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Palacios C, Wang P, Wang N, Brown MA, Capatosto L, Du J, Jiang J, Zhang Q, Dahal N, Lamichhaney S. Genomic Variation, Population History, and Long-Term Genetic Adaptation to High Altitudes in Tibetan Partridge (Perdix hodgsoniae). Mol Biol Evol 2023; 40:msad214. [PMID: 37768198 PMCID: PMC10583571 DOI: 10.1093/molbev/msad214] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Revised: 09/09/2023] [Accepted: 09/25/2023] [Indexed: 09/29/2023] Open
Abstract
Species residing across elevational gradients display adaptations in response to environmental changes such as oxygen availability, ultraviolet radiation, and temperature. Here, we study genomic variation, gene expression, and long-term adaptation in Tibetan Partridge (Perdix hodgsoniae) populations residing across the elevational gradient of the Tibetan Plateau. We generated a high-quality draft genome and used it to carry out downstream population genomic and transcriptomic analysis. The P. hodgsoniae populations residing across various elevations were genetically distinct, and their phylogenetic clustering was consistent with their geographic distribution. We identified possible evidence of gene flow between populations residing in <3,000 and >4,200 m elevation that is consistent with known habitat expansion of high-altitude populations of P. hodgsoniae to a lower elevation. We identified a 60 kb haplotype encompassing the Estrogen Receptor 1 (ESR1) gene, showing strong genetic divergence between populations of P. hodgsoniae. We identified six single nucleotide polymorphisms within the ESR1 gene fixed for derived alleles in high-altitude populations that are strongly conserved across vertebrates. We also compared blood transcriptome profiles and identified differentially expressed genes (such as GAPDH, LDHA, and ALDOC) that correlated with differences in altitude among populations of P. hodgsoniae. These candidate genes from population genomics and transcriptomics analysis were enriched for neutrophil degranulation and glycolysis pathways, which are known to respond to hypoxia and hence may contribute to long-term adaptation to high altitudes in P. hodgsoniae. Our results highlight Tibetan Partridges as a useful model to study molecular mechanisms underlying long-term adaptation to high altitudes.
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Affiliation(s)
- Catalina Palacios
- Department of Biological Sciences, Kent State University, Kent, OH 44242, USA
| | - Pengcheng Wang
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing 210023, P. R. China
| | - Nan Wang
- School of Ecology and Nature Conservation, Beijing Forestry University, Beijing 100083, P. R. China
| | - Megan A Brown
- Department of Biological Sciences, Kent State University, Kent, OH 44242, USA
| | - Lukas Capatosto
- Department of Biological Sciences, Kent State University, Kent, OH 44242, USA
| | - Juan Du
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, P. R. China
| | - Jiahu Jiang
- School of Ecology and Nature Conservation, Beijing Forestry University, Beijing 100083, P. R. China
| | - Qingze Zhang
- School of Ecology and Nature Conservation, Beijing Forestry University, Beijing 100083, P. R. China
| | - Nishma Dahal
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur, HP 176061, India
| | - Sangeet Lamichhaney
- Department of Biological Sciences, Kent State University, Kent, OH 44242, USA
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Shen R, Aspöck H, Aspöck U, Plant J, Dai Y, Liu X. Unraveling the evolutionary history of the snakefly family Inocelliidae (Insecta: Raphidioptera) through integrative phylogenetics. Cladistics 2022; 38:515-537. [PMID: 35349190 DOI: 10.1111/cla.12503] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Revised: 02/21/2022] [Accepted: 02/26/2022] [Indexed: 01/31/2023] Open
Abstract
Inocelliidae is one of the two extant families of the holometabolan order Raphidioptera (snakeflies), with the modern fauna represented by seven genera and 44 species. The evolutionary history of the family is little-known. Here we present the first phylogenetic and biogeographical analyses based on a worldwide sampling of taxa and datasets combined with morphological characters and mitochondrial genomes, aiming to investigate the intergeneric phylogeny and historical biogeography of Inocelliidae. The phylogenetic inference from the combined analysis of morphological and molecular data recovered the sister-group relationship between a clade of (Negha + Indianoinocellia) + Sininocellia and a clade of Fibla + the Inocellia clade (interiorly nested by Amurinocellia and Parainocellia). Amurinocellia stat.r. and Parainocellia stat.r. et emend.n. are relegated to subgeneric status within Inocellia, whereas a newly erected subgenus of Inocellia, Epinocellia subgen.n., accommodates the former Parainocellia burmana (U. Aspöck and H. Aspöck, 1968) plus a new species Inocellia (Epinocellia) weii sp.n. Further, the Inocellia crassicornis group constitutes the nominotypical subgenus Inocellia stat.n., but the Inocellia fulvostigmata group is paraphyletic. Diversification within Inocelliidae is distinguished by an Eocene divergence leading to extant genera and a Miocene radiation of species. A biogeographical scenario depicts how the diverse inocelliid fauna from East Asia could have originated from western North America via dispersal across the Beringia during the early Tertiary, and how the Miocene ancestors of Inocellia could have accomplished long-distance dispersals via the Tibet-Himalayan corridor or eastern Palaearctic to western Palaearctic. Our results shed new light specifically on the evolution of Inocelliidae and, in general, the Raphidioptera.
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Affiliation(s)
- Rongrong Shen
- Department of Entomology, China Agricultural University, Beijing, 100193, China
| | - Horst Aspöck
- Institute of Specific Prophylaxis and Tropical Medicine, Medical Parasitology, Medical University of Vienna, Kinderspitalgasse 15, Vienna, A-1090, Austria
| | - Ulrike Aspöck
- Naturhistorisches Museum Wien, Zweite Zoologische Abteilung, Burgring 7, Vienna, A-1010, Austria.,Unit for Integrative Zoology, Department of Evolutionary Biology, University of Vienna, Djerassiplatz 1, Vienna, A-1030, Austria
| | - John Plant
- Unit for Integrative Zoology, Department of Evolutionary Biology, University of Vienna, Djerassiplatz 1, Vienna, A-1030, Austria
| | - Yuting Dai
- Wujiang Customs, Suzhou, Jiangsu, 215200, China
| | - Xingyue Liu
- Department of Entomology, China Agricultural University, Beijing, 100193, China
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Yang MX, Werth S, Wang LS, Scheidegger C. Phylogeographic analyses of an epiphytic foliose lichen show multiple dispersal events westward from the Hengduan Mountains of Yunnan into the Himalayas. Ecol Evol 2022; 12:e9308. [PMID: 36177127 PMCID: PMC9475131 DOI: 10.1002/ece3.9308] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Revised: 08/24/2022] [Accepted: 08/26/2022] [Indexed: 11/09/2022] Open
Abstract
Lobaria pindarensis is an endemic species of the Himalayas and the Hengduan Mountains. Little information is available on the phylogeography genetics and colonization history of this species or how its distribution patterns changed in response to the orographic history of the Himalayas and Hengduan Mountains. Based on samples covering a major part of the species' distribution range, we used 443 newly generated sequences of nine loci for molecular coalescent analyses in order to reconstruct the evolutionary history of L. pindarensis, and to reconstruct the species' ancestral phylogeographic distributions using Bayesian binary MCMC analyses. The results suggest that current populations originated from the Yunnan region of the Hengduan Mountains in the middle Pliocene, and that the Himalayas of Bhutan were colonized by a lineage that diverged from Yunnan ca. 2.72 Ma. The analysis additionally indicates that the Nepal and Xizang areas of the Himalayas were colonized from Yunnan as well, and that there was later a second dispersal event from Yunnan to Bhutan. We conclude that the change in climate and habitat related to the continuous uplift of the Himalayas and the Hengduan Mountains in the late Pliocene and middle Pleistocene influenced the geographic distribution pattern of L. pindarensis.
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Affiliation(s)
- Mei-Xia Yang
- Biodiversity and Conservation Biology Swiss Federal Institute for Forest, Snow and Landscape Research WSL Birmensdorf Switzerland.,Institute of Plant Sciences University of Bern Bern Switzerland.,Division of Life Science and Center for Chinese Medicine The Hong Kong University of Science and Technology Hong Kong China
| | - Silke Werth
- Systematics, Biodiversity and Evolution of Plants, Ludwig Maximilian University Munich Munich Germany
| | - Li-Song Wang
- Key Laboratory for Plant Diversity and Biogeography of East Asia Kunming Institute of Botany, Chinese Academy of Sciences Kunming China
| | - Christoph Scheidegger
- Biodiversity and Conservation Biology Swiss Federal Institute for Forest, Snow and Landscape Research WSL Birmensdorf Switzerland
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Yin H, Zhou H, Wang W, Tran LSP, Zhang B. Transcriptome Analysis Reveals Potential Roles of Abscisic Acid and Polyphenols in Adaptation of Onobrychis viciifolia to Extreme Environmental Conditions in the Qinghai-Tibetan Plateau. Biomolecules 2020; 10:biom10060967. [PMID: 32604957 PMCID: PMC7356597 DOI: 10.3390/biom10060967] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2020] [Revised: 06/22/2020] [Accepted: 06/23/2020] [Indexed: 11/16/2022] Open
Abstract
A detailed understanding of the molecular mechanisms of plant stress resistance in the face of ever-changing environmental stimuli will be helpful for promoting the growth and production of crop and forage plants. Investigations of plant responses to various single abiotic or biotic factors, or combined stresses, have been extensively reported. However, the molecular mechanisms of plants in responses to environmental stresses under natural conditions are not clearly understood. In this study, we carried out a transcriptome analysis using RNA-sequencing to decipher the underlying molecular mechanisms of Onobrychis viciifolia responding and adapting to the extreme natural environment in the Qinghai-Tibetan Plateau (QTP). The transcriptome data of plant samples collected from two different altitudes revealed a total of 8212 differentially expressed genes (DEGs), including 5387 up-regulated and 2825 down-regulated genes. Detailed analysis of the identified DEGs uncovered that up-regulation of genes potentially leading to changes in hormone homeostasis and signaling, particularly abscisic acid-related ones, and enhanced biosynthesis of polyphenols play vital roles in the adaptive processes of O. viciifolia. Interestingly, several DEGs encoding uridine diphosphate glycosyltransferases, which putatively regulate phytohormone homeostasis to resist environmental stresses, were also discovered. Furthermore, numerous DEGs encoding transcriptional factors, such as members of the myeloblastosis (MYB), homeodomain-leucine zipper (HD-ZIP), WRKY, and nam-ataf1,2-cuc2 (NAC) families, might be involved in the adaptive responses of O. viciifolia to the extreme natural environmental conditions. The DEGs identified in this study represent candidate targets for improving environmental stress resistance of O. viciifolia grown in higher altitudes of the QTP, and can provide deep insights into the molecular mechanisms underlying the responses of this plant species to the extreme natural environmental conditions of the QTP.
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Affiliation(s)
- Hengxia Yin
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining 810016, China;
| | - Huakun Zhou
- The Key Laboratory of Restoration Ecology in Cold Region of Qinghai Province, Northwest Institute of Plateau Biology, Chinese Academy of Science, Xining 810008, China;
| | - Wenying Wang
- School of Life Science, Qinghai Normal University, Xining 810008, China;
| | - Lam-Son Phan Tran
- Institute of Research and Development, Duy Tan University, 03 Quang Trung, Da Nang 550000, Vietnam
- Correspondence: (L.-S.P.T.); (B.Z.)
| | - Benyin Zhang
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining 810016, China;
- College of Eco-Environmental Engineering, Qinghai University, Xining 810016, China
- Correspondence: (L.-S.P.T.); (B.Z.)
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Ye M, Zhu X, Gao P, Jiang L, Wu R. Identification of Quantitative Trait Loci for Altitude Adaptation of Tree Leaf Shape With Populus szechuanica in the Qinghai-Tibetan Plateau. FRONTIERS IN PLANT SCIENCE 2020; 11:632. [PMID: 32536931 PMCID: PMC7267013 DOI: 10.3389/fpls.2020.00632] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Accepted: 04/24/2020] [Indexed: 06/11/2023]
Abstract
As an important functional organ of plants, leaves alter their shapes in response to a changing environment. The variation of leaf shape has long been an important evolutionary and developmental force in plants. Despite an increasing amount of investigations into the genetic controls of leaf morphology, few have systematically studied the genetic architecture controlling shape differences among distinct altitudes. Altitude denotes a comprehensive complex of environmental factors affecting plant growth in many aspects, e.g., UV-light radiation, temperature, and humidity. To reveal how plants alter ecological adaptation to altitude through genes, we used Populus szechuanica var. tibetica growing on the Qinghai-Tibetan plateau. F ST between the low- and high- altitude population was 0.00748, Q ST for leaf width, length and area were 0.00924, 0.1108, 0.00964 respectively. With the Elliptic Fourier-based morphometric model, association study of leaf shape was allowed, the dissection of the pleiotropic expression of genes mediating altitude-derived leaf shape variation was performed. For high and low altitudes, 130 and 131 significant single-nucleotide polymorphisms (SNPs) were identified. QTLs that affected leaf axis length and leaf width were expressed in both-altitude population, while QTLs regulating "leaf tip" and "leaf base" were expressed in low-altitude population. Pkinase and PRR2 were common significant genes in both types of populations. Auxin-related and differentiation-related genes included PIN1, CDK-like, and CAK1AT at high altitude, whereas they included NAP5, PIN-LIKES, and SCL1 at low altitude. The presence of Stress-antifung gene, CIPK3 and CRPK1 in high-altitude population suggested an interaction between genes and harsh environment in mediating leaf shape, while the senescence repression-related genes (EIN2 and JMJ18) and JMT in jasmonic acid pathway in low-altitude population suggested their crucial roles in ecological adaptability. These data provide new information that strengthens the understanding of genetic control with respect to leaf shape and constitute an entirely novel perspective regarding leaf adaptation and development in plants.
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Affiliation(s)
- Meixia Ye
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing, China
- Center for Computational Biology, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | - Xuli Zhu
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing, China
- Center for Computational Biology, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | - Pan Gao
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing, China
- Center for Computational Biology, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | - Libo Jiang
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing, China
- Center for Computational Biology, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | - Rongling Wu
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing, China
- Center for Computational Biology, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
- Center for Statistical Genetics, The Pennsylvania State University, Hershey, PA, United States
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Li Y, Zhang C, Yang K, Shi J, Ding Y, Gao Z. De novo sequencing of the transcriptome reveals regulators of the floral transition in Fargesia macclureana (Poaceae). BMC Genomics 2019; 20:1035. [PMID: 31888463 PMCID: PMC6937737 DOI: 10.1186/s12864-019-6418-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2019] [Accepted: 12/19/2019] [Indexed: 12/25/2022] Open
Abstract
Background Fargesia macclureana (Poaceae) is a woody bamboo species found on the Qinghai–Tibet Plateau (QTP) approximately 2000 ~ 3800 m above sea level. It rarely blossoms in the QTP, but it flowered 20 days after growing in our lab, which is in a low-altitude area outside the QTP. To date, little is known regarding the molecular mechanism of bamboo flowering, and no studies of flowering have been conducted on wild bamboo plants growing in extreme environments. Here, we report the first de novo transcriptome sequence for F. macclureana to investigate the putative mechanisms underlying the flowering time control used by F. macclureana to adapt to its environment. Results Illumina deep sequencing of the F. macclureana transcriptome generated 140.94 Gb of data, assembled into 99,056 unigenes. A comprehensive analysis of the broadly, specifically and differentially expressed unigenes (BEUs, SEUs and DEUs) indicated that they were mostly involved in metabolism and signal transduction, as well as DNA repair and plant-pathogen interactions, which may be of adaptive importance. In addition, comparison analysis between non-flowering and flowering tissues revealed that expressions of FmFT and FmHd3a, two putative F. macclureana orthologs, were differently regulated in NF- vs F- leaves, and carbohydrate metabolism and signal transduction were two major KEGG pathways that DEUs were enriched in. Finally, we detected 9296 simple sequence repeats (SSRs) that may be useful for further molecular marker-assisted breeding. Conclusions F. macclureana may have evolved specific reproductive strategies for flowering-related pathways in response to photoperiodic cues to ensure long vegetation growing period. Our findings will provide new insights to future investigations into the mechanisms of flowering time control and adaptive evolution in plants growing at high altitudes.
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Affiliation(s)
- Ying Li
- State Forestry and Grassland Administration Key Open Laboratory on the Science and Technology of Bamboo and Rattan, Institute of Gene Science and Industrialization for Bamboo and Rattan Resources, International Centre for Bamboo and Rattan, Beijing, 100102, China
| | - Chunxia Zhang
- Bamboo Research Institute, Nanjing Forestry University, Nanjing, 210037, Jiangsu, China
| | - Kebin Yang
- State Forestry and Grassland Administration Key Open Laboratory on the Science and Technology of Bamboo and Rattan, Institute of Gene Science and Industrialization for Bamboo and Rattan Resources, International Centre for Bamboo and Rattan, Beijing, 100102, China
| | - Jingjing Shi
- State Forestry and Grassland Administration Key Open Laboratory on the Science and Technology of Bamboo and Rattan, Institute of Gene Science and Industrialization for Bamboo and Rattan Resources, International Centre for Bamboo and Rattan, Beijing, 100102, China
| | - Yulong Ding
- Bamboo Research Institute, Nanjing Forestry University, Nanjing, 210037, Jiangsu, China
| | - Zhimin Gao
- State Forestry and Grassland Administration Key Open Laboratory on the Science and Technology of Bamboo and Rattan, Institute of Gene Science and Industrialization for Bamboo and Rattan Resources, International Centre for Bamboo and Rattan, Beijing, 100102, China.
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Liu Y, Dietrich CH, Wei C. Genetic divergence, population differentiation and phylogeography of the cicada Subpsaltria yangi based on molecular and acoustic data: an example of the early stage of speciation? BMC Evol Biol 2019; 19:5. [PMID: 30621591 PMCID: PMC6323834 DOI: 10.1186/s12862-018-1317-8] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2018] [Accepted: 12/04/2018] [Indexed: 11/17/2022] Open
Abstract
Background Geographical isolation combined with historical climatic fluctuations have been identified as two major factors that contribute to the formation of new species. On the other hand, biotic factors such as competition and predation are also able to drive the evolution and diversification of organisms. To determine whether geographical barriers contributed to population divergence or speciation in the rare endemic cicada Subpsaltria yangi the population differentiation, genetic structure and phylogeography of the species were investigated in the Loess Plateau and adjacent areas of northwestern China by analysing mitochondrial and nuclear DNA and comparing the calling song structure of 161 male individuals. Results The results reveal a low level of genetic differentiation and relatively simple phylogeographic structure for this species, but two independent clades corresponding to geographically isolated populations were recognised. Genetic and geographical distances were significantly correlated among lineages. Results of divergence-time estimation are consistent with a scenario of isolation due to glacial refugia and interglacial climate oscillation in northwestern China. Significant genetic divergence was found between the population occurring in the Helan Mountains and other populations, and recent population expansion has occurred in the Helan Mountains and/or adjacent areas. This population is also significantly different in calling song structure from other populations. Conclusions Geographical barriers (i.e., the deserts and semi-deserts surrounding the Helan Mountains), possibly coupled with related ecological differences, may have driven population divergence and allopatric speciation. This provides a possible example of incipient speciation in Cicadidae, improves understanding of population differentiation, acoustic signal diversification and phylogeographic relationships of this rare cicada species of conservation concern, and informs future studies on population differentiation, speciation and phylogeography of other insects with a high degree of endemism in the Helan Mountains and adjacent areas. Electronic supplementary material The online version of this article (10.1186/s12862-018-1317-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Yunxiang Liu
- State Key Laboratory of Crop Stress Biology for Arid Areas, and Key Laboratory of Plant Protection Resources and Pest Management, Ministry of Education, College of Plant Protection, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Christopher H Dietrich
- Illinois Natural History Survey, Prairie Research Institute, University of Illinois, Champaign, IL, 61820, USA
| | - Cong Wei
- State Key Laboratory of Crop Stress Biology for Arid Areas, and Key Laboratory of Plant Protection Resources and Pest Management, Ministry of Education, College of Plant Protection, Northwest A&F University, Yangling, 712100, Shaanxi, China.
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Yang H, Lin CP, Liang AP. Phylogeography of the Rice Spittle Bug (Callitettix versicolor) Implies Two Long-Term Mountain Barriers in South China. Zoolog Sci 2017; 33:592-602. [PMID: 27927096 DOI: 10.2108/zs160042] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
South China is a region of remarkable topographic complexity. However, the impact of climate fluctuations in the Pleistocene on the local fauna and especially insects has not been extensively studied. We integrated mitochondrial DNA (mtDNA) and microsatellite data of the rice spittle bug, Callitettix versicolor, to determine the genetic structure, potential biogeographic barriers, and historical demography of this species. The mtDNA data revealed two distinct lineages (Western and Eastern) congruent with the geographically separated western and eastern sub-regions of the Hengduan Mountains. The Eastern lineage was subdivided into two sub-lineages, E1 and E2, congruent with the geographically separated northern and southern sub-regions of the Dabie Mountains. E2 was further subdivided into two sub-groups, E2-1 and E2-2, with a hybrid zone (Guizhou and Hunan Provinces) in which their areas were contiguous. The genetic structures constructed using mtDNA were corroborated by four clusters (G1-G4) of microsatellite data. The populations of each cluster were nearly consistent with a sub-lineage of the mtDNA gene tree (G1-G4 corresponded to the Western, E1, E2-2 and E2-1 lineages, respectively). The divergence time estimated between the Western and Eastern lineages was 1.17 (0.50-2.37) to 0.89 (0.39-1.78) Mya, indicating that the lineages diversified on both geographic and temporal scales. The historical demography of the Eastern lineage showed continuous population growth after the Last Interglacial (LIG) and a stable population during the Last Glacial Maximum (LGM) period. However, the Western lineage remained largely unchanged during the LIG and LGM periods. This suggests that the historical demography of C. versicolor is probably related not only to the paleoclimate of South China, but also to the geological restriction and specific habitat preferences of species.
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Affiliation(s)
- Han Yang
- 1 Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Chung-Ping Lin
- 2 Department of Life Science, National Taiwan Normal University, Taipei, Taiwan
| | - Ai-Ping Liang
- 1 Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
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Song S, Jiang B, Liu NF. Phylogeography of chukar partridge (Alectoris chukar) in China based on mtDNA control region. Mitochondrial DNA A DNA Mapp Seq Anal 2016; 28:473-481. [PMID: 27159688 DOI: 10.3109/19401736.2015.1137901] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
The chukar partridge (Alectoris chukar) is distributed in north and northwest of China, in mountainous areas that were heavily affected by cyclic climate and landscape changes during the last Pleistocene glaciations. Some partridge populations have colonized and expanded their present ranges only after deglaciation and recent deforestation by human. Consequently, partridges from different areas could be genetically differentiated. In this study, a 1152-1154 bp portion of the mitochondrial DNA control region were analyzed for all 279 specimens collected from 28 populations through their distribution in China. A total number of 91 haplotypes were defined by 113 variable sites. The mean haplotype diversity and nucleotide diversity were 0.939 ± 0.008 and 0.0030 ± 0.0017, respectively, for chukar. Haplotype diversity among the 28 populations varied from 0.600 ± 0.215 (HH) to 1.000 ± 0.272 (SBC), and nucleotide diversity ranged from 0.0006 ± 0.0007 (HJ) to (0.0071 ± 0.0041) (HEG). The nucleotide diversity of chukar was descending from west to east and a possible historical scenario might be that A. chukar inhabited central Asia, and then dispersed eastward. Phylogenetic analyses indicated that there was no distinct phylogeographic structure in chukar populations in China. Haplotype network of chukar was star-like with some common haplotypes shared by different samples came from different populations as center. Both unstructured phylogeographic tree and star-like haplotype network are signatures of population expansion.
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Affiliation(s)
- Sen Song
- a School of Life Sciences, Lanzhou University , Lanzhou , P.R. China
| | - Bo Jiang
- a School of Life Sciences, Lanzhou University , Lanzhou , P.R. China
| | - Nai-Fa Liu
- a School of Life Sciences, Lanzhou University , Lanzhou , P.R. China
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Liu S, Jiang N, Xue D, Cheng R, Qu Y, Li X, Lei F, Han H. Evolutionary history ofApocheima cinerarius(Lepidoptera: Geometridae), a female flightless moth in northern China. ZOOL SCR 2015. [DOI: 10.1111/zsc.12147] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Shuxian Liu
- Key Laboratory of Zoological Systematics and Evolution; Institute of Zoology; Chinese Academy of Sciences; Beijing 100101 China
- University of the Chinese Academy of Sciences; Beijing 100049 China
| | - Nan Jiang
- Key Laboratory of Zoological Systematics and Evolution; Institute of Zoology; Chinese Academy of Sciences; Beijing 100101 China
| | - Dayong Xue
- Key Laboratory of Zoological Systematics and Evolution; Institute of Zoology; Chinese Academy of Sciences; Beijing 100101 China
| | - Rui Cheng
- Key Laboratory of Zoological Systematics and Evolution; Institute of Zoology; Chinese Academy of Sciences; Beijing 100101 China
- University of the Chinese Academy of Sciences; Beijing 100049 China
| | - Yanhua Qu
- Key Laboratory of Zoological Systematics and Evolution; Institute of Zoology; Chinese Academy of Sciences; Beijing 100101 China
| | - Xinxin Li
- Key Laboratory of Zoological Systematics and Evolution; Institute of Zoology; Chinese Academy of Sciences; Beijing 100101 China
- University of the Chinese Academy of Sciences; Beijing 100049 China
| | - Fumin Lei
- Key Laboratory of Zoological Systematics and Evolution; Institute of Zoology; Chinese Academy of Sciences; Beijing 100101 China
| | - Hongxiang Han
- Key Laboratory of Zoological Systematics and Evolution; Institute of Zoology; Chinese Academy of Sciences; Beijing 100101 China
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11
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Pan T, Wang H, Hu C, Sun Z, Zhu X, Meng T, Meng X, Zhang B. Species Delimitation in the Genus Moschus (Ruminantia: Moschidae) and Its High-Plateau Origin. PLoS One 2015; 10:e0134183. [PMID: 26280166 PMCID: PMC4539215 DOI: 10.1371/journal.pone.0134183] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2015] [Accepted: 07/06/2015] [Indexed: 11/29/2022] Open
Abstract
The authenticity of controversial species is a significant challenge for systematic biologists. Moschidae is a small family of musk deer in the Artiodactyla, composing only one genus, Moschus. Historically, the number of species in the Moschidae family has been debated. Presently, most musk deer species were restricted in the Tibetan Plateau and surrounding/adjacent areas, which implied that the evolution of Moschus might have been punctuated by the uplift of the Tibetan Plateau. In this study, we aimed to determine the evolutionary history and delimit the species in Moschus by exploring the complete mitochondrial genome (mtDNA) and other mitochondrial gene. Our study demonstrated that six species, M. leucogaster, M. fuscus, M. moschiferus, M. berezovskii, M. chrysogaster and M. anhuiensis, were authentic species in the genus Moschus. Phylogenetic analysis and molecular dating showed that the ancestor of the present Moschidae originates from Tibetan Plateau which suggested that the evolution of Moschus was prompted by the most intense orogenic movement of the Tibetan Plateau during the Pliocene age, and alternating glacial-interglacial geological eras.
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Affiliation(s)
- Tao Pan
- Anhui Key Laboratory of Eco-engineering and Bio-technique, School of Life Sciences, Anhui University, Hefei, 230601, Anhui, China
| | - Hui Wang
- Anhui Key Laboratory of Eco-engineering and Bio-technique, School of Life Sciences, Anhui University, Hefei, 230601, Anhui, China
| | - Chaochao Hu
- School of Life Science, Nanjing Normal University, Nanjing, 230039, Jiangsu, China
| | - Zhonglou Sun
- Anhui Key Laboratory of Eco-engineering and Bio-technique, School of Life Sciences, Anhui University, Hefei, 230601, Anhui, China
| | - Xiaoxue Zhu
- Anhui Key Laboratory of Eco-engineering and Bio-technique, School of Life Sciences, Anhui University, Hefei, 230601, Anhui, China
| | - Tao Meng
- Guangxi Forest Inventory and Planning Institute, Nanning, 530011, Guangxi, China
| | - Xiuxiang Meng
- School of Environment and Natural Resources, Renmin University of China, Beijing, 100872, China
| | - Baowei Zhang
- Anhui Key Laboratory of Eco-engineering and Bio-technique, School of Life Sciences, Anhui University, Hefei, 230601, Anhui, China
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Wang Y, Yan G. Molecular phylogeography and population genetic structure of O. longilobus and O. taihangensis (Opisthopappus) on the Taihang mountains. PLoS One 2014; 9:e104773. [PMID: 25148249 PMCID: PMC4141751 DOI: 10.1371/journal.pone.0104773] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2014] [Accepted: 07/15/2014] [Indexed: 11/19/2022] Open
Abstract
Historic events such as the uplift of mountains and climatic oscillations in the Quaternary periods greatly affected the evolution and modern distribution of the flora. We sequenced the trnL–trnF, ndhJ-trnL and ITS from populations throughout the known distributions of O. longilobus and O. taihangensis to understand the evolutionary history and the divergence related to the past shifts of habitats in the Taihang Mountains regions. The results showed high genetic diversity and pronounced genetic differentiation among the populations of the two species with a significant phylogeographical pattern (NST>GST, P<0.05), which imply restricted gene flow among the populations and significant geographical or environmental isolation. Ten chloroplast DNA (cpDNA) and eighteen nucleus ribosome DNA (nrDNA) haplotypes were identified and clustered into two lineages. Two corresponding refuge areas were revealed across the entire distribution ranges of O. longilobus and at least three refuge areas for O. taihangensis. O. longilobus underwent an evolutionary historical process of long-distance dispersal and colonization, whereas O. taihangensis underwent a population expansion before the main uplift of Taihang Mountains. The differentiation time between O. longilobus and O. taihangensis is estimated to have occurred at the early Pleistocene. Physiographic complexity and paleovegetation transition of Taihang Mountains mainly shaped the specific formation and effected the present distribution of these two species. The results therefore support the inference that Quaternary refugial isolation promoted allopatric speciation in Taihang Mountains. This may help to explain the existence of high diversity and endemism of plant species in central/northern China.
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Affiliation(s)
- Yiling Wang
- College of Life Sciences, Shanxi Normal University, Linfen, China
| | - Guiqin Yan
- College of Life Sciences, Shanxi Normal University, Linfen, China
- * E-mail:
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