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31 results for “Genome wide SNPs”

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Genome-wide SNPs detect no evidence of genetic population structure for reef manta rays (Mobula alfredi) in southern Mozambique

Little is known about the extent of genetic connectivity along continuous coastlines in manta rays or whether site visitation is influenced by relatedness. Such information is pertinent to defining population boundaries and understanding localised dispersal patterns and behaviour. Here, we use 3057 genome-wide single nucleotide polymorphisms (SNPs) to evaluate population genetic structure and assess levels of relatedness at aggregation sites of reef manta rays (Mobula alfredi) in southern Mozambique (n = 114). Contrary to indications of limited dispersal along the southern Mozambican coastline inferred from photo identification and telemetry studies, our results show no evidence of population structure (non-significant FST <0.001) for M. alfredi along this coast. We also found no evidence that individuals sampled at the same site were more related than expected by chance for males, females or across both sexes, suggesting kinship may not influence visitation pattern s at these sites. We estimated the effective population size (Ne) of this population to be 375 (95% CI = 369-380). Comparison to a distant eastern Indian Ocean site (Western Australia; n = 15) revealed strong genetic differentiation between Mozambique and Western Australia (FST = 0.377), identifying the Indian Ocean basin as a barrier to dispersal. Our findings show that genetic connectivity in M. alfredi extends for several hundred kilometres along continuous coastlines. We therefore recommend the population in Mozambique be considered a discrete management unit and future conservation plans should prioritize integrated strategies along the entire southern coastline.

opencc-zeroSep 2020View details →

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Data from: Genome-wide SNPs resolve phylogenetic relationships in the North American spruce budworm (Choristoneura fumiferana) species complex

High throughput sequencing technologies have revolutionized the potential to reconcile incongruence between gene and species trees, and numerous approaches have been developed to take advantage of these advances. Genotyping-by-sequencing is becoming a regular tool for gathering phylogenetic data, yet comprehensive evaluations of phylogenetic methods using these data are sparse. Here we use multiple phylogenetic and population genetic methods for genotyping-by-sequencing data to assess species relationships in a group of forest insect pests, the spruce budworm (Choristoneura fumiferana) species complex. With few exceptions, all methods agree on the same relationships, most notably placing C. pinus as basal to the remainder of the group, rather than C. fumiferana as previously suggested. We found strong support for the monophyly of C. pinus, C. fumiferana, and C. retinana, but more ambiguous relationships and signatures of introgression in a clade of western lineages, including C. carnana, C. lambertiana, C. occidentalis occidentalis, C. occidentalis biennis, and C. orae. This represents the most taxonomically comprehensive genomic treatment of the spruce budworm species group, which is further supported by the broad agreement among multiple methodologies.

opencc-zeroDec 2016View details →

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Genetic diversity and signatures of selection in 15 Chinese indigenous dog breeds revealed by genome-wide SNPs

<a name="_Hlk15722205">There are dozens of recognized indigenous dog breeds in China. However, these breeds have not had extensive studies to describe their population structure, genomic linkage disequilibrium (LD) patterns, and selection signatures. </a>Here, <a name="_Hlk15722444">we systematically surveyed the genomes </a>of 169 unrelated dogs that were from<a name="_Hlk15722467">15 diverse Chinese dog breeds</a>. Canine 170K SNP chips were used to<a name="_Hlk15722535">compare the genomic structures of Chinese and Western dogs</a>. The genotyping data of 170K SNP chips in Western dogswere downloadedfrom the LUPA (a European initiative of canine genome project) database. Chinese indigenous dogs had lower LD and shorter accumulative runs of homozygosity (ROH) in the genome. The genetic distances between individuals within each Chinese breed were larger than those within Western breeds. Principal component analysis (PCA) and neighbor-joining (NJ)-tree analysis indicated distinct phylogenetic affinities between Chinese and Western dogs. <a name="_Hlk15722638">We found evidence for historical introgression of Western dogs</a>into Chinese Kazakhstan shepherd and Mongolia Xi dogs. We suggested that Greenland sledge dog, Spanish Papillon, and European Eurasier have Chinese dog lineages. The distatistic estimation identified genome-wide selection signatures of each Chinese breed and three breed groups. This study highlights several candidate genes that have undergone natural selection and might be responsible for breed-typical phenotypes. Several genes, e.g. EPAS1and DNAH9, showed signatures of natural selection in Qinghai-Tibetan plateau dogs and are important for genetic adaptation to high altitude. RBP7,NMNAT1,SLC2A5,and H6PDgenes exhibit signatures of natural selection in Chinese mountain hounds and are likely associated with hunting abilities (endurance and night vision). Moreover, the selective sweep analysis suggested that NOL8,KRT9, RORBand CAMTA1might be candidate genes for dog running speed. The resultsabout genomic and population structures, and <a name="_Hlk15722685">selection signatures of Chinese dog breeds reinforce the conclusion that </a>Chinese indigenous dogs with great variations of phenotypes are important resources for identifying genes responsible for complex traits.

opencc-zeroNov 2019View details →

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