scholarly journals Refinement of Global Domestic Horse Biogeography Using Historic Landrace Chinese Mongolian Populations

2019 ◽  
Author(s):  
Haige Han ◽  
Kenneth Bryan ◽  
Wunierfu Shiraigol ◽  
Dongyi Bai ◽  
Yiping Zhao ◽  
...  
Keyword(s):  
Sequence Data ◽  
Genomic Diversity ◽  
Data Sets ◽  
Domestic Horse ◽  
Snp Data ◽  
Genome Wide ◽  
History Of ◽  
Genomic Characterization ◽  
Mongolian Horse ◽  
Free Ranging

Abstract The Mongolian horse is one of the oldest extant horse populations and although domesticated, most animals are free-ranging and experience minimal human intervention. As an ancient population originating in one of the key domestication centers, the Mongolian horse may play a key role in understanding the origins and recent evolutionary history of horses. Here we describe an analysis of high-density genome-wide single-nucleotide polymorphism (SNP) data in 40 globally dispersed horse populations (n = 895). In particular, we have focused on new results from Chinese Mongolian horses (n = 100) that represent 5 distinct populations. These animals were genotyped for 670K SNPs and the data were analyzed in conjunction with 35K SNP data for 35 distinct breeds. Analyses of these integrated SNP data sets demonstrated that the Chinese Mongolian populations were genetically distinct from other modern horse populations. In addition, compared to other domestic horse breeds, the Chinese Mongolian horse populations exhibited relatively high genomic diversity. These results suggest that, in genetic terms, extant Chinese Mongolian horses may be the most similar modern populations to the animals originally domesticated in this region of Asia. Chinese Mongolian horse populations may therefore retain ancestral genetic variants from the earliest domesticates. Further genomic characterization of these populations in conjunction with archaeogenetic sequence data should be prioritized for understanding recent horse evolution and the domestication process that has led to the wealth of diversity observed in modern global horse breeds.

scholarly journals On the origin of mongrels: evolutionary history of free-breeding dogs in Eurasia

2015 ◽  
Vol 282 (1820) ◽  
pp. 20152189 ◽  
Author(s):  
Małgorzata Pilot ◽  
Tadeusz Malewski ◽  
Andre E. Moura ◽  
Tomasz Grzybowski ◽  
Kamil Oleński ◽  
...  
Keyword(s):  
East Asian ◽  
Domestic Dog ◽  
Indigenous Status ◽  
Westward Expansion ◽  
Pure Breed ◽  
Archaeological Data ◽  
Genome Wide ◽  
History Of ◽  
Western Eurasia ◽  
Free Ranging

Although a large part of the global domestic dog population is free-ranging and free-breeding, knowledge of genetic diversity in these free-breeding dogs (FBDs) and their ancestry relations to pure-breed dogs is limited, and the indigenous status of FBDs in Asia is still uncertain. We analyse genome-wide SNP variability of FBDs across Eurasia, and show that they display weak genetic structure and are genetically distinct from pure-breed dogs rather than constituting an admixture of breeds. Our results suggest that modern European breeds originated locally from European FBDs. East Asian and Arctic breeds show closest affinity to East Asian FBDs, and they both represent the earliest branching lineages in the phylogeny of extant Eurasian dogs. Our biogeographic reconstruction of ancestral distributions indicates a gradual westward expansion of East Asian indigenous dogs to the Middle East and Europe through Central and West Asia, providing evidence for a major expansion that shaped the patterns of genetic differentiation in modern dogs. This expansion was probably secondary and could have led to the replacement of earlier resident populations in Western Eurasia. This could explain why earlier studies based on modern DNA suggest East Asia as the region of dog origin, while ancient DNA and archaeological data point to Western Eurasia.

scholarly journals Stable Species Boundaries Despite Ten Million Years of Hybridization in Tropical Eels

2019 ◽  
Author(s):  
Julia M. I. Barth ◽  
Chrysoula Gubili ◽  
Michael Matschiner ◽  
Ole K. Tørresen ◽  
Shun Watanabe ◽  
...  
Keyword(s):  
Sequence Data ◽  
F1 Hybrids ◽  
Species Boundaries ◽  
Hybrid Breakdown ◽  
Genome Wide ◽  
Dynamic Scenario ◽  
Stable Species ◽  
Species Pairs ◽  
History Of ◽  
Tropical Eels

AbstractGenomic evidence is increasingly underpinning that hybridization between taxa is commonplace, challenging our views on the mechanisms that maintain their boundaries. Here, we focus on seven catadromous eel species (genusAnguilla), and use genome-wide sequence data from more than 450 individuals sampled across the tropical Indo-Pacific, morphological information, and three newly assembled draft genomes to compare contemporary patterns of hybridization with signatures of past gene flow across a time-calibrated phylogeny. We show that the seven species have remained distinct entities for up to 10 million years, despite a dynamic scenario of incomplete isolation whereby the current frequencies of hybridization across species pairs (over 5% of all individuals were either F1 hybrids or backcrosses) contrast remarkably with patterns of past introgression. Based on near-complete asymmetry in the directionality of hybridization and decreasing frequencies of later-generation hybrids, we identify cytonuclear incompatibilities and hybrid breakdown as two powerful mechanisms that can support species cohesion even when hybridization has been pervasive throughout the evolutionary history of entire clades.

scholarly journals Molecular phylogenetics of mormolyca (orchidaceae: maxillariinae) based on combined molecular data sets

Lankesteriana ◽  
2013 ◽  
Author(s):  
Rafael Arévalo ◽  
Kenneth M. Cameron
Keyword(s):  
Molecular Phylogenetics ◽  
Sequence Data ◽  
Intergenic Spacer ◽  
Molecular Data ◽  
Data Sets ◽  
History Of ◽  
Trnk Intron ◽  
Vegetative Characters ◽  
High Level ◽  
Pollination Systems

The Neotropical orchid genus Mormolyca Fenzl, as currently circumscribed, encompasses a diverse group of ca. 27species. Many of these were included traditionally in Maxillaria sect. Rufescens, when similarity of floral morphology was considered foremost in their classification rather than the evolutionary history of the taxa. In order to begin revising species delimitation and clarifying the evolution and biology of the genus, we present a phylogenetic hypothesis using sequence data from five plastid loci (rpoC1, matK gene and flanking trnK intron, atpB-rbcL intergenic spacer, and the 3’ portion of ycf1) and the nuclear ribosomal internal and external transcribed spacers (ITS, ETS). Resulting trees using both Bayesian and parsimony inference are congruent with each other, and generally well resolved. Based on current level of sampling across Maxillariinae, these molecular data support the monophyly of Mormolyca and shed light on the interspecific phylogenetic patterns within the genus. These include an early divergent paraphyletic grade of Mormolyca species successively sister to a clade with at least two definable subclades within. The latter are characterized by two different flower morphologies that are likely related to their pollination systems. Although not all relationships within the genus are fully resolved or supported, these results offer a first glimpse into the phylogeny of a small group of epiphytic orchids characterized by an unusually high level of variable vegetative characters, floral fragrance profiles, and pollination systems.

scholarly journals Inferring the History of Population Size Change from Genome-Wide SNP Data

2012 ◽  
Vol 29 (12) ◽  
pp. 3653-3667 ◽  
Author(s):  
Christoph Theunert ◽  
Kun Tang ◽  
Michael Lachmann ◽  
Sile Hu ◽  
Mark Stoneking
Keyword(s):  
Population Size ◽  
Size Change ◽  
Snp Data ◽  
Genome Wide ◽  
History Of ◽  
Population Size Change

scholarly journals Human cytomegalovirus haplotype reconstruction reveals high diversity due to superinfection and evidence of within-host recombination

2019 ◽  
Vol 116 (12) ◽  
pp. 5693-5698 ◽  
Author(s):  
Juliana Cudini ◽  
Sunando Roy ◽  
Charlotte J. Houldcroft ◽  
Josephine M. Bryant ◽  
Daniel P. Depledge ◽  
...  
Keyword(s):  
Human Cytomegalovirus ◽  
Nucleotide Diversity ◽  
Sequence Data ◽  
Dna Viruses ◽  
Single Strain ◽  
Recombinant Fragment ◽  
Genome Wide ◽  
Short Read Sequence ◽  
History Of ◽  
Hepatitis C Viruses

Recent sequencing efforts have led to estimates of human cytomegalovirus (HCMV) genome-wide intrahost diversity that rival those of persistent RNA viruses [Renzette N, Bhattacharjee B, Jensen JD, Gibson L, Kowalik TF (2011)PLoS Pathog7:e1001344]. Here, we deep sequence HCMV genomes recovered from single and longitudinally collected blood samples from immunocompromised children to show that the observations of high within-host HCMV nucleotide diversity are explained by the frequent occurrence of mixed infections caused by genetically distant strains. To confirm this finding, we reconstructed within-host viral haplotypes from short-read sequence data. We verify that within-host HCMV nucleotide diversity in unmixed infections is no greater than that of other DNA viruses analyzed by the same sequencing and bioinformatic methods and considerably less than that of human immunodeficiency and hepatitis C viruses. By resolving individual viral haplotypes within patients, we reconstruct the timing, likely origins, and natural history of superinfecting strains. We uncover evidence for within-host recombination between genetically distinct HCMV strains, observing the loss of the parental virus containing the nonrecombinant fragment. The data suggest selection for strains containing the recombinant fragment, generating testable hypotheses about HCMV evolution and pathogenesis. These results highlight that high HCMV diversity present in some samples is caused by coinfection with multiple distinct strains and provide reassurance that within the host diversity for single-strain HCMV infections is no greater than for other herpesviruses.

scholarly journals Demographic model and biological adaptation inferred from the genome-wide SNP data reveal tripartite origins of southernmost Chinese Huis

2021 ◽  
Author(s):  
Guanglin He ◽  
Zhi-Quan Fan ◽  
Xing Zou ◽  
Xiaohui Deng ◽  
Hui-Yuan Yeh ◽  
...  
Keyword(s):  
Indigenous Populations ◽  
Genetic Admixture ◽  
Historical Period ◽  
Demographic Model ◽  
Biological Adaptation ◽  
Snp Data ◽  
Genome Wide ◽  
Maritime Silk Road ◽  
History Of ◽  
Cultural Origins

The culturally unique Sanya Hui (SYH) people are regarded as the descendants of ancient Cham people in Central Vietnam (CV) and exhibit a scenario of complex migration and admixture history, who were likely to first migrate from Central and South Asia (CSA) to CV and then to South Hainan and finally assimilated with indigenous populations and resided in the tropical island environments since then. A long-standing hypothesis posits that SYH derives from different genetic and cultural origins, which hypothesizes that SYH people are different from the genetically attested admixture history of northern Hui people possessing major Han-related ancestry and minor western Eurasian ancestry. However, the effect of the cultural admixture from CSA and East Asia (EA) on the genetic admixture of SYH people remains unclear. Here, we reported the first batch of genome-wide SNP data from 94 SYH people from Hainan and comprehensively characterized their genetic structure, origin, and admixture history. Our results found that SYH people were genetically different from the northern Chinese Hui people and harbored a close genomic affinity with indigenous Vietnamese but a distinct relationship with Cham, which confirmed the hypothesis of documented recent historical migration from CV and assimilation with Hainan indigenous people. The fitted admixture models and reconstructed demographic frameworks revealed an additional influx of CSA and EA ancestries during the historical period, consisting of the frequent cultural communication along the Southern Maritime Silk Road and extensive interaction with EA. Analyses focused on natural-selected signatures of SYH people revealed a similar pattern with mainland East Asians, which further confirmed the possibility of admixture-induced biological adaptation of island environments. Generally, three genetically attested ancestries from CV, EA, and CSA in modern SYH people supported their tripartite model of genomic origins.

scholarly journals Extensive ethnolinguistic diversity in Vietnam reflects multiple sources of genetic diversity

2019 ◽  
Author(s):  
Dang Liu ◽  
Nguyen Thuy Duong ◽  
Nguyen Dang Ton ◽  
Nguyen Van Phong ◽  
Brigitte Pakendorf ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Linguistic Diversity ◽  
Published Data ◽  
Multiple Sources ◽  
Austronesian Languages ◽  
Snp Data ◽  
Genome Wide ◽  
Genome Wide Data ◽  
History Of ◽  
Dense Sampling

AbstractVietnam features extensive ethnolinguistic diversity and occupies a key position in Mainland Southeast Asia (MSEA). Yet, the genetic diversity of Vietnam remains relatively unexplored, especially with genome-wide data, because previous studies have focused mainly on the majority Kinh group. Here we analyze newly-generated genome-wide SNP data for the Kinh and 21 additional ethnic groups in Vietnam, encompassing all five major language families in MSEA. In addition to analyzing the allele and haplotype sharing within the Vietnamese groups, we incorporate published data from both nearby modern populations and ancient samples for comparison. We find that the Vietnamese ethnolinguistic groups harbor multiple sources of genetic diversity that are associated with heterogeneous ancestry sharing profiles in each language family. However, linguistic diversity does not completely match genetic diversity; there have been extensive interactions between the Hmong-Mien and Tai-Kadai groups, and a likely case of cultural diffusion in which some Austro-Asiatic groups shifted to Austronesian languages. Overall, our results highlight the importance of genome-wide data from dense sampling of ethnolinguistic groups in providing new insights into the genetic diversity and history of an ethnolinguistically-diverse region, such as Vietnam.

scholarly journals Diverse demographic histories in a guild of hymenopteran parasitoids

2019 ◽  
Author(s):  
William Walton ◽  
Graham N Stone ◽  
Konrad Lohse
Keyword(s):  
Population Size ◽  
Sequence Data ◽  
Demographic History ◽  
Whole Genome Sequence ◽  
Parasitoid Wasps ◽  
Effective Population ◽  
Glacial Cycles ◽  
Genome Wide ◽  
History Of ◽  
Hymenopteran Parasitoids

AbstractSignatures of changes in population size have been detected in genome-wide variation in many species. However, the causes of such changes and the extent to which they are shared across co-distributed species remain poorly understood. During Pleistocene glacial maxima, many temperate European species were confined to southern refugia. While vicariance and range expansion processes associated with glacial cycles have been widely studied, little is known about the demographic history of refugial populations, and the extent and causes of demographic variation among codistributed species. We used whole genome sequence data to reconstruct and compare demographic histories during the Quaternary for Iberian refuge populations in a single ecological guild (seven species of chalcid parasitoid wasps associated with oak cynipid galls). We find support for large changes in effective population size (Ne) through the Pleistocene that coincide with major climate change events. However, there is little evidence that the timing, direction and magnitude of demographic change are shared across species, suggesting that demographic histories are largely idiosyncratic. Our results are compatible with the idea that specialist parasitoids attacking a narrow range of hosts experience greater fluctuations in Ne than generalists.

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