1
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Martínez A, Bonaglia S, Di Domenico M, Fonseca G, Ingels J, Jörger KM, Laumer C, Leasi F, Zeppilli D, Baldrighi E, Bik H, Cepeda D, Curini-Galletti M, Cutter AD, Dos Santos G, Fattorini S, Frisch D, Gollner S, Jondelius U, Kerbl A, Kocot KM, Majdi N, Mammola S, Martín-Durán JM, Menegotto A, Montagna PA, Nascimento FJA, Puillandre N, Rognant A, Sánchez N, Santos IR, Schmidt-Rhaesa A, Schratzberger M, Semprucci F, Shimabukuro M, Sommerfield PJ, Struck TH, Sørensen MV, Wallberg A, Worsaae K, Yamasaki H, Fontaneto D. Fundamental questions in meiofauna research highlight how small but ubiquitous animals can improve our understanding of Nature. Commun Biol 2025; 8:449. [PMID: 40097602 PMCID: PMC11914145 DOI: 10.1038/s42003-025-07888-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2024] [Accepted: 03/05/2025] [Indexed: 03/19/2025] Open
Affiliation(s)
- Alejandro Martínez
- Molecular Ecology Group (MEG), Water Research Institute (CNR-IRSA), National Research Council, 28922, Verbania Pallanza, Italy.
| | - Stefano Bonaglia
- Department of Marine Sciences, University of Gothenburg, Gothenburg, Sweden
| | - Maikon Di Domenico
- Center for Marine Studies (CEM), Federal University of Paraná (UFPR), Pontal do Paraná, Paraná, Brazil
| | - Gustavo Fonseca
- Marine Science Institute, Federal University of São Paulo, Santos, Brazil
| | - Jeroen Ingels
- National Institute of Water and Atmospheric Research, 301 Evans Bay Parade, Hataitai, 6021, Wellington, New Zealand
| | | | | | - Francesca Leasi
- Department of Biology, Geology, and Environmental Science, University of Tennessee at Chattanooga, Chattanooga, TN, USA
| | - Daniela Zeppilli
- UMR6197 Biologie et Écologie des Ecosystèmes Marins Profonds, University Brest, CNRS, Ifremer, 29280, Plouzané, France
| | - Elisa Baldrighi
- Department of Biology, The University of Nevada, Reno, NV, USA
| | - Holly Bik
- Department of Marine Science & Institute of Bioinformatics, University of Georgia, Athens, GA, USA
| | - Diego Cepeda
- Department of Life Sciences, University of Alcalá (UAH), Ctra. Madrid-Barcelona Km.33, 600. 28805 Alcalá de Henares, Madrid, Spain
| | - Marco Curini-Galletti
- Department of Veterinary Medicine, University of Sassari, Sassari, Italy
- National Biodiversity Future Center (NBFC), Palermo, Italy
| | - Asher D Cutter
- Department of Ecology & Evolutionary Biology. University of Toronto, Toronto, ON, M5S3B2, Canada
| | - Giovanni Dos Santos
- Zoology Department, Federal University of Pernambuco, 50670-901, Recife-PE, Brazil
| | - Simone Fattorini
- Department of Life, Health & Environmental Sciences, University of L'Aquila, Via Vetoio - Coppito, 67100, L'Aquila, Italy
| | - Dagmar Frisch
- Department of Evolutionary and Integrative Ecology, IGB Leibniz-Institute of Freshwater Ecology and Inland Fisheries, Berlin, Germany
| | - Sabine Gollner
- Department of Ocean Systems (OCS), Royal Netherlands Institute for Sea Research (NIOZ), Landsdiep 4, 1797 SZ 't Horntje, Texel, The Netherlands
| | - Ulf Jondelius
- Swedish Museum of Natural History, Department of Zoology, POB 50007, SE-104 05, Stockholm, Sweden
| | - Alexandra Kerbl
- Department for Evolutionary Neurobiology, Centre for Organismal Studies, University Heidelberg. Im Neuenheimer Feld 230, 69120, Heidelberg, Germany
| | - Kevin M Kocot
- Department of Biological Sciences, University of Alabama, Tuscaloosa, AL, USA
| | - Nabil Majdi
- Réserve Naturelle Nationale de la Forêt de la Massane, Sorbonne Université, UPMC Université Paris 06, Observatoire Océanologique de Banyuls, 66650, Banyuls-sur-Mer, France
| | - Stefano Mammola
- Molecular Ecology Group (MEG), Water Research Institute (CNR-IRSA), National Research Council, 28922, Verbania Pallanza, Italy
- National Biodiversity Future Center (NBFC), Palermo, Italy
- Laboratory for Integrative Biodiversity Research (LIBRe), Finnish Museum of Natural History (LUOMUS), University of Helsinki, Helsinki, Finland
| | - José M Martín-Durán
- School of Biological and Behavioural Sciences. Queen Mary University of London. Mile End Road, E1 4NS, London, UK
| | - André Menegotto
- Department of Ecology, Research Centre for Biodiversity and Global Change, Autonomous University of Madrid (CIBC-UAM), C/ Darwin 2, 28049, Madrid, Spain
- Terrestrial Ecology Group (TEG-UAM), Department of Ecology, Autonomous University of Madrid, 28049, Madrid, Spain
- Department of Ecology, ICB, Federal University of Goiás, Goiânia, 74690-900, Brazil
| | - Paul A Montagna
- Harte Research Institute, Texas A&M University-Corpus Christi, Corpus Christi, TX, USA
| | | | - Nicolas Puillandre
- Institut Systématique Evolution Biodiversité (ISYEB), Muséum national d'Histoire naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, 57 rue Cuvier, CP51, Paris, France
| | - Anne Rognant
- Océanopolis. Port de Plaisance du Moulin blanc. B.P. 91039. Brest Cedex 1, Brest, 29210, France
| | - Nuria Sánchez
- Facultad de Ciencias Biológicas, Departamento de Biodiversidad, Ecología y Evolución José Antonio Novais, 12. Planta 10. 28040 Madrid, Spain. Universidad Complutense de Madrid, Madrid, Spain
| | - Isaac R Santos
- Department of Marine Sciences, University of Gothenburg, Gothenburg, Sweden
| | | | | | - Federica Semprucci
- Dipartimento di Scienze Biomolecolari., Università degli Studi di Urbino Carlo Bo, Marche, Italy
| | - Mauricio Shimabukuro
- Universidade Federal do Rio Grande (FURG) - Instituto de Oceanografia, Rio Grande, Brazil
| | | | - Torsten H Struck
- Natural History Museum, University of Oslo, 1172, Blindern, 0318, Oslo, Norway
| | - Martin V Sørensen
- Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Andreas Wallberg
- Department of Medical Biochemistry and Microbiology, Uppsala University; Husargatan 3, 751 23, Uppsala, Sweden
| | - Katrine Worsaae
- Marine Biological Section, Department of Biology, University of Copenhagen, Universitetsparken 4, 2100, Copenhagen, Denmark
| | | | - Diego Fontaneto
- Molecular Ecology Group (MEG), Water Research Institute (CNR-IRSA), National Research Council, 28922, Verbania Pallanza, Italy
- National Biodiversity Future Center (NBFC), Palermo, Italy
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2
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Khan A, Sil M, Thekaekara T, Garg KM, Sinha I, Khurana R, Sukumar R, Ramakrishnan U. Divergence and serial colonization shape genetic variation and define conservation units in Asian elephants. Curr Biol 2024; 34:4692-4703.e5. [PMID: 39341203 DOI: 10.1016/j.cub.2024.08.062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Revised: 05/15/2024] [Accepted: 08/30/2024] [Indexed: 09/30/2024]
Abstract
Asian elephants (Elephas maximus) are the largest extant terrestrial megaherbivores native to Asia, with 60% of their wild population found in India. Despite ecological and cultural importance, their population genetic structure and diversity, demographic history, and ensuing implications for management/conservation remain understudied. We analyzed 34 whole genomes (between 11× and 32×) from most known elephant landscapes in India and identified five management/conservation units corresponding to elephants in Northern (Northwestern/Northeastern), Central, and three in Southern India. Our data reveal signatures of divergence and serial colonization and a potential dilution of genetic diversity from north to south of India. The northern populations diverged from others more than 70,000 years ago, have higher genetic diversity, and have low inbreeding (pi = 0.0016 ± 0.0001; FROH > 1 MB = 0.09 ± 0.03). Two of three populations in Southern India have low diversity and are inbred, with very low effective population sizes compared with census sizes (pi = 0.0014 ± 0.00009 and 0.0015 ± 0.0001; FROH > 1 MB = 0.25 ± 0.09 and 0.17 ± 0.02). Analyses of genetic load reveal the purging of potentially high-effect insertion/deletion (indel) deleterious alleles in the southern populations and a decreasing number of deleterious alleles from north to south in India. However, despite dilution and purging for the damaging mutation load in Southern India, the load that remains is homozygous. High homozygosity of deleterious alleles, coupled with low neutral genetic diversity, make southernmost populations high priority for conservation attention. Most surprisingly, our study suggests that patterns of genetic diversity and genetic load can correspond to genomic signatures of serial founding events, even in large, highly mobile, endangered mammals.
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Affiliation(s)
- Anubhab Khan
- National Centre for Biological Sciences, TIFR, GKVK campus, Bangalore 560065, India; School of Biodiversity, One Health and Veterinary Medicine, University of Glasgow, Glasgow G128QQ, UK.
| | - Maitreya Sil
- National Centre for Biological Sciences, TIFR, GKVK campus, Bangalore 560065, India; National Institute of Science Education and Research, Bhubaneshwar 752050, India
| | - Tarsh Thekaekara
- National Centre for Biological Sciences, TIFR, GKVK campus, Bangalore 560065, India; The Shola Trust, Gudalur 643211, India
| | - Kritika M Garg
- Centre for Interdisciplinary Archaeological Research, Ashoka University, Sonipat 131029, India; Department of Biology, Ashoka University, Sonipat 131029, India
| | - Ishani Sinha
- National Centre for Biological Sciences, TIFR, GKVK campus, Bangalore 560065, India
| | - Rupsy Khurana
- Centre for Ecological Sciences, Indian Institute of Science, Bangalore 560012, India
| | - Raman Sukumar
- Centre for Ecological Sciences, Indian Institute of Science, Bangalore 560012, India.
| | - Uma Ramakrishnan
- National Centre for Biological Sciences, TIFR, GKVK campus, Bangalore 560065, India.
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3
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Defourneaux É, Herranz M, Armenteros M, Sørensen MV, Norenburg JL, Park T, Worsaae K. Circumtropical distribution and cryptic species of the meiofaunal enteropneust Meioglossus (Harrimaniidae, Hemichordata). Sci Rep 2024; 14:9296. [PMID: 38654022 DOI: 10.1038/s41598-024-57591-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Accepted: 03/20/2024] [Indexed: 04/25/2024] Open
Abstract
Hemichordata has always played a central role in evolutionary studies of Chordata due to their close phylogenetic affinity and shared morphological characteristics. Hemichordates had no meiofaunal representatives until the surprising discovery of a microscopic, paedomorphic enteropneust Meioglossus psammophilus (Harrimaniidae, Hemichordata) from the Caribbean in 2012. No additional species have been described since, questioning the broader distribution and significance of this genus. However, being less than a millimeter long and superficially resembling an early juvenile acorn worm, Meioglossus may easily be overlooked in both macrofauna and meiofauna surveys. We here present the discovery of 11 additional populations of Meioglossus from shallow subtropical and tropical coralline sands of the Caribbean Sea, Red Sea, Indian Ocean, and East China Sea. These geographically separated populations show identical morphology but differ genetically. Our phylogenetic reconstructions include four gene markers and support the monophyly of Meioglossus. Species delineation analyses revealed eight new cryptic species, which we herein describe using DNA taxonomy. This study reveals a broad circumtropical distribution, supporting the validity and ecological importance of this enigmatic meiobenthic genus. The high cryptic diversity and apparent morphological stasis of Meioglossus may exemplify a potentially common evolutionary 'dead-end' scenario, where groups with highly miniaturized and simplified body plan lose their ability to diversify morphologically.
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Affiliation(s)
- Éloïse Defourneaux
- Marine Biological Section, Department of Biology, University of Copenhagen, Universitetsparken 4, DK-2100, Copenhagen, Denmark
| | - Maria Herranz
- Marine Biological Section, Department of Biology, University of Copenhagen, Universitetsparken 4, DK-2100, Copenhagen, Denmark
- Area of Biodiversity and Conservation, Superior School of Experimental Science and Technology (ESCET), Rey Juan Carlos University, C/ Tulipán S/N, 28933, Mostoles, Madrid, Spain
| | - Maickel Armenteros
- Unidad Académica Mazatlán, Instituto de Ciencias del Mar y Limnología, Universidad Nacional Autónoma de México, Av. Joel Montes Camarena S/N, 82040, Mazatlán, México
| | - Martin V Sørensen
- Natural History Museum Denmark, University of Copenhagen, Universitetsparken 15, DK-2100, Copenhagen, Denmark
| | - Jon L Norenburg
- Smithsonian National Museum of Natural History, Washington, DC, USA
| | - Taeseo Park
- Species Diversity Research Division, National Institute of Biological Resources, Hwangyeong-Ro 42, Incheon, 22689, South Korea
| | - Katrine Worsaae
- Marine Biological Section, Department of Biology, University of Copenhagen, Universitetsparken 4, DK-2100, Copenhagen, Denmark.
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4
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Cerca J. Understanding natural selection and similarity: Convergent, parallel and repeated evolution. Mol Ecol 2023; 32:5451-5462. [PMID: 37724599 DOI: 10.1111/mec.17132] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Revised: 08/26/2023] [Accepted: 08/30/2023] [Indexed: 09/21/2023]
Abstract
Parallel and convergent evolution offer some of the most compelling evidence for the significance of natural selection in evolution, as the emergence of similar adaptive solutions is unlikely to occur by random chance alone. However, these terms are often employed inconsistently, leading to misinterpretation and confusion, and recently proposed definitions have unintentionally diminished the emphasis on the evolution of similar adaptive solutions. Here, I examine various conceptual frameworks and definitions related to parallel and convergent evolution and propose a consolidated framework that enhances our comprehension of these evolutionary patterns. The primary aim of this framework is to harmonize the concepts of parallel and convergent evolution together with natural selection and the idea of similarity. Both concepts involve the evolution of similar adaptive solutions as a result of environmental challenges. The distinction lies in ancestral phenotypes. Parallel evolution takes place when the ancestral phenotypes (before selection) of the lineages are similar. Convergent evolution happens when the lineages have distinct ancestral phenotypes (before selection). Because an ancestral-based distinction will inevitably lead to cases where uncertainty in the distinction may arise, the framework includes a general term, repeated evolution, which can be used as a term applying to the evolution of similar phenotypes and genotypes as well as similar responses to environmental pressures. Based on the argument that genetic similarity may frequently arise without selection, the framework posits that the similarity of genetic sequences is not of great interest unless linked to the actions of natural selection or to the origins (mutation, standing genetic variation, gene flow) and locations of the similar sequences.
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Affiliation(s)
- José Cerca
- CEES - Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, Oslo, Norway
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5
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Fleming JF, Struck TH. nRCFV: a new, dataset-size-independent metric to quantify compositional heterogeneity in nucleotide and amino acid datasets. BMC Bioinformatics 2023; 24:145. [PMID: 37046225 PMCID: PMC10099917 DOI: 10.1186/s12859-023-05270-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Accepted: 04/04/2023] [Indexed: 04/14/2023] Open
Abstract
MOTIVATION Compositional heterogeneity-when the proportions of nucleotides and amino acids are not broadly similar across the dataset-is a cause of a great number of phylogenetic artefacts. Whilst a variety of methods can identify it post-hoc, few metrics exist to quantify compositional heterogeneity prior to the computationally intensive task of phylogenetic tree reconstruction. Here we assess the efficacy of one such existing, widely used, metric: Relative Composition Frequency Variability (RCFV), using both real and simulated data. RESULTS Our results show that RCFV can be biased by sequence length, the number of taxa, and the number of possible character states within the dataset. However, we also find that missing data does not appear to have an appreciable effect on RCFV. We discuss the theory behind this, the consequences of this for the future of the usage of the RCFV value and propose a new metric, nRCFV, which accounts for these biases. Alongside this, we present a new software that calculates both RCFV and nRCFV, called nRCFV_Reader. AVAILABILITY AND IMPLEMENTATION nRCFV has been implemented in RCFV_Reader, available at: https://github.com/JFFleming/RCFV_Reader . Both our simulation and real data are available at Datadryad: https://doi.org/10.5061/dryad.wpzgmsbpn .
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Affiliation(s)
- James F Fleming
- University of Oslo Natural History Museum, Sars' Gata 1, Oslo, Norway.
| | - Torsten H Struck
- University of Oslo Natural History Museum, Sars' Gata 1, Oslo, Norway
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6
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Newton LG, Starrett J, Jochim EE, Bond JE. Phylogeography and cohesion species delimitation of California endemic trapdoor spiders within the Aptostichus icenoglei sibling species complex (Araneae: Mygalomorphae: Euctenizidae). Ecol Evol 2023; 13:e10025. [PMID: 37122769 PMCID: PMC10133383 DOI: 10.1002/ece3.10025] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Revised: 03/30/2023] [Accepted: 04/05/2023] [Indexed: 05/02/2023] Open
Abstract
Species delimitation is an imperative first step toward understanding Earth's biodiversity, yet what constitutes a species and the relative importance of the various processes by which new species arise continue to be debatable. Species delimitation in spiders has traditionally used morphological characters; however, certain mygalomorph spiders exhibit morphological homogeneity despite long periods of population-level isolation, absence of gene flow, and consequent high degrees of molecular divergence. Studies have shown strong geographic structuring and significant genetic divergence among several species complexes within the trapdoor spider genus Aptostichus, most of which are restricted to the California Floristic Province (CAFP) biodiversity hotspot. Specifically, the Aptostichus icenoglei complex, which comprises the three sibling species, A. barackobamai, A. isabella, and A. icenoglei, exhibits evidence of cryptic mitochondrial DNA diversity throughout their ranges in Northern, Central, and Southern California. Our study aimed to explicitly test species hypotheses within this assemblage by implementing a cohesion species-based approach. We used genomic-scale data (ultraconserved elements, UCEs) to first evaluate genetic exchangeability and then assessed ecological interchangeability of genetic lineages. Biogeographical analysis was used to assess the likelihood of dispersal versus vicariance events that may have influenced speciation pattern and process across the CAFP's complex geologic and topographic landscape. Considering the lack of congruence across data types and analyses, we take a more conservative approach by retaining species boundaries within A. icenoglei.
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Affiliation(s)
- Lacie G. Newton
- Department of Entomology & NematologyUniversity of CaliforniaDavisCaliforniaUSA
| | - James Starrett
- Department of Entomology & NematologyUniversity of CaliforniaDavisCaliforniaUSA
| | - Emma E. Jochim
- Department of Entomology & NematologyUniversity of CaliforniaDavisCaliforniaUSA
| | - Jason E. Bond
- Department of Entomology & NematologyUniversity of CaliforniaDavisCaliforniaUSA
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7
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Bachmann L, Beermann J, Brey T, de Boer HJ, Dannheim J, Edvardsen B, Ericson PGP, Holston KC, Johansson VA, Kloss P, Konijnenberg R, Osborn KJ, Pappalardo P, Pehlke H, Piepenburg D, Struck TH, Sundberg P, Markussen SS, Teschke K, Vanhove MPM. The role of systematics for understanding ecosystem functions: Proceedings of the Zoologica Scripta Symposium, Oslo, Norway, 25 August 2022. ZOOL SCR 2023. [DOI: 10.1111/zsc.12593] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/28/2023]
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8
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Nickel J, Cordellier M. Cost-saving population genomic investigation of Daphnia longispina complex resting eggs using whole-genome amplification and pre-sequencing screening. Ecol Evol 2022; 12:e9682. [PMID: 36582775 PMCID: PMC9793289 DOI: 10.1002/ece3.9682] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Revised: 11/02/2022] [Accepted: 12/07/2022] [Indexed: 12/28/2022] Open
Abstract
Resting stages of aquatic organisms that accumulate in the sediment over time are an exceptional resource that allows direct insights into past populations and addressing evolutionary questions. This is of particular interest in taxa that face relatively new environmental challenges, e.g., climate change and eutrophication, such as the Daphnia longispina species complex, a keystone zooplankton group in European freshwater ecosystems. However, genomic analysis might be challenging as DNA yield from many of these resting stages can be low and the material degraded. To reliably allow the resequencing of single Daphnia resting eggs from different sediment layers and characterize genomic changes through time, we performed whole-genome amplification to obtain DNA amounts suitable for genome resequencing and tested multiple protocols involving egg isolation, whole-genome amplification kits, and library preparation. A pre-sequencing contamination screening was developed, consisting of amplifying mitochondrial Daphnia and bacterial markers, to quickly assess and exclude possibly contaminated samples. In total, we successfully amplified and sequenced nine genomes from Daphnia resting eggs that could be identified as Daphnia longispina species. We analyzed the genome coverage and heterozygosity of these samples to optimize this method for future projects involving population genomic investigation of the resting egg bank.
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Affiliation(s)
- Jana Nickel
- Institute of Animal Cell and Systems BiologyUniversity of HamburgHamburgGermany
| | - Mathilde Cordellier
- Institute of Animal Cell and Systems BiologyUniversity of HamburgHamburgGermany
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9
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Decoupling in Diversification and Body Size Rates During the Radiation of Phyllodactylus: Evidence Suggests Minor Role of Ecology in Shaping Phenotypes. Evol Biol 2022. [DOI: 10.1007/s11692-022-09575-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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10
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Aguado MT, Ponz-Segrelles G, Glasby CJ, Ribeiro RP, Nakamura M, Oguchi K, Omori A, Kohtsuka H, Fisher C, Ise Y, Jimi N, Miura T. Ramisyllis kingghidorahi n. sp., a new branching annelid from Japan. ORG DIVERS EVOL 2022. [DOI: 10.1007/s13127-021-00538-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
AbstractAmong over 20,000 species of Annelida, only two branching species with a highly modified body-pattern are known until now: the Syllidae Syllis ramosa McIntosh, 1879, and Ramisyllis multicaudata Glasby et al. (Zoological Journal of the Linnean Society, 164, 481–497, 2012). Both have unusual ramified bodies with one head and multiple branches and live inside the canals of host sponges. Using an integrative approach (combining morphology, internal anatomy, ecology, phylogeny, genetic divergence, and the complete mitochondrial genome), we describe a new branching species from Japan, Ramisyllis kingghidorahi n. sp., inhabiting an undescribed species of Petrosia (Porifera: Demospongiae) from shallow waters. We compare the new species with its closest relative, R. multicaudata; emend the diagnosis of Ramisyllis; and discuss previous reports of S. ramosa. This study suggests a much higher diversity of branching syllids than currently known. Finally, we discuss possible explanations for the feeding behaviour in the new species in relation to its highly ciliated wall of the digestive tubes (especially at the distal branches and anus), and provide a hypothesis for the evolution of branching body patterns as the result of an adaptation to the host sponge labyrinthic canal system.
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11
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Sowersby W, Cerca J, Wong BBM, Lehtonen TK, Chapple DG, Leal-Cardín M, Barluenga M, Ravinet M. Pervasive admixture and the spread of a large-lipped form in a cichlid fish radiation. Mol Ecol 2021; 30:5551-5571. [PMID: 34418206 DOI: 10.1111/mec.16139] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2019] [Revised: 07/31/2021] [Accepted: 08/11/2021] [Indexed: 12/30/2022]
Abstract
Adaptive radiations have proven important for understanding the mechanisms and processes underlying biological diversity. The convergence of form and function, as well as admixture and adaptive introgression, are common in adaptive radiations. However, distinguishing between these two scenarios remains a challenge for evolutionary research. The Midas cichlid species complex (Amphilophus spp.) is a prime example of adaptive radiation, with phenotypic diversification occurring at various stages of genetic differentiation. One species, A. labiatus, has large fleshy lips, is associated with rocky lake substrates, and occurs patchily within Lakes Nicaragua and Managua. By contrast, the similar, but thin-lipped, congener, A. citrinellus, is more common and widespread. We investigated the evolutionary history of the large-lipped form, specifically regarding whether the trait has evolved independently in both lakes from ancestral thin-lipped populations, or via dispersal and/or admixture events. We collected samples from distinct locations in both lakes, and assessed differences in morphology and ecology. Using RAD-seq, we genotyped thousands of SNPs to measure population structure and divergence, demographic history, and admixture. We found significant between-species differences in ecology and morphology, local intraspecific differences in body shape and trophic traits, but only limited intraspecific variation in lip shape. Despite clear ecological differences, our genomic approach uncovered pervasive admixture between the species and low genomic differentiation, with species within lakes being genetically more similar than species between lakes. Taken together, our results suggest a single origin of large-lips, followed by pervasive admixture and adaptive introgression, with morphology being driven by local ecological opportunities, despite ongoing gene-flow.
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Affiliation(s)
- Will Sowersby
- School of Biological Sciences, Monash University, Melbourne, Victoria, Australia.,Department of Biology, Osaka City University, Osaka, Japan
| | - José Cerca
- Frontiers of Evolutionary Zoology Research Group, Natural History Museum, University of Oslo, Oslo, Norway.,Department of Environmental Science, Policy and Management, University of California, Berkeley, Berkeley, California, USA.,Department of Natural History, NTNU University Museum, Norwegian University of Science and Technology, Trondheim, Norway
| | - Bob B M Wong
- School of Biological Sciences, Monash University, Melbourne, Victoria, Australia
| | - Topi K Lehtonen
- School of Biological Sciences, Monash University, Melbourne, Victoria, Australia.,Department of Biology, University of Turku, Turku, Finland.,Organismal and Evolutionary Biology, University of Helsinki, Helsinki, Finland
| | - David G Chapple
- School of Biological Sciences, Monash University, Melbourne, Victoria, Australia
| | - Mariana Leal-Cardín
- Department of Biodiversity and Evolutionary Biology, Museo Nacional de Ciencias Naturales, CSIC, Madrid, Spain.,Universidad de Alcalá de Henares, Madrid, Spain
| | - Marta Barluenga
- Department of Biodiversity and Evolutionary Biology, Museo Nacional de Ciencias Naturales, CSIC, Madrid, Spain
| | - Mark Ravinet
- Centre for Ecological and Evolutionary Synthesis, University of Oslo, Oslo, Norway.,Division of Population Genetics, National Institute of Genetics, Mishima, Japan.,School of Life Sciences, University of Nottingham, Nottingham, UK
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12
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Kobmoo N, Arnamnart N, Pootakham W, Sonthirod C, Khonsanit A, Kuephadungphan W, Suntivich R, Mosunova O, Giraud T, Luangsa-ard J. The integrative taxonomy of Beauveria asiatica and B. bassiana species complexes with whole-genome sequencing, morphometric and chemical analyses. PERSOONIA 2021; 47:136-150. [PMID: 38352976 PMCID: PMC10784665 DOI: 10.3767/persoonia.2023.47.04] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Figures] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Accepted: 08/12/2021] [Indexed: 02/16/2024]
Abstract
Fungi are rich in complexes of cryptic species that need a combination of different approaches to be delimited, including genomic information. Beauveria (Cordycipitaceae, Hypocreales) is a well-known genus of entomopathogenic fungi, used as a biocontrol agent. In this study we present a polyphasic taxonomy regarding two widely distributed complexes of Beauveria: B. asiatica and B. bassiana s.lat. Some of the genetic groups as previously detected within both taxa were either confirmed or fused using population genomics. High levels of divergence were found between two clades in B. asiatica and among three clades in B. bassiana, supporting their subdivision as distinct species. Morphological examination focusing on the width and the length of phialides and conidia showed no difference among the clades within B. bassiana while conidial length was significantly different among clades within B. asiatica. The secondary metabolite profiles obtained by liquid chromatography-mass spectrometry (LC-MS) allowed a distinction between B. asiatica and B. bassiana, but not between the clades therein. Based on these genomic, morphological, chemical data, we proposed a clade of B. asiatica as a new species, named B. thailandica, and two clades of B. bassiana to respectively represent B. namnaoensis and B. neobassiana spp. nov. Such closely related but divergent species with different host ranges have potential to elucidate the evolution of host specificity, with potential biocontrol application. Citation: Kobmoo N, Arnamnart N, Pootakham W, et al. 2021. The integrative taxonomy of Beauveria asiatica and B. bassiana species complexes with whole-genome sequencing, morphometric and chemical analyses. Persoonia 47: 136-150. https://doi.org/10.3767/persoonia.2021.47.04.
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Affiliation(s)
- N. Kobmoo
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), 113 Thailand Science Park, Phahonyothin Rd., Khlong Nueng, Khlong Luang, Pathum Thani 12120, Thailand
| | - N. Arnamnart
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), 113 Thailand Science Park, Phahonyothin Rd., Khlong Nueng, Khlong Luang, Pathum Thani 12120, Thailand
| | - W. Pootakham
- National Omics Center, National Science and Technology Development Agency (NSTDA), Pathum Thani, Thailand
| | - C. Sonthirod
- National Omics Center, National Science and Technology Development Agency (NSTDA), Pathum Thani, Thailand
| | - A. Khonsanit
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), 113 Thailand Science Park, Phahonyothin Rd., Khlong Nueng, Khlong Luang, Pathum Thani 12120, Thailand
| | - W. Kuephadungphan
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), 113 Thailand Science Park, Phahonyothin Rd., Khlong Nueng, Khlong Luang, Pathum Thani 12120, Thailand
| | - R. Suntivich
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), 113 Thailand Science Park, Phahonyothin Rd., Khlong Nueng, Khlong Luang, Pathum Thani 12120, Thailand
| | - O.V. Mosunova
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
| | - T. Giraud
- Ecologie Systématique Evolution, CNRS, AgroParisTech, Université Paris-Saclay, Orsay, France
| | - J.J. Luangsa-ard
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), 113 Thailand Science Park, Phahonyothin Rd., Khlong Nueng, Khlong Luang, Pathum Thani 12120, Thailand
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Zhou X, Zhang ZC, Huang YB, Xiao HW, Wu JJ, Qi ZC, Wei YK. Conservation Genomics of Wild Red Sage ( Salvia miltiorrhiza) and Its Endangered Relatives in China: Population Structure and Interspecific Relationships Revealed From 2b-RAD Data. Front Genet 2021; 12:688323. [PMID: 34046061 PMCID: PMC8144715 DOI: 10.3389/fgene.2021.688323] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Accepted: 04/13/2021] [Indexed: 12/28/2022] Open
Abstract
Red sage (Salvia miltiorrhiza) is a widely used medicinal plant for treatment of cardiovascular and cerebrovascular diseases. Because of excessive excavation by huge market demand and habitat loss by human activities, the wild population resources of S. miltiorrhiza have reduced drastically in recent years. Meanwhile, population status of two closely related species S. bowleyana and S. paramiltiorrhiza were in a trend of decreasing due to their potential replacement of S. miltiorrhiza. Particularly, S. paramiltiorrhiza was threatened and endemic to a small region in eastern China. However, to date there has been no conservation genetic research reported for wild S. miltiorrhiza population and its endangered relatives. Assess the wild germplasm diversity for S. miltiorrhiza and its related species would provide fundamental genetic background for cultivation and molecular breeding of this medicinally important species. In the present study, we investigated the genetic diversity, population structure, and intra/inter-specific differentiation of S. miltiorrhiza and above two relatives using 2b-RAD genome-wide genotyping method. By investigating 81 individuals of S. miltiorrhiza, 55 individuals of S. bowleyana and 15 individuals of S. paramiltiorrhiza from 23 locations in China, we obtained 23,928 SNPs in total. A comparatively high genetic diversity was observed in S. miltiorrhiza (π = 0.0788, H e = 0.0783 ± 0.0007). The observed and expected heterozygosity in populations of these three species ranged from 0.0297 to 0.1481 and 0.0251 to 0.831, respectively. Two major lineage groups were detected in the examined S. miltiorrhiza populations. The results indicated that Dabie Mountain as a genetic diversity center of S. miltiorrhiza and possible complex inter-specific genetic exchange/hybridization occurred between S. miltiorrhiza and the two relatives. We suggest that strategic conservation and germplasm preservation should be considered not only for wild populations of S. miltiorrhiza, but also for its related S. bowleyana and S. paramiltiorrhiza.
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Affiliation(s)
- Xuan Zhou
- Zhejiang Province Key Laboratory of Plant Secondary Metabolism and Regulation, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, China
- Shanghai Key Laboratory of Plant Functional Genomics and Resources and Eastern China Conservation Center for Wild Endangered Plant Resources, Shanghai Chenshan Botanical Garden, Shanghai, China
| | - Zhi-Cheng Zhang
- Zhejiang Province Key Laboratory of Plant Secondary Metabolism and Regulation, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, China
- Shanghai Key Laboratory of Plant Functional Genomics and Resources and Eastern China Conservation Center for Wild Endangered Plant Resources, Shanghai Chenshan Botanical Garden, Shanghai, China
| | - Yan-Bo Huang
- Shanghai Key Laboratory of Plant Functional Genomics and Resources and Eastern China Conservation Center for Wild Endangered Plant Resources, Shanghai Chenshan Botanical Garden, Shanghai, China
| | - Han-Wen Xiao
- Shanghai Key Laboratory of Plant Functional Genomics and Resources and Eastern China Conservation Center for Wild Endangered Plant Resources, Shanghai Chenshan Botanical Garden, Shanghai, China
| | - Jun-Jie Wu
- Zhejiang Province Key Laboratory of Plant Secondary Metabolism and Regulation, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, China
| | - Zhe-Chen Qi
- Zhejiang Province Key Laboratory of Plant Secondary Metabolism and Regulation, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, China
- Shaoxing Academy of Biomedicine of Zhejiang Sci-Tech University, Shaoxing, China
| | - Yu-Kun Wei
- Shanghai Key Laboratory of Plant Functional Genomics and Resources and Eastern China Conservation Center for Wild Endangered Plant Resources, Shanghai Chenshan Botanical Garden, Shanghai, China
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