepted: 09/21/2023] [Indexed: 10/23/2023]
Abstract
BACKGROUND Activated sludge (AS) systems in wastewater treatment plants (WWTPs) harbor enormous viruses that regulate microbial metabolism and nutrient cycling, significantly influencing the stability of AS systems. However, our knowledge about the diversity of viral taxonomic groups and functional traits in global AS systems is still limited. To address this gap, we investigated the global diversity and biogeography of DNA viral communities in AS systems using 85,114 viral operational taxonomic units (vOTUs) recovered from 144 AS samples collected across 54 WWTPs from 13 different countries. RESULTS AS viral communities and their functional traits exhibited distance-decay relationship (DDR) at the global scale and latitudinal diversity gradient (LDG) from equator to mid-latitude. Furthermore, it was observed that AS viral community and functional gene structures were largely driven by the geographic factors and wastewater types, of which the geographic factors were more important. Carrying and disseminating auxiliary metabolic genes (AMGs) associated with the degradation of polysaccharides, sulfate reduction, denitrification, and organic phosphoester hydrolysis, as well as the lysis of crucial functional microbes that govern biogeochemical cycles were two major ways by which viruses could regulate AS functions. It was worth noting that our study revealed a high abundance of antibiotic resistance genes (ARGs) in viral genomes, suggesting that viruses were key reservoirs of ARGs in AS systems. CONCLUSIONS Our results demonstrated the highly diverse taxonomic groups and functional traits of viruses in AS systems. Viral lysis of host microbes and virus-mediated HGT can regulate the biogeochemical and nutrient cycles, thus affecting the performance of AS systems. These findings provide important insights into the viral diversity, function, and ecology in AS systems on a global scale. Video Abstract.
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Affiliation(s)
- Xiangyu Fan
- School of Biological Science and Technology, University of Jinan, Jinan, Shandong Province, China.
- Artificial Intelligence Institute, University of Jinan, Jinan, Shandong Province, China.
| | - Mengzhi Ji
- School of Biological Science and Technology, University of Jinan, Jinan, Shandong Province, China
- Institute of Marine Science and Technology, Shandong University, Qingdao, Shandong Province, China
| | - Dashuai Mu
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao, Shandong Province, China
- Marine College, Shandong University, Weihai, Shandong Province, China
| | - Xianghe Zeng
- School of Biological Science and Technology, University of Jinan, Jinan, Shandong Province, China
| | - Zhen Tian
- Artificial Intelligence Institute, University of Jinan, Jinan, Shandong Province, China
| | - Kaili Sun
- School of Biological Science and Technology, University of Jinan, Jinan, Shandong Province, China
| | - Rongfeng Gao
- School of Biological Science and Technology, University of Jinan, Jinan, Shandong Province, China
| | - Yang Liu
- Artificial Intelligence Institute, University of Jinan, Jinan, Shandong Province, China
| | - Xinyuan He
- Artificial Intelligence Institute, University of Jinan, Jinan, Shandong Province, China
| | - Linwei Wu
- Institute of Ecology, Key Laboratory for Earth Surface Processes of the Ministry of Education, College of Urban and Environmental Sciences, Peking University, Beijing, China.
| | - Qiang Li
- School of Biological Science and Technology, University of Jinan, Jinan, Shandong Province, China.
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AlShamakhi HS, Al-Sadi AM, Cook LG. Phylogenetic Relationships of the Mutualistic Fungi Associated with Macrotermes subhyalinus in Oman. Mycobiology 2023; 51:281-287. [PMID: 37929007 PMCID: PMC10621247 DOI: 10.1080/12298093.2023.2258623] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Accepted: 09/11/2023] [Indexed: 11/07/2023]
Abstract
The symbiotic association between fungus-gardening termites Macrotermes and its fungal symbiont has a moderate degree of specificity-although the symbiotic fungi (Termitomyces) form a monophyletic clade, there is not a one-to-one association between termite species and their fungus-garden associates. Here, we aim to determine the origin and phylogenetic relationships of Termitomyces in Oman. We used sequences of the internal transcribed spacer region (ITS) and the nuclear large subunit ribosomal RNA (LSU rRNA, 25S) gene and analyzed these with sequences of Termitomyces from other geographic areas. We find no evidence for more than a single colonization of Oman by Termitomyces. Unexpectedly, we find Termitomyces in Oman is most closely related to the symbiont of M. subhyalinus in West Africa rather than to those of geographically closer populations in East Africa.
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Affiliation(s)
| | - Abdullah M. Al-Sadi
- Department of Plant Sciences, College of Agricultural and Marine Sciences, Sultan Qaboos University, Al-Khoud, Oman
| | - Lyn G. Cook
- School of Biological Sciences, The University of Queensland, Brisbane, QLD, Australia
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Raman G, Choi KS, Lee EM, Morden CW, Shim H, Kang JS, Yang TJ, Park S. Extensive characterization of 28 complete chloroplast genomes of Hydrangea species: A perspective view of their organization and phylogenetic and evolutionary relationships. Comput Struct Biotechnol J 2023; 21:5073-5091. [PMID: 37867966 PMCID: PMC10589384 DOI: 10.1016/j.csbj.2023.10.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Revised: 10/04/2023] [Accepted: 10/06/2023] [Indexed: 10/24/2023] Open
Abstract
The tribe Hydrangeeae displays a unique, distinctive disjunct distribution encompassing East Asia, North America and Hawaii. Despite its complex trait variations and polyphyletic nature, comprehensive phylogenomic and biogeographical studies on this tribe have been lacking. To address this gap, we sequenced and characterized 28 plastomes of Hydrangeeae. Our study highlights the highly conserved nature of Hydrangeaceae chloroplast (cp) genomes in terms of gene content and arrangement. Notably, synapomorphic characteristics of tandem repeats in the conserved domain of accD were observed in the Macrophyllae, Chinenses, and Dichroa sections within the Hydrangeeae tribe. Additionally, we found lower expression of accD in these sections using structure prediction and quantitative real-time PCR analysis. Phylogenomic analyses revealed the subdivision of the Hydrangeeae tribe into two clades with robust support values. Consistent with polyphyletic relationships, sect. Broussaisia was identified as the basal group in the tribe Hydrangeeae. Our study also provides insights into the phylogenetic relationships of Hydrangea petiolaris in the Jeju and Ulleung Island populations, suggesting the need for further studies with more samples and molecular data. Divergence time estimation and biogeographical analyses suggested that the common ancestors of the tribe Hydrangeeae likely originated from North America and East Asia during the Paleocene period via the Bering Land Bridge, potentially facilitating migration within the tribe between these regions. In conclusion, this study enhances our understanding of the evolutionary history and biogeography of the tribe Hydrangeeae, shedding light on the dispersal patterns and origins of this intriguing plant group with its unique disjunct distribution.
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Affiliation(s)
- Gurusamy Raman
- Department of Life Sciences, Yeungnam University, Gyeongsan, Gyeongsan-buk, Republic of Korea
| | - Kyoung-Su Choi
- Department of Life Sciences, Yeungnam University, Gyeongsan, Gyeongsan-buk, Republic of Korea
- Plant Research Team, Animal and Plant Research Department, Nakdonggang National Institute of Biological Resources, Sangju, Republic of Korea
| | - Eun Mi Lee
- Department of Life Sciences, Yeungnam University, Gyeongsan, Gyeongsan-buk, Republic of Korea
| | - Clifford W. Morden
- School of Life Sciences, University of Hawai]i at Mānoa, Honolulu, HI, USA
| | - Hyeonah Shim
- Department of Agriculture, Forestry and Bioresources, Plant Genomics and Breeding Institute, Research Institute of Agriculture and Life Science, College of Agriculture and Life Sciences, Seoul National University, Seoul, Republic of Korea
| | - Jong-Soo Kang
- Department of Agriculture, Forestry and Bioresources, Plant Genomics and Breeding Institute, Research Institute of Agriculture and Life Science, College of Agriculture and Life Sciences, Seoul National University, Seoul, Republic of Korea
| | - Tae-Jin Yang
- Department of Agriculture, Forestry and Bioresources, Plant Genomics and Breeding Institute, Research Institute of Agriculture and Life Science, College of Agriculture and Life Sciences, Seoul National University, Seoul, Republic of Korea
| | - SeonJoo Park
- Department of Life Sciences, Yeungnam University, Gyeongsan, Gyeongsan-buk, Republic of Korea
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Riewluang S, Wakeman KC. Biodiversity of symbiotic microalgae associated with meiofaunal marine acoels in Southern Japan. PeerJ 2023; 11:e16078. [PMID: 37814628 PMCID: PMC10560497 DOI: 10.7717/peerj.16078] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Accepted: 08/21/2023] [Indexed: 10/11/2023] Open
Abstract
Acoels in the family Convolutidae are commonly found with microalgal symbionts. Convolutids can host green algal Tetraselmis and dinoflagellates within the family Symbiodiniaceae and the genus Amphidinium. The diversity of these microalgae has not been well surveyed. In this study, we used PCR and culture techniques to demonstrate the biodiversity of Tetraselmis and dinoflagellates in symbiosis with meiofaunal acoels. Here, 66 acoels were collected from seven localities around Okinawa, Ishigaki, and Kochi, Japan. While convolutids were heavily represented in this sampling, some acoels formed a clade outside Convolutidae and are potentially a new family of acoels harboring symbiotic microalgae. From the acoels collected, a total of 32 Tetraselmis and 26 Symbiodiniaceae cultures were established. Molecular phylogenies were constructed from cultured material (and from total host DNA) using the 18S rRNA gene (Tetraselmis) and 28S rRNA gene (dinoflagellates). The majority of Tetraselmis sequences grouped within the T. astigmatica clade but strains closely related to T. convolutae, T. marina, and T. gracilis were also observed. This is the first report of Tetraselmis species, other than T. convolutae, naturally associating with acoels. For dinoflagellates, members of Cladocopium and Miliolidium were observed, but most Symbiodiniaceae sequences formed clusters within Symbiodinium, grouping with S. natans, or sister to S. tridacnidorum. Several new Symbiodinium sequences from this study may represent novel species. This is the first molecular record of Miliolidium and Symbiodinium from acoels. Microalgal strains from this study will provide a necessary framework for future taxonomic studies and research on symbiotic relationships between acoels and microalgae.
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Affiliation(s)
| | - Kevin C Wakeman
- Institute for the Advancement of Higher Education, Hokkaido University, Sapporo, Hokkaido, Japan
- Graduate School of Science, Hokkaido University, Sapporo, Hokkaido, Japan
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Takenaka M, Yano K, Tojo K. Phylogeography of the true freshwater crab, Geothelphusa dehaani: Detected dual dispersal routes via land and sea. ZOOLOGY 2023; 160:126118. [PMID: 37683516 DOI: 10.1016/j.zool.2023.126118] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Revised: 08/19/2023] [Accepted: 08/21/2023] [Indexed: 09/10/2023]
Abstract
Dispersal is an important factor that determines the potential for colonization to pioneer sites. Although most decapods employ seaward migration for reproduction with a planktonic larval phase, true freshwater crabs spend their entire life cycle in freshwater. Therefore, it is expected that genetic regionality can be easily detected. In this study, we focused on true freshwater crabs, Geothelphusa Stimpson, 1858. Herein, we reveal the evolutionary history and dispersal patterns of freshwater crustaceans. We collected and genetically analyzed 283 specimens at 138 localities across the Japanese Islands. Phylogenetic analyses were conducted on the combined dataset (mtDNA COI, 16S, and nDNA ITS1, histone H3 regions) and the data set based on the mtDNA COI region. The phylogenetic relationships detected 10 clades that were highly monophyletic. The highlights of this study were the discovery of several cryptic species or undescribed species, and the completely different heterogeneous dual dispersal pathways within a single species; i.e., both land and ocean routes. Although it was concluded that Japanese crabs are basically genetically divided by straits, strong evidence for dispersion via ocean currents was also detected (i.e., a "sweepstake"). It was also confirmed that Geothelphusa dehaani (White, 1847) could survive in seawater.
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Affiliation(s)
- Masaki Takenaka
- Department of Biology, Faculty of Science, Shinshu University, Asahi 3-1-1, Matsumoto 390-8621, Japan; Institute of Mountain Science, Shinshu University, Asahi 3-1-1, Matsumoto 390-8621, Japan; Faculty of Life and Environmental Sciences, University of Tsukuba, Sugadairakogen 1278-294, Ueda 386-2204, Japan
| | - Koki Yano
- Department of Biology, Faculty of Science, Shinshu University, Asahi 3-1-1, Matsumoto 390-8621, Japan; Division of Evolutionary Developmental Biology, National Institute for Basic Biology, Nishigonaka 38, Okazaki 444-0867, Japan
| | - Koji Tojo
- Department of Biology, Faculty of Science, Shinshu University, Asahi 3-1-1, Matsumoto 390-8621, Japan; Institute of Mountain Science, Shinshu University, Asahi 3-1-1, Matsumoto 390-8621, Japan.
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50
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Becz Á, Török JK. Life history of Apocarchesium arndti Norf & Foissner, 2010 (Ciliophora, Peritrichia) including recognition of a novel type of zooid. Eur J Protistol 2023; 91:126022. [PMID: 37774456 DOI: 10.1016/j.ejop.2023.126022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Revised: 08/15/2023] [Accepted: 09/11/2023] [Indexed: 10/01/2023]
Abstract
Apocarchesium rosettum and A. arndti were originally discovered in Japan (Lake Biwa) and Germany (River Rhine), respectively. We report the first record of A. arndti in the Danube and provide a detailed description of its colony development. Our findings support the theory of moderate endemicity and reveal a new, smaller zooid type in A. arndti. This zooid remains attached to the colony, connected to the stalk myoneme but lacks an aboral ciliary wreath. Unlike microzooids, it is incapable of leaving the colony. It exhibits a less spherical shape and arises from the fourth division of the colony-founder cell. Although its specific function is unknown, it is hypothesized to support the stalk dish. Our results have significant implications for understanding the systematics of vorticellids, suggesting their ancestral nature as colonial organisms characterized by a helically contracting stalk myoneme. Furthermore, the exclusive retention of the stalk myoneme by the parental cell after binary fission may serve as a synapomorphy for the Vorticellidae. We provide a descriptive analysis of the ecological environment and microhabitat of A. arndti in the Danube, revealing its preference for well-developed, detritus-rich biofilms during summer, absence in late winter and spring, emergence during peak summer, and subsequent decline until mid-winter.
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Affiliation(s)
- Álmos Becz
- Doctoral School of Biology, Institute of Biology, ELTE Eötvös Loránd University, 1117 Budapest, Hungary.
| | - Júlia Katalin Török
- Department of Systematic Zoology and Ecology, Institute of Biology, ELTE Eötvös Loránd University, 1117 Budapest, Hungary
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