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USGS2011

Population fragmentation and inter-ecosystem movements of grizzly bears in Western Canada and the Northern United States

Population fragmentation compromises population viability, reduces a species ability to respond to climate change, and ultimately may reduce biodiversity. We studied the current state and potential causes of fragmentation in grizzly bears over approximately 1,000,000 km 2 of western Canada, the northern United States (US), and southeast Alaska. We compiled much of our data from projects undertaken with a variety of research objectives including population estimation and trend, landscape fragmentation, habitat selection, vital rates, and response to human development. Our primary analytical techniques stemmed from genetic analysis of 3,134 bears, supplemented with radiotelemetry data from 792 bears. We used 15 locus microsatellite data coupled withmeasures of genetic distance, isolation-by-distance (IBD) analysis, analysis of covariance (ANCOVA), linear multiple regression, multi-factorial correspondence analysis (to identify population divisions or fractures with no a priori assumption of group membership), and population-assignment methods to detect individual migrants between immediately adjacent areas. These data corroborated observations of inter-area movements from our telemetry database. In northern areas, we found a spatial genetic pattern of IBD, although there was evidence of natural fragmentation from the rugged heavily glaciated coast mountains of British Columbia (BC) and the Yukon. These results contrasted with the spatial pattern of fragmentation in more southern parts of their distribution. Near the Canada-US border area, we found extensive fragmentation that corresponded to settled mountain valleys andmajor highways. Genetic distances across developed valleys were elevated relative to those across undeveloped valleys in central and northern BC. In disturbed areas, most inter-area movements detected were made by male bears, with few female migrants identified. North-south movements within mountain ranges (Mts) and across BC Highway 3 were more common than east-west movements across settled mountain valleys separating Mts. Our results suggest that relatively distinct subpopulations exist in this region, including the Cabinet, Selkirk South, and the decadesisolated Yellowstone populations. Current movement rates do not appear sufficient to consider the subpopulations we identify along the Canada-US border as 1 inter-breeding unit. Although we detected enough male movement to mediate gene flow, the current low rate of female movement detected among areas is insufficient to provide a demographic rescue effect between areas in the immediate future (0-15 yr). In Alberta, we found fragmentation corresponded to major east-west highways (Highways 3, 11, 16, and 43) and most inter-area movements were made by males. Gene flow and movement rates between Alberta and BC were highest across the Continental Divide south of Highway 1 and north of Highway 16. In the central region between Highways 1 and 11, we found evidence of natural fragmentation associated with the extensive glaciers and icefields along the Continental Divide. The discontinuities that we identified would form appropriate boundaries formanagement units. We related sex-specific movement rates between adjacent areas to several metrics of human use (highway traffic, settlement, and humancaused mortality) to understand the causes of fragmentation. This analysis used data from 1,508 bears sampled over a 161,500-km 2 area in southeastern BC, western Alberta, northern Idaho, and northern Montana during 1979-2007. This area was bisected by numerous human transportation and settlement corridors of varying intensity and complexity. We used multiple linear regression and ANCOVA to document the responses of female and male bears to disturbance. Males and females both demonstrated reduced movement rates with increasing settlement and traffic. However, females reduced their movement rates dramatically when settlement increased to >20% of the fracture zone. At this same

Wildlife Monographs↗

USGS2023

Genetic diversity goals and targets have improved, but remain insufficient for clear implementation of the post-2020 global biodiversity framework

Genetic diversity among and within populations of all species is necessary for people and nature to survive and thrive in a changing world. Over the past three years, commitments for conserving genetic diversity have become more ambitious and specific under the Convention on Biological Diversity’s (CBD) draft post-2020 global biodiversity framework (GBF). This Perspective article comments on how goals and targets of the GBF have evolved, the improvements that are still needed, lessons learned from this process, and connections between goals and targets and the actions and reporting that will be needed to maintain, protect, manage and monitor genetic diversity. It is possible and necessary that the GBF strives to maintain genetic diversity within and among populations of all species, to restore genetic connectivity, and to develop national genetic conservation strategies, and to report on these using proposed, feasible indicators.

Conservation Genetics↗

USGS1998

Incubation temperature, developmental biology, and the divergence of sockeye salmon ( Oncorhynchus nerka ) within Lake Washington

Sockeye salmon ( Oncorhynchus nerka) introduced into Lake Washington in the 1930s and 1940s now spawn at several different sites and over a period of more than 3 months. To test for evolutionary divergence within this derived lineage, embryos that would have incubated in different habitats (Cedar River or Pleasure Point Beach) or at different times (October, November, or December in the Cedar River) were reared in the laboratory at 5, 9, and 12.5??C. Some developmental variation mirrored predictions of adaptive divergence: (i) survival at 12.5??C was highest for embryos most likely to experience such temperatures in the wild (Early Cedar), (ii) development rate was fastest for progeny of late spawners (Late Cedar), and (iii) yolk conversion efficiency was matched to natural incubation temperatures. These patterns likely had a genetic basis because they were observed in a common environment and could not be attributed to differences in egg size. The absolute magnitude of divergence in development rates was moderate (Late Cedar embryos emerged only 6 days earlier at 9??C) and some predictions regarding development rates were not supported. Nonetheless our results provide evidence of adaptive divergence in only 9-14 generations.

Washington↗

USGS2019

Landscape genetics reveals unique and shared effects of urbanization for two sympatric pool-breeding amphibians

Metapopulation-structured species can be negatively affected when landscape fragmentation impairs connectivity. We investigated the effects of urbanization on genetic diversity and gene flow for two sympatric amphibian species, spotted salamanders ( Ambystoma maculatum ) and wood frogs ( Lithobates sylvaticus ), across a large (>35,000 km 2 ) landscape in Maine, USA, containing numerous natural and anthropogenic gradients. Isolation-by-distance (IBD) patterns differed between the species. Spotted salamanders showed a linear and relatively high variance relationship between genetic and geographic distances ( r = .057, p < .001), whereas wood frogs exhibited a strongly nonlinear and lower variance relationship ( r = 0.429, p < .001). Scale dependence analysis of IBD found gene flow has its most predictable influence (strongest IBD correlations) at distances up to 9 km for spotted salamanders and up to 6 km for wood frogs. Estimated effective migration surfaces revealed contrasting patterns of high and low genetic diversity and gene flow between the two species. Population isolation, quantified as the mean IBD residuals for each population, was associated with local urbanization and less genetic diversity in both species. The influence of geographic proximity and urbanization on population connectivity was further supported by distance-based redundancy analysis and multiple matrix regression with randomization. Resistance surface modeling found interpopulation connectivity to be influenced by developed land cover, light roads, interstates, and topography for both species, plus secondary roads and rivers for wood frogs. Our results highlight the influence of anthropogenic landscape features within the context of natural features and broad spatial genetic patterns, in turn supporting the premise that while urbanization significantly restricts interpopulation connectivity for wood frogs and spotted salamanders, specific landscape elements have unique effects on these two sympatric species.

Maine↗

USGS2023

Glacial vicariance and secondary contact shape demographic histories in a freshwater mussel species complex

Characterizing the mechanisms influencing the distribution of genetic variation in aquatic species can be difficult due to the dynamic nature of hydrological landscapes. In North America’s Central Highlands, a complex history of glacial dynamics, long-term isolation, and secondary contact have shaped genetic variation in aquatic species. Although the effects of glacial history have been demonstrated in many taxa, responses are often lineage- or species-specific and driven by organismal ecology. In this study, we reconstruct the evolutionary history of a freshwater mussel species complex using a suite of mitochondrial and nuclear loci to resolve taxonomic and demographic uncertainties. Our findings do not support Pleurobema rubrum as a valid species, which is proposed for listing as threatened under the U.S. Endangered Species Act. We synonymize P. rubrum under Pleurobema sintoxia —a common and widespread species found throughout the Mississippi River Basin. Further investigation of patterns of genetic variation in P. sintoxia identified a complex demographic history, including ancestral vicariance and secondary contact, within the Eastern Highlands. We hypothesize these patterns were shaped by ancestral vicariance driven by the formation of Lake Green and subsequent secondary contact after the last glacial maximum. Our inference aligns with demographic histories observed in other aquatic taxa in the region and mirrors patterns of genetic variation of a freshwater fish species ( Erimystax dissimilis ) confirmed to serve as a parasitic larval host for P. sintoxia . Our findings directly link species ecology to observed patterns of genetic variation and may have significant implications for future conservation and recovery actions of freshwater mussels.

Mississippi River basin↗

USGS2018

Implications of introgression for wildlife translocations: the case of North American martens

The evolutionary consequences of natural introgression provide a rare opportunity to retrospectively evaluate how the introduction of exotics or genetic rescue efforts may impact endemic faunas. Phylogeographic structure among mainland, endemic insular, and introduced North American marten ( Martes americana and M. caurina ) populations have been shaped by a complex history of natural, post-glacial population expansion followed by a series of anthropogenic introductions. In some cases, both natural colonization and translocations facilitated secondary contact, offering a series of replicated experiments that demonstrate how introgression, in these cases following isolation (insular and refugial), shapes genetic diversity. We test whether genetic exchange is occurring between North American marten species using mitochondrial genomes and ten nuclear loci. We present evidence of biased nuclear introgression from M. caurina into M. americana across two natural hybrid zones (insular and mainland) and found no remnant evidence of M. caurina on islands that received M. americana translocations, suggesting prior absence, potential extirpation, or genetic swamping of M. caurina from these islands. Our results highlight the importance of understanding phylogeographic variation prior to identifying source populations for wildlife translocations and caution the use of genetic rescue for North American marten populations. Although previously managed as a single species, these two species show substantial genetic divergence. When the two are placed into contact, they exhibit unidirectional, asymmetric introgression with potentially negative consequences for M. caurina , underscoring the value of mindful consideration of introgression in wildlife management.

Conservation Genetics↗

USGS2023

Genetic architecture and evolution of color variation in American black bears

Color variation is a frequent evolutionary substrate for camouflage in small mammals, but the underlying genetics and evolutionary forces that drive color variation in natural populations of large mammals are mostly unexplained. The American black bear, Ursus americanus ( U. americanus ), exhibits a range of colors including the cinnamon morph, which has a similar color to the brown bear, U. arctos , and is found at high frequency in the American southwest. Reflectance and chemical melanin measurements showed little distinction between U. arctos and cinnamon U. americanus individuals. We used a genome-wide association for hair color as a quantitative trait in 151 U. americanus individuals and identified a single major locus (p < 10 −13 ). Additional genomic and functional studies identified a missense alteration (R153C) in Tyrosinase-related protein 1 ( TYRP1 ) that likely affects binding of the zinc cofactor, impairs protein localization, and results in decreased pigment production. Population genetic analyses and demographic modeling indicated that the R153C variant arose 9.36 kya in a southwestern population where it likely provided a selective advantage, spreading both northwards and eastwards by gene flow. A different TYRP1 allele, R114C, contributes to the characteristic brown color of U. arctos but is not fixed across the range.

Current Biology↗

USGS2025

Population genetics of the endangered narrowly endemic Island Marble butterfly (Euchloe ausonides insulanus)

The Island Marble butterfly ( Euchloe ausonides insulanus ) is an endangered species endemic to the San Juan Islands off the coast of Washington State, United States, and British Columbia, Canada. The species was thought to be extinct for ~ 90 years before it was rediscovered at American Camp, San Juan Island National Historical Park in 1998. Here, we report the results of the first population genetic analyses for insulanus , using DNA collected non-invasively from individuals in the last known stronghold for the species. We used DNA extracted from meconium, larval exuviae, and natural mortalities to generate and test thirteen new microsatellite markers to estimate genetic diversity, population structure, and kinship. We assembled and annotated mitochondrial genomes, which were used alongside museum specimens of insulanus collected ~ 100 years ago from Vancouver Island, and other members of the E. ausonides species complex, to infer the evolutionary history of the species. The results indicated that insulanus experiences low heterozygosity, a small effective population size (N e ), and low allelic diversity. High levels of inbreeding were found in some individuals, but inbreeding was uneven across the population. No population structure or partitioning of genetic variation by host plant was detected. The mitogenomes of extant insulanus were all identical and modern samples showed a loss of allelic diversity compared to insulanus from museums. Extant insulanus formed a clade with museum specimens and we identified multiple putatively diagnostic alleles to differentiate insulanus from other subspecies. Based on these results, we outline considerations for species management and genetic monitoring.

British Columbia, Washington↗

USGS2011

Genetic identity of Thamnophis sp. using microsatellite genetic markers

Butler’s gartersnake (Thamnophis butleri) was previously listed by the Wisconsin Department of Natural Resources as a state threatened species. Several key questions associated with species identity, integrity, and hybridization with other gartersnake species needed to be addressed to further refi ne the management plan for this species. The objectives of this research were: 1) to determine if genetic markers developed in the initial phase of research could identify discrete genetic groups of Wisconsin gartersnakes, 2) to determine if any or all genetic groups delineated in objective one were consistent with Butler’s gartersnake, plains gartersnake (T. radix), and/or common gartersnake (T. sirtalis), and 3) to determine if any of the genetic data were consistent with hybridization occurring between gartersnakes in Wisconsin. Snakes were sampled from various Midwestern locations with a focus on sites in Wisconsin. All snakes were photo-vouchered, morphological landmarks were taken, and a tail snip was collected for genetic analysis. Genetic data from previously developed microsatellite markers discriminated three genetic groups from a composite 13-locus dataset (N=815) using the Bayesian admixture analysis in STRUCTURE v2.3.3. These units were highly consistent with species-groups based on the membership of a small number of known snakes from areas where the species are not thought to co-occur. Using a threshold q-value (proportional genotype) of ≥80%, 498 Butler’s gartersnakes, 93 plains gartersnakes, and 107 common gartersnakes were identifi ed in Wisconsin samples; putative hybrid snakes of Butler’s gartersnake x plain gartersnake (34), Butler’s gartersnake x common gartersnake (8), and a single ambiguous snake were also identifi ed in Wisconsin samples. Levels of divergence among the species groups from Wisconsin were lower than between species groups from other states consistent with either larger than expected Wisconsin population sizes or signifi cant gene fl ow (introgressive hybridization) having occurred among species. Regardless, levels of divergence and overall integrity of the three groups were such that the presence of three species of gartersnakes in Wisconsin was supported and hybridization, at a minimum between Butler’s gartersnakes and the two other species, was shown to occur.

Wisconsin DNR Research Report↗

USGS2025

Bovine SNP array-based genetic assessment of American plains bison at American Prairie

American plains bison ( Bison bison bison , bison hereafter) experienced an extreme demographic bottleneck in the late 1800s. The species has since rebounded but is primarily managed as small and isolated herds due to habitat and sociopolitical limitations. Thus, reintroducing bison and allowing herds to achieve as much of their natural dynamics as possible is a major conservation goal. Concerns about genetic diversity loss in small, isolated herds and the persistence of cattle-origin variants from historical crossbreeding efforts have made genetic analysis an important part of bison conservation. The limitations of the current conservation genetic tools which are based on traditional markers such as microsatellites and mitochondrial DNA sequences, may be overcome with genome-wide genotyping panels commonly developed for agricultural species. Bison reintroduction in the grasslands at American Prairie began in 2005. Genetic analysis on these herds has yet to be conducted. We used the Illumina 777K Bovine genotyping panel to obtain data from 197 bison and 179 domestic cows to understand the current population genetic state of bison at American Prairie and gain insight on cattle ( Bos taurus ) introgression. Overall, bison at American Prairie currently have relatively high genetic diversity, low inbreeding, and no obvious signs of cattle introgression. A more comprehensive evaluation of introgression, likely including whole-genome sequence data, would clarify this finding. These results can serve as a baseline for future comparison as part of a genetic monitoring framework.

Journal of Heredity↗

USGS2022

Scat as a source of DNA for population monitoring

Sampling fecal droppings (scat) to genetically identify individual animals is an established method for monitoring mammal populations and could be highly useful for monitoring reptile populations. Whereas existing protocols for obtaining DNA from reptile scat focus on analyses of whole, fresh scat deposited during animal handling, the collection of scat naturally deposited by reptiles in situ, as required for non-invasive population monitoring, requires protocols to extract highly degraded DNA. Using surface swabs from such scats can reduce PCR inhibition, ecological impacts of removing scat, and zoonotic risks. We report on three related but independently designed studies of DNA analyses from scat swabs of herbivorous reptiles under natural desert conditions: two free-ranging desert tortoise species (Agassiz's desert tortoise, Gopherus agassizii , California, US, and Morafka's desert tortoise, G. morafkai , Arizona, US) and the common chuckwalla (Sauromalus atar ) (Arizona, US, and Sonora, MX). We analyzed samples from both tortoise species with the same set of 16 microsatellites and chuckwalla samples with four mtDNA markers; studies also varied in swab preservation medium and DNA extraction method. Microsatellite amplification success per sample, defined as ≥9 loci with amplification, varied between studies, with 15% for Agassiz's desert tortoise and 42% Morafka's desert tortoise. For chuckwallas, we successfully amplified and sequenced 50% of samples. We recovered fragments up to 400 bp for tortoises and 980 bp for chuckwallas from scat swab samples. This study demonstrates that genotypes can successfully be obtained from swabs of herbivorous reptile scat collected in the field under natural environmental conditions and emphasizes that repeat amplifications are necessary for genetic identification of individuals from non-invasive samples.

Arizona, California↗

USGS2014

A nuclear DNA perspective on delineating evolutionarily significant lineages in polyploids: the case of the endangered shortnose sturgeon ( Acipenser brevirostrum )

The shortnose sturgeon, Acipenser brevirostrum , oft considered a phylogenetic relic, is listed as an “endangered species threatened with extinction” in the US and “Vulnerable” on the IUCN Red List. Effective conservation of A. brevirostrum depends on understanding its diversity and evolutionary processes, yet challenges associated with the polyploid nature of its nuclear genome have heretofore limited population genetic analysis to maternally inherited haploid characters. We developed a suite of polysomic microsatellite DNA markers and characterized a sample of 561 shortnose sturgeon collected from major extant populations along the North American Atlantic coast. The 181 alleles observed at 11 loci were scored as binary loci and the data were subjected to multivariate ordination, Bayesian clustering, hierarchical partitioning of variance, and among-population distance metric tests. The methods uncovered moderately high levels of gene diversity suggesting population structuring across and within three metapopulations (Northeast, Mid-Atlantic, and Southeast) that encompass seven demographically discrete and evolutionarily distinct lineages. The predicted groups are consistent with previously described behavioral patterns, especially dispersal and migration, supporting the interpretation that A. brevirostrum exhibit adaptive differences based on watershed. Combined with results of prior genetic (mitochondrial DNA) and behavioral studies, the current work suggests that dispersal is an important factor in maintaining genetic diversity in A. brevirostrum and that the basic unit for conservation management is arguably the local population.

PLoS ONE↗

USGS2003

Native plants for effective coastal wetland restoration

Plant communities, along with soils and appropriate water regimes, are essential components of healthy wetland systems. In Louisiana, the loss of wetland habitat continues to be an issue of major concern. Wetland loss is caused by several interacting factors, both natural and human-induced (e.g., erosion and saltwater intrusion from the construction of canals and levees). Recent estimates of annual coastal land loss rates of about 62 km2 (24 mi2 ) over the past decade emphasize the magnitude of this problem. In an attempt to slow the rate of loss and perhaps halt the overall trend, resource managers in Louisiana apply various techniques to restore damaged or degraded habitats to functioning wetland systems. Researchers at the U.S. Geological Survey’s National Wetlands Research Center (NWRC) have cooperated with the Louisiana Department of Natural Resources in studies that address effective restoration strategies for coastal wetlands. The studies have identified differences in growth that naturally exist in native Louisiana wetland plant species and genetic varieties (i.e., clones) within species. Clones of a species have a distinctive genetic identity, and some clones may also have distinctive growth responses under various environmental conditions (i.e., preferences). Indeed, large areas of coastal marsh are typically populated by several clones of a plant species, each growing in a microenvironment suited to its preferences. These studies will provide information that will assist resource managers in selecting plant species and clones of species with known growth characteristics that can be matched to environmental conditions at potential restoration sites. Before the studies began, a collection of several clones from four plant species native to coastal Louisiana was established. The species collected included saltgrass (Distichlis spicata), common reed (Phragmites australis), giant bulrush (Schoenoplectus californicus), and saltmarsh bulrush (Schoenoplectus robustus). Plants connected by roots were collected from public lands across the coastal zone, and then allowed to grow several months and produce new stems and plants from underground stems called “rhizomes.” These procedures maintained the genetic identity of the clones and allowed the plants to adjust to greenhouse conditions before experimental treatments began.

Fact Sheet↗

USGS2016

A century of landscape disturbance and urbanization of the San Francisco Bay region affects the present-day genetic diversity of the California Ridgway’s rail (Rallus obsoletus obsoletus)

Fragmentation and loss of natural habitat have important consequences for wild populations and can negatively affect long-term viability and resilience to environmental change. Salt marsh obligate species, such as those that occupy the San Francisco Bay Estuary in western North America, occupy already impaired habitats as result of human development and modifications and are highly susceptible to increased habitat loss and fragmentation due to global climate change. We examined the genetic variation of the California Ridgway’s rail ( Rallus obsoletus obsoletus ), a state and federally endangered species that occurs within the fragmented salt marsh of the San Francisco Bay Estuary. We genotyped 107 rails across 11 microsatellite loci and a single mitochondrial gene to estimate genetic diversity and population structure among seven salt marsh fragments and assessed demographic connectivity by inferring patterns of gene flow and migration rates. We found pronounced genetic structuring among four geographically separate genetic clusters across the San Francisco Bay. Gene flow analyses supported a stepping stone model of gene flow from south-to-north. However, contemporary gene flow among the regional embayments was low. Genetic diversity among occupied salt marshes and genetic clusters were not significantly different. We detected low effective population sizes and significantly high relatedness among individuals within salt marshes. Preserving genetic diversity and connectivity throughout the San Francisco Bay may require attention to salt marsh restoration in the Central Bay where habitat is both most limited and most fragmented. Incorporating periodic genetic sampling into the management regime may help evaluate population trends and guide long-term management priorities.

California↗

USGS2015

Population and genetic outcomes 20 years after reintroducing bobcats ( Lynx rufus ) to Cumberland Island, Georgia USA

In 1988–1989, 32 bobcats Lynx rufus were reintroduced to Cumberland Island (CUIS), Georgia, USA, from which they had previously been extirpated. They were monitored intensively for 3 years immediately post-reintroduction, but no estimation of the size or genetic diversity of the population had been conducted in over 20 years since reintroduction. We returned to CUIS in 2012 to estimate abundance and effective population size of the present-day population, as well as to quantify genetic diversity and inbreeding. We amplified 12 nuclear microsatellite loci from DNA isolated from scats to establish genetic profiles to identify individuals. We used spatially explicit capture–recapture population estimation to estimate abundance. From nine unique genetic profiles, we estimate a population size of 14.4 (SE = 3.052) bobcats, with an effective population size ( N e ) of 5–8 breeding individuals. This is consistent with predictions of a population viability analysis conducted at the time of reintroduction, which estimated the population would average 12–13 bobcats after 10 years. We identified several pairs of related bobcats (parent-offspring and full siblings), but ~75% of the pairwise comparisons were typical of unrelated individuals, and only one individual appeared inbred. Despite the small population size and other indications that it has likely experienced a genetic bottleneck, levels of genetic diversity in the CUIS bobcat population remain high compared to other mammalian carnivores. The reintroduction of bobcats to CUIS provides an opportunity to study changes in genetic diversity in an insular population without risk to this common species. Opportunities for natural immigration to the island are limited; therefore, continued monitoring and supplemental bobcat reintroductions could be used to evaluate the effect of different management strategies to maintain genetic diversity and population viability. The successful reintroduction and maintenance of a bobcat population on CUIS illustrates the suitability of translocation as a management tool for re-establishing felid populations.

Georgia↗

USGS2017

Restricted gene flow between resident Oncorhynchus mykiss and an admixed population of anadromous steelhead

The species Oncorhynchus mykiss is characterized by a complex life history that presents a significant challenge for population monitoring and conservation management. Many factors contribute to genetic variation in O. mykiss populations, including sympatry among migratory phenotypes, habitat heterogeneity, hatchery introgression, and immigration (stray) rates. The relative influences of these and other factors are contingent on characteristics of the local environment. The Rock Creek subbasin in the middle Columbia River has no history of hatchery supplementation and no dams or artificial barriers. Limited intervention and minimal management have led to a dearth of information regarding the genetic distinctiveness of the extant O. mykiss population in Rock Creek and its tributaries. We used 192 SNP markers and collections sampled over a 5‐year period to evaluate the temporal and spatial genetic structures of O. mykiss between upper and lower watersheds of the Rock Creek subbasin. We investigated potential limits to gene flow within the lower watershed where the stream is fragmented by seasonally dry stretches of streambed, and between upper and lower watershed regions. We found minor genetic differentiation within the lower watershed occupied by anadromous steelhead ( F ST = 0.004), and evidence that immigrant influences were prevalent and ubiquitous. Populations in the upper watershed above partial natural barriers were highly distinct ( F ST = 0.093) and minimally impacted by apparent introgression. Genetic structure between watersheds paralleled differences in local demographics (e.g., variation in size), migratory restrictions, and habitat discontinuity. The evidence of restricted gene flow between putative remnant resident populations in the upper watershed and the admixed anadromous population in the lower watershed has implications for local steelhead productivity and regional conservation.

Washington↗

USGS2018

Genetic diversity and structure from Antillean manatee (Trichechus manatus manatus) in the southern Gulf of Mexico: Comparison between connected and isolated populations

Antillean manatees ( Trichechus manatus manatus ), a subspecies of the West Indian manatee, is listed as endangered species in the Red List of Threatened Species of the International Union for Conservation of Nature. The aims of this research were to survey on the possible regional genetic structure in the southern Gulf of Mexico and to compare genetic status of a landlocked population in Laguna de las Ilusiones (IL) with individuals from localities with no barriers to displacement and breed (open population [OP]). We analyzed 45 manatee skin samples collected from different locations in Tabasco ( n = 38, including 19 from IL), Veracruz ( n = 3), Campeche ( n = 2), and Chiapas ( n = 2). The genomic DNA was isolated and PCR amplifications were performed for each sample using 28 microsatellite loci, previously designed for West Indian manatees and described as polymorphic for this species. Two clusters ( k = 2) were identified by STRUCTURE. The analysis of both a priori populations (IL and OP) indicate that the global values of F ST and R ST ( F ST =0.049, R ST =0.077) were significant. The H E for IL was 0.38 ± 0.03 and for OP was 0.49 ± 0.01. The average number of alleles N A for IL was 2.21 ± 0.09 and for OP was 2.32 ± 0.09. The overall inbreeding coefficient was F IS =−0.013 for analyzed populations. Genetic diversity was low. The IL population had slightly lower genetic diversity compared with OP, which could be explained by isolation of that small group, so conservation plans for IL should be considered as priority.

Tropical Conservation Science↗

USGS2007

Population response to habitat fragmentation in a stream-dwelling brook trout population

Fragmentation can strongly influence population persistence and expression of life-history strategies in spatially-structured populations. In this study, we directly estimated size-specific dispersal, growth, and survival of stream-dwelling brook trout in a stream network with connected and naturally-isolated tributaries. We used multiple-generation, individual-based data to develop and parameterize a size-class and location-based population projection model, allowing us to test effects of fragmentation on population dynamics at local (i.e., subpopulation) and system-wide (i.e., metapopulation) scales, and to identify demographic rates which influence the persistence of isolated and fragmented populations. In the naturally-isolated tributary, persistence was associated with higher early juvenile survival (-45% greater), shorter generation time (one-half) and strong selection against large body size compared to the open system, resulting in a stage-distribution skewed towards younger, smaller fish. Simulating barriers to upstream migration into two currently-connected tribuory populations caused rapid (2-6 generations) local extinction. These local extinctions in turn increased the likelihood of system-wide extinction, as tributaries could no longer function as population sources. Extinction could be prevented in the open system if sufficient immigrants from downstream areas were available, but the influx of individuals necessary to counteract fragmentation effects was high (7-46% of the total population annually). In the absence of sufficient immigration, a demographic change (higher early survival characteristic of the isolated tributary) was also sufficient to rescue the population from fragmentation, suggesting that the observed differences in size distributions between the naturally-isolated and open system may reflect an evolutionary response to isolation. Combined with strong genetic divergence between the isolated tributary and open system, these results suggest that local adaptation can 'rescue' isolated populations, particularly in one-dimensional stream networks where both natural and anthropegenically-mediated isolation is common. However, whether rescue will occur before extinction depends critically on the race between adaptation and reduced survival in response to fragmentation.

PLoS ONE↗