Rangewide American shad microsatellite data

Microsatellite dataset for 13 loci genotyped across 33 populations of American shad from across the species native range

Appendix A. A table showing the results of GLM analyses.

A table showing the results of GLM analyses

Deciphering Hatchery Stock Influences on Wild Populations of Vermont Lake Trout

<div><p></p><p>To better understand the influence of hatchery practices on wild populations of Lake Trout <i>Salvelinus namaycush</i>, we used a landscape genetic approach to tease apart the population genetic patterns expected due to natural processes versus hatchery stocking, i.e., human-mediated gene flow. In several lakes across our study area in Vermont, the presence of exogenous mitochondrial DNA haplotypes supported our human-mediated gene flow hypothesis. Microsatellite DNA analyses showed introgression of hatchery genotypes into the wild populations. Nonetheless, clustering patterns within river drainages and signatures of isolation by distance were consistent with natural postglacial colonization. We conclude that though the genetic makeup of Vermont Lake Trout populations has been influenced by stocking, a lack of genetic bottlenecks and concordance with landscape processes suggests that much of the indigenous genetic diversity remains intact. We were able to attribute departures from expectations based on natural genetic patterns to hatchery introgression in specific lakes. To preserve the adaptive potential of local populations that have persisted since the last ice age, we suggest areas for which hatchery supplementation could be minimized.</p><p>Received June 16, 2014; accepted September 12, 2014</p></div

Barcoding Atlantic Canada’s mesopelagic and upper bathypelagic marine fishes

<div><p>DNA barcode sequences were developed from 557 mesopelagic and upper bathypelagic teleost specimens collected in waters off Atlantic Canada. Confident morphological identifications were available for 366 specimens, of 118 species and 93 genera, which yielded 328 haplotypes. Five of the species were novel to the Barcode of Life Database (BOLD). Most of the 118 species conformed to expectations of monophyly and the presence of a “barcode gap”, though some known weaknesses in existing taxonomy were confirmed and a deficiency in published keys was revealed. Of the specimens for which no firm morphological identification was available, 156 were successfully identified to species, and a further 11 to genus, using their barcode sequences and a combination of distance- and character-based methods. The remaining 24 specimens were from species for which no reference barcode is yet available or else ones confused by apparent misidentification of publicly available sequences in BOLD. Addition of the new sequences to those previously in BOLD contributed support to recent taxonomic revisions of <i>Chiasmodon</i> and <i>Poromitra</i>, while it also revealed 18 cases of potential cryptic speciation. Most of the latter appear to result from genetic divergence among populations in different ocean basins, while the general lack of strong horizontal environmental gradients within the deep sea has allowed morphology to be conserved. Other examples of divergence appear to distinguish individuals living under the sub-tropical gyre of the North Atlantic from those under that ocean’s sub-polar gyre. In contrast, the available sequences for two myctophid species, <i>Benthosema glaciale</i> and <i>Notoscopelus elongatus</i>, showed genetic structuring on finer geographic scales. The observed structure was not consistent with recent suggestions that “resident” populations of myctophids can maintain allopatry despite the mixing of ocean waters. Rather, it indicates that the very rapid speciation characteristic of the Myctophidae is both on-going and detectable using barcodes.</p></div

Distribution of northern fur seal breeding sites.

<p>Distribution of northern fur seal breeding sites.</p

Additional file 5: of Genetic and phenotypic variation along an ecological gradient in lake trout Salvelinus namaycush

First and second principal coordinate (PC) scores (PC1 and PC2) of an individual-based PC analysis on ecotype genotype. Populations were grouped by approximate confidence ellipses for each ecotype (lean = black circles; humper = light grey circles; siscowet = dark grey circles; redfin = red circles). (DOCX 67 kb

Isolation by distance based on mitochondrial DNA analysis in northern fur seals including the relationship between genetic distance, pairwise comparisons of rookeries (Φ_ST ) and the natural log of the geographic distance between the rookery pairs.

<p>Isolation by distance based on mitochondrial DNA analysis in northern fur seals including the relationship between genetic distance, pairwise comparisons of rookeries (Φ_ST ) and the natural log of the geographic distance between the rookery pairs.</p

Minimum spanning network of 112 core mitochondrial DNA haplotypes of northern fur seals.

<p>Branch lengths are the minimum number of steps between haplotypes. The size of the circle representing the individual haplotypes corresponds to the abundance of that haplotype. Numbers identify the most abundant haplotypes. Dashed lines represent alternative groupings.</p

K2P distances within species, genera and families for the 75 species represented by two or more sequences in the reference data set.

<p>K2P distances within species, genera and families for the 75 species represented by two or more sequences in the reference data set.</p

Map showing capture locations of specimens in the reference data set.

<p>The yellow dot represents the specimens in the ACMB BOLD project and marks the location of The Gully. The other dots represent the specimens in the ACMF project, ones caught in close proximity being grouped together for clarity. (Projection: Lambert Conformal Conic).</p