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Huang J, Liu XL, Du L, Bernstein JM, Liu S, Yang Y, Yu G, Wu Z. A new species of Bush frog (Anura, Rhacophoridae, Raorchestes) from southeastern Yunnan, China. Zookeys 2023; 1151:47-65. [DOI: 10.3897/zookeys.1151.95616] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2022] [Accepted: 12/20/2022] [Indexed: 03/06/2023] Open
Abstract
In this study, based on morphological and molecular data, a new bush frog species is described from Yunnan, China. Eleven samples of Raorchestes malipoensissp. nov. were collected from Malipo County, southeastern Yunnan. This species can be distinguished from other congeners by a combination of 13 morphological characters. Phylogenetic analyses based on the 16S rRNA gene indicate that these individuals form a monophyletic group, and genetic divergence between this clade and its closest relatives is higher than 3.1%, which is comparable to the divergence between recognized Raorchestes species. The discovery of this new species suggests that additional extensive surveys in the southeastern Yunnan would yield more amphibian lineages yet unknown to science.
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Dufresnes C, Mahony S, Prasad VK, Kamei RG, Masroor R, Khan MA, Al-Johany AM, Gautam KB, Gupta SK, Borkin LJ, Melnikov DA, Rosanov JM, Skorinov DV, Borzée A, Jablonski D, Litvinchuk SN. Shedding light on taxonomic chaos: Diversity and distribution of South Asian skipper frogs (Anura, Dicroglossidae, Euphlyctis). SYST BIODIVERS 2022. [DOI: 10.1080/14772000.2022.2102686] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
Affiliation(s)
- Christophe Dufresnes
- LASER, College of Biology and the Environment, Nanjing Forestry University, Nanjing, People’s Republic of China
| | - Stephen Mahony
- School of Biology and Environmental Science, University College Dublin, Dublin 4, Ireland
- Department of Life Sciences, The Natural History Museum, London, UK
| | - Vishal Kumar Prasad
- Laboratory of Animal Behaviour and Conservation, College of Biology and the Environment, Nanjing Forestry University, People’s Republic of China
- Wildlife Institute of India, Chandrabani, Uttarakhand, India
| | - Rachunliu G. Kamei
- Department of Life Sciences, The Natural History Museum, London, UK
- 566 Kohima-Meriema Road (AH1), Meriema, Kohima, 797001, Nagaland, India
| | - Rafaqat Masroor
- Zoological Sciences Division, Pakistan Museum of Natural History, Garden Avenue, Shakarparian, 44000, Islamabad Pakistan
| | - Muazzam Ali Khan
- Department of Botany, Bacha Khan University Charsadda, Charsadda, KP, Pakistan
| | - Awadh M. Al-Johany
- Department of Zoology, King Saud University, Riyadh, 11451, Kingdom of Saudi Arabia
| | | | | | - Leo J. Borkin
- Laboratory of Herpetology, Zoological Institute, Russian Academy of Sciences, Saint Petersburg, 199034, Russia
| | - Daniel A. Melnikov
- Laboratory of Herpetology, Zoological Institute, Russian Academy of Sciences, Saint Petersburg, 199034, Russia
| | - Juriy M. Rosanov
- Institute of Cytology, Russian Academy of Sciences, Saint Petersburg, Russia
| | - Dmitriy V. Skorinov
- Institute of Cytology, Russian Academy of Sciences, Saint Petersburg, Russia
| | - Amaël Borzée
- Laboratory of Animal Behaviour and Conservation, College of Biology and the Environment, Nanjing Forestry University, People’s Republic of China
| | - Daniel Jablonski
- Department of Zoology, Comenius University, in Bratislava, Mlynská dolina, Ilkovičova 6, Bratislava, 842 15, Slovakia
| | - Spartak N. Litvinchuk
- Institute of Cytology, Russian Academy of Sciences, Saint Petersburg, Russia
- Dagestan State University, Makhachkala, Russia
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3
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Rawien J, Jairam-Doerga S. Predicted Batrachochytrium dendrobatidis infection sites in Guyana, Suriname, and French Guiana using the species distribution model maxent. PLoS One 2022; 17:e0270134. [PMID: 35834475 PMCID: PMC9282542 DOI: 10.1371/journal.pone.0270134] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Accepted: 06/03/2022] [Indexed: 11/19/2022] Open
Abstract
The fungal pathogen Batrachochytrium dendrobatidis (Bd) which causes that amphibian disease chytridiomycosis is expanding its worldwide range from an Asian origin, infecting amphibians in a growing number of countries. Modelling the potential range of this amphibian pathogen using environmental variables and presence data could advance our understanding of at-risk areas and species in locations with limited surveillance to date. We used a species distribution model to assess Bd habitat suitability in the three Guiana's (Guyana, Suriname, and French Guiana) in South America. The model output showed that all three countries have substantial areas where Bd could grow and proliferate, and maximum temperature of the warmest month was the top predictor of suitable Bd habitat, inversely correlated with modeled Bd occurrence. Predicted Bd infection areas in Guyana and French Guiana were large and localized whereas possible sites in Suriname were more scattered throughout the country. The areas projected as potential suitable in Suriname were mostly high elevation regions. These results could help inform efficiencies for development of a proactive monitoring program that could alert managers of novel Bd outbreaks for focused mitigation actions to forestall the spread of this amphibian disease.
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Affiliation(s)
- Jairam Rawien
- Anton de Kom University of Suriname, National Zoological Collection Suriname, Paramaribo, Suriname
| | - Sabitrie Jairam-Doerga
- Anton de Kom University of Suriname, National Herbarium of Suriname, Paramaribo, Suriname
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4
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Phylogeographic structure suggests environmental gradient speciation in a montane frog from the northern Andes of Colombia. ORG DIVERS EVOL 2022. [DOI: 10.1007/s13127-022-00549-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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5
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The role of climate and islands in species diversification and reproductive-mode evolution of Old World tree frogs. Commun Biol 2022; 5:347. [PMID: 35411020 PMCID: PMC9001633 DOI: 10.1038/s42003-022-03292-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Accepted: 03/17/2022] [Indexed: 11/21/2022] Open
Abstract
Large diversifications of species are known to occur unevenly across space and evolutionary lineages, but the relative importance of their driving mechanisms, such as climate, ecological opportunity and key evolutionary innovations (KEI), remains poorly understood. Here, we explore the remarkable diversification of rhacophorid frogs, which represent six percent of global amphibian diversity, utilize four distinct reproductive modes, and span a climatically variable area across mainland Asia, associated continental islands, and Africa. Using a complete species-level phylogeny, we find near-constant diversification rates but a highly uneven distribution of species richness. Montane regions on islands and some mainland regions have higher phylogenetic diversity and unique assemblages of taxa; we identify these as cool-wet refugia. Starting from a centre of origin, rhacophorids reached these distant refugia by adapting to new climatic conditions (‘niche evolution’-dominant), especially following the origin of KEIs such as terrestrial reproduction (in the Late Eocene) or by dispersal during periods of favourable climate (‘niche conservatism’-dominant). By examining climate, geographical and phylogenetic data, the diversification and evolution of rhacophorid frogs is explored
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6
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Ellepola G, Herath J, Manamendra-Arachchi K, Wijayathilaka N, Senevirathne G, Pethiyagoda R, Meegaskumbura M. Molecular species delimitation of shrub frogs of the genus Pseudophilautus (Anura, Rhacophoridae). PLoS One 2021; 16:e0258594. [PMID: 34665841 PMCID: PMC8525734 DOI: 10.1371/journal.pone.0258594] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2021] [Accepted: 09/30/2021] [Indexed: 11/17/2022] Open
Abstract
Sri Lanka is an amphibian hotspot of global significance. Its anuran fauna is dominated by the shrub frogs of the genus Pseudophilautus. Except for one small clade of four species in Peninsular India, these cool-wet adapted frogs, numbering some 59 extant species, are distributed mainly across the montane and lowland rain forests of the island. With species described primarily by morphological means, the diversification has never yet been subjected to a molecular species delimitation analysis, a procedure now routinely applied in taxonomy. Here we test the species boundaries of Pseudophilautus in the context of the phylogenetic species concept (PSC). We use all the putative species for which credible molecular data are available (nDNA-Rag-1; mt-DNA- 12S rRNA, 16S rRNA) to build a well resolved phylogeny, which is subjected to species delimitation analyses. The ABGD, bPTP, mPTP and bGMYC species delimitation methods applied to the 16S rRNA frog barcoding gene (for all species), 12S rRNA and Rag-1 nDNA grouped P. procax and P. abundus; P. hallidayi and P. fergusonianus; P. reticulatus and P. pappilosus; P. pleurotaenia and P. hoipolloi; P. hoffmani and P. asankai; P. silvaticus and P. limbus; P. dilmah and P. hankeni; P. fulvus and P. silus.. Surprisingly, all analyses recovered 14 unidentified potential new species as well. The geophylogeny affirms a distribution across the island's aseasonal 'wet zone' and its three principal hill ranges, suggestive of allopatric speciation playing a dominant role, especially between mountain masses. Among the species that are merged by the delimitation analyses, a pattern leading towards a model of parapatric speciation emerges-ongoing speciation in the presence of gene flow. This delimitation analysis reinforces the species hypotheses, paving the way to a reasonable understanding of Sri Lankan Pseudophilautus, enabling both deeper analyses and conservation efforts of this remarkable diversification. http://zoobank.org/urn:lsid:zoobank.org:pub:DA869B6B-870A-4ED3-BF5D-5AA3F69DDD27.
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Affiliation(s)
- Gajaba Ellepola
- College of Forestry, Guangxi Key Lab for Forest Ecology and Conservation, Guangxi University, Nanning, PR China.,Faculty of Science, University of Peradeniya, Peradeniya, Sri Lanka
| | - Jayampathi Herath
- College of Forestry, Guangxi Key Lab for Forest Ecology and Conservation, Guangxi University, Nanning, PR China
| | | | - Nayana Wijayathilaka
- Department of Zoology, Faculty of Applied Sciences, University of Sri Jayewardenepura, Nugegoda, Sri Lanka
| | - Gayani Senevirathne
- Department of Organismal Biology and Anatomy, University of Chicago, Chicago, Illinois, United States of America
| | - Rohan Pethiyagoda
- Ichthyology Section, Australian Museum, Sydney, New South Wales, Australia
| | - Madhava Meegaskumbura
- College of Forestry, Guangxi Key Lab for Forest Ecology and Conservation, Guangxi University, Nanning, PR China
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7
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Akram A, Rais M, Lopez‐Hervas K, Tarvin RD, Saeed M, Bolnick DI, Cannatella DC. An insight into molecular taxonomy of bufonids, microhylids, and dicroglossid frogs: First genetic records from Pakistan. Ecol Evol 2021; 11:14175-14216. [PMID: 34707849 PMCID: PMC8525160 DOI: 10.1002/ece3.8134] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2021] [Revised: 08/30/2021] [Accepted: 09/03/2021] [Indexed: 11/19/2022] Open
Abstract
The current study was focused on documentation of amphibian assemblage in North Punjab and Islamabad Capital Territory, Pakistan, by using mitochondrial gene sequences of 16S rRNA. Our study entailed 37% of the known amphibian species of the country. We provided a phylogenetic analysis based on 74 newly generated mitochondrial 16S rRNAs from nine species of genus Microlyla, Duttaphrynus, Allopaa, Nanorana, Sphaerotheca, Minervarya, Hoplobatrachus, and Euphlyctis. We employed the maximum-likelihood inference and Bayesian analysis to assess the taxonomic status of the samples obtained from Pakistan, with respect to other congeneric species from surrounding regions. Our findings confirmed the taxonomic status of South Asian anuran species Duttaphrynus stomaticus, Duttaphrynus melanostictus, Microhyla nilphamariensis, Allopaa hazarensis, Nanorana vicina, Sphaerotheca maskeyi (synonym: S. pashchima), Minervarya pierrei, Hoplobatrachus tigerinus, and Euphlyctis kalasgramensis in Pakistan. We have reported new country records of genus Minervarya ( M. pierrei). Minervarya pierrei was previously misidentified as Fejervarya limnocharis, due to dearth of genetic information. We provided the first genetic records of our endemic species N. vicina. The results revealed the taxonomic placement of N. vicina with respect to its congeners and validated the taxonomic status of N. vicina from its type locality (Murree) for the first time. The findings of the present study also indicated the paraphyletic relationship of A.- hazarensis with Nanorana species. So, based on our phylogenetic inferences, morphological characters, and habitat preferences, validity of generic status of A. hazarensis is undecided. As our data were not enough to resolve this issue, we suggest sequencing of additional mitochondrial and nuclear genes in the future studies to get a better resolution. We recommend carrying out extensive surveys throughout the country for proper scientific documentation of amphibians of Pakistan. Many new species, some of them might be endemic to Pakistan, are expected to be discovered, and taxonomic status of other species would be resolved.
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Affiliation(s)
- Ayesha Akram
- Herpetology LabDepartment of Wildlife ManagementPir Mehr Ali Shah Arid Agriculture University RawalpindiRawalpindiPakistan
| | - Muhammad Rais
- Herpetology LabDepartment of Wildlife ManagementPir Mehr Ali Shah Arid Agriculture University RawalpindiRawalpindiPakistan
| | - Karem Lopez‐Hervas
- Department of Wetland EcologyDoñana Biological StationConsejo Superior de Investigaciones CientíficasSevilleSpain
| | - Rebecca D. Tarvin
- Department of Integrative BiologyUniversity of California BerkeleyBerkeleyCaliforniaUSA
- Museum of Vertebrate Zoology and Department of Integrative BiologyUniversity of California BerkeleyBerkeleyCaliforniaUSA
| | - Muhammad Saeed
- Herpetology LabDepartment of Wildlife ManagementPir Mehr Ali Shah Arid Agriculture University RawalpindiRawalpindiPakistan
| | - Daniel I. Bolnick
- Department of Ecology and Evolutionary BiologyUniversity of ConnecticutStorrsConnecticutUSA
| | - David C. Cannatella
- Department of Integrative Biology and Biodiversity CenterUniversity of TexasAustinTexasUSA
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8
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Edwards SV, Robin V, Ferrand N, Moritz C. The evolution of comparative phylogeography: putting the geography (and more) into comparative population genomics. Genome Biol Evol 2021; 14:6339579. [PMID: 34347070 PMCID: PMC8743039 DOI: 10.1093/gbe/evab176] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/28/2021] [Indexed: 11/13/2022] Open
Abstract
Comparative population genomics is an ascendant field using genomic comparisons between species to draw inferences about forces regulating genetic variation. Comparative phylogeography, by contrast, focuses on the shared lineage histories of species codistributed geographically and is decidedly organismal in perspective. Comparative phylogeography is approximately 35 years old, and, by some metrics, is showing signs of reduced growth. Here, we contrast the goals and methods of comparative population genomics and comparative phylogeography and argue that comparative phylogeography offers an important perspective on evolutionary history that succeeds in integrating genomics with landscape evolution in ways that complement the suprageographic perspective of comparative population genomics. Focusing primarily on terrestrial vertebrates, we review the history of comparative phylogeography, its milestones and ongoing conceptual innovations, its increasingly global focus, and its status as a bridge between landscape genomics and the process of speciation. We also argue that, as a science with a strong “sense of place,” comparative phylogeography offers abundant “place-based” educational opportunities with its focus on geography and natural history, as well as opportunities for collaboration with local communities and indigenous peoples. Although comparative phylogeography does not yet require whole-genome sequencing for many of its goals, we conclude that it nonetheless plays an important role in grounding our interpretation of genetic variation in the fundamentals of geography and Earth history.
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Affiliation(s)
- Scott V Edwards
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, 02138, USA.,Museum of Comparative Zoology, Harvard University, Cambridge, MA, 02138, USA
| | - Vv Robin
- Indian Institute of Science Education and Research (IISER) Tirupati, Karakambadi Road, Tirupati, Andhra Pradesh, 517507, India
| | - Nuno Ferrand
- CIBIO/InBIO, Laboratório Associado, Centro de Investigação em Biodiversidade e Recursos Genéticos, Campus Agrário de Vairão, Universidade do Porto, Portugal
| | - Craig Moritz
- Research School of Biology, The Australian National University, Canberra, ACT, 0200, Australia
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9
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Günther R, Richards S. Description of six new species of Xenorhina Peters, 1863 from southern Papua New Guinea (Amphibia, Anura, Microhylidae). ZOOSYST EVOL 2021. [DOI: 10.3897/zse.97.59696] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
We describe six new species of the microhylid frog genus Xenorhina from the southern slopes of Papua New Guinea’s central cordillera and adjacent lowlands, based on a combination of morphological (including osteology) and bioacoustic features. All of the new species are fossorial or terrestrial inhabitants of tropical rainforest habitats and belong to a group of Xenorhina having a single, enlarged odontoid spike on each vomeropalatine bone. Advertisement calls and habitat preferences are described for each species, one of which is amongst the smallest hitherto members of the genus. Description of these six species brings the total number of Xenorhina known to 40 and emphasises the importance of the high-rainfall belt that extends along the southern flanks of New Guinea’s central cordillera as a hotspot of Melanesian amphibian diversity.
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10
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Etter L, Haas A, Lee CC, Min PY, Das I, Hertwig ST. Out of the trap: A new phytothelm‐breeding species of
Philautus
and an updated phylogeny of Bornean bush frogs (Anura: Rhacophoridae). J ZOOL SYST EVOL RES 2021. [DOI: 10.1111/jzs.12465] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Laurence Etter
- Institute of Ecology and Evolution University of Bern Bern Switzerland
| | - Alexander Haas
- Centrum für Naturkunde Universität Hamburg Hamburg Germany
| | - Chien C. Lee
- Institute of Biodiversity and Environmental Conservation Universiti Malaysia Sarawak Kota Samarahan, Sarawak Malaysia
| | - Pui Yong Min
- Institute of Biodiversity and Environmental Conservation Universiti Malaysia Sarawak Kota Samarahan, Sarawak Malaysia
| | - Indraneil Das
- Institute of Biodiversity and Environmental Conservation Universiti Malaysia Sarawak Kota Samarahan, Sarawak Malaysia
| | - Stefan T. Hertwig
- Institute of Ecology and Evolution University of Bern Bern Switzerland
- Naturhistorisches Museum der Burgergemeinde Bern Bern Switzerland
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11
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Garg S, Suyesh R, Das S, Bee MA, Biju SD. An integrative approach to infer systematic relationships and define species groups in the shrub frog genus Raorchestes, with description of five new species from the Western Ghats, India. PeerJ 2021; 9:e10791. [PMID: 33717674 PMCID: PMC7936570 DOI: 10.7717/peerj.10791] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Accepted: 12/26/2020] [Indexed: 11/21/2022] Open
Abstract
The genus Raorchestes is a large radiation of Old World tree frogs for which the Western Ghats in Peninsular India is the major center for origin and diversification. Extensive studies on this group during the past two decades have resolved long-standing taxonomic confusions and uncovered several new species, resulting in a four-fold increase in the number of known Raorchestes frogs from this region. Our ongoing research has revealed another five new species in the genus, formally described as Raorchestes drutaahu sp. nov., Raorchestes kakkayamensis sp. nov., Raorchestes keirasabinae sp. nov., Raorchestes sanjappai sp. nov., and Raorchestes vellikkannan sp. nov., all from the State of Kerala in southern Western Ghats. Based on new collections, we also provide insights on the taxonomic identity of three previously known taxa. Furthermore, since attempts for an up-to-date comprehensive study of this taxonomically challenging genus using multiple integrative taxonomic approaches have been lacking, here we review the systematic affinities of all known Raorchestes species and define 16 species groups based on evidence from multi-gene (2,327 bp) phylogenetic analyses, several morphological characters (including eye colouration and pattern), and acoustic parameters (temporal and spectral properties, as well as calling height). The results of our study present novel insights to facilitate a better working taxonomy for this rather speciose and morphologically conserved radiation of shrub frogs. This will further enable proper field identification, provide momentum for multi-disciplinary studies, as well as assist conservation of one of the most colourful and acoustically diverse frog groups of the Western Ghats biodiversity hotspot.
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Affiliation(s)
- Sonali Garg
- Systematics Lab, Department of Environmental Studies, University of Delhi, Delhi, India
| | - Robin Suyesh
- Systematics Lab, Department of Environmental Studies, University of Delhi, Delhi, India.,Department of Environmental Studies, Sri Venkateswara College, University of Delhi, Delhi, India
| | - Sandeep Das
- Forest Ecology and Biodiversity Conservation Division, Kerala Forest Research Institute, Peechi, Kerala, India.,EDGE of Existence programme, Conservation and Policy, Zoological Society of London, London, UK
| | - Mark A Bee
- Department of Ecology, Evolution, and Behavior, University of Minnesota - Twin Cities, St. Paul, MN, USA
| | - S D Biju
- Systematics Lab, Department of Environmental Studies, University of Delhi, Delhi, India
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12
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Species richness patterns, hotspots and phytogeographic affinities of thalloid liverworts (Marchantiophyta) and hornworts (Anthocerotophyta) of Sri Lanka. Trop Ecol 2021. [DOI: 10.1007/s42965-020-00132-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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13
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Chaplin K, Sumner J, Hipsley CA, Melville J. An Integrative Approach Using Phylogenomics and High-Resolution X-Ray Computed Tomography for Species Delimitation in Cryptic Taxa. Syst Biol 2020; 69:294-307. [PMID: 31372642 DOI: 10.1093/sysbio/syz048] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2019] [Revised: 06/18/2019] [Accepted: 07/12/2019] [Indexed: 11/14/2022] Open
Abstract
Morphologically cryptic taxa have proved to be a long-standing challenge for taxonomists. Lineages that show strong genomic structuring across the landscape but are phenotypically similar pose a conundrum, with traditional morphological analyses of these cryptic lineages struggling to keep up with species delimitation advances. Micro X-ray computed tomography (CT) combined with geometric morphometric analyses provides a promising avenue for identification of morphologically cryptic taxa, given its ability to detect subtle differences in anatomical structures. However, this approach has yet to be used in combination with genomic data in a comparative analytical framework to distinguish cryptic taxa. We present an integrative approach incorporating genomic and geometric morphometric evidence to assess the species delimitation of grassland earless dragons (Tympanocryptis spp.) in north-eastern Australia. Using mitochondrial and nuclear genes (ND2 and RAG1, respectively), along with $>$8500 SNPs (nuclear single nucleotide polymorphisms), we assess the evolutionary independence of target lineages and several closely related species. We then integrate phylogenomic data with osteological cranial variation between lineages using landmark-based analyses of three-dimensional CT models. High levels of genomic differentiation between the three target lineages were uncovered, also supported by significant osteological differences. By incorporating multiple lines of evidence, we provide strong support for three undescribed cryptic lineages of Tympanocryptis in north-eastern Australia that warrant taxonomic review. Our approach demonstrates the successful application of CT with integrative taxonomic approaches for cryptic species delimitation, which is broadly applicable across vertebrates containing morphologically similar yet genetically distinct lineages. Additionally, we provide a review of recent integrative taxonomic approaches for cryptic species delimitation and an assessment of how our approach can value-add to taxonomic research.
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Affiliation(s)
- Kirilee Chaplin
- Department of Sciences, Museums Victoria, GPO Box 666, Melbourne, Victoria 3001, Australia.,School of BioSciences The University of Melbourne Parkville Campus Victoria 3010, Australia
| | - Joanna Sumner
- Department of Sciences, Museums Victoria, GPO Box 666, Melbourne, Victoria 3001, Australia
| | - Christy A Hipsley
- Department of Sciences, Museums Victoria, GPO Box 666, Melbourne, Victoria 3001, Australia.,School of BioSciences The University of Melbourne Parkville Campus Victoria 3010, Australia
| | - Jane Melville
- Department of Sciences, Museums Victoria, GPO Box 666, Melbourne, Victoria 3001, Australia
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14
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Al-Razi H, Maria M, Muzaffar SB. A new species of cryptic Bush frog (Anura, Rhacophoridae, Raorchestes) from northeastern Bangladesh. Zookeys 2020; 927:127-151. [PMID: 32341678 PMCID: PMC7180169 DOI: 10.3897/zookeys.927.48733] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2019] [Accepted: 02/26/2020] [Indexed: 11/12/2022] Open
Abstract
Raorchestes is a speciose genus of bush frogs with high diversity occurring in the Western Ghats of India. Relatively fewer species have been recorded across India, through Bangladesh, southern China, into Vietnam and Peninsular Malaysia. Many bush frogs are morphologically cryptic and therefore remain undescribed. Here, a new species, Raorchestes rezakhani sp. nov., is described from northeastern Bangladesh based on morphological characters, genetics, and bioacoustics. The 16S rRNA gene distinguished this species from 48 known species of this genus. Bayesian Inference and Maximum Likelihood analyses indicated that the new species was most similar to R. tuberohumerus, a species found in the Western Ghats, and to R. gryllus, a species found in Vietnam. Bioacoustics indicated that their calls were similar in pattern to most Raorchestes species, although number of pulses, duration of pulses, pulse intervals and amplitude differentiated it from a few other species. It is suggested that northeastern India, Bangladesh, northern Myanmar, and southern China represent important, relatively unexplored areas that could yield additional species of Raorchestes. Since many remaining habitat patches in Bangladesh are under severe threat from deforestation, efforts should be made to protect these last patches from further degradation.
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Affiliation(s)
- Hassan Al-Razi
- Faculty of Life and Earth Science, Department of Zoology, Jagannath University, Dhaka, BangladeshJagannath UniversityDhakaBangladesh
| | - Marjan Maria
- Faculty of Life and Earth Science, Department of Zoology, Jagannath University, Dhaka, BangladeshJagannath UniversityDhakaBangladesh
| | - Sabir Bin Muzaffar
- Department of Biology, United Arab Emirates University, Al Ain, United Arab EmiratesJagannath UniversityAl AinUnited Arab Emirates
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15
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Fu M, Waldman B. Ancestral chytrid pathogen remains hypervirulent following its long coevolution with amphibian hosts. Proc Biol Sci 2019; 286:20190833. [PMID: 31161901 DOI: 10.1098/rspb.2019.0833] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
Many amphibian species around the world, except in Asia, suffer morbidity and mortality when infected by the emerging infectious pathogen Batrachochytrium dendrobatidis (Bd). A lineage of the amphibian chytrid fungus isolated from South Korean amphibians (BdAsia-1) is evolutionarily basal to recombinant global pandemic lineages (BdGPL) associated with worldwide amphibian population declines. In Asia, the Bd pathogen and its amphibian hosts have coevolved over 100 years or more. Thus, resilience of Asian amphibian populations to infection might result from attenuated virulence of endemic Bd lineages, evolved immunity to the pathogen or both. We compared susceptibilities of an Australasian amphibian, Litoria caerulea, known to lack resistance to BdGPL, with those of three Korean species, Bufo gargarizans, Bombina orientalis and Hyla japonica, after inoculation with BdAsia-1, BdGPL or a blank solution. Subjects became infected in all experimental treatments but Korean species rapidly cleared themselves of infection, regardless of Bd lineage. They survived with no apparent secondary effects. By contrast, L. caerulea, after infection by either BdAsia-1 or BdGPL, suffered deteriorating body condition and carried progressively higher Bd loads over time. Subsequently, most subjects died. Comparing their effects on L. caerulea, BdAsia-1 induced more rapid disease progression than BdGPL. The results suggest that genomic recombination with other lineages was not necessary for the ancestral Bd lineage to evolve hypervirulence over its long period of coevolution with amphibian hosts. The pathogen's virulence may have driven strong selection for immune responses in endemic Asian amphibian host species.
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Affiliation(s)
- Minjie Fu
- 1 Laboratory of Behavioral and Population Ecology, School of Biological Sciences, Seoul National University , Seoul 08826 , South Korea
| | - Bruce Waldman
- 1 Laboratory of Behavioral and Population Ecology, School of Biological Sciences, Seoul National University , Seoul 08826 , South Korea.,2 Department of Integrative Biology, Oklahoma State University , Stillwater, OK 74078 , USA
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16
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Integrative evidence confirms new endemic island frogs and transmarine dispersal of amphibians between Madagascar and Mayotte (Comoros archipelago). Naturwissenschaften 2019; 106:19. [DOI: 10.1007/s00114-019-1618-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2018] [Revised: 04/07/2019] [Accepted: 04/11/2019] [Indexed: 10/26/2022]
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17
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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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18
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Diversification of shrub frogs (Rhacophoridae, Pseudophilautus) in Sri Lanka – Timing and geographic context. Mol Phylogenet Evol 2019; 132:14-24. [DOI: 10.1016/j.ympev.2018.11.004] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2018] [Revised: 11/07/2018] [Accepted: 11/10/2018] [Indexed: 11/17/2022]
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19
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Kanesharatnam N, P. Benjamin S. Multilocus genetic and morphological phylogenetic analysis reveals a radiation of shiny South Asian jumping spiders (Araneae, Salticidae). Zookeys 2019; 839:1-81. [PMID: 31065224 PMCID: PMC6482596 DOI: 10.3897/zookeys.839.28312] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2018] [Accepted: 12/20/2018] [Indexed: 11/26/2022] Open
Abstract
This study presents a systematic revision of South Asian members of the Tribe Chrysillini Simon, 1901. Genetic and morphological variations were analysed of a "similar-looking" group of species that were initially identified as members of the jumping spider genera Chrysilla Thorell, 1887 and Phintella Strand, in Bösenberg and Strand 1906 to determine their phylogenetic relationships. Results suggest that the assessed morphospecies complex constitute of three evolutionary lineages, two previously unrecognised, which are described and diagnosed as two new genera: Phintelloides gen. n. and Proszynskia gen. n. The third lineage, Phintella, is sister to these proposed genera. The following new species are described: Phintelloidesalborea sp. n., P.brunne sp. n., P.flavoviri sp. n., P.flavumi sp. n., P.orbisa sp. n., Phintellaargentea sp. n., and P.jaleeli sp. n. Sri Lanka is rich in biodiversity but currently has one of the highest rates of deforestation. Lack of clarity on diversity and distribution of the islands' biodiversity can lead to underestimations during threat assessments and thus downgrading of conservation needs of individual species.
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Affiliation(s)
- Nilani Kanesharatnam
- National Institute of Fundamental Studies, Hantana Road, Kandy, Sri LankaNational Institute of Fundamental StudiesKandySri Lanka
- Department of Zoology, Faculty of Science, Eastern University, Vantharumoolai, Sri LankaEastern UniversityVantharumoolaiSri Lanka
| | - Suresh P. Benjamin
- National Institute of Fundamental Studies, Hantana Road, Kandy, Sri LankaNational Institute of Fundamental StudiesKandySri Lanka
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20
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Lajmi A, Bansal R, Giri V, Karanth P. Phylogeny and biogeography of the endemic Hemidactylus geckos of the Indian subregion suggest multiple dispersals from Peninsular India to Sri Lanka. Zool J Linn Soc 2018. [DOI: 10.1093/zoolinnean/zly047] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Affiliation(s)
- Aparna Lajmi
- Centre for Ecological Sciences, Indian Institute of Science, Bengaluru, India
- National Centre for Biological Sciences, Bengaluru, India
| | - Rohini Bansal
- Department of Medical Neurobiology, School of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Varad Giri
- National Centre for Biological Sciences, Bengaluru, India
| | - Praveen Karanth
- Centre for Ecological Sciences, Indian Institute of Science, Bengaluru, India
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21
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The interplay of past diversification and evolutionary isolation with present imperilment across the amphibian tree of life. Nat Ecol Evol 2018; 2:850-858. [DOI: 10.1038/s41559-018-0515-5] [Citation(s) in RCA: 273] [Impact Index Per Article: 45.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2017] [Accepted: 02/21/2018] [Indexed: 02/02/2023]
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22
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Suwannapoom C, Yuan ZY, A Poyarkov N, Yan F, Kamtaeja S, W Murphy R, Che J. A new species of genus Fejervarya (Anura: Dicroglossidae) from northern Thailand. Zool Res 2018; 37:327-337. [PMID: 28105797 PMCID: PMC5359320 DOI: 10.13918/j.issn.2095-8137.2016.6.327] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022] Open
Abstract
We describe a new species of frog in the dicroglossid genus Fejervarya from Ban Monjong, Omkoi District, Chiang Mai Province, northern Thailand. Analysis of DNA sequence data from the mitochondrial gene 16S, advertisement calls, and morphological distinctiveness support recognition of the new species. Matrilineal genealogy suggests that the new population from Chiang Mai is a sister taxon to the South Asian clade that includes F. syhadrensis, F. granosa, and F. pierrei. The new species, Fejervarya chiangmaiensissp. nov., differs morphologically from its congeners by its relatively small body size and proportions and the presence of dorsal warts and dermal ridges. Discovery of this new species indicates that the biodiversity of amphibians in this region remains underestimated.
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Affiliation(s)
- Chatmongkon Suwannapoom
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming Yunnan 650223, China; Division of Fishery, School of Agriculture and Natural Resources, University of Phayao, Phayao 56000, Thailand; Southeast Asia Biodiversity Research Institute, Chinese Academy of Sciences, Mengla Yunnan 666303, China
| | - Zhi-Yong Yuan
- College of Forestry, Southwest Forestry University, Kunming Yunnan 650224, China; Southeast Asia Biodiversity Research Institute, Chinese Academy of Sciences, Mengla Yunnan 666303, China
| | - Nikolay A Poyarkov
- Department of Vertebrate Zoology, Biological Faculty, Lomonosov Moscow State University, Leninskiye Gory Moscow 119991, Russia; Joint Russian-Vietnamese Tropical Research and Technological Center Under the A. N. Severtsov Institute of Ecology and Evolution RAS, South Branch, Ho Chi Minh City, Vietnam
| | - 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, Mengla Yunnan 666303, China
| | - Somboon Kamtaeja
- Faculty of Education, Chiang Rai Rajabhat University, Chiang Rai 57100, Thailand
| | - Robert W Murphy
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming Yunnan 650223, China; Centre for Biodiversity and Conservation Biology, Royal Ontario Museum, Toronto M5S 2C6, Canada
| | - Jing Che
- 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, Mengla Yunnan 666303, China.
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23
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Espíndola A, Ruffley M, Smith ML, Carstens BC, Tank DC, Sullivan J. Identifying cryptic diversity with predictive phylogeography. Proc Biol Sci 2017; 283:rspb.2016.1529. [PMID: 27798300 DOI: 10.1098/rspb.2016.1529] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2016] [Accepted: 09/27/2016] [Indexed: 01/14/2023] Open
Abstract
Identifying units of biological diversity is a major goal of organismal biology. An increasing literature has focused on the importance of cryptic diversity, defined as the presence of deeply diverged lineages within a single species. While most discoveries of cryptic lineages proceed on a taxon-by-taxon basis, rapid assessments of biodiversity are needed to inform conservation policy and decision-making. Here, we introduce a predictive framework for phylogeography that allows rapidly identifying cryptic diversity. Our approach proceeds by collecting environmental, taxonomic and genetic data from codistributed taxa with known phylogeographic histories. We define these taxa as a reference set, and categorize them as either harbouring or lacking cryptic diversity. We then build a random forest classifier that allows us to predict which other taxa endemic to the same biome are likely to contain cryptic diversity. We apply this framework to data from two sets of disjunct ecosystems known to harbour taxa with cryptic diversity: the mesic temperate forests of the Pacific Northwest of North America and the arid lands of Southwestern North America. The predictive approach presented here is accurate, with prediction accuracies placed between 65% and 98.79% depending of the ecosystem. This seems to indicate that our method can be successfully used to address ecosystem-level questions about cryptic diversity. Further, our application for the prediction of the cryptic/non-cryptic nature of unknown species is easily applicable and provides results that agree with recent discoveries from those systems. Our results demonstrate that the transition of phylogeography from a descriptive to a predictive discipline is possible and effective.
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Affiliation(s)
- Anahí Espíndola
- Department of Biological Sciences, University of Idaho, 875 Perimeter Drive MS 3051, Moscow, ID 83844-3051, USA .,Biological Sciences, Institute for Bioinformatics and Evolutionary Studies (IBEST), 875 Perimeter Drive MS 3051, Moscow, ID 83844-3051, USA
| | - Megan Ruffley
- Department of Biological Sciences, University of Idaho, 875 Perimeter Drive MS 3051, Moscow, ID 83844-3051, USA.,Biological Sciences, Institute for Bioinformatics and Evolutionary Studies (IBEST), 875 Perimeter Drive MS 3051, Moscow, ID 83844-3051, USA
| | - Megan L Smith
- Department of Evolution, Ecology, and Organismal Biology, The Ohio State University, 318 W. 12th Avenue, 300 Aronoff Labs, Columbus, OH 43210-1293, USA
| | - Bryan C Carstens
- Department of Evolution, Ecology, and Organismal Biology, The Ohio State University, 318 W. 12th Avenue, 300 Aronoff Labs, Columbus, OH 43210-1293, USA
| | - David C Tank
- Department of Biological Sciences, University of Idaho, 875 Perimeter Drive MS 3051, Moscow, ID 83844-3051, USA.,Biological Sciences, Institute for Bioinformatics and Evolutionary Studies (IBEST), 875 Perimeter Drive MS 3051, Moscow, ID 83844-3051, USA
| | - Jack Sullivan
- Department of Biological Sciences, University of Idaho, 875 Perimeter Drive MS 3051, Moscow, ID 83844-3051, USA.,Biological Sciences, Institute for Bioinformatics and Evolutionary Studies (IBEST), 875 Perimeter Drive MS 3051, Moscow, ID 83844-3051, USA
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24
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Model-based analyses reveal insular population diversification and cryptic frog species in the Ischnocnema parva complex in the Atlantic forest of Brazil. Mol Phylogenet Evol 2017; 112:68-78. [DOI: 10.1016/j.ympev.2017.04.007] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2016] [Revised: 03/29/2017] [Accepted: 04/07/2017] [Indexed: 11/18/2022]
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25
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Oliver PM, Iannella A, Richards SJ, Lee MS. Mountain colonisation, miniaturisation and ecological evolution in a radiation of direct-developing New Guinea Frogs ( Choerophryne, Microhylidae). PeerJ 2017; 5:e3077. [PMID: 28382230 PMCID: PMC5376113 DOI: 10.7717/peerj.3077] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2016] [Accepted: 02/08/2017] [Indexed: 11/20/2022] Open
Abstract
AIMS Mountain ranges in the tropics are characterised by high levels of localised endemism, often-aberrant evolutionary trajectories, and some of the world's most diverse regional biotas. Here we investigate the evolution of montane endemism, ecology and body size in a clade of direct-developing frogs (Choerophryne, Microhylidae) from New Guinea. METHODS Phylogenetic relationships were estimated from a mitochondrial molecular dataset using Bayesian and maximum likelihood approaches. Ancestral state reconstruction was used to infer the evolution of elevational distribution, ecology (indexed by male calling height), and body size, and phylogenetically corrected regression was employed to examine the relationships between these three traits. RESULTS We obtained strong support for a monophyletic lineage comprising the majority of taxa sampled. Within this clade we identified one subclade that appears to have diversified primarily in montane habitats of the Central Cordillera (>1,000 m a.s.l.), with subsequent dispersal to isolated North Papuan Mountains. A second subclade (characterised by moderately to very elongated snouts) appears to have diversified primarily in hill forests (<1,000 m a.s.l.), with inferred independent upwards colonisations of isolated montane habitats, especially in isolated North Papuan Mountains. We found no clear relationship between extremely small body size (adult SVL less than 15 mm) and elevation, but a stronger relationship with ecology-smaller species tend to be more terrestrial. CONCLUSIONS Orogeny and climatic oscillations have interacted to generate high montane biodiversity in New Guinea via both localised diversification within montane habitats (centric endemism) and periodic dispersal across lowland regions (eccentric endemism). The correlation between extreme miniaturisation and terrestrial habits reflects a general trend in frogs, suggesting that ecological or physiological constraints limit niche usage by miniaturised frogs, even in extremely wet environments such as tropical mountains.
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Affiliation(s)
- Paul M. Oliver
- Division of Ecology and Evolution, Research School of Biology & Centre for Biodiversity Analysis, Australian National University, Canberra, Australian Capital Territory, Australia
| | - Amy Iannella
- School of Biological Sciences, The University of Adelaide, Adelaide, South Australia, Australia
| | | | - Michael S.Y. Lee
- South Australian Museum, Adelaide, South Australia, Australia
- School of Biological Sciences, Flinders University, Adelaide, South Australia, Australia
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26
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Senevirathne G, Kerney R, Meegaskumbura M. Comparative Postembryonic Skeletal Ontogeny in Two Sister Lineages of Old World Tree Frogs (Rhacophoridae: Taruga, Polypedates). PLoS One 2017; 12:e0167939. [PMID: 28060923 PMCID: PMC5218391 DOI: 10.1371/journal.pone.0167939] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2016] [Accepted: 11/22/2016] [Indexed: 11/19/2022] Open
Abstract
Rhacophoridae, a family of morphologically cryptic frogs, with many genetically distinct evolutionary lineages, is understudied with respect to skeletal morphology, life history traits and skeletal ontogeny. Here we analyze two species each from two sister lineages, Taruga and Polypedates, and compare their postembryonic skeletal ontogeny, larval chondrocrania and adult osteology in the context of a well-resolved phylogeny. We further compare these ontogenetic traits with the direct-developing Pseudophilautus silus. For each species, we differentially stained a nearly complete developmental series of tadpoles from early postembryonic stages through metamorphosis to determine the intraspecific and interspecific differences of cranial and postcranial bones. Chondrocrania of the four species differ in 1) size; 2) presence/absence of anterolateral and posterior process; and 3) shape of the suprarostral cartilages. Interspecific variation of ossification sequences is limited during early stages, but conspicuous during later development. Early cranial ossification is typical of other anuran larvae, where the frontoparietal, exoccipital and parasphenoid ossify first. The ossification sequences of the cranial bones vary considerably within the four species. Both species of Taruga show a faster cranial ossification rate than Polypedates. Seven cranial bones form when larvae near metamorphic climax. Ossification of all 18 cranial bones is initiated by larval Gosner stage 46 in T. eques. However, some cranial bone formation is not initiated until after metamorphosis in the other three species. Postcranial sequence does not vary significantly. The comparison of adult osteology highlights two characters, which have not been previously recorded: presence/absence of the parieto-squamosal plates and bifurcated base of the omosternum. This study will provide a starting point for comparative analyses of rhacophorid skeletal ontogeny and facilitate the study of the evolution of ontogenetic repatterning associated with the life history variation in the family.
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Affiliation(s)
- Gayani Senevirathne
- Department of Molecular Biology and Biotechnology, Faculty of Science, University of Peradeniya, Peradeniya, Sri Lanka
- Postgraduate Institute of Science, Faculty of Science, University of Peradeniya, Sri Lanka
| | - Ryan Kerney
- Department of Biology, Gettysburg College, Gettysburg, Pennsylvania, United States of America
| | - Madhava Meegaskumbura
- Department of Molecular Biology and Biotechnology, Faculty of Science, University of Peradeniya, Peradeniya, Sri Lanka
- Postgraduate Institute of Science, Faculty of Science, University of Peradeniya, Sri Lanka
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27
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Ecology and demography of the Critically Endangered Kandian torrent toadAdenomus kandianus: a long-lost endemic species of Sri Lanka. ORYX 2016. [DOI: 10.1017/s0030605316000594] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
Abstract
AbstractThe tropical island nation of Sri Lanka is a biodiversity hotspot with a high diversity and endemism of amphibians. The endemic, stream-dwelling Kandian torrent toadAdenomus kandianusis Critically Endangered and was considered to be extinct until its rediscovery in 2012. The species is now known from two localities in tropical montane forests. We conducted a 4-year study using transect surveys and opportunistic excursions to assess habitat associations, demographics and abundance ofA. kandianusin and around Pidurutalagala Conservation Forest. We recorded a mean of 44.25 post-metamorphs per year, with a density of < 1 individual per 100 m2, with occurrence within a narrow extent (c. 0.005 km2) of the stream channel. Behaviour and microhabitat selection varied depending on sex and stage of maturity. The species preferred moderately sized montane streams with rocky substrates and woody debris, colder temperatures, and closed-canopy, intact riparian forests. We noted size-based reversed sexual dimorphism and a strong ontogenetic relationship between snout–vent length and body weight. Anthropogenic activities such as intensive crop farming deterred the species; proximity to croplands had a negative influence on abundance. We recommend re-delineation of the boundary of Pidurutalagala Conservation Forest to incorporate the toad's habitat into the core of the reserve and thus limit the impacts of human activities. Conservation and management actions such as ex-situ breeding, population monitoring, and restoration of degraded habitats could also contribute towards the persistence of this toad. Our findings provide useful insights into ecological research on and conservation of range-restricted aquatic amphibians.
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An Acoustic Analysis of the Genus Microhyla (Anura: Microhylidae) of Sri Lanka. PLoS One 2016; 11:e0159003. [PMID: 27403744 PMCID: PMC4942061 DOI: 10.1371/journal.pone.0159003] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2016] [Accepted: 06/25/2016] [Indexed: 11/19/2022] Open
Abstract
Vocalizing behavior of frogs and toads, once quantified, is useful for systematics, rapid species identification, behavioral experimentation and conservation monitoring. But yet, for many lineages vocalizations remain unknown or poorly quantified, especially in diversity rich tropical regions. Here we provide a quantitative acoustical analysis for all four Sri Lankan congeners of the genus Microhyla. Three of these species are endemic to the island, but Microhyla ornata is regionally widespread. Two of these endemics, M. karunaratnei (Critically Endangered) and M. zeylanica (Endangered), are highly threatened montane isolates; the other, M. mihintalei, is relatively common across the dry lowlands. We recorded and analyzed 100 advertisement calls from five calling males for each species, except for M. zeylanica, which only had 53 calls from three males suitable for analyses. All four species call in choruses and their vocal repertoires are simple compared to most frogs. Their calls contain multiple pulses and no frequency modulation. We quantified eight call characters. Call duration and number of pulses were higher for the two montane isolates (inhabiting cooler habitats at higher altitudes) compared to their lowland congeners. Microhyla zeylanica has the longest call duration (of 1.8 ± 0.12 s) and the highest number of pulses (of 61–92 pulses). The smallest of the species, Microhyla karunaratnei (16.2–18.3 mm), has the highest mean dominant frequency (3.3 ± 0.14 kHz) and pulse rate (77 ± 5.8 pulses per second). The calls separate well in the Principal Component space: PC1 axis is mostly explained by the number of pulses per call and call duration; PC2 is mostly explained by the pulse rate. A canonical means plot of a Discriminant Function analysis shows non-overlapping 95% confidence ellipses. This suggests that some call parameters can be used to distinguish these species effectively. We provide detailed descriptions for eight call properties and compare these with congeners for which data is available. This work provides a foundation for comparative bioacoustic analyses and species monitoring while facilitating the systematics of Microhyla across its range.
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29
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Jablonski D, Jandzik D, Mikulíček P, Džukić G, Ljubisavljević K, Tzankov N, Jelić D, Thanou E, Moravec J, Gvoždík V. Contrasting evolutionary histories of the legless lizards slow worms (Anguis) shaped by the topography of the Balkan Peninsula. BMC Evol Biol 2016; 16:99. [PMID: 27165497 PMCID: PMC4863322 DOI: 10.1186/s12862-016-0669-1] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2016] [Accepted: 04/25/2016] [Indexed: 11/27/2022] Open
Abstract
Background Genetic architecture of a species is a result of historical changes in population size and extent of distribution related to climatic and environmental factors and contemporary processes of dispersal and gene flow. Population-size and range contractions, expansions and shifts have a substantial effect on genetic diversity and intraspecific divergence, which is further shaped by gene-flow limiting barriers. The Balkans, as one of the most important sources of European biodiversity, is a region where many temperate species persisted during the Pleistocene glaciations and where high topographic heterogeneity offers suitable conditions for local adaptations of populations. In this study, we investigated the phylogeographical patterns and demographic histories of four species of semifossorial slow-worm lizards (genus Anguis) present in the Balkan Peninsula, and tested the relationship between genetic diversity and topographic heterogeneity of the inhabited ranges. Results We inferred phylogenetic relationships, compared genetic structure and historical demography of slow worms using nucleotide sequence variation of mitochondrial DNA. Four Anguis species with mostly parapatric distributions occur in the Balkan Peninsula. They show different levels of genetic diversity. A signature of population growth was detected in all four species but with various courses in particular populations. We found a strong correlation between genetic diversity of slow-worm populations and topographic ruggedness of the ranges (mountain systems) they inhabit. Areas with more rugged terrain harbour higher genetic diversity. Conclusions Phylogeographical pattern of the genus Anguis in the Balkans is concordant with the refugia-within-refugia model previously proposed for both several other taxa in the region and other main European Peninsulas. While slow-worm populations from the southern refugia mostly have restricted distributions and have not dispersed much from their refugial areas, populations from the extra-Mediterranean refugia in northern parts of the Balkans have colonized vast areas of eastern, central, and western Europe. Besides climatic historical events, the heterogeneous topography of the Balkans has also played an important role in shaping genetic diversity of slow worms. Electronic supplementary material The online version of this article (doi:10.1186/s12862-016-0669-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Daniel Jablonski
- Department of Zoology, Comenius University in Bratislava, Mlynská dolina, Ilkovičova 6, 842 15, Bratislava, Slovakia.
| | - David Jandzik
- Department of Zoology, Comenius University in Bratislava, Mlynská dolina, Ilkovičova 6, 842 15, Bratislava, Slovakia.,Department of Ecology and Evolutionary Biology (EBIO), University of Colorado, Ramaley N122, Campus, Box 334, 80309-0334, Boulder, CO, USA
| | - Peter Mikulíček
- Department of Zoology, Comenius University in Bratislava, Mlynská dolina, Ilkovičova 6, 842 15, Bratislava, Slovakia
| | - Georg Džukić
- Department of Evolutionary Biology, Institute for Biological Research "Siniša Stanković", 11060, Belgrade, Serbia
| | - Katarina Ljubisavljević
- Department of Evolutionary Biology, Institute for Biological Research "Siniša Stanković", 11060, Belgrade, Serbia
| | - Nikolay Tzankov
- Department of Vertebrates, National Museum of Natural History, Tsar Osvoboditel Blvd. 1, 1000, Sofia, Bulgaria
| | - Dušan Jelić
- Croatian Institute for Biodiversity, Croatian Herpetological Society Hyla, I, Breznička 5a, 10000, Zagreb, Croatia
| | - Evanthia Thanou
- Department of Biology, Section of Animal Biology, School of Natural Sciences, University of Patras, GR-26500, Patras, Greece
| | - Jiří Moravec
- Department of Zoology, National Museum, 193 00, Prague, Czech Republic
| | - Václav Gvoždík
- Department of Zoology, National Museum, 193 00, Prague, Czech Republic.,Institute of Vertebrate Biology, Czech Academy of Sciences, 603 65, Brno, Czech Republic
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Touchon JC, Worley JL. Oviposition site choice under conflicting risks demonstrates that aquatic predators drive terrestrial egg-laying. Proc Biol Sci 2016; 282:20150376. [PMID: 25948689 DOI: 10.1098/rspb.2015.0376] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Laying eggs out of water was crucial to the transition to land and has evolved repeatedly in multiple animal phyla. However, testing hypotheses about this transition has been difficult because extant species only breed in one environment. The pantless treefrog, Dendropsophus ebraccatus, makes such tests possible because they lay both aquatic and arboreal eggs. Here, we test the oviposition site choices of D. ebraccatus under conflicting risks of arboreal egg desiccation and aquatic egg predation, thereby estimating the relative importance of each selective agent on reproduction. We also measured discrimination between habitats with and without predators and development of naturally laid aquatic and arboreal eggs. Aquatic embryos in nature developed faster than arboreal embryos, implying no cost to aquatic egg laying. In choice tests, D. ebraccatus avoided habitats with fish, showing that they can detect aquatic egg predators. Most importantly, D. ebraccatus laid most eggs in the water when faced with only desiccation risk, but switched to laying eggs arboreally when desiccation risk and aquatic predators were both present. This provides the first experimental evidence to our knowledge that aquatic predation risk influences non-aquatic oviposition and strongly supports the hypothesis that it was a driver of the evolution of terrestrial reproduction.
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Affiliation(s)
- Justin C Touchon
- Department of Biology, Vassar College, 124 Raymond Avenue, Poughkeepsie, NY 12604, USA Department of Biology, Boston University, 5 Cummington Mall, Boston, MA 02215, USA
| | - Julie L Worley
- Biology Department, Portland State University, 1719 SW 10th Avenue, Portland, OR 97201, USA
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Meegaskumbura M, Senevirathne G, Biju SD, Garg S, Meegaskumbura S, Pethiyagoda R, Hanken J, Schneider CJ. Patterns of reproductive-mode evolution in Old World tree frogs (Anura, Rhacophoridae). ZOOL SCR 2015. [DOI: 10.1111/zsc.12121] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Madhava Meegaskumbura
- Department of Molecular Biology & Biotechnology; Faculty of Science; University of Peradeniya; Peradeniya KY 20400 Sri Lanka
| | - Gayani Senevirathne
- Department of Molecular Biology & Biotechnology; Faculty of Science; University of Peradeniya; Peradeniya KY 20400 Sri Lanka
| | - S. D. Biju
- Department of Environmental Studies; University of Delhi; Delhi 110 007 India
| | - Sonali Garg
- Department of Environmental Studies; University of Delhi; Delhi 110 007 India
| | - Suyama Meegaskumbura
- Department of Zoology Faculty of Science; University of Peradeniya; Peradeniya KY 20400 Sri Lanka
| | | | - James Hanken
- Museum of Comparative Zoology; Harvard University; Cambridge MA 02138 USA
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32
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Dang NX, Sun FH, Lv YY, Zhao BH, Wang JC, Murphy RW, Wang WZ, Li JT. DNA barcoding and the identification of tree frogs (Amphibia: Anura: Rhacophoridae). Mitochondrial DNA A DNA Mapp Seq Anal 2015; 27:2574-84. [PMID: 26004249 DOI: 10.3109/19401736.2015.1041113] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
The DNA barcoding gene COI (cytochrome c oxidase subunit I) effectively identifies many species. Herein, we barcoded 172 individuals from 37 species belonging to nine genera in Rhacophoridae to test if the gene serves equally well to identify species of tree frogs. Phenetic neighbor joining and phylogenetic Bayesian inference were used to construct phylogenetic trees, which resolved all nine genera as monophyletic taxa except for Rhacophorus, two new matrilines for Liuixalus, and Polypedates leucomystax species complex. Intraspecific genetic distances ranged from 0.000 to 0.119 and interspecific genetic distances ranged from 0.015 to 0.334. Within Rhacophorus and Kurixalus, the intra- and interspecific genetic distances did not reveal an obvious barcode gap. Notwithstanding, we found that COI sequences unambiguously identified rhacophorid species and helped to discover likely new cryptic species via the synthesis of genealogical relationships and divergence patterns. Our results supported that COI is an effective DNA barcoding marker for Rhacophoridae.
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Affiliation(s)
- Ning-Xin Dang
- a Chengdu Institute of Biology, Chinese Academy of Sciences , Chengdu , China .,b College of Life Sciences, Sichuan University , Chengdu , China
| | - Feng-Hui Sun
- c School of Medical Laboratory Science, Chengdu Medical College , Chengdu , China
| | - Yun-Yun Lv
- a Chengdu Institute of Biology, Chinese Academy of Sciences , Chengdu , China
| | - Bo-Han Zhao
- a Chengdu Institute of Biology, Chinese Academy of Sciences , Chengdu , China .,b College of Life Sciences, Sichuan University , Chengdu , China
| | - Ji-Chao Wang
- d Department of Tropical Animal and Plant Ecology , College of Life Sciences, Hainan Normal University , Haikou , China
| | - Robert W Murphy
- e Department of Conservation Biology , Royal Ontario Museum , Toronto , Ontario , Canada , and
| | - Wen-Zhi Wang
- f State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences , Kunming , China
| | - Jia-Tang Li
- a Chengdu Institute of Biology, Chinese Academy of Sciences , Chengdu , China
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Howlader MSA, Nair A, Gopalan SV, Merilä J. A new species of Microhyla (Anura: Microhylidae) from Nilphamari, Bangladesh. PLoS One 2015; 10:e0119825. [PMID: 25806804 PMCID: PMC4373918 DOI: 10.1371/journal.pone.0119825] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2014] [Accepted: 02/03/2015] [Indexed: 11/19/2022] Open
Abstract
A new species of Microhyla frog from the Nilphamari district of Bangladesh is described and compared with its morphologically similar and geographically proximate congeners. Molecular phylogeny derived from mitochondrial DNA sequences revealed that although the new species--designated here as Microhyla nilphamariensis sp. nov.--forms a clade with M. ornate, it is highly divergent from M. ornata and all of its congeners, with 5.7-13.2% sequence divergence at the 16S rRNA gene. The new species can be identified phenotypically on the basis of a set of diagnostic (both qualitative and quantitative) characters as follows: head length is 77% of head width, distance from front of eyes to the nostril is roughly six times greater than nostril-snout length, internarial distance is roughly five times greater than nostril-snout length, interorbital distance is two times greater than internarial distance, and distance from back of mandible to back of the eye is 15% of head length. Furthermore, inner metacarpal tubercle is small and ovoid-shaped, whereas outer metacarpal tubercle is very small and rounded. Toes have rudimentary webbing, digital discs are absent, inner metatarsal tubercle is small and round, outer metatarsal tubercle is ovoid-shaped, minute, and indistinct.
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Affiliation(s)
| | - Abhilash Nair
- Ecological Genetics Research Unit, Department of Biosciences, University of Helsinki, Helsinki, Finland
| | - Sujith V. Gopalan
- Molecular Ecology Laboratory, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram, Kerala, India
| | - Juha Merilä
- Ecological Genetics Research Unit, Department of Biosciences, University of Helsinki, Helsinki, Finland
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Somaweera R, Wijayathilaka N, Bowatte G, Meegaskumbura M. Conservation in a changing landscape: habitat occupancy of the critically endangered Tennent’s leaf-nosed lizard (Ceratophora tennentii) in Sri Lanka. J NAT HIST 2015. [DOI: 10.1080/00222933.2015.1006280] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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35
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Kieswetter CM, Schneider CJ. Phylogeography in the northern Andes: Complex history and cryptic diversity in a cloud forest frog, Pristimantis w-nigrum (Craugastoridae). Mol Phylogenet Evol 2013; 69:417-29. [DOI: 10.1016/j.ympev.2013.08.007] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2013] [Revised: 08/01/2013] [Accepted: 08/08/2013] [Indexed: 10/26/2022]
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36
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Pyron RA, Burbrink FT. Phylogenetic estimates of speciation and extinction rates for testing ecological and evolutionary hypotheses. Trends Ecol Evol 2013; 28:729-36. [PMID: 24120478 DOI: 10.1016/j.tree.2013.09.007] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2013] [Revised: 09/03/2013] [Accepted: 09/15/2013] [Indexed: 10/26/2022]
Abstract
Phylogenies are used to estimate rates of speciation and extinction, reconstruct historical diversification scenarios, and link these to ecological and evolutionary factors, such as climate or organismal traits. Recent models can now estimate the effects of binary, multistate, continuous, and biogeographic characters on diversification rates. Others test for diversity dependence (DD) in speciation and extinction, which has become recognized as an important process in numerous clades. A third class incorporates flexible time-dependent functions, enabling reconstruction of major periods of both expanding and contracting diversity. Although there are some potential problems (particularly for estimating extinction), these methods hold promise for answering many classic questions in ecology and evolution, such as the origin of adaptive radiations, and the latitudinal gradient in species richness.
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Affiliation(s)
- R Alexander Pyron
- Department of Biological Sciences, The George Washington University, 2023 G St. NW, Washington, DC 20052, USA.
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37
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Diversification in a biodiversity hotspot – The evolution of Southeast Asian rhacophorid tree frogs on Borneo (Amphibia: Anura: Rhacophoridae). Mol Phylogenet Evol 2013; 68:567-81. [DOI: 10.1016/j.ympev.2013.04.001] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2012] [Revised: 03/28/2013] [Accepted: 04/01/2013] [Indexed: 12/24/2022]
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Abstract
The evolutionary removal of the tadpole from the frog life history is a very successful strategy, particularly in the tropics. These direct developers form limbs and a frog-like head early in embryogenesis, and they have reduced or lost tadpole-specific structures, like gills, a long, coiled intestine, and tadpole teeth and jaws. Despite the apparently continuous development to the frog morphology, the direct developer, Eleutherodactylus coqui, undergoes a cryptic metamorphosis requiring thyroid hormone. As in Xenopus laevis, there is a stimulation by corticotrophin-releasing factor (CRF) and an upregulation of thyroid hormone receptor β (thrb). In addition to changes in skin and muscle, thyroid hormone stimulates yolk utilization for froglet growth from a novel tissue, the nutritional endoderm. The activities of CRF and corticosterone (CORT) in metamorphosis may provide the basis for the multiple evolutionary origins of direct development in anuran amphibians. Potential roles for maternally supplied thyroid hormone and its receptor and for deiodinases in regulating tissue sensitivity to thyroid hormone should be the subjects of future investigations.
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Affiliation(s)
- Richard P Elinson
- Department of Biological Sciences, Duquesne University, Pittsburgh, Pennsylvania, USA.
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39
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From widespread to microendemic: molecular and acoustic analyses show that Ischnocnema guentheri (Amphibia: Brachycephalidae) is endemic to Rio de Janeiro, Brazil. CONSERV GENET 2013. [DOI: 10.1007/s10592-013-0488-5] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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40
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Crawford AJ, Cruz C, Griffith E, Ross H, Ibáñez R, Lips KR, Driskell AC, Bermingham E, Crump P. DNA barcoding applied to ex situ tropical amphibian conservation programme reveals cryptic diversity in captive populations. Mol Ecol Resour 2012; 13:1005-18. [PMID: 23280343 DOI: 10.1111/1755-0998.12054] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2012] [Revised: 11/10/2012] [Accepted: 11/21/2012] [Indexed: 11/26/2022]
Abstract
Amphibians constitute a diverse yet still incompletely characterized clade of vertebrates, in which new species are still being discovered and described at a high rate. Amphibians are also increasingly endangered, due in part to disease-driven threats of extinctions. As an emergency response, conservationists have begun ex situ assurance colonies for priority species. The abundance of cryptic amphibian diversity, however, may cause problems for ex situ conservation. In this study we used a DNA barcoding approach to survey mitochondrial DNA (mtDNA) variation in captive populations of 10 species of Neotropical amphibians maintained in an ex situ assurance programme at El Valle Amphibian Conservation Center (EVACC) in the Republic of Panama. We combined these mtDNA sequences with genetic data from presumably conspecific wild populations sampled from across Panama, and applied genetic distance-based and character-based analyses to identify cryptic lineages. We found that three of ten species harboured substantial cryptic genetic diversity within EVACC, and an additional three species harboured cryptic diversity among wild populations, but not in captivity. Ex situ conservation efforts focused on amphibians are therefore vulnerable to an incomplete taxonomy leading to misidentification among cryptic species. DNA barcoding may therefore provide a simple, standardized protocol to identify cryptic diversity readily applicable to any amphibian community.
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Affiliation(s)
- Andrew J Crawford
- Smithsonian Tropical Research Institute, Apartado 0843-03092, Panama, Republic of Panama; Círculo Herpetológico de Panamá, Apartado 0824-00122, Panama, Republic of Panama; Departamento de Ciencias Biológicas, Universidad de los Andes, A.A. 4976, Bogotá, Colombia
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41
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Genus-level phylogeny of snakes reveals the origins of species richness in Sri Lanka. Mol Phylogenet Evol 2012; 66:969-78. [PMID: 23261713 DOI: 10.1016/j.ympev.2012.12.004] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2012] [Revised: 11/27/2012] [Accepted: 12/05/2012] [Indexed: 11/20/2022]
Abstract
Snake diversity in the island of Sri Lanka is extremely high, hosting at least 89 inland (i.e., non-marine) snake species, of which at least 49 are endemic. This includes the endemic genera Aspidura, Balanophis, Cercaspis, Haplocercus, and Pseudotyphlops, which are of uncertain phylogenetic affinity. We present phylogenetic evidence from nuclear and mitochondrial loci showing the relationships of 40 snake species from Sri Lanka (22 endemics) to the remaining global snake fauna. To determine the phylogenetic placement of these species, we create a molecular dataset containing 10 genes for all global snake genera, while also sampling all available species for genera with endemic species occurring in Sri Lanka. Our sampling comprises five mitochondrial genes (12S, 16S, cyt-b, ND2, and ND4) and five nuclear genes (BDNF, c-mos, NT3 RAG-1, and RAG-2), for a total of up to 9582bp per taxon. We find that the five endemic genera represent portions of four independent colonizations of Sri Lanka, with Cercaspis nested within Colubrinae, Balanophis in Natricinae, Pseudotyphlops in Uropeltidae, and that Aspidura+Haplocercus represents a distinct, ancient lineage within Natricinae. We synonymize two endemic genera that render other genera paraphyletic (Haplocercus with Aspidura, and Cercaspis with Lycodon), and discover that further endemic radiations may be present on the island, including a new taxon from the blindsnake family Typhlopidae, suggesting a large endemic radiation. Despite its small size relative to other islands such as New Guinea, Borneo, and Madagascar, Sri Lanka has one of the most phylogenetically diverse island snake faunas in the world, and more research is needed to characterize the island's biodiversity, with numerous undescribed species in multiple lineages.
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42
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Touchon JC. A treefrog with reproductive mode plasticity reveals a changing balance of selection for nonaquatic egg laying. Am Nat 2012; 180:733-43. [PMID: 23149398 DOI: 10.1086/668079] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Nonaquatic reproduction has evolved repeatedly, but the factors that select for laying eggs on land are not well understood. The treefrog Dendropsophus ebraccatus has plasticity in its reproductive mode, laying eggs that successfully develop in or out of water. This permits the first experimental comparison of the selective agents that shape adult oviposition behavior and embryo developmental capacity. I quantified the sources and strengths of arboreal and aquatic egg mortality and how mortality varies with weather patterns, and I assessed 39 years of daily rainfall patterns to infer historic levels of egg mortality and effects of climate change on the selective balance between aquatic and nonaquatic egg deposition. Aquatic predators and desiccation were the strongest selective agents in water and air, respectively. Egg mortality varied with weather such that aquatic oviposition was advantageous when rainfall was low but laying eggs out of water increased survival when rainfall was high. Additionally, I found that since 1972 there have been significant changes in the rainfall patterns in central Panama, and this has altered the selective landscape acting on egg-laying behavior. This work provides insight into the evolution and maintenance of adaptive phenotypic plasticity as well as historic and current selection on reproduction.
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43
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Gehring PS, Tolley KA, Eckhardt FS, Townsend TM, Ziegler T, Ratsoavina F, Glaw F, Vences M. Hiding deep in the trees: discovery of divergent mitochondrial lineages in Malagasy chameleons of the Calumma nasutum group. Ecol Evol 2012; 2:1468-79. [PMID: 22957155 PMCID: PMC3434913 DOI: 10.1002/ece3.269] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2012] [Revised: 03/28/2012] [Accepted: 03/31/2012] [Indexed: 11/29/2022] Open
Abstract
We conducted a comprehensive molecular phylogenetic study for a group of chameleons from Madagascar (Chamaeleonidae: Calumma nasutum group, comprising seven nominal species) to examine the genetic and species diversity in this widespread genus. Based on DNA sequences of the mitochondrial gene (ND2) from 215 specimens, we reconstructed the phylogeny using a Bayesian approach. Our results show deep divergences among several unnamed mitochondrial lineages that are difficult to identify morphologically. We evaluated lineage diversification using a number of statistical phylogenetic methods (general mixed Yule-coalescent model; SpeciesIdentifier; net p-distances) to objectively delimit lineages that we here consider as operational taxonomic units (OTUs), and for which the taxonomic status remains largely unknown. In addition, we compared molecular and morphological differentiation in detail for one particularly diverse clade (the C. boettgeri complex) from northern Madagascar. To assess the species boundaries within this group we used an integrative taxonomic approach, combining evidence from two independent molecular markers (ND2 and CMOS), together with genital and other external morphological characters, and conclude that some of the newly discovered OTUs are separate species (confirmed candidate species, CCS), while others should best be considered as deep conspecific lineages (DCLs). Our analysis supports a total of 33 OTUs, of which seven correspond to described species, suggesting that the taxonomy of the C. nasutum group is in need of revision.
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Affiliation(s)
- Philip-Sebastian Gehring
- Zoological Institute, Technical University of BraunschweigMendelssohnstr. 4, 38106 Braunschweig, Germany
| | - Krystal A Tolley
- Applied Biodiversity Research Division, South African National Biodiversity InstituteClaremont 7735, Cape Town, South Africa
- Department of Botany and Zoology, University of StellenboschMatieland 7602, South Africa
| | - Falk Sebastian Eckhardt
- Zoological Institute, Technical University of BraunschweigMendelssohnstr. 4, 38106 Braunschweig, Germany
- Tierärztliche Hochschule Hannover, Zoological InstituteBünteweg 17, 30559 Hannover, Germany
| | - Ted M Townsend
- Department of Biology, San Diego State UniversitySan Diego, California 92182
| | | | - Fanomezana Ratsoavina
- Zoological Institute, Technical University of BraunschweigMendelssohnstr. 4, 38106 Braunschweig, Germany
- Département de Biologie Animale, Université d’AntananarivoBP 906, Antananarivo 101, Madagascar
| | - Frank Glaw
- Zoologische Staatssammlung MünchenMünchhausenstr. 21, 81247 München, Germany
| | - Miguel Vences
- Zoological Institute, Technical University of BraunschweigMendelssohnstr. 4, 38106 Braunschweig, Germany
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KURAISHI NORIHIRO, MATSUI MASAFUMI, HAMIDY AMIR, BELABUT DAICUSM, AHMAD NORHAYATI, PANHA SOMSAK, SUDIN AHMAD, YONG HOIS, JIANG JIANPING, OTA HIDETOSHI, THONG HOT, NISHIKAWA KANTO. Phylogenetic and taxonomic relationships of thePolypedates leucomystaxcomplex (Amphibia). ZOOL SCR 2012. [DOI: 10.1111/j.1463-6409.2012.00562.x] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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45
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Hasan M, Islam MM, Khan MR, Alam MS, Kurabayashi A, Igawa T, Kuramoto M, Sumida M. Cryptic anuran biodiversity in Bangladesh revealed by mitochondrial 16S rRNA gene sequences. Zoolog Sci 2012; 29:162-72. [PMID: 22379983 DOI: 10.2108/zsj.29.162] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
To survey the diversity of anuran species in Bangladesh, we compared mitochondrial 16S rRNA gene sequences (approximately 1.4 kbp) from 107 Bangladesh frog specimens. The results of genetic divergence and phylogenetic analyses incorporating data from related species revealed the occurrence of at least eight cryptic species. Hoplobatrachus tigerinus from two districts diverged considerably, indicating the involvement of a cryptic species. Two Fejervarya sp. (large and medium types) and Hylarana cf. taipehensis formed lineages distinct from related species and are probably new species. Microhyla cf. ornata differed from M. ornata with respect to type locality area and involved two distinct species. In addition, we found that Hylarana sp. and Microhyla sp. did not match congeners examined to date in either morphology or 16S rRNA sequence. The occurrence of M. fissipes was tentatively suggested. Consequently, at least, 19 species were found from Bangladesh in this study. These findings revealed a rich anuran biodiversity in Bangladesh, which is unexpected considering the rather simple topographic features of the country.
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Affiliation(s)
- Mahmudul Hasan
- Institute for Amphibian Biology, Hiroshima University, Higashihiroshima, Japan
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46
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Elinson RP, del Pino EM. Developmental diversity of amphibians. WILEY INTERDISCIPLINARY REVIEWS. DEVELOPMENTAL BIOLOGY 2012; 1:345-69. [PMID: 22662314 PMCID: PMC3364608 DOI: 10.1002/wdev.23] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
The current model amphibian, Xenopus laevis, develops rapidly in water to a tadpole which metamorphoses into a frog. Many amphibians deviate from the X. laevis developmental pattern. Among other adaptations, their embryos develop in foam nests on land or in pouches on their mother's back or on a leaf guarded by a parent. The diversity of developmental patterns includes multinucleated oogenesis, lack of RNA localization, huge non-pigmented eggs, and asynchronous, irregular early cleavages. Variations in patterns of gastrulation highlight the modularity of this critical developmental period. Many species have eliminated the larva or tadpole and directly develop to the adult. The wealth of developmental diversity among amphibians coupled with the wealth of mechanistic information from X. laevis permit comparisons that provide deeper insights into developmental processes.
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Affiliation(s)
- Richard P Elinson
- Department of Biological Sciences, Duquesne University, Pittsburgh, PA, USA.
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47
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Mouquet N, Devictor V, Meynard CN, Munoz F, Bersier LF, Chave J, Couteron P, Dalecky A, Fontaine C, Gravel D, Hardy OJ, Jabot F, Lavergne S, Leibold M, Mouillot D, Münkemüller T, Pavoine S, Prinzing A, Rodrigues ASL, Rohr RP, Thébault E, Thuiller W. Ecophylogenetics: advances and perspectives. Biol Rev Camb Philos Soc 2012; 87:769-85. [PMID: 22432924 DOI: 10.1111/j.1469-185x.2012.00224.x] [Citation(s) in RCA: 206] [Impact Index Per Article: 17.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Ecophylogenetics can be viewed as an emerging fusion of ecology, biogeography and macroevolution. This new and fast-growing field is promoting the incorporation of evolution and historical contingencies into the ecological research agenda through the widespread use of phylogenetic data. Including phylogeny into ecological thinking represents an opportunity for biologists from different fields to collaborate and has provided promising avenues of research in both theoretical and empirical ecology, towards a better understanding of the assembly of communities, the functioning of ecosystems and their responses to environmental changes. The time is ripe to assess critically the extent to which the integration of phylogeny into these different fields of ecology has delivered on its promise. Here we review how phylogenetic information has been used to identify better the key components of species interactions with their biotic and abiotic environments, to determine the relationships between diversity and ecosystem functioning and ultimately to establish good management practices to protect overall biodiversity in the face of global change. We evaluate the relevance of information provided by phylogenies to ecologists, highlighting current potential weaknesses and needs for future developments. We suggest that despite the strong progress that has been made, a consistent unified framework is still missing to link local ecological dynamics to macroevolution. This is a necessary step in order to interpret observed phylogenetic patterns in a wider ecological context. Beyond the fundamental question of how evolutionary history contributes to shape communities, ecophylogenetics will help ecology to become a better integrative and predictive science.
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Affiliation(s)
- Nicolas Mouquet
- Institut des Sciences de l'Evolution, UMR, CNRS, Université Montpellier, France.
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Castroviejo-Fisher S, Pérez-Peña PE, Padial JM, Guayasamin JM. A Second Species of the Family Allophrynidae (Amphibia: Anura). AMERICAN MUSEUM NOVITATES 2012. [DOI: 10.1206/3739.2] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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Dissanayake R, Oshida T. The systematics of the dusky striped squirrel,Funambulus sublineatus(Waterhouse, 1838) (Rodentia: Sciuridae) and its relationships to Layard's squirrel,Funambulus layardiBlyth, 1849. J NAT HIST 2012. [DOI: 10.1080/00222933.2011.626126] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/15/2022]
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Kudavidanage EP, Wanger TC, Alwis C, Sanjeewa S, Kotagama SW. Amphibian and butterfly diversity across a tropical land-use gradient in Sri Lanka; implications for conservation decision making. Anim Conserv 2011. [DOI: 10.1111/j.1469-1795.2011.00507.x] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
| | | | - C. Alwis
- Faculty of Applied Sciences; Sabaragamuwa University of Sri Lanka; Belihuloya; Sri Lanka
| | - S. Sanjeewa
- Faculty of Applied Sciences; Sabaragamuwa University of Sri Lanka; Belihuloya; Sri Lanka
| | - S. W. Kotagama
- Department of Zoology; University of Colombo; Colombo; Sri Lanka
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