scholarly journals Effects of landscapes and range expansion on population structure and local adaptation

2020 ◽  
Vol 228 (1) ◽  
pp. 330-343
Author(s):  
Wei Zhao ◽  
Yan‐Qiang Sun ◽  
Jin Pan ◽  
Alexis R. Sullivan ◽  
Michael L. Arnold ◽  
...  
Keyword(s):  
Population Structure ◽  
Local Adaptation ◽  
Range Expansion

Local adaptation shapes pattern of mitochondrial population structure in Sebastiscus marmoratus

2017 ◽  
Vol 100 (7) ◽  
pp. 763-774 ◽  
Author(s):  
Sheng-Yong Xu ◽  
Dian-Rong Sun ◽  
Na Song ◽  
Tian-Xiang Gao ◽  
Zhi-Qiang Han ◽  
...  
Keyword(s):  
Population Structure ◽  
Local Adaptation ◽  
Sebastiscus Marmoratus ◽  
Mitochondrial Population

scholarly journals Population structure, demographic history and local adaptation of the grass carp

BMC Genomics ◽  
2019 ◽  
Vol 20 (1) ◽  
Author(s):  
Yubang Shen ◽  
Le Wang ◽  
Jianjun Fu ◽  
Xiaoyan Xu ◽  
Gen Hua Yue ◽  
...  
Keyword(s):  
Population Structure ◽  
Local Adaptation ◽  
Grass Carp ◽  
Demographic History

scholarly journals The role of gene flow asymmetry along an environmental gradient in constraining local adaptation and range expansion

2012 ◽  
Vol 25 (8) ◽  
pp. 1676-1685 ◽  
Author(s):  
K. M. FEDORKA ◽  
W. E. WINTERHALTER ◽  
K. L. SHAW ◽  
W. R. BROGAN ◽  
T. A. MOUSSEAU
Keyword(s):  
Gene Flow ◽  
Local Adaptation ◽  
Range Expansion ◽  
Environmental Gradient ◽  
Flow Asymmetry

scholarly journals In the presence of population structure: From genomics to candidate genes underlying local adaptation

2019 ◽  
Author(s):  
Nicholas Price ◽  
Lua Lopez ◽  
Adrian E. Platts ◽  
Jesse R. Lasky ◽  
John K. McKay
Keyword(s):  
Population Structure ◽  
Flowering Time ◽  
Local Adaptation ◽  
Evolutionary Biology ◽  
Indirect Evidence ◽  
Mixed Linear Model ◽  
Functional Constraint ◽  
Heterogeneous Environments ◽  
Functional Sites ◽  
And Function

AbstractUnderstanding the genomic signatures, genes, and traits underlying local adaptation of organisms to heterogeneous environments is of central importance to the field evolutionary biology. Mixed linear mrsodels that identify allele associations to environment, while controlling for genome-wide variation at other loci, have emerged as the method of choice when studying local adaptation. Despite their importance, it is unclear whether this approach performs better than identifying environmentally-associated SNPs without accounting for population structure. To examine this, we first use the mixed linear model GEMMA, and simple Spearman correlations, to identify SNPs showing significant associations to climate with and without accounting for population structure. Subsequently, using Italy and Sweden populations, we compare evidence of allele frequency differentiation (FST), linkage disequilibrium (LD), fitness variation, and functional constraint, underlying these SNPs. Using a lenient cut-off for significance, we find that SNPs identified by both approaches, and SNPs uniquely identified by Spearman correlations, were enriched at sites showing genomic evidence of local adaptation and function but were limited across Quantitative Trait Loci (QTL) explaining fitness variation. SNPs uniquely identified by GEMMA, showed no direct or indirect evidence of local adaptation, and no enrichment along putative functional sites. Finally, SNPs that showed significantly high FST and LD, were enriched along fitness QTL peaks and cis-regulatory/nonsynonymous sites showing significant functional constraint. Using these SNPs, we identify genes underlying fitness QTL, and genes linking flowering time to local adaptation. These include a regulator of abscisic-acid (FLDH) and flowering time genes PIF3, FIO1, and COL5.

scholarly journals A comprehensive map of genetic variation in the world’s largest ethnic group - Han Chinese

2017 ◽  
Author(s):  
Charleston W. K. Chiang ◽  
Serghei Mangul ◽  
Christopher R. Robles ◽  
Warren W. Kretzschmar ◽  
Na Cai ◽  
...  
Keyword(s):  
Population Structure ◽  
Ethnic Group ◽  
Local Adaptation ◽  
Chinese Women ◽  
Han Chinese ◽  
Data Set ◽  
Novel Variants ◽  
Study Population ◽  
Low Coverage ◽  
Geographical Space

AbstractAs are most non-European populations around the globe, the Han Chinese are relatively understudied in population and medical genetics studies. From low-coverage whole-genome sequencing of 11,670 Han Chinese women we present a catalog of 25,057,223 variants, including 548,401 novel variants that are seen at least 10 times in our dataset. Individuals from our study come from 19 out of 22 provinces across China, allowing us to study population structure, genetic ancestry, and local adaptation in Han Chinese. We identify previously unrecognized population structure along the East-West axis of China and report unique signals of admixture across geographical space, such as European influences among the Northwestern provinces of China. Finally, we identified a number of highly differentiated loci, indicative of local adaptation in the Han Chinese. In particular, we detected extreme differentiation among the Han Chinese at MTHFR, ADH7, and FADS loci, suggesting that these loci may not be specifically selected in Tibetan and Inuit populations as previously suggested. On the other hand, we find that Neandertal ancestry does not vary significantly across the provinces, consistent with admixture prior to the dispersal of modern Han Chinese. Furthermore, contrary to a previous report, Neandertal ancestry does not explain a significant amount of heritability in depression. Our findings provide the largest genetic data set so far made available for Han Chinese and provide insights into the history and population structure of the world’s largest ethnic group.

scholarly journals Going with the flow: analysis of population structure reveals high gene flow shaping invasion pattern and inducing range expansion of Mikania micrantha in Asia

2020 ◽  
Vol 125 (7) ◽  
pp. 1113-1126
Author(s):  
Achyut Kumar Banerjee ◽  
Zhuangwei Hou ◽  
Yuting Lin ◽  
Wentao Lan ◽  
Fengxiao Tan ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Genetic Variation ◽  
Gene Flow ◽  
Genetic Distance ◽  
Range Expansion ◽  
Mikania Micrantha ◽  
High Gene Flow ◽  
Genetic Pattern ◽  
High Gene

Abstract Background and Aims Mikania micrantha, a climbing perennial weed of the family Asteraceae, is native to Latin America and is highly invasive in the tropical belt of Asia, Oceania and Australia. This study was framed to investigate the population structure of M. micrantha at a large spatial scale in Asia and to identify how introduction history, evolutionary forces and landscape features influenced the genetic pattern of the species in this region. Methods We assessed the genetic diversity and structure of 1052 individuals from 46 populations for 12 microsatellite loci. The spatial pattern of genetic variation was investigated by estimating the relationship between genetic distance and geographical, climatic and landscape resistances hypothesized to influence gene flow between populations. Key Results We found high genetic diversity of M. micrantha in this region, as compared with the genetic diversity parameters of other invasive species. Spatial and non-spatial clustering algorithms identified the presence of multiple genetic clusters and admixture between populations. Most of the populations showed heterozygote deficiency, primarily due to inbreeding, and the founder populations showed evidence of a genetic bottleneck. Persistent gene flow throughout the invasive range caused low genetic differentiation among populations and provided beneficial genetic variation to the marginal populations in a heterogeneous environment. Environmental suitability was found to buffer the detrimental effects of inbreeding at the leading edge of range expansion. Both linear and non-linear regression models demonstrated a weak relationship between genetic distance and geographical distance, as well as bioclimatic variables and environmental resistance surfaces. Conclusions These findings provide evidence that extensive gene flow and admixture between populations have influenced the current genetic pattern of M. micrantha in this region. High gene flow across the invaded landscape may facilitate adaptation, establishment and long-term persistence of the population, thereby indicating the range expansion ability of the species.

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