Australian arboreal mammals are experiencing significant population declines, particularly due to land clearing and resulting habitat fragmentation. The squirrel glider, Petaurus norfolcensis, is a threatened species in New South Wales, with a stronghold population in the Lake Macquarie Local Government Area (LGA) where fragmentation due to urbanization is an ongoing problem for the species conservation. Here we report on the use of squirrel glider mitochondrial (385 bp cytochrome b gene, 70 individuals) and nuclear DNA (6,834 SNPs, 87 individuals) markers to assess their population genetic structure and connectivity across 14 locations sampled in the Lake Macquarie LGA. The mitochondrial DNA sequences detected evidence of a historical genetic bottleneck, while the genome-wide SNPs detected significant population structure in the Lake Macquarie squirrel glider populations at scales as fine as one kilometer. There was no evidence of inbreeding within patches, however there were clear effects of habitat fragmentation and biogeographical barriers on gene flow. A least cost path analysis identified thin linear corridors that have high priority for conservation. These areas should be protected to avoid further isolation of squirrel glider populations and the loss of genetic diversity through genetic drift.

The Nashville crayfish (Faxonius shoupi, Hobbs 1948) was federally listed as an endangered species in 1986 due to its limited distribution in the Mill Creek watershed; this waterway lies in the rapidly developing Nashville basin and has experienced habitat degradation due to agricultural run-off, contamination, and urban development. Recovery efforts, including dam removal and restoration of riparian zones, have improved conditions in Mill Creek and F. shoupi has increased in numbers and recolonized extirpated stream segments. However, a history of demographic bottlenecks and restricted gene flow may have negatively impacted the long-term recovery of this species. A recently discovered population of F. shoupi in a disjunct segment of the Lower Tennessee River at the Pickwick Tailwater may provide an additional source of genetic variation. Uncertainty surrounding the origins of the Pickwick population and its taxonomic relationship to F. shoupi in Mill Creek raises questions about the conservation and management implications of this population. We used mitochondrial sequencing and SNP genotyping to assess genetic variation and connectivity of F. shoupi in the Mill Creek drainage and to investigate the taxonomy and demographic history of the newly discovered population at Pickwick. We found substantial genetic variation and evidence of connectivity for samples throughout Mill Creek for both mitochondrial and genome-wide SNPs. Our results also suggest a recently severed connection between crayfish in Pickwick and Mill Creek. Unique mitochondrial haplotypes and SNP variation in the Pickwick population highlight the need for prioritizing this population in future conservation and management plans for this species.

Pond physical characteristics (connectivity, hydroperiod) have shown to be highly relevant in explaining species presence, reproductive success, and survival in breeding-pond amphibians. However, few studies have addressed the influence that these factors may have on the genetic variability of pond populations. We examined genetic variation at 11 microsatellite loci in Iberian endemic, the pygmy newt (Triturus pygmaeus), from 58 breeding ponds in the Doñana National Park (Andalusia), including both temporary ponds and artificially deepened ponds that remain wet during the whole year. Temporary ponds are located in the North part of the region where the surrounding habitat-wet meadows-facilitates the connectivity among populations, whereas the deepest ponds (‘zacallones’) are located in the southern edge embedded in a matrix of unsuitable habitat (thickets and dry underbrush). We investigated genetic diversity and structure within and among ponds. Our results show that both regions (Doñana-North and Doñana-South) are well-differentiated and form two main clusters. We found higher genetic diversity within ponds from the North region, which also exhibited a higher degree of genetic admixture in comparison with populations from the southern edge. Although we found an isolation-by-distance pattern within each cluster, it arose due to the effect of a few isolated ponds located on the edge of each zone, suggesting the existence of substantial gene flow between ponds in the core area. According to our findings, landscape’s permeability to movement (pond connectivity) may constitute a more important factor than hydroperiod length in determining the genetic diversity and viability of pygmy newt populations in this area. Although Doñana populations show a good state, more peripheral and isolated populations present a more worrisome condition as a result of fragmentation and thus, require conservation efforts. Our study provides key insights that could help guide management practices of this threatened and poorly-studied salamander.

Genome-wide evaluations of genetic diversity and population structure are important for informing management and conservation of trailing-edge populations. North American moose (Alces alces) are declining along portions of the southern edge of their range due to disease, species interactions, and marginal habitat, all of which may be exacerbated by climate change. We employed a genotyping by sequencing (GBS) approach in an effort to collect baseline information on the genetic variation of moose inhabiting the species’ southern range periphery in the contiguous United States. We identified 1920 single nucleotide polymorphisms (SNPs) from 155 moose representing three subspecies from five states: A. a. americana (New Hampshire), A. a. andersoni (Minnesota), and A. a. shirasi (Idaho, Montana, and Wyoming). Molecular analyses supported three geographically isolated clusters, congruent with currently recognized subspecies. Additionally, while moderately low genetic diversity was observed, there was little evidence of inbreeding. Results also indicated > 20% shared ancestry proportions between A. a. shirasi samples from northern Montana and A. a. andersoni samples from Minnesota, indicating a putative hybrid zone warranting further investigation. GBS has proven to be a simple and effective method for genome-wide SNP discovery in moose and provides robust data for informing herd management and conservation priorities. With increasing disease, predation, and climate related pressure on range edge moose populations in the United States, the use of SNP data to identify gene flow between subspecies may prove a powerful tool for moose management and recovery, particularly if hybrid moose are more able to adapt.

Landscape features impact gene flow and the spatial patterns of genetic variation between populations of a species. Because many Magnoliaceae species occur in fragmented and highly disturbed landscapes, the family provide an excellent model for landscape genetic studies. This research focuses on the subspecies and subpopulations of Magnolia cubensis and aims to: (1) compare the genetic diversity between the different subspecies and their subpopulations, (2) search for patterns between the spatial and genetic distance, (3) quantify the functional connectivity and (4) assess the structural connectivity of the landscape. This study employs 21 microsatellite markers to quantify the genetic diversity, complemented with seven landscape characteristics of the Guamuhaya and Sierra Maestra massifs in Cuba. Magnolia cubensis subsp. acunae does not have a well-defined spatial genetic pattern: there is no evidence of isolation by distance or spatial autocorrelation and the little genetic differentiation between the two subpopulations does not reflect the characteristics of the landscape that separates them or the cost values to cross it. Magnolia cubensis subsp. cubensis presents evidence of isolation by distance and the autocorrelation analyses indicate that the approximate scale of the genetic neighborhood is between 35 and 40 km. There is a marked genetic structure with probability values that indicate the existence of three genetic groups. Large genetic differentiation was only found between Gran Piedra and the other subpopulations, which reflects low gene flow. Our results support the recognition of these subspecies at the species level. We define one evolutionary significant unit in Magnolia cubensis subsp. acunae and two evolutionary significant units in Magnolia cubensis subsp. cubensis. These results must be combined with ecological, social and distribution data, in order to obtain a more accurate and realistic perspective of the conservation management strategies for these taxa.

Functional connectivity (i.e., the movement of individuals across a landscape) is essential for the maintenance of genetic variation and persistence of rare species. However, illuminating the processes influencing functional connectivity and ultimately translating this knowledge into management practice remains a fundamental challenge. Here, we combine various population structure analyses with pairwise, population-specific demographic modeling to investigate historical functional connectivity in Graham’s beardtongue (Penstemon grahamii), a rare plant narrowly distributed across a dryland region of the western US. While principal component and population structure analyses indicated an isolation-by-distance pattern of differentiation across the species’ range, spatial inferences of effective migration exposed an abrupt shift in population ancestry near the range center. To understand these seemingly conflicting patterns, we tested various models of historical gene flow and found evidence for recent admixture (~ 3400 generations ago) between populations near the range center. This historical perspective reconciles population structure patterns and suggests management efforts should focus on maintaining connectivity between these previously isolated lineages to promote the ongoing transfer of genetic variation. Beyond providing species-specific knowledge to inform management options, our study highlights how understanding demographic history may be critical to guide conservation efforts when interpreting population genetic patterns and inferring functional connectivity.

The ability of tree species to adapt to water stress and increased frequency of bark beetle outbreaks with climate change may increase with population size and standing genetic variation, calling into question the resilience of small, rare plant populations. The Torrey pine (Pinus torreyana) is a rare, genetically depauperate conifer that occurs naturally in a mainland and island population in southern California. Due to recent declines in the mainland population coinciding with drought and Ips paraconfusus bark beetle outbreaks, the species would benefit from an assessment of adaptive genetic diversity. Here, we use RNA-Seq to survey gene-coding diversity across 40 individuals to (1) characterize patterns of genetic diversity in the species and (2) test for genetic differentiation between trees that succumbed to beetle attack or survived following an outbreak. Consistent with previous studies, we found few genetic variants, with most SNPs occurring as fixed differences between populations. However, we found structure within the mainland and polymorphisms segregating in both populations. Interestingly, we found differentiation in genotypes between attacked and surviving trees and 11 SNPs associated with survival status, several of which had defense-related functions. While low diversity suggests limited adaptive capacity, genetic associations with survival in functionally relevant genes suggest adaptive potential for bark beetle defense. This initial study prompts future research to explore the genetic basis of putative resistance and suggests conservation efforts should protect surviving genotypes and the full spectrum of genetic diversity across populations to preserve the evolutionary potential of the species.