scholarly journals Population Transcriptomics Reveals Gene Flow and Introgression Between Two Non-sister Alpine Gentians

2021 ◽  
Vol 9 ◽  
Author(s):  
Chunlin Chen ◽  
Wenjie Yang ◽  
Jianquan Liu ◽  
Zhenxiang Xi ◽  
Lei Zhang ◽  
...  
Keyword(s):  
Gene Flow ◽  
Phylogenetic Analyses ◽  
Population Data ◽  
Tibet Plateau ◽  
Interspecific Gene Flow ◽  
Climatic Oscillations ◽  
Distributional Shifts ◽  
Qinghai Tibet Plateau ◽  
Two Populations ◽  
Hybridization And Introgression

Distributional shifts driven by Quaternary climatic oscillations have been suggested to cause interspecific hybridization and introgression. In this study, we aimed to test this hypothesis by using population transcriptomes and coalescent modeling of two alpine none-sister gentians. Previous studies suggested that historical hybridizations occurred between Gentiana siphonantha and G. straminea in the high-altitude Qinghai-Tibet Plateau although both species are not sister to each other with the most recent divergence. In the present study, we sequenced transcriptomes of 33 individuals from multiple populations of G. siphonantha and G. straminea. The two species are well delimited by nuclear genomic SNPs while phylogenetic analyses of plastomes clustered one G. straminea individual into the G. siphonantha group. Further population structure analyses of the nuclear SNPs suggested that two populations of G. siphonantha were admixed with around 15% ancestry from G. straminea. These analyses suggested genetic introgressions from G. straminea to G. siphonantha. In addition, our coalescent-based modeling results revealed that gene flow occurred between the two species since Last Glacier Maximum after their initial divergence, which might have leaded to the observed introgressions. Our results underscore the significance of transcriptome population data in determining timescale of interspecific gene flow and direction of the resulting introgression.

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

2010 ◽  
Vol 60 (4) ◽  
pp. 449-465
Author(s):  
Wen Longying ◽  
Zhang Lixun ◽  
An Bei ◽  
Luo Huaxing ◽  
Liu Naifa ◽  
...  
Keyword(s):  
Demographic History ◽  
Phylogenetic Analyses ◽  
Divergence Time ◽  
Population Expansion ◽  
Population History ◽  
Tibet Plateau ◽  
Phylogeographic Structure ◽  
Mitochondrial Cytochrome B ◽  
History Of ◽  
Qinghai Tibet Plateau

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.

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

2019 ◽  
Vol 71 (3) ◽  
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.

Genomic evidence for polyphyletic origins and interlineage gene flow within complex taxa: a case study ofPicea brachytylain the Qinghai-Tibet Plateau

2016 ◽  
Vol 25 (11) ◽  
pp. 2373-2386 ◽  
Author(s):  
Dafu Ru ◽  
Kangshan Mao ◽  
Lei Zhang ◽  
Xiaojuan Wang ◽  
Zhiqiang Lu ◽  
...  
Keyword(s):  
Gene Flow ◽  
Tibet Plateau ◽  
Qinghai Tibet Plateau

Exploring the diversity of Asian Cryptocercus (Blattodea : Cryptocercidae): species delimitation based on chromosome numbers, morphology and molecular analysis

2018 ◽  
Vol 32 (1) ◽  
pp. 69 ◽  
Author(s):  
Qikun Bai ◽  
Lili Wang ◽  
Zongqing Wang ◽  
Nathan Lo ◽  
Yanli Che
Keyword(s):  
Chromosome Number ◽  
Species Delimitation ◽  
Phylogenetic Analyses ◽  
Western China ◽  
Tibet Plateau ◽  
28S Rrna ◽  
Candidate Species ◽  
The Rich ◽  
Coi Sequences ◽  
Qinghai Tibet Plateau

Woodroaches from the genus Cryptocercus Scudder, 1862 are known to display low levels of morphological divergence, yet significant genetic divergence and variability in chromosome number. Compared with Cryptocercus taxa from North America, the diversity of the genus in Asia has received relatively little attention. We performed morphological and karyotypic examinations of multiple taxa from several previously unsampled mountainous areas of central and south-western China, and identified nine candidate species primarily on the basis of chromosome number. We then investigated diversity across all Asian Cryptocercus, through phylogenetic analyses of 135 COI sequences and 74 28S rRNA sequences from individuals of 28 localities, including species delimitation analysis in General Mixed Yule Coalescent (GMYC) and Automatic Barcode Gap Discovery (ABGD). Phylogenetic results indicated that individuals from the same locality constituted well supported clades. The congruence of GMYC and ABGD results were in almost perfect accord, with 28 candidate species described on the basis of karyotypes (including the nine identified in this study). We provide evidence that each valley population in the Hengduan Mountains contains a separate evolving lineage. We conclude that the principal cause of the rich Cryptocercus diversity in China has been the uplift of the Qinghai-Tibet Plateau.

scholarly journals Mumia zhuanghuii sp. nov., isolated from the intestinal contents of plateau pika (Ochotona curzoniae) on the Qinghai–Tibet Plateau

2020 ◽  
Vol 70 (4) ◽  
pp. 2233-2238 ◽  
Author(s):  
Zhi Tian ◽  
Shan Lu ◽  
Dong Jin ◽  
Jing Yang ◽  
Ji Pu ◽  
...  
Keyword(s):  
Cell Wall ◽  
Type Species ◽  
Phylogenetic Analyses ◽  
Tibet Plateau ◽  
Plateau Pika ◽  
Content Type ◽  
Link Type ◽  
Ochotona Curzoniae ◽  
Intestinal Contents ◽  
Qinghai Tibet Plateau

Two Gram-staining-positive, catalase-positive, oxidase-negative, aerobic, non-motile, irregular rod-shaped bacterial strains (Z350T and Z527) were isolated from intestinal contents of plateau pika (Ochotona curzoniae) from the Qinghai–Tibet Plateau, PR China. Results of phylogenetic analyses based on 16S rRNA gene sequences indicated that strain Z350T belongs to the genus Mumia (family Nocardioidaceae ) but clearly differs from the currently recognized species Mumia xiangluensis DSM 101040T (98.4 % similarity) and Mumia flava DSM 27763T (97.4 %). Strain Z350T had a DNA G+C content of 70.7 mol% and shared 80.4 and 76.7 % average nucleotide identity values and 23.4 and 20.6 % in silico DNA–DNA hybridization relatedness with M. xiangluensis DSM 101040T and M. flava DSM 27763T, respectively. Further phylogenetic analyses based on 497 core genes indicated that our isolates were members of the genus Mumia but separated from all existing genera within the family Nocardioidaceae . The major cellular fatty acids were C18 : 1 ω9c and 10-methyl C18 : 0. The cell wall contained ll-diaminopimelic acid as the diamino acid, and rhamnose, ribose and glucose as whole cell-wall sugars. MK-9(H4) was detected as the major menaquinone. Polar lipids present were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol, phosphatidylinositol mannoside and one unidentified phospholipid. Based on distinct differences in the genotypic and phenotypic data from the two Mumia species, a novel species, Mumia zhuanghuii sp. nov., is proposed. The type strain is Z350T (=CGMCC 4.7464T=DSM 106288T).

Eutrema tianshanense (Brassicaceae), a new species from Tian Shan Mountains of central Asia

Phytotaxa ◽  
2016 ◽  
Vol 286 (1) ◽  
pp. 23 ◽  
Author(s):  
GUOQIAN HAO ◽  
IHSAN A. AL-SHEHBAZ ◽  
QIANLONG LIANG ◽  
QIAN WANG ◽  
JIANQUAN LIU
Keyword(s):  
New Species ◽  
Central Asia ◽  
Phylogenetic Analyses ◽  
Tibet Plateau ◽  
Long Distance ◽  
North Asia ◽  
Tian Shan Mountains ◽  
Qinghai Tibet Plateau ◽  
A New Species ◽  
Tian Shan

Eutrema tianshanense, a new species of Brassicaceae growing near to the permanent glaciation area in the Tian Shan Mountains of central Asia, is described. It is quite similar morphologically to E. heterophyllum, and E. racemosum from the Qinghai-Tibet Plateau and adjacent regions, and to E. edwardsii of Qinghai-Tibet Plateau, Central and North Asia, and northern North America, but with rounder and smaller leaves. In addition to its long-distance disjunction from the ranges of the above three species, phylogenetic analyses based on sequence variations of multiple chloroplast DNA markers and nuclear ITS suggested that E. tianshanense and these species represent two independently evolved lineages in Tian Shan Mountains and the Qinghai-Tibet Plateau. Their morphological similarities may have resulted from the same selection pressures in the alpine habitats where they grow.

scholarly journals Effects of hypoxia on the thermal physiology of a high-elevation lizard: implications for upslope-shifting species

2021 ◽  
Vol 17 (3) ◽  
Author(s):  
Zhong-Wen Jiang ◽  
Liang Ma ◽  
Chun-Rong Mi ◽  
Wei-Guo Du
Keyword(s):  
Thermal Tolerance ◽  
High Elevation ◽  
Tibet Plateau ◽  
Body Temperatures ◽  
Hypoxic Conditions ◽  
Fitness Traits ◽  
Thermal Maximum ◽  
Qinghai Tibet Plateau ◽  
Two Populations ◽  
Hypoxia Treatment

Montane reptiles are predicted to move to higher elevations in response to climate warming. However, whether upwards-shifting reptiles will be physiologically constrained by hypoxia at higher elevations remains unknown. We investigated the effects of hypoxic conditions on preferred body temperatures (T pref ) and thermal tolerance capacity of a montane lizard ( Phrynocephalus vlangalii ) from two populations on the Qinghai–Tibet Plateau. Lizards from 2600 m a.s.l. were exposed to O 2 levels mimicking those at 2600 m (control) and 3600 m (hypoxia treatment). Lizards from 3600 m a.s.l. were exposed to O 2 levels mimicking those at 3600 m (control) and 4600 m (hypoxia treatment). The T pref did not differ between the control and hypoxia treatments in lizards from 2600 m. However, lizards from 3600 m selected lower body temperatures when exposed to the hypoxia treatment mimicking the O 2 level at 4600 m. Additionally, the hypoxia treatment induced lower critical thermal minimum (CT min ) in lizards from both populations, but did not affect the critical thermal maximum (CT max ) in either population. Our results imply that upwards-shifting reptiles may be constrained by hypoxia if a decrease in T pref reduces thermally dependent fitness traits, despite no observed effect on their heat tolerance.

Mycolicibacterium baixiangningiae sp. nov. and Mycolicibacterium mengxianglii sp. nov., two new rapidly growing mycobacterial species

2021 ◽  
Vol 71 (12) ◽  
Author(s):  
Yanpeng Cheng ◽  
Wenjing Lei ◽  
Xiaoxia Wang ◽  
Zhi Tian ◽  
Haican Liu ◽  
...  
Keyword(s):  
Type Species ◽  
Phylogenetic Analyses ◽  
Tibet Plateau ◽  
Bacterial Strains ◽  
Content Type ◽  
Link Type ◽  
Faecal Samples ◽  
Respective Type ◽  
Mycobacterium Aurum ◽  
Qinghai Tibet Plateau

Four bacterial strains (LJ126T/S18 and Z-34T/S20) recovered from faecal samples of Tibetan antelopes on the Qinghai–Tibet Plateau of China were analysed using a polyphasic approach. All four isolates were aerobic, short rod-shaped, non-motile, Gram-stain-positive, acid-fast and fast-growing. Phylogenetic analyses based upon 16S rRNA and whole-genome sequences showed that the two pair of strains formed two distinct branches within the evolutionary radiation of the genus Mycolicibacterium . Strains LJ126T/S18 and Z-34T/S20 were most closely related to Mycolicibacterium austroafricanum CCUG 37667T, Mycobacterium aurum NCTC 10437T, Mycobacterium pyrenivorans DSM 44605T, Mycobacterium monacense JCM 15658T, Mycolicibacterium sarraceniae JCM 30395T, Mycolicibacterium tokaiense JCM 6373T and Mycobacterium murale JCM 13392T, but readily distinguished from the known species by a combination of chemotaxonomic and phenotypic features and by low average nucleotide identity values (74.4–84.9 %). Consequently, the two strain pairs are considered to represent different novel species of Mycolicibacterium for which the names Mycolicibacterium baixiangningiae sp. nov. and Mycolicibacterium mengxianglii sp. nov. are proposed, with LJ126T (=CGMCC 1.1992T=KCTC 49535T) and Z-34T (=CGMCC 1.1993T=DSM 106172T) as the respective type strains.

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