Sampling affects the detection of genetic subdivision and conservation implications for fisher in the Sierra Nevada

Spatial genetic structure and seed quality of a southernmost Abies nephrolepis population

Abies nephrolepis (Trautv. ex Maxim.) Maxim. has its southernmost populations in South Korea and they are expected to decline under climate change. To establish a strategic conservation plan, this study aimed to investigate the spatial genetic structure and seed characteristics of A. nephrolepis. We used nine microsatellite markers on 165 individuals of A. nephrolepis and sampled seeds in a southernmost population at Mt. Hambaeksan, South Korea. We observed a high level of heterozygosity, and a simulation study found that sampling 20 individuals was enough to secure sufficient genetic diversity on average. Spatial autocorrelation analysis revealed that individuals had a positive genetic relationship until 30 m. Bayesian clustering models, STRUCTURE and GENELAND, failed to achieve a consensus in the optimal number of population (K), estimating K = 1 and K = 2, respectively. Principal coordinate analysis supported the absence of genetic substructure within the study population. There was a large variance in seed production among mother trees. On average, seeds of A. nephrolepis from Mt. Hambaeksan had a purity of 70.4% and a germination percentage of 32.2%. We found that seed weight was the most effective indicator of seed quality. Mother trees at higher altitudes had poorer purity which is threatening to A. nephrolepis considering the upslope retreat of subalpine species under climate change. Our results provide insights into the interactions among spatial processes, genetic structure, and seed quality within a population of A. nephrolepis.

Where to draw the line? Expanding the delineation of conservation units to highly mobile taxa

Conservation units (CUs) are an essential tool for maximizing evolutionary potential and prioritizing areas across a species' range for protection when implementing conservation and management measures. However, current workflows for identifying CUs on the basis of neutral and adaptive genomic variation largely ignore information contained in patterns of isolation by distance (IBD), frequently the primary signal of population structure in highly mobile taxa, such as birds, bats, and marine organisms with pelagic larval stages. While individuals located on either end of a species' distribution may exhibit clear genetic, phenotypic, and ecological differences, IBD produces subtle changes in allele frequencies across space, making it difficult to draw clear boundaries for conservation purposes in the absence of discrete population structure. Here, we highlight potential pitfalls that arise when applying common methods for delineating CUs to continuously distributed organisms and review existing methods for detecting subtle breakpoints in patterns of IBD that can indicate barriers to gene flow in highly mobile taxa. In addition, we propose a new framework for identifying CUs in all organisms, including those characterized by continuous genomic differentiation, and suggest several possible ways to harness the information contained in patterns of IBD to guide conservation and management decisions.

Mega-disturbances cause rapid decline of mature conifer forest habitat in California

Mature forests provide important wildlife habitat and support critical ecosystem functions globally. Within the dry conifer forests of the western United States, past management and fire exclusion have contributed to forest conditions that are susceptible to increasingly severe wildfire and drought. We evaluated declines in conifer forest cover in the southern Sierra Nevada of California during a decade of record disturbance by using spatially comprehensive forest structure estimates, wildfire perimeter data, and the eDaRT forest disturbance tracking algorithm. Primarily due to the combination of wildfires, drought, and drought-associated beetle epidemics, 30% of the region's conifer forest extent transitioned to nonforest vegetation during 2011-2020. In total, 50% of mature forest habitat and 85% of high density mature forests either transitioned to lower density forest or nonforest vegetation types. California spotted owl protected activity centers (PAC) experienced greater canopy cover decline (49% of 2011 cover) than non-PAC areas (42% decline). Areas with high initial canopy cover and without tall trees were most vulnerable to canopy cover declines, likely explaining the disproportionate declines of mature forest habitat and within PACs. Drought and beetle attack caused greater cumulative declines than areas where drought and wildfire mortality overlapped, and both types of natural disturbance far outpaced declines attributable to mechanical activities. Drought mortality that disproportionately affects large conifers is particularly problematic to mature forest specialist species reliant on large trees. However, patches of degraded forests within wildfire perimeters were larger with greater core area than those outside burned areas, and remnant forest habitats were more fragmented within burned perimeters than those affected by drought and beetle mortality alone. The percentage of mature forest that survived and potentially benefited from lower severity wildfire increased over time as the total extent of mature forest declined. These areas provide some opportunity for improved resilience to future disturbances, but strategic management interventions are likely also necessary to mitigate worsening mega-disturbances. Remaining dry mature forest habitat in California may be susceptible to complete loss in the coming decades without a rapid transition from a conservation paradigm that attempts to maintain static conditions to one that manages for sustainable disturbance dynamics.

New strategies for characterizing genetic structure in wide-ranging, continuously distributed species: A Greater Sage-grouse case study

Characterizing genetic structure across a species’ range is relevant for management and conservation as it can be used to define population boundaries and quantify connectivity. Wide-ranging species residing in continuously distributed habitat pose substantial challenges for the characterization of genetic structure as many analytical methods used are less effective when isolation by distance is an underlying biological pattern. Here, we illustrate strategies for overcoming these challenges using a species of significant conservation concern, the Greater Sage-grouse (Centrocercus urophasianus), providing a new method to identify centers of genetic differentiation and combining multiple methods to help inform management and conservation strategies for this and other such species. Our objectives were to (1) describe large-scale patterns of population genetic structure and gene flow and (2) to characterize genetic subpopulation centers across the range of Greater Sage-grouse. Samples from 2,134 individuals were genotyped at 15 microsatellite loci. Using standard STRUCTURE and spatial principal components analyses, we found evidence for four or six areas of large-scale genetic differentiation and, following our novel method, 12 subpopulation centers of differentiation. Gene flow was greater, and differentiation reduced in areas of contiguous habitat (eastern Montana, most of Wyoming, much of Oregon, Nevada, and parts of Idaho). As expected, areas of fragmented habitat such as in Utah (with 6 subpopulation centers) exhibited the greatest genetic differentiation and lowest effective migration. The subpopulation centers defined here could be monitored to maintain genetic diversity and connectivity with other subpopulation centers. Many areas outside subpopulation centers are contact zones where different genetic groups converge and could be priorities for maintaining overall connectivity. Our novel method and process of leveraging multiple different analyses to find common genetic patterns provides a path forward to characterizing genetic structure in wide-ranging, continuously distributed species.

Population genetics of the wolverine in Finland: the road to recovery?

After decades, even centuries of persecution, large carnivore populations are widely recovering in Europe. Considering the recent recovery of the wolverine (Gulo gulo) in Finland, our aim was to evaluate genetic variation using 14 microsatellites and mtDNA control region (579 bp) in order (1) to determine whether the species is represented by a single genetic population within Finland, (2) to quantify the genetic diversity, and (3) to estimate the effective population size. We found two major genetic clusters divided between eastern and northern Finland based on microsatellites (FST = 0.100) but also a significant pattern of isolation by distance. Wolverines in western Finland had a genetic signature similar to the northern cluster, which can be explained by former translocations of wolverines from northern to western Finland. For both main clusters, most estimates of the effective population size Ne were below 50. Nevertheless, the genetic diversity was higher in the eastern cluster (HE = 0.57, AR = 4.0, AP = 0.3) than in the northern cluster (HE = 0.49, AR = 3.7, AP = 0.1). Migration between the clusters was low. Two mtDNA haplotypes were found: one common and identical to Scandinavian wolverines; the other rare and not previously detected. The rare haplotype was more prominent in the eastern genetic cluster. Combining all available data, we infer that the genetic population structure within Finland is shaped by a recent bottleneck, isolation by distance, human-aided translocations and postglacial recolonization routes.

Assessing arrays of multiple trail cameras to detect North American mammals

Motion triggered camera traps are an increasingly popular tool for wildlife research and can be used to survey for multiple species simultaneously. As with all survey techniques, it is crucial to conduct camera trapping research following study designs that include adequate spatial and temporal replication, and sufficient probability of detecting species presence. The use and configuration of multiple camera traps within a single survey site are understudied considerations that could have a substantial impact on detection probability. Our objective was to test the role that camera number (one, two or three units), and spacing along a linear transect (100 m or 150 m), have on the probability of detecting a species given it is present. From January to March, 2017 we collected data on six mammal species in Maine, USA: coyote (Canis latrans), fisher (Pekania pennanti), American marten (Martes americana), short-tailed weasel (Mustela erminea), snowshoe hare (Lepus americanus), and American red squirrel (Tamiasciurus hudsonicus). We used multi-scale occupancy modelling to compare pooled detection histories of different configuration of five cameras deployed at the same survey site (n = 32), and how the configuration would influence the probability of detecting a species given it was available at the site. Across all six species, we found substantial increases in probability of detection as the number of cameras increased from one to two (22 to 400 percent increase), regardless of the spacing between cameras. For most species the magnitude of the increase was less substantial when adding a third camera (4 to 85 percent increase), with coyote and snowshoe hare showing a pronounced effect. The influence of survey station features also varied by species. We suggest that using pooled data from two or three cameras at a survey site is a cost effective approach to increase detection success over a single camera.

Ecological correlates of the spatial co-occurrence of sympatric mammalian carnivores worldwide

The composition of local mammalian carnivore communities has far-reaching effects on terrestrial ecosystems worldwide. To better understand how carnivore communities are structured, we analysed camera trap data for 108 087 trap days across 12 countries spanning five continents. We estimate local probabilities of co-occurrence among 768 species pairs from the order Carnivora and evaluate how shared ecological traits correlate with probabilities of co-occurrence. Within individual study areas, species pairs co-occurred more frequently than expected at random. Co-occurrence probabilities were greatest for species pairs that shared ecological traits including similar body size, temporal activity pattern and diet. However, co-occurrence decreased as compared to other species pairs when the pair included a large-bodied carnivore. Our results suggest that a combination of shared traits and top-down regulation by large carnivores shape local carnivore communities globally.

Phylogeography of Daphnia magna Straus (Crustacea: Cladocera) in Northern Eurasia: Evidence for a deep longitudinal split between mitochondrial lineages

Species with a large geographic distributions present a challenge for phylogeographic studies due to logistic difficulties of obtaining adequate sampling. For instance, in most species with a Holarctic distribution, the majority of studies has concentrated on the European or North American part of the distribution, with the Eastern Palearctic region being notably understudied. Here, we study the phylogeography of the freshwater cladoceran Daphnia magna Straus, 1820 (Crustacea: Cladocera), based on partial mitochondrial COI sequences and using specimens from populations spread longitudinally from westernmost Europe to easternmost Asia, with many samples from previously strongly understudied regions in Siberia and Eastern Asia. The results confirm the previously suspected deep split between Eastern and Western mitochondrial haplotype super-clades. We find a narrow contact zone between these two super-clades in the eastern part of Western Siberia, with proven co-occurrence in a single lake in the Novosibirsk region. However, at present there is no evidence suggesting that the two mitochondrial super-clades represent cryptic species. Rather, they may be explained by secondary contact after expansion from different refugia. Interestingly, Central Siberia has previously been found to be an important contact zone also in other cladoceran species, and may thus be a crucial area for understanding the Eurasian phylogeography of freshwater invertebrates. Together, our study provides an unprecedented complete, while still not global, picture of the phylogeography of this important model species.

Genetic diversity and structure related to expansion history and habitat isolation: stone marten populating rural-urban habitats

Background

Population genetic diversity and structure are determined by past and current evolutionary processes, among which spatially limited dispersal, genetic drift, and shifts in species distribution boundaries have major effects. In most wildlife species, environmental modifications by humans often lead to contraction of species’ ranges and/or limit their dispersal by acting as environmental barriers. However, in species well adapted to anthropogenic habitat or open landscapes, human induced environmental changes may facilitate dispersal and range expansions. In this study, we analysed whether isolation by distance and deforestation, among other environmental features, promotes or restricts dispersal and expansion in stone marten (Martes foina) populations.

Results

We genotyped 298 martens from eight sites at twenty-two microsatellite loci to characterize the genetic variability, population structure and demographic history of stone martens in Poland. At the landscape scale, limited genetic differentiation between sites in a mosaic of urban, rural and forest habitats was mostly influenced by isolation by distance. Statistical clustering and multivariate analyses showed weak genetic structuring with two to four clusters and a high rate of gene flow between them. Stronger genetic differentiation was detected for one stone marten population (NE1) located inside a large forest complex. Genetic differentiation between this site and all others was 20% higher than between other sites separated by similar distances. The genetic uniqueness index of NE1 was also twofold higher than in other sites. Past demographic history analyses showed recent expansion of this species in north-eastern Poland. A decrease in genetic diversity from south to north, and MIGRAINE analyses indicated the direction of expansion of stone marten.

Conclusions

Our results showed that two processes, changes in species distribution boundaries and limited dispersal associated with landscape barriers, affect genetic diversity and structure in stone marten. Analysis of local barriers that reduced dispersal and large scale analyses of genetic structure and demographic history highlight the importance of isolation by distance and forest cover for the past colonization of central Europe by stone marten. This confirmed the hypothesis that human-landscape changes (deforestation) accelerated stone marten expansion, to which climate warming probably has also been contributing over the last few decades.

Electronic supplementary material

The online version of this article (10.1186/s12898-017-0156-6) contains supplementary material, which is available to authorized users.

Genetic Diversity and Population Structure of Mesoamerican Jaguars (Panthera onca): Implications for Conservation and Management

Mesoamerican jaguars (Panthera onca) have been extirpated from over 77% of their historic range, inhabiting fragmented landscapes at potentially reduced population sizes. Maintaining and restoring genetic diversity and connectivity across human-altered landscapes has become a major conservation priority; nonetheless large-scale genetic monitoring of natural populations is rare. This is the first regional conservation genetic study of jaguars to primarily use fecal samples collected in the wild across five Mesoamerican countries: Belize, Costa Rica, Guatemala, Honduras, and Mexico. We genotyped 445 jaguar fecal samples and examined patterns of genetic diversity and connectivity among 115 individual jaguars using data from 12 microsatellite loci. Overall, moderate levels of genetic variation were detected (NA = 4.50 ± 1.05, AR = 3.43 ± 0.22, HE = 0.59 ± 0.04), with Mexico having the lowest genetic diversity, followed by Honduras, Guatemala, Belize, and Costa Rica. Population-based gene flow measures (FST = 0.09 to 0.15, Dest = 0.09 to 0.21), principal component analysis, and Bayesian clustering applied in a hierarchical framework revealed significant genetic structure in Mesoamerican jaguars, roughly grouping individuals into four genetic clusters with varying levels of admixture. Gene flow was highest among Selva Maya jaguars (northern Guatemala and central Belize), whereas genetic differentiation among all other sampling sites was moderate. Genetic subdivision was most pronounced between Selva Maya and Honduran jaguars, suggesting limited jaguar movement between these close geographic regions and ultimately refuting the hypothesis of contemporary panmixia. To maintain a critical linkage for jaguars dispersing through the Mesoamerican landscape and ensure long-term viability of this near threatened species, we recommend continued management and maintenance of jaguar corridors. The baseline genetic data provided by this study underscores the importance of understanding levels of genetic diversity and connectivity to making informed management and conservation decisions with the goal to maintain functional connectivity across the region.

The effect of a major drainage divide on the gene flow of a semiaquatic carnivore, the Eurasian otter

Major drainage divides (separating the water flow draining to different seas) may significantly affect the dispersal, distribution, and genetic structure of semiaquatic animals. Assessing this effect is important for the proper management of both endangered and invasive riparian species. Here, I determined the fine-scale impact of the drainage divide between the Baltic Sea and the Black Sea drainage basins on the genetic structure and dispersal of the Eurasian otter (Lutra lutra) in the Bieszczady Mountains (Poland and Slovakia). I investigated the genetic structure of the otter population and assessed 3 alternative dispersal models using 6 landscape genetics methods. The analyses were based on 48 individual genotypes obtained from 622 fecal and gland secretion samples collected in 2008–2011. Results indicate that the major drainage divide is not a barrier to gene flow for this population. This was established by analyses of population genetic structure and confirmed by analysis of the spatial distribution of samples originating from closely related individuals. In line with these findings, the best-supported dispersal model assumed that otters migrate through mountain passes, away from streams, thus revealing that they are able to cross a drainage divide. The genetic structure of the population studied exhibits an isolation-by-distance pattern; however, the locations of several repeatedly recorded or closely related individuals revealed the occurrence of long-distance movements. Confirmation of the high mobility of otters and their ability to cross a major drainage divide ridge suggest that landscape obstacles and discontinuity of river network are unlikely to stop otter dispersal, gene flow, and recolonization of new areas.

Assessing Genetic Structure in Common but Ecologically Distinct Carnivores: The Stone Marten and Red Fox

The identification of populations and spatial genetic patterns is important for ecological and conservation research, and spatially explicit individual-based methods have been recognised as powerful tools in this context. Mammalian carnivores are intrinsically vulnerable to habitat fragmentation but not much is known about the genetic consequences of fragmentation in common species. Stone martens (Martes foina) and red foxes (Vulpes vulpes) share a widespread Palearctic distribution and are considered habitat generalists, but in the Iberian Peninsula stone martens tend to occur in higher quality habitats. We compared their genetic structure in Portugal to see if they are consistent with their differences in ecological plasticity, and also to illustrate an approach to explicitly delineate the spatial boundaries of consistently identified genetic units. We analysed microsatellite data using spatial Bayesian clustering methods (implemented in the software BAPS, GENELAND and TESS), a progressive partitioning approach and a multivariate technique (Spatial Principal Components Analysis-sPCA). Three consensus Bayesian clusters were identified for the stone marten. No consensus was achieved for the red fox, but one cluster was the most probable clustering solution. Progressive partitioning and sPCA suggested additional clusters in the stone marten but they were not consistent among methods and were geographically incoherent. The contrasting results between the two species are consistent with the literature reporting stricter ecological requirements of the stone marten in the Iberian Peninsula. The observed genetic structure in the stone marten may have been influenced by landscape features, particularly rivers, and fragmentation. We suggest that an approach based on a consensus clustering solution of multiple different algorithms may provide an objective and effective means to delineate potential boundaries of inferred subpopulations. sPCA and progressive partitioning offer further verification of possible population structure and may be useful for revealing cryptic spatial genetic patterns worth further investigation.

Survival of fishers in the southern Sierra Nevada region of California

Fishers in the western United States were recently proposed for listing under the U.S. Endangered Species Act because of concerns for loss of suitable habitat and evidence of a diversity of mortality risks that reduce survival. One of 2 remnant populations of fishers in California is in the southern Sierra Nevada region, where we studied them at 2 research sites in the Sierra National Forest. Our objectives were to evaluate whether survival was lower for male fishers and dispersal-aged individuals or if survival varied seasonally. We captured and monitored 232 radiocollared fishers from March 2007 to March 2014 and used model analyses to identify important predictors of survival. Fifty-two percent ( n = 120) of the radiocollared fishers died, and survival varied by sex and season, but not by age or between study sites. There was no evidence that dispersal-aged fishers experienced lower survival than older fishers. Annual survival trended lower for male (0.62 [95% CI 0.54–0.70]) compared to female fishers (0.72 [95% CI 0.67–0.78]), was lowest in the spring to mid-summer season (0.83 [95% CI 0.78–0.87]), and highest in late fall and winter (0.92 [95% CI 0.89–0.94]). Lower survival among male fishers appeared linked to males moving over large areas to locate mates, while lower survival for females was potentially related to high energetic cost of reproduction. It was possible but unknown if lower survival among all fishers in spring was linked to secondary exposure to toxicants dispersed around illicit marijuana grow sites. Six-month survival of juvenile fishers was 0.85 for females and 0.79 for males, but lower at 0.62 for females and 0.57 for males when adjusted for deaths before late September. Annual survival among adult female fishers was 20% lower than 0.90, a value that prior modeling suggested was required for population expansion in the overall southern Sierra Nevada. Survival data from our study imply a greater challenge for maintaining self-sustaining fisher populations in the southern Sierra Nevada region, and resource managers are working to mitigate several of the human-associated factors that limit population growth.

Inferring Population Genetic Structure in Widely and Continuously Distributed Carnivores: The Stone Marten (Martes foina) as a Case Study

The stone marten is a widely distributed mustelid in the Palaearctic region that exhibits variable habitat preferences in different parts of its range. The species is a Holocene immigrant from southwest Asia which, according to fossil remains, followed the expansion of the Neolithic farming cultures into Europe and possibly colonized the Iberian Peninsula during the Early Neolithic (ca. 7,000 years BP). However, the population genetic structure and historical biogeography of this generalist carnivore remains essentially unknown. In this study we have combined mitochondrial DNA (mtDNA) sequencing (621 bp) and microsatellite genotyping (23 polymorphic markers) to infer the population genetic structure of the stone marten within the Iberian Peninsula. The mtDNA data revealed low haplotype and nucleotide diversities and a lack of phylogeographic structure, most likely due to a recent colonization of the Iberian Peninsula by a few mtDNA lineages during the Early Neolithic. The microsatellite data set was analysed with a) spatial and non-spatial Bayesian individual-based clustering (IBC) approaches (STRUCTURE, TESS, BAPS and GENELAND), and b) multivariate methods [discriminant analysis of principal components (DAPC) and spatial principal component analysis (sPCA)]. Additionally, because isolation by distance (IBD) is a common spatial genetic pattern in mobile and continuously distributed species and it may represent a challenge to the performance of the above methods, the microsatellite data set was tested for its presence. Overall, the genetic structure of the stone marten in the Iberian Peninsula was characterized by a NE-SW spatial pattern of IBD, and this may explain the observed disagreement between clustering solutions obtained by the different IBC methods. However, there was significant indication for contemporary genetic structuring, albeit weak, into at least three different subpopulations. The detected subdivision could be attributed to the influence of the rivers Ebro, Tagus and Guadiana, suggesting that main watercourses in the Iberian Peninsula may act as semi-permeable barriers to gene flow in stone martens. To our knowledge, this is the first phylogeographic and population genetic study of the species at a broad regional scale. We also wanted to make the case for the importance and benefits of using and comparing multiple different clustering and multivariate methods in spatial genetic analyses of mobile and continuously distributed species.

Population structure among octocoral adults and recruits identifies scale dependent patterns of population isolation in The Bahamas

Patterns of dispersal and connectivity of the Caribbean gorgonian Antillogorgia elisabethae in The Bahamas were assessed in both adults and recently settled recruits from 13 sites using microsatellite loci. Adult populations along the Little Bahama Bank (LBB) exhibited a clear pattern of isolation by distance (IBD) which described 86% of the variance in pairwise genetic distances. Estimates of dispersal based on the IBD model suggested dispersal distances along the LBB on the order of 100 m. Increasing the spatial scale to include sites separated by open ocean generated an apparent IBD signal but the relationship had a greater slope and explained less of the variance. This relationship with distance reflected both stepping stone based IBD and regional differentiation probably created by ocean currents and barriers to dispersal that are correlated with geographic distance. Analysis of recruits from 4 sites on the LBB from up to 6 years did not detect differences between years nor differences with adult populations. The result suggests that neither selection on recruits nor inter-annual variation in dispersal affected adult population structure. Assignment tests of recruits indicated the most likely sources of the recruits were the local or adjacent populations. Most of the patterning in population structure in the northern Bahamas can be explained by geographic distance and oceanographic connectivity. Recognition of these complex patterns is important in developing management plans for A. elisabethae and in understanding the effects of disturbance to adult populations of A. elisabethae and similar species with limited dispersal.