Genome-wide SNPs reveal complex fine scale population structure in the California market squid fishery (Doryteuthis opalescens)

2020 ◽  
Author(s):  
Samantha H. Cheng ◽  
Mark Gold ◽  
Nichole Rodriguez ◽  
Paul H. Barber
Keyword(s):  
Population Structure ◽  
Fine Scale ◽  
Genome Wide ◽  
Doryteuthis Opalescens ◽  
Scale Population

scholarly journals Genome-wide survey of single-nucleotide polymorphisms reveals fine-scale population structure and signs of selection in the threatened Caribbean elkhorn coral, Acropora palmata

2017 ◽  
Author(s):  
Meghann D Durante ◽  
Iliana B Baums
Keyword(s):  
Population Structure ◽  
Single Nucleotide Polymorphisms ◽  
Ex Situ ◽  
Fine Scale ◽  
Nucleotide Polymorphisms ◽  
Acropora Palmata ◽  
Single Nucleotide ◽  
Major Barrier ◽  
Genome Wide ◽  
Scale Population

The advent of next-generation sequencing tools has made it possible to conduct fine-scale surveys of population differentiation and genome-wide scans for signatures of selection in non-model organisms. Such surveys are of particular importance in sharply declining coral species, since knowledge of population boundaries and signs of local adaptation can inform restoration and conservation efforts. Here, genome-wide surveys of single-nucleotide polymorphisms in the threatened Caribbean elkhorn coral, Acropora palmata, reveal fine-scale population structure and place the major barrier to gene flow that separates the eastern and western Caribbean populations between the Bahamas and Puerto Rico. The exact location of this break had been subject to discussion because two previous studies based on microsatellite data had come to differing conclusions. We investigate this contradiction by analyzing an extended set of 12 microsatellite markers including the five previously employed and discovered that one of the original microsatellite loci is apparently under selection. Exclusion of this locus reconciles the results from the SNP and the microsatellite datasets. Scans for outlier loci in the SNP data detected 12 candidate loci under positive selection. Together, these results suggest that restoration of populations should use local sources and utilize existing functional variation among populations in ex situ crossing experiments to improve stress resistance of this species.

scholarly journals A different view on fine-scale population structure in Western African populations

2019 ◽  
Vol 139 (1) ◽  
pp. 45-59 ◽  
Author(s):  
Kridsadakorn Chaichoompu ◽  
Fentaw Abegaz ◽  
Bruno Cavadas ◽  
Verónica Fernandes ◽  
Bertram Müller-Myhsok ◽  
...  
Keyword(s):  
Population Structure ◽  
A Priori ◽  
Scale Structure ◽  
Fine Scale ◽  
Computationally Efficient ◽  
Structure Detection ◽  
Genome Wide ◽  
African Populations ◽  
Scale Population ◽  
Southwest Usa

Abstract Due to its long genetic evolutionary history, Africans exhibit more genetic variation than any other population in the world. Their genetic diversity further lends itself to subdivisions of Africans into groups of individuals with a genetic similarity of varying degrees of granularity. It remains challenging to detect fine-scale structure in a computationally efficient and meaningful way. In this paper, we present a proof-of-concept of a novel fine-scale population structure detection tool with Western African samples. These samples consist of 1396 individuals from 25 ethnic groups (two groups are African American descendants). The strategy is based on a recently developed tool called IPCAPS. IPCAPS, or Iterative Pruning to CApture Population Structure, is a genetic divisive clustering strategy that enhances iterative pruning PCA, is robust to outliers and does not require a priori computation of haplotypes. Our strategy identified in total 12 groups and 6 groups were revealed as fine-scale structure detected in the samples from Cameroon, Gambia, Mali, Southwest USA, and Barbados. Our finding helped to explain evolutionary processes in the analyzed West African samples and raise awareness for fine-scale structure resolution when conducting genome-wide association and interaction studies.

scholarly journals Fine-scale population structure in the UK Biobank: implications for genome-wide association studies

2020 ◽  
Vol 29 (16) ◽  
pp. 2803-2811
Author(s):  
James P Cook ◽  
Anubha Mahajan ◽  
Andrew P Morris
Keyword(s):  
Population Structure ◽  
Association Studies ◽  
Genome Wide Association ◽  
Genome Wide Association Studies ◽  
Fine Scale ◽  
Uk Biobank ◽  
Genome Wide ◽  
Scale Population ◽  
The Uk ◽  
The Impact

Abstract The UK Biobank is a prospective study of more than 500 000 participants, which has aggregated data from questionnaires, physical measures, biomarkers, imaging and follow-up for a wide range of health-related outcomes, together with genome-wide genotyping supplemented with high-density imputation. Previous studies have highlighted fine-scale population structure in the UK on a North-West to South-East cline, but the impact of unmeasured geographical confounding on genome-wide association studies (GWAS) of complex human traits in the UK Biobank has not been investigated. We considered 368 325 white British individuals from the UK Biobank and performed GWAS of their birth location. We demonstrate that widely used approaches to adjust for population structure, including principal component analysis and mixed modelling with a random effect for a genetic relationship matrix, cannot fully account for the fine-scale geographical confounding in the UK Biobank. We observe significant genetic correlation of birth location with a range of lifestyle-related traits, including body-mass index and fat mass, hypertension and lung function, even after adjustment for population structure. Variants driving associations with birth location are also strongly associated with many of these lifestyle-related traits after correction for population structure, indicating that there could be environmental factors that are confounded with geography that have not been adequately accounted for. Our findings highlight the need for caution in the interpretation of lifestyle-related trait GWAS in UK Biobank, particularly in loci demonstrating strong residual association with birth location.

scholarly journals Genome-wide survey of single-nucleotide polymorphisms reveals fine-scale population structure and signs of selection in the threatened Caribbean elkhorn coral, Acropora palmata

PeerJ ◽  
2017 ◽  
Vol 5 ◽  
pp. e4077 ◽  
Author(s):  
Meghann K. Devlin-Durante ◽  
Iliana B. Baums
Keyword(s):  
Population Structure ◽  
Single Nucleotide Polymorphisms ◽  
Ex Situ ◽  
Fine Scale ◽  
Nucleotide Polymorphisms ◽  
Acropora Palmata ◽  
Single Nucleotide ◽  
Major Barrier ◽  
Genome Wide ◽  
Scale Population

The advent of next-generation sequencing tools has made it possible to conduct fine-scale surveys of population differentiation and genome-wide scans for signatures of selection in non-model organisms. Such surveys are of particular importance in sharply declining coral species, since knowledge of population boundaries and signs of local adaptation can inform restoration and conservation efforts. Here, we use genome-wide surveys of single-nucleotide polymorphisms in the threatened Caribbean elkhorn coral, Acropora palmata, to reveal fine-scale population structure and infer the major barrier to gene flow that separates the eastern and western Caribbean populations between the Bahamas and Puerto Rico. The exact location of this break had been subject to discussion because two previous studies based on microsatellite data had come to differing conclusions. We investigate this contradiction by analyzing an extended set of 11 microsatellite markers including the five previously employed and discovered that one of the original microsatellite loci is apparently under selection. Exclusion of this locus reconciles the results from the SNP and the microsatellite datasets. Scans for outlier loci in the SNP data detected 13 candidate loci under positive selection, however there was no correlation between available environmental parameters and genetic distance. Together, these results suggest that reef restoration efforts should use local sources and utilize existing functional variation among geographic regions in ex situ crossing experiments to improve stress resistance of this species.

scholarly journals Fine-scale human population structure in southern Africa reflects ecological boundaries

2016 ◽  
Author(s):  
Caitlin Uren ◽  
Minju Kim ◽  
Alicia R Martin ◽  
Dean Bobo ◽  
Christopher R Gignoux ◽  
...  
Keyword(s):  
Population Structure ◽  
Southern Africa ◽  
Population History ◽  
Fine Scale ◽  
Hunter Gatherers ◽  
Kalahari Desert ◽  
Genome Wide ◽  
African Populations ◽  
Scale Population ◽  
Northern Cape

Recent genetic studies have established that the KhoeSan populations of southern Africa are distinct from all other African populations and have remained largely isolated during human prehistory until about 2,000 years ago. Dozens of different KhoeSan groups exist, belonging to three different language families, but very little is known about population history within southern Africa. We examine new genome-wide polymorphism data and whole mitochondrial genomes for more than one hundred South Africans from the ≠Khomani San and Nama populations of the Northern Cape, analyzed in conjunction with 19 additional southern African populations. Our analyses reveal fine-scale population structure in and around the Kalahari Desert. Surprisingly, this structure does not always correspond to linguistic or subsistence categories as previously suggested, but rather reflects the role of geographic barriers and the ecology of the greater Kalahari Basin. Regardless of subsistence strategy, the indigenous Khoe-speaking Nama pastoralists and the N|u-speaking ≠Khomani (formerly hunter-gatherers) share recent ancestry with other Khoe-speaking forager populations that forms a rim around the Kalahari Desert. We reconstruct earlier migration patterns and estimate that the southern Kalahari populations were among the last to experience gene flow from Bantu-speakers, approximately 14 generations ago. We conclude that local adoption of pastoralism, at least by the Nama, appears to have been primarily a cultural process with limited impact from eastern African genetic diffusion.

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