Identification of microsatellites, or simple sequence repeats (SSRs), can be a time-consuming and costly investment requiring enrichment, cloning, and sequencing of candidate loci. Recently, however, high throughput sequencing (with or without prior enrichment for specific SSR loci) has been utilized to identify SSR loci. The direct “Seq-to-SSR” approach has an advantage over enrichment-based strategies in that it does not require a priori selection of particular motifs, or prior knowledge of genomic SSR content. It has been more expensive per SSR locus recovered, however, particularly for genomes with few SSR loci, such as bird genomes. The longer but relatively more expensive 454 reads have been preferred over less expensive Illumina reads. Here, we use Illumina paired-end sequence data to identify potentially amplifiable SSR loci (PALs) from a snake (the Burmese python, Python molurus bivittatus), and directly compare these results to those from 454 data. We also compare the python results to results from Illumina sequencing of two bird genomes (Gunnison Sage-grouse, Centrocercus minimus, and Clark's Nutcracker, Nucifraga columbiana), which have considerably fewer SSRs than the python. We show that direct Illumina Seq-to-SSR can identify and characterize thousands of potentially amplifiable SSR loci for as little as $10 per sample – a fraction of the cost of 454 sequencing. Given that Illumina Seq-to-SSR is effective, inexpensive, and reliable even for species such as birds that have few SSR loci, it seems that there are now few situations for which prior hybridization is justifiable.

Environmental DNA (eDNA) methods are used to detect DNA that is shed into the aquatic environment by cryptic or low density species. Applied in eDNA studies, occupancy models can be used to estimate occurrence and detection probabilities and thereby account for imperfect detection. However, occupancy terminology has been applied inconsistently in eDNA studies, and many have calculated occurrence probabilities while not considering the effects of imperfect detection. Low detection of invasive giant constrictors using visual surveys and traps has hampered the estimation of occupancy and detection estimates needed for population management in southern Florida, USA. Giant constrictor snakes pose a threat to native species and the ecological restoration of the Florida Everglades. To assist with detection, we developed species-specific eDNA assays using quantitative PCR (qPCR) for the Burmese python (Python molurus bivittatus), Northern African python (P. sebae), boa constrictor (Boa constrictor), and the green (Eunectes murinus) and yellow anaconda (E. notaeus). Burmese pythons, Northern African pythons, and boa constrictors are established and reproducing, while the green and yellow anaconda have the potential to become established. We validated the python and boa constrictor assays using laboratory trials and tested all species in 21 field locations distributed in eight southern Florida regions. Burmese python eDNA was detected in 37 of 63 field sampling events; however, the other species were not detected. Although eDNA was heterogeneously distributed in the environment, occupancy models were able to provide the first estimates of detection probabilities, which were greater than 91%. Burmese python eDNA was detected along the leading northern edge of the known population boundary. The development of informative detection tools and eDNA occupancy models can improve conservation efforts in southern Florida and support more extensive studies of invasive constrictors. Generic sampling design and terminology are proposed to standardize and clarify interpretations of eDNA-based occupancy models.

Quaternary climatic oscillations greatly influenced the present-day population genetic structure of animals and plants. For species with high dispersal and reproductive potential, phylogeographic patterns resulting from historical processes can be cryptic, overshadowed by contemporary processes. Here we report a study of the phylogeography of Odocoileus hemionus, a large, vagile ungulate common throughout western North America. We examined sequence variation of mitochondrial DNA (control region and cytochrome b) within and among 70 natural populations across the entire range of the species. Among the 1766 individual animals surveyed, we recovered 496 haplotypes. Although fine-scale phylogenetic structure was weakly resolved using phylogenetic methods, network analysis clearly revealed the presence of 12 distinct haplogroups. The spatial distribution of haplogroups showed a strong genetic discontinuity between the two morphological types of O. hemionus, mule deer and black-tailed deer, east and west of the Cascade Mountains in the Pacific Northwest. Within the mule deer lineage, we identified several haplogroups that expanded before or during the Last Glacial Maximum, suggesting that mule deer persisted in multiple refugia south of the ice sheets. Patterns of genetic diversity within the black-tailed deer lineage suggest a single refugium along the Pacific Northwest coast, and refute the hypothesis that black-tailed deer persisted in one or more northern refugia. Our data suggest that black-tailed deer recolonized areas in accordance with the pattern of glacial retreat, with initial recolonization northward along a coastal route and secondary recolonization inland.

The raccoon (Procyon lotor (L., 1758)), a generalist mesocarnivore, has thrived in anthropogenically fragmented landscapes. In this study we utilized 13 microsatellites to analyze the population genetic structure in raccoons occupying an agriculturally fragmented habitat. Our analyses revealed low, but significant, levels of genetic structure (FST = 0.022, P < 0.001) among 645 raccoons inhabiting 29 spatially distinct habitat patches (neighborhoods). We found no evidence for the presence of either isolation by distance or barriers. However, spatial autocorrelation revealed evidence for social structure at the raccoon-neighborhood scale. About 30% of the variance in levels of social structure among raccoon neighborhoods was explained by effects of habitat-patch size and the percentage of land cover represented by forest around the individual habitat patch. We found strong evidence of sex-biased dispersal using direct (parentage analysis) and indirect (relatedness and assignment indices) genetic estimators. However, our analysis revealed that among dispersing raccoons there was no difference in dispersal distance between sexes and that dispersal events are randomly distributed with respect to distance. Our study provides evidence that demographic and behavioral processes affecting raccoon spatial organization may be most critical at very fine scales of biological organization, such as within individual habitat patches.Résumé : Le raton laveur (Procyon lotor (L., 1758)), un mésocarnivore généraliste, a prospéré dans les paysages fragmentés par l'activité humaine. Nous utilisons, dans notre étude, 13 microsatellites pour déterminer la structure génétique de la population chez des ratons laveurs qui vivent dans un habitat fragmenté par l'agriculture. Nos analyses révèlent des niveaux bas, mais significatifs, de structure génétique (F ST = 0,022, P < 0,001) parmi 645 ratons laveurs vivant dans 29 taches d'habitat distinctes (quartiers). Il n'y a aucune indication d'isolement par la distance, ni de barrières. Cependant, l'autocorrélation spatiale donne des indications d'une structure sociale à l'échelle des quartiers de ratons laveurs. Environ 30 % de la variance des niveaux de structure sociale entre les quartiers de ratons laveurs s'explique par les effets de la taille de la tache d'habitat et le pourcentage de la couverture du sol autour des taches individuelles d'habitat qui est repré-senté par de la forêt. Des estimateurs génétiques directs (analyse de filiation) et indirects (indices de consanguinité et d'attribution) indiquent clairement une dispersion variable en fonction du sexe. Cependant, notre analyse révèle que, parmi les ratons laveurs qui se dispersent, il n'y a pas de différence de distance de dispersion en fonction des sexes et que les événe-ments de dispersion sont répartis au hasard en fonction de la distance. Notre étude fournit des indications que les processus démographiques et comportementaux qui affectent l'organisation spatiale des ratons laveurs peuvent agir de la façon la plus critique aux éch...

Given the significance of animal dispersal to population dynamics and geographic variability, understanding how dispersal is impacted by landscape patterns has major ecological and conservation importance. Speaking to the importance of dispersal, the use of linear mixed models to compare genetic differentiation with pairwise resistance derived from landscape resistance surfaces has presented new opportunities to disentangle the menagerie of factors behind effective dispersal across a given landscape. Here, we combine these approaches with novel resistance surface parameterization to determine how the distribution of high- and low-quality seasonal habitat and individual landscape components shape patterns of gene flow for the greater sage-grouse (Centrocercus urophasianus) across Wyoming. We found that pairwise resistance derived from the distribution of low-quality nesting and winter, but not summer, seasonal habitat had the strongest correlation with genetic differentiation. Although the patterns were not as strong as with habitat distribution, multivariate models with sagebrush cover and landscape ruggedness or forest cover and ruggedness similarly had a much stronger fit with genetic differentiation than an undifferentiated landscape. In most cases, landscape resistance surfaces transformed with 17.33-km-diameter moving windows were preferred, suggesting small-scale differences in habitat were unimportant at this large spatial extent. Despite the emergence of these overall patterns, there were differences in the selection of top models depending on the model selection criteria, suggesting research into the most appropriate criteria for landscape genetics is required. Overall, our results highlight the importance of differences in seasonal habitat preferences to patterns of gene flow and suggest the combination of habitat suitability modeling and linear mixed models with our resistance parameterization is a powerful approach to discerning the effects of landscape on gene flow.