Genetic diversity and population structure of<i>Arabidopsis thaliana</i>along an altitudinal gradient

Tyagi, Antariksh; Singh, Shivani; Mishra, Parneeta; Singh, Akanksha; Tripathi, Alok; Jena, Satya Narayan; Roy, Sribash

doi:10.1093/aobpla/plv145

Cited by 24 publications

(32 citation statements)

References 74 publications

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“…Particularly surprising was the finding that all African populations, including South Africans and Tanzanians, are native and that all sampled African individuals represent relicts when compared to the major Eurasian clade (Durvasula et al ., ). Other notable findings are that the island of Madeira harbors the most extremely diverged individuals sampled to date (Fulgione et al ., ) and that diverged samples from Central Asia (Tibet, Zeng et al ., ; Yunnan, Zou et al ., ; Western Himalayas, Tyagi et al ., ; the Altai Mountains, Yin et al ., ) suggest additional refugia.…”

Section: New Genomic Data From Outside Eurasia Challenge Our View Of mentioning

confidence: 97%

Archaic lineages broaden our view on the history of Arabidopsis thaliana

Fulgione

Hancock

2018

New Phytologist

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Contents Summary 1194 I. Introduction 1194 II. Origin of the A. thaliana species 1194 III. The classic model of the history of A. thaliana 1195 IV. New genomic data from outside Eurasia challenge our view of A. thaliana history 1195 V. Conclusions 1197 Acknowledgements 1197 References 1197 SUMMARY: Natural variation in Arabidopsis thaliana has contributed to discoveries in diverse areas of plant biology. While A. thaliana has typically been considered a weed associated primarily with human-mediated environments, including agricultural and urban sites and railways, it has recently been shown that it is also native in remote natural areas, including high altitude sites in Eurasia and Africa, from the Atlas mountains in Morocco to the afro-alpine regions in Eastern and South Africa to Yunnan in China, the Himalayas and the Tibetan Plateau. This finding suggests that while A. thaliana has been extensively studied in Europe and Western Asia there are still many open questions about its population history, genotype-phenotype relationships and mechanisms of adaptation.

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Section: New Genomic Data From Outside Eurasia Challenge Our View Of mentioning

confidence: 97%

Archaic lineages broaden our view on the history of Arabidopsis thaliana

Fulgione

Hancock

2018

New Phytologist

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“…Microsatellite markers are proven appropriate for population structure and differentiation studies (Pálsson 2000; Song et al 2006; Tyagi et al 2016; Volis et al 2016) and for investigating the relationship among closely related taxa (Korpelainen et al 2010; Talve et al 2013, 2014). …”

Section: Discussionmentioning

confidence: 99%

Two closely related species differ in their regional genetic differentiation despite admixing

2018

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Genetic differences between regions are usually studied for individual species. However, many species can reproduce with each other. We studied whether gene flow between two closely related sedge species influences regional differences. Our molecular genetic data support considerable gene flow between the species. Still, we detected clear genetic differences between species and regions, and more pronounced regional differences for the less common one. Thus, gene flow between the species appeared too weak to neutralize differences between the regional genetic structure of our study species. We encourage further regional differentiation studies in groups of cross-compatible species.

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“…The accession information for these complete cp genome data is shown in Supplementary Table S1. Yin et al (2010) and Tyagi et al (2015) carried out phylogenetic and population genetic studies of Chinese and Western Himalayan populations based on 11 cpDNA markers (GenBank accession numbers are GU293237-GU293316, GU293317-GU293396, GU293397-GU293476, GU293477-GU293556, GU293557-GU293636, GU293637-GU293716, GU293717-GU293796, GU293797-GU293876, GU293877-GU293956, GU293957-GU294036, GU294037-GU294116). Therefore, we also retrieved the nucleotide sequence data of 68 A. thaliana individuals with these 11 cpDNA markers.…”

Section: Data Matrixmentioning

confidence: 99%

“…Geographic origins of all the accessions (accurate to the country). According to their geographic locations and previous A. thaliana population genomic research (Yin et al, 2010;Tyagi et al, 2015;1001Genomes Consortium, 2016, all the populations are divided into four groups: Remaining Asia region (green), European region (pink), China-India region (hyacinthine), Relicts (yellow). Clades 1-7 ( Fig.…”

Section: Data Matrixmentioning

confidence: 99%

“…Therefore, it is important to compare the different genealogies among cp gene trees and nuclear gene trees to improve our understanding of the complete historical evolutionary landscape of A. thaliana. Nevertheless, while several previous studies (e.g., Yin et al, 2010;Tyagi et al, 2015) reported extensive phylogeographic and population genetic analyses of local populations of this species, the maternal history of A. thaliana across its geographic distribution areas is little known. Moreover, the evolutionary histories of the chloroplast genomes and the nuclear genomes have seldom been compared.…”

Section: Introductionmentioning

confidence: 99%

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Maternal phylogeographic patterns and coalescent times of <i>Arabidopsis thaliana</i> based on chloroplast DNA analyses

2019

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Arabidopsis thaliana, one of the most important model plants, has played an essential role in every biological field including evolutionary biology. Recent population genomic studies have gradually clarified the origin and evolution of this species. Nevertheless, incongruent patterns among gene trees based on cytogenetic data have highlighted the importance of understanding the life history evolution and landscape biogeography of extant A. thaliana populations. Here, we focus on the maternally inherited chloroplast genome in A. thaliana and carry out phylogeographic analyses and coalescent time estimations. The maternal lineage of A. thaliana originated in the European to West and Central Asian regions in the Early Pleistocene. Relicts, the ancient lineages suggested by population genomic data, are not ancestral maternal lineages, but are derived from the European population. Part of the European population then dispersed eastward and spread to the Indian region, and finally extended to the Yangtze River region. The branching patterns and evolutionary time scales of the maternal genealogy are significantly different from those estimated from analyses of autosomal genes, and these cannot be explained by incomplete lineage sorting of the ancestral polymorphisms during the coalescent process due to large differences in the evolutionary time scale involved.

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Genetic diversity and population structure ofArabidopsis thalianaalong an altitudinal gradient

Cited by 24 publications

References 74 publications

Archaic lineages broaden our view on the history of Arabidopsis thaliana

Archaic lineages broaden our view on the history of Arabidopsis thaliana

Two closely related species differ in their regional genetic differentiation despite admixing

Maternal phylogeographic patterns and coalescent times of <i>Arabidopsis thaliana</i> based on chloroplast DNA analyses

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