1
|
Hofmann S, Rödder D, Andermann T, Matschiner M, Riedel J, Baniya CB, Flecks M, Yang J, Jiang K, Jianping J, Litvinchuk SN, Martin S, Masroor R, Nothnagel M, Vershinin V, Zheng Y, Jablonski D, Schmidt J, Podsiadlowski L. Exploring Paleogene Tibet's warm temperate environments through target enrichment and phylogenetic niche modelling of Himalayan spiny frogs (Paini, Dicroglossidae). Mol Ecol 2024; 33:e17446. [PMID: 38946613 DOI: 10.1111/mec.17446] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2024] [Revised: 05/25/2024] [Accepted: 06/17/2024] [Indexed: 07/02/2024]
Abstract
The Cenozoic topographic development of the Himalaya-Tibet orogen (HTO) substantially affected the paleoenvironment and biodiversity patterns of High Asia. However, concepts on the evolution and paleoenvironmental history of the HTO differ massively in timing, elevational increase and sequence of surface uplift of the different elements of the orogen. Using target enrichment of a large set of transcriptome-derived markers, ancestral range estimation and paleoclimatic niche modelling, we assess a recently proposed concept of a warm temperate paleo-Tibet in Asian spiny frogs of the tribe Paini and reconstruct their historical biogeography. That concept was previously developed in invertebrates. Because of their early evolutionary origin, low dispersal capacity, high degree of local endemism, and strict dependence on temperature and humidity, the cladogenesis of spiny frogs may echo the evolution of the HTO paleoenvironment. We show that diversification of main lineages occurred during the early to Mid-Miocene, while the evolution of alpine taxa started during the late Miocene/early Pliocene. Our distribution and niche modelling results indicate range shifts and niche stability that may explain the modern disjunct distributions of spiny frogs. They probably maintained their (sub)tropical or (warm)temperate preferences and moved out of the ancestral paleo-Tibetan area into the Himalaya as the climate shifted, as opposed to adapting in situ. Based on ancestral range estimation, we assume the existence of low-elevation, climatically suitable corridors across paleo-Tibet during the Miocene along the Kunlun, Qiangtang and/or Gangdese Shan. Our results contribute to a deeper understanding of the mechanisms and processes of faunal evolution in the HTO.
Collapse
Affiliation(s)
- Sylvia Hofmann
- Leibniz Institute for the Analysis of Biodiversity Change, Museum Koenig, Bonn, Germany
| | - Dennis Rödder
- Leibniz Institute for the Analysis of Biodiversity Change, Museum Koenig, Bonn, Germany
| | - Tobias Andermann
- Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden
| | | | - Jendrian Riedel
- Leibniz Institute for the Analysis of Biodiversity Change, Museum Koenig, Bonn, Germany
| | - Chitra B Baniya
- Central Department of Botany, Tribhuvan University, Kathmandu, Nepal
| | - Morris Flecks
- Leibniz Institute for the Analysis of Biodiversity Change, Museum Koenig, Bonn, Germany
| | - Jianhuan Yang
- Kadoorie Conservation China, Kadoorie Farm and Botanic Garden, Hong Kong, China
| | - Ke Jiang
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
| | - Jiang Jianping
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
| | | | - Sebastian Martin
- Leibniz Institute for the Analysis of Biodiversity Change, Museum Koenig, Bonn, Germany
| | | | - Michael Nothnagel
- Statistical Genetics and Bioinformatics, Cologne Center for Genomics, University of Cologne, Cologne, Germany
| | - Vladimir Vershinin
- Institute of Plant and Animal Ecology, Ural Branch of the Russian Academy of Sciences, Yekaterinburg, Russia
- Institute of Natural Sciences and Mathematics, Eltsyn Ural Federal University, Yekaterinburg, Russia
| | - Yuchi Zheng
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
| | - Daniel Jablonski
- Department of Zoology, Comenius University in Bratislava, Bratislava, Slovakia
| | - Joachim Schmidt
- General and Systematic Zoology, Institute of Biosciences, University of Rostock, Rostock, Germany
| | - Lars Podsiadlowski
- Leibniz Institute for the Analysis of Biodiversity Change, Museum Koenig, Bonn, Germany
| |
Collapse
|
2
|
Karuno AP, Mi X, Chen Y, Zou DH, Gao W, Zhang BL, Xu W, Jin JQ, Shen WJ, Huang S, Zhou WW, Che J. Impacts of climate change on herpetofauna diversity in the Qinghai-Tibetan Plateau. CONSERVATION BIOLOGY : THE JOURNAL OF THE SOCIETY FOR CONSERVATION BIOLOGY 2023; 37:e14155. [PMID: 37551770 DOI: 10.1111/cobi.14155] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/08/2023] [Revised: 06/07/2023] [Accepted: 06/12/2023] [Indexed: 08/09/2023]
Abstract
Although numerous studies on the impacts of climate change on biodiversity have been published, only a handful are focused on the intraspecific level or consider population-level models (separate models per population). We endeavored to fill this knowledge gap relative to the Qinghai-Tibetan plateau (QTP) by combining species distribution modeling (SDMs) with population genetics (i.e., population-level models) and phylogenetic methods (i.e., phylogenetic tree reconstruction and phylogenetic diversity analyses). We applied our models to 11 endemic and widely distributed herpetofauna species inhabiting high elevations in the QTP. We aimed to determine the influence of environmental heterogeneity on species' responses to climate change, the magnitude of climate-change impacts on intraspecific diversity, and the relationship between species range loss and intraspecific diversity losses under 2 shared socioeconomic pathways (SSP245 and SSP585) and 3 future periods (2050s, 2070s, and 2090s). The effects of global climatic change were more pronounced at the intraspecific level (22% of haplotypes lost and 36% of populations lost) than the morphospecies level in the SSP585 climate change scenario. Maintenance of genetic diversity was in general determined by a combination of factors including range changes, species genetic structure, and the part of the range predicted to be lost. This is owing to the fact that the loss and survival of populations were observed in species irrespective of the predicted range changes (contraction or expansion). In the southeast (mountainous regions), climate change had less of an effect on range size (>100% in 3 species) than in central and northern QTP plateau regions (range size <100% in all species). This may be attributed to environmental heterogeneity, which provided pockets of suitable climate in the southeast, whereas ecosystems in the north and central regions were homogeneous. Generally, our results imply that mountainous regions with high environmental heterogeneity and high genetic diversity may buffer the adverse impacts of climate change on species distribution and intraspecific diversity. Therefore, genetic structure and characteristics of the ecosystem may be crucial for conservation under climate change.
Collapse
Affiliation(s)
- Alex Plimo Karuno
- State Key Laboratory of Genetic Resources and Evolution & Yunnan key laboratory of Biodiversity and Ecological Conservation of Gaoligong Mountain, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, P. R. China
- Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, P. R. China
| | - Xue Mi
- State Key Laboratory of Genetic Resources and Evolution & Yunnan key laboratory of Biodiversity and Ecological Conservation of Gaoligong Mountain, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, P. R. China
- Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, P. R. China
| | - Youhua Chen
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, P. R. China
| | - Da-Hu Zou
- State Key Laboratory of Genetic Resources and Evolution & Yunnan key laboratory of Biodiversity and Ecological Conservation of Gaoligong Mountain, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, P. R. China
- Research Center for Ecology, College of Science, Tibet University, Lhasa, P. R. China
| | - Wei Gao
- State Key Laboratory of Genetic Resources and Evolution & Yunnan key laboratory of Biodiversity and Ecological Conservation of Gaoligong Mountain, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, P. R. China
| | - Bao-Lin Zhang
- State Key Laboratory of Genetic Resources and Evolution & Yunnan key laboratory of Biodiversity and Ecological Conservation of Gaoligong Mountain, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, P. R. China
| | - Wei Xu
- State Key Laboratory of Genetic Resources and Evolution & Yunnan key laboratory of Biodiversity and Ecological Conservation of Gaoligong Mountain, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, P. R. China
| | - Jie-Qiong Jin
- State Key Laboratory of Genetic Resources and Evolution & Yunnan key laboratory of Biodiversity and Ecological Conservation of Gaoligong Mountain, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, P. R. China
| | - Wen-Jing Shen
- State Key Laboratory of Genetic Resources and Evolution & Yunnan key laboratory of Biodiversity and Ecological Conservation of Gaoligong Mountain, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, P. R. China
| | - Song Huang
- College of Life Sciences, Anhui Normal University, Wuhu, P. R. China
| | - Wei-Wei Zhou
- State Key Laboratory of Genetic Resources and Evolution & Yunnan key laboratory of Biodiversity and Ecological Conservation of Gaoligong Mountain, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, P. R. China
- State Key Laboratory of Grassland Agro-ecosystems, Institute of Innovation Ecology & College of Life Sciences, Lanzhou University, Lanzhou, P. R. China
| | - Jing Che
- State Key Laboratory of Genetic Resources and Evolution & Yunnan key laboratory of Biodiversity and Ecological Conservation of Gaoligong Mountain, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, P. R. China
| |
Collapse
|
3
|
Tang S, Liu S, Yu G. A New Species of Nanorana (Anura: Dicroglossidae) from Northwestern Yunnan, China, with Comments on the Taxonomy of Nanorana arunachalensis and Allopaa. Animals (Basel) 2023; 13:3427. [PMID: 37958182 PMCID: PMC10649098 DOI: 10.3390/ani13213427] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Revised: 10/28/2023] [Accepted: 11/04/2023] [Indexed: 11/15/2023] Open
Abstract
The genus Nanorana contains three subgenera, namely Nanorana, Paa, and Chaparana, and currently, there are four species known to science in Nanorana (Nanorana). In this study, we describe a new species belonging to the subgenus Nanorana from northwestern Yunnan, China. Phylogenetically, the new species, Nanorana laojunshanensissp. nov., is the sister to the clade of N. pleskei and N. ventripunctata. Morphologically, the new species can be distinguished from known congeners by the combination of following characters: present tympanum, equal fingers I and II, small body size, yellow ventral surface of limbs, distinct vomerine teeth, indistinct subarticular tubercles, head width greater than head length, slender supratympanic fold, absent dorsolateral fold, nuptial spines present on fingers I and II in adult males, absent vocal sac, and paired brown spines on the chest. Moreover, we suggest moving the genus Allopaa into Nanorana (Chaparana) and consider that N. arunachalensis is neither an Odorrana species nor a member of the subfamily Dicroglossinae (therefore Nanorana), but probably represents a distinct genus closely related to Ingerana or belongs to Ingerana, pending more data. Additionally, we consider that Nanorana minica deserves the rank of an independent subgenus, and we suggest assigning N. arnoldi, N. blanfordii, N. ercepeae, N. polunini, N. rarica, N. rostandi, N. vicina, N. xuelinensis, and N. zhaoermii into the subgenus Paa and placing N. kangxianensis, N. phrynoides, and N. sichuanensis in the subgenus Chaparana.
Collapse
Affiliation(s)
- Shangjing Tang
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection (Guangxi Normal University), Ministry of Education, Guilin 541004, China;
- Guangxi Key Laboratory of Rare and Endangered Animal Ecology, College of Life Science, Guangxi Normal University, Guilin 541004, China
| | - Shuo Liu
- Kunming Natural History Museum of Zoology, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
| | - Guohua Yu
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection (Guangxi Normal University), Ministry of Education, Guilin 541004, China;
- Guangxi Key Laboratory of Rare and Endangered Animal Ecology, College of Life Science, Guangxi Normal University, Guilin 541004, China
| |
Collapse
|
4
|
Du Y, Zhang Y, Lou Z, Wang T. Unrecognized diversity, genetic structuring, and phylogeography of the genus Triplophysa (Cypriniformes: Nemacheilidae) sheds light on two opposite colonization routes during Quaternary glaciation that occurred in the Qilian Mountains. Ecol Evol 2023; 13:e10003. [PMID: 37091569 PMCID: PMC10116023 DOI: 10.1002/ece3.10003] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Revised: 03/21/2023] [Accepted: 03/30/2023] [Indexed: 04/25/2023] Open
Abstract
In recent years, the influence of historical geological and climatic events on the evolution of flora and fauna in the Tibetan Plateau has been a hot research topic. The Qilian Mountain region is one of the most important sources of biodiversity on the Qinghai-Tibet Plateau. Many species existed in the region during the Pleistocene glacial oscillation, and the complex geographical environment provided suitable conditions for the survival of local species. The shrinkage, expansion, and transfer of the distribution range and population size of species have significant effects on genetic diversity and intraspecific differentiation. To reveal the effects of geological uplift and climate oscillation on the evolution of fish populations in the Qilian Mountains, we investigated the genetic structure, phylogenetic relationship, and phylogeographical characteristics of genus Triplophysa species in the Qilian Mountains using the mitochondrial DNA gene (COI), three nuclear genes (RAG1, sRH, and Myh6) and 11 pairs of nuclear microsatellite markers. We collected 11 species of genus Triplophysa living in the Qilian Mountains, among which Triplophysa hsutschouensis and Triplophysa papillosolabiata are widely distributed in the rivers on the northern slope of the Qilian Mountains. There was a high degree of lineage differentiation among species, and the genetic diversity of endemic species was low. The different geographical groups of T. papillosolabiata presented some allogeneic adaptation and differentiation, which was closely related to the changes in the river system. Except for the population expansion event of T. hsutschouensis during the last glacial period of the Qinghai-Tibet Plateau (0.025 MYA), the population sizes of other plateau loach species remained stable without significant population expansion. Starting from the east and west sides of the Qilian Mountains, T. hsutschouensis, and T. papillosolabiata showed two species colonization routes in opposite directions. The geological events of the uplift of the Qinghai-Tibet Plateau and the climatic oscillation of the Quaternary glaciation had a great influence on the genetic structure of the plateau loach in the Qilian Mountains, which promoted the genetic differentiation of the plateau loach and formed some unique new species. The results of this study have important guiding significance for fish habitat protection in the Qilian Mountains.
Collapse
Affiliation(s)
- Yan‐yan Du
- Gansu Key Laboratory of Cold Water Fishes Germplasm Resources and Genetics BreedingGansu Fisheries Research InstituteLanzhouChina
| | - Yan‐ping Zhang
- Gansu Key Laboratory of Cold Water Fishes Germplasm Resources and Genetics BreedingGansu Fisheries Research InstituteLanzhouChina
| | - Zhong‐yu Lou
- Gansu Key Laboratory of Cold Water Fishes Germplasm Resources and Genetics BreedingGansu Fisheries Research InstituteLanzhouChina
| | - Tai Wang
- Gansu Key Laboratory of Cold Water Fishes Germplasm Resources and Genetics BreedingGansu Fisheries Research InstituteLanzhouChina
| |
Collapse
|
5
|
Hou J, Xiang J, Li D, Liu X. Prediction of Potential Suitable Distribution Areas of Quasipaa spinosa in China Based on MaxEnt Optimization Model. BIOLOGY 2023; 12:biology12030366. [PMID: 36979059 PMCID: PMC10045758 DOI: 10.3390/biology12030366] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Revised: 02/17/2023] [Accepted: 02/23/2023] [Indexed: 03/03/2023]
Abstract
Quasipaa spinosa is a large cold-water frog unique to China, with great ecological and economic value. In recent years, due to the impact of human activities on the climate, its habitat has been destroyed, resulting in a sharp decline in natural population resources. Based on the existing distribution records of Q. spinosa, this study uses the optimized MaxEnt model and ArcGis 10.2 software to screen out 10 factors such as climate and altitude to predict its future potential distribution area because of climate change. The results show that when the parameters are FC = LQHP and RM = 3, the MaxEnt model is optimal and AUC values are greater than 0.95. The precipitation of the driest month (bio14), temperature seasonality (bio4), elevation (ele), isothermality (bio3), and the minimum temperature of coldest month (bio6) were the main environmental factors affecting the potential range of the Q. spinosa. At present, high-suitability areas are mainly in the Hunan, Fujian, Jiangxi, Chongqing, Guizhou, Anhui, and Sichuan provinces of China. In the future, the potential distribution area of Q. spinosa may gradually extend to the northwest and north. The low-concentration emissions scenario in the future can increase the area of suitable habitat for Q. spinosa and slow down the reduction in the amount of high-suitability areas to a certain extent. In conclusion, the habitat of Q. spinosa is mainly distributed in southern China. Because of global climate change, the high-altitude mountainous areas in southern China with abundant water resources may be the main potential habitat area of Q. spinosa. Predicting the changes in the distribution patterns of Q. spinosa can better help us understand the biogeography of Q. spinosa and develop conservation strategies to minimize the impacts of climate change.
Collapse
|
6
|
Phylogeography of the Plateau Pika (Ochotona curzoniae) in Response to the Uplift of the Qinghai-Tibet Plateau. DIVERSITY 2023. [DOI: 10.3390/d15020307] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/22/2023]
Abstract
The evolution and current distribution of species on the Qinghai-Tibet Plateau have been significantly impacted by historical occurrences, including the uplift of the plateau and the Quaternary climate upheaval. As a remnant species, the plateau pika (Ochotona curzoniae) is a great model for researching historical events. In this study, 302 samples from 42 sample sites were utilized to analyze the impact of historical events on the evolution and distribution pattern of plateau pikas. The genetic diversity, patterns of differentiation, and historical dynamics of the plateau pika were investigated using molecular markers that included four mitochondrial genes (COI, D-loop, Cytb, and 12S rRNA) and three nuclear genes (GHR, IRBP, and RAG1). The results showed that: (1) The genetic diversity of the plateau pika was high in the Tibetan Plateau (Hd = 0.9997, π = 0.01205), and the plateau pika evolved into five lineages that occupied different geographical areas, with lineage 1 (Group 1) in the south of the Yarlung Zangbo River, lineage 2 (Group 2) in the hinterland of the plateau, lineage 3 (Group 3) in the northeastern part of the plateau, lineage 4 (Group 4) in the Hengduan Mountains, and lineage 5 (Group 5) in the eastern part of the plateau. (2) The gene flow among the five lineages was low, and the differentiation level was high (Nm < 0.25; Fst > 0.25), indicating that the geographical barriers between the five lineages, such as the Yarlung Zangbo River, the Qaidam-Ghuong-Guide Basin, and the Lancang River, effectively promoted the population differentiation of the plateau pika. (3) The plateau pika first spread from the Hengduan Mountains to the entire Qinghai-Tibet Plateau and then conducted small-scale migration and dispersal in several refuges across the plateau in response to climate changes during the glacial and interglacial periods. (4) Except for Group 1 and Group 4, all the other populations exhibited a rapid expansion between 0.06 and 0.01 Mya, but the expansion was considerably delayed or halted by the effects of climate change during the last glacial maximum (0.02 Mya). Overall, the plateau pika on the Qinghai-Tibet Plateau exhibits high genetic diversity, and topographic obstacles, including mountains, valleys, and basins, created by the uplift of the plateau and climatic changes since the Quaternary period have played an important role in the differentiation and historical dynamics of the plateau pika population.
Collapse
|
7
|
Zhao C, Jiang J, Xie F, Li C, Zhao T. Assessment of Amphibians Vulnerability to Climate Change in China. Front Ecol Evol 2022. [DOI: 10.3389/fevo.2022.826910] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Global climate change is considered to be one of the main threats to organisms. As poikilothermic animals, amphibians are in particular sensitive because they cannot adapt to the dramatic climate change through active physiological regulation. Using 104 representative species, the present study conducted an assessment of amphibians vulnerability to climate change in China through the combination of two approaches. Specifically, 18 vulnerability criteria belonging to five categories (i.e., thermal tolerance, individual reproductive, population diffusion and diversity, food and habitat, and climate conditions) were first selected and scored based on literatures and experts opinions. Species were then ranked into three levels of climate change vulnerability (i.e., high, moderate, and low) by calculating vulnerability scores and conducting natural breaks analyses, as well as performing a principal coordinate analysis (PCoA) and k-means cluster analyses, respectively. To integrate the two results, a matrix with the ranks from each result was developed to produce a final integrated list. Our results indicated that the 104 amphibian species were classified into three types by natural breaks, with 54 low vulnerable species, 41 moderately vulnerable species, and nine highly vulnerable species. Based on the results of PCoA and k-means cluster analyses, five species were highly vulnerable, 38 species were moderately vulnerable, and 61 species were low vulnerable. The combination of the two ranks suggested that 36 species such as Hyla tsinlingensis and Liangshantriton taliangensis were of low vulnerability, 54 species such as Echinotriton chinhaiensis and Hynobius chinensis were of moderate vulnerability, and 14 species such as Ichthyophis kohtaoensis and Zhangixalus prasinatus were of high vulnerability. Overall, our results indicated that climate change could have strong potential effects on amphibians in China. And the highly vulnerable species such as Ichthyophis kohtaoensis, Zhangixalus prasinatus, and Theloderma corticale should be the priority in future conservation activities.
Collapse
|
8
|
Amiri N, Vaissi S, Aghamir F, Saberi‐Pirooz R, Rödder D, Ebrahimi E, Ahmadzadeh F. Tracking climate change in the spatial distribution pattern and the phylogeographic structure of Hyrcanian wood frog,
Rana pseudodalmatina
(Anura: Ranidae). J ZOOL SYST EVOL RES 2021. [DOI: 10.1111/jzs.12503] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- Negar Amiri
- Department of Biodiversity and Ecosystem Management Environmental Sciences Research Institute Shahid Beheshti University Tehran Iran
| | - Somaye Vaissi
- Department of Biology Faculty of Science Razi University Kermanshah Iran
| | - Fateme Aghamir
- Department of Agroecology Environmental Sciences Research Institute Shahid Beheshti University Tehran Iran
| | - Reihaneh Saberi‐Pirooz
- Department of Biodiversity and Ecosystem Management Environmental Sciences Research Institute Shahid Beheshti University Tehran Iran
| | - Dennis Rödder
- Herpetology Section Zoologisches Forschungsmuseum Alexander Koenig (ZFMK) Bonn Germany
| | - Elham Ebrahimi
- Department of Biodiversity and Ecosystem Management Environmental Sciences Research Institute Shahid Beheshti University Tehran Iran
| | - Faraham Ahmadzadeh
- Department of Biodiversity and Ecosystem Management Environmental Sciences Research Institute Shahid Beheshti University Tehran Iran
| |
Collapse
|
9
|
Hu J, Huang Y, Jiang J, Guisan A. Genetic diversity in frogs linked to past and future climate changes on the roof of the world. J Anim Ecol 2019; 88:953-963. [PMID: 30861112 DOI: 10.1111/1365-2656.12974] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2018] [Revised: 12/05/2018] [Accepted: 02/13/2019] [Indexed: 11/29/2022]
Abstract
Mountains, representing storehouses of biodiversity, endemism and threatened species, are biodiversity hotspots of great conservation importance. However, increasing evidence indicates that mountain species throughout the world are responding to climate change, past or contemporary, by shifting their geographic distributions and patterns of genetic diversity, potentially affecting their adaptive capacity and increasing risk of extinction. Using the iconic high-elevation frog Nanorana parkeri as indicator, we showed how spatial analyses of climatic stability combined with genetic data allow unravelling amphibian responses to past and future climate changes on 'the roof of the world'-the Qinghai-Tibetan Plateau. We found that areas along the Yarlung Tsangpo Valley were climatically more stable relative to other regions, apparently serving as a large climatic refugium during Quaternary glaciations, but that these areas will likely be affected by future climate change. As populations closer to Quaternary refugia usually had higher genetic diversity, current genetic diversity can be explained in the largest part by distance to historically stable areas, outweighing other historical and contemporary factors. Along with the dynamics of suitable range, a fluctuating habitat fragmentation supported the pattern of historical changes in genetic diversity (Ne ) over time. Our results emphasize strong relationships between amphibian genetic diversity, past range dynamics and where to preserve suitable habitats in the face of future climate changes. More generally, our findings highlighted a central role of refugia during Quaternary climatic fluctuations, and how isolation from refugia may have modulated amphibian genetic diversity across the Qinghai-Tibetan Plateau.
Collapse
Affiliation(s)
- Junhua Hu
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration and Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
| | - Yan Huang
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration and Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
| | - Jianping Jiang
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration and Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
| | - Antoine Guisan
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland.,Institute of Earth Surface Dynamics, University of Lausanne, Lausanne, Switzerland
| |
Collapse
|
10
|
Jiang L, You Z, Yu P, Ruan Q, Chen W. The first complete mitochondrial genome sequence of Nanorana parkeri and Nanorana ventripunctata (Amphibia: Anura: Dicroglossidae), with related phylogenetic analyses. Ecol Evol 2018; 8:6972-6987. [PMID: 30073060 PMCID: PMC6065340 DOI: 10.1002/ece3.4214] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2017] [Revised: 04/20/2018] [Accepted: 04/24/2018] [Indexed: 11/24/2022] Open
Abstract
Members of the Nanorana genus (family Dicroglossidae) are often referred to as excellent model species with which to study amphibian adaptations to extreme environments and also as excellent keystone taxa for providing insights into the evolution of the Dicroglossidae. However, a complete mitochondrial genome is currently only available for Nanorana pleskei. Thus, we analyzed the complete mitochondrial genomes of Nanorana parkeri and Nanorana ventripunctata to investigate their evolutionary relationships within Nanorana and their phylogenetic position in the family Dicroglossidae. Our results showed that the genomes of N. parkeri (17,837 bp) and N. ventripunctata (18,373 bp) encode 13 protein‐coding genes (PCGs), two ribosomal RNA genes, 23 transfer RNA (tRNA) genes, and a noncoding control region. Overall sequences and genome structure of the two species showed high degree of similarity with N. pleskei, although the motif structures and repeat sequences of the putative control region showed clear differences among these three Nanorana species. In addition, a tandem repeat of the tRNA‐Met gene was found located between the tRNA‐Gln and ND2 genes. On both the 5′ and 3′‐sides, the control region possessed distinct repeat regions; however, the CSB‐2 motif was not found in N. pleskei. Based on the nucleotide sequences of 13 PCGs, our phylogenetic analyses, using Bayesian inference and maximum‐likelihood methods, illustrate the taxonomic status of Nanorana with robust support showing that N. ventripunctata and N. pleskei are more closely related than they are to N. parkeri. In conclusion, our analyses provide a more robust and reliable perspective on the evolutionary history of Dicroglossidae than earlier analyses, which used only a single species (N. pleskei).
Collapse
Affiliation(s)
- Lichun Jiang
- Ecological Security and Protection Key Laboratory of Sichuan Province Mianyang Normal University Mianyang Sichuan China.,Key Laboratory for Molecular Biology and Biopharmaceutics School of Life Science and Technology Mianyang Normal University Mianyang Sichuan China
| | - Zhangqiang You
- Ecological Security and Protection Key Laboratory of Sichuan Province Mianyang Normal University Mianyang Sichuan China
| | - Peng Yu
- Key Laboratory for Molecular Biology and Biopharmaceutics School of Life Science and Technology Mianyang Normal University Mianyang Sichuan China
| | - Qiping Ruan
- Key Laboratory for Molecular Biology and Biopharmaceutics School of Life Science and Technology Mianyang Normal University Mianyang Sichuan China
| | - Wei Chen
- Ecological Security and Protection Key Laboratory of Sichuan Province Mianyang Normal University Mianyang Sichuan China
| |
Collapse
|
11
|
Wang GD, Zhang BL, Zhou WW, Li YX, Jin JQ, Shao Y, Yang HC, Liu YH, Yan F, Chen HM, Jin L, Gao F, Zhang Y, Li H, Mao B, Murphy RW, Wake DB, Zhang YP, Che J. Selection and environmental adaptation along a path to speciation in the Tibetan frog Nanorana parkeri. Proc Natl Acad Sci U S A 2018; 115:E5056-E5065. [PMID: 29760079 PMCID: PMC5984489 DOI: 10.1073/pnas.1716257115] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Tibetan frogs, Nanorana parkeri, are differentiated genetically but not morphologically along geographical and elevational gradients in a challenging environment, presenting a unique opportunity to investigate processes leading to speciation. Analyses of whole genomes of 63 frogs reveal population structuring and historical demography, characterized by highly restricted gene flow in a narrow geographic zone lying between matrilines West (W) and East (E). A population found only along a single tributary of the Yalu Zangbu River has the mitogenome only of E, whereas nuclear genes of W comprise 89-95% of the nuclear genome. Selection accounts for 579 broadly scattered, highly divergent regions (HDRs) of the genome, which involve 365 genes. These genes fall into 51 gene ontology (GO) functional classes, 14 of which are likely to be important in driving reproductive isolation. GO enrichment analyses of E reveal many overrepresented functional categories associated with adaptation to high elevations, including blood circulation, response to hypoxia, and UV radiation. Four genes, including DNAJC8 in the brain, TNNC1 and ADORA1 in the heart, and LAMB3 in the lung, differ in levels of expression between low- and high-elevation populations. High-altitude adaptation plays an important role in maintaining and driving continuing divergence and reproductive isolation. Use of total genomes enabled recognition of selection and adaptation in and between populations, as well as documentation of evolution along a stepped cline toward speciation.
Collapse
Affiliation(s)
- Guo-Dong Wang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming 650223, China
| | - Bao-Lin Zhang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
- Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming 650204, Yunnan, China
| | - Wei-Wei Zhou
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
- Southeast Asia Biodiversity Research Institute, Chinese Academy of Sciences, Yezin, 05282 Nay Pyi Taw, Myanmar
| | - Yong-Xin Li
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
- Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming 650204, Yunnan, China
| | - Jie-Qiong Jin
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
| | - Yong Shao
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
| | - He-Chuan Yang
- Human Genetics, Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore 138672, Singapore
| | - Yan-Hu Liu
- Laboratory for Conservation and Utilization of Bio-Resources & Key Laboratory for Microbial Resources of the Ministry of Education, Yunnan University, Kunming 650091, China
| | - Fang Yan
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
| | - Hong-Man Chen
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
| | - Li Jin
- Key Laboratory of Freshwater Fish Reproduction and Development of the Ministry of Education and Key Laboratory of Aquatic Science of Chongqing, Southwest University School of Life Sciences, Chongqing 400715, China
| | - Feng Gao
- CAS Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Yaoguang Zhang
- Key Laboratory of Freshwater Fish Reproduction and Development of the Ministry of Education and Key Laboratory of Aquatic Science of Chongqing, Southwest University School of Life Sciences, Chongqing 400715, China
| | - Haipeng Li
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming 650223, China
- CAS Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Bingyu Mao
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming 650223, China
| | - Robert W Murphy
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
- Centre for Biodiversity and Conservation Biology, Royal Ontario Museum, Toronto, ON, Canada M5S 2C6
| | - David B Wake
- Department of Integrative Biology and Museum of Vertebrate Zoology, University of California, Berkeley, CA 94720-3160
| | - Ya-Ping Zhang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China;
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming 650223, China
| | - Jing Che
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China;
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming 650223, China
- Southeast Asia Biodiversity Research Institute, Chinese Academy of Sciences, Yezin, 05282 Nay Pyi Taw, Myanmar
| |
Collapse
|
12
|
Wang B, Xie F, Li J, Wang G, Li C, Jiang J. Phylogeographic investigation and ecological niche modelling of the endemic frog species Nanorana pleskei revealed multiple refugia in the eastern Tibetan Plateau. PeerJ 2017; 5:e3770. [PMID: 28924497 PMCID: PMC5598431 DOI: 10.7717/peerj.3770] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2016] [Accepted: 08/16/2017] [Indexed: 11/22/2022] Open
Abstract
The largest plateau Tibetan Plateau supplied an excellent opportunity to investigate the influence of the Pleistocene events on the high-elevation species. To test for the alternative hypotheses of Pleistocene glacial refugia, we used partial sequences of two mitochondrial genes and one nuclear gene to examine the phylogeographic patterns of the endemic frog species Nanorana pleskei across its known range in the eastern Tibetan Plateau, and conducted species distribution modelling (SDM) to explore changes of its distribution range through current and paleo periods. In all data sets, the species was divided into lineage north occupying open plateau platform and lineage south colonizing the mountainous plateau. The divergence of two major clades was estimated at the early Pleistocene. In mtDNA, lineage north contained northeastern and northwestern sublineages, and lineage south had two overlapping-distributed sublineages. Different lineages possessed distinct demographic characteristics, i.e., subdivision in the northeastern sublineage, historical bottleneck effects and recent expansions in the northwestern sublineage and the southeastern sublineage. SDMs depicted that stable suitable habitats had existed in the upper-middle streams of the Yellow River, Dadu River, Jinsha River and Yalong River. These regions were also recognized as the ancestral areas of different lineages. In conclusion, Nanorana pleskei lineages have probably experienced long-term separations. Stable suitable habitats existing in upper-middle streams of major rivers on the eastern Tibetan Plateau and distinct demographic dynamics of different lineages indicated that the lineages possessed independent evolutionary processes in multiple glacial refugia. The findings verified the profound effects of Pleistocene climatic fluctuations on the plateau endemic species.
Collapse
Affiliation(s)
- Bin Wang
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization, Ecological Restoration and Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, Sichuan, China
| | - Feng Xie
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization, Ecological Restoration and Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, Sichuan, China
| | - Jiannan Li
- Nanjing Institute of Environmental Sciences Under Ministry of Environmental Protection, Nanjing, Jiangsu, China
| | - Gang Wang
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization, Ecological Restoration and Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, Sichuan, China
| | - Cheng Li
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization, Ecological Restoration and Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, Sichuan, China
| | - Jianping Jiang
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization, Ecological Restoration and Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, Sichuan, China
| |
Collapse
|
13
|
Cheng J, Lv X, Xia L, Ge D, Zhang Q, Lu L, Yang Q. Impact of Orogeny and Environmental Change on Genetic Divergence and Demographic History of Dipus sagitta (Dipodoidea, Dipodinae) since the Pliocene in Inland East Asia. J MAMM EVOL 2017. [DOI: 10.1007/s10914-017-9397-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
|
14
|
Zhou W, Jin J, Wu J, Chen H, Yang J, Murphy RW, Che J. Mountains too high and valleys too deep drive population structuring and demographics in a Qinghai-Tibetan Plateau frog Nanorana pleskei (Dicroglossidae). Ecol Evol 2016; 7:240-252. [PMID: 28070287 PMCID: PMC5214757 DOI: 10.1002/ece3.2646] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2016] [Revised: 11/09/2016] [Accepted: 11/13/2016] [Indexed: 12/31/2022] Open
Abstract
Pleistocene glacial–interglacial climatic oscillations greatly shaped the current genetic structure of many species. However, geographic features may influence the impact of climatic cycling. Distinct geographic and environmental characters between northern and southern parts of the eastern Qinghai–Tibetan Plateau (EQTP) facilitate explorations into the impacts of geographic features on species. The northern parts of EQTP contain large areas of marsh, and the environment is rather homogeneous. In contrast, the southern EQTP harbors complex alpine valleys and a much more heterogeneous setting. We evaluate DNA sequence variation from both the mitochondrial and nuclear genomes in Nanorana pleskei, a species endemic to the EQTP. Hypothesis testing on the evolutionary history of N. pleskei indicates that northern populations can disperse freely, but alpine valleys isolate southern populations. Demographic histories between northern and southern populations also differ. Northern populations appear to have experienced population expansions, while southern frogs exhibit a far more stable demographic history. By combining climatic analyses and species' distribution models, our study suggests that geographic and environmental features drive the differences between the northern and southern EQTP.
Collapse
Affiliation(s)
- Weiwei Zhou
- State Key Laboratory of Genetic Resources and Evolution Kunming Institute of Zoology Chinese Academy of Sciences Kunming China
| | - Jieqiong Jin
- State Key Laboratory of Genetic Resources and Evolution Kunming Institute of Zoology Chinese Academy of Sciences Kunming China
| | - Jun Wu
- Nanjing Institute of Environmental Sciences Ministry of Environmental Protection Nanjing China
| | - Hongman Chen
- State Key Laboratory of Genetic Resources and Evolution Kunming Institute of Zoology Chinese Academy of Sciences Kunming China
| | - Junxiao Yang
- State Key Laboratory of Genetic Resources and Evolution Kunming Institute of Zoology Chinese Academy of Sciences Kunming China; Kunming College of Life Science University of Chinese Academy of Sciences Kunming China
| | - Robert W Murphy
- State Key Laboratory of Genetic Resources and Evolution Kunming Institute of Zoology Chinese Academy of Sciences Kunming China; Centre for Biodiversity and Conservation Biology Royal Ontario Museum Toronto ON Canada
| | - Jing Che
- State Key Laboratory of Genetic Resources and Evolution Kunming Institute of Zoology Chinese Academy of Sciences Kunming China
| |
Collapse
|
15
|
Chen W, Shen Y, Gan X, Wang X, He S. Genetic diversity and evolutionary history of the Schizothorax species complex in the Lancang River (upper Mekong). Ecol Evol 2016; 6:6023-36. [PMID: 27648223 PMCID: PMC5016629 DOI: 10.1002/ece3.2319] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2016] [Revised: 06/20/2016] [Accepted: 06/21/2016] [Indexed: 11/28/2022] Open
Abstract
The genus Schizothorax (Cyprinidae), one of the most diverse genera of ichthyofauna of the Qinghai‐Tibetan Plateau (QTP), is a good candidate for investigating patterns of genetic variation and evolutionary mechanisms. In this study, sequences from the mitochondrial control region, the cytochrome b gene, and two nuclear genes were used to re‐examine the genetic diversity and investigate the evolutionary history of the Schizothorax species complex inhabiting the Lancang River. Three maternal clades were detected in the Schizothorax species complex, but frequent nuclear allele sharing also occurred among the three maternal clades. A discrepancy between topologies of mitochondrial and nuclear loci might result from introgression or/and incomplete lineage sorting. The divergence of the clades of the Schizothorax species complex was closely related to the Late Pliocene and Early Pleistocene orogenesis of the QTP and Southwest Mountains of China. Demographic analyses indicated that the species complex subsequently persisted in situ with stable populations during Pleistocene glacial cycling, which suggested that Pleistocene climate changes did not exert a remarkable influence on the species complex. Our study provides a comprehensive analysis of the genetic diversity and evolutionary history of the Schizothorax species complex in the Lancang River.
Collapse
Affiliation(s)
- Weitao Chen
- The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences Institute of Hydrobiology Chinese Academy of Sciences Wuhan Hubei 430072 China; Graduate School of Chinese Academy of Sciences Beijing 10001 China
| | - Yanjun Shen
- The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences Institute of Hydrobiology Chinese Academy of Sciences Wuhan Hubei 430072 China; Graduate School of Chinese Academy of Sciences Beijing 10001 China
| | - Xiaoni Gan
- The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences Institute of Hydrobiology Chinese Academy of Sciences Wuhan Hubei 430072 China
| | - Xuzhen Wang
- The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences Institute of Hydrobiology Chinese Academy of Sciences Wuhan Hubei 430072 China
| | - Shunping He
- The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences Institute of Hydrobiology Chinese Academy of Sciences Wuhan Hubei 430072 China
| |
Collapse
|