Museum Genomics Provide Evidence for Persistent Genetic Differentiation in a Threatened Seabird Species in the Western Atlantic.

Connectivity among wildlife populations facilitates exchange of genetic material between groups. Changes to historical connectivity patterns resulting from anthropogenic activities can therefore have negative consequences for genetic diversity, particularly for small or isolated populations. DNA obtained from museum specimens can enable direct comparison of temporal changes in connectivity among populations, which can aid in conservation planning and contribute to the understanding of population declines. However, museum DNA can be degraded and only available in low quantities, rendering it challenging for use in population genomic analyses. Applications of genomic methodologies such as targeted sequencing address this issue by enabling capture of shared variable sites, increasing quantity and quality of recovered genomic information. We used targeted sequencing of ultra-conserved Elements (UCEs) to evaluate potential changes in connectivity and genetic diversity of roseate terns (Sterna dougallii) with a breeding distribution in the northwestern Atlantic and the Caribbean. Both populations experienced range contractions and population declines due to anthropogenic activity in the 20th century, which has the potential to alter historical connectivity regimes. Instead, we found that the two populations were differentiated historically as well as contemporaneously, with little evidence of migration between them for either time period. We also found no evidence for temporal changes in genetic diversity, although these interpretations may have been limited due to sequencing artifacts caused by the degraded nature of the museum samples. Population structuring in migratory seabirds is typically reflective of low rates of divergence and high connectivity among geographically segregated subpopulations. Our contrasting results suggest the potential presence of ecological mechanisms driving population differentiation, and highlight the value of targeted sequencing on DNA derived from museum specimens to uncover long-term patterns of genetic differentiation in wildlife populations.

Waste not, want not: Microsatellites remain an economical and informative technology for conservation genetics.

Comparisons of microsatellites and single-nucleotide polymorphisms (SNPs) have found that SNPs outperform microsatellites in population genetic analyses, questioning the continued utility of microsatellites in population and landscape genetics. Yet, highly polymorphic markers may be of value in species that have reduced genetic variation. This study repeated previous analyses that used microsatellites with SNPs developed from ddRAD sequencing in the black-capped vireo source-sink system. SNPs provided greater resolution of genetic diversity, population differentiation, and migrant detection but could not reconstruct parentage relationships due to insufficient heterozygosities. The biological inferences made by both sets of markers were similar: asymmetrical gene flow from source sites to the remaining sink sites. With the landscape genetic analyses, we found different results between the two molecular markers, but associations of the top environmental features (riparian, open habitat, agriculture, and human development) with dispersal estimates were shared between marker types. Despite the higher precision of SNPs, we find that microsatellites effectively uncover population processes and patterns and are superior for parentage analyses in this species with reduced genetic diversity. This study illustrates the continued applicability and relevance of microsatellites in population genetic research.

Breeding Brown Pelicans Improve Foraging Performance as Energetic Needs Rise.

Optimal foraging theory states that animals should maximize resource acquisition rates with respect to energy expenditure, which may involve alteration of strategies in response to changes in resource availability and energetic need. However, field-based studies of changes in foraging behavior at fine spatial and temporal scales are rare, particularly among species that feed on highly mobile prey across broad landscapes. To derive information on changes in foraging behavior of breeding brown pelicans (Pelecanus occidentalis) over time, we used GPS telemetry and distribution models of their dominant prey species to relate bird movements to changes in foraging habitat quality in the northern Gulf of Mexico. Over the course of each breeding season, pelican cohorts began by foraging in suboptimal habitats relative to the availability of high-quality patches, but exhibited a marked increase in foraging habitat quality over time that outpaced overall habitat improvement trends across the study site. These findings, which are consistent with adjustment of foraging patch use in response to increased energetic need, highlight the degree to which animal populations can optimize their foraging behaviors in the context of uncertain and dynamic resource availability, and provide an improved understanding of how landscape-level features can impact behavior.

Asymmetrical gene flow of the recently delisted passerine black-capped vireo (Vireo atricapilla) indicates source-sink dynamics in central Texas.

Habitat fragmentation can produce metapopulations or source-sink systems in which dispersal in crucial for population maintenance. Our objective was to investigate connectivity among black-capped vireo (Vireo atricapilla) populations in tandem with a demographic study (Biological Conservation, 2016, 203, 108-118) to elucidate if central Texas populations act as a source-sink system. We genotyped 343 individuals at 12 microsatellite loci to elucidate the movement ecology of the black-capped vireo in central Texas surrounding Fort Hood; the largest and most stable breeding population of black-capped vireos inhabit Fort Hood. To gain insight into gene flow among populations, we analyzed genetic differentiation, migration rates, number of migrants, and parentage. We found statistically significant, but low levels of genetic differentiation among several populations, suggesting some limited restriction to gene flow. Across approaches to estimate migration, we found consistent evidence for asymmetrical movement from Fort Hood to the other central Texas sites consistent with source-sink dynamics. Our results are complementary to black-capped vireo demographic studies done in tandem showing that portions of Fort Hood are acting as a source population to smaller central Texas populations.

Impacts of human recreation on carnivores in protected areas.

Mammalian carnivores can be particularly sensitive to human disturbance, even within protected areas (PAs). Our objective was to understand how human disturbance affects carnivore communities in southern Arizona, USA by studying habitat occupancy based on data collected using non-invasive methods in three PAs with different levels of human disturbance. Carnivore occupancy varied based on human disturbance variables (i.e., roads, trails, etc.). Common carnivore species (coyotes, gray foxes, and bobcats) had high occupancy probability in highly disturbed sites, while all other carnivore species had a higher probability of occupancy in low disturbance protected areas. Additionally, overall carnivore diversity was higher in PAs with low human disturbance. Edges of PAs appeared to negatively impact occupancy of nearly all carnivore species. We also found the presence of roads and trails, and not necessarily how much they are used, had a significant negative impact on the occupancy of most carnivore species. Furthermore, the overall level of disturbance within a PA influenced how sensitive carnivores were to human disturbance variables. Carnivores were more sensitive in PAs with higher levels of disturbance and were relatively unaffected by disturbance variables in a PA with low base levels of disturbance. Increased visitation to PAs, expected with the region's high level of population growth, is likely to cause shifts in the carnivore communities favoring species that are less sensitive to disturbance.

Genetic structure of brown pelicans (Pelecanus occidentalis) in the northern Gulf of Mexico in the context of human management and disturbance.

Environmental disturbances, both natural and anthropogenic, have the capacity to substantially impact animal behavior and abundance, which can in turn influence patterns of genetic diversity and gene flow. However, little empirical information is available on the nature and degree of such changes due to the relative rarity of longitudinal genetic sampling of wild populations at appropriate intervals. Addressing this knowledge gap is therefore of interest to evolutionary biologists, policy makers, and managers. In the past half century, populations of the brown pelican (Pelecanus occidentalis) in the southeastern United States have been exposed to regional extirpations, translocations, colony losses, and oil spills, but potential impacts on genetic diversity and population structure remain unknown. To investigate the cumulative impacts of recent disturbances and management actions, we analyzed seven microsatellite loci using genetic samples collected from 540 nestlings across twelve pelican colonies from two time periods, corresponding to before (n = 305) and after (n = 235) the 2010 Deepwater Horizon oil spill. Pre-2010 populations in Texas were significantly differentiated from Louisiana, Alabama, and Florida populations to the east, with reintroduced populations in southeastern Louisiana having less genetic diversity than sites in Texas, consistent with a recent bottleneck. In contrast, there was no evidence of a geographic component to genetic structure among colonies sampled after the spill, consistent with increased dispersal among sites following the event. This pattern may be associated with reduced philopatry in response to colony abandonment in the areas most heavily impacted by the Deepwater Horizon event, though other factors (e.g., rehabilitation and translocation of oiled birds or colony loss due to erosion and tropical storms) were likely also involved. Future monitoring is necessary to determine if bottlenecks and loss of genetic variation are associated with the oil spill over time, and is recommended for other systems in which disturbance effects may be inferred via repeated genetic sampling.

Closing the gaps for animal seed dispersal: Separating the effects of habitat loss on dispersal distances and seed aggregation.

Habitat loss can alter animal movements and disrupt animal seed dispersal mutualisms; however, its effects on spatial patterns of seed dispersal are not well understood. To explore the effects of habitat loss on seed dispersal distances and seed dispersion (aggregation), we created a spatially explicit, individual-based model of an animal dispersing seeds (SEADS-Spatially Explicit Animal Dispersal of Seeds) in a theoretical landscape of 0%-90% habitat loss based on three animal traits: movement distance, gut retention time, and time between movements. Our model design had three objectives: to determine the effects of (1) animal traits and (2) habitat loss on seed dispersal distances and dispersion and (3) determine how animal traits could mitigate the negative effects of habitat loss on these variables. SEADS results revealed a complex interaction involving all animal traits and habitat loss on dispersal distances and dispersion, driven by a novel underlying mechanism of fragment entrapment. Unexpectedly, intermediate habitat loss could increase dispersal distances and dispersion relative to low and high habitat loss for some combinations of animal traits. At intermediate habitat loss, movement between patches was common, and increased dispersal distances and dispersion compared to continuous habitats because animals did not stop in spaces between fragments. However, movement between patches was reduced at higher habitat loss as animals became trapped in fragments, often near the parent plant, and dispersed seeds in aggregated patterns. As movement distance increased, low time between movements and high gut retention time combinations permitted more movement to adjacent patches than other combinations of animal traits. Because habitat loss affects movement in a nonlinear fashion under some conditions, future empirical tests would benefit from comparisons across landscapes with more than two levels of fragmentation.

Using Genealogical Mapping and Genetic Neighborhood Sizes to Quantify Dispersal Distances in the Neotropical Passerine, the Black-Capped Vireo.

Dispersal is a key demographic process, ultimately responsible for genetic connectivity among populations. Despite its importance, quantifying dispersal within and between populations has proven difficult for many taxa. Even in passerines, which are among the most intensely studied, individual movement and its relation to gene flow remains poorly understood. In this study we used two parallel genetic approaches to quantify natal dispersal distances in a Neotropical migratory passerine, the black-capped vireo. First, we employed a strategy of sampling evenly across the landscape coupled with parentage assignment to map the genealogical relationships of individuals across the landscape, and estimate dispersal distances; next, we calculated Wright's neighborhood size to estimate gene dispersal distances. We found that a high percentage of captured individuals were assigned at short distances within the natal population, and males were assigned to the natal population more often than females, confirming sex-biased dispersal. Parentage-based dispersal estimates averaged 2400m, whereas gene dispersal estimates indicated dispersal distances ranging from 1600-4200 m. Our study was successful in quantifying natal dispersal distances, linking individual movement to gene dispersal distances, while also providing a detailed look into the dispersal biology of Neotropical passerines. The high-resolution information was obtained with much reduced effort (sampling only 20% of breeding population) compared to mark-resight approaches, demonstrating the potential applicability of parentage-based approaches for quantifying dispersal in other vagile passerine species.

Development of novel microsatellite markers for the secret cave cricket, Ceuthophilus secretus.

The secret cave cricket, Ceuthophilus secretes Scudder (Orthroptera: Rhaphidophoridae), is an obligate trogloxene endemic to central Texas, USA, and is a primary source of energy and nutrients for sensitive cave ecosystems. In this study, nine polymorphic microsatellite markers were developed from genomic DNA of C. secretes. Genotypes of 120 individuals sampled from four localities on the Fort Hood Military Reservation, Killeen, Texas, were analyzed to characterize the polymorphism at each locus. The number of alleles ranged from 19 to 46. All paired loci were in linkage equilibrium. Four loci had significant deviations from Hardy-Weinberg equilibrium. Observed heterozygosity varied from 0.793 to 0.959. These loci provide a means of characterizing population genetic structure in this species.

Birds in space and time: genetic changes accompanying anthropogenic habitat fragmentation in the endangered black-capped vireo (Vireo atricapilla).

Anthropogenic alterations in the natural environment can be a potent evolutionary force. For species that have specific habitat requirements, habitat loss can result in substantial genetic effects, potentially impeding future adaptability and evolution. The endangered black-capped vireo (Vireo atricapilla) suffered a substantial contraction of breeding habitat and population size during much of the 20th century. In a previous study, we reported significant differentiation between remnant populations, but failed to recover a strong genetic signal of bottlenecks. In this study, we used a combination of historical and contemporary sampling from Oklahoma and Texas to (i) determine whether population structure and genetic diversity have changed over time and (ii) evaluate alternate demographic hypotheses using approximate Bayesian computation (ABC). We found lower genetic diversity and increased differentiation in contemporary samples compared to historical samples, indicating nontrivial impacts of fragmentation. ABC analysis suggests a bottleneck having occurred in the early part of the 20th century, resulting in a magnitude decline in effective population size. Genetic monitoring with temporally spaced samples, such as used in this study, can be highly informative for assessing the genetic impacts of anthropogenic fragmentation on threatened or endangered species, as well as revealing the dynamics of small populations over time.

How far is too close? restricted, sex-biased dispersal in black-capped vireos.

Understanding the interplay of dispersal and how it translates into gene flow is key to understanding population processes, and especially so for endangered species occupying fragmented habitats. In migratory songbirds, there is evidence that long-distance movement capabilities do not translate well into observed dispersal. Our objectives were to (i) define the fine-scale spatial genetic structure in endangered black-capped vireos to characterize dispersal patterns and (ii) to correlate dispersal dynamics to overall population genetic structure using a simulation approach. We sampled 160 individuals over 2 years to (i) describe the fine-scale genetic structuring and (ii) used this information to model scenarios to compare with actual data on change in population structuring over a 100-year interval. We found that black-capped vireos exhibit male philopatry and restricted dispersal distances, relative to females. Our simulations also support a sex-biased dispersal model. Additionally, we find that fragmentation related changes in rates of dispersal might be a likely cause for increasing levels of population structure over a 100-year period. We show that restricted sex-biased dispersal can explain population structuring in this species and that changes in dispersal rates due to fragmentation may be a continuing threat to genetic viability in this species.

Heritability of heat tolerance in a small livebearing fish, Heterandria formosa.

Climate change is expected to result in an increased occurrence of heat stress. The long-term population-level impact of this stress would be lessened in populations able to genetically adapt to higher temperatures. Adaptation requires the presence of genetically-based variation. At-risk populations may undergo strong declines in population size that lower the amount of genetic variation. The objectives of this study were to quantify the heritability of heat tolerance in populations of the least killifish, Heterandria formosa, and to determine if heritabilities were reduced following a population bottleneck. Heritabilities of heat tolerance were determined for two lines of each of two source populations; two bottlenecked lines (established with one pair of fish) and two regular lines. Heat tolerance was quantified as temperature-at-death (TAD), when fish acclimated at 28 °C were subjected to an increase in water temperature of 2 °C/day. Mid-parent/mean offspring regressions and full-sib analyses were used to estimate the heritability of TAD. Heritability estimates from parent/offspring regressions ranged from 0.185 to 0.462, while those from sib analyses ranged from 0 to 0.324, with an overall estimate of 0.203 (0.230 for the regular lines, 0.168 for bottlenecked ones). Fish from the bottlenecked line from one source population (but not the other) had a lower heritability than did those from the regular line. These results show that the populations tested had some potential for adaptation to elevated water temperatures, and that this potential may be reduced following a population bottleneck. This should not be construed as evidence that natural populations will not suffer negative consequences from global warming; this study only showed that these specific populations have some potential to adapt under a very specific set of conditions.

Population structure in an endangered songbird: maintenance of genetic differentiation despite high vagility and significant population recovery.

Black-capped vireos (Vireo atricapilla), an endangered, migratory species dependent upon early successional habitat, have experienced significant recovery since its protection. In light of its vagility and known increase in population size and range, limited genetic differentiation would be expected in the species. Using 15 microsatellite loci and an extensive sampling regime, we detected significant overall genetic differentiation (F(ST) = 0.021) and high interpopulation differentiation compared to other migratory birds. Although proximate sites (separated by < 20 km) tended to be genetically similar, there was no apparent association of either geographical distance or landscape attributes with differentiation between sites. Evidence of a population bottleneck was also detected in a site located near other large concentrations of birds. Although black-capped vireos are capable of large-scale movements and the population has experienced a recent expansion, dispersal appears too insufficient to eliminate the genetic differentiation resulting from restricted colonization of ephemeral habitats.

Habitat fragmentation and genetic diversity of an endangered, migratory songbird, the golden-cheeked warbler (Dendroica chrysoparia).

Landscape genetic approaches offer the promise of increasing our understanding of the influence of habitat features on genetic structure. We assessed the genetic diversity of the endangered golden-cheeked warbler (Dendroica chrysoparia) across their breeding range in central Texas and evaluated the role of habitat loss and fragmentation in shaping the population structure of the species. We determined genotypes across nine microsatellite loci of 109 individuals from seven sites representing the major breeding concentrations of the species. No evidence of a recent population bottleneck was found. Differences in allele frequencies were highly significant among sites. The sampled sites do not appear to represent isolated lineages requiring protection as separate management units, although the amount of current gene flow is insufficient to prevent genetic differentiation. Measures of genetic differentiation were negatively associated with habitat connectivity and the percentage of forest cover between sites, and positively associated with geographic distance and the percentage of agricultural land between sites. The northernmost site was the most genetically differentiated and was isolated from other sites by agricultural lands. Fragmentation of breeding habitat may represent barriers to dispersal of birds which would pose no barrier to movement during other activities such as migration.

Role of inbreeding depression and purging in captive breeding and restoration programmes.

Inbreeding depression is a major force affecting the evolution and viability of small populations in captive breeding and restoration programmes. Populations that experience small sizes may be less susceptible to future inbreeding depression because they have been purged of deleterious recessive alleles. We review issues related to purging, as they apply to the management of small populations, and discuss an experiment we conducted examining purging in populations of mosquitofish (Gambusia affinis). Purging is an important process in many small populations, but the literature contains a diversity of responses to purging both within and among studies. With the exception that slow inbreeding results in more purging and less threat to population viability, there seem to be few consistent trends that aid in prediction of how a purging event will affect a population. In our examination of purging on population viability in mosquitofish, single or multiple bottlenecks do not appear to have resulted in any purging of the influence of genetic load on population growth. Rather, serial bottlenecks resulted in a marked decline in population growth and an increase in extinction. Our results, taken together with those of reviewed studies, suggest that in small populations there is great uncertainty regarding the success of any single purging event in eliminating inbreeding depression, together with the high likelihood that purging will depress population viability through the fixation of deleterious alleles. In management of captive breeding and restoration programmes, the common practice of avoiding inbreeding and small population sizes should be followed whenever possible.

Adaptation as a potential response to sea-level rise: a genetic basis for salinity tolerance in populations of a coastal marsh fish.

Relative sea-level rise is resulting in the intrusion of saline waters into marshes historically dominated by fresh water. Saltwater intrusions can potentially affect resident marsh species, especially when storm-related tidal surges cause rapid changes in salinity. We examined the role of historical salinity exposure on the survival of Gambusia affinis from two locations in coastal Louisiana. At each location, we sampled fish populations from fresh, intermediate and brackish marshes. Individuals were then exposed to a salinity of 25‰ and survival time was measured. We found that fish from brackish and intermediate marshes had an increased tolerance to salinity stress relative to fish from freshwater environments. We then tested the descendents of fish from the fresh and brackish marshes, reared for two generation in fresh water, to determine if there was a genetic basis for differential survival. We found that descendents of individuals from brackish marshes showed elevated survivals relative to the descendents of fish with no historical exposure to salinity. The most reasonable mechanism to account for the differences in survival relative to historical exposure is genetic adaptation, suggesting that natural selection may play a role in the responses of resident marsh fishes to future increases in salinity.

Laboratory culturing and selection for increased resistance to cadmium reduce genetic variation in the least killifish, Heterandria formosa.

Populations exposed to environmental contaminants can undergo intense selection pressures, which in turn can lead to a loss of genetic variation. We assessed this loss of genetic variation in the least killifish Heterandria formosa for laboratory populations that had undergone eight generations of selection for an increased resistance to cadmium. Using microsatellite markers, we compared genetic variation between three selection and three control laboratory populations and between these laboratory populations and the source population. Heterozygosity was lower in each selection population than it was in its paired control population, with this difference being statistically significant in two of the three comparisons. This is evidence that adaptation to environmental contaminants can result in an overall loss of genetic variation. Furthermore, the laboratory populations had much lower heterozygosity than did the source population. The latter loss of genetic variation, probably a result of random drift, did not prevent the laboratory populations from showing a strong response to the selection for cadmium resistance. The loss of genetic variation resulting from maintaining populations in the laboratory demonstrates that it is important to maintain a large population size for such populations and that the potential for loss of genetic variation in laboratory populations is taken into consideration in ecotoxicology when extrapolating from laboratory to natural populations.

Breeding distributions of north American bird species moving north as a result of climate change.

Geographic changes in species distributions toward traditionally cooler climes is one hypothesized indicator of recent global climate change. We examined distribution data on 56 bird species. If global warming is affecting species distributions across the temperate northern hemisphere, these data should show the same northward range expansions of birds that have been reported for Great Britain. Because a northward shift of distributions might be due to multidirectional range expansions for multiple species, we also examined the possibility that birds with northern distributions may be expanding their ranges southward. There was no southward expansion of birds with a northern distribution, indicating that there is no evidence of overall range expansion of insectivorous and granivorous birds in North America. As predicted, the northern limit of birds with a southern distribution showed a significant shift northward (2.35 km/year). This northward shift is similar to that observed in previous work conducted in Great Britain: the widespread nature of this shift in species distributions over two distinct geographical regions and its coincidence with a period of global warming suggests a connection with global climate change.

Multiple paternity in a salamander with socially monogamous behaviour.

In the majority of birds and mammals, social monogamy is not congruent with genetic monogamy. No research to date has compared social and genetic monogamy in amphibians. We analysed paternity in clutches of red-backed salamanders (Plethodon cinereus), a species in which social monogamy has been demonstrated in the laboratory, and 28% of individuals in the forest are found in male-female pairs in the noncourtship season. We collected 16 clutches of eggs of P. cinereus in the southern Appalachian Mountains of Virginia and collected tail clippings from attending mothers. We genotyped embryos and adults at five microsatellite loci in order to analyse paternity of clutches. Most clutches (84.6%) had multiple sires, with two to three sires per clutch. In this study, 25% of clutches had males in addition to females attending eggs. None of the mothers of these clutches were genetically monogamous. All attending males sired some of the offspring in the clutch that they attended (between 9% and 50%) but never sired a majority in that clutch. We conclude that, at least in this population, social monogamy in P. cinereus is not concomitant with genetic monogamy.

ENHANCING THE RETRDEVABILITY OF POPULATION GENETIC SURVEY DATA? AN ASSESSMENT OF ANIMAL MITOCHONDRIAL DNA STUDIES.

Surveys of genetic variation in natural populations represent a valuable and often irreplaceable resource. It may be desirable to reanalyze data as new methods are developed for comparisons with other populations or for comparisons with the same populations at different times. We evaluated existing mechanisms of data preservation in a survey of 627 published surveys of mitochondrial DNA variation in animal and found that over half of the datasets (56%) contained insufficient information for reanalysis. In many cases, publication of complete data would not have added excessively to the length of the publication. Because at present, publications represent the main archive of population genetic data, we offer recommendations for how the essential data from mtDNA surveys can be presented in a form that is complete and concise.