Phylogeographic structure and gene flow of Himalayan snowcock (Tetraogallus himalayensis)

AbstractWe have used phylogeographic methods to investigate the genetic structure and population history of the endangered Himalayan snowcock (Tetraogallus himalayensis) in northwestern China. The mitochondrial cytochrome b gene was sequenced of 102 individuals sampled throughout the distribution range. In total, we found 26 different haplotypes defined by 28 polymorphic sites. Phylogenetic analyses indicated that the samples were divided into two major haplogroups corresponding to one western and one eastern clade. The divergence time between these major clades was estimated to be approximately one million years. An analysis of molecular variance showed that 40% of the total genetic variability was found within local populations, 12% among populations within regional groups and 48% among groups. An analysis of the demographic history of the populations suggested that major expansions have occurred in the Himalayan snowcock populations and these correlate mainly with the first and the second largest glaciations during the Pleistocene. In addition, the data indicate that there was a population expansion of the Tianshan population during the uplift of the Qinghai-Tibet Plateau, approximately 2 million years ago.

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Population structure and demographic history of the chukar partridge Alectoris chukar in China

Current Zoology ◽

10.1093/czoolo/59.4.458 ◽

2013 ◽

Vol 59 (4) ◽

pp. 458-474 ◽

Cited By ~ 2

Author(s):

Sen Song ◽

Shijie Bao ◽

Ying Wang ◽

Xinkang Bao ◽

Bei An ◽

...

Keyword(s):

Genetic Diversity ◽

Gene Flow ◽

North America ◽

Demographic History ◽

Population Expansion ◽

Northwest China ◽

Population History ◽

Extant Species ◽

History Of ◽

Chukar Partridge

Abstract Pleistocene climate fluctuations have shaped the patterns of genetic diversity observed in extant species. Although the effects of recent glacial cycles on genetic diversity have been well studied on species in Europe and North America, genetic legacy of species in the Pleistocene in north and northwest of China where glaciations was not synchronous with the ice sheet development in the Northern Hemisphere or or had little or no ice cover during the glaciations’ period, remains poorly understood. Here we used phylogeographic methods to investigate the genetic structure and population history of the chukar partridge Alec-toris chukar in north and northwest China. A 1,152 – 1,154 bp portion of the mtDNA CR were sequenced for all 279 specimens and a total number of 91 haplotypes were defined by 113 variable sites. High levels of gene flow were found and gene flow estimates were greater than 1 for most population pairs in our study. The AMOVA analysis showed that 81% and 16% of the total genetic variability was found within populations and among populations within groups, respectively. The demographic history of chukar was examined using neutrality tests and mismatch distribution analyses and results indicated Late Pleistocene population expansion. Results revealed that most populations of chukar experienced population expansion during 0.027 ? 0.06 Ma. These results are at odds with the results found in Europe and North America, where population expansions occurred after Last Glacial Maximum (LGM, 0.023 to 0.018 Ma). Our results are not consistent with the results from avian species of Tibetan Plateau, either, where species experienced population expansion following the retreat of the extensive glaciation period (0.5 to 0.175 Ma).

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Molecular phylogenetic and phylogeography of Soriculus nigrescens in southwest China

10.22541/au.161470351.19785260/v1 ◽

2021 ◽

Author(s):

Haijun Jiang ◽

Changkun Fu ◽

Keyi Tang ◽

Fengjun Li ◽

Fei Xie ◽

...

Keyword(s):

Southwest China ◽

Ecological Niche Modeling ◽

Demographic History ◽

Phylogenetic Analyses ◽

Divergence Time ◽

Species Status ◽

Putative Species ◽

Molecular Phylogenetic ◽

History Of ◽

Different Altitudes

The Himalayan Shrew belongs to the genus Soriculus, which is a monotypic genus. We investigated the phylogeographic patterns, speciation, divergence time, and demographic history of Soriculus nigrescens in southwestern China. A total of 128 samples from 29 regions were analyzed for both mitochondrial and nuclear genes. Phylogenetic analyses of the concatenated mtDNA and nuDNA data revealed three highly divergent lineages within the S. nigrescens. One group represented subspecies S. n. minors, another group represented subspecies S. n. nigrescens, which is made up of two Clades A and B. The species delimitation analyses, based on two methods, supported the species status of the two Clades of S. n. nigrescens. In addtion, it was found that individuals at different altitudes in Motuo were divided into two Clades. Bayesian skyline plotting analyses and ecological niche modeling also supported demographic and range expansions during the LGM for S. n. nigrescens. We propose that S. n. nigrescens appears to be composed of two putative species, and S. n. minor should be elevated to species status. Our study also suggested that climate change since the Miocene periods and the uplift of the QTP may have resulted in the diversification and speciation of S. nigrescens.

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Distinctiveness, speciation and demographic history of the rare endemic conifer Juniperus erectopatens in the eastern Qinghai-Tibet Plateau

Conservation Genetics ◽

10.1007/s10592-019-01211-2 ◽

2019 ◽

Vol 20 (6) ◽

pp. 1289-1301 ◽

Cited By ~ 2

Author(s):

Jingjing Xu ◽

Xinya Song ◽

Markus Ruhsam ◽

Tingxuan Liu ◽

Jialiang Li ◽

...

Keyword(s):

Demographic History ◽

Tibet Plateau ◽

History Of ◽

Rare Endemic ◽

Qinghai Tibet Plateau

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Phylogeographic Patterns in Motacilla Flava and Motacilla Citreola: Species Limits and Population History

The Auk ◽

10.1093/auk/120.3.744 ◽

2003 ◽

Vol 120 (3) ◽

pp. 744-758

Author(s):

Alexandra Pavlova ◽

Robert M. Zink ◽

Sergei V. Drovetski ◽

Yaroslav Red'kin ◽

Sievert Rohwer

Keyword(s):

Dna Sequences ◽

Isolation By Distance ◽

Population Expansion ◽

Population History ◽

Phylogeographic Structure ◽

Restricted Gene Flow ◽

Western Group ◽

History Of ◽

Group A ◽

Past Population

Abstract We conducted phylogeographic analyses of Motacilla flava (Yellow Wagtail) and M. citreola (Citrine Wagtail). We analyzed mitochondrial DNA sequences from 167 M. flava specimens obtained from 17 localities throughout Eurasia and Alaska, and 38 specimens of M. citreola obtained from 7 Eurasian localities. Phylogenetic analysis revealed three clades within traditionally recognized M. flava: Europe and southwestern Asia, northeastern Eurasia, and southeastern Asia. Those groups should be considered species, because together they are not monophyletic, and are interspersed with M. citreola, M. cinerea, and M. alba. Motacilla citreola also is paraphyletic, consisting of two species-level groups. Northeastern and southeastern groups of M. flava each appear to be sister taxa to eastern and western groups of M. citreola, respectively. Together those four groups form a clade, whereas the western M. flava group is considerably more distant. Within each of the three groups of M. flava, and the two groups of M. citreola, little phylogeographic structure was detected. Signatures of past population expansion are evident for some populations of M. flava; expansion is more recent in Moscow, Kursk (western group), Yamal, and Anabar (northeastern group), and older in Tyva and Vyatka (western group). A history of population stability is inferred for the Yamal population of M. citreola. Nested-clade analyses detected contiguous range expansion for southeastern M. flava and restricted gene flow with isolation by distance for northeastern M. flava and eastern M. citreola.

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Evolutionary history of two rare endemic conifer species from the eastern Qinghai-Tibet Plateau

Annals of Botany ◽

10.1093/aob/mcab114 ◽

2021 ◽

Author(s):

Jibin Miao ◽

Perla Farhat ◽

Wentao Wang ◽

Markus Ruhsam ◽

Richard Milne ◽

...

Keyword(s):

Genetic Diversity ◽

Evolutionary History ◽

Demographic History ◽

Genetic Load ◽

Tibet Plateau ◽

Interspecific Gene Flow ◽

Mountainous Regions ◽

Quaternary Climate ◽

History Of ◽

Qinghai Tibet Plateau

Abstract Background and Aims Understanding the population genetics and evolutionary history of endangered species is urgently needed in an era of accelerated biodiversity loss. This knowledge is most important for regions with high endemism that are ecologically vulnerable, such as the Qinghai-Tibet Plateau (QTP). Methods The genetic variation of 84 juniper trees from six populations of Juniperus microsperma and one population of Juniperus erectopatens, two narrow endemic junipers from the QTP that are sister to each other, was surveyed using RNA-seq data. Coalescent-based analyses were used to test speciation, migration, and demographic scenarios. Furthermore, positively selected and climate-associated genes were identified, and the genetic load was assessed for both species. Key Results Analyses of 149,052 single nucleotide polymorphisms showed that the two species are well-differentiated and monophyletic. They diverged around the late Pliocene, but interspecific gene flow continued until the Last Glacial Maximum. Demographic reconstruction by Stairway Plot detected two severe bottlenecks for J. microsperma and only one bottleneck for J. erectopatens. The identified positive selected genes and climate-associated genes revealed habitat adaptation of the two species. Furthermore, although J. microsperma had a much wider geographical distribution than J. erectopatens, the former possesses lower genetic diversity and a higher genetic load than the latter. Conclusions This study sheds light on the evolution of two endemic juniper species from the QTP and their responses to Quaternary climate fluctuations. Our findings emphasize the importance of speciation and demographic history reconstructions in the understanding of the current distribution pattern and genetic diversity of threatened species in mountainous regions.

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Demographic history and genomic response to environmental changes in a rapid radiation of wild rats

Molecular Biology and Evolution ◽

10.1093/molbev/msaa334 ◽

2021 ◽

Author(s):

Deyan Ge ◽

Anderson Feijó ◽

Zhixin Wen ◽

Alexei V Abramov ◽

Liang Lu ◽

...

Keyword(s):

Environmental Changes ◽

Demographic History ◽

Terrestrial Ecosystems ◽

Tibet Plateau ◽

Global Changes ◽

Rapid Radiation ◽

Protein Functions ◽

Wild Rats ◽

Qinghai Tibet Plateau ◽

Genomic Response

Abstract For organisms to survive and prosper in a harsh environment, particularly under rapid climate change, poses tremendous challenges. Recent studies have highlighted the continued loss of megafauna in terrestrial ecosystems and the subsequent surge of small mammals, such as rodents, bats, lagomorphs, and insectivores. However, the ecological partitioning of these animals will likely lead to large variation in their responses to environmental change. In the present study, we investigated the evolutionary history and genetic adaptations of white-bellied rats (Niviventer Marshall, 1976), which are widespread in the natural terrestrial ecosystems in Asia but also known as important zoonotic pathogen vectors and transmitters. The southeastern Qinghai-Tibet Plateau (QHTP) was inferred as the origin center of this genus, with parallel diversification in temperate and tropical niches. Demographic history analyses from mitochondrial and nuclear sequences of Niviventer demonstrated population size increases and range expansion for species in Southeast Asia, and habitat generalists elsewhere. Unexpectedly, population increases were seen in N. eha, which inhabits the highest elevation among Niviventer species. Genome scans of nuclear exons revealed that among the congeneric species, N. eha has the largest number of positively selected genes. Protein functions of these genes are mainly related to olfaction, taste and tumor suppression. Extensive genetic modification presents a major strategy in response to global changes in these alpine species.

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Actinomyces marmotae sp. nov. and Actinomyces procaprae sp. nov. isolated from wild animals and reclassification of Actinomyces liubingyangii and Actinomyces tangfeifanii as Boudabousia liubingyangii comb. nov. and Boudabousia tangfeifanii comb. nov., respectively

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY ◽

10.1099/ijsem.0.004696 ◽

2019 ◽

Vol 71 (3) ◽

Cited By ~ 16

Author(s):

Caixin Yang ◽

Yibo Bai ◽

Kui Dong ◽

Jing Yang ◽

Xin-He Lai ◽

...

Keyword(s):

Type Species ◽

Phylogenetic Analyses ◽

Brain Heart Infusion ◽

Tibet Plateau ◽

Rrna Gene ◽

Bacterial Strains ◽

Content Type ◽

Link Type ◽

Pr China ◽

Qinghai Tibet Plateau

Four Gram-stain-positive, catalase-negative, non-spore-forming, rod-shaped bacterial strains (zg-325T, zg329, dk561T and dk752) were isolated from the respiratory tract of marmot (Marmota himalayana) and the faeces of Tibetan gazelle (Procapra picticaudata) from the Qinghai-Tibet Plateau of PR China. The results of 16S rRNA gene sequence-based phylogenetic analyses indicated that strains zg-325T and dk561T represent members of the genus Actinomyces , most similar to Actinomyces denticolens DSM 20671T and Actinomyces ruminicola B71T, respectively. The DNA G+C contents of strains zg-325T and dk561T were 71.6 and 69.3 mol%, respectively. The digital DNA–DNA hybridization values of strains zg-325T and dk561T with their most closely related species were below the 70 % threshold for species demarcation. The four strains grew best at 35 °C in air containing 5 % CO2 on brain heart infusion (BHI) agar with 5 % sheep blood. All four strains had C18:1ω9c and C16:0 as the major cellular fatty acids. MK-8 and MK-9 were the major menaquinones in zg-325T while MK-10 was predominant in dk561T. The major polar lipids included diphosphatidylglycerol and phosphatidylinositol. On the basis of several lines of evidence from phenotypic and phylogenetic analyses, zg-325T and dk561T represent novel species of the genus Actinomyces , for which the name Actinomyces marmotae sp. nov. and Actinomyces procaprae sp. nov. are proposed. The type strains are zg-325T (=GDMCC 1.1724T=JCM 34091T) and dk561T (=CGMCC 4.7566T=JCM 33484T). We also propose, on the basis of the phylogenetic results herein, the reclassification of Actinomyces liubingyangii and Actinomyces tangfeifanii as Boudabousia liubingyangii comb. nov. and Boudabousia tangfeifanii comb. nov., respectively.

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Morphological and molecular phylogenetic analyses of Zepedanulus ishikawai (Arachnida: Opiliones: Laniatores: Epedanidae) in the southern part of the Ryukyu Archipelago

The Canadian Entomologist ◽

10.4039/tce.2021.42 ◽

2021 ◽

pp. 1-28

Author(s):

Yoshimasa Kumekawa ◽

Haruka Fujimoto ◽

Osamu Miura ◽

Ryo Arakawa ◽

Jun Yokoyama ◽

...

Keyword(s):

Phylogenetic Tree ◽

Phylogenetic Analyses ◽

Divergence Time ◽

Morphological Characters ◽

Ryukyu Archipelago ◽

Divergence Time Estimates ◽

Time Estimates ◽

Molecular Phylogenetic ◽

History Of ◽

Polymerase Chain

Abstract Harvestmen (Arachnida: Opiliones) are soil animals with extremely low dispersal abilities that experienced allopatric differentiation. To clarify the morphological and phylogenetic differentiation of the endemic harvestman Zepedanulus ishikawai (Suzuki, 1971) (Laniatores: Epedanidae) in the southern part of the Ryukyu Archipelago, we conducted molecular phylogenetic analyses and divergence time estimates based on CO1 and 16S rRNA sequences of mtDNA, the 28S rRNA sequence of nrDNA, and the external morphology. A phylogenetic tree based on mtDNA sequences indicated that individuals of Z. ishikawai were monophyletic and were divided into clade I and clade II. This was supported by the nrDNA phylogenetic tree. Although clades I and II were distributed sympatrically on all three islands examined (Ishigaki, Iriomote, and Yonaguni), heterogeneity could not be detected by polymerase chain reaction–restriction fragment length polymorphism of nrDNA, indicating that clades I and II do not have a history of hybridisation. Also, several morphological characters differed significantly between individuals of clade I and clade II. The longstanding isolation of the southern Ryukyus from the surrounding islands enabled estimation of the original morphological characters of both clades of Z. ishikawai.

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Whole-genome resequencing provides insights into the evolution and divergence of the native domestic yaks of the Qinghai–Tibet Plateau

BMC Evolutionary Biology ◽

10.1186/s12862-020-01702-8 ◽

2020 ◽

Vol 20 (1) ◽

Author(s):

Zhi-xin Chai ◽

Jin-wei Xin ◽

Cheng-fu Zhang ◽

Dawayangla ◽

Luosang ◽

...

Keyword(s):

Population Genomics ◽

Tibet Plateau ◽

Human Beings ◽

Trade Routes ◽

High Altitude Area ◽

History Of ◽

Whole Genome Resequencing ◽

Qinghai Tibet Plateau ◽

Selective Analysis ◽

The Silk Road

Abstract Background On the Qinghai–Tibet Plateau, known as the roof ridge of the world, the yak is a precious cattle species that has been indispensable to the human beings living in this high-altitude area. However, the origin of domestication, dispersal route, and the divergence of domestic yaks from different areas are poorly understood. Results Here, we resequenced the genome of 91 domestic yak individuals from 31 populations and 1 wild yaks throughout China. Using a population genomics approach, we observed considerable genetic variation. Phylogenetic analysis suggested that the earliest domestications of yak occurred in the south-eastern QTP, followed by dispersal to the west QTP and northeast to SiChuang, Gansu, and Qinghai by two routes. Interestingly, we also found potential associations between the distribution of some breeds and historical trade routes such as the Silk Road and Tang-Tibet Ancient Road. Selective analysis identified 11 genes showing differentiation between domesticated and wild yaks and the potentially positively selected genes in each group were identified and compared among domesticated groups. We also detected an unbalanced pattern of introgression among domestic yak, wild yak, and Tibetan cattle. Conclusions Our research revealed population genetic evidence for three groups of domestic yaks. In addition to providing genomic evidence for the domestication history of yaks, we identified potential selected genes and introgression, which provide a theoretical basis and resources for the selective breeding of superior characters and high-quality yak.

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