Comparing mixed models and Random Forest association tests using naturalgwas and a Striped Bass SNP data set.

In this study, we used the phenotype simulation package naturalgwas to test the performance of Zhao's Random Forest method in comparison to an uncorrected Random Forest test, latent factor mixed models (LFMM), genome-wide efficient mixed models (GEMMA), and confounder adjusted linear regression (CATE). We created 400 sets of phenotypes, corresponding to five effect sizes and two, five, 15, or 30 causal loci, simulated from two empirical data sets containing SNPs from Striped Bass representing three and 13 populations. All association methods were evaluated for their ability to detect genotype-phenotype associations based on power, false discovery rates, and number of false positives. Genomic inflation was highest for uncorrected Random Forest and LFMM tests and lowest for Gemma and Zhao's Random Forest. All association tests had similar power to detect causal loci, and Zhao's Random Forest had the lowest false discovery rate in all scenarios. To measure the performance of association tests in small data sets with few loci surrounding a causal gene we also ran analyses again after removing causal loci from each data set. All association tests were only able to find true positives, defined as loci located within 30 kbp of a causal locus, in 3%-18% of simulations. In contrast, at least one false positive was found in 17%-44% of simulations. Zhao's Random Forest again identified the fewest false positives of all association tests studied. The ability to test the power of association tests for individual empirical data sets can be an extremely useful first step when designing a GWAS study.

Genomic population structure of Striped Bass (Morone saxatilis) from the Gulf of St. Lawrence to Cape Fear River.

Striped Bass, Morone saxatilis (Walbaum, 1792), is an anadromous fish species that supports fisheries throughout North America and is native to the North American Atlantic Coast. Due to long coastal migrations that span multiple jurisdictions, a detailed understanding of population genomics is required to untangle demographic patterns, understand local adaptation, and characterize population movements. This study used 1,256 single nucleotide polymorphism (SNP) loci to investigate genetic structure of 477 Striped Bass sampled from 15 locations spanning the North American Atlantic coast from the Gulf of St. Lawrence, Canada, to the Cape Fear River, United States. We found striking differences in neutral divergence among Canadian sites, which were isolated from each other and US populations, compared with US populations that were much less isolated. Our SNP dataset was able to assign 99% of Striped Bass back to six reporting groups, a 39% improvement over previous genetic markers. Using this method, we found (a) evidence of admixture within Saint John River, indicating that migrants from the United States and from Shubenacadie River occasionally spawn in the Saint John River; (b) Striped Bass collected in the Mira River, Cape Breton, Canada, were found to be of both Miramichi River and US origin; (c) juveniles in the newly restored Kennebec River population had small and nonsignificant differences from the Hudson River; and (d) tributaries within the Chesapeake Bay showed a mixture of homogeny and small differences among each other. This study introduces new hypotheses about the dynamic zoogeography of Striped Bass at its northern range and has important implications for the local and international management of this species.

Population structure of Purple Sandpipers (Calidris maritima) as revealed by mitochondrial DNA and microsatellites.

The Purple Sandpiper (Calidris maritima) is a medium-sized shorebird that breeds in the Arctic and winters along northern Atlantic coastlines. Migration routes and affiliations between breeding grounds and wintering grounds are incompletely understood. Some populations appear to be declining, and future management policies for this species will benefit from understanding their migration patterns. This study used two mitochondrial DNA markers and 10 microsatellite loci to analyze current population structure and historical demographic trends. Samples were obtained from breeding locations in Nunavut (Canada), Iceland, and Svalbard (Norway) and from wintering locations along the coast of Maine (USA), Nova Scotia, New Brunswick, and Newfoundland (Canada), and Scotland (UK). Mitochondrial haplotypes displayed low genetic diversity, and a shallow phylogeny indicating recent divergence. With the exception of the two Canadian breeding populations from Nunavut, there was significant genetic differentiation among samples from all breeding locations; however, none of the breeding populations was a monophyletic group. We also found differentiation between both Iceland and Svalbard breeding populations and North American wintering populations. This pattern of divergence is consistent with a previously proposed migratory pathway between Canadian breeding locations and wintering grounds in the United Kingdom, but argues against migration between breeding grounds in Iceland and Svalbard and wintering grounds in North America. Breeding birds from Svalbard also showed a genetic signature intermediate between Canadian breeders and Icelandic breeders. Our results extend current knowledge of Purple Sandpiper population genetic structure and present new information regarding migration routes to wintering grounds in North America.