1
|
Bernstein JM, Voris HK, Stuart BL, Karns DR, McGuire JA, Iskandar DT, Riyanto A, Calderón-Acevedo CA, Brown RM, Gehara M, Soto-Centeno JA, Ruane S. Integrative methods reveal multiple drivers of diversification in rice paddy snakes. Sci Rep 2024; 14:4727. [PMID: 38472264 DOI: 10.1038/s41598-024-54744-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Accepted: 02/15/2024] [Indexed: 03/14/2024] Open
Abstract
Divergence dating analyses in systematics provide a framework to develop and test biogeographic hypotheses regarding speciation. However, as molecular datasets grow from multilocus to genomic, sample sizes decrease due to computational burdens, and the testing of fine-scale biogeographic hypotheses becomes difficult. In this study, we use coalescent demographic models to investigate the diversification of poorly known rice paddy snakes from Southeast Asia (Homalopsidae: Hypsiscopus), which have conflicting dates of origin based on previous studies. We use coalescent modeling to test the hypothesis that Hypsiscopus diversified 2.5 mya during the Khorat Plateau uplift in Thailand. Additionally, we use ecological niche analyses to identify potential differences in the niche space of the two most widely distributed species in the past and present. Our results suggest Hypsiscopus diversified ~ 2.4 mya, supporting that the Khorat Plateau may have initiated the diversification of rice paddy snakes. We also find significant niche differentiation and shifts between species of Hypsiscopus, indicating that environmental differences may have sustained differentiation of this genus after the Khorat Plateau uplift. Our study expands on the diversification history of snakes in Southeast Asia, and highlights how results from smaller multilocus datasets can be useful in developing and testing biogeographic hypotheses alongside genomic datasets.
Collapse
Affiliation(s)
- Justin M Bernstein
- Center for Genomics, University of Kansas, Dyche Hall, 1345 Jayhawk Blvd, Lawrence, KS, 66045, USA.
| | - Harold K Voris
- Life Sciences Section, Negaunee Integrative Research Center, Field Museum, 1400 S. Lake Shore Drive, Chicago, IL, 60605, USA
| | - Bryan L Stuart
- Section of Research and Collections, North Carolina Museum of Natural Sciences, Raleigh, NC, 27601, USA
| | - Daryl R Karns
- Biology Department, Hanover College, Hanover, IN, 47243, USA
| | - Jimmy A McGuire
- Museum of Vertebrate Zoology and Department of Integrative Biology, University of California, Berkeley, CA, 94720, USA
| | - Djoko T Iskandar
- School of Life Sciences and Technology, Institut Teknologi Bandung, Bandung, Indonesia
| | - Awal Riyanto
- Museum Zoologicum Bogoriense, Research Center for Biology, National Research and Innovation Agency of Indonesia (BRIN), Cibinong, 16911, Indonesia
| | - Camilo A Calderón-Acevedo
- State University of New York: College of Environmental Science and Forestry, Syracuse, NY, 13210, USA
| | - Rafe M Brown
- Department of Ecology and Evolutionary Biology and Biodiversity Institute, University of Kansas, Lawrence, KS, 66045, USA
| | - Marcelo Gehara
- Department of Earth and Environmental Science, Rutgers University-Newark, Newark, NJ, 07102, USA
| | - J Angel Soto-Centeno
- Department of Earth and Environmental Science, Rutgers University-Newark, Newark, NJ, 07102, USA
- Department of Mammalogy, American Museum of Natural History, New York, NY, 10024, USA
| | - Sara Ruane
- Life Sciences Section, Negaunee Integrative Research Center, Field Museum, 1400 S. Lake Shore Drive, Chicago, IL, 60605, USA
| |
Collapse
|
2
|
Huang JF, Li SQ, Xu R, Peng YQ. East‒West genetic differentiation across the Indo-Burma hotspot: evidence from two closely related dioecious figs. BMC PLANT BIOLOGY 2023; 23:321. [PMID: 37322436 DOI: 10.1186/s12870-023-04324-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Accepted: 05/30/2023] [Indexed: 06/17/2023]
Abstract
BACKGROUND Understanding biodiversity patterns and their underlying mechanisms is of interest to ecologists, biogeographers and conservationists and is critically important for conservation efforts. The Indo-Burma hotspot features high species diversity and endemism, yet it also faces significant threats and biodiversity losses; however, few studies have explored the genetic structure and underlying mechanisms of Indo-Burmese species. Here, we conducted a comparative phylogeographic analysis of two closely related dioecious Ficus species, F. hispida and F. heterostyla, based on wide and intensive population sampling across Indo-Burma ranges, using chloroplast (psbA-trnH, trnS-trnG) and nuclear microsatellite (nSSR) markers, as well as ecological niche modeling. RESULTS The results indicated large numbers of population-specific cpDNA haplotypes and nSSR alleles in the two species. F. hispida showed slightly higher chloroplast diversity but lower nuclear diversity than F. heterostyla. Low-altitude mountainous areas of northern Indo-Burma were revealed to have high genetic diversity and high habitat suitability, suggesting potential climate refugia and conservation priority areas. Strong phylogeographic structure and a marked east‒west differentiation pattern were observed in both species, due to the interactions between biotic and abiotic factors. Interspecific dissimilarities at fine-scale genetic structure and asynchronized historical dynamics of east‒west differentiation between species were also detected, which were attributed to different species-specific traits. CONCLUSIONS We confirm hypothesized predictions that interactions between biotic and abiotic factors largely determine the patterns of genetic diversity and phylogeographic structure of Indo-Burmese plants. The east‒west genetic differentiation pattern observed in two targeted figs can be generalized to some other Indo-Burmese plants. The results and findings of this work will contribute to the conservation of Indo-Burmese biodiversity and facilitate targeted conservation efforts for different species.
Collapse
Affiliation(s)
- Jian-Feng Huang
- CAS Key Laboratory of Tropical Forest Ecoloy, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla, 666303, China.
| | - Shu-Qiong Li
- CAS Key Laboratory of Tropical Forest Ecoloy, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla, 666303, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Rui Xu
- Yunnan Academy of Biodiversity/College of Biodiversity and Conservation, Southwest Forestry University, Kunming, China
| | - Yan-Qiong Peng
- CAS Key Laboratory of Tropical Forest Ecoloy, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla, 666303, China.
| |
Collapse
|
3
|
Carvalho PS, Santana DJ, Zaher H, Myers EA. Effects of Environmental Variation in Structuring Population Genetic Variation in the False-Water Cobras (Xenodontinae: Hydrodynastes). Evol Biol 2023. [DOI: 10.1007/s11692-023-09601-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/05/2023]
|
4
|
Arifin U, Smart U, Husemann M, Hertwig ST, Smith EN, Iskandar DT, Haas A. Phylogeographic inference of Sumatran ranids bearing gastromyzophorous tadpoles with regard to the Pleistocene drainage systems of Sundaland. Sci Rep 2022; 12:12013. [PMID: 35853951 PMCID: PMC9296532 DOI: 10.1038/s41598-022-14722-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Accepted: 06/10/2022] [Indexed: 11/18/2022] Open
Abstract
Rivers are known to act as biogeographic barriers in several strictly terrestrial taxa, while possibly serving as conduits of dispersal for freshwater-tolerant or -dependent species. However, the influence of river systems on genetic diversity depends on taxa-specific life history traits as well as other geographic factors. In amphibians, several studies have demonstrated that river systems have only minor influence on their divergence. Here, we assess the role of the paleodrainage systems of the Sunda region (with a focus on the island of Sumatra) in shaping the evolutionary history of two genera of frogs (Sumaterana and Wijayarana) whose tadpoles are highly dependent on cascading stream habitats. Our phylogenetic results show no clear association between the genetic diversification patterns of both anurans genera and the existence of paleodrainage systems. Time-calibrated phylogenies and biogeographical models suggest that these frogs colonized Sumatra and diversified on the island before the occurrence of the Pleistocene drainage systems. Both genera demonstrate phylogenetic structuring along a north–south geographic axis, the temporal dynamics of which coincide with the geological chronology of proto Sumatran and -Javan volcanic islands. Our results also highlight the chronic underestimation of Sumatran biodiversity and call for more intense sampling efforts on the island.
Collapse
Affiliation(s)
- Umilaela Arifin
- Centre for Taxonomy and Morphology, Leibniz Institute for the Analysis of Biodiversity Change, Martin-Luther-King-Platz 3, 20146, Hamburg, Germany. .,Universität Hamburg, Edmund-Siemers-Allee 1, 20148, Hamburg, Germany.
| | - Utpal Smart
- Department of Biology, Texas State University, 601 University Drive, San Marcos, TX, 78666, USA.,Amphibian & Reptile Diversity Research Center Department of Biology, University of Texas at Arlington, Arlington, TX, 76019-0498, USA
| | - Martin Husemann
- Centre for Taxonomy and Morphology, Leibniz Institute for the Analysis of Biodiversity Change, Martin-Luther-King-Platz 3, 20146, Hamburg, Germany.,Universität Hamburg, Edmund-Siemers-Allee 1, 20148, Hamburg, Germany
| | - Stefan T Hertwig
- Naturhistorisches Museum der Burgergemeinde Bern, Bernastrasse 15, 3005, Bern, Switzerland.,Institute of Ecology and Evolution, University of Bern, Baltzerstrasse 6, 3012, Bern, Switzerland
| | - Eric N Smith
- Amphibian & Reptile Diversity Research Center Department of Biology, University of Texas at Arlington, Arlington, TX, 76019-0498, USA
| | - Djoko T Iskandar
- Basic Science Committee, Indonesian Academy of Sciences, Jalan Medan Merdeka Selatan 11, Jakarta, 10110, Indonesia
| | - Alexander Haas
- Centre for Taxonomy and Morphology, Leibniz Institute for the Analysis of Biodiversity Change, Martin-Luther-King-Platz 3, 20146, Hamburg, Germany.,Universität Hamburg, Edmund-Siemers-Allee 1, 20148, Hamburg, Germany
| |
Collapse
|
5
|
Platt SG, Thongsavath O, Leslie SC, Brakels P, Dawson JE, Ihlow F, Rainwater TR. On the Occurrence of the Khorat Snail-Eating Turtle (Malayemys khoratensis) in Lao People's Democratic Republic with Notes on Traditional Ecological Knowledge and Exploitation. CHELONIAN CONSERVATION AND BIOLOGY 2022. [DOI: 10.2744/ccb-1525.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Steven G. Platt
- Wildlife Conservation Society–Lao Program, PO Box 6712, Vientiane, Lao PDR [; ; ]
| | - Oudomxay Thongsavath
- Wildlife Conservation Society–Lao Program, PO Box 6712, Vientiane, Lao PDR [; ; ]
| | - Samuel C. Leslie
- Wildlife Conservation Society–Lao Program, PO Box 6712, Vientiane, Lao PDR [; ; ]
| | - Peter Brakels
- IUCN, 391/24 Bourichane Road, Ban Naxay, Vientiane, Lao PDR []
| | - Jeffery E. Dawson
- Museum of Zoology, Senckenberg Dresden, B. Meyer Building, Königsbrücker Landstraße 159, 01109 Dresden, Germany [; ]
| | - Flora Ihlow
- Museum of Zoology, Senckenberg Dresden, B. Meyer Building, Königsbrücker Landstraße 159, 01109 Dresden, Germany [; ]
| | - Thomas R. Rainwater
- Tom Yawkey Wildlife Center and Belle W. Baruch Institute of Coastal Ecology and Forest Science, Clemson University, PO Box 596, Georgetown, South Carolina 29442 USA []
| |
Collapse
|
6
|
Homogenized Phylogeographic Structure across the Indo-Burma Ranges of a Large Monoecious Fig, Ficus altissima Blume. DIVERSITY 2021. [DOI: 10.3390/d13120654] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
As well as bountiful natural resources, the Indo-Burma biodiversity hotspot features high rates of habitat destruction and fragmentation due to increasing human activity; however, most of the Indo-Burma species are poorly studied. The exploration of plants closely associated with human activity will further assist us to understand our influence in the context of the ongoing extinction events in the Anthropocene. This study, based on widely and intensively sampled F. altissima across Indo-Burma and the adjacent south China ranges, using both the chloroplast psbA-trnH spacer and sixteen newly developed nuclear microsatellite markers (nSSRs), aims to explore its spatial genetic structure. The results indicated low chloroplast haplotype diversity and a moderate level of nuclear genetic diversity. Although limited seed flow was revealed by psbA-trnH, no discernible phylogeographic structure was shown due to the low resolution of cpDNA markers and dominance of an ancestral haplotype. From the nSSRs data set, phylogeographic structure was homogenized, most likely due to extensive pollen flow mediated by pollinating fig wasps. Additionally, human cultivation and human-mediated transplanting further confounded the analyses of population structure. No geographic barriers are evident across the large study range, with F. altissima constituting a single population, and extensive human cultivation is likely to have had beneficial consequences for protecting the genetic diversity of F. altissima.
Collapse
|
7
|
Morgan B, Huang JP. Isolation by geographical distance after release from Pleistocene refugia explains genetic and phenotypic variation in Xylotrupes siamensis (Coleoptera: Scarabaeidae). Zool J Linn Soc 2021. [DOI: 10.1093/zoolinnean/zlaa106] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Abstract
Consistent and objective species delimitation is crucial to biodiversity studies, but challenges remain when conflicting taxonomic decisions have been made because different data sets and analytical methods were used to delineate species. In the rhinoceros beetle, Xylotrupes siamensis, the use of different morphological characters has resulted in taxonomic disagreement between studies. We used three molecular loci (mitochondrial CO1 and nuclear ITS2 and H3) to investigate the genetic divergence between populations exhibiting different male horn phenotypes. We also applied an approximate Bayesian computation approach to test alternative historical hypotheses that might explain the present genetic diversity among geographical populations. Furthermore, we used species distribution models to estimate the temporal variation in the geographical distribution of suitable habitats. The results show that the two phenotypic taxa within X. siamensis are not genetically structured and that their genetic structure can be explained using isolation by geographical distance. The emergence of the two phenotypic taxa might have been associated with historical isolation in separate refugia. However, spatial expansion and genetic interchange between populations might have gradually eroded the spatial genetic structure. We demonstrate that understanding the historical processes responsible for phenotypic divergence and genetic diversity among current populations could help with making evolutionarily coherent taxonomic decisions.
Collapse
Affiliation(s)
- Brett Morgan
- Biodiversity Research Center, Academia Sinica, Nankang, Taipei, Taiwan
| | - Jen-Pan Huang
- Biodiversity Research Center, Academia Sinica, Nankang, Taipei, Taiwan
| |
Collapse
|
8
|
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.
Collapse
|
9
|
Klabacka RL, Wood PL, McGuire JA, Oaks JR, Grismer LL, Grismer JL, Aowphol A, Sites JW. Rivers of Indochina as potential drivers of lineage diversification in the spotted flying lizard (Draco maculatus) species complex. Mol Phylogenet Evol 2020; 150:106861. [PMID: 32497832 DOI: 10.1016/j.ympev.2020.106861] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Revised: 05/21/2020] [Accepted: 05/21/2020] [Indexed: 12/25/2022]
Abstract
Southeast Asia hosts a rich concentration of biodiversity within multiple biodiversity hotspots. Indochina, a region with remarkably high levels of in situ diversification, possesses five major rivers (Ayeyarwady, Chiang Mai, Mekong, Red, and Salween), several of which coincide with phylogenetic breaks of terrestrial taxa. Draco maculatus possesses a range that stretches across Indochina, which widespread geographic distribution along with potential discrete variation within subspecies alludes to the possibility of this taxon constituting multiple divergent lineages. Using sequence data from three mitochondrial (12S, 16S, and ND2) and three nuclear (BDNF, CMOS, and PNN) genes, we provide the first estimated phylogeny of this hypothesized species complex and examine its phylogeographic architecture with maximum likelihood and Bayes factor delimitation (BFD) approaches. Our results support multiple divergent lineages with phylogenetic breaks coincident with rivers, indicating that river barriers may be contributing to the elevated levels of in situ diversification of Indochina.
Collapse
Affiliation(s)
- Randy L Klabacka
- Department of Biological Sciences and Museum of Natural History, Auburn University, 331 Funchess Hall, Auburn, AL 36849, United States; Department of Biology and M.I. Bean Life Science Museum, Brigham Young University, 150 East Bulldog Boulevard, Provo, UT 84602, United States.
| | - Perry L Wood
- Department of Biological Sciences and Museum of Natural History, Auburn University, 331 Funchess Hall, Auburn, AL 36849, United States; Department of Biology and M.I. Bean Life Science Museum, Brigham Young University, 150 East Bulldog Boulevard, Provo, UT 84602, United States.
| | - Jimmy A McGuire
- Museum of Vertebrate Zoology, University of California, 3101 Valley Life Sciences Building, Berkeley, CA 94720, United States.
| | - Jamie R Oaks
- Department of Biological Sciences and Museum of Natural History, Auburn University, 331 Funchess Hall, Auburn, AL 36849, United States.
| | - L Lee Grismer
- Herpetology Laboratory, Department of Biology, La Sierra University, 4500 Riverwalk Parkway, Riverside, CA 92515, United States.
| | - Jesse L Grismer
- Herpetology Laboratory, Department of Biology, La Sierra University, 4500 Riverwalk Parkway, Riverside, CA 92515, United States.
| | - Anchalee Aowphol
- Faculty of Science, Department of Zoology, Kasetsart University, Chatuchak, Bankok, Thailand.
| | - Jack W Sites
- Department of Biology and M.I. Bean Life Science Museum, Brigham Young University, 150 East Bulldog Boulevard, Provo, UT 84602, United States; Department of Biology, Austin Peay State University, Clarksville, TN 37044, United States
| |
Collapse
|
10
|
Jeratthitikul E, Phuangphong S, Sutcharit C, Prasankok P, Kongim B, Panha S. Integrative taxonomy reveals phenotypic plasticity in the freshwater mussel Contradens contradens (Bivalvia: Unionidae) in Thailand, with a description of a new species. SYST BIODIVERS 2019. [DOI: 10.1080/14772000.2018.1554607] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Affiliation(s)
- Ekgachai Jeratthitikul
- Animal Systematics and Molecular Ecology Laboratory, Department of Biology, Faculty of Science, Mahidol University, Bangkok, 10400, Thailand
| | - Supanat Phuangphong
- Animal Systematics and Molecular Ecology Laboratory, Department of Biology, Faculty of Science, Mahidol University, Bangkok, 10400, Thailand
| | - Chirasak Sutcharit
- Animal Systematics Research Unit, Department of Biology, Faculty of Science, Chulalongkorn University, Bangkok, 10330, Thailand
| | - Pongpun Prasankok
- School of Biology, Institute of Science, Suranaree University of Technology, Nakhon Ratchasima, 30000, Thailand
| | - Bangon Kongim
- Biodiversity and Traditional Knowledge Research Unit, Department of Biology, Faculty of Science, Mahasarakham University, Maha Sarakham, 44150, Thailand
| | - Somsak Panha
- Animal Systematics Research Unit, Department of Biology, Faculty of Science, Chulalongkorn University, Bangkok, 10330, Thailand
| |
Collapse
|
11
|
Genetic diversity and population structure of blue-crested lizard, Calotes mystaceus Duméril & Bibron, 1837 (Squamata: Agamidae) in Thailand. J Genet 2018; 96:377-382. [PMID: 28674239 DOI: 10.1007/s12041-017-0767-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
The blue-crested lizard, Calotes mystaceus Duméril & Bibron, 1837, is listed as a protected wild animal in Thailand. Its population is likely to be dramatically reduced due to massive hunting in several areas in this country. Basic information on its population genetics is therefore needed to facilitate its conservation. Thus, in this study we investigated the mitochondrial cytochrome c oxidase subunit 1 (CO1) sequence variation of 238 individualC.mystaceus from 42 different geographical localities of the north, west, central, east and northeast regions of Thailand. High genetic diversity and genetic differentiation at the intrapopulation and interpopulation levels was observed.We detected 63 unique haplotypes and 12 common/shared haplotypes. The phylogenetic analysis reveals two major lineages, I and II. These two lineages are separated by mountain ranges, which play an important role as natural barriers blocking gene flow. Our finding reveal at least two cryptic lineages represented in C. mystaceus populations in Thailand. However, a comprehensive investigation of the morphology, biology, ecology and genetic diversity of C. mystaceus in other regions within its area of distribution is needed.
Collapse
|
12
|
Ihlow F, Vamberger M, Flecks M, Hartmann T, Cota M, Makchai S, Meewattana P, Dawson JE, Kheng L, Rödder D, Fritz U. Integrative Taxonomy of Southeast Asian Snail-Eating Turtles (Geoemydidae: Malayemys) Reveals a New Species and Mitochondrial Introgression. PLoS One 2016; 11:e0153108. [PMID: 27050302 PMCID: PMC4822821 DOI: 10.1371/journal.pone.0153108] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2015] [Accepted: 03/22/2016] [Indexed: 11/18/2022] Open
Abstract
Based on an integrative taxonomic approach, we examine the differentiation of Southeast Asian snail-eating turtles using information from 1863 bp of mitochondrial DNA, 12 microsatellite loci, morphology and a correlative species distribution model. Our analyses reveal three genetically distinct groups with limited mitochondrial introgression in one group. All three groups exhibit distinct nuclear gene pools and distinct morphology. Two of these groups correspond to the previously recognized species Malayemys macrocephala (Chao Phraya Basin) and M. subtrijuga (Lower Mekong Basin). The third and genetically most divergent group from the Khorat Basin represents a previously unrecognized species, which is described herein. Although Malayemys are extensively traded and used for religious release, only few studied turtles appear to be translocated by humans. Historic fluctuations in potential distributions were assessed using species distribution models (SDMs). The Last Glacial Maximum (LGM) projection of the predictive SDMs suggests two distinct glacial distribution ranges, implying that the divergence of M. macrocephala and M. subtrijuga occurred in allopatry and was triggered by Pleistocene climate fluctuations. Only the projection derived from the global circulation model MIROC reveals a distinct third glacial distribution range for the newly discovered Malayemys species.
Collapse
Affiliation(s)
- Flora Ihlow
- Herpetology Section, Zoologisches Forschungsmuseum Alexander Koenig, Bonn, Germany
| | | | - Morris Flecks
- Herpetology Section, Zoologisches Forschungsmuseum Alexander Koenig, Bonn, Germany
| | - Timo Hartmann
- Herpetology Section, Zoologisches Forschungsmuseum Alexander Koenig, Bonn, Germany
| | - Michael Cota
- Thailand Natural History Museum, National Science Museum, Khlong Luang, Pathum Thani, Thailand
- Phranakhon Rajabhat University, Bang Khen, Bangkok, Thailand
| | - Sunchai Makchai
- Thailand Natural History Museum, National Science Museum, Khlong Luang, Pathum Thani, Thailand
| | | | - Jeffrey E. Dawson
- Charles H. Hoessle Herpetarium, Saint Louis Zoo, St. Louis, Missouri, United States of America
| | - Long Kheng
- General Department of Administration for Nature Conservation and Protection, Ministry of Environment, Chamkar Mon, Phnom Penh, Cambodia
| | - Dennis Rödder
- Herpetology Section, Zoologisches Forschungsmuseum Alexander Koenig, Bonn, Germany
| | - Uwe Fritz
- Museum of Zoology, Senckenberg Dresden, Dresden, Germany
| |
Collapse
|
13
|
Zhu F, Liu Q, Che J, Zhang L, Chen X, Yan F, Murphy R, Guo C, Guo P. Molecular phylogeography of white-lipped tree viper (Trimeresurus; Viperidae). ZOOL SCR 2016. [DOI: 10.1111/zsc.12156] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Fei Zhu
- Sichuan Key Laboratory of Bio-resources and Eco-enviroment; Ministry of Education, College of Life Sciences; Sichuan University; Chengdu, Sichuan 610065 China
| | - Qin Liu
- Department of Life Sciences and Food Engineering; Yibin University; , 8 Jiusheng Rd, 1 4 Wuliangye Ave., Yibin, Sichuan 644007 China
| | - Jing Che
- Southeast Asia Biodiversity Research Institute; Chinese Academy of Sciences; Kunming, Yunnan 650223 China
| | - Liang Zhang
- South China Institute of Endangered Animals; Guangzhou, Guangdong 510260 China
| | - Xin Chen
- Department of Biology; The College of Staten Island; The City University of New York, Staten Island; NY 10314 USA
| | - Fang Yan
- State Key Laboratory of Genetic Resources and Evolution, and Yunnan Laboratory of Molecular Biology of Domestic Animals; Kunming Institute of Zoology; Kunming, Yunnan 650223 China
| | - Robert Murphy
- State Key Laboratory of Genetic Resources and Evolution, and Yunnan Laboratory of Molecular Biology of Domestic Animals; Kunming Institute of Zoology; Kunming, Yunnan 650223 China
| | - Cong Guo
- Sichuan Key Laboratory of Bio-resources and Eco-enviroment; Ministry of Education, College of Life Sciences; Sichuan University; Chengdu, Sichuan 610065 China
| | - Peng Guo
- Department of Life Sciences and Food Engineering; Yibin University; , 8 Jiusheng Rd, 1 4 Wuliangye Ave., Yibin, Sichuan 644007 China
| |
Collapse
|
14
|
Siriwut W, Edgecombe GD, Sutcharit C, Panha S. The Centipede Genus Scolopendra in Mainland Southeast Asia: Molecular Phylogenetics, Geometric Morphometrics and External Morphology as Tools for Species Delimitation. PLoS One 2015; 10:e0135355. [PMID: 26270342 PMCID: PMC4536039 DOI: 10.1371/journal.pone.0135355] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2015] [Accepted: 07/21/2015] [Indexed: 12/31/2022] Open
Abstract
Seven Scolopendra species from the Southeast Asian mainland delimited based on standard external morphological characters represent monophyletic groups in phylogenetic trees inferred from concatenated sequences of three gene fragments (cytochrome c oxidase subunit 1, 16S rRNA and 28S rRNA) using Maximum likelihood and Bayesian inference. Geometric morphometric description of shape variation in the cephalic plate, forcipular coxosternite, and tergite of the ultimate leg-bearing segment provides additional criteria for distinguishing species. Colouration patterns in some Scolopendra species show a high degree of fit to phylogenetic trees at the population level. The most densely sampled species, Scolopendra dehaani Brandt, 1840, has three subclades with allopatric distributions in mainland SE Asia. The molecular phylogeny of S. pinguis Pocock, 1891, indicated ontogenetic colour variation among its populations. The taxonomic validation of S. dawydoffi Kronmüller, 2012, S. japonica Koch, 1878, and S. dehaani Brandt, 1840, each a former subspecies of S. subspinipes Leach, 1814 sensu Lewis, 2010, as full species was supported by molecular information and additional morphological data. Species delimitation in these taxonomically challenging animals is facilitated by an integrative approach that draws on both morphology and molecular phylogeny.
Collapse
Affiliation(s)
- Warut Siriwut
- Biological Sciences Program, Faculty of Science, Chulalongkorn University, Bangkok, Thailand
- Animal Systematics Research Unit, Department of Biology, Chulalongkorn University, Bangkok, Thailand
| | - Gregory D. Edgecombe
- Department of Earth Sciences, The Natural History Museum, London, United Kingdom
| | - Chirasak Sutcharit
- Animal Systematics Research Unit, Department of Biology, Chulalongkorn University, Bangkok, Thailand
| | - Somsak Panha
- Animal Systematics Research Unit, Department of Biology, Chulalongkorn University, Bangkok, Thailand
| |
Collapse
|
15
|
|