Conservation status of buff-breasted sandpipers (Tryngites subruficollis) in the Western Hemisphere: a conservation genetic approach

Master of ScienceDivision of BiologySamantha M. WiselyRange-wide estimates of shorebird (Aves: Charadriiformes) populations suggest sharp declines in population sizes across a range of species. Efforts to accurately assess the conservation status of wild populations are becoming increasingly vital to species management. One shorebird of conservation concern, the Buff-breasted Sandpiper (Tryngites subruficollis), is a New World migrant which winters in southeastern South America and breeds in the arctic. To establish an updated conservation status for Buff-breasted Sandpipers, we conducted a molecular survey of wild populations on spatial and temporal scales. We analyzed patterns of global population structure, demographic trends, and phylogeography using nine polymorphic microsatellites and two mitochondrial DNA (mtDNA) markers, cytochrome b and the control region, among 477 individuals across their distributional range. To empirically assess the impact of population declines on genetic diversity, we also surveyed segments of the same two mtDNA markers from 220 museum specimens collected across a 135-year period. Contemporary microsatellite and mtDNA analyses revealed that Buff-breasted Sandpipers are admixed on a global scale, with effective population size estimates ranging from 2,657 to 16,400 birds and no signal of a recent genetic bottleneck. Contemporary mtDNA analyses suggested a pattern of haplotype diversity consistent with a historic radiation from a single refugium which we estimated to have occurred between 8,000−45,000 years before present. Using five measures of mtDNA diversity (haplotype and nucleotide diversity, trend analyses of haplotype richness, Watterson’s estimate of theta, and phi-statistics), as well as a Bayesian Skyline reconstruction of demographic trends in effective population size (N[subscript]e[subscript]f), we concluded that substantial mtDNA diversity and N[subscript]e[subscript]f had not been lost as a result of the population declines in this species. While genetic diversity did not appear to have been lost due to population losses, management efforts must focus on preventing future losses in order for wild populations to remain viable. Our results suggested that the global population of Buff-breasted Sandpipers should be treated as a single, panmictic conservation unit and that successful management must focus on preventing further declines and habitat fragmentation

Identification of 12 EST-derived SSR markers in Lumbricus rubellus

While many species of earthworms are globally distributed, very little is known about the genetic population dynamics of this diverse group. We present the characterization of novel simple sequence repeat (SSR) markers, including primer information, number of alleles, repeat motif, and approximate size ranges, to be used in population genetic analyses of the earthworm Lumbricus rubellus Hoffmeister 1843. Specifically, we designed and characterized 12 novel, polymorphic markers derived from published expressed sequence tags (EST) for amplification in L. rubellus. The mean number of alleles per locus was 6.25 ± 1.91, indicating these markers will be sufficiently polymorphic for population genetic studies of this species

Draft genome of tule elk Cervus canadensis nannodes [version 2; referees: 2 approved]

This paper presents the first draft genome of the tule elk (Cervus elaphus nannodes), a subspecies native to California that underwent an extreme genetic bottleneck in the late 1800s.  The genome was generated from Illumina HiSeq 3000 whole genome sequencing of four individuals, resulting in the assembly of 2.395 billion base pairs (Gbp) over 602,862 contigs over 500 bp and N50 = 6,885 bp. This genome provides a resource to facilitate future genomic research on elk and other cervids

Draft genome of tule elk Cervus canadensis nannodes.

This paper presents the first draft genome of the tule elk ( Cervus elaphus nannodes), a subspecies native to California that underwent an extreme genetic bottleneck in the late 1800s.  The genome was generated from Illumina HiSeq 3000 whole genome sequencing of four individuals, resulting in the assembly of 2.395 billion base pairs (Gbp) over 602,862 contigs over 500 bp and N50 = 6,885 bp. This genome provides a resource to facilitate future genomic research on elk and other cervids

Metadata and genotypes for tule elk and contigs containing microsatellites

Metadata and genotypes for tule elk and contigs containing microsatellite

Data from: Development and characterization of 15 polymorphic di-nucleotide microsatellite markers for tule elk using HiSeq3000

The tule elk (Cervus elaphus nannodes) experienced a severe bottleneck in the 1800s, resulting in low genetic diversity. There is a need for high-resolution genetic assays that can be used to differentiate individual elk, including close relatives, with high confidence. An efficient assay requires multiple markers both polymorphic and that can be amplified in concert with other markers in multiplex reactions. To develop such markers, we employed 150-bp paired-end whole genome shotgun sequencing on an Illumina HiSeq3000 platform to discover dinucleotide microsatellite markers. After preliminary screening of these markers, we selected and screened 15 candidate loci and 5 existing tetra nucleotide markers in 56 tule elk. We combined these markers in 2 multiplex reactions and report primer concentrations and PCR conditions enabling their efficient amplification

Sequencing Red Fox Y Chromosome Fragments to Develop Phylogenetically Informative SNP Markers and Glimpse Male-Specific Trans-Pacific Phylogeography.

The red fox (Vulpes vulpes) has a wide global distribution with many ecotypes and has been bred in captivity for various traits, making it a useful evolutionary model system. The Y chromosome represents one of the most informative markers of phylogeography, yet it has not been well-studied in the red fox due to a lack of the necessary genomic resources. We used a target capture approach to sequence a portion of the red fox Y chromosome in a geographically diverse red fox sample, along with other canid species, to develop single nucleotide polymorphism (SNP) markers, 13 of which we validated for use in subsequent studies. Phylogenetic analyses of the Y chromosome sequences, including calibration to outgroups, confirmed previous estimates of the timing of two intercontinental exchanges of red foxes, the initial colonization of North America from Eurasia approximately half a million years ago and a subsequent continental exchange before the last Pleistocene glaciation (~100,000 years ago). However, in contrast to mtDNA, which showed unidirectional transfer from Eurasia to North America prior to the last glaciation, the Y chromosome appears to have been transferred from North America to Eurasia during this period. Additional sampling is needed to confirm this pattern and to further clarify red fox Y chromosome phylogeography

Additional Evidence for DDB2 T338M as a Genetic Risk Factor for Ocular Squamous Cell Carcinoma in Horses.

Squamous cell carcinoma (SCC) is the most common periocular cancer in horses and the second most common tumor of the horse overall. A missense mutation in damage-specific DNA-binding protein 2 (DDB2, c.1012 C>T, p.Thr338Met) was previously found to be strongly associated with ocular SCC in Haflinger and Belgian horses, explaining 76% of cases across both breeds. To determine if this same variant in DDB2 contributes to risk for ocular SCC in the Arabian, Appaloosa, and Percheron breeds and to determine if the variant contributes to risk for oral or urogenital SCC, histologically confirmed SCC cases were genotyped for the DDB2 variant and associations were investigated. Horses with urogenital SCC that were heterozygous for the DDB2 risk allele were identified in the Appaloosa breed, but a significant association between the DDB2 variant and SCC occurring at any location in this breed was not detected. The risk allele was not identified in Arabians, and no Percherons were homozygous for the risk allele. High-throughput sequencing data from six Haflingers were analyzed to ascertain if any other variant from the previously associated 483 kb locus on ECA12 was more concordant with the SCC phenotype than the DDB2 variant. Sixty polymorphisms were prioritized for evaluation, and no other variant from this locus explained the genetic risk better than the DDB2 allele (P = 3.39 × 10-17, n = 118). These data provide further support of the DDB2 variant contributing to risk for ocular SCC, specifically in the Haflinger and Belgian breeds