The recent development of fecal-genetic capture-mark-recapture (CMR) methods has increased the feasibility of estimating abundance of forest-dwelling ungulates that are difficult to survey using visual methods. Unless genetic markers differentiating sex are incorporated into such studies, however, genetic CMR approaches risk missing sex-specific differences in population trends. We developed a singlereaction genetic assay for sex and individual identification, including 10 microsatellites and an SRY marker, and applied it in the context of a post-fawning CMR study of Columbian black-tailed deer (Odocoileus hemionus columbianus) in forested habitat of coastal California during 2011 and 2012. We measured sexspecific abundance and sex ratios in high-quality summer habitats encompassing 4 distinct fawning areas. We detected a significant interaction between sex and year, indicating different trends in the abundance of males and females. We also detected a significant decline in abundance of females between years (P ¼ 0.045), which agreed with independent telemetry-based estimates, and significant differences in female abundance among fawning areas (P ¼ 0.020) but no significant differences in the abundance of males for either variable (F 1-3,20 < 0.710, P > 0.410). When sex was not considered in the analysis, we found no significant differences in abundance between the 2 years, suggesting that differing trends between the 2 sexes obscured the femalespecific patterns. We estimated average local (i.e., on the high-quality summer ranges) density (D) for females at 41.0 (AE 5.9) deer/km 2 in 2011 and 29.1 (AE 6.8) deer/km 2 in 2012, and local density of males at 15.7 (AE 3.0) deer/km 2 across the 2 study years. Accordingly, sex ratios differed between years (95% CI ¼ 3.0-4.2 F:M ratio in 2011, 2.0-2.3 F:M ratio in 2012). Incorporating sex and individual markers into a single assay provided a cost-effective means of applying CMR estimation based on fecal DNA to a high-density ungulate population in a forested ecosystem and emphasized the importance of explicitly modeling sex in abundance estimation. Ó

Domestic dogs have been central to life in the North American Arctic for millennia. The ancestors of the Inuit were the first to introduce the widespread usage of dog sledge transportation technology to the Americas, but whether the Inuit adopted local Palaeo-Inuit dogs or introduced a new dog population to the region remains unknown. To test these hypotheses, we generated mitochondrial DNA and geometric morphometric data of skull and dental elements from a total of 922 North American Arctic dogs and wolves spanning over 4500 years. Our analyses revealed that dogs from Inuit sites dating from 2000 BP possess morphological and genetic signatures that distinguish them from earlier Palaeo-Inuit dogs, and identified a novel mitochondrial clade in eastern Siberia and Alaska. The genetic legacy of these Inuit dogs survives today in modern Arctic sledge dogs despite phenotypic differences between archaeological and modern Arctic dogs. Together, our data reveal that Inuit dogs derive from a secondary pre-contact migration of dogs distinct from Palaeo-Inuit dogs, and probably aided the Inuit expansion across the North American Arctic beginning around 1000 BP.

Native to sub-Saharan Africa, Aethina tumida Murray (Coleoptera: Nitidulidae) is now an invasive pest of honey bee, Apis mellifera L., colonies in Australia and North America. Knowledge about the introduction (s) of this beetle from Africa into and among the current ranges will elucidate pest populations and invasion pathways and contribute to knowledge of how a parasite expands in new populations. We examined genetic variation in adult beetle samples from the United States, Australia, Canada, and Africa by sequencing a 912-base pair region of the mitochondrial DNA cytochrome c oxidase subunit I gene and screening 10 informative microsatellite loci. One Canadian introduction of small hive beetles can be traced to Australia, whereas the second introduction seems to have come from the United States. Beetles now resident in Australia were of a different African origin than were beetles in North America. North American beetles did not show covariance between two mitochondrial haplotypes and their microsatellite frequencies, suggesting that these beetles have a shared source despite having initial genetic structure within their introduced range. Excellent dispersal of beetles, aided in some cases by migratory beekeeping and the bee trade, seems to lead to panmixis in the introduced populations as well as in Africa.

Use of complete mitochondrial genomes (mitogenomes) can greatly increase the resolution achievable in phylogeographic and historical demographic studies. Using next-generation sequencing methods, it is now feasible to efficiently sequence mitogenomes of large numbers of individuals once a reference mitogenome is available. However, assembling the initial mitogenomes of nonmodel organisms can present challenges, for example, in birds, where mtDNA is often subject to gene rearrangements and duplications. We developed a workflow based on Illumina paired-end, whole-genome shotgun sequencing, which we used to generate complete 19-kilobase mitogenomes for each of three species of North Pacific albatross, a group of birds known to carry a tandem duplication. Although this duplication had been described previously, our procedure did not depend on this prior knowledge, nor did it require a closely related reference mitogenome (e.g. a mammalian mitogenome was sufficient). We employed an iterative process including de novo assembly, reference-guided assembly and gap closing, which enabled us to detect duplications, determine gene order and identify sequence for primer positioning to resolve any mitogenome ambiguity (via minimal targeted Sanger sequencing). We present full mtDNA annotations, including 22 tRNAs, 2 rRNAs, 13 protein-coding genes, a control region and a duplicated feature for all three species. Pairwise comparisons supported previous hypotheses regarding the phylogenetic relationships within this group and occurrence of a shared tandem duplication. The resulting mitogenome sequences will enable rapid, high-throughput NGS mitogenome sequencing of North Pacific albatrosses via direct reference-guided assembly. Moreover, our approach to assembling mitogenomes should be applicable to any taxon.

Noninvasive DNA sampling from scats can provide powerful tools for wildlife research depending in large part on how scats are collected in the field. Preservation of scat in 95-100% ethanol can be highly effective, but not always practical. Use of swabs to sample the mucous layer from scats is a popular alternative, but has not been adequately tested in arid environments, where the mucous layer can rapidly desiccate. We conducted a paired comparison of methods, extraction from scats stored in ethanol ("direct method") versus from swabs ("swab method"), for carnivore scats collected under typical field conditions during May-September 2013 and January-February 2015 in northern California, USA. Direct quantification of DNA indicated that the extracts from ethanol-preserved direct-method samples contained, on average, an order of magnitude (14Â) more target DNA than extracts from swab method (P < 0.03). For mitochondrial sequencing, which is typically used for species-typing, we obtained slightly higher success for the direct (81%) than the swab (73%) extracts, but not significantly so (P ¼ 0.25, n ¼ 104). Among 62 canid scats, microsatellite genotyping (typically used for individual identification) was much more successful for the direct extracts (74%) than the swab extracts (35%; P < 0.001, n ¼ 62). Together, our findings indicated a substantial advantage of ethanol preservation followed by extraction directly from scats over swabbing in our arid study area. Our results apply most specifically to canids in the arid study environment; swabbing is potentially more effective in humid environments or in other carnivore species. Nevertheless, our findings highlight the importance of conducting pilot studies before committing to swabbing as a means of fecal DNA collection. Ó 2015 The Wildlife Society.

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.

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Abstract.-Range-wide monitoring of shorebirds (Aves: Charadriiformes) suggests that many species are declining. For most species, it is unknown whether distinct population units exist, which makes management and conservation difficult. One shorebird of conservation concern, the Buff-breasted Sandpiper (Tryngites subruficollis), is a New World migrant that breeds at Arctic latitudes in North America and Russia and winters in southeastern South America. We conducted a molecular survey of samples representing each of three migratory regions (breeding, migration, and wintering) using nine polymorphic microsatellite loci and 1.5 kb of highly variable mitochondrial DNA (mtDNA) from the cytochrome b gene and mtDNA control region. We analyzed contemporary population structure, demographic trends, and phylogeographic patterns. Overall, microsatellite and mtDNA analyses revealed that Buff-breasted Sandpipers are panmictic both regionally and at a global scale, with no signal of a recent genetic bottleneck. The mtDNA analyses revealed a pattern of haplotype diversity consistent with an expansion from a single refugium (Tajima's D: -2.27, P < 0.01; Fu's F S : -30.6, P < 0.0001), after the height of the Wisconsinan glaciation (8,400-45,000 years before present). Overall, our molecular analyses suggest that Buff-breasted Sandpipers should be treated as a single conservation unit, and management efforts for this species should focus on limiting future declines to ensure that genetic viability is maintained. Received 30 October 2012, accepted 22 February 2013 Key words: Buff-breasted Sandpiper, microsatellites, mtDNA, phylogeography, population bottleneck, shorebird, Tryngites subruficollis, wader. Genética de la Conservación de Tryngites subruficollis en Toda su DistribuciónResumen.-El monitoreo de aves playeras (Aves: Charadriiformes) a través de toda su distribución sugiere que muchas especies presentan disminuciones poblacionales. Para la mayoría de las especies no se conoce si existen distintas unidades poblacionales, lo que dificulta su manejo y conservación. Un ave playera de interés para la conservación, Tryngites subruficollis, es un migrante del Nuevo Mundo que se reproduce en latitudes árticas en Norte América y Rusia, y pasa el invierno en el sureste de Sur América. Hicimos un estudio molecular de muestras que representan cada una de tres regiones migratorias (sitios de reproducción, migración e invernada) usando nueve loci de microsatélites polimórficos y 1.5 kb de ADN mitocondrial altamente variable (ADNmt) del gen citocromo b y la región control del ADNmt. Analizamos la estructura poblacional contemporánea, las tendencias demográficas y los patrones filogeográficos. En general, los análisis de microsatélites y de ADNmt revelaron que T. subruficollis tiene una estuctura poblacional panmíctica tanto a escala regional como a escala global, sin señales genéticas de cuellos de botella recientes. Los análisis de ADNmt revelaron un patrón de diversidad haplotípica consistente con una expansión desde un único refugio (D...