scholarly journals Green turtle population structure in the Pacific: new insights from single nucleotide polymorphisms and microsatellites

2013 ◽  
Vol 20 (3) ◽  
pp. 227-234 ◽  
Author(s):  
SE Roden ◽  
PA Morin ◽  
A Frey ◽  
GH Balazs ◽  
P Zarate ◽  
...  
Keyword(s):  
Population Structure ◽  
Single Nucleotide Polymorphisms ◽  
Green Turtle ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
The Pacific ◽  
Turtle Population

scholarly journals The efficacy of short tandem repeat polymorphisms versus single-nucleotide polymorphisms for resolving population structure

BMC Genetics ◽  
2005 ◽  
Vol 6 (Suppl 1) ◽  
pp. S84 ◽  
Author(s):  
John SK Kauwe ◽  
Sarah Bertelsen ◽  
Laura Bierut ◽  
Gerald Dunn ◽  
Anthony L Hinrichs ◽  
...  
Keyword(s):  
Population Structure ◽  
Single Nucleotide Polymorphisms ◽  
Tandem Repeat ◽  
Short Tandem Repeat ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Short Tandem

Population structure of pigs determined by single nucleotide polymorphisms observed in assembled expressed sequence tags

2011 ◽  
Vol 83 (1) ◽  
pp. 14-22 ◽  
Author(s):  
Toshimi MATSUMOTO ◽  
Naohiko OKUMURA ◽  
Hirohide UENISHI ◽  
Takeshi HAYASHI ◽  
Noriyuki HAMASIMA ◽  
...  
Keyword(s):  
Population Structure ◽  
Single Nucleotide Polymorphisms ◽  
Expressed Sequence Tags ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Expressed Sequence

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 Assessment of population structure by single nucleotide polymorphisms (SNPs) in goat breeds☆

2006 ◽  
Vol 833 (1) ◽  
pp. 117-120 ◽  
Author(s):  
L. Pariset ◽  
I. Cappuccio ◽  
P. Ajmone Marsan ◽  
S. Dunner ◽  
G. Luikart ◽  
...  
Keyword(s):  
Population Structure ◽  
Single Nucleotide Polymorphisms ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide

scholarly journals A Whole-Genome Scan for Association with Invasion Success in the Fruit Fly Drosophila suzukii Using Contrasts of Allele Frequencies Corrected for Population Structure

2020 ◽  
Vol 37 (8) ◽  
pp. 2369-2385 ◽  
Author(s):  
Laure Olazcuaga ◽  
Anne Loiseau ◽  
Hugues Parrinello ◽  
Mathilde Paris ◽  
Antoine Fraimout ◽  
...  
Keyword(s):  
Population Structure ◽  
Single Nucleotide Polymorphisms ◽  
Genome Wide Association Study ◽  
Allele Frequencies ◽  
Invasion Success ◽  
Nucleotide Polymorphisms ◽  
Drosophila Suzukii ◽  
Single Nucleotide ◽  
A Genome ◽  
Invasive Status

Abstract Evidence is accumulating that evolutionary changes are not only common during biological invasions but may also contribute directly to invasion success. The genomic basis of such changes is still largely unexplored. Yet, understanding the genomic response to invasion may help to predict the conditions under which invasiveness can be enhanced or suppressed. Here, we characterized the genome response of the spotted wing drosophila Drosophila suzukii during the worldwide invasion of this pest insect species, by conducting a genome-wide association study to identify genes involved in adaptive processes during invasion. Genomic data from 22 population samples were analyzed to detect genetic variants associated with the status (invasive versus native) of the sampled populations based on a newly developed statistic, we called C2, that contrasts allele frequencies corrected for population structure. We evaluated this new statistical framework using simulated data sets and implemented it in an upgraded version of the program BayPass. We identified a relatively small set of single-nucleotide polymorphisms that show a highly significant association with the invasive status of D. suzukii populations. In particular, two genes, RhoGEF64C and cpo, contained single-nucleotide polymorphisms significantly associated with the invasive status in the two separate main invasion routes of D. suzukii. Our methodological approaches can be applied to any other invasive species, and more generally to any evolutionary model for species characterized by nonequilibrium demographic conditions for which binary covariables of interest can be defined at the population level.

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