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Wilenzik IV, Barger BB, Pyron RA. Fossil-informed biogeographic analysis suggests Eurasian regionalization in crown Squamata during the early Jurassic. PeerJ 2024; 12:e17277. [PMID: 38708352 PMCID: PMC11067913 DOI: 10.7717/peerj.17277] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Accepted: 04/01/2024] [Indexed: 05/07/2024] Open
Abstract
Background Squamata (lizards, snakes, and amphisbaenians) is a Triassic lineage with an extensive and complex biogeographic history, yet no large-scale study has reconstructed the ancestral range of early squamate lineages. The fossil record indicates a broadly Pangaean distribution by the end- Cretaceous, though many lineages (e.g., Paramacellodidae, Mosasauria, Polyglyphanodontia) subsequently went extinct. Thus, the origin and occupancy of extant radiations is unclear and may have been localized within Pangaea to specific plates, with potential regionalization to distinct Laurasian and Gondwanan landmasses during the Mesozoic in some groups. Methods We used recent tectonic models to code extant and fossil squamate distributions occurring on nine discrete plates for 9,755 species, with Jurassic and Cretaceous fossil constraints from three extinct lineages. We modeled ancestral ranges for crown Squamata from an extant-only molecular phylogeny using a suite of biogeographic models accommodating different evolutionary processes and fossil-based node constraints from known Jurassic and Cretaceous localities. We hypothesized that the best-fit models would not support a full Pangaean distribution (i.e., including all areas) for the origin of crown Squamata, but would instead show regionalization to specific areas within the fragmenting supercontinent, likely in the Northern Hemisphere where most early squamate fossils have been found. Results Incorporating fossil data reconstructs a localized origin within Pangaea, with early regionalization of extant lineages to Eurasia and Laurasia, while Gondwanan regionalization did not occur until the middle Cretaceous for Alethinophidia, Scolecophidia, and some crown Gekkotan lineages. While the Mesozoic history of extant squamate biogeography can be summarized as a Eurasian origin with dispersal out of Laurasia into Gondwana, their Cenozoic history is complex with multiple events (including secondary and tertiary recolonizations) in several directions. As noted by previous authors, squamates have likely utilized over-land range expansion, land-bridge colonization, and trans-oceanic dispersal. Tropical Gondwana and Eurasia hold more ancient lineages than the Holarctic (Rhineuridae being a major exception), and some asymmetries in colonization (e.g., to North America from Eurasia during the Cenozoic through Beringia) deserve additional study. Future studies that incorporate fossil branches, rather than as node constraints, into the reconstruction can be used to explore this history further.
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Affiliation(s)
- Ian V. Wilenzik
- Department of Biology, George Washington University, Washington D.C., United States of America
| | - Benjamin B. Barger
- Department of Biology, George Washington University, Washington D.C., United States of America
| | - R. Alexander Pyron
- Department of Biology, George Washington University, Washington D.C., United States of America
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2
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Portik DM, Streicher JW, Wiens JJ. Frog phylogeny: A time-calibrated, species-level tree based on hundreds of loci and 5,242 species. Mol Phylogenet Evol 2023; 188:107907. [PMID: 37633542 DOI: 10.1016/j.ympev.2023.107907] [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: 01/15/2023] [Revised: 08/15/2023] [Accepted: 08/15/2023] [Indexed: 08/28/2023]
Abstract
Large-scale, time-calibrated phylogenies from supermatrix studies have become crucial for evolutionary and ecological studies in many groups of organisms. However, in frogs (anuran amphibians), there is a serious problem with existing supermatrix estimates. Specifically, these trees are based on a limited number of loci (15 or fewer), and the higher-level relationships estimated are discordant with recent phylogenomic estimates based on much larger numbers of loci. Here, we attempted to rectify this problem by generating an expanded supermatrix and combining this with data from phylogenomic studies. To assist in aligning ribosomal sequences for this supermatrix, we developed a new program (TaxonomyAlign) to help perform taxonomy-guided alignments. The new combined matrix contained 5,242 anuran species with data from 307 markers, but with 95% missing data overall. This dataset represented a 71% increase in species sampled relative to the previous largest supermatrix analysis of anurans (adding 2,175 species). Maximum-likelihood analyses generated a tree in which higher-level relationships (and estimated clade ages) were generally concordant with those from phylogenomic analyses but were more discordant with the previous largest supermatrix analysis. We found few obvious problems arising from the extensive missing data in most species. We also generated a set of 100 time-calibrated trees for use in comparative analyses. Overall, we provide an improved estimate of anuran phylogeny based on the largest number of combined taxa and markers to date. More broadly, we demonstrate the potential to combine phylogenomic and supermatrix analyses in other groups of organisms.
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Affiliation(s)
- Daniel M Portik
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ 85721 USA; California Academy of Sciences, San Francisco, CA 94118, USA
| | | | - John J Wiens
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ 85721 USA.
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Skeels A, Boschman LM, McFadden IR, Joyce EM, Hagen O, Jiménez Robles O, Bach W, Boussange V, Keggin T, Jetz W, Pellissier L. Paleoenvironments shaped the exchange of terrestrial vertebrates across Wallace's Line. Science 2023; 381:86-92. [PMID: 37410831 DOI: 10.1126/science.adf7122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Accepted: 06/01/2023] [Indexed: 07/08/2023]
Abstract
Faunal turnover in Indo-Australia across Wallace's Line is one of the most recognizable patterns in biogeography and has catalyzed debate about the role of evolutionary and geoclimatic history in biotic interchanges. Here, analysis of more than 20,000 vertebrate species with a model of geoclimate and biological diversification shows that broad precipitation tolerance and dispersal ability were key for exchange across the deep-time precipitation gradient spanning the region. Sundanian (Southeast Asian) lineages evolved in a climate similar to the humid "stepping stones" of Wallacea, facilitating colonization of the Sahulian (Australian) continental shelf. By contrast, Sahulian lineages predominantly evolved in drier conditions, hampering establishment in Sunda and shaping faunal distinctiveness. We demonstrate how the history of adaptation to past environmental conditions shapes asymmetrical colonization and global biogeographic structure.
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Affiliation(s)
- A Skeels
- Department of Environmental Systems Science, Ecosystems and Landscape Evolution, Institute of Terrestrial Ecosystems, ETH Zurich, 8092 Zurich, Switzerland
- Swiss Federal Institute for Forest, Snow and Landscape Research WSL, 8903 Birmensdorf, Switzerland
- Research School of Biology, Australian National University, Canberra 0200, Australia
| | - L M Boschman
- Department of Earth Sciences, Utrecht University, 3584 CB Utrecht, Netherlands
| | - I R McFadden
- Department of Environmental Systems Science, Ecosystems and Landscape Evolution, Institute of Terrestrial Ecosystems, ETH Zurich, 8092 Zurich, Switzerland
- Swiss Federal Institute for Forest, Snow and Landscape Research WSL, 8903 Birmensdorf, Switzerland
- Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, 1090 GE Amsterdam, Netherlands
| | - E M Joyce
- Systematics, Biodiversity and Evolution of Plants, Ludwig Maximilian University of Munich, 80331 Munich, Germany
| | - O Hagen
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, 04103 Leipzig, Germany
| | - O Jiménez Robles
- Research School of Biology, Australian National University, Canberra 0200, Australia
- Institute of Biology, École Normale Supérieure, 75005 Paris, France
| | - W Bach
- Department of Environmental Systems Science, Ecosystems and Landscape Evolution, Institute of Terrestrial Ecosystems, ETH Zurich, 8092 Zurich, Switzerland
- Swiss Federal Institute for Forest, Snow and Landscape Research WSL, 8903 Birmensdorf, Switzerland
| | - V Boussange
- Department of Environmental Systems Science, Ecosystems and Landscape Evolution, Institute of Terrestrial Ecosystems, ETH Zurich, 8092 Zurich, Switzerland
- Swiss Federal Institute for Forest, Snow and Landscape Research WSL, 8903 Birmensdorf, Switzerland
| | - T Keggin
- Department of Environmental Systems Science, Ecosystems and Landscape Evolution, Institute of Terrestrial Ecosystems, ETH Zurich, 8092 Zurich, Switzerland
- Swiss Federal Institute for Forest, Snow and Landscape Research WSL, 8903 Birmensdorf, Switzerland
| | - W Jetz
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT 06520, USA
- Center for Biodiversity and Global Change, Yale University, New Haven, CT 06520, USA
| | - L Pellissier
- Department of Environmental Systems Science, Ecosystems and Landscape Evolution, Institute of Terrestrial Ecosystems, ETH Zurich, 8092 Zurich, Switzerland
- Swiss Federal Institute for Forest, Snow and Landscape Research WSL, 8903 Birmensdorf, Switzerland
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Population genetic structure and evolutionary demographic patterns of Phrynoderma karaavali, an edible frog species of Kerala, India. J Genet 2022. [DOI: 10.1007/s12041-022-01407-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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Abstract
Salamanders are an important group of living amphibians and model organisms for understanding locomotion, development, regeneration, feeding, and toxicity in tetrapods. However, their origin and early radiation remain poorly understood, with early fossil stem-salamanders so far represented by larval or incompletely known taxa. This poor record also limits understanding of the origin of Lissamphibia (i.e., frogs, salamanders, and caecilians). We report fossils from the Middle Jurassic of Scotland representing almost the entire skeleton of the enigmatic stem-salamander Marmorerpeton. We use computed tomography to visualize high-resolution three-dimensional anatomy, describing morphologies that were poorly characterized in early salamanders, including the braincase, scapulocoracoid, and lower jaw. We use these data in the context of a phylogenetic analysis intended to resolve the relationships of early and stem-salamanders, including representation of important outgroups alongside data from high-resolution imaging of extant species. Marmorerpeton is united with Karaurus, Kokartus, and others from the Middle Jurassic-Lower Cretaceous of Asia, providing evidence for an early radiation of robustly built neotenous stem-salamanders. These taxa display morphological specializations similar to the extant cryptobranchid "giant" salamanders. Our analysis also demonstrates stem-group affinities for a larger sample of Jurassic species than previously recognized, highlighting an unappreciated diversity of stem-salamanders and cautioning against the use of single species (e.g., Karaurus) as exemplars for stem-salamander anatomy. These phylogenetic findings, combined with knowledge of the near-complete skeletal anatomy of Mamorerpeton, advance our understanding of evolutionary changes on the salamander stem-lineage and provide important data on early salamanders and the origins of Batrachia and Lissamphibia.
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Comparative Mitogenomics of True Frogs (Ranidae, Anura), and Its Implications for the Phylogeny and Evolutionary History of Rana. Animals (Basel) 2022; 12:ani12101250. [PMID: 35625095 PMCID: PMC9137629 DOI: 10.3390/ani12101250] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Revised: 05/09/2022] [Accepted: 05/09/2022] [Indexed: 12/04/2022] Open
Abstract
Simple Summary The true frogs of the genus Rana are a complex and diverse group. Many new species have been discovered with the help of molecular markers and morphological traits. However, the evolutionary history in Rana were not well understood. In this study, we sequenced and annotated the complete mitochondrial genome of R. longicrus and R. zhenhaiensis. In 13 protein codon genes, the COI was the most conserved, and ATP8 had a fast rate of evolution. The Ka/Ks ratio analysis among Rana indicated the protein-coding genes were suffering purify selection. There were three kinds of gene arrangement patterns found. This study provides mitochondrial genetic information, improving our understanding of mitogenomic structure and evolution, and recognizes the phylogenetic relationship and taxonomy among Rana. Abstract The true frogs of the genus Rana are a complex and diverse group, containing approximately 60 species with wide distribution across Eurasia and the Americas. Recently, many new species have been discovered with the help of molecular markers and morphological traits. However, the evolutionary history in Rana was not well understood and might be limited by the absence of mitogenome information. In this study, we sequenced and annotated the complete mitochondrial genome of R. longicrus and R. zhenhaiensis, containing 22 tRNAs, 13 protein-coding genes, two ribosomal RNAs, and a non-coding region, with 17,502 bp and 18,006 bp in length, respectively. In 13 protein codon genes, the COI was the most conserved, and ATP8 had a fast rate of evolution. The Ka/Ks ratio analysis among Rana indicated the protein-coding genes were suffering purify selection. There were three kinds of gene arrangement patterns found. The mitochondrial gene arrangement was not related to species diversification, and several independent shifts happened in evolutionary history. Climate fluctuation and environmental change may have played an essential role in species diversification in Rana. This study provides mitochondrial genetic information, improving our understanding of mitogenomic structure and evolution, and recognizes the phylogenetic relationship and taxonomy among Rana.
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Dufresnes C, Litvinchuk SN. Diversity, distribution and molecular species delimitation in frogs and toads from the Eastern Palaearctic. Zool J Linn Soc 2021. [DOI: 10.1093/zoolinnean/zlab083] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Abstract
Biodiversity analyses can greatly benefit from coherent species delimitation schemes and up-to-date distribution data. In this article, we have made the daring attempt to delimit and map described and undescribed lineages of anuran amphibians in the Eastern Palaearctic (EP) region in its broad sense. Through a literature review, we have evaluated the species status considering reproductive isolation and genetic divergence, combined with an extensive occurrence dataset (nearly 85k localities). Altogether 274 native species from 46 genera and ten families were retrieved, plus eight additional species introduced from other realms. Independent hotspots of species richness were concentrated in southern Tibet (Medog County), the circum-Sichuan Basin region, Taiwan, the Korean Peninsula and the main Japanese islands. Phylogeographic breaks responsible for recent in situ speciation events were shared around the Sichuan Mountains, across Honshu and between the Ryukyu Island groups, but not across shallow water bodies like the Yellow Sea and the Taiwan Strait. Anuran compositions suggested to restrict the zoogeographical limits of the EP to East Asia. In a rapidly evolving field, our study provides a checkpoint to appreciate patterns of species diversity in the EP under a single, spatially explicit, species delimitation framework that integrates phylogeographic data in taxonomic research.
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Affiliation(s)
- Christophe Dufresnes
- LASER, College of Biology & Environment, Nanjing Forestry University, Nanjing, China
| | - Spartak N Litvinchuk
- Institute of Cytology, Russian Academy of Sciences, St. Petersburg, Russia
- Department of Biology, Dagestan State University, Makhachkala, Russia
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8
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Yamahira K, Ansai S, Kakioka R, Yaguchi H, Kon T, Montenegro J, Kobayashi H, Fujimoto S, Kimura R, Takehana Y, Setiamarga DHE, Takami Y, Tanaka R, Maeda K, Tran HD, Koizumi N, Morioka S, Bounsong V, Watanabe K, Musikasinthorn P, Tun S, Yun LKC, Masengi KWA, Anoop VK, Raghavan R, Kitano J. Mesozoic origin and 'out-of-India' radiation of ricefishes (Adrianichthyidae). Biol Lett 2021; 17:20210212. [PMID: 34343438 DOI: 10.1098/rsbl.2021.0212] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The Indian subcontinent has an origin geologically different from Eurasia, but many terrestrial animal and plant species on it have congeneric or sister species in other parts of Asia, especially in the Southeast. This faunal and floral similarity between India and Southeast Asia is explained by either of the two biogeographic scenarios, 'into-India' or 'out-of-India'. Phylogenies based on complete mitochondrial genomes and five nuclear genes were undertaken for ricefishes (Adrianichthyidae) to examine which of these two biogeographic scenarios fits better. We found that Oryzias setnai, the only adrianichthyid distributed in and endemic to the Western Ghats, a mountain range running parallel to the western coast of the Indian subcontinent, is sister to all other adrianichthyids from eastern India and Southeast-East Asia. Divergence time estimates and ancestral area reconstructions reveal that this western Indian species diverged in the late Mesozoic during the northward drift of the Indian subcontinent. These findings indicate that adrianichthyids dispersed eastward 'out-of-India' after the collision of the Indian subcontinent with Eurasia, and subsequently diversified in Southeast-East Asia. A review of geographic distributions of 'out-of-India' taxa reveals that they may have largely fuelled or modified the biodiversity of Eurasia.
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Affiliation(s)
- Kazunori Yamahira
- Tropical Biosphere Research Center, University of the Ryukyus, Okinawa, Japan
| | - Satoshi Ansai
- Graduate School of Life Sciences, Tohoku University, Sendai, Japan
| | - Ryo Kakioka
- Tropical Biosphere Research Center, University of the Ryukyus, Okinawa, Japan
| | - Hajime Yaguchi
- Tropical Biosphere Research Center, University of the Ryukyus, Okinawa, Japan.,School of Science and Technology, Kwansei Gakuin University, Sanda, Japan
| | - Takeshi Kon
- Center for Strategic Research Project, University of the Ryukyus, Okinawa, Japan
| | - Javier Montenegro
- Tropical Biosphere Research Center, University of the Ryukyus, Okinawa, Japan
| | - Hirozumi Kobayashi
- Tropical Biosphere Research Center, University of the Ryukyus, Okinawa, Japan
| | - Shingo Fujimoto
- Tropical Biosphere Research Center, University of the Ryukyus, Okinawa, Japan
| | - Ryosuke Kimura
- Graduate School of Medicine, University of the Ryukyus, Okinawa, Japan
| | - Yusuke Takehana
- Faculty of Bio-Science, Nagahama Institute of Bio-Science and Technology, Japan
| | - Davin H E Setiamarga
- Department of Applied Chemistry and Biochemistry, National Institute of Technology, Wakayama College, Wakayama, Japan
| | - Yasuoki Takami
- Graduate School of Human Development and Environment, Kobe University, Kobe, Japan
| | - Rieko Tanaka
- World Medaka Aquarium, Nagoya Higashiyama Zoo and Botanical Gardens, Nagoya, Japan
| | - Ken Maeda
- Marine Eco-Evo-Devo Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa, Japan
| | - Hau D Tran
- Faculty of Biology, Hanoi National University of Education, Hanoi, Vietnam
| | - Noriyuki Koizumi
- Strategic Planning Headquarters, National Agriculture and Food Research Organization, Ibaraki, Japan
| | - Shinsuke Morioka
- Fisheries Division, Japan International Research Center for Agricultural Sciences, Ibaraki, Japan
| | | | - Katsutoshi Watanabe
- Division of Biological Sciences, Graduate School of Science, Kyoto University, Kyoto, Japan
| | | | - Sein Tun
- Inlay Lake Wildlife Sanctuary, Ministry of Natural Resources and Environmental Conservation, Nyaungshwe, Myanmar
| | - L K C Yun
- Inlay Lake Wildlife Sanctuary, Ministry of Natural Resources and Environmental Conservation, Nyaungshwe, Myanmar
| | | | - V K Anoop
- School of Ocean Science and Technology, Kerala University of Fisheries and Ocean Studies, Kochi, India
| | - Rajeev Raghavan
- Department of Fisheries Resource Management, Kerala University of Fisheries and Ocean Studies, Kochi, India
| | - Jun Kitano
- Ecological Genetics Laboratory, National Institute of Genetics, Mishima, Japan
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Bakkes DK, Ropiquet A, Chitimia-Dobler L, Matloa DE, Apanaskevich DA, Horak IG, Mans BJ, Matthee CA. Adaptive radiation and speciation in Rhipicephalus ticks: A medley of novel hosts, nested predator-prey food webs, off-host periods and dispersal along temperature variation gradients. Mol Phylogenet Evol 2021; 162:107178. [PMID: 33892098 DOI: 10.1016/j.ympev.2021.107178] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2020] [Revised: 03/18/2021] [Accepted: 04/13/2021] [Indexed: 01/22/2023]
Abstract
Rhipicephalus are a species-diverse genus of ticks, mainly distributed in the Afrotropics with some species in the Palearctic and Oriental regions. Current taxonomic consensus comprise nine informal species groups/lineages based on immature morphology. This work integrates biogeographic, ecological and molecular lines of evidence to better understand Rhipicephalus evolution. Phylogenetic analysis based on four genes (12S, 16S, 28S-D2 and COI) recovered five distinct clades with nine descendant clades that are generally congruent with current taxonomy, with some exceptions. Historical biogeography is inferred from molecular divergence times, ancestral distribution areas, host-use and climate niches of four phylogenetically significant bioclimatic variables (isothermality, annual, seasonal and diurnal temperature range). Novel hosts enabled host-linked dispersal events into new environments, and ticks exploited new hosts through nested predator-prey connections in food webs. Diversification was further induced by climate niche partitioning along gradients in temperature range during off-host periods. Ancestral climate niche estimates corroborated dispersal events by indicating hypothetical ancestors moved into environments with different annual and seasonal temperature ranges along latitudinal gradients. Host size for immature and adult life stages was important for dispersal and subsequent diversification rates. Clades that utilise large, mobile hosts (ungulates and carnivores) early in development have wider geographic ranges but slower diversification rates, and those utilising small, less mobile hosts (rodents, lagomorphs and afroinsectivores) early in development have smaller ranges but higher diversification rates. These findings suggest diversification is driven by a complex set of factors linked to both host-associations (host size, ranges and mobility) and climate niche partitioning along annual and seasonal temperature range gradients that vary with latitude. Moreover, competitive interactions can reinforce these processes and drive speciation. Off-host periods facilitate adaptive radiation by enabling host switches along nested predator-prey connections in food webs, but at the cost of environmental exposure that partitions niches among dispersing progenitors, disrupting geneflow and driving diversification. As such, the evolution and ecological niches of Rhipicephalus are characterised by trade-offs between on- and off-host periods, and these trade-offs interact with nested predator-prey connections in food webs, host-use at different life stages, as well as gradients in annual and seasonal temperature ranges to drive adaptive radiation and speciation.
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Affiliation(s)
- Deon K Bakkes
- Gertrud Theiler Tick Museum - Epidemiology, Parasites and Vectors, Agricultural Research Council - Onderstepoort Veterinary Research, Pretoria 0110, South Africa; Evolutionary Genomics Group, Department of Botany and Zoology, Stellenbosch University, Private Bag X1, Matieland 7602, South Africa.
| | - Anne Ropiquet
- Evolutionary Genomics Group, Department of Botany and Zoology, Stellenbosch University, Private Bag X1, Matieland 7602, South Africa; Middlesex University, Department of Natural Sciences- Faculty of Science and Technology, London NW4 4BT, United Kingdom
| | | | - Dikeledi E Matloa
- Gertrud Theiler Tick Museum - Epidemiology, Parasites and Vectors, Agricultural Research Council - Onderstepoort Veterinary Research, Pretoria 0110, South Africa
| | - Dmitry A Apanaskevich
- United States National Tick Collection, the James H. Oliver, Jr. Institute for Coastal Plain Science, Georgia Southern University, Statesboro, GA 30460-8042, USA; Biology Department, Georgia Southern University, Statesboro, GA 30460, USA; Zoological Institute, Russian Academy of Sciences, St. Petersburg 199034, Russia
| | - Ivan G Horak
- Department of Veterinary Tropical Diseases, University of Pretoria, Pretoria, South Africa
| | - Ben J Mans
- Gertrud Theiler Tick Museum - Epidemiology, Parasites and Vectors, Agricultural Research Council - Onderstepoort Veterinary Research, Pretoria 0110, South Africa; Department of Veterinary Tropical Diseases, University of Pretoria, Pretoria, South Africa; Department of Life and Consumer Sciences, University of South Africa, South Africa
| | - Conrad A Matthee
- Evolutionary Genomics Group, Department of Botany and Zoology, Stellenbosch University, Private Bag X1, Matieland 7602, South Africa
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Loria SF, Prendini L. Out of India, thrice: diversification of Asian forest scorpions reveals three colonizations of Southeast Asia. Sci Rep 2020; 10:22301. [PMID: 33339838 PMCID: PMC7749168 DOI: 10.1038/s41598-020-78183-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2019] [Accepted: 11/04/2020] [Indexed: 11/10/2022] Open
Abstract
The 'Out of India' hypothesis is often invoked to explain patterns of distribution among Southeast Asian taxa. According to this hypothesis, Southeast Asian taxa originated in Gondwana, diverged from their Gondwanan relatives when the Indian subcontinent rifted from Gondwana in the Late Jurassic, and colonized Southeast Asia when it collided with Eurasia in the early Cenozoic. A growing body of evidence suggests these events were far more complex than previously understood, however. The first quantitative reconstruction of the biogeography of Asian forest scorpions (Scorpionidae Latreille, 1802: Heterometrinae Simon, 1879) is presented here. Divergence time estimation, ancestral range estimation, and diversification analyses are used to determine the origins, dispersal and diversification patterns of these scorpions, providing a timeline for their biogeographical history that can be summarized into four major events. (1) Heterometrinae diverged from other Scorpionidae on the African continent after the Indian subcontinent became separated in the Cretaceous. (2) Environmental stresses during the Cretaceous-Tertiary (KT) mass extinction caused range contraction, restricting one clade of Heterometrinae to refugia in southern India (the Western Ghats) and Sri Lanka (the Central Highlands). (3) Heterometrinae dispersed to Southeast Asia three times during India's collision with Eurasia, the first dispersal event occurring as the Indian subcontinent brushed up against the western side of Sumatra, and the other two events occurring as India moved closer to Eurasia. (4) Indian Heterometrinae, confined to southern India and Sri Lanka during the KT mass extinction, recolonized the Deccan Plateau and northern India, diversifying into new, more arid habitats after environmental conditions stabilized. These hypotheses, which are congruent with the geological literature and biogeographical analyses of other taxa from South and Southeast Asia, contribute to an improved understanding of the dispersal and diversification patterns of taxa in this biodiverse and geologically complex region.
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Affiliation(s)
- Stephanie F Loria
- Richard Gilder Graduate School, American Museum of Natural History, Central Park West at 79th St., New York, NY, 10024-5192, USA.
- Scorpion Systematics Research Group, Division of Invertebrate Zoology, American Museum of Natural History, Central Park West at 79th St., New York, NY, 10024-5192, USA.
| | - Lorenzo Prendini
- Scorpion Systematics Research Group, Division of Invertebrate Zoology, American Museum of Natural History, Central Park West at 79th St., New York, NY, 10024-5192, USA
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11
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Jiang L, Zhang M, Deng L, Xu Z, Shi H, Jia X, Lai Z, Ruan Q, Chen W. Characteristics of the mitochondrial genome of Rana omeimontis and related species in Ranidae: Gene rearrangements and phylogenetic relationships. Ecol Evol 2020; 10:12817-12837. [PMID: 33304496 PMCID: PMC7713938 DOI: 10.1002/ece3.6824] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Revised: 08/16/2020] [Accepted: 08/20/2020] [Indexed: 12/01/2022] Open
Abstract
The Omei wood frog (Rana omeimontis), endemic to central China, belongs to the family Ranidae. In this study, we achieved detail knowledge about the mitogenome of the species. The length of the genome is 20,120 bp, including 13 protein-coding genes (PCGs), 22 tRNA genes, two rRNA genes, and a noncoding control region. Similar to other amphibians, we found that only nine genes (ND6 and eight tRNA genes) are encoded on the light strand (L) and other genes on the heavy strand (H). Totally, The base composition of the mitochondrial genome included 27.29% A, 28.85% T, 28.87% C, and 15.00% G, respectively. The control regions among the Rana species were found to exhibit rich genetic variability and A + T content. R. omeimontis was clustered together with R. chaochiaoensis in phylogenetic tree. Compared to R. amurensis and R. kunyuensi, it was more closely related to R. chaochiaoensis, and a new way of gene rearrangement (ND6-trnE-Cytb-D-loop-trnL2 (CUN)-ND5-D-loop) was also found in the mitogenome of R. amurensis and R. kunyuensi. Our results about the mitochondrial genome of R. omeimontis will contribute to the future studies on phylogenetic relationship and the taxonomic status of Rana and related Ranidae species.
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Affiliation(s)
- Lichun Jiang
- Key Laboratory for Molecular Biology and BiopharmaceuticsSchool of Life Science and TechnologyMianyang Normal UniversityMianyangChina
- Ecological Security and Protection Key Laboratory of Sichuan ProvinceMianyang Normal UniversityMianyangChina
| | - Min Zhang
- Key Laboratory for Molecular Biology and BiopharmaceuticsSchool of Life Science and TechnologyMianyang Normal UniversityMianyangChina
| | - Lu Deng
- Key Laboratory for Molecular Biology and BiopharmaceuticsSchool of Life Science and TechnologyMianyang Normal UniversityMianyangChina
| | - Zhongwen Xu
- Key Laboratory for Molecular Biology and BiopharmaceuticsSchool of Life Science and TechnologyMianyang Normal UniversityMianyangChina
| | - Hongyan Shi
- Key Laboratory for Molecular Biology and BiopharmaceuticsSchool of Life Science and TechnologyMianyang Normal UniversityMianyangChina
| | - Xiaodong Jia
- Key Laboratory for Molecular Biology and BiopharmaceuticsSchool of Life Science and TechnologyMianyang Normal UniversityMianyangChina
| | - Zhenli Lai
- Key Laboratory for Molecular Biology and BiopharmaceuticsSchool of Life Science and TechnologyMianyang Normal UniversityMianyangChina
| | - Qiping Ruan
- Key Laboratory for Molecular Biology and BiopharmaceuticsSchool of Life Science and TechnologyMianyang Normal UniversityMianyangChina
| | - Wei Chen
- Ecological Security and Protection Key Laboratory of Sichuan ProvinceMianyang Normal UniversityMianyangChina
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12
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Najibzadeh M, Ehl S, Feldmeier S, Pesarakloo A, Veith M. Unequal sisters - Past and potential future range development of Anatolian and Hyrcanian brown frogs. ZOOLOGY 2020; 144:125873. [PMID: 33296820 DOI: 10.1016/j.zool.2020.125873] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2019] [Revised: 11/02/2020] [Accepted: 11/03/2020] [Indexed: 11/28/2022]
Abstract
Phylogeography can reconstruct historical evolutionary processes by comparing historical patterns of gene flow, divergence among species and by using species distribution models (SDM) upon geographic distribution. We investigate the phylogeographic patterns of Anatolian brown frogs including R. macrocnemis and R. tavasensis as well as the Hyrcanian brown frog, R. pseudodalmatina, using a fragment of the mitochondrial 16S rRNA gene for 145 specimens across the entire range of these frogs. We calculate parameters of molecular diversity, such as the number of variable sites (S), the number of haplotypes (h), haplotype diversity (Hd) and nucleotide diversity (π). We generated a haplotype network and used three methods (Neutrality tests, mismatch distributions and Bayesian skyline plots) to reconstruct the demographic histories of R. macrocnemis and R. pseudodalmatina. Finally, we used SDMs to predict the habitat suitability for three periods: The Present Day, the Last Glacial Maximum (LGM) and the future until 2070 for R. macrocnemis and R. pseudodalmatina. Our phylogenetic analyses support a late Miocene origin of Anatolian and Hyrcanian lineages. Hyrcanian brown frogs were enclosed in lowlands of the southern coast of the Caspian Sea after the uplift of the Elburz range and the Armenian plateau. The formation of a salinity belt from the north Aegean corridor (the south western Turkey) to northward during the Late Tortonian led to the subdivision of ancestor of the Anatolian lineage into today isolated western and eastern populations. The salinity belt had a considerable impact on the divergence of R. tavasensis from R. macrocnemis. Combined historical demographic analyses and SDMs revealed a rapid expansion occurring during the Pleistocene in R. macrocnemis and R. pseudodalmatina. Currently, suitable habitat for R. macrocnemis has declined compared to the LGM, and the species is predicted to do even worse under future climatic conditions. In contrast, R. pseudodalmatina found suitable habitat from the LGM to present within its restricted distribution area; it is predicted to do fine even under future climate.
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Affiliation(s)
- M Najibzadeh
- Iranian Plateau Herpetology Research Group (IPHRG), Razi University, Bagh e Abrisham 6714967346 Kermanshah, Iran.
| | - S Ehl
- Department of Biogeography, Trier University, Universitätsring 15, 54296 Trier, Germany
| | - S Feldmeier
- Department of Biogeography, Trier University, Universitätsring 15, 54296 Trier, Germany
| | - A Pesarakloo
- Department of Biology, Faculty of Science, Arak University, Sardasht, 3813853945 Arak, Iran
| | - M Veith
- Department of Biogeography, Trier University, Universitätsring 15, 54296 Trier, Germany
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13
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Blackburn DC, Nielsen SV, Barej MF, Doumbia J, Hirschfeld M, Kouamé NG, Lawson D, Loader S, Ofori‐Boateng C, Stanley EL, Rödel M. Evolution of the African slippery frogs (Anura:
Conraua
), including the world’s largest living frog. ZOOL SCR 2020. [DOI: 10.1111/zsc.12447] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Affiliation(s)
- David C. Blackburn
- Department of Natural History Florida Museum of Natural History University of Florida Gainesville FL USA
| | - Stuart V. Nielsen
- Department of Natural History Florida Museum of Natural History University of Florida Gainesville FL USA
- Department of Biological Sciences Marquette University Milwaukee WI USA
| | - Michael F. Barej
- Museum für Naturkunde ‐ Leibniz Institute for Evolution and Biodiversity Science Berlin Germany
| | | | - Mareike Hirschfeld
- Museum für Naturkunde ‐ Leibniz Institute for Evolution and Biodiversity Science Berlin Germany
| | | | - Dwight Lawson
- Oklahoma City Zoo and Botanical Garden Oklahoma City OK USA
| | | | | | - Edward L. Stanley
- Department of Natural History Florida Museum of Natural History University of Florida Gainesville FL USA
| | - Mark‐Oliver Rödel
- Museum für Naturkunde ‐ Leibniz Institute for Evolution and Biodiversity Science Berlin Germany
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14
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Kundu S, Lalremsanga HT, Purkayastha J, Biakzuala L, Chandra K, Kumar V. DNA barcoding elucidates the new altitude record and range-extension of lesser-known bullfrog ( Hoplobatrachus litoralis) in northeast India. Mitochondrial DNA B Resour 2020. [DOI: 10.1080/23802359.2020.1787259] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022] Open
Affiliation(s)
- Shantanu Kundu
- Centre for DNA Taxonomy, Molecular Systematics Division, Zoological Survey of India, Kolkata, India
| | - Hmar Tlawmte Lalremsanga
- Developmental Biology and Herpetology Laboratory, Department of Zoology, Mizoram University, Mizoram, India
| | | | - Lal Biakzuala
- Developmental Biology and Herpetology Laboratory, Department of Zoology, Mizoram University, Mizoram, India
| | - Kailash Chandra
- Centre for DNA Taxonomy, Molecular Systematics Division, Zoological Survey of India, Kolkata, India
| | - Vikas Kumar
- Centre for DNA Taxonomy, Molecular Systematics Division, Zoological Survey of India, Kolkata, India
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15
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Costa L, Jimenez H, Carvalho R, Carvalho-Sobrinho J, Escobar I, Souza G. Divide to Conquer: Evolutionary History of Allioideae Tribes (Amaryllidaceae) Is Linked to Distinct Trends of Karyotype Evolution. FRONTIERS IN PLANT SCIENCE 2020; 11:320. [PMID: 32318079 PMCID: PMC7155398 DOI: 10.3389/fpls.2020.00320] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/15/2019] [Accepted: 03/04/2020] [Indexed: 06/11/2023]
Abstract
Allioideae (e.g., chives, garlics, onions) comprises three mainly temperate tribes: Allieae (800 species from the northern hemisphere), Gilliesieae (80 South American species), and Tulbaghieae (26 Southern African species). We reconstructed the phylogeny of Allioideae (190 species plus 257 species from Agapanthoideae and Amaryllidoideae) based on ITS, matK, ndhF, and rbcL to investigate its historical biogeography and karyotype evolution using newly generated cytomolecular data for Chilean Gilliesieae genera Gethyum, Miersia, Solaria, and Speea. The crown group of Allioideae diversified ∼62 Mya supporting a Gondwanic origin for the subfamily and vicariance as the cause of the intercontinental disjunction of the tribes. Our results support the hypothesis of the Indian tectonic plate carrying Allieae to northern hemisphere ('out-of-India' hypothesis). The colonization of the northern hemisphere (∼30 Mya) is correlated with a higher diversification rate in Allium associated to stable x = 8, increase of polyploidy and the geographic expansion in Europe and North America. Tulbaghieae presented x = 6, but with numerical stability (2n = 12). In contrast, the tribe Gilliesieae (x = 6) varied considerably in genome size (associated with Robertsonian translocations), rDNA sites distribution and chromosome number. Our data indicate that evolutionary history of Allioideae tribes is linked to distinct trends of karyotype evolution.
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Affiliation(s)
- Lucas Costa
- Laboratory of Plant Cytogenetics and Evolution, Department of Botany, Federal University of Pernambuco, Recife, Brazil
| | - Horace Jimenez
- Laboratory of Plant Cytogenetics, Department of Biology, Federal Rural University of Pernambuco, Recife, Brazil
| | - Reginaldo Carvalho
- Laboratory of Plant Cytogenetics, Department of Biology, Federal Rural University of Pernambuco, Recife, Brazil
| | - Jefferson Carvalho-Sobrinho
- Laboratory of Plant Cytogenetics, Department of Biology, Federal Rural University of Pernambuco, Recife, Brazil
| | - Inelia Escobar
- Department of Botany, University of Concepción, Concepción, Chile
| | - Gustavo Souza
- Laboratory of Plant Cytogenetics and Evolution, Department of Botany, Federal University of Pernambuco, Recife, Brazil
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16
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Early Pliocene anuran fossils from Kanapoi, Kenya, and the first fossil record for the African burrowing frog Hemisus (Neobatrachia: Hemisotidae). J Hum Evol 2020; 140:102353. [DOI: 10.1016/j.jhevol.2017.06.008] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2016] [Revised: 05/26/2017] [Accepted: 06/23/2017] [Indexed: 11/20/2022]
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17
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Sil M, Aravind NA, Karanth KP. Into-India or out-of-India? Historical biogeography of the freshwater gastropod genus Pila (Caenogastropoda: Ampullariidae). Biol J Linn Soc Lond 2020. [DOI: 10.1093/biolinnean/blz171] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Abstract
The biota of the Indian subcontinent was assembled through multiple associations with various landmasses during a period spanning the Late Cretaceous to the present. It consists of Gondwanan elements that subsequently dispersed ‘out-of-India’ and biota that dispersed ‘into-India’ after the subcontinent collided with Asia. However, the relative contribution of these connections to the current biotic assembly of the subcontinent has been under-explored. Our aim here was to understand the relative importance of these various routes of biotic assembly in India by studying the historical biogeography of the tropical Old World freshwater snail genus Pila. We reconstructed a near-complete phylogeny, based on nuclear and mitochondrial markers, of Ampullariidae including all the described Pila species from India and Ampullariids worldwide. Thereafter, molecular dating and ancestral range estimation analyses were carried out to ascertain the time frame and route of colonization of India by Pila. The results showed that Pila dispersed into India as well as other parts of tropical Asia from Africa after both India and Africa collided with Eurasia. Furthermore, multiple dispersals took place between Southeast Asia and India. These findings corroborate increasing evidence that much of the current Indian assemblage of biota actually dispersed ‘into-India’ after it collided with Asia.
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Affiliation(s)
- Maitreya Sil
- Centre for Ecological Sciences, Indian Institute of Science, Bangalore, India
- Ashoka Trust for Research in Ecology and the Environment, Bangalore, India
| | - N A Aravind
- Ashoka Trust for Research in Ecology and the Environment, Bangalore, India
- Yenepoya Research Centre, Yenepoya (Deemed to be University), University road, Derlakatte, Mangalore, India
| | - K Praveen Karanth
- Centre for Ecological Sciences, Indian Institute of Science, Bangalore, India
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18
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An integrative phylogenomic approach illuminates the evolutionary history of Old World tree frogs (Anura: Rhacophoridae). Mol Phylogenet Evol 2019; 145:106724. [PMID: 31881327 DOI: 10.1016/j.ympev.2019.106724] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2019] [Revised: 11/14/2019] [Accepted: 12/23/2019] [Indexed: 11/24/2022]
Abstract
Rhacophoridae are one of the most speciose and ecologically diverse families of amphibians. Resolution of their evolutionary relationships is key to understanding the accumulation of biodiversity, yet previous hypotheses based on Sanger sequencing exhibit much discordance amongst generic relationships. This conflict precludes the making of sound macroevolutionary conclusions. Herein, we conduct the first phylogenomic study using broad-scale sampling and sequences of 352 nuclear DNA loci obtained using anchored hybrid enrichment targeted sequencing. The robust time-calibrated phylogenetic hypothesis clarifies several long-disputed relationships and facilitates the testing of evolutionary hypotheses on spatiotemporal diversification and reproductive modes. The major extant lineages of Rhacophoridae appear to have radiated in mainland Asia, and the spatiotemporal process corresponds with several common accumulations of biodiversity in Asia. Analyses do not detect any case of "Out of Himalaya" in Rhacophoridae. All transitions of reproductive modes appear to have evolved in an ordered, gradual sequence associated with gaining independence of standing water for larval development. The different reproductive modes are phylogenetically conserved and the completion of their transitions appear to have occurred over a period of ~30 Ma, which does not fit a pattern of a rapid burst of diversification. Innovations in reproductive modes associate statistically with the uneven distribution of species-richness between clades, where higher diversification is linked to increased terrestrial modes of reproduction. These results strengthen the hypothesis that breeding innovations drive diversification by providing new opportunities for ecological release and dispersion.
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19
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Hofmann S, Baniya CB, Litvinchuk SN, Miehe G, Li J, Schmidt J. Phylogeny of spiny frogs Nanorana (Anura: Dicroglossidae) supports a Tibetan origin of a Himalayan species group. Ecol Evol 2019; 9:14498-14511. [PMID: 31938536 PMCID: PMC6953589 DOI: 10.1002/ece3.5909] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2019] [Revised: 11/09/2019] [Accepted: 11/18/2019] [Indexed: 11/29/2022] Open
Abstract
Recent advances in the understanding of the evolution of the Asian continent challenge the long-held belief of a faunal immigration into the Himalaya. Spiny frogs of the genus Nanorana are a characteristic faunal group of the Himalaya-Tibet orogen (HTO). We examine the phylogeny of these frogs to explore alternative biogeographic scenarios for their origin in the Greater Himalaya, namely, immigration, South Tibetan origin, strict vicariance. We sequenced 150 Nanorana samples from 62 localities for three mitochondrial (1,524 bp) and three nuclear markers (2,043 bp) and complemented the data with sequence data available from GenBank. We reconstructed a gene tree, phylogenetic networks, and ancestral areas. Based on the nuDNA, we also generated a time-calibrated species tree. The results revealed two major clades (Nanorana and Quasipaa), which originated in the Lower Miocene from eastern China and subsequently spread into the HTO (Nanorana). Five well-supported subclades are found within Nanorana: from the East, Central, and Northwest Himalaya, the Tibetan Plateau, and the southeastern Plateau margin. The latter subclade represents the most basal group (subgenus Chaparana), the Plateau group (Nanorana) represents the sister clade to all species of the Greater Himalaya (Paa). We found no evidence for an east-west range expansion of Paa along the Himalaya, nor clear support for a strict vicariance model. Diversification in each of the three Himalayan subclades has probably occurred in distinct areas. Specimens from the NW Himalaya are placed basally relative to the highly diverse Central Himalayan group, while the lineage from the Tibetan Plateau is placed within a more terminal clade. Our data indicate a Tibetan origin of Himalayan Nanorana and support a previous hypothesis, which implies that a significant part of the Himalayan biodiversity results from primary diversification of the species groups in South Tibet before this part of the HTO was uplifted to its recent heights.
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Affiliation(s)
- Sylvia Hofmann
- Department of Conservation BiologyUFZ – Helmholtz Centre for Environmental ResearchLeipzigGermany
| | | | | | - Georg Miehe
- Faculty of GeographyPhilipps University MarburgMarburgGermany
| | - Jia‐Tang Li
- Department of HerpetologyChengdu Institute of BiologyChinese Academy of SciencesChengduChina
| | - Joachim Schmidt
- Institute of Biosciences, General and Systematic ZoologyUniversity of RostockRostockGermany
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20
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Vijayakumar SP, Pyron RA, Dinesh KP, Torsekar VR, Srikanthan AN, Swamy P, Stanley EL, Blackburn DC, Shanker K. A new ancient lineage of frog (Anura: Nyctibatrachidae: Astrobatrachinae subfam. nov.) endemic to the Western Ghats of Peninsular India. PeerJ 2019; 7:e6457. [PMID: 30881763 PMCID: PMC6419720 DOI: 10.7717/peerj.6457] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2018] [Accepted: 01/16/2019] [Indexed: 11/20/2022] Open
Abstract
The Western Ghats (WG) is an escarpment on the west coast of Peninsular India, housing one of the richest assemblages of frogs in the world, with three endemic families. Here, we report the discovery of a new ancient lineage from a high-elevation massif in the Wayanad Plateau of the southern WG. Phylogenetic analysis reveals that the lineage belongs to Natatanura and clusters with Nyctibatrachidae, a family endemic to the WG/Sri Lanka biodiversity hotspot. Based on geographic distribution, unique morphological traits, deep genetic divergence, and phylogenetic position that distinguishes the lineage from the two nyctibatrachid subfamilies Nyctibatrachinae Blommers-Schlösser, 1993 and Lankanectinae Dubois & Ohler, 2001, we erect a new subfamily Astrobatrachinae subfam. nov. (endemic to the WG, Peninsular India), and describe a new genus Astrobatrachus gen. nov. and species, Astrobatrachus kurichiyana sp. nov. The discovery of this species adds to the list of deeply divergent and monotypic or depauperate lineages with narrow geographic ranges in the southern massifs of the WG. The southern regions of the WG have long been considered geographic and climatic refugia, and this new relict lineage underscores their evolutionary significance. The small range of this species exclusively outside protected areas highlights the significance of reserve forest tracts in the WG in housing evolutionary novelty. This reinforces the need for intensive sampling to uncover new lineages and advance our understanding of the historical biogeography of this ancient landmass.
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Affiliation(s)
- Seenapuram Palaniswamy Vijayakumar
- Centre for Ecological Sciences, Indian Institute of Science, Bangalore, Karnataka, India
- Department of Biological Sciences, The George Washington University, Washington, DC, USA
| | - Robert Alexander Pyron
- Department of Biological Sciences, The George Washington University, Washington, DC, USA
| | - K. P. Dinesh
- Western Regional Centre, Zoological Survey of India, Pune, Maharashtra, India
| | - Varun R. Torsekar
- Centre for Ecological Sciences, Indian Institute of Science, Bangalore, Karnataka, India
| | | | - Priyanka Swamy
- Centre for Ecological Sciences, Indian Institute of Science, Bangalore, Karnataka, India
| | - Edward L. Stanley
- Florida Museum of Natural History, University of Florida, Gainesville, FL, USA
| | - David C. Blackburn
- Florida Museum of Natural History, University of Florida, Gainesville, FL, USA
| | - Kartik Shanker
- Centre for Ecological Sciences, Indian Institute of Science, Bangalore, Karnataka, India
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21
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Rebelo AD, Measey J. Locomotor performance constrained by morphology and habitat in a diverse clade of African frogs (Anura: Pyxicephalidae). Biol J Linn Soc Lond 2019. [DOI: 10.1093/biolinnean/blz007] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Affiliation(s)
- Alexander D Rebelo
- Centre for Invasion Biology, Department of Botany & Zoology, Stellenbosch University, Matieland, South Africa
| | - John Measey
- Centre for Invasion Biology, Department of Botany & Zoology, Stellenbosch University, Matieland, South Africa
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22
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Garg S, Biju SD. New microhylid frog genus from Peninsular India with Southeast Asian affinity suggests multiple Cenozoic biotic exchanges between India and Eurasia. Sci Rep 2019; 9:1906. [PMID: 30760773 PMCID: PMC6374391 DOI: 10.1038/s41598-018-38133-x] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2017] [Accepted: 12/20/2018] [Indexed: 11/08/2022] Open
Abstract
Anurans in Peninsular India exhibit close biogeographical links with Gondwana as well as Laurasia, often explainable by the geological history of the Indian subcontinent; its breakup from Gondwanan landmasses followed by long isolation that resulted in diversification of endemic lineages, and subsequent land connections with Asia that enabled dispersal of widespread groups. Although widely distributed, the frog subfamily Microhylinae mostly comprises of geographically restricted genera found either in Southeast and East Asia or Peninsular India and Sri Lanka. Here we report a previously unknown microhylid from the Western Ghats in Peninsular India with closest relatives found over 2,000 km away in Southeast Asia. Based on integrated evidence from mitochondrial and nuclear DNA, adult and tadpole morphology, hand musculature, male advertisement call, and geographical distance, we recognize this enigmatic frog as a distinct new species and genus endemic to the Western Ghats. The discovery of Mysticellus franki gen. et sp. nov. and its close evolutionary relationship with the Southeast Asian genus Micryletta also provide insights on the biogeography of Microhylinae. Genus-level divergences within the subfamily suggest multiple Cenozoic biotic exchange events between India and Eurasia, particularly through postulated Eocene land bridges via Southeast Asia prior to accretion of the two landmasses.
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Affiliation(s)
- Sonali Garg
- Systematics Lab, Department of Environmental Studies, University of Delhi, Delhi, 110 007, India
| | - S D Biju
- Systematics Lab, Department of Environmental Studies, University of Delhi, Delhi, 110 007, India.
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23
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Zang JC, Sun T. The complete mitochondrial genome of seed pest from Sophora moorcroftiana. Mitochondrial DNA B Resour 2019. [DOI: 10.1080/23802359.2018.1544857] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022] Open
Affiliation(s)
- Jian-cheng Zang
- aPlant Science College, Tibet Agriculture & Animal Husbandry University, Nyingchi, Tibet, China
| | - Tao Sun
- aPlant Science College, Tibet Agriculture & Animal Husbandry University, Nyingchi, Tibet, China
- bCollege of Life Science, Huaibei Normal University, Huaibei, China
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24
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Yuan ZY, Zhang BL, Raxworthy CJ, Weisrock DW, Hime PM, Jin JQ, Lemmon EM, Lemmon AR, Holland SD, Kortyna ML, Zhou WW, Peng MS, Che J, Prendini E. Natatanuran frogs used the Indian Plate to step-stone disperse and radiate across the Indian Ocean. Natl Sci Rev 2018; 6:10-14. [PMID: 34691821 PMCID: PMC8294181 DOI: 10.1093/nsr/nwy092] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2018] [Revised: 08/30/2018] [Accepted: 09/02/2018] [Indexed: 12/02/2022] Open
Affiliation(s)
- Zhi-Yong Yuan
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
- Key Laboratory for Forest Resources Conservation and Utilization in the Southwest Mountains of China, Ministry of Education, Southwest Forestry University, Kunming, China
| | - Bao-Lin Zhang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
- Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, China
| | | | | | - Paul M Hime
- Department of Biology, University of Kentucky, Lexington, USA
- Biodiversity Institute, University of Kansas, Lawrence, USA
| | - Jie-Qiong Jin
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
- Southeast Asia Biodiversity Research Institute, Chinese Academy of Sciences, Yezin, Myanmar
| | - Emily M Lemmon
- Department of Biological Science, Florida State University, Tallahassee, USA
| | - Alan R Lemmon
- Department of Scientific Computing, Florida State University, Tallahassee, USA
| | - Sean D Holland
- Department of Biological Science, Florida State University, Tallahassee, USA
| | - Michelle L Kortyna
- Department of Biological Science, Florida State University, Tallahassee, USA
| | - Wei-Wei Zhou
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
- Southeast Asia Biodiversity Research Institute, Chinese Academy of Sciences, Yezin, Myanmar
| | - Min-Sheng Peng
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Kunming, China
| | - Jing Che
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
- Southeast Asia Biodiversity Research Institute, Chinese Academy of Sciences, Yezin, Myanmar
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, China
| | - Elizabeth Prendini
- Department of Herpetology, American Museum of Natural History, New York, USA
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25
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Jiang L, You Z, Yu P, Ruan Q, Chen W. The first complete mitochondrial genome sequence of Nanorana parkeri and Nanorana ventripunctata (Amphibia: Anura: Dicroglossidae), with related phylogenetic analyses. Ecol Evol 2018; 8:6972-6987. [PMID: 30073060 PMCID: PMC6065340 DOI: 10.1002/ece3.4214] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2017] [Revised: 04/20/2018] [Accepted: 04/24/2018] [Indexed: 11/24/2022] Open
Abstract
Members of the Nanorana genus (family Dicroglossidae) are often referred to as excellent model species with which to study amphibian adaptations to extreme environments and also as excellent keystone taxa for providing insights into the evolution of the Dicroglossidae. However, a complete mitochondrial genome is currently only available for Nanorana pleskei. Thus, we analyzed the complete mitochondrial genomes of Nanorana parkeri and Nanorana ventripunctata to investigate their evolutionary relationships within Nanorana and their phylogenetic position in the family Dicroglossidae. Our results showed that the genomes of N. parkeri (17,837 bp) and N. ventripunctata (18,373 bp) encode 13 protein‐coding genes (PCGs), two ribosomal RNA genes, 23 transfer RNA (tRNA) genes, and a noncoding control region. Overall sequences and genome structure of the two species showed high degree of similarity with N. pleskei, although the motif structures and repeat sequences of the putative control region showed clear differences among these three Nanorana species. In addition, a tandem repeat of the tRNA‐Met gene was found located between the tRNA‐Gln and ND2 genes. On both the 5′ and 3′‐sides, the control region possessed distinct repeat regions; however, the CSB‐2 motif was not found in N. pleskei. Based on the nucleotide sequences of 13 PCGs, our phylogenetic analyses, using Bayesian inference and maximum‐likelihood methods, illustrate the taxonomic status of Nanorana with robust support showing that N. ventripunctata and N. pleskei are more closely related than they are to N. parkeri. In conclusion, our analyses provide a more robust and reliable perspective on the evolutionary history of Dicroglossidae than earlier analyses, which used only a single species (N. pleskei).
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Affiliation(s)
- Lichun Jiang
- Ecological Security and Protection Key Laboratory of Sichuan Province Mianyang Normal University Mianyang Sichuan China.,Key Laboratory for Molecular Biology and Biopharmaceutics School of Life Science and Technology Mianyang Normal University Mianyang Sichuan China
| | - Zhangqiang You
- Ecological Security and Protection Key Laboratory of Sichuan Province Mianyang Normal University Mianyang Sichuan China
| | - Peng Yu
- Key Laboratory for Molecular Biology and Biopharmaceutics School of Life Science and Technology Mianyang Normal University Mianyang Sichuan China
| | - Qiping Ruan
- Key Laboratory for Molecular Biology and Biopharmaceutics School of Life Science and Technology Mianyang Normal University Mianyang Sichuan China
| | - Wei Chen
- Ecological Security and Protection Key Laboratory of Sichuan Province Mianyang Normal University Mianyang Sichuan China
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Jongsma GF, Barej MF, Barratt CD, Burger M, Conradie W, Ernst R, Greenbaum E, Hirschfeld M, Leaché AD, Penner J, Portik DM, Zassi-Boulou AG, Rödel MO, Blackburn DC. Diversity and biogeography of frogs in the genus Amnirana (Anura: Ranidae) across sub-Saharan Africa. Mol Phylogenet Evol 2018; 120:274-285. [DOI: 10.1016/j.ympev.2017.12.006] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2017] [Revised: 11/30/2017] [Accepted: 12/05/2017] [Indexed: 10/18/2022]
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27
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Heinicke MP, Lemmon AR, Lemmon EM, McGrath K, Hedges SB. Phylogenomic support for evolutionary relationships of New World direct-developing frogs (Anura: Terraranae). Mol Phylogenet Evol 2018; 118:145-155. [DOI: 10.1016/j.ympev.2017.09.021] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2017] [Revised: 09/15/2017] [Accepted: 09/25/2017] [Indexed: 10/18/2022]
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Lau Q, Igawa T, Minei R, Kosch TA, Satta Y. Transcriptome analyses of immune tissues from three Japanese frogs (genus Rana ) reveals their utility in characterizing major histocompatibility complex class II. BMC Genomics 2017; 18:994. [PMID: 29281968 PMCID: PMC5745589 DOI: 10.1186/s12864-017-4404-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2017] [Accepted: 12/19/2017] [Indexed: 01/05/2023] Open
Abstract
Background In Japan and East Asia, endemic frogs appear to be tolerant or not susceptible to chytridiomycosis, a deadly amphibian disease caused by the chytrid fungus Batrachochytridium dendrobatidis (Bd). Japanese frogs may have evolved mechanisms of immune resistance to pathogens such as Bd. This study characterizes immune genes expressed in various tissues of healthy Japanese Rana frogs. Results We generated transcriptome data sets of skin, spleen and blood from three adult Japanese Ranidae frogs (Japanese brown frog Rana japonica, the montane brown frog Rana ornativentris, and Tago’s brown frog Rana tagoi tagoi) as well as whole body of R. japonica and R. ornativentris tadpoles. From this, we identified tissue- and stage-specific differentially expressed genes; in particular, the spleen was most enriched for immune-related genes. A specific immune gene, major histocompatibility complex class IIB (MHC-IIB), was further characterized due to its role in pathogen recognition. We identified a total of 33 MHC-IIB variants from the three focal species (n = 7 individuals each), which displayed evolutionary signatures related to increased MHC variation, including balancing selection. Our supertyping analyses of MHC-IIB variants from Japanese frogs and previously studied frog species identified potential physiochemical properties of MHC-II that may be important for recognizing and binding chytrid-related antigens. Conclusions This is one of the first studies to generate transcriptomic resources for Japanese frogs, and contributes to further understanding the immunogenetic factors associated with resistance to infectious diseases in amphibians such as chytridiomycosis. Notably, MHC-IIB supertyping analyses identified unique functional properties of specific MHC-IIB alleles that may partially contribute to Bd resistance, and such properties provide a springboard for future experimental validation. Electronic supplementary material The online version of this article (10.1186/s12864-017-4404-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Quintin Lau
- Department of Evolutionary Studies of Biosystems, Sokendai, The Graduate University for Advanced Studies, Kamiyamaguchi 1560-35, Hayama, Kanagawa, 240-0193, Japan.
| | - Takeshi Igawa
- Amphibian Research Center, Hiroshima University, 1-3-1, Higashi-Hiroshima, Hiroshima, 739-8526, Japan
| | - Ryuhei Minei
- Department of Bioscience, Nagahama Institute of Bio-Science and Technology, Tamura-cho 1266, Nagahama, Shiga, 526-0829, Japan
| | - Tiffany A Kosch
- One Health Research Group, College of Public Health, Medical and Veterinary Sciences, James Cook University, Townsville, QLD, 4811, Australia
| | - Yoko Satta
- Department of Evolutionary Studies of Biosystems, Sokendai, The Graduate University for Advanced Studies, Kamiyamaguchi 1560-35, Hayama, Kanagawa, 240-0193, Japan
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Brown RM, Prue A, Onn CK, Gaulke M, Sanguila MB, Siler CD. Taxonomic Reappraisal of the Northeast Mindanao Stream Frog, Sanguirana albotuberculata(Inger 1954), Validation ofRana mearnsi, Stejneger 1905, and Description of a New Species from the Central Philippines. HERPETOLOGICAL MONOGRAPHS 2017. [DOI: 10.1655/herpmonographs-d-16-00009.1] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Affiliation(s)
- Rafe M. Brown
- Department of Ecology and Evolutionary Biology and Biodiversity Institute, University of Kansas, Lawrence, KS 66045-7561, USA
| | - Allyson Prue
- Department of Ecology and Evolutionary Biology and Biodiversity Institute, University of Kansas, Lawrence, KS 66045-7561, USA
- Haskell Indian Nations University, Lawrence, KS 66045, USA
| | - Chan Kin Onn
- Department of Ecology and Evolutionary Biology and Biodiversity Institute, University of Kansas, Lawrence, KS 66045-7561, USA
| | - Maren Gaulke
- GeoBio Center LMU, Richard-Wagner-Strasse 10, 80333 München, Germany
| | - Marites B. Sanguila
- Biodiversity Informatics and Research Center, Father Saturnino Urios University, San Francisco Street, 8600, Butuan City, Philippines
| | - Cameron D. Siler
- Department of Biology and Sam Noble Oklahoma Museum of Natural History, University of Oklahoma, Norman, OK 73072-7029, USA
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Feng YJ, Blackburn DC, Liang D, Hillis DM, Wake DB, Cannatella DC, Zhang P. Phylogenomics reveals rapid, simultaneous diversification of three major clades of Gondwanan frogs at the Cretaceous-Paleogene boundary. Proc Natl Acad Sci U S A 2017; 114:E5864-E5870. [PMID: 28673970 PMCID: PMC5530686 DOI: 10.1073/pnas.1704632114] [Citation(s) in RCA: 171] [Impact Index Per Article: 24.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Frogs (Anura) are one of the most diverse groups of vertebrates and comprise nearly 90% of living amphibian species. Their worldwide distribution and diverse biology make them well-suited for assessing fundamental questions in evolution, ecology, and conservation. However, despite their scientific importance, the evolutionary history and tempo of frog diversification remain poorly understood. By using a molecular dataset of unprecedented size, including 88-kb characters from 95 nuclear genes of 156 frog species, in conjunction with 20 fossil-based calibrations, our analyses result in the most strongly supported phylogeny of all major frog lineages and provide a timescale of frog evolution that suggests much younger divergence times than suggested by earlier studies. Unexpectedly, our divergence-time analyses show that three species-rich clades (Hyloidea, Microhylidae, and Natatanura), which together comprise ∼88% of extant anuran species, simultaneously underwent rapid diversification at the Cretaceous-Paleogene (K-Pg) boundary (KPB). Moreover, anuran families and subfamilies containing arboreal species originated near or after the KPB. These results suggest that the K-Pg mass extinction may have triggered explosive radiations of frogs by creating new ecological opportunities. This phylogeny also reveals relationships such as Microhylidae being sister to all other ranoid frogs and African continental lineages of Natatanura forming a clade that is sister to a clade of Eurasian, Indian, Melanesian, and Malagasy lineages. Biogeographical analyses suggest that the ancestral area of modern frogs was Africa, and their current distribution is largely associated with the breakup of Pangaea and subsequent Gondwanan fragmentation.
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Affiliation(s)
- Yan-Jie Feng
- State Key Laboratory of Biocontrol, College of Ecology and Evolution, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510006, China
| | - David C Blackburn
- Department of Natural History, Florida Museum of Natural History, University of Florida, Gainesville, FL 32611
| | - Dan Liang
- State Key Laboratory of Biocontrol, College of Ecology and Evolution, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510006, China
| | - David M Hillis
- Department of Integrative Biology and Biodiversity Collections, University of Texas, Austin, TX 78712
| | - David B Wake
- Museum of Vertebrate Zoology and Department of Integrative Biology, University of California, Berkeley, CA 94720
| | - David C Cannatella
- Department of Integrative Biology and Biodiversity Collections, University of Texas, Austin, TX 78712;
| | - Peng Zhang
- State Key Laboratory of Biocontrol, College of Ecology and Evolution, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510006, China;
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Yang BT, Zhou Y, Min MS, Matsui M, Dong BJ, Li PP, Fong JJ. Diversity and phylogeography of Northeast Asian brown frogs allied to Rana dybowskii (Anura, Ranidae). Mol Phylogenet Evol 2017; 112:148-157. [DOI: 10.1016/j.ympev.2017.04.026] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2016] [Revised: 02/10/2017] [Accepted: 04/29/2017] [Indexed: 11/27/2022]
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32
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Jiang L, Zhao L, Cheng D, Zhu L, Zhang M, Ruan Q, Chen W. The complete mitochondrial genome sequence of the Sichuan Digging Frog, Kaloula rugifera (Anura: Microhylidae) and its phylogenetic implications. Gene 2017; 626:367-375. [PMID: 28536079 DOI: 10.1016/j.gene.2017.05.039] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2017] [Revised: 04/30/2017] [Accepted: 05/19/2017] [Indexed: 10/19/2022]
Abstract
The Sichuan Digging Frog (Kaloula rugifera) belongs to the family Dicroglossidae, which is endemic to northeastern Sichuan and southernmost Gansu provinces, in southwestern China. In this study, the complete mitochondrial genome of K. rugifera was sequenced. The mitogenome was 17,074bp in length, consisting of 13 protein-coding genes, 22 transfer RNA (tRNA) genes, two ribosomal RNA (rRNA) genes, and a non-coding control region. As in other vertebrates, most mitochondrial genes are encoded on the heavy strand, except for ND6 and eight tRNA genes which are encoded on the light strand. The overall base composition of the K. rugifera is 30.32% A, 25.76% C, 29.72% T, and 14.20% G, which is consistent with the lowest frequency for G content in typical amphibian animals' mitochondrial genomes. The alignment of the Kaloula species control regions exhibited high genetic variability and rich A+T content. Besides, 3 types of tandem repeat units were also identified in the control region. Phylogenetic tree demonstrated that K. rugifera was clustered together with K. borealis and K. verrucosa and they had a close relationship with each other. The complete mitogenome of K. rugifera can provide an important data for the studies on phylogenetic relationship to further explore the taxonomic status of Kaloula species.
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Affiliation(s)
- Lichun Jiang
- Ecological Security and Protection Key Laboratory of Sichuan Province, Mianyang Normal University, Mianyang, Sichuan 621000, PR China; Key Laboratory for Molecular Biology and Biopharmaceutics, School of Life Science and Technology, Mianyang Normal University, Mianyang, Sichuan 621000, PR China
| | - Li Zhao
- Key Laboratory for Molecular Biology and Biopharmaceutics, School of Life Science and Technology, Mianyang Normal University, Mianyang, Sichuan 621000, PR China
| | - Dongmei Cheng
- Key Laboratory for Molecular Biology and Biopharmaceutics, School of Life Science and Technology, Mianyang Normal University, Mianyang, Sichuan 621000, PR China
| | - Lilan Zhu
- Key Laboratory for Molecular Biology and Biopharmaceutics, School of Life Science and Technology, Mianyang Normal University, Mianyang, Sichuan 621000, PR China
| | - Min Zhang
- Key Laboratory for Molecular Biology and Biopharmaceutics, School of Life Science and Technology, Mianyang Normal University, Mianyang, Sichuan 621000, PR China
| | - Qiping Ruan
- Key Laboratory for Molecular Biology and Biopharmaceutics, School of Life Science and Technology, Mianyang Normal University, Mianyang, Sichuan 621000, PR China.
| | - Wei Chen
- Ecological Security and Protection Key Laboratory of Sichuan Province, Mianyang Normal University, Mianyang, Sichuan 621000, PR China.
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Zhou Y, Wang S, Zhu H, Li P, Yang B, Ma J. Phylogeny and biogeography of South Chinese brown frogs (Ranidae, Anura). PLoS One 2017; 12:e0175113. [PMID: 28369142 PMCID: PMC5378408 DOI: 10.1371/journal.pone.0175113] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2016] [Accepted: 03/21/2017] [Indexed: 01/05/2023] Open
Abstract
Few studies have explored the role of Cenozoic tectonic evolution in shaping the patterns and processes of extant animal distributions in and around East Asia. In this study, we selected South Chinese brown frogs as a model to examine the phylogenetic and biogeographical consequences of Miocene tectonic events within South China and its margins. We used mitochondrial and nuclear molecular data to reconstruct phylogenetic interrelationships among Chinese brown frogs using Bayesian and maximum likelihood analyses. The phylogeny results show that there are four main clades of Chinese brown frogs. Excepting the three commonly known Chinese brown frog species groups, R. maoershanensis forms an independent clade nearest to the R. japonica group. Phylogeny and P-distance analyses confirmed R. maoershanensis as a valid species. Among South Chinese brown frogs, there are four subclades associated with four geographical areas: (I) R. maoershanensis; (II) R. japonica; (III) R. chaochiaoensis; and (IV) other species of the R. longicrus species group. Divergence times, estimated using mitochondrial sequences, place the vicariance events among the four subclades in the middle to late Miocene epoch. Our results suggest that (1) South Chinese brown frogs originated due to a vicariance event separating them from the R. chensinensis species group at the time of the Geological movement (~18 million years ago, Ma) in southern Tibet and the Himalayan region; (2) the separation and speciation of R. maoershanensis from the R. japonica group occurred due to the dry climate at approximately 16 Ma; (3) South Chinese brown frogs migrated from South China to Japan at the time (~10.8 Ma) that the global sea-level fell and the East China Sea Shelf Basin was swamp facies, when a land gallery may have formed across the sea to connect the two areas; and (4) R. chaochiaoensis separated from other species of the R. longicrus species group during the uplift of the Tibetan Plateau at approximately 9.5 Ma.
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Affiliation(s)
- Yu Zhou
- College of Wildlife Resources, Northeast Forestry University, Harbin, Heilongjiang, China
- Feline Research Center of the Chinese State Forestry Administration, Northeast Forestry University, Harbin, China
| | - Sirui Wang
- College of Wildlife Resources, Northeast Forestry University, Harbin, Heilongjiang, China
| | - Hedan Zhu
- College of Wildlife Resources, Northeast Forestry University, Harbin, Heilongjiang, China
| | - Pipeng Li
- College of Life Sciences, Shenyang Normal University, Shenyang, Liaoning, China
- * E-mail: (PL); (BY); (JM)
| | - Baotian Yang
- College of Life Sciences, Shenyang Normal University, Shenyang, Liaoning, China
- * E-mail: (PL); (BY); (JM)
| | - Jianzhang Ma
- College of Wildlife Resources, Northeast Forestry University, Harbin, Heilongjiang, China
- Feline Research Center of the Chinese State Forestry Administration, Northeast Forestry University, Harbin, China
- * E-mail: (PL); (BY); (JM)
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Chen Z, Li H, Zhu Y, Feng Q, He Y, Chen X. Molecular phylogeny of the family Dicroglossidae (Amphibia: Anura) inferred from complete mitochondrial genomes. BIOCHEM SYST ECOL 2017. [DOI: 10.1016/j.bse.2017.01.006] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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35
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Jin H, Yonezawa T, Zhong Y, Kishino H, Hasegawa M. Cretaceous origin of giant rhinoceros beetles (Dynastini; Coleoptera) and correlation of their evolution with the Pangean breakup. Genes Genet Syst 2017; 91:209-215. [PMID: 27557976 DOI: 10.1266/ggs.16-00003] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
The giant rhinoceros beetles (Dynastini, Scarabaeidae, Coleoptera) are distributed in tropical and temperate regions in Asia, America and Africa. Recent molecular phylogenetic studies have revealed that the giant rhinoceros beetles can be divided into three clades representing Asia, America and Africa. Although a correlation between their evolution and the continental drift during the Pangean breakup was suggested, there is no accurate divergence time estimation among the three clades based on molecular data. Moreover, there is a long chronological gap between the timing of the Pangean breakup (Cretaceous: 110-148 Ma) and the emergence of the oldest fossil record (Oligocene: 33 Ma). In this study, we estimated their divergence times based on molecular data, using several combinations of fossil calibration sets, and obtained robust estimates. The inter-continental divergence events among the clades were estimated to have occurred about 99 Ma (Asian clade and others) and 78 Ma (American clade and African clade), both of which are after the Pangean breakup. These estimates suggest their inter-continental divergences occurred by overseas sweepstakes dispersal, rather than by vicariances of the population caused by the Pangean breakup.
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Affiliation(s)
- Haofei Jin
- School of Life Sciences, Fudan University
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36
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Garg S, Biju SD. Molecular and Morphological Study of Leaping Frogs (Anura, Ranixalidae) with Description of Two New Species. PLoS One 2016; 11:e0166326. [PMID: 27851823 PMCID: PMC5112961 DOI: 10.1371/journal.pone.0166326] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2016] [Accepted: 10/24/2016] [Indexed: 11/19/2022] Open
Abstract
The monotypic anuran family Ranixalidae is endemic to India, with a predominant distribution in the Western Ghats, a region that is home to several unique amphibian lineages. It is also one of the three ancient anuran families that diversified on the Indian landmass long before several larger radiations of extant frogs in this region. In recent years, ranixalids have been subjected to DNA barcoding and systematic studies. Nearly half of the presently recognized species in this family have been described over the last three years, along with recognition of a new genus to accommodate three previously known members. Our surveys in the Western Ghats further suggest the presence of undescribed diversity in this group, thereby increasing former diversity estimates. Based on rapid genetic identification using a mitochondrial gene, followed by phylogenetic analyses with an additional nuclear gene and detailed morphological studies including examination of museum specimens, new collections, and available literature, here we describe two new species belonging to the genus Indirana from the Western Ghats states of Karnataka and Kerala. We also provide new genetic and morphological data along with confirmed distribution records for all the species known prior to this study. This updated systematic revision of family Ranixalidae will facilitate future studies and provide vital information for conservation assessment of these relic frogs.
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Affiliation(s)
- Sonali Garg
- Systematics Lab, Department of Environmental Studies, University of Delhi, Delhi, 110 007, India
| | - S. D. Biju
- Systematics Lab, Department of Environmental Studies, University of Delhi, Delhi, 110 007, India
- * E-mail:
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37
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Portik DM, Blackburn DC. The evolution of reproductive diversity in Afrobatrachia: A phylogenetic comparative analysis of an extensive radiation of African frogs. Evolution 2016; 70:2017-32. [PMID: 27402182 PMCID: PMC5129497 DOI: 10.1111/evo.12997] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2016] [Revised: 05/13/2016] [Accepted: 06/24/2016] [Indexed: 11/28/2022]
Abstract
The reproductive modes of anurans (frogs and toads) are the most diverse of terrestrial vertebrates, and a major challenge is identifying selective factors that promote the evolution or retention of reproductive modes across clades. Terrestrialized anuran breeding strategies have evolved repeatedly from the plesiomorphic fully aquatic reproductive mode, a process thought to occur through intermediate reproductive stages. Several selective forces have been proposed for the evolution of terrestrialized reproductive traits, but factors such as water systems and co-evolution with ecomorphologies have not been investigated. We examined these topics in a comparative phylogenetic framework using Afrobatrachian frogs, an ecologically and reproductively diverse clade representing more than half of the total frog diversity found in Africa (∼400 species). We infer direct development has evolved twice independently from terrestrialized reproductive modes involving subterranean or terrestrial oviposition, supporting evolution through intermediate stages. We also detect associations between specific ecomorphologies and oviposition sites, and demonstrate arboreal species exhibit an overall shift toward using lentic water systems for breeding. These results indicate that changes in microhabitat use associated with ecomorphology, which allow access to novel sites for reproductive behavior, oviposition, or larval development, may also promote reproductive mode diversity in anurans.
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Affiliation(s)
- Daniel M Portik
- Department of Biology, The University of Texas at Arlington, Arlington, Texas.
- Department of Integrative Biology and Museum of Vertebrate Zoology, University of California, Berkeley, California.
| | - David C Blackburn
- Florida Museum of Natural History, University of Florida, Gainesville, Florida
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38
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Phylogenetics and biogeography of the endemic Madagascan millipede assassin bugs (Hemiptera: Reduviidae: Ectrichodiinae). Mol Phylogenet Evol 2016; 100:219-233. [DOI: 10.1016/j.ympev.2016.03.011] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2015] [Revised: 01/27/2016] [Accepted: 03/11/2016] [Indexed: 12/23/2022]
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39
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Yuan ZY, Zhou WW, Chen X, Poyarkov NA, Chen HM, Jang-Liaw NH, Chou WH, Matzke NJ, Iizuka K, Min MS, Kuzmin SL, Zhang YP, Cannatella DC, Hillis DM, Che J. Spatiotemporal Diversification of the True Frogs (GenusRana): A Historical Framework for a Widely Studied Group of Model Organisms. Syst Biol 2016; 65:824-42. [DOI: 10.1093/sysbio/syw055] [Citation(s) in RCA: 101] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2015] [Accepted: 05/31/2015] [Indexed: 11/12/2022] Open
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40
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Larson TR, Castro D, Behangana M, Greenbaum E. Evolutionary history of the river frog genus Amietia (Anura: Pyxicephalidae) reveals extensive diversification in Central African highlands. Mol Phylogenet Evol 2016; 99:168-181. [PMID: 27026115 PMCID: PMC4898062 DOI: 10.1016/j.ympev.2016.03.017] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2015] [Revised: 03/10/2016] [Accepted: 03/13/2016] [Indexed: 10/22/2022]
Abstract
The African river frog genus Amietia is found near rivers and other lentic water sources throughout central, eastern, and southern Africa. Because the genus includes multiple morphologically conservative species, taxonomic studies of river frogs have been relatively limited. We sampled 79 individuals of Amietia from multiple localities in and near the Albertine Rift (AR) of Burundi, Democratic Republic of the Congo, and Uganda. We utilized single-gene (16S) and concatenated (12S, 16S, cyt b and RAG1) gene-tree analyses and coalescent species-tree analyses to construct phylogenetic trees. Two divergence dating approaches were used in BEAST, including secondary calibration points with 12S, 16S, cyt b and RAG1, and a molecular clock with the 12S, 16S, and cyt b genes. All analyses recovered Amietia as monophyletic with strong support, and revealed several well-supported cryptic lineages, which is consistent with other recent phylogeography studies of AR amphibians. Dating estimates were similar, and Amietia diversification is coincident with global cooling and aridification events in the Miocene and Pliocene, respectively. Our results suggest additional taxonomic work is needed to describe multiple new species of AR Amietia, some of which have limited geographic distributions that are likely to be of conservation concern.
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Affiliation(s)
- Thornton R Larson
- Department of Biological Sciences, University of Texas at El Paso, 500 W. University Ave., El Paso, TX 79968, USA
| | - Delilah Castro
- Department of Biological Sciences, University of Texas at El Paso, 500 W. University Ave., El Paso, TX 79968, USA
| | | | - Eli Greenbaum
- Department of Biological Sciences, University of Texas at El Paso, 500 W. University Ave., El Paso, TX 79968, USA.
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Eberle J, Fabrizi S, Lago P, Ahrens D. A historical biogeography of megadiverse Sericini-another story “out of Africa”? Cladistics 2016; 33:183-197. [DOI: 10.1111/cla.12162] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/06/2016] [Indexed: 02/04/2023] Open
Affiliation(s)
- Jonas Eberle
- Centre of Taxonomy and Evolutionary Research; Zoologisches Forschungsmuseum Alexander Koenig Bonn; Adenauerallee 160 53113 Bonn Germany
| | - Silvia Fabrizi
- Centre of Taxonomy and Evolutionary Research; Zoologisches Forschungsmuseum Alexander Koenig Bonn; Adenauerallee 160 53113 Bonn Germany
| | - Paul Lago
- Department of Biology; University of Mississippi; University MS 38677 USA
| | - Dirk Ahrens
- Centre of Taxonomy and Evolutionary Research; Zoologisches Forschungsmuseum Alexander Koenig Bonn; Adenauerallee 160 53113 Bonn Germany
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Interspecific variation in larval anuran anti-parasite behavior: a test of the adaptive plasticity hypothesis. Evol Ecol 2016. [DOI: 10.1007/s10682-016-9831-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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43
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Goutte S, Dubois A, Howard SD, Marquez R, Rowley JJL, Dehling JM, Grandcolas P, Rongchuan X, Legendre F. Environmental constraints and call evolution in torrent-dwelling frogs. Evolution 2016; 70:811-26. [PMID: 26960074 DOI: 10.1111/evo.12903] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2014] [Revised: 02/09/2016] [Accepted: 02/16/2016] [Indexed: 02/02/2023]
Abstract
Although acoustic signals are important for communication in many taxa, signal propagation is affected by environmental properties. Strong environmental constraints should drive call evolution, favoring signals with greater transmission distance and content integrity in a given calling habitat. Yet, few empirical studies have verified this prediction, possibly due to a shortcoming in habitat characterization, which is often too broad. Here we assess the potential impact of environmental constraints on the evolution of advertisement call in four groups of torrent-dwelling frogs in the family Ranidae. We reconstruct the evolution of calling site preferences, both broadly categorized and at a finer scale, onto a phylogenetic tree for 148 species with five markers (∼3600 bp). We test models of evolution for six call traits for 79 species with regard to the reconstructed history of calling site preferences and estimate their ancestral states. We find that in spite of existing morphological constraints, vocalizations of torrent-dwelling species are most probably constrained by the acoustic specificities of torrent habitats and particularly their high level of ambient noise. We also show that a fine-scale characterization of calling sites allows a better perception of the impact of environmental constraints on call evolution.
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Affiliation(s)
- Sandra Goutte
- Muséum National d'Histoire Naturelle, Institut de Systématique, Evolution, Biodiversité, ISYEB - UMR 7205 CNRS MNHN UPMC EPHE, Sorbonne Universités, 57 rue Cuvier, 75231, Paris Cedex 05, France. .,Laboratório de História Natural de Anfíbios Brasileiros, Instituto de Biologia, Universidade Estadual de Campinas, rua Monteiro Lobato, 255, CEP 13083-862, Campinas, São Paulo, Brazil.
| | - Alain Dubois
- Muséum National d'Histoire Naturelle, Institut de Systématique, Evolution, Biodiversité, ISYEB - UMR 7205 CNRS MNHN UPMC EPHE, Sorbonne Universités, 57 rue Cuvier, 75231, Paris Cedex 05, France
| | - Samuel D Howard
- Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, 117543, Singapore
| | - Rafael Marquez
- Fonoteca Zoológica, Departamento de Biodiversidad y Biología Evolutiva, Museo Nacional de Ciencias Naturales (CSIC), C/José Gutiérrez Abascal, 2, 28006, Madrid, Spain
| | - Jodi J L Rowley
- Australian Museum Research Institute, Australian museum 1 College Street, Sydney, NSW, 2010, Australia
| | - J Maximilian Dehling
- Institut für Integrierte Naturwissenschaften, Abteilung Biologie, Universität Koblenz-Landau, Universitätsstraße 1, 56070, Koblenz, Germany
| | - Philippe Grandcolas
- Muséum National d'Histoire Naturelle, Institut de Systématique, Evolution, Biodiversité, ISYEB - UMR 7205 CNRS MNHN UPMC EPHE, Sorbonne Universités, 57 rue Cuvier, 75231, Paris Cedex 05, France
| | - Xiong Rongchuan
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China
| | - Frédéric Legendre
- Muséum National d'Histoire Naturelle, Institut de Systématique, Evolution, Biodiversité, ISYEB - UMR 7205 CNRS MNHN UPMC EPHE, Sorbonne Universités, 57 rue Cuvier, 75231, Paris Cedex 05, France
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44
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Bittencourt-Silva GB, Conradie W, Siu-Ting K, Tolley KA, Channing A, Cunningham M, Farooq HM, Menegon M, Loader SP. The phylogenetic position and diversity of the enigmatic mongrel frog Nothophryne Poynton, 1963 (Amphibia, Anura). Mol Phylogenet Evol 2016; 99:89-102. [PMID: 27001603 DOI: 10.1016/j.ympev.2016.03.021] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2015] [Revised: 03/14/2016] [Accepted: 03/16/2016] [Indexed: 11/18/2022]
Abstract
The phylogenetic relationships of the African mongrel frog genus Nothophryne are poorly understood. We provide the first molecular assessment of the phylogenetic position of, and diversity within, this monotypic genus from across its range-the Afromontane regions of Malawi and Mozambique. Our analysis using a two-tiered phylogenetic approach allowed us to place the genus in Pyxicephalidae. Within the family, Nothophryne grouped with Tomopterna, a hypothesis judged significantly better than alternative hypotheses proposed based on morphology. Our analyses of populations across the range of Nothophryne suggest the presence of several cryptic species, at least one species per mountain. Formal recognition of these species is pending but there is a major conservation concern for these narrowly distributed populations in an area impacted by major habitat change. The phylogenetic tree of pyxicephalids is used to examine evolution of life history, ancestral habitat, and biogeography of this group.
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Affiliation(s)
| | - Werner Conradie
- Port Elizabeth Museum (Bayworld), Humewood 6013, South Africa; South African Institute for Aquatic Biodiversity, Grahamstown 6140, South Africa
| | - Karen Siu-Ting
- Ecological and Evolutionary Genomics Lab, IBERS, Aberystwyth University, Aberystwyth SY23 3FG, United Kingdom; School of Biotechnology, Dublin City University, Glasnevin, Dublin 9, Ireland; Departamento de Herpetología, Museo de Historia Natural UNMSM, Av. Arenales 1256, Jesus María, Lima, Peru
| | - Krystal A Tolley
- South African National Biodiversity Institute, Rhodes Drive, Private Bag X7, Newlands, Claremont 7735, Cape Town, South Africa
| | - Alan Channing
- Biodiversity and Conservation Biology Department, University of the Western Cape, Bellville 7525, South Africa
| | - Michael Cunningham
- South African Institute for Aquatic Biodiversity, Grahamstown 6140, South Africa; Department of Genetics, University of Pretoria, Private Bag X20, Hatfield 0028, South Africa
| | - Harith M Farooq
- Faculty of Natural Sciences, Lúrio University, Pemba 958, Mozambique
| | - Michele Menegon
- Tropical Biodiversity Section, Museo delle Scienze, Viale del Lavoro e della Scienza, 3, 38122 Trento, Italy
| | - Simon P Loader
- Department of Environmental Sciences, University of Basel, Basel 4056, Switzerland; University of Roehampton, London SW15 4JD, United Kingdom
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45
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Toussaint EFA, Fikáček M, Short AEZ. India-Madagascar vicariance explains cascade beetle biogeography. Biol J Linn Soc Lond 2016. [DOI: 10.1111/bij.12791] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Emmanuel F. A. Toussaint
- Department of Ecology & Evolutionary Biology & Division of Entomology; Biodiversity Institute; University of Kansas; Lawrence KS USA
| | - Martin Fikáček
- Department of Entomology; National Museum; Cirkusova 1740, CZ-19800 Praha 9 Czech Republic
- Department of Zoology; Faculty of Science; Charles University in Prague; Viničná 7, CZ-12843 Praha 2 Czech Republic
| | - Andrew E. Z. Short
- Department of Ecology & Evolutionary Biology & Division of Entomology; Biodiversity Institute; University of Kansas; Lawrence KS USA
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Yan F, Jiang K, Wang K, Jin JQ, Suwannapoom C, Li C, Vindum JV, Brown RM, Che J. The Australasian frog family Ceratobatrachidae in China, Myanmar and Thailand: discovery of a new Himalayan forest frog clade. DONG WU XUE YAN JIU = ZOOLOGICAL RESEARCH 2016; 37:7-14. [PMID: 26828029 DOI: 10.13918/j.issn.2095-8137.2016.1.7] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 11/01/2022]
Abstract
In an effort to study the systematic affinities and specieslevel phylogenetic relationships of the enigmatic anurans variably assigned to the genera Ingerana or Limnonectes (family Dicroglossidae), we collected new molecular sequence data for five species including four Himalayan taxa, Limnonectes xizangensis, Lim. medogensis, Lim. alpina, [corrected] Ingerana borealis and one southeast Asian species, I. tasanae, and analyzed these together with data from previous studies involving other ostensibly related taxa. Our surprising results demonstrate unequivocally that Lim. xizangensis, Lim. medogensis and Lim. alpina [corrected] form a strongly supported clade, the sister-group of the family Australasian forest frog family Ceratobatrachidae. This discovery requires an expansion of the definition of Ceratobatrachidae and represents the first record of this family in China. These three species are distinguished from the species of Ingerana and Limnonectes by the: (1) absence of interdigital webbing of the foot, (2) absence of terminal discs on fingers and toes, (3) absence of circumarginal grooves on the fingers and toes, and (4) absence of tarsal folds. Given their phylogenetic and morphological distinctiveness, we assign them to the oldest available generic name for this clade, Liurana Dubois 1987, and transfer Liurana from Dicroglossidae to the family Ceratobatrachidae. In contrast, Ingerana tasanae was found to be clustered with strong support with the recently described genus Alcalus (Ceratobatrachidae), a small clade of otherwise Sundaic species; this constitutes a new record of the family Ceratobatrachidae for Myanmar and Thailand. Finally, Ingerana borealis clustered with the "true" Ingerana (family Dicroglossidae), for which the type species is I. tenasserimensis.
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Affiliation(s)
- Fang Yan
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming Yunnan 650223, China;Southeast Asia Biodiversity Research Institute, Chinese Academy of Sciences, Yezin, Nay Pyi Taw 05282, Myanmar
| | - Ke Jiang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming Yunnan 650223, China;Southeast Asia Biodiversity Research Institute, Chinese Academy of Sciences, Yezin, Nay Pyi Taw 05282, Myanmar
| | - Kai Wang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming Yunnan 650223, China; Sam Noble Oklahoma Museum of Natural History and Department of Biology, University of Oklahoma, Norman OK 73072-7029, U.S.A
| | - Jie-Qiong Jin
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming Yunnan 650223, China
| | - Chatmongkon Suwannapoom
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming Yunnan 650223, China; School of Agriculture and Natural Resources, University of Phayao, Phayao 56000, Thailand
| | - Cheng Li
- Imaging Biodiversity Expedition, Beijing 100107, China
| | - Jens V Vindum
- Department of Herpetology, California Academy of Sciences, California 94118, U.S.A
| | - Rafe M Brown
- Biodiversity Institute and Department of Ecology and Evolutionary Biology, 1345 Jayhawk Blvd, University of Kansas, Lawrence KS 66045, U.S.A
| | - Jing Che
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming Yunnan 650223, China.
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47
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Frazão A, da Silva HR, Russo CADM. The Gondwana Breakup and the History of the Atlantic and Indian Oceans Unveils Two New Clades for Early Neobatrachian Diversification. PLoS One 2015; 10:e0143926. [PMID: 26618546 PMCID: PMC4664409 DOI: 10.1371/journal.pone.0143926] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2015] [Accepted: 11/11/2015] [Indexed: 11/20/2022] Open
Abstract
The largest anuran diversity belongs to the Neobatrachia, which harbor more than five thousand extant species. Here, we propose a new hypothesis for the historical aspects of the neobatrachian evolution with a formal biogeographical analysis. We selected 12 genes for 144 neobatrachian genera and four archaeobatrachian outgroups and performed a phylogenetic analysis using a maximum likelihood algorithm with the rapid bootstrap test. We also estimated divergence times for major lineages using a relaxed uncorrelated clock method. According to our time scale, the diversification of crown Neobatrachia began around the end of the Early Cretaceous. Our phylogenetic tree suggests that the first split of Neobatrachia is related to the geological events in the Atlantic and Indian Oceans. Hence, we propose names for these clades that indicate this connection, i.e., Atlanticanura and Indianura. The Atlanticanura is composed of three major neobatrachian lineages: Heleophrynidae, Australobatrachia and Nobleobatrachia. On the other hand, the Indianura consists of two major lineages: Sooglossoidea and Ranoides. The biogeographical analysis indicates that many neobatrachian splits occurred as a result of geological events such as the separation between South America and Africa, between India and the Seychelles, and between Australia and South America.
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Affiliation(s)
- Annelise Frazão
- Departamento de Genética, Instituto de Biologia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Hélio Ricardo da Silva
- Departamento de Biologia Animal, Instituto de Biologia, Universidade Federal Rural do Rio de Janeiro, Seropédica, Rio de Janeiro, Brazil
| | - Claudia Augusta de Moraes Russo
- Departamento de Genética, Instituto de Biologia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Rio de Janeiro, Brazil
- * E-mail:
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48
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Moen DS, Morlon H, Wiens JJ. Testing Convergence Versus History: Convergence Dominates Phenotypic Evolution for over 150 Million Years in Frogs. Syst Biol 2015; 65:146-60. [DOI: 10.1093/sysbio/syv073] [Citation(s) in RCA: 80] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2014] [Accepted: 09/22/2015] [Indexed: 11/14/2022] Open
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49
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Li Y, Wu X, Zhang H, Yan P, Xue H, Wu X. Vicariance and Its Impact on the Molecular Ecology of a Chinese Ranid Frog Species-Complex (Odorrana schmackeri, Ranidae). PLoS One 2015; 10:e0138757. [PMID: 26394403 PMCID: PMC4578928 DOI: 10.1371/journal.pone.0138757] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2015] [Accepted: 09/03/2015] [Indexed: 11/26/2022] Open
Abstract
Paleogeological events and Pleistocene climatic fluctuations have had profound influences on the genetic patterns and phylogeographic structure of species in southern China. In this study, we investigated the population genetic structure and Phylogeography of the Odorrana schmackeri species complex, mountain stream-dwelling odorous frogs, endemic to southern China. We obtained mitochondrial sequences (1,151bp) of the complete ND2 gene and two flanking tRNAs of 511 individuals from 25 sites for phylogeographic analyses. Phylogenetic reconstruction revealed seven divergent evolutionary lineages, with mean pairwise (K2P) sequence distances from 7.8% to 21.1%, except for a closer ND2 distance (3.4%). The complex geological history of southern China drove matrilineal divergence in the O. schmackeri species complex into highly structured geographical units. The first divergence between lineage A+B and other lineages (C-G) had likely been influenced by the uplift of coastal mountains of Southeast China during the Mio-Pliocene period. The subsequent divergences between the lineages C-G may have followed the formation of the Three Gorges and the intensification of the East Asian summer monsoon during the late Pliocene and early Pleistocene. Demographic analyses indicated that major lineages A and C have been experienced recent population expansion (c. 0.045–0.245 Ma) from multiple refugia prior to the Last Glacial Maximum (LGM). Molecular analysis suggest that these seven lineages may represent seven different species, three described species and four cryptic species and should at least be separated into seven management units corresponding to these seven geographic lineages for conservation.
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Affiliation(s)
- Yongmin Li
- Anhui Province Key Laboratory for Conservation and Exploitation of Biological Resource, College of Life Sciences, Anhui Normal University, Wuhu, Anhui, China
- School of Life Sciences, Fuyang Teachers College, Fuyang, Anhui, China
| | - Xiaoyou Wu
- Anhui Province Key Laboratory for Conservation and Exploitation of Biological Resource, College of Life Sciences, Anhui Normal University, Wuhu, Anhui, China
| | - Huabin Zhang
- Anhui Province Key Laboratory for Conservation and Exploitation of Biological Resource, College of Life Sciences, Anhui Normal University, Wuhu, Anhui, China
| | - Peng Yan
- Anhui Province Key Laboratory for Conservation and Exploitation of Biological Resource, College of Life Sciences, Anhui Normal University, Wuhu, Anhui, China
| | - Hui Xue
- Anhui Province Key Laboratory for Conservation and Exploitation of Biological Resource, College of Life Sciences, Anhui Normal University, Wuhu, Anhui, China
| | - Xiaobing Wu
- Anhui Province Key Laboratory for Conservation and Exploitation of Biological Resource, College of Life Sciences, Anhui Normal University, Wuhu, Anhui, China
- * E-mail:
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50
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Brown RM. A New Species of Stream Frog of the Genus Hylarana from the Mountains of Southern Mindanao Island, Philippines. HERPETOLOGICA 2015. [DOI: 10.1655/herpetologica-d-14-00075] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Affiliation(s)
- Rafe M. Brown
- Biodiversity Institute and Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, KS 66045, USA
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