Evolutionary history of Purple cone spruce (Picea purpurea) in the Qinghai-Tibet Plateau: homoploid hybrid origin and Pleistocene expansion

2013 ◽  
Vol 23 (2) ◽  
pp. 343-359 ◽  
Author(s):  
Yongshuai Sun ◽  
Richard J. Abbott ◽  
Lili Li ◽  
Long Li ◽  
Jiabin Zou ◽  
...  
Keyword(s):  
Evolutionary History ◽  
Hybrid Origin ◽  
Tibet Plateau ◽  
History Of ◽  
Homoploid Hybrid ◽  
Qinghai Tibet Plateau

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

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.

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.

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

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.

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

2019 ◽  
Vol 20 (6) ◽  
pp. 1289-1301 ◽  
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

scholarly journals THE EVOLUTIONARY HISTORY OF PARTHENOGENETICCNEMIDOPHORUS LEMNISCATUS(SAURIA, TEIIDAE). I. EVIDENCE FOR A HYBRID ORIGIN

Evolution ◽  
1990 ◽  
Vol 44 (4) ◽  
pp. 906-921 ◽  
Author(s):  
Jack W. Sites ◽  
Denise M. Peccinini-Seale ◽  
Craig Moritz ◽  
John W. Wright ◽  
Wesley M. Brown
Keyword(s):  
Evolutionary History ◽  
Hybrid Origin ◽  
History Of

scholarly journals A taxonomic and molecular survey of the pteridophytes of the Nectandra Cloud Forest Reserve, Costa Rica

PLoS ONE ◽  
2020 ◽  
Vol 15 (11) ◽  
pp. e0241231
Author(s):  
Joel H. Nitta ◽  
Atsushi Ebihara ◽  
Alan R. Smith
Keyword(s):  
Costa Rica ◽  
Evolutionary History ◽  
Cloud Forest ◽  
Dna Barcode ◽  
Hybrid Origin ◽  
Forest Reserve ◽  
Biogeographic History ◽  
Molecular Phylogenetic ◽  
History Of ◽  
Ferns And Lycophytes

Floristic surveys are crucial to the conservation of biodiversity, but the vast majority of such surveys are limited to listing species names, and few take into account the evolutionary history of species. Here, we combine classical taxonomic and molecular phylogenetic (DNA barcoding) approaches to catalog the biodiversity of pteridophytes (ferns and lycophytes) of the Nectandra Cloud Forest Reserve, Costa Rica. Surveys were carried out over three field seasons (2008, 2011, and 2013), resulting in 176 species representing 69 genera and 22 families of pteridophytes. Our literature survey of protected areas in Costa Rica shows that Nectandra has an exceptionally diverse pteridophyte flora for its size. Plastid rbcL was selected as a DNA barcode marker and obtained for >95% of pteridophyte taxa at this site. Combined molecular and morphological analyses revealed two previously undescribed taxa that appear to be of hybrid origin. The utility of rbcL for species identification was assessed by calculating minimum interspecific distances and found to have a failure rate of 18%. Finally we compared the distribution of minimum interspecific rbcL distances with two other areas that have been the focus of pteridophyte molecular surveys: Japan and Tahiti. The comparison shows that Nectandra is more similar to Japan than Tahiti, which may reflect the biogeographic history of these floras.

scholarly journals Comparative genomics of apomictic root-knot nematodes: hybridization, ploidy, and dynamic genome change

2017 ◽  
Author(s):  
Amir Szitenberg ◽  
Laura Salazar-Jaramillo ◽  
Vivian C. Blok ◽  
Dominik R. Laetsch ◽  
Soumi Joseph ◽  
...  
Keyword(s):  
Evolutionary History ◽  
Hybrid Origin ◽  
Root Knot Nematodes ◽  
Geographic Origins ◽  
Dynamic Genome ◽  
History Of ◽  
Global Agriculture ◽  
Variable Success ◽  
Ploidy Changes ◽  
Genomic Basis

AbstractThe Root-Knot Nematodes (RKN; genus Meloidogyne) are important plant parasites causing substantial agricultural losses. The Meloidogyne incognita group (MIG) of species, most of which are obligatory apomicts (mitotic parthenogens), are extremely polyphagous and important problems for global agriculture. While understanding the genomic basis for their variable success on different crops could benefit future agriculture, analyses of their genomes pose challenges due to complex evolutionary histories that may incorporate hybridization, ploidy changes, and chromosomal fragmentation. Here we sequence 19 genomes, representing five species of key RKN collected from different geographic origins. We show that a hybrid origin that predated speciation within the MIG has resulted in each species possessing two divergent genomic copies. Additionally, the MIG apomicts are hypotriploids, with a proportion of one genome present in a second copy, and this proportion varies among species. The evolutionary history of the MIG genomes is revealed to be very dynamic, with non-crossover recombination both homogenising the genomic copies, and acting as a mechanism for generating divergence between species. Interestingly, the automictic MIG species M. floridensis differs from the apomict species in that it has become homozygous throughout much of its genome.

scholarly journals The Aquilegia genome reveals a hybrid origin of core eudicots

2018 ◽  
Author(s):  
Gökçe Aköz ◽  
Magnus Nordborg
Keyword(s):  
Evolutionary History ◽  
Genetic Material ◽  
Diploid Species ◽  
Hybrid Origin ◽  
The Core ◽  
Whole Genome Duplications ◽  
Core Eudicots ◽  
Eventual Return ◽  
Genome Duplications ◽  
History Of

AbstractBackgroundWhole-genome duplications (WGD) have dominated the evolutionary history of plants. One consequence of WGD is a dramatic restructuring of the genome as it undergoes diploidization, a process under which deletions and rearrangements of various sizes scramble the genetic material, leading to a repacking of the genome and eventual return to diploidy. Here, we investigate the history of WGD in the columbine genus Aquilegia, a basal eudicot, and use it to illuminate the origins of the core eudicots.ResultsWithin-genome synteny confirms that columbines are ancient tetraploids, and comparison with the grape genome reveals that this tetraploidy appears to be shared with the core eudicots. Thus, the ancient gamma hexaploidy found in all core eudicots must have involved a two-step process: first tetraploidy in the ancestry of all eudicots, then hexaploidy in the ancestry of core eudicots. Furthermore, the precise pattern of synteny sharing suggests that the latter involved allopolyploidization, and that core eudicots thus have a hybrid origin.ConclusionsNovel analyses of synteny sharing together with the well-preserved structure of the columbine genome reveal that the gamma hexaploidy at the root of core eudicots is likely a result of hybridization between a tetraploid and a diploid species.

scholarly journals Population genomics of wall lizards reflects the dynamic history of the Mediterranean Basin

2021 ◽  
Author(s):  
Weizhao Yang ◽  
Nathalie Feiner ◽  
Daniele Salvi ◽  
Hanna Laakkonen ◽  
Daniel Jablonski ◽  
...  
Keyword(s):  
Genetic Structure ◽  
Mediterranean Basin ◽  
Evolutionary History ◽  
Central Italy ◽  
Hybrid Origin ◽  
Recent Common Ancestor ◽  
Extant Species ◽  
History Of ◽  
The Mediterranean ◽  
The Mediterranean Basin

The Mediterranean Basin has experienced extensive change in geology and climate over the past six million years. Yet, the relative importance of key geological events for the distribution and genetic structure of the Mediterranean fauna remains poorly understood. Here, we use population genomic and phylogenomic analyses to establish the evolutionary history and genetic structure of common wall lizards (Podarcis muralis). This species is particularly informative because, in contrast to other Mediterranean lizards, it is widespread across the Iberian, Italian, and Balkan peninsulas, and in extra-Mediterranean regions. We found strong support for six major lineages within P. muralis, which were largely discordant with the phylogenetic relationship of mitochondrial DNA. The most recent common ancestor of extant P. muralis was likely distributed in the Italian Peninsula, and experienced an Out-of-Italy expansion following the Messinian salinity crisis (~5 Mya), resulting in the differentiation into the extant lineages on the Iberian, Italian and Balkan peninsulas. Introgression analysis revealed that both inter- and intraspecific gene flow have been pervasive throughout the evolutionary history of P. muralis. For example, the Southern Italy lineage has a hybrid origin, formed through admixture between the Central Italy lineage and an ancient lineage that was the sister to all other P. muralis. More recent genetic differentiation is associated with the onset of the Quaternary glaciations, which influenced population dynamics and genetic diversity of contemporary lineages. These results demonstrate the pervasive role of Mediterranean geology and climate for the evolutionary history and population genetic structure of extant species.

scholarly journals The Quaternary evolutionary history, potential distribution dynamics, and conservation implications for a Qinghai–Tibet Plateau endemic herbaceous perennial, Anisodus tanguticus (Solanaceae)

2016 ◽  
Vol 6 (7) ◽  
pp. 1977-1995 ◽  
Author(s):  
Dong‐Shi Wan ◽  
Jian‐Ju Feng ◽  
De‐Chun Jiang ◽  
Kang‐Shan Mao ◽  
Yuan‐Wen Duan ◽  
...  
Keyword(s):  
Potential Distribution ◽  
Evolutionary History ◽  
Tibet Plateau ◽  
Distribution Dynamics ◽  
Conservation Implications ◽  
Qinghai Tibet Plateau ◽  
Herbaceous Perennial
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