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Wilenzik IV, Barger BB, Pyron RA. Fossil-informed biogeographic analysis suggests Eurasian regionalization in crown Squamata during the early Jurassic. PeerJ 2024; 12:e17277. [PMID: 38708352 PMCID: PMC11067913 DOI: 10.7717/peerj.17277] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Accepted: 04/01/2024] [Indexed: 05/07/2024] Open
Abstract
Background Squamata (lizards, snakes, and amphisbaenians) is a Triassic lineage with an extensive and complex biogeographic history, yet no large-scale study has reconstructed the ancestral range of early squamate lineages. The fossil record indicates a broadly Pangaean distribution by the end- Cretaceous, though many lineages (e.g., Paramacellodidae, Mosasauria, Polyglyphanodontia) subsequently went extinct. Thus, the origin and occupancy of extant radiations is unclear and may have been localized within Pangaea to specific plates, with potential regionalization to distinct Laurasian and Gondwanan landmasses during the Mesozoic in some groups. Methods We used recent tectonic models to code extant and fossil squamate distributions occurring on nine discrete plates for 9,755 species, with Jurassic and Cretaceous fossil constraints from three extinct lineages. We modeled ancestral ranges for crown Squamata from an extant-only molecular phylogeny using a suite of biogeographic models accommodating different evolutionary processes and fossil-based node constraints from known Jurassic and Cretaceous localities. We hypothesized that the best-fit models would not support a full Pangaean distribution (i.e., including all areas) for the origin of crown Squamata, but would instead show regionalization to specific areas within the fragmenting supercontinent, likely in the Northern Hemisphere where most early squamate fossils have been found. Results Incorporating fossil data reconstructs a localized origin within Pangaea, with early regionalization of extant lineages to Eurasia and Laurasia, while Gondwanan regionalization did not occur until the middle Cretaceous for Alethinophidia, Scolecophidia, and some crown Gekkotan lineages. While the Mesozoic history of extant squamate biogeography can be summarized as a Eurasian origin with dispersal out of Laurasia into Gondwana, their Cenozoic history is complex with multiple events (including secondary and tertiary recolonizations) in several directions. As noted by previous authors, squamates have likely utilized over-land range expansion, land-bridge colonization, and trans-oceanic dispersal. Tropical Gondwana and Eurasia hold more ancient lineages than the Holarctic (Rhineuridae being a major exception), and some asymmetries in colonization (e.g., to North America from Eurasia during the Cenozoic through Beringia) deserve additional study. Future studies that incorporate fossil branches, rather than as node constraints, into the reconstruction can be used to explore this history further.
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Affiliation(s)
- Ian V. Wilenzik
- Department of Biology, George Washington University, Washington D.C., United States of America
| | - Benjamin B. Barger
- Department of Biology, George Washington University, Washington D.C., United States of America
| | - R. Alexander Pyron
- Department of Biology, George Washington University, Washington D.C., United States of America
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2
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Title PO, Singhal S, Grundler MC, Costa GC, Pyron RA, Colston TJ, Grundler MR, Prates I, Stepanova N, Jones MEH, Cavalcanti LBQ, Colli GR, Di-Poï N, Donnellan SC, Moritz C, Mesquita DO, Pianka ER, Smith SA, Vitt LJ, Rabosky DL. The macroevolutionary singularity of snakes. Science 2024; 383:918-923. [PMID: 38386744 DOI: 10.1126/science.adh2449] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Accepted: 01/02/2024] [Indexed: 02/24/2024]
Abstract
Snakes and lizards (Squamata) represent a third of terrestrial vertebrates and exhibit spectacular innovations in locomotion, feeding, and sensory processing. However, the evolutionary drivers of this radiation remain poorly known. We infer potential causes and ultimate consequences of squamate macroevolution by combining individual-based natural history observations (>60,000 animals) with a comprehensive time-calibrated phylogeny that we anchored with genomic data (5400 loci) from 1018 species. Due to shifts in the dynamics of speciation and phenotypic evolution, snakes have transformed the trophic structure of animal communities through the recurrent origin and diversification of specialized predatory strategies. Squamate biodiversity reflects a legacy of singular events that occurred during the early history of snakes and reveals the impact of historical contingency on vertebrate biodiversity.
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Affiliation(s)
- Pascal O Title
- Department of Ecology and Evolution, Stony Brook University, Stony Brook, NY 11794, USA
- Environmental Resilience Institute, Indiana University, Bloomington, IN 47408, USA
- Museum of Zoology and Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Sonal Singhal
- Museum of Zoology and Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109, USA
- Department of Biology, California State University, Dominguez Hills, Carson, CA 90747, USA
| | - Michael C Grundler
- Museum of Zoology and Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Gabriel C Costa
- Museum of Zoology and Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109, USA
- Department of Biology and Environmental Sciences, Auburn University at Montgomery, Montgomery, AL 36117, USA
| | - R Alexander Pyron
- Department of Biological Sciences, The George Washington University, Washington, DC 20052, USA
- Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, DC, 20560, USA
| | - Timothy J Colston
- Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, DC, 20560, USA
- Biology Department, University of Puerto Rico at Mayagüez, Mayagüez 00680, Puerto Rico
| | - Maggie R Grundler
- Museum of Zoology and Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109, USA
- Department of Environmental Science, Policy, and Management, University of California, Berkeley, Berkeley, CA 94720, USA
- Museum of Vertebrate Zoology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Ivan Prates
- Museum of Zoology and Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Natasha Stepanova
- Museum of Zoology and Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Marc E H Jones
- Science Group: Fossil Reptiles, Amphibians and Birds Section, Natural History Museum, London SW7 5BD, UK
- Research Department of Cell and Developmental Biology, University College London, London WC1E 6BT, UK
- Biological Sciences, University of Adelaide, Adelaide, SA 5005, Australia
| | - Lucas B Q Cavalcanti
- Departamento de Sistemática e Ecologia, Universidade Federal da Paraíba, João Pessoa, Paraíba 58051-900, Brazil
| | - Guarino R Colli
- Departamento de Zoologia, Universidade de Brasília, Brasília, Distrito Federal 70910-900, Brazil
| | - Nicolas Di-Poï
- Institute of Biotechnology, Helsinki Institute of Life Science, University of Helsinki, 00014 Helsinki, Finland
| | | | - Craig Moritz
- Research School of Biology, The Australian National University, Canberra, ACT 2600, Australia
| | - Daniel O Mesquita
- Departamento de Sistemática e Ecologia, Universidade Federal da Paraíba, João Pessoa, Paraíba 58051-900, Brazil
| | - Eric R Pianka
- Department of Integrative Biology, The University of Texas at Austin, Austin, TX 78712, USA
| | - Stephen A Smith
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Laurie J Vitt
- Sam Noble Museum and Department of Biology, University of Oklahoma, Norman, OK, USA
| | - Daniel L Rabosky
- Museum of Zoology and Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109, USA
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3
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Sitthivong S, Brakels P, Xayyasith S, Maury N, Idiiatullina S, Pawangkhanant P, Wang K, Nguyen TV, Poyarkov NA. Hiding on jagged karst pinnacles: A new microendemic genus and species of a limestone-dwelling agamid lizard (Squamata: Agamidae: Draconinae) from Khammouan Province, Laos. Zool Res 2023; 44:1039-1051. [PMID: 37872005 PMCID: PMC10802101 DOI: 10.24272/j.issn.2095-8137.2023.062] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Accepted: 10/09/2023] [Indexed: 10/25/2023] Open
Abstract
We describe a unique new species and genus of agamid lizard from the karstic massifs of Khammouan Province, central Laos. Laodracon carsticola Gen. et sp. nov. is an elusive medium-sized lizard (maximum snout-vent length 101 mm) specifically adapted to life on limestone rocks and pinnacles. To assess the phylogenetic position of the new genus amongst other agamids, we generated DNA sequences from two mitochondrial gene fragments (16S rRNA and ND2) and three nuclear loci ( BDNF, RAG1 and c-mos), with a final alignment comprising 7 418 base pairs for 64 agamid species. Phylogenetic analyses unambiguously place the new genus in the mainland Asia subfamily Draconinae, where it forms a clade sister to the genus Diploderma from East Asia and the northern part of Southeast Asia. Morphologically, the new genus is distinguished from all other genera in Draconinae by possessing a notably swollen tail base with enlarged scales on its dorsal and ventral surfaces. Our work provides further evidence that limestone regions of Indochina represent unique "arks of biodiversity" and harbor numerous relict lineages. To date, Laodracon carsticola Gen. et sp. nov. is known from only two adult male specimens and its distribution seems to be restricted to a narrow limestone massif on the border of Khammouan and Bolikhamxai provinces of Laos. Additional studies are required to understand its life history, distribution, and conservation status.
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Affiliation(s)
- Saly Sitthivong
- Faculty of Forestry, National University of Laos, Vientiane 01170, Lao PDR
| | | | - Santi Xayyasith
- Faculty of Environmental Sciences, National University of Laos, Vientiane 01170, Lao PDR
| | - Nathanaël Maury
- Chelonian Conservation Center Laos, World Encyclopedia of Herpetofauna, Vientiane 01000, Lao PDR
| | - Sabira Idiiatullina
- Department of Vertebrate Zoology, Biological Faculty, Lomonosov Moscow State University, Moscow 119234, Russia
| | | | - Kai Wang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China
- Southeast Asia Biodiversity Research Institute, Chinese Academy of Sciences, Yezin , Nay Pyi Taw 05282, Myanmar. E-mail:
| | - Tan Van Nguyen
- Institute for Research and Training in Medicine, Biology and Pharmacy, Duy Tan University, Da Nang 550000, Vietnam
- College of Medicine & Pharmacy, Duy Tan University, Da Nang 550000, Vietnam. E-mail:
| | - Nikolay A Poyarkov
- Department of Vertebrate Zoology, Biological Faculty, Lomonosov Moscow State University, Moscow 119234, Russia
- Joint Russian-Vietnamese Tropical Research and Technological Center, Nghia Do, Cau Giay, Hanoi 122000, Vietnam. E-mail:
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4
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Chaitanya R, McGuire JA, Karanth P, Meiri S. Their fates intertwined: diversification patterns of the Asian gliding vertebrates may have been forged by dipterocarp trees. Proc Biol Sci 2023; 290:20231379. [PMID: 37583322 PMCID: PMC10427812 DOI: 10.1098/rspb.2023.1379] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Accepted: 07/19/2023] [Indexed: 08/17/2023] Open
Abstract
The repeated evolution of gliding in diverse Asian vertebrate lineages is hypothesized to have been triggered by the dominance of tall dipterocarp trees in the tropical forests of Southeast Asia. These dipterocarp forests have acted as both centres of diversification and climatic refugia for gliding vertebrates, and support most of their extant diversity. We predict similarities in the diversification patterns of dipterocarp trees and gliding vertebrates, and specifically test whether episodic diversification events such as rate shifts and/or mass extinctions were temporally congruent in these groups. We analysed diversification patterns in reconstructed timetrees of Asian dipterocarps, the most speciose gliding vertebrates from different classes (Draco lizards, gliding frogs and Pteromyini squirrels) and compared them with similar-sized clades of non-gliding relatives (Diploderma lizards, Philautus frogs and Callosciurinae squirrels) from Southeast Asia. We found significant declines in net-diversification rates of dipterocarps and the gliding vertebrates during the Pliocene-Pleistocene, but not in the non-gliding groups. We conclude that the homogeneity and temporal coincidence of these rate declines point to a viable ecological correlation between dipterocarps and the gliding vertebrates. Further, we suggest that while the diversification decay in dipterocarps was precipitated by post-Miocene aridification of Asia, the crises in the gliding vertebrates were induced by both events concomitantly.
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Affiliation(s)
| | - Jimmy A. McGuire
- Museum of Vertebrate Zoology and Department of Integrative Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Praveen Karanth
- Centre for Ecological Sciences, Indian Institute of Science, Bangalore, Karnataka 560012, India
| | - Shai Meiri
- School of Zoology, Tel Aviv University 6997801, Tel Aviv, Israel
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5
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Luo A, Zhang C, Zhou QS, Ho SYW, Zhu CD. Impacts of Taxon-Sampling Schemes on Bayesian Tip Dating Under the Fossilized Birth-Death Process. Syst Biol 2023; 72:781-801. [PMID: 36919368 PMCID: PMC10405359 DOI: 10.1093/sysbio/syad011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2021] [Revised: 01/18/2023] [Accepted: 03/14/2023] [Indexed: 03/16/2023] Open
Abstract
Evolutionary timescales can be inferred by molecular-clock analyses of genetic data and fossil evidence. Bayesian phylogenetic methods such as tip dating provide a powerful framework for inferring evolutionary timescales, but the most widely used priors for tree topologies and node times often assume that present-day taxa have been sampled randomly or exhaustively. In practice, taxon sampling is often carried out so as to include representatives of major lineages, such as orders or families. We examined the impacts of different densities of diversified sampling on Bayesian tip dating on unresolved fossilized birth-death (FBD) trees, in which fossil taxa are topologically constrained but their exact placements are averaged out. We used synthetic data generated by simulations of nucleotide sequence evolution, fossil occurrences, and diversified taxon sampling. Our analyses under the diversified-sampling FBD process show that increasing taxon-sampling density does not necessarily improve divergence-time estimates. However, when informative priors were specified for the root age or when tree topologies were fixed to those used for simulation, the performance of tip dating on unresolved FBD trees maintains its accuracy and precision or improves with taxon-sampling density. By exploring three situations in which models are mismatched, we find that including all relevant fossils, without pruning off those that are incompatible with the diversified-sampling FBD process, can lead to underestimation of divergence times. Our reanalysis of a eutherian mammal data set confirms some of the findings from our simulation study, and reveals the complexity of diversified taxon sampling in phylogenomic data sets. In highlighting the interplay of taxon-sampling density and other factors, the results of our study have practical implications for using Bayesian tip dating to infer evolutionary timescales across the Tree of Life. [Bayesian tip dating; eutherian mammals; fossilized birth-death process; phylogenomics; taxon sampling.].
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Affiliation(s)
- Arong Luo
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Chi Zhang
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing 100044, China
- Center for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Beijing 100044, China
| | - Qing-Song Zhou
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Simon Y W Ho
- School of Life and Environmental Sciences, University of Sydney, Sydney, New South Wales 2006, Australia
| | - Chao-Dong Zhu
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- State Key Laboratory of Integrated Pest Management, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
- International College, University of Chinese Academy of Sciences, Beijing, 100049, China
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6
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Srinivasulu A, Srinivasulu B, Kusuminda T, Amarasinghe C, Ukuwela KDB, Karunarathna M, Mannakkara A, Yapa WB, Srinivasulu C. Taxonomic status of the Lesser Woolly Horseshoe bats (Chiroptera, Rhinolophidae, Rhinolophus beddomei) in peninsular India and Sri Lanka. Zootaxa 2023; 5301:199-218. [PMID: 37518565 DOI: 10.11646/zootaxa.5301.2.3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Indexed: 08/01/2023]
Abstract
Insularity provides ample opportunities for species diversification. Sri Lanka is home to a large diversity of species, many of which are endemic but morphologically similar to species found in southern India, due to recent speciation events, suggesting a complex evolutionary history. However, in some taxa although morphological diversity has been noted, the genetic level variations are minimal. Among the wide-ranging horseshoe bats such a phenomenon is noted. In this study, we used bioacoustics, morphometric and molecular data to evaluate the relationships between the taxa of lesser woolly horseshoe bats in the India and Sri Lanka. Our study reveals that the two taxa-Rhinolophus beddomei Andersen, 1905 and here we have validated the existing subspecies from peninsular India and R. sobrinus Andersen, 1918 from Sri Lanka are genetically very close to R. perniger Hodgson, 1843. Currently the taxa-beddomei and sobrinus are recognized as subspecies of Rhinolophus beddomei Andersen, 1905. We provide a detailed description of the taxa beddomei and sobrinus as the original descriptions are limited in nature.
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Affiliation(s)
- Aditya Srinivasulu
- Ecology and Conservation Lab; School of Biological Sciences; University of Reading; Whiteknights; Reading; UK.
| | - Bhargavi Srinivasulu
- Wildlife Biology and Taxonomy Lab; Department of Zoology; Osmania University; Hyderabad; Telangana State 500007; India; Systematics; Ecology and Conservation Laboratory; Zoo Outreach Organization; 96; Kumudham Nagar; Vilankurichi Road; Coimbatore; Tamil Nadu 641035; India.
| | - Tharaka Kusuminda
- Department of Agricultural Biology; Faculty of Agriculture; University of Ruhuna; Mapalana; Kamburupitiya; Sri Lanka.
| | - Chamara Amarasinghe
- Department of Zoology and Environment Sciences; Faculty of Science; University of Colombo; Colombo; Sri Lanka.
| | - Kanishka D B Ukuwela
- Department of Biological Sciences; Faculty of Applied Sciences; Rajarata University of Sri Lanka; Mihintale; Sri Lanka.
| | | | - Amani Mannakkara
- Department of Agricultural Biology; Faculty of Agriculture; University of Ruhuna; Mapalana; Kamburupitiya; Sri Lanka.
| | - Wipula B Yapa
- Department of Zoology and Environment Sciences; Faculty of Science; University of Colombo; Colombo; Sri Lanka.
| | - Chelmala Srinivasulu
- Centre for Biodiversity and Conservation Studies; Osmania University; Hyderabad; Telangana State 500007; India.
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7
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Harvey MB, Sarker GC, Sidik I, Kurniawan N, Smith EN. A Contribution to the Systematics of Sunda Shelf Angle-Headed Dragons (Agamidae: Gonocephalus) with the Description of New Taxa from Sumatra. HERPETOLOGICAL MONOGRAPHS 2023. [DOI: 10.1655/herpmonographs-d-22-00001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/30/2023]
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8
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Ananjeva NB, Gordeev DA, Tao NT, Orlov NL. Analysis of Urotomy and Regeneration in Agamid Lizards of the Genus Mantheyus (Reptilia: Sauria: Agamidae: Draconinae) Using X-ray Methods and a Computed Microtomography. BIOL BULL+ 2022. [DOI: 10.1134/s1062359022040033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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9
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Reynolds RG, Miller AH, Pasachnik SA, Knapp CR, Welch ME, Colosimo G, Gerber GP, Drawert B, Iverson JB. Phylogenomics and historical biogeography of West Indian Rock Iguanas (genus Cyclura). Mol Phylogenet Evol 2022; 174:107548. [PMID: 35690377 DOI: 10.1016/j.ympev.2022.107548] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Revised: 04/22/2022] [Accepted: 05/26/2022] [Indexed: 10/18/2022]
Abstract
The genus Cyclura includes nine extant species and six subspecies of West Indian Rock Iguanas and is one of the most imperiled genera of squamate reptiles globally. An understanding of species diversity, evolutionary relationships, diversification, and historical biogeography in this group is crucial for implementing sound long-term conservation strategies. We collected DNA samples from 1 to 10 individuals per taxon from all Cyclura taxa (n = 70 ingroup individuals), focusing where possible on incorporating individuals from different populations of each species. We also collected 1-2 individuals from each of seven outgroup species of iguanas (Iguana delicatissima; five Ctenosaura species) and Anolis sagrei (n = 12 total outgroup individuals). We used targeted genomic sequence capture to isolate and to sequence 1,872 loci comprising of 687,308 base pairs (bp) from each of the 82 individuals from across the nuclear genome. We extracted mitochondrial reads and assembled and annotated mitogenomes for all Cyclura taxa plus outgroup species. We present well-supported phylogenomic gene tree/species tree analyses for all extant species of Cyclura using ASTRAL-III, SVDQuartets, and StarBEAST2 methods, and discuss the taxonomic, biogeographic, and conservation implications of these data. We find a most recent common ancestor of the genus 9.91 million years ago. The earliest divergence within Cyclura separates C. pinguis from a clade comprising all other Cyclura. Within the latter group, a clade comprising C. carinata from the southern Lucayan Islands and C. ricordii from Hispaniola is the sister taxon to a clade comprising the other Cyclura. Among the other Cyclura, the species C. cornuta and C. stejnegeri (from Hispaniola and Isla Mona) form the sister taxon to a clade of species from Jamaica (C. collei), Cuba and Cayman Islands (C. nubila and C. lewisi), and the eastern (C. rileyi) and western (C. cychlura) Lucayan Islands. Cyclura cychlura and C. rileyi form a clade whose sister taxa are C. nubila and C. lewisi. Cyclura collei is the sister taxon to these four species combined.
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Affiliation(s)
- R Graham Reynolds
- Department of Biology, University of North Carolina Asheville, One University Heights, Asheville, NC 28804, USA.
| | - Aryeh H Miller
- Department of Biology, University of North Carolina Asheville, One University Heights, Asheville, NC 28804, USA; Department of Biology, Washington University in St. Louis, St. Louis, MO 63130, USA
| | | | - Charles R Knapp
- Daniel P. Haerther Center for Conservation and Research, John G. Shedd Aquarium, 1200 S. Lake Shore Dr., Chicago, IL 60605, USA
| | - Mark E Welch
- Department of Biological Sciences, Mississippi State University, Starkville, MS 39762
| | - Giuliano Colosimo
- Department of Biology, University of Rome Tor Vergata, Rome, Latium 00133, Italy
| | - Glenn P Gerber
- San Diego Zoo Wildlife Alliance, Escondido, CA 92027, USA
| | - Brian Drawert
- Department of Computer Science, University of North Carolina Asheville, One University Heights, Asheville, NC 28804, USA
| | - John B Iverson
- Dept. of Biology, Earlham College, Richmond, IN 47374, USA
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10
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Grismer LL, Poyarkov NA, Quah ES, Grismer JL, Wood Jr PL. The biogeography of bent-toed geckos, Cyrtodactylus (Squamata: Gekkonidae). PeerJ 2022; 10:e13153. [PMID: 35341041 PMCID: PMC8953499 DOI: 10.7717/peerj.13153] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Accepted: 03/01/2022] [Indexed: 01/12/2023] Open
Abstract
The gekkonid genus Cyrtodactylus is the third largest vertebrate genus on the planet with well over 300 species that range across at least eight biogeographic regions from South Asia to Melanesia. The ecological and morphological plasticity within the genus, has contributed to its ability to disperse across ephemeral seaways, river systems, basins, land bridges, and mountain ranges-followed by in situ diversification within specific geographic areas. Ancestral ranges were reconstructed on a mitochondrial phylogeny with 346 described and undescribed species from which it was inferred that Cyrtodactylus evolved in a proto-Himalaya region during the early Eocene. From there, it dispersed to what is currently Indoburma and Indochina during the mid-Eocene-the latter becoming the first major center of origin for the remainder of the genus that seeded dispersals to the Indian subcontinent, Papua, and Sundaland. Sundaland became a second major center of radiation during the Oligocene and gave rise to a large number of species that radiated further within Sundaland and dispersed to Wallacea, the Philippines, and back to Indochina. One Papuan lineage dispersed west to recolonize and radiate in Sundaland. Currently, Indochina and Sundaland still harbor the vast majority of species of Cyrtodactylus.
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Affiliation(s)
- L. Lee Grismer
- Department of Biology, La Sierra University, Riverside, CA, United States of America
| | - Nikolay A. Poyarkov
- Faculty of Biology, Department of Vertebrate Zoology, Moscow State University, Moscow, Russia,Joint Russian-Vietnamese Tropical Research and Technological Center, Hanoi, Vietnam
| | - Evan S.H. Quah
- Department of Biology, La Sierra University, Riverside, CA, United States of America,Institute for Tropical Biology and Conservation, Universiti Malaysia Sabah, Jalan UMS, Kota Kinabalu, SabahMalaysia
| | - Jesse L. Grismer
- Department of Biology, La Sierra University, Riverside, CA, United States of America
| | - Perry L. Wood Jr
- Department of Biological Sciences & Museum of Natural History, Auburn University, Auburn, AL, United States of America,Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI, United States of America
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11
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Poyarkov NA, Nguyen TV, Pawangkhanant P, Yushchenko PV, Brakels P, Nguyen LH, Nguyen HN, Suwannapoom C, Orlov N, Vogel G. An integrative taxonomic revision of slug-eating snakes (Squamata: Pareidae: Pareineae) reveals unprecedented diversity in Indochina. PeerJ 2022; 10:e12713. [PMID: 35047234 PMCID: PMC8757378 DOI: 10.7717/peerj.12713] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Accepted: 12/09/2021] [Indexed: 01/07/2023] Open
Abstract
Slug-eating snakes of the subfamily Pareinae are an insufficiently studied group of snakes specialized in feeding on terrestrial mollusks. Currently Pareinae encompass three genera with 34 species distributed across the Oriental biogeographic region. Despite the recent significant progress in understanding of Pareinae diversity, the subfamily remains taxonomically challenging. Here we present an updated phylogeny of the subfamily with a comprehensive taxon sampling including 30 currently recognized Pareinae species and several previously unknown candidate species and lineages. Phylogenetic analyses of mtDNA and nuDNA data supported the monophyly of the three genera Asthenodipsas, Aplopeltura, and Pareas. Within both Asthenodipsas and Pareas our analyses recovered deep differentiation with each genus being represented by two morphologically diagnosable clades, which we treat as subgenera. We further apply an integrative taxonomic approach, including analyses of molecular and morphological data, along with examination of available type materials, to address the longstanding taxonomic questions of the subgenus Pareas, and reveal the high level of hidden diversity of these snakes in Indochina. We restrict the distribution of P. carinatus to southern Southeast Asia, and recognize two subspecies within it, including one new subspecies proposed for the populations from Thailand and Myanmar. We further revalidate P. berdmorei, synonymize P. menglaensis with P. berdmorei, and recognize three subspecies within this taxon, including the new subspecies erected for the populations from Laos and Vietnam. Furthermore, we describe two new species of Pareas from Vietnam: one belonging to the P. carinatus group from southern Vietnam, and a new member of the P. nuchalis group from the central Vietnam. We provide new data on P. temporalis, and report on a significant range extension for P. nuchalis. Our phylogeny, along with molecular clock and ancestral area analyses, reveal a complex diversification pattern of Pareinae involving a high degree of sympatry of widespread and endemic species. Our analyses support the "upstream" colonization hypothesis and, thus, the Pareinae appears to have originated in Sundaland during the middle Eocene and then colonized mainland Asia in early Oligocene. Sundaland and Eastern Indochina appear to have played the key roles as the centers of Pareinae diversification. Our results reveal that both vicariance and dispersal are responsible for current distribution patterns of Pareinae, with tectonic movements, orogeny and paleoclimatic shifts being the probable drivers of diversification. Our study brings the total number of Pareidae species to 41 and further highlights the importance of comprehensive taxonomic revisions not only for the better understanding of biodiversity and its evolution, but also for the elaboration of adequate conservation actions.
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Affiliation(s)
- Nikolay A. Poyarkov
- Laboratory of Tropical Ecology, Joint Russian-Vietnamese Tropical Research and Technological Center, Hanoi, Vietnam,Faculty of Biology, Department of Vertebrate Zoology, Moscow State University, Moscow, Russia
| | - Tan Van Nguyen
- Department of Species Conservation, Save Vietnam’s Wildlife, Ninh Binh, Vietnam
| | - Parinya Pawangkhanant
- Division of Fishery, School of Agriculture and Natural Resources, University of Phayao, Phayao, Thailand
| | - Platon V. Yushchenko
- Faculty of Biology, Department of Vertebrate Zoology, Moscow State University, Moscow, Russia
| | | | - Linh Hoang Nguyen
- Department of Zoology, Southern Institute of Ecology, Vietnam Academy of Science and Technology, Ho Chi Minh City, Vietnam
| | - Hung Ngoc Nguyen
- Department of Zoology, Southern Institute of Ecology, Vietnam Academy of Science and Technology, Ho Chi Minh City, Vietnam
| | - Chatmongkon Suwannapoom
- Division of Fishery, School of Agriculture and Natural Resources, University of Phayao, Phayao, Thailand
| | - Nikolai Orlov
- Department of Herpetology, Zoological Institute, Russian Academy of Sciences, St. Petersburg, Russia
| | - Gernot Vogel
- Society for Southeast Asian Herpetology, Heidelberg, Germany
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12
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Heckwolf MJ, Morim T, Riccioli F, Baltazar-Soares M. Fresh start after rough rides: understanding patterns of genetic differentiation upon human-mediated translocations. Biol Invasions 2021. [DOI: 10.1007/s10530-021-02605-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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13
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Yamahira K, Ansai S, Kakioka R, Yaguchi H, Kon T, Montenegro J, Kobayashi H, Fujimoto S, Kimura R, Takehana Y, Setiamarga DHE, Takami Y, Tanaka R, Maeda K, Tran HD, Koizumi N, Morioka S, Bounsong V, Watanabe K, Musikasinthorn P, Tun S, Yun LKC, Masengi KWA, Anoop VK, Raghavan R, Kitano J. Mesozoic origin and 'out-of-India' radiation of ricefishes (Adrianichthyidae). Biol Lett 2021; 17:20210212. [PMID: 34343438 DOI: 10.1098/rsbl.2021.0212] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The Indian subcontinent has an origin geologically different from Eurasia, but many terrestrial animal and plant species on it have congeneric or sister species in other parts of Asia, especially in the Southeast. This faunal and floral similarity between India and Southeast Asia is explained by either of the two biogeographic scenarios, 'into-India' or 'out-of-India'. Phylogenies based on complete mitochondrial genomes and five nuclear genes were undertaken for ricefishes (Adrianichthyidae) to examine which of these two biogeographic scenarios fits better. We found that Oryzias setnai, the only adrianichthyid distributed in and endemic to the Western Ghats, a mountain range running parallel to the western coast of the Indian subcontinent, is sister to all other adrianichthyids from eastern India and Southeast-East Asia. Divergence time estimates and ancestral area reconstructions reveal that this western Indian species diverged in the late Mesozoic during the northward drift of the Indian subcontinent. These findings indicate that adrianichthyids dispersed eastward 'out-of-India' after the collision of the Indian subcontinent with Eurasia, and subsequently diversified in Southeast-East Asia. A review of geographic distributions of 'out-of-India' taxa reveals that they may have largely fuelled or modified the biodiversity of Eurasia.
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Affiliation(s)
- Kazunori Yamahira
- Tropical Biosphere Research Center, University of the Ryukyus, Okinawa, Japan
| | - Satoshi Ansai
- Graduate School of Life Sciences, Tohoku University, Sendai, Japan
| | - Ryo Kakioka
- Tropical Biosphere Research Center, University of the Ryukyus, Okinawa, Japan
| | - Hajime Yaguchi
- Tropical Biosphere Research Center, University of the Ryukyus, Okinawa, Japan.,School of Science and Technology, Kwansei Gakuin University, Sanda, Japan
| | - Takeshi Kon
- Center for Strategic Research Project, University of the Ryukyus, Okinawa, Japan
| | - Javier Montenegro
- Tropical Biosphere Research Center, University of the Ryukyus, Okinawa, Japan
| | - Hirozumi Kobayashi
- Tropical Biosphere Research Center, University of the Ryukyus, Okinawa, Japan
| | - Shingo Fujimoto
- Tropical Biosphere Research Center, University of the Ryukyus, Okinawa, Japan
| | - Ryosuke Kimura
- Graduate School of Medicine, University of the Ryukyus, Okinawa, Japan
| | - Yusuke Takehana
- Faculty of Bio-Science, Nagahama Institute of Bio-Science and Technology, Japan
| | - Davin H E Setiamarga
- Department of Applied Chemistry and Biochemistry, National Institute of Technology, Wakayama College, Wakayama, Japan
| | - Yasuoki Takami
- Graduate School of Human Development and Environment, Kobe University, Kobe, Japan
| | - Rieko Tanaka
- World Medaka Aquarium, Nagoya Higashiyama Zoo and Botanical Gardens, Nagoya, Japan
| | - Ken Maeda
- Marine Eco-Evo-Devo Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa, Japan
| | - Hau D Tran
- Faculty of Biology, Hanoi National University of Education, Hanoi, Vietnam
| | - Noriyuki Koizumi
- Strategic Planning Headquarters, National Agriculture and Food Research Organization, Ibaraki, Japan
| | - Shinsuke Morioka
- Fisheries Division, Japan International Research Center for Agricultural Sciences, Ibaraki, Japan
| | | | - Katsutoshi Watanabe
- Division of Biological Sciences, Graduate School of Science, Kyoto University, Kyoto, Japan
| | | | - Sein Tun
- Inlay Lake Wildlife Sanctuary, Ministry of Natural Resources and Environmental Conservation, Nyaungshwe, Myanmar
| | - L K C Yun
- Inlay Lake Wildlife Sanctuary, Ministry of Natural Resources and Environmental Conservation, Nyaungshwe, Myanmar
| | | | - V K Anoop
- School of Ocean Science and Technology, Kerala University of Fisheries and Ocean Studies, Kochi, India
| | - Rajeev Raghavan
- Department of Fisheries Resource Management, Kerala University of Fisheries and Ocean Studies, Kochi, India
| | - Jun Kitano
- Ecological Genetics Laboratory, National Institute of Genetics, Mishima, Japan
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14
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Gowande GG, Bhosale HS, Phansalkar PU, Sawant M, Mirza ZA. On the systematics and the phylogenetic position of the poorly known, montane dragon-lizard species Pseudocalotes austeniana (Annandale, 1908) (Squamata, Agamidae, Draconinae). EVOLUTIONARY SYSTEMATICS 2021. [DOI: 10.3897/evolsyst.5.67137] [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
The montane agamid species Pseudocalotes austeniana has had a complicated taxonomic history, as the species was initially described as a member of the genus Salea Gray, 1845. Later, the species was placed in a monotypic genus Mictopholis Smith, 1935, which was erected only to include this species; however, the species was later on transferred to the genus Pseudocalotes Fitzinger, 1843, owing to the morphological similarities, and lack of strong characters to diagnose the genus Mictopholis. Nonetheless, its precise phylogenetic and systematic position has remained unresolved due to the lack of molecular sequence data. During a herpetological expedition to Arunachal Pradesh, specimens of P. austeniana were collected from the hills near the type locality. The mitochondrial 16S rRNA, ND2 and ND4, and the nuclear RAG1 regions were subjected to molecular phylogenetics. Maximum Likelihood and Bayesian Inference gene trees revealed that P. austeniana is a member of the subfamily Draconinae. The analyses showed that the genus Pseudocalotes is polyphyletic, and P. austeniana was embedded within the genus Japalura Gray, 1853 sensu stricto. We here, thus, propose to transfer the species P. austeniana to the genus Japlaura, as Japalura austenianacomb. nov. Biogeographic and evolutionary significance of the findings are discussed.
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15
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Reilly SB, Stubbs AL, Arida E, Karin BR, Arifin U, Kaiser H, Bi K, Iskandar DT, McGuire JA. Phylogenomic Analysis Reveals Dispersal-Driven Speciation and Divergence with Gene Flow in Lesser Sunda Flying Lizards (Genus Draco). Syst Biol 2021; 71:221-241. [PMID: 34117769 DOI: 10.1093/sysbio/syab043] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Revised: 05/30/2021] [Accepted: 06/02/2021] [Indexed: 12/13/2022] Open
Abstract
The Lesser Sunda Archipelago offers exceptional potential as a model system for studying the dynamics of dispersal-driven diversification. The geographic proximity of the islands suggests the possibility for successful dispersal, but this is countered by the permanence of the marine barriers and extreme intervening currents that are expected to hinder gene flow. Phylogenetic and species delimitation analyses of flying lizards (genus Draco) using single mitochondrial genes, complete mitochondrial genomes, and exome-capture data sets identified 9-11 deeply divergent lineages including single-island endemics, lineages that span multiple islands, and parapatrically-distributed non-sister lineages on the larger islands. Population clustering and PCA confirmed these genetic boundaries with isolation-by-distance playing a role in some islands or island sets. While gdi estimates place most candidate species comparisons in the ambiguous zone, migration estimates suggest 9 or 10 species exist with nuclear introgression detected across some intra-island contact zones. Initial entry of Draco into the archipelago occurred at 5.5-7.5 Ma, with most inter-island colonization events having occurred between 1-3 Ma. Biogeographical model testing favors scenarios integrating geographic distance and historical island connectivity, including an initial stepping-stone dispersal process from the Greater Sunda Shelf through the Sunda Arc as far eastward as Lembata Island. However, rather than reaching the adjacent island of Pantar by dispersing over the 15-km wide Alor Strait, Draco ultimately reached Pantar (and much of the rest of the archipelago) by way of a circuitous route involving at least five over-water dispersal events. These findings suggest that historical geological and oceanographic conditions heavily influenced dispersal pathways and gene flow, which in turn drove species formation and shaped species boundaries.
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Affiliation(s)
- Sean B Reilly
- Museum of Vertebrate Zoology and Department of Integrative Biology, University of California, Berkeley, CA 94720, USA
| | - Alexander L Stubbs
- Museum of Vertebrate Zoology and Department of Integrative Biology, University of California, Berkeley, CA 94720, USA
| | - Evy Arida
- Museum Zoologicum Bogoriense, Indonesian Institute of Sciences, Cibinong, Indonesia
| | - Benjamin R Karin
- Museum of Vertebrate Zoology and Department of Integrative Biology, University of California, Berkeley, CA 94720, USA
| | - Umilaela Arifin
- School of Life Sciences and Technology, Institut Teknologi Bandung, Bandung, Indonesia
| | - Hinrich Kaiser
- Department of Vertebrate Zoology, Zoologisches Forschungsmuseum Alexander Koenig, Adenauerallee 160, 53113 Bonn, Germany; and Department of Biology, Victor Valley College, Victorville, California 92395, USA
| | - Ke Bi
- Museum of Vertebrate Zoology and Department of Integrative Biology, University of California, Berkeley, CA 94720, USA.,Computational Genomics Resource Laboratory, California Institute for Quantitative Biosciences, University of California, Berkeley, CA 94720, USA
| | | | - Jimmy A McGuire
- Museum of Vertebrate Zoology and Department of Integrative Biology, University of California, Berkeley, CA 94720, USA
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16
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Harvey MB, Rech I, Riyanto A, Kurniawan N, Smith EN. A New Angle-Headed Dragon (Agamidae: Gonocephalus) from Montane Forests of the Southern Bukit Barisan Range of Sumatra. HERPETOLOGICA 2021. [DOI: 10.1655/herpetologica-d-20-00044.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Affiliation(s)
- Michael B. Harvey
- Department of Biological Sciences, Broward College, 3501 SW Davie Road, Davie, FL 33314, USA
| | - Inna Rech
- Zoologisches Forschungsmuseum Alexander Koenig, Adenauerallee 160, Bonn 53113, Germany
| | - Awal Riyanto
- Laboratory of Herpetology, Museum Zoologicum Bogoriense, Research Center for Biology, Indonesian Institute of Sciences–LIPI, Jl. Raya Jakarta Bogor km 46, Cibinong, West Java, 16911, Indonesia
| | - Nia Kurniawan
- Department of Biology, Universitas Brawijaya, Jl. Veteran, Malang, East Java, 65145, Indonesia
| | - Eric N. Smith
- The Amphibian and Reptile Diversity Research Center and Department of Biology, University of Texas at Arlington, 501 S Nedderman Drive, Arlington, TX 76010, USA
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17
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Phylogenetics of mud snakes (Squamata: Serpentes: Homalopsidae): A paradox of both undescribed diversity and taxonomic inflation. Mol Phylogenet Evol 2021; 160:107109. [PMID: 33609712 DOI: 10.1016/j.ympev.2021.107109] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Revised: 11/20/2020] [Accepted: 02/05/2021] [Indexed: 12/30/2022]
Abstract
Mud snakes (Serpentes: Homalopsidae) are a family of 55 described, mainly aquatic, species primarily distributed throughout mainland Southeast Asia and the Indo-Australian Archipelago. Although they have been the focus of prior research, the basic relationships amongst genera and species remain poorly known. We used a combined mitochondrial and nuclear gene dataset to infer their phylogenetic relationships, using the highest levels of taxon and geographic sampling for any homalopsid phylogeny to date (62% generic and 62% species coverage; 140 individuals). Our results recover two reciprocally monophyletic groups: the fangless Brachyorrhos and its sister clade comprised of all rear-fanged homalopsids. Most genera and interspecific relationships were monophyletic and strongly supported, but intergeneric relationships and intraspecific population structure lack support. We find evidence of both undescribed diversity as well as cases of taxonomic inflation within several species. Tree-based species delimitation approaches (mPTP) support potential new candidate species as distinct from their conspecifics and also suggest that many named taxa may not be distinct species. Divergence date estimation and lineage-through-time analyses indicate lower levels of speciation in the Eocene, with a subsequent burst in diversification in the Miocene. Homalopsids may have diversified most rapidly during the Pliocene and Pleistocene, possibly in relation to tectonic shifts and sea-level fluctuations that took place in Sundaland and the Sahul Shelf. Our analyses provide new insights on homalopsid taxonomy, a baseline phylogeny for the family, and further biogeographic implications demonstrating how dynamic tectonics and Quaternary sea level changes may have shaped a widespread, diverse family of snakes.
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18
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Li F, Shao L, Li S. Tropical Niche Conservatism Explains the Eocene Migration from India to Southeast Asia in Ochyroceratid Spiders. Syst Biol 2021; 69:987-998. [PMID: 32011715 DOI: 10.1093/sysbio/syaa006] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2019] [Revised: 01/23/2020] [Accepted: 01/29/2020] [Indexed: 12/11/2022] Open
Abstract
Biological migrations between India and Southeast (SE) Asia provide an ideal system for exploring the effects of geology and climate on species ranges. Geologists have confirmed that the direct collision between India and Eurasia occurred in the Early Eocene, but most migrations occurred between the Indian subcontinent and SE Asia rather than the former and the southern margin of Eurasia. To explain this seemingly paradoxical disconnect between the routes of plate movement and biological migration, we studied the evolutionary history of the tropical spider family Ochyroceratidae based on 101 globally distributed species. We infer a robust dated phylogeny using both transcriptomic data and a data set of classical markers and relate these to biogeographic and climatic analyses. Our results indicate that the monophyly of Ochyroceratidae is strongly supported, and the divergence times suggest a Cretaceous Gondwanan origin of the family. Reconstructed biogeographic histories support a dispersal event from the Indian subcontinent to islands of SE Asia 55-38 Ma. Climatic analyses and the fossil record reveal that ochyroceratids are characterized by a high degree of tropical niche conservatism, and that the ancestor of the Indian and SE Asian clades originated in very warm, wet environments. Early Eocene tropical, perhumid climates in India, and SE Asia may have facilitated ochyroceratid migration, whereas the dry or seasonal climate extending from the eastern coast of China to Central Asia may have acted as a barrier, preventing dispersal. Our analyses suggest that climate plays a more important role than geology in biological migration from the Indian subcontinent to SE Asia, providing new insights into the Indian-Asian biogeographic link. [Biogeography; ecology; geological connections; macroevolution; paleoclimate.].
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Affiliation(s)
- Fengyuan Li
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Lili Shao
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Shuqiang Li
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
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19
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Sidharthan C, Karanth KP. India's biogeographic history through the eyes of blindsnakes- filling the gaps in the global typhlopoid phylogeny. Mol Phylogenet Evol 2020; 157:107064. [PMID: 33387646 DOI: 10.1016/j.ympev.2020.107064] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2020] [Revised: 12/05/2020] [Accepted: 12/24/2020] [Indexed: 11/25/2022]
Abstract
The Indian subcontinent's unique geological history is reflected in the diverse assemblage of its biota. The blindsnake superfamily Typhlopoidea, with its unique mix of ancient as well as younger lineages in Asia, provides an opportunity to understand the various biotic exchange scenarios proposed for the Indian landmass. In this study, we aim to understand the biogeographic origins of the four genera of typhlopoids found in India and to decipher their times and modes of arrival in the subcontinent. Five nuclear markers were sequenced for 12 samples collected from across India, encompassing all four genera under study. Published sequences of typhlopoid genera were compiled and combined with Indian sequences to generate a global dataset. Phylogenetic relationships were reconstructed using maximum likelihood and Bayesian inference methods. Divergence times were estimated using BEAST 1.8.2. Ancestral geographical ranges were estimated using DEC + J, implemented in BioGeoBEARS. Divergence time estimates suggest that Gerrhopilus is an ancient lineage, and the lineage leading to it was present on the Indian landmass since the last 100 million years. The other three genera are more recent dispersals into India, possibly trans-oceanic. Biogeographic reconstructions suggest an East Gondwanan origin for Typhlopoidea, an African origin for Grypotyphlops and an Asian origin for Indotyphlops and Argyrophis. It appears that India harbours a combination of ancient and more recently dispersed lineages of typhlopoids. The genus Gerrhopilus is of Gondwanan origin that likely dispersed out of India into Southeast Asia. The other genera are intrusive elements that dispersed into India from Africa (Grypotyphlops) and Asia (Indotyphlops and possibly Argyrophis) post break-up of Gondwana. Thus, our study provides further evidence on the ability of blindsnakes to undergo long distance trans-oceanic dispersal. Results also suggest an Asian origin for typhlopoids from Australasia, Philippines and Wallacea.
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Affiliation(s)
- Chinta Sidharthan
- Centre for Ecological Sciences, Indian Institute of Science, Bangalore 560012, India.
| | - K Praveen Karanth
- Centre for Ecological Sciences, Indian Institute of Science, Bangalore 560012, India
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20
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Shaney KJ, Harvey MB, Hamidy A, Kurniawan N, Smith EN. Phylogeny and biogeography of Sumatra´s cloud forest lizards of the genus Dendragama and status of Acanthosaura schneideri. Zookeys 2020; 995:127-153. [PMID: 33281471 PMCID: PMC7688618 DOI: 10.3897/zookeys.995.49355] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2019] [Accepted: 09/08/2020] [Indexed: 12/02/2022] Open
Abstract
Lizards of the genus Dendragama are endemic to the highland cloud forests of Sumatra’s Barisan Mountain Range in western Indonesia, and recent studies have uncovered widespread diversity within the genus. Here, a suite of morphological characters and mitochondrial DNA are used to compare three geographically isolated populations of D.boulengeri from (1) Mount Kerinci in Jambi province, (2) Mount Marapi of west Sumatra, and (3) the Karo Highlands of north Sumatra. Additional phylogeographic analyses with two recently described sister species, D.australis and D.dioidema were conducted. Five genetically distinct clades of Dendragama, all distributed allopatrically of one another were identified and some are suspected to inhabit small distributions. Morphological and genetic data confirm the Karo Highlands population D.schneideri (previously Acanthosauraschneideri Ahl, 1926) should be revalidated from the synonymy of D.boulengeri. Dendragamaschneideri is endemic to montane forests of the Karo Highlands surrounding Lake Toba in Sumatra Utara province. Pairwise genetic distances of 6–11% separate D.schneideri from congeners. Two distinct clades of D.boulengeri from Mount Kerinci and Mount Marapi were identified, which are 5.0% genetically distant from one another. Using morphological characters, we provide the first key for distinguishing between species of Dendragama. Based on biogeographic patterns and levels of genetic variation it is suspected that at least 18 other isolated cloud forest locations may hold new species or divergent populations of Dendragama but lack survey work. Collectively, these comparisons among populations of montane lizards further elucidate the complex biogeographic history of Sumatra’s montane forest species and the first phylogeny of the genus Dendragama.
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Affiliation(s)
- Kyle J Shaney
- Departamento de Ecología de la Biodiversidad, Instituto de Ecología, Universidad Nacional Autónoma de México, Ap. Postal 70-275, Ciudad Universitaria, Ciudad de México, 04510, México University of Texas Arlington United States of America.,The Amphibian and Reptile Diversity Research Center and Department of Biology; University of Texas at Arlington; 501 S. Nedderman Drive; Arlington, TX 76010; 775-351-5277, USA Universitas Brawijaya Malang Indonesia
| | - Michael B Harvey
- Department of Biological Sciences; Broward College; 3501 S.W. Davie Road; Davie, FL 33314, USA Indonesian Institute of Sciences Bogor Indonesia
| | - Amir Hamidy
- Laboratory of Herpetology; Museum Zoologicum Bogoriense; Research Center for Biology, Indonesian Institute of Sciences-LIPI; Jl. Raya Jakarta Bogor km 46; Cibinong, west Java, 16911, Indonesia Universidad Nacional Autónoma de México Ciudad de México Mexico
| | - Nia Kurniawan
- Department of Biology; Universitas Brawijaya; Jl. Veteran; Malang, East Java, 65145, Indonesia Broward College Davie United States of America
| | - Eric N Smith
- The Amphibian and Reptile Diversity Research Center and Department of Biology; University of Texas at Arlington; 501 S. Nedderman Drive; Arlington, TX 76010; 775-351-5277, USA Universitas Brawijaya Malang Indonesia
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21
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Kurita T, Kojima Y, Hossman MY, Nishikawa K. Phylogenetic position of a bizarre lizard Harpesaurus implies the co-evolution between arboreality, locomotion, and reproductive mode in Draconinae (Squamata: Agamidae). SYST BIODIVERS 2020. [DOI: 10.1080/14772000.2020.1795741] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Affiliation(s)
- Takaki Kurita
- Natural History Museum and Institute, Chiba. Aoba-cho 955-2, Chuo-ku, Chiba, 260-8682, Japan
| | - Yosuke Kojima
- Department of Biology, Toho University, 2-2-1 Miyama, Funabashi, 274-8510, Chiba, Japan
| | - Mohamad Yazid Hossman
- Research Development and Innovation Division, Section of Biodiversity Fauna, Forest Department Sarawak, Kuching, 93250, Sarawak, Malaysia
| | - Kanto Nishikawa
- Graduate School of Human and Environmental Studies, Kyoto University, Yoshida Nihonmatsu-cho, Sakyo-ku, Kyoto, 606-8501, Japan
- Graduate School of Global Environmental Studies, Kyoto University, Yoshida Hon-machi, Sakyo-ku, Kyoto, 606-8501, Japan
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22
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Gorin VA, Solovyeva EN, Hasan M, Okamiya H, Karunarathna DS, Pawangkhanant P, de Silva A, Juthong W, Milto KD, Nguyen LT, Suwannapoom C, Haas A, Bickford DP, Das I, Poyarkov NA. A little frog leaps a long way: compounded colonizations of the Indian Subcontinent discovered in the tiny Oriental frog genus Microhyla (Amphibia: Microhylidae). PeerJ 2020; 8:e9411. [PMID: 32685285 PMCID: PMC7337035 DOI: 10.7717/peerj.9411] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Accepted: 06/03/2020] [Indexed: 11/22/2022] Open
Abstract
Frogs of the genus Microhyla include some of the world's smallest amphibians and represent the largest radiation of Asian microhylids, currently encompassing 50 species, distributed across the Oriental biogeographic region. The genus Microhyla remains one of the taxonomically most challenging groups of Asian frogs and was found to be paraphyletic with respect to large-sized fossorial Glyphoglossus. In this study we present a time-calibrated phylogeny for frogs in the genus Microhyla, and discuss taxonomy, historical biogeography, and morphological evolution of these frogs. Our updated phylogeny of the genus with nearly complete taxon sampling includes 48 nominal Microhyla species and several undescribed candidate species. Phylogenetic analyses of 3,207 bp of combined mtDNA and nuDNA data recovered three well-supported groups: the Glyphoglossus clade, Southeast Asian Microhyla II clade (includes M. annectens species group), and a diverse Microhyla I clade including all other species. Within the largest major clade of Microhyla are seven well-supported subclades that we identify as the M. achatina, M. fissipes, M. berdmorei, M. superciliaris, M. ornata, M. butleri, and M. palmipes species groups. The phylogenetic position of 12 poorly known Microhyla species is clarified for the first time. These phylogenetic results, along with molecular clock and ancestral area analyses, show the Microhyla-Glyphoglossus assemblage to have originated in Southeast Asia in the middle Eocene just after the first hypothesized land connections between the Indian Plate and the Asian mainland. While Glyphoglossus and Microhyla II remained within their ancestral ranges, Microhyla I expanded its distribution generally east to west, colonizing and diversifying through the Cenozoic. The Indian Subcontinent was colonized by members of five Microhyla species groups independently, starting with the end Oligocene-early Miocene that coincides with an onset of seasonally dry climates in South Asia. Body size evolution modeling suggests that four groups of Microhyla have independently achieved extreme miniaturization with adult body size below 15 mm. Three of the five smallest Microhyla species are obligate phytotelm-breeders and we argue that their peculiar reproductive biology may be a factor involved in miniaturization. Body size increases in Microhyla-Glyphoglossus seem to be associated with a burrowing adaptation to seasonally dry habitats. Species delimitation analyses suggest a vast underestimation of species richness and diversity in Microhyla and reveal 15-33 undescribed species. We revalidate M. nepenthicola, synonymize M. pulverata with M. marmorata, and provide insights on taxonomic statuses of a number of poorly known species. Further integrative studies, combining evidence from phylogeny, morphology, advertisement calls, and behavior will result in a better systematic understanding of this morphologically cryptic radiation of Asian frogs.
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Affiliation(s)
- Vladislav A. Gorin
- Faculty of Biology, Department of Vertebrate Zoology, Lomonosov Moscow State University, Moscow, Russia
| | | | - Mahmudul Hasan
- Department of Fisheries, Bangamata Sheikh Fazilatunnesa Mujib Science & Technology University, Jamalpur, Bangladesh
| | - Hisanori Okamiya
- Department of Biological Science, Faculty of Science, Tokyo Metropolitan University, Tokyo, Japan
| | | | | | - Anslem de Silva
- Amphibia and Reptile Research Organization of Sri Lanka, Gampola, Sri Lanka
| | | | | | | | | | - Alexander Haas
- Center for Natural History, Universität Hamburg, Hamburg, Germany
| | | | - Indraneil Das
- Institute of Biodiversity and Environmental Conservation, Universiti Malaysia Sarawak, Kota Samarahan, Malaysia
| | - Nikolay A. Poyarkov
- Faculty of Biology, Department of Vertebrate Zoology, Lomonosov Moscow State University, Moscow, Russia
- Joint Russian-Vietnamese Tropical Research and Technological Center, Hanoi, Vietnam
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23
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Agarwal I, Thackeray T, Pal S, Khandekar A. Granite boulders act as deep‐time climate refugia: A Miocene divergent clade of rupicolous
Cnemaspis
Strauch, 1887 (Squamata: Gekkonidae) from the Mysore Plateau, India, with descriptions of three new species. J ZOOL SYST EVOL RES 2020. [DOI: 10.1111/jzs.12391] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Affiliation(s)
- Ishan Agarwal
- Thackeray Wildlife Foundation Mumbai India
- National Centre for Biological Sciences Tata Institute of Fundamental Research Bengaluru India
| | | | - Saunak Pal
- Centre for Ecological Sciences Indian Institute of Science Bangalore India
- Bombay Natural History Society Mumbai India
| | - Akshay Khandekar
- Thackeray Wildlife Foundation Mumbai India
- National Centre for Biological Sciences Tata Institute of Fundamental Research Bengaluru India
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24
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Shaney KJ, Maldonado J, Smart U, Thammachoti P, Fujita M, Hamidy A, Kurniawan N, Harvey MB, Smith EN. Phylogeography of montane dragons could shed light on the history of forests and diversification processes on Sumatra. Mol Phylogenet Evol 2020; 149:106840. [PMID: 32305510 DOI: 10.1016/j.ympev.2020.106840] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2019] [Revised: 04/12/2020] [Accepted: 04/13/2020] [Indexed: 12/15/2022]
Abstract
Biogeographical evidence, both, for and against the "regional endemism paradigm" hypothesis has been uncovered across the Greater Sunda Region (Sundaland) of Southeast Asia. Additionally, there are competing hypotheses regarding how Pleistocene forests may have impacted biological patterns and processes in Sumatra. Using montane agamid lizards from Sumatra, we derived and analyzed a phylogenetic dataset, genetic divergence estimates, and contemporary distributional patterns among species. We tested whether (1) Sumatra's highland Draconinae diversification fits the regional endemism paradigm hypothesis and (2) Draconinae phylogeography provides biological evidence for Pleistocene forest extent at various points in history. Our results suggest in situ diversification was the main driver behind montane Draconinae lizard diversification in Sumatra, rejecting the "regional endemism paradigm". Contemporary distribution of endemic species and their genetic relationships may potentially provide biologicalevidence for determining more precise elevational lower limits of montane forests during the Pleistocene epoch. Our data suggests montane forests did not retreat more than 700-750 m during glacial maxima because lower retreating forests would have become interconnected, allowing for widespread dispersal, exchange of gene flow and sympatric distributions contemporarily. To the contrary, our divergence estimates show that cloud forest dragons have been isolated for millions of years, suggesting there may have been a continuous disconnect between some areas, predating the Pleistocene. There may also be other ecological and evolutionary factors that impacted Draconinae distributions, such as competition, making this an excellent system for testing questions regarding montane biogeography. Additionally, we provide the first phylogeny for a wide range of Sundaland agamid species and identify some biogeographic pressures that may have triggered montane Draconinae diversification in Sumatra.
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Affiliation(s)
- Kyle J Shaney
- Institute of Ecology, National Autonomous University of Mexico, Mexico City, Mexico; University of Texas at Arlington and Amphibian and Reptile Diversity Research Center, Department of Biology, 501 S. Nedderman Road, Arlington, TX 76010, USA.
| | - Jose Maldonado
- University of Texas at Arlington and Amphibian and Reptile Diversity Research Center, Department of Biology, 501 S. Nedderman Road, Arlington, TX 76010, USA
| | - Utpal Smart
- University of Texas at Arlington and Amphibian and Reptile Diversity Research Center, Department of Biology, 501 S. Nedderman Road, Arlington, TX 76010, USA; Center for Human Identification, University of North Texas Health Science Center, 3500 Camp Bowie Blvd., Fort Worth, Texas 76107, USA
| | - Panupong Thammachoti
- University of Texas at Arlington and Amphibian and Reptile Diversity Research Center, Department of Biology, 501 S. Nedderman Road, Arlington, TX 76010, USA; Department of Biology, Faculty of Science, Chulalongkorn University, Payathai Road, Pathumwan District, Bangkok 10330, Thailand
| | - Matthew Fujita
- University of Texas at Arlington and Amphibian and Reptile Diversity Research Center, Department of Biology, 501 S. Nedderman Road, Arlington, TX 76010, USA
| | - Amir Hamidy
- Laboratory of Herpetology, Museum Zoologicum Bogoriense, Research Center for Biology, Indonesian Institute of Sciences-LIPI, Jl. Raya Jakarta Bogor km 46, Cibinong, West Java 16911, Indonesia
| | - Nia Kurniawan
- Department of Biology, Universitas Brawijaya, Jl. Veteran, Malang, East Java 65145, Indonesia
| | - Michael B Harvey
- Department of Biological Sciences, Broward College, 3501 S.W. Davie Road, Davie, FL 33314, USA
| | - Eric N Smith
- University of Texas at Arlington and Amphibian and Reptile Diversity Research Center, Department of Biology, 501 S. Nedderman Road, Arlington, TX 76010, USA
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25
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Harvey MB, Larson TR, Jacobs JL, Shaney K, Streicher JW, Hamidy A, Kurniawan N, Smith EN. Phoxophrys After 60 Years: Review of Morphology, Phylogeny, Status of Pelturagonia, and a New Species from Southeastern Kalimantan. HERPETOLOGICAL MONOGRAPHS 2020. [DOI: 10.1655/herpmonographs-d-19-00006.1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Affiliation(s)
- Michael B. Harvey
- Department of Biological Sciences, Broward College, 3501 Southwest Davie Road, Davie, FL 33314, USA
| | - Thorton R. Larson
- The Amphibian and Reptile Diversity Research Center and Department of Biology, University of Texas at Arlington, 501 South Nedderman Drive, Arlington, TX 76010, USA
| | - Justin L. Jacobs
- The Amphibian and Reptile Diversity Research Center and Department of Biology, University of Texas at Arlington, 501 South Nedderman Drive, Arlington, TX 76010, USA
| | - Kyle Shaney
- The Amphibian and Reptile Diversity Research Center and Department of Biology, University of Texas at Arlington, 501 South Nedderman Drive, Arlington, TX 76010, USA
| | | | - Amir Hamidy
- Laboratory of Herpetology, Museum Zoologicum Bogoriense, Research Center for Biology, Indonesian Institute of Sciences–LIPI, Jl Raya Jakarta Bogor km 46, Cibinong, West Java, 16911, Indonesia
| | - Nia Kurniawan
- Department of Biology, Universitas Brawijaya, Jl Veteran, Malang, East Java, 65145, Indonesia
| | - Eric N. Smith
- The Amphibian and Reptile Diversity Research Center and Department of Biology, University of Texas at Arlington, 501 South Nedderman Drive, Arlington, TX 76010, USA
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26
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Karin BR, Gamble T, Jackman TR. Optimizing Phylogenomics with Rapidly Evolving Long Exons: Comparison with Anchored Hybrid Enrichment and Ultraconserved Elements. Mol Biol Evol 2020; 37:904-922. [PMID: 31710677 PMCID: PMC7038749 DOI: 10.1093/molbev/msz263] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Marker selection has emerged as an important component of phylogenomic study design due to rising concerns of the effects of gene tree estimation error, model misspecification, and data-type differences. Researchers must balance various trade-offs associated with locus length and evolutionary rate among other factors. The most commonly used reduced representation data sets for phylogenomics are ultraconserved elements (UCEs) and Anchored Hybrid Enrichment (AHE). Here, we introduce Rapidly Evolving Long Exon Capture (RELEC), a new set of loci that targets single exons that are both rapidly evolving (evolutionary rate faster than RAG1) and relatively long in length (>1,500 bp), while at the same time avoiding paralogy issues across amniotes. We compare the RELEC data set to UCEs and AHE in squamate reptiles by aligning and analyzing orthologous sequences from 17 squamate genomes, composed of 10 snakes and 7 lizards. The RELEC data set (179 loci) outperforms AHE and UCEs by maximizing per-locus genetic variation while maintaining presence and orthology across a range of evolutionary scales. RELEC markers show higher phylogenetic informativeness than UCE and AHE loci, and RELEC gene trees show greater similarity to the species tree than AHE or UCE gene trees. Furthermore, with fewer loci, RELEC remains computationally tractable for full Bayesian coalescent species tree analyses. We contrast RELEC to and discuss important aspects of comparable methods, and demonstrate how RELEC may be the most effective set of loci for resolving difficult nodes and rapid radiations. We provide several resources for capturing or extracting RELEC loci from other amniote groups.
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Affiliation(s)
- Benjamin R Karin
- Department of Biology, Villanova University, Villanova, PA
- Museum of Vertebrate Zoology and Department of Integrative Biology, University of California, Berkeley, CA
| | - Tony Gamble
- Department of Biological Sciences, Marquette University, Milwaukee, WI
- Milwaukee Public Museum, Milwaukee, WI
- Bell Museum of Natural History, University of Minnesota, St. Paul, MN
| | - Todd R Jackman
- Department of Biology, Villanova University, Villanova, PA
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27
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Rüber L, Tan HH, Britz R. Snakehead (Teleostei: Channidae) diversity and the Eastern Himalaya biodiversity hotspot. J ZOOL SYST EVOL RES 2019. [DOI: 10.1111/jzs.12324] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Affiliation(s)
- Lukas Rüber
- Naturhistorisches Museum Bern Bern Switzerland
- Aquatic Ecology and Evolution, Institute of Ecology and Evolution University of Bern Bern Switzerland
| | - Heok Hui Tan
- Lee Kong Chian Natural History Museum National University of Singapore Singapore Singapore
| | - Ralf Britz
- Department of Life Sciences The Natural History Museum London UK
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28
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Gustafson GT, Alexander A, Sproul JS, Pflug JM, Maddison DR, Short AEZ. Ultraconserved element (UCE) probe set design: Base genome and initial design parameters critical for optimization. Ecol Evol 2019; 9:6933-6948. [PMID: 31312430 PMCID: PMC6617817 DOI: 10.1002/ece3.5260] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2019] [Revised: 04/26/2019] [Accepted: 04/28/2019] [Indexed: 01/10/2023] Open
Abstract
Targeted capture and enrichment approaches have proven effective for phylogenetic study. Ultraconserved elements (UCEs) in particular have exhibited great utility for phylogenomic analyses, with the software package phyluce being among the most utilized pipelines for UCE phylogenomics, including probe design. Despite the success of UCEs, it is becoming increasing apparent that diverse lineages require probe sets tailored to focal taxa in order to improve locus recovery. However, factors affecting probe design and methods for optimizing probe sets to focal taxa remain underexplored. Here, we use newly available beetle (Coleoptera) genomic resources to investigate factors affecting UCE probe set design using phyluce. In particular, we explore the effects of stringency during initial design steps, as well as base genome choice on resulting probe sets and locus recovery. We found that both base genome choice and initial bait design stringency parameters greatly alter the number of resultant probes included in final probe sets and strongly affect the number of loci detected and recovered during in silico testing of these probe sets. In addition, we identify attributes of base genomes that correlated with high performance in probe design. Ultimately, we provide a recommended workflow for using phyluce to design an optimized UCE probe set that will work across a targeted lineage, and use our findings to develop a new, open-source UCE probe set for beetles of the suborder Adephaga.
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Affiliation(s)
- Grey T. Gustafson
- Department of Ecology and Evolutionary BiologyUniversity of KansasLawrenceKansas
- Biodiversity InstituteUniversity of KansasLawrenceKansas
| | - Alana Alexander
- Biodiversity InstituteUniversity of KansasLawrenceKansas
- Department of Anatomy, School of Biomedical SciencesUniversity of OtagoDunedinNew Zealand
| | - John S. Sproul
- Department of Integrative BiologyOregon State UniversityCorvallisOregon
- Department of BiologyUniversity of RochesterRochesterNew York
| | - James M. Pflug
- Department of Integrative BiologyOregon State UniversityCorvallisOregon
| | - David R. Maddison
- Department of Integrative BiologyOregon State UniversityCorvallisOregon
| | - Andrew E. Z. Short
- Department of Ecology and Evolutionary BiologyUniversity of KansasLawrenceKansas
- Biodiversity InstituteUniversity of KansasLawrenceKansas
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29
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Garg S, Biju SD. New microhylid frog genus from Peninsular India with Southeast Asian affinity suggests multiple Cenozoic biotic exchanges between India and Eurasia. Sci Rep 2019; 9:1906. [PMID: 30760773 PMCID: PMC6374391 DOI: 10.1038/s41598-018-38133-x] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2017] [Accepted: 12/20/2018] [Indexed: 11/08/2022] Open
Abstract
Anurans in Peninsular India exhibit close biogeographical links with Gondwana as well as Laurasia, often explainable by the geological history of the Indian subcontinent; its breakup from Gondwanan landmasses followed by long isolation that resulted in diversification of endemic lineages, and subsequent land connections with Asia that enabled dispersal of widespread groups. Although widely distributed, the frog subfamily Microhylinae mostly comprises of geographically restricted genera found either in Southeast and East Asia or Peninsular India and Sri Lanka. Here we report a previously unknown microhylid from the Western Ghats in Peninsular India with closest relatives found over 2,000 km away in Southeast Asia. Based on integrated evidence from mitochondrial and nuclear DNA, adult and tadpole morphology, hand musculature, male advertisement call, and geographical distance, we recognize this enigmatic frog as a distinct new species and genus endemic to the Western Ghats. The discovery of Mysticellus franki gen. et sp. nov. and its close evolutionary relationship with the Southeast Asian genus Micryletta also provide insights on the biogeography of Microhylinae. Genus-level divergences within the subfamily suggest multiple Cenozoic biotic exchange events between India and Eurasia, particularly through postulated Eocene land bridges via Southeast Asia prior to accretion of the two landmasses.
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Affiliation(s)
- Sonali Garg
- Systematics Lab, Department of Environmental Studies, University of Delhi, Delhi, 110 007, India
| | - S D Biju
- Systematics Lab, Department of Environmental Studies, University of Delhi, Delhi, 110 007, India.
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30
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Wang K, Che J, Lin S, Deepak V, Aniruddha DR, Jiang K, Jin J, Chen H, Siler CD. Multilocus phylogeny and revised classification for mountain dragons of the genusJapalura s.l. (Reptilia: Agamidae: Draconinae) from Asia. Zool J Linn Soc 2018. [DOI: 10.1093/zoolinnean/zly034] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Kai Wang
- Sam Noble Oklahoma Museum of Natural History and Department of Biology, University of Oklahoma, Norman, OK, USA
- State Key Laboratory of Genetics and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Jing Che
- State Key Laboratory of Genetics and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China
- Ashoka Trust for Research in Ecology and Evolution (ATREE), Royal Enclave, Sriramapura, Jakkur, Bangalore, Karnataka, India
| | - Simin Lin
- Department of Life Science, National Taiwan Normal University, Taipei, Taiwan
| | - V Deepak
- Center for Ecological Sciences, Indian Institute of Science, Bangalore, Karnataka, India
- Department of Life Sciences, The Natural History Museum, London, UK
| | - Datta-Roy Aniruddha
- Center for Ecological Sciences, Indian Institute of Science, Bangalore, Karnataka, India
- Ashoka Trust for Research in Ecology and Evolution (ATREE), Royal Enclave, Sriramapura, Jakkur, Bangalore, Karnataka, India
| | - Ke Jiang
- State Key Laboratory of Genetics and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China
- Southeast Asia Biodiversity Institute, Chinese Academy of Sciences, Yezin, Nay Pyi Taw, Myanmar
| | - Jieqiong Jin
- State Key Laboratory of Genetics and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China
- Southeast Asia Biodiversity Institute, Chinese Academy of Sciences, Yezin, Nay Pyi Taw, Myanmar
| | - Hongman Chen
- State Key Laboratory of Genetics and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China
- Southeast Asia Biodiversity Institute, Chinese Academy of Sciences, Yezin, Nay Pyi Taw, Myanmar
| | - Cameron D Siler
- Sam Noble Oklahoma Museum of Natural History and Department of Biology, University of Oklahoma, Norman, OK, USA
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31
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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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32
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Wang K, Jiang K, Deepak V, Abhijit D, Hou M, Che J, Siler CD. On the Occurrences ofJapalura kumaonensisandJapalura tricarinata(Reptilia: Sauria: Draconinae) in China. HERPETOLOGICA 2018. [DOI: 10.1655/herpetologica-d-17-00018.1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Affiliation(s)
- Kai Wang
- Sam Noble Oklahoma Museum of Natural History and Department of Biology, University of Oklahoma, Norman, OK 73072, USA
| | - Ke Jiang
- Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China
- Southeast Asia Biodiversity Research Institute, Chinese Academy of Sciences, Menglun, Yunnan 666303, China
| | - V. Deepak
- Center for Ecological Sciences, Indian Institute of Science, Bangalore, Karnataka 560012, India
| | - Das Abhijit
- Wildlife Institute of India, Chandrabani, Dehradun 248002, India
| | - Mian Hou
- Academy of Continuing Education, Sichuan Normal University, Chengdu, Sichuan 610068, China
| | - Jing Che
- Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China
- Southeast Asia Biodiversity Research Institute, Chinese Academy of Sciences, Menglun, Yunnan 666303, China
| | - Cameron D. Siler
- Sam Noble Oklahoma Museum of Natural History and Department of Biology, University of Oklahoma, Norman, OK 73072, USA
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33
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Deepak V, Karanth P. Aridification driven diversification of fan-throated lizards from the Indian subcontinent. Mol Phylogenet Evol 2017; 120:53-62. [PMID: 29197684 DOI: 10.1016/j.ympev.2017.11.016] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2017] [Revised: 11/14/2017] [Accepted: 11/27/2017] [Indexed: 10/18/2022]
Abstract
The establishment of monsoon climate and the consequent aridification has been one of the most important climate change episodes in the Indian subcontinent. However, little is known about how these events might have shaped the diversification patterns among the widely distributed taxa. Fan-throated lizards (FTL) (Genus: Sitana, Sarada) are widespread, diurnal and restricted to the semi-arid zones of the Indian subcontinent. We sampled FTL in 107 localities across its range. We used molecular species delimitation method and delineated 15 species including six putative species. Thirteen of them were distinguishable based on morphology but two sister species were indistinguishable and have minor overlaps in distribution. Five fossils were used to calibrate and date the phylogeny. Diversification of fan-throated lizards lineage started ~18 mya and higher lineage diversification was observed after 11 my. The initial diversification corresponds to the time when monsoon climate was established and the latter was a period of intensification of monsoon and initiation of aridification. Thirteen out of the fifteen FTL species delimited are from Peninsular India; this is probably due to the landscape heterogeneity in this region. The species poor sister genus Otocryptis is paraphyletic and probably represents relict lineages which are now confined to forested areas. Thus, the seasonality led changes in habitat, from forests to open habitats appear to have driven diversification of fan-throated lizards.
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Affiliation(s)
- V Deepak
- Centre for Ecological Sciences, Indian Institute of Science, Bangalore 560012, India; Department of Life Sciences, The Natural History Museum, London SW7 5BD, United Kingdom.
| | - Praveen Karanth
- Centre for Ecological Sciences, Indian Institute of Science, Bangalore 560012, India
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34
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Panzera A, Leaché AD, D'Elía G, Victoriano PF. Phylogenomic analysis of the Chilean clade of Liolaemus lizards (Squamata: Liolaemidae) based on sequence capture data. PeerJ 2017; 5:e3941. [PMID: 29085750 PMCID: PMC5660876 DOI: 10.7717/peerj.3941] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2017] [Accepted: 09/27/2017] [Indexed: 01/19/2023] Open
Abstract
The genus Liolaemus is one of the most ecologically diverse and species-rich genera of lizards worldwide. It currently includes more than 250 recognized species, which have been subject to many ecological and evolutionary studies. Nevertheless, Liolaemus lizards have a complex taxonomic history, mainly due to the incongruence between morphological and genetic data, incomplete taxon sampling, incomplete lineage sorting and hybridization. In addition, as many species have restricted and remote distributions, this has hampered their examination and inclusion in molecular systematic studies. The aims of this study are to infer a robust phylogeny for a subsample of lizards representing the Chilean clade (subgenus Liolaemus sensu stricto), and to test the monophyly of several of the major species groups. We use a phylogenomic approach, targeting 541 ultra-conserved elements (UCEs) and 44 protein-coding genes for 16 taxa. We conduct a comparison of phylogenetic analyses using maximum-likelihood and several species tree inference methods. The UCEs provide stronger support for phylogenetic relationships compared to the protein-coding genes; however, the UCEs outnumber the protein-coding genes by 10-fold. On average, the protein-coding genes contain over twice the number of informative sites. Based on our phylogenomic analyses, all the groups sampled are polyphyletic. Liolaemus tenuis tenuis is difficult to place in the phylogeny, because only a few loci (nine) were recovered for this species. Topologies or support values did not change dramatically upon exclusion of L. t. tenuis from analyses, suggesting that missing data did not had a significant impact on phylogenetic inference in this data set. The phylogenomic analyses provide strong support for sister group relationships between L. fuscus, L. monticola, L. nigroviridis and L. nitidus, and L. platei and L. velosoi. Despite our limited taxon sampling, we have provided a reliable starting hypothesis for the relationships among many major groups of the Chilean clade of Liolaemus that will help future work aimed at resolving the Liolaemus phylogeny.
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Affiliation(s)
- Alejandra Panzera
- Departamento de Zoología, Facultad de Ciencias Naturales y Oceanográficas, Universidad de Concepción, Concepción, Chile.,Programa de Doctorado en Sistemática y Biodiversidad, Universidad de Concepción, Concepción, Chile
| | - Adam D Leaché
- Department of Biology & Burke Museum of Natural History and Culture, University of Washington, Seattle, WA, United States of America
| | - Guillermo D'Elía
- Instituto de Ciencias Ambientales y Evolutivas, Universidad Austral de Chile, Valdivia, Chile
| | - Pedro F Victoriano
- Departamento de Zoología, Facultad de Ciencias Naturales y Oceanográficas, Universidad de Concepción, Concepción, Chile
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A comprehensive phylogeny of the genus Kurixalus (Rhacophoridae, Anura) sheds light on the geographical range evolution of frilled swamp treefrogs. Mol Phylogenet Evol 2017; 121:224-232. [PMID: 28987637 DOI: 10.1016/j.ympev.2017.09.019] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2017] [Revised: 08/18/2017] [Accepted: 09/25/2017] [Indexed: 11/23/2022]
Abstract
Currently, the genus Kurixalus comprises 14 species distributed in Southern, Southeast and East Asia. Because of their relatively low dispersal capability and intolerance of seawater, this group is ideal for the study of terrestrial range evolution, especially that portion of its range that extends into the island archipelagos of Southern Asia. We assembled a large dataset of mitochondrial and nuclear genes, and estimated phylogeny by maximum likelihood and Bayesian methods, and we explored the history of each species via divergence-time estimation based on fossil-calibrations. A variety of ancestral-area reconstruction strategies were employed to estimate past changes of the species' geographical range, and to evaluate the impact of different abiotic barriers on range evolution. We found that frilled swamp treefrogs probably originated in Taiwan or South Vietnam in the Oligocene. Alternatively, the lineage leading to Kurixalus appendiculatus strongly supports a hypothesis of terrestrial connection between the Indian and Asian continents in the Oligocene. The outcome of both our divergence-time estimates and ancestral-area reconstruction suggests that the divergence between species from Indochina and Taiwan can probably be attributed to the opening of the South China Sea, approximately 33 million years ago. We could not find evidence for dispersal between mainland China and Taiwan Island. Formation of both Mekong and Red River valleys did not have any impact on Kurixalus species diversification. However, coincidence in timing of climate change and availability of plausible dispersal routes from the Oligocene to the middle Miocene, plausibly implied that Kurixalus diversification in Asia resulted from contemporaneous, climate-induced environmental upheaval (Late Oligocene Warming at 29 Ma; Mi-1 glaciation since 24.4-21.5 Ma; Mid-Miocene Climatic Optimum at 14 Ma), which alternatively opened and closed dispersal routes.
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Cyriac VP, Kodandaramaiah U. Paleoclimate determines diversification patterns in the fossorial snake family Uropeltidae Cuvier, 1829. Mol Phylogenet Evol 2017; 116:97-107. [PMID: 28867076 DOI: 10.1016/j.ympev.2017.08.017] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2017] [Revised: 08/17/2017] [Accepted: 08/24/2017] [Indexed: 11/15/2022]
Abstract
Understanding how and why diversification rates vary across evolutionary time is central to understanding how biodiversity is generated and maintained. Recent mathematical models that allow estimation of diversification rates across time from reconstructed phylogenies have enabled us to make inferences on how biodiversity copes with environmental change. Here, we explore patterns of temporal diversification in Uropeltidae, a diverse fossorial snake family. We generate a time-calibrated phylogenetic hypothesis for Uropeltidae and show a significant correlation between diversification rate and paleotemperature during the Cenozoic. We show that the temporal diversification pattern of this group is punctuated by one rate shift event with a decrease in diversification and turnover rate between ca. 11Ma to present, but there is no strong support for mass extinction events. The analysis indicates higher turnover during periods of drastic climatic fluctuations and reduced diversification rates associated with contraction and fragmentation of forest habitats during the late Miocene. Our study highlights the influence of environmental fluctuations on diversification rates in fossorial taxa such as uropeltids, and raises conservation concerns related to present rate of climate change.
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Affiliation(s)
- Vivek Philip Cyriac
- IISER-TVM Centre for Research and Education in Ecology and Evolution (ICREEE) and School of Biology, Indian Institute of Science Education and Research Thiruvananthapuram, Maruthamala P.O., Vithura, Thiruvananthapuram, Kerala 695551, India.
| | - Ullasa Kodandaramaiah
- IISER-TVM Centre for Research and Education in Ecology and Evolution (ICREEE) and School of Biology, Indian Institute of Science Education and Research Thiruvananthapuram, Maruthamala P.O., Vithura, Thiruvananthapuram, Kerala 695551, India
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37
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Agarwal I, Biswas S, Bauer AM, Greenbaum E, Jackman TR, Silva AD, Batuwita S. Cryptic species, taxonomic inflation, or a bit of both? New species phenomenon in Sri Lanka as suggested by a phylogeny of dwarf geckos (Reptilia, Squamata, Gekkonidae, Cnemaspis). SYST BIODIVERS 2017. [DOI: 10.1080/14772000.2017.1282553] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Affiliation(s)
- Ishan Agarwal
- Department of Biology, Villanova University, 800 Lancaster Avenue, Villanova, Pennsylvania 19085, USA
| | - Sayantan Biswas
- Department of Biology, Villanova University, 800 Lancaster Avenue, Villanova, Pennsylvania 19085, USA
| | - Aaron M. Bauer
- Department of Biology, Villanova University, 800 Lancaster Avenue, Villanova, Pennsylvania 19085, USA
| | - Eli Greenbaum
- Department of Biology, Villanova University, 800 Lancaster Avenue, Villanova, Pennsylvania 19085, USA
- Department of Biological Sciences, University of Texas at El Paso, 500 West University Avenue, El Paso, Texas 79968, USA
| | - Todd R. Jackman
- Department of Biology, Villanova University, 800 Lancaster Avenue, Villanova, Pennsylvania 19085, USA
| | | | - Sudesh Batuwita
- Wildlife Heritage Trust of Sri Lanka, 95 Cotta Road, Colombo, Sri Lanka
- College of Biology and the Environment, Nanjing Forestry University, Nanjing, China
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38
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Alexander AM, Su Y, Oliveros CH, Olson KV, Travers SL, Brown RM. Genomic data reveals potential for hybridization, introgression, and incomplete lineage sorting to confound phylogenetic relationships in an adaptive radiation of narrow‐mouth frogs. Evolution 2016; 71:475-488. [DOI: 10.1111/evo.13133] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2015] [Accepted: 11/07/2016] [Indexed: 12/30/2022]
Affiliation(s)
| | - Yong‐Chao Su
- Biodiversity Institute University of Kansas Lawrence Kansas 66045
- Department of Biological Sciences National University of Singapore 117543 Singapore
| | - Carl H. Oliveros
- Biodiversity Institute University of Kansas Lawrence Kansas 66045
- Department of Biological Sciences Louisiana State University Baton Rouge Louisiana 70803
| | - Karen V. Olson
- Biodiversity Institute University of Kansas Lawrence Kansas 66045
| | - Scott L. Travers
- Biodiversity Institute University of Kansas Lawrence Kansas 66045
| | - Rafe M. Brown
- Biodiversity Institute University of Kansas Lawrence Kansas 66045
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Welton LJ, Siler CD, Grismer LL, Diesmos AC, Sites JW, Brown RM. Archipelago-wide survey of Philippine forest dragons (Agamidae:Gonocephalus): multilocus phylogeny uncovers unprecedented levels of genetic diversity in a biodiversity hotspot. Biol J Linn Soc Lond 2016. [DOI: 10.1111/bij.12878] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Affiliation(s)
- Luke J. Welton
- Department of Biology; 4102 LSB, Brigham Young University; Provo UT 84602 USA
- Biodiversity Institute and Department of Ecology and Evolutionary Biology; 1345 Jayhawk Blvd., University of Kansas; Lawrence KS 66045-7561 USA
| | - Cameron D. Siler
- Sam Noble Oklahoma Museum of Natural History and Department of Biology; 2401 Chautauqua Ave., University of Oklahoma; Norman OK 73072-7029 USA
| | - L. L. Grismer
- Department of Biology; 4500 Riverwalk Parkway, La Sierra University; Riverside CA 92515-8247 USA
| | - Arvin C. Diesmos
- Herpetology Section; Zoology Division; National Museum of the Philippines; Rizal Park Padre Burgos Avenue Manila Philippines
| | - Jack W. Sites
- Department of Biology; 4102 LSB, Brigham Young University; Provo UT 84602 USA
| | - Rafe M. Brown
- Biodiversity Institute and Department of Ecology and Evolutionary Biology; 1345 Jayhawk Blvd., University of Kansas; Lawrence KS 66045-7561 USA
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