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

2020 ◽  
Vol 10 (4) ◽  
pp. 1889-1904 ◽  
Author(s):  
Nicholas Price ◽  
Lua Lopez ◽  
Adrian E. Platts ◽  
Jesse R. Lasky
Keyword(s):  
Population Structure ◽  
Candidate Genes ◽  
Local Adaptation

scholarly journals Candidate Genes for the High-Altitude Adaptations of Two Mountain Pine Taxa

2021 ◽  
Vol 22 (7) ◽  
pp. 3477
Author(s):  
Julia Zaborowska ◽  
Bartosz Łabiszak ◽  
Annika Perry ◽  
Stephen Cavers ◽  
Witold Wachowiak
Keyword(s):  
Population Structure ◽  
Candidate Genes ◽  
Genetic Basis ◽  
Redox Homeostasis ◽  
Snp Markers ◽  
Regulation Of Transcription ◽  
Single Nucleotide ◽  
Homeostasis Regulation ◽  
Genomic Regions ◽  
Mountain Plants

Mountain plants, challenged by vegetation time contractions and dynamic changes in environmental conditions, developed adaptations that help them to balance their growth, reproduction, survival, and regeneration. However, knowledge regarding the genetic basis of species adaptation to higher altitudes remain scarce for most plant species. Here, we attempted to identify such corresponding genomic regions of high evolutionary importance in two closely related European pines, Pinus mugo and P. uncinata, contrasting them with a reference lowland relative—P. sylvestris. We genotyped 438 samples at thousands of single nucleotide polymorphism (SNP) markers, tested their genetic differentiation and population structure followed by outlier detection and gene ontology annotations. Markers clearly differentiated the species and uncovered patterns of population structure in two of them. In P. uncinata three Pyrenean sites were grouped together, while two outlying populations constituted a separate cluster. In P. sylvestris, Spanish population appeared distinct from the remaining four European sites. Between mountain pines and the reference species, 35 candidate genes for altitude-dependent selection were identified, including such encoding proteins responsible for photosynthesis, photorespiration and cell redox homeostasis, regulation of transcription, and mRNA processing. In comparison between two mountain pines, 75 outlier SNPs were found in proteins involved mainly in the gene expression and metabolism.

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 Genome-wide scan for runs of homozygosity identifies potential candidate genes associated with local adaptation in Valle del Belice sheep

2017 ◽  
Vol 49 (1) ◽  
Author(s):  
Salvatore Mastrangelo ◽  
Marco Tolone ◽  
Maria T. Sardina ◽  
Gianluca Sottile ◽  
Anna M. Sutera ◽  
...  
Keyword(s):  
Candidate Genes ◽  
Local Adaptation ◽  
Potential Candidate ◽  
Runs Of Homozygosity ◽  
Genome Wide ◽  
Genome Wide Scan

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 Genetic structure of immunologically associated candidate genes suggests arctic rabies variants exert differential selection in arctic fox populations

PLoS ONE ◽  
2021 ◽  
Vol 16 (10) ◽  
pp. e0258975
Author(s):  
Tristan M. Baecklund ◽  
Michael E. Donaldson ◽  
Karsten Hueffer ◽  
Christopher J. Kyle
Keyword(s):  
Genetic Structure ◽  
Candidate Genes ◽  
Local Adaptation ◽  
Genotyping By Sequencing ◽  
Past Research ◽  
Disease Spread ◽  
The Arctic ◽  
Arctic Fox ◽  
Primary Host ◽  
Differential Selection

Patterns of local adaptation can emerge in response to the selective pressures diseases exert on host populations as reflected in increased frequencies of respective, advantageous genotypes. Elucidating patterns of local adaptation enhance our understanding of mechanisms of disease spread and the capacity for species to adapt in context of rapidly changing environments such as the Arctic. Arctic rabies is a lethal disease that largely persists in northern climates and overlaps with the distribution of its natural host, arctic fox. Arctic fox populations display little neutral genetic structure across their North American range, whereas phylogenetically unique arctic rabies variants are restricted in their geographic distributions. It remains unknown if arctic rabies variants impose differential selection upon host populations, nor what role different rabies variants play in the maintenance and spread of this disease. Using a targeted, genotyping-by-sequencing assay, we assessed correlations of arctic fox immunogenetic variation with arctic rabies variants to gain further insight into the epidemiology of this disease. Corroborating past research, we found no neutral genetic structure between sampled regions, but did find moderate immunogenetic structuring between foxes predominated by different arctic rabies variants. FST outliers associated with host immunogenetic structure included SNPs within interleukin and Toll-like receptor coding regions (IL12B, IL5, TLR3 and NFKB1); genes known to mediate host responses to rabies. While these data do not necessarily reflect causation, nor a direct link to arctic rabies, the contrasting genetic structure of immunologically associated candidate genes with neutral loci is suggestive of differential selection and patterns of local adaptation in this system. These data are somewhat unexpected given the long-lived nature and dispersal capacities of arctic fox; traits expected to undermine local adaptation. Overall, these data contribute to our understanding of the co-evolutionary relationships between arctic rabies and their primary host and provide data relevant to the management of this disease.

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