1
|
Wu N, Wang S, Dujsebayeva TN, Chen D, Ali A, Guo X. Geography and past climate changes have shaped the evolution of a widespread lizard in arid Central Asia. Mol Phylogenet Evol 2023; 184:107781. [PMID: 37044189 DOI: 10.1016/j.ympev.2023.107781] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Revised: 04/06/2023] [Accepted: 04/06/2023] [Indexed: 04/14/2023]
Abstract
The complex orogenic history and structure of Central Asia, coupled with Pleistocene glacial cycles have generated its stepwise aridification. Such events would have significantly influenced the evolution of many mid-latitude species in arid Central Asia (ACA). In this study, we employed two mitochondrial genes (CO1 and ND2) and genome-wide SNPs, coupled with ecological niche modeling, to investigate the lineage diversification and historical demography within a widespread lizard Phrynocepahlus helioscopus, and their associations with geography and past climate change. We obtained themtDNA dataset for 300 individuals from 96 localities within the known range of the lizard, among which 51 individuals from 27 localities were selected for generating the SNP dataset via genotyping-by-sequencing approach. Phylogenetic analyses of the concatenated mtDNA dataset revealed eight geographically correlated lineages that diverged by 4.21-10.41% for the CO1 gene, which were estimated to have coalesced ∼4.47 million years ago. However, we observed mito-nuclear discordance pattern regarding the population of Clade V (P. helioscopus sergeevi) from Tajikistan. Ancestral area estimations suggested that P. helioscopus originated from the Fergana Valley and then dispersed into the adjacent areas in ACA along with a history of multiple allopatric divergence processes, suggesting that Fergana may have been the cradle of diversification of P. helioscopus. The intensification of aridification across Central Asia during the Late Pliocene may have facilitated the rapid radiation of this arid-adapted lizard throughout this vast territory. Subsequently, the geological events (e.g., uplift of the Hissar-Alay, transgressions of the Caspian Sea) and geographic barriers (e.g., Amu Darya River, Zerarshan River) during the Pleistocene triggered the progressive diversification of P. helioscopus. Interestingly, Clade VIII (P. helioscopus varius) experienced rapid population growth coupled with range expansion while Clade IV (P. helioscopus cameranoi) underwent drastic population expansion associated with range contraction during the Last Glacial Maximum. In Clade IV, but not in Clade VIII, environmental turnover contributes more to mitochondrial genetic distinctiveness than geographic distance. Overall, the SNP dataset demonstrates that geographic distance plays a greater role than environmental distance. Both the mtDNA dataset and the SNP dataset suggest local-scale genetic differentiation in Clade IV and Clade VIII, revealing potential geographic barriers in the Ili River Valley and the Junggar Basin, respectively. Twenty-seven outlier SNPs associated with environmental factors (precipitation and temperature) were identified, which supports the signature of local adaptation to the arid desert environment. Finally, our finding suggests taxonomic implications, such as support for full species status for P. saidalievi (Clade II) and P. meridionalis (Clade I). Future analyses based on further evidence and increased taxon and geographic sampling should be carried out to corroborate our findings.
Collapse
Affiliation(s)
- Na Wu
- Chengdu Institute of Biology Chinese Academy of Sciences, Chengdu 610041, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Song Wang
- Chengdu Institute of Biology Chinese Academy of Sciences, Chengdu 610041, China
| | - Tatjana N Dujsebayeva
- Laboratory of Ornithology and Herpetology, Institute of Zoology, Ministry of Sciences and High Education of Republic of Kazakhstan, Almaty 050060, Kazakhstan
| | - Dali Chen
- Department of Pathogenic Biology, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu 610041, China
| | - Abid Ali
- Chengdu Institute of Biology Chinese Academy of Sciences, Chengdu 610041, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xianguang Guo
- Chengdu Institute of Biology Chinese Academy of Sciences, Chengdu 610041, China.
| |
Collapse
|
2
|
Yu M, Liu Q, Wu Y, Guo P, Yang K. Genetic diversity and sex‐biased dispersal in the brown spotted pitviper (
Protobothrops mucrosquamatus
): Evidence from microsatellite markers. Ecol Evol 2022; 12:e8652. [PMID: 35261743 PMCID: PMC8888261 DOI: 10.1002/ece3.8652] [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: 10/23/2021] [Revised: 01/20/2022] [Accepted: 01/28/2022] [Indexed: 11/18/2022] Open
Abstract
Dispersal plays a vital role in the geographical distribution, population genetic structure, quantity dynamics, and evolution of a species. Sex‐biased dispersal is common among vertebrates and many studies have documented a tendency toward male‐biased dispersal in mammals and female‐biased dispersal in birds. However, dispersal patterns in reptiles remain poorly understood. In this study, we explored the genetic diversity and dispersal patterns of the widely distributed Asian pitviper Protobothrops mucrosquamatus. In total, 16 polymorphic microsatellite loci were screened in 150 snakes (48 males, 44 females, 58 samples without sex information) covering most of their distribution. Microsatellite analysis revealed high genetic diversity in P. mucrosquamatus. Bayesian clustering of population assignment identified two major clusters for all populations, somewhat inconsistent with the mitochondrial DNA phylogeny of P. mucrosquamatus reported in previous research. Analyses based on 92 sex‐determined and 37 samples of P. mucrosquamatus from three small sites in Sichuan, China (Mingshan, Yibin, and Zizhong) consistently suggested female‐biased dispersal in P. mucrosquamatus, which is the first example of this pattern in snakes. The female‐biased dispersal patterns in P. mucrosquamatus may be explained by local resource competition.
Collapse
Affiliation(s)
- Min Yu
- Institute of Qinghai‐Tibetan Plateau Southwest Minzu University Chengdu China
- Faculty of Agriculture, Forest and Food Engineering Yibin University Yibin China
| | - Qin Liu
- Faculty of Agriculture, Forest and Food Engineering Yibin University Yibin China
| | - Ya‐Yong Wu
- Faculty of Agriculture, Forest and Food Engineering Yibin University Yibin China
| | - Peng Guo
- Faculty of Agriculture, Forest and Food Engineering Yibin University Yibin China
| | - Kong Yang
- Institute of Qinghai‐Tibetan Plateau Southwest Minzu University Chengdu China
- Faculty of Agriculture, Forest and Food Engineering Yibin University Yibin China
| |
Collapse
|
3
|
Dickerson AL, Rankin KJ, Cadena V, Endler JA, Stuart-Fox D. Rapid beard darkening predicts contest outcome, not copulation success, in bearded dragon lizards. Anim Behav 2020. [DOI: 10.1016/j.anbehav.2020.10.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
|
4
|
Zhu Q, Damba I, Zhao Q, Yi K, Batbayar N, Natsagdorj T, Davaasuren B, Wang X, Rozenfeld S, Moriguchi S, Zhan A, Cao L, Fox AD. Lack of conspicuous sex-biased dispersal patterns at different spatial scales in an Asian endemic goose species breeding in unpredictable steppe wetlands. Ecol Evol 2020; 10:7006-7020. [PMID: 32760508 PMCID: PMC7391341 DOI: 10.1002/ece3.6382] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2019] [Revised: 04/20/2020] [Accepted: 04/21/2020] [Indexed: 12/01/2022] Open
Abstract
Dispersal affects the spatial distribution and population structure of species. Dispersal is often male-biased in mammals while female-biased in birds, with the notable exception of the Anatidae. In this study, we tested genetic evidence for sex-biased dispersal (SBD) in the Swan Goose Anser cygnoides, an Asian endemic and IUCN vulnerable species, which has been increasingly restricted to breeding on Mongolian steppe wetlands. We analyzed the genotypes of 278 Swan Geese samples from 14 locations at 14 microsatellite loci. Results from assignment indices, analysis of molecular variance, and five other population descriptors all failed to support significant SBD signals for the Swan Goose at the landscape level. Although overall results showed significantly high relatedness within colonies (suggesting high levels of philopatry in both sexes), local male genetic structure at the 1,050 km distance indicated greater dispersal distance for females from the eastern sector of the breeding range. Hence, local dispersal is likely scale-dependent and female-biased within the eastern breeding range. These findings are intriguing considering the prevailing expectation for there to be female fidelity in most goose species. We suggest that while behavior-related traits may have facilitated the local genetic structure for the Swan Goose, several extrinsic factors, including the decreasing availability of the nesting sites and the severe fragmentation of breeding habitats, could have contributed to the absence of SBD at the landscape level. The long-distance molt migration that is typical of goose species such as the Swan Goose may also have hampered our ability to detect SBD. Hence, we urge further genetic sampling from other areas in summer to extend our results, complemented by field observations to confirm our DNA analysis conclusions about sex-specific dispersal patterns at different spatial scales in this species.
Collapse
Affiliation(s)
- Qin Zhu
- School of Life SciencesUniversity of Science and Technology of ChinaHefeiChina
| | - Iderbat Damba
- State Key Laboratory of Urban and Regional EcologyResearch Center for Eco‐Environmental SciencesChinese Academy of SciencesBeijingChina
- University of Chinese Academy of SciencesBeijingChina
- Ornithology LaboratoryInstitute of BiologyMongolian Academy of SciencesUlaanbaatarMongolia
| | - Qingshan Zhao
- State Key Laboratory of Urban and Regional EcologyResearch Center for Eco‐Environmental SciencesChinese Academy of SciencesBeijingChina
| | - Kunpeng Yi
- State Key Laboratory of Urban and Regional EcologyResearch Center for Eco‐Environmental SciencesChinese Academy of SciencesBeijingChina
| | | | | | | | - Xin Wang
- State Key Laboratory of Urban and Regional EcologyResearch Center for Eco‐Environmental SciencesChinese Academy of SciencesBeijingChina
| | - Sonia Rozenfeld
- Bird Ringing Centre of RussiaInstitute of Ecology and EvolutionRussian Academy of SciencesMoscowRussia
| | - Sachiko Moriguchi
- Faculty of Veterinary ScienceNippon Veterinary and Life Science UniversityTokyoJapan
| | - Aibin Zhan
- University of Chinese Academy of SciencesBeijingChina
- Key Laboratory of Environmental BiotechnologyResearch Center for Eco‐Environmental SciencesChinese Academy of SciencesBeijingChina
| | - Lei Cao
- State Key Laboratory of Urban and Regional EcologyResearch Center for Eco‐Environmental SciencesChinese Academy of SciencesBeijingChina
- University of Chinese Academy of SciencesBeijingChina
| | | |
Collapse
|
5
|
Wang W, Li J, Wang H, Ran Y, Wu H. Genetic evidence reveals male‐biased dispersal of the Omei tree frog. J Zool (1987) 2019. [DOI: 10.1111/jzo.12749] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Affiliation(s)
- W. Wang
- Institute of Evolution and Ecology School of Life Sciences Central China Normal University Wuhan China
| | - J. Li
- Institute of Evolution and Ecology School of Life Sciences Central China Normal University Wuhan China
| | - H. Wang
- Institute of Evolution and Ecology School of Life Sciences Central China Normal University Wuhan China
| | - Y. Ran
- Institute of Evolution and Ecology School of Life Sciences Central China Normal University Wuhan China
| | - H. Wu
- Institute of Evolution and Ecology School of Life Sciences Central China Normal University Wuhan China
| |
Collapse
|
6
|
Jin Y, Brown RP. Morphological species and discordant mtDNA: A genomic analysis of Phrynocephalus lizard lineages on the Qinghai-Tibetan Plateau. Mol Phylogenet Evol 2019; 139:106523. [DOI: 10.1016/j.ympev.2019.106523] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2018] [Revised: 02/14/2019] [Accepted: 05/29/2019] [Indexed: 11/27/2022]
|
7
|
Bernardo PH, Sánchez-Ramírez S, Sánchez-Pacheco SJ, Álvarez-Castañeda ST, Aguilera-Miller EF, Mendez-de la Cruz FR, Murphy RW. Extreme mito-nuclear discordance in a peninsular lizard: the role of drift, selection, and climate. Heredity (Edinb) 2019; 123:359-370. [PMID: 30833746 PMCID: PMC6781153 DOI: 10.1038/s41437-019-0204-4] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2018] [Revised: 02/13/2019] [Accepted: 02/18/2019] [Indexed: 12/22/2022] Open
Abstract
Nuclear and mitochondrial genomes coexist within cells but are subject to different tempos and modes of evolution. Evolutionary forces such as drift, mutation, selection, and migration are expected to play fundamental roles in the origin and maintenance of diverged populations; however, divergence may lag between genomes subject to different modes of inheritance and functional specialization. Herein, we explore whole mitochondrial genome data and thousands of nuclear single nucleotide polymorphisms to evidence extreme mito-nuclear discordance in the small black-tailed brush lizard, Urosaurus nigricaudus, of the Peninsula of Baja California, Mexico and southern California, USA, and discuss potential drivers. Results show three deeply divergent mitochondrial lineages dating back to the later Miocene (ca. 5.5 Ma) and Pliocene (ca. 2.8 Ma) that likely followed geographic isolation due to trans-peninsular seaways. This contrasts with very low levels of genetic differentiation in nuclear loci (FST < 0.028) between mtDNA lineages. Analyses of protein-coding genes reveal substantial fixed variation between mitochondrial lineages, of which a significant portion comes from non-synonymous mutations. A mixture of drift and selection is likely responsible for the rise of these mtDNA groups, albeit with little evidence of marked differences in climatic niche space between them. Finally, future investigations can look further into the role that mito-nuclear incompatibilities and mating systems play in explaining contrasting nuclear gene flow.
Collapse
Affiliation(s)
- Pedro Henrique Bernardo
- Department of Ecology and Evolutionary Biology, University of Toronto, 25 Willcocks Street, Toronto, ON, M5S 3B2, Canada. .,Department of Natural History, Royal Ontario Museum, Toronto, ON, Canada.
| | - Santiago Sánchez-Ramírez
- Department of Ecology and Evolutionary Biology, University of Toronto, 25 Willcocks Street, Toronto, ON, M5S 3B2, Canada.,Department of Natural History, Royal Ontario Museum, Toronto, ON, Canada
| | - Santiago J Sánchez-Pacheco
- Department of Ecology and Evolutionary Biology, University of Toronto, 25 Willcocks Street, Toronto, ON, M5S 3B2, Canada.,Department of Natural History, Royal Ontario Museum, Toronto, ON, Canada
| | | | | | | | - Robert W Murphy
- Department of Ecology and Evolutionary Biology, University of Toronto, 25 Willcocks Street, Toronto, ON, M5S 3B2, Canada.,Department of Natural History, Royal Ontario Museum, Toronto, ON, Canada
| |
Collapse
|
8
|
Solovyeva EN, Lebedev VS, Dunayev EA, Nazarov RA, Bannikova AA, Che J, Murphy RW, Poyarkov NA. Cenozoic aridization in Central Eurasia shaped diversification of toad-headed agamas ( Phrynocephalus; Agamidae, Reptilia). PeerJ 2018; 6:e4543. [PMID: 29576991 PMCID: PMC5863718 DOI: 10.7717/peerj.4543] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2017] [Accepted: 03/06/2018] [Indexed: 12/03/2022] Open
Abstract
We hypothesize the phylogenetic relationships of the agamid genus Phrynocephalus to assess how past environmental changes shaped the evolutionary and biogeographic history of these lizards and especially the impact of paleogeography and climatic factors. Phrynocephalus is one of the most diverse and taxonomically confusing lizard genera. As a key element of Palearctic deserts, it serves as a promising model for studies of historical biogeography and formation of arid habitats in Eurasia. We used 51 samples representing 33 of 40 recognized species of Phrynocephalus covering all major areas of the genus. Molecular data included four mtDNA (COI, ND2, ND4, Cytb; 2,703 bp) and four nuDNA protein-coding genes (RAG1, BDNF, AKAP9, NKTR; 4,188 bp). AU-tests were implemented to test for significant differences between mtDNA- and nuDNA-based topologies. A time-calibrated phylogeny was estimated using a Bayesian relaxed molecular clock with nine fossil calibrations. We reconstructed the ancestral area of origin, biogeographic scenarios, body size, and the evolution of habitat preference. Phylogenetic analyses of nuDNA genes recovered a well-resolved and supported topology. Analyses detected significant discordance with the less-supported mtDNA genealogy. The position of Phrynocephalus mystaceus conflicted greatly between the two datasets. MtDNA introgression due to ancient hybridization best explained this result. Monophyletic Phrynocephalus contained three main clades: (I) oviparous species from south-western and Middle Asia; (II) viviparous species of Qinghai–Tibetan Plateau (QTP); and (III) oviparous species of the Caspian Basin, Middle and Central Asia. Phrynocephalus originated in late Oligocene (26.9 Ma) and modern species diversified during the middle Miocene (14.8–13.5 Ma). The reconstruction of ancestral areas indicated that Phrynocephalus originated in Middle East–southern Middle Asia. Body size miniaturization likely occurred early in the history of Phrynocephalus. The common ancestor of Phrynocephalus probably preferred sandy substrates with the inclusion of clay or gravel. The time of Agaminae radiation and origin of Phrynocephalus in the late Oligocene significantly precedes the landbridge between Afro-Arabia and Eurasia in the Early Miocene. Diversification of Phrynocephalus coincides well with the mid-Miocene climatic transition when a rapid cooling of climate drove progressing aridification and the Paratethys salinity crisis. These factors likely triggered the spreading of desert habitats in Central Eurasia, which Phrynocephalus occupied. The origin of the viviparous Tibetan clade has been associated traditionally with uplifting of the QTP; however, further studies are needed to confirm this. Progressing late Miocene aridification, the decrease of the Paratethys Basin, orogenesis, and Plio–Pleistocene climate oscillations likely promoted further diversification within Phrynocephalus. We discuss Phrynocephalus taxonomy in scope of the new analyses.
Collapse
Affiliation(s)
| | | | - Evgeniy A Dunayev
- Zoological Museum, Lomonosov Moscow State University, Moscow, Russia
| | - Roman A Nazarov
- Zoological Museum, Lomonosov Moscow State University, Moscow, Russia
| | - Anna A Bannikova
- Biological Faculty, Department of Vertebrate Zoology, Lomonosov Moscow State University, Moscow, Russia
| | - Jing Che
- State Key Laboratory of Genetic Resources and Evolution, and Center for Excellence in Animal Evolution and Genetics, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China.,Southeast Asia Biodiversity Research Institute, Chinese Academy of Sciences, Yezin, Nay Pyi Taw, Myanmar
| | - Robert W Murphy
- State Key Laboratory of Genetic Resources and Evolution, and Center for Excellence in Animal Evolution and Genetics, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China.,Faculty of Arts and Science, Department of Ecology & Evolutionary Biology, University of Toronto, Toronto, ON, Canada
| | - Nikolay A Poyarkov
- Biological Faculty, Department of Vertebrate Zoology, Lomonosov Moscow State University, Moscow, Russia
| |
Collapse
|
9
|
Šmíd J, Moravec J, Gvoždík V, Štundl J, Frynta D, Lymberakis P, Kapli P, Wilms T, Schmitz A, Shobrak M, Yousefkhani SH, Rastegar-Pouyani E, Castilla AM, Els J, Mayer W. Cutting the Gordian Knot: Phylogenetic and ecological diversification of theMesalina brevirostrisspecies complex (Squamata, Lacertidae). ZOOL SCR 2017. [DOI: 10.1111/zsc.12254] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Jiří Šmíd
- Department of Zoology; National Museum; Prague Czech Republic
- South African National Biodiversity Institute; Claremont Cape Town South Africa
| | - Jiří Moravec
- Department of Zoology; National Museum; Prague Czech Republic
| | - Václav Gvoždík
- Department of Zoology; National Museum; Prague Czech Republic
| | - Jan Štundl
- Department of Zoology; National Museum; Prague Czech Republic
- Department of Zoology; Faculty of Science; Charles University; Prague Czech Republic
| | - Daniel Frynta
- Department of Zoology; Faculty of Science; Charles University; Prague Czech Republic
| | - Petros Lymberakis
- Natural History Museum of Crete - University of Crete; Herakleio Greece
| | - Paschalia Kapli
- The Exelixis Lab; Scientific Computing Group; Heidelberg Institute for Theoretical Studies; Heidelberg Germany
| | | | - Andreas Schmitz
- Department of Herpetology and Ichthyology; Natural History Museum of Geneva; Geneva Switzerland
| | - Mohammed Shobrak
- Biology Department; Faculty of Science; Taif University; Taif Saudi Arabia
| | | | | | - Aurora M. Castilla
- Qatar Environment and Energy Research Institute; Hamad Bin Khalifa University (Qatar Foundation); Doha Qatar
| | - Johannes Els
- Breeding Centre for Endangered Arabian Wildlife, Environment and Protected Areas Authority; Sharjah United Arab Emirates
| | | |
Collapse
|
10
|
Pipoly I, Bókony V, Kirkpatrick M, Donald PF, Székely T, Liker A. The genetic sex-determination system predicts adult sex ratios in tetrapods. Nature 2015; 527:91-4. [DOI: 10.1038/nature15380] [Citation(s) in RCA: 78] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2015] [Accepted: 08/05/2015] [Indexed: 11/09/2022]
|