Janna R. Willoughby

The impacts of inbreeding, drift and selection on genetic diversity in captive breeding populations

The goal of captive breeding programmes is often to maintain genetic diversity until re‐introductions can occur. However, due in part to changes that occur in captive populations, approximately one‐third of re‐introductions fail. We evaluated genetic changes in captive populations using microsatellites and mtDNA. We analysed six populations of white‐footed mice that were propagated for 20 generations using two replicates of three protocols: random mating (RAN), minimizing mean kinship (MK) and selection for docility (DOC). We found that MK resulted in the slowest loss of microsatellite genetic diversity compared to RAN and DOC. However, the loss of mtDNA haplotypes was not consistent among replicate lines. We compared our empirical data to simulated data and found no evidence of selection. Our results suggest that although the effects of drift may not be fully mitigated, MK reduces the loss of alleles due to inbreeding more effectively than random mating or docility selection. Therefore, MK should be preferred for captive breeding. Furthermore, our simulations show that incorporating microsatellite data into the MK framework reduced the magnitude of drift, which may have applications in long‐term or extremely genetically depauperate captive populations.

Of contigs and quagmires: next-generation sequencing pitfalls associated with transcriptomic studies.

Molecular ecologists have good reasons to be excited about the newest DNA/RNA sequencing technologies. However, this exuberance should be tempered with a hefty dose of reality: new sequencing technologies come with significant new challenges. Herein, we offer a brief overview of some practical problems encountered during transcriptomics studies conducted in our laboratory, and of nontrivial issues that prospective practitioners should consider. These include template contamination (e.g. from xenobiotics) and the cutting‐room floor problem, whereby most of the data are often unassembled, unannotated and unused. We also highlight computational requirements, including hardware, personnel time and associated skill sets. We are very optimistic about the future of molecular ecology, but we hope this cautionary overview will help neophytes better recognize some key challenges associated with new technologies.

Mechanistic insights into landscape genetic structure of two tropical amphibians using field‐derived resistance surfaces

Conversion of forests to agriculture often fragments distributions of forest species and can disrupt gene flow. We examined effects of prevalent land uses on genetic connectivity of two amphibian species in northeastern Costa Rica. We incorporated data from field surveys and experiments to develop resistance surfaces that represent local mechanisms hypothesized to modify dispersal success of amphibians, such as habitat‐specific predation and desiccation risk. Because time lags can exist between forest conversion and genetic responses, we evaluated landscape effects using land‐cover data from different time periods. Populations of both species were structured at similar spatial scales but exhibited differing responses to landscape features. Litter frog population differentiation was significantly related to landscape resistances estimated from abundance and experiment data. Model support was highest for experiment‐derived surfaces that represented responses to microclimate variation. Litter frog genetic variation was best explained by contemporary landscape configuration, indicating rapid population response to land‐use change. Poison frog genetic structure was strongly associated with geographic isolation, which explained up to 45% of genetic variation, and long‐standing barriers, such as rivers and mountains. However, there was also partial support for abundance‐ and microclimate response‐derived resistances. Differences in species responses to landscape features may be explained by overriding effects of population size on patterns of differentiation for poison frogs, but not litter frogs. In addition, pastures are likely semi‐permeable to poison frog gene flow because the species is known to use pastures when remnant vegetation is present, but litter frogs do not. Ongoing reforestation efforts will probably increase connectivity in the region by increasing tree cover and reducing area of pastures.

Segregating the effects of seed traits and common ancestry of hardwood trees on eastern gray squirrel foraging decisions

The evolution of specific seed traits in scatter-hoarded tree species often has been attributed to granivore foraging behavior. However, the degree to which foraging investments and seed traits correlate with phylogenetic relationships among trees remains unexplored. We presented seeds of 23 different hardwood tree species (families Betulaceae, Fagaceae, Juglandaceae) to eastern gray squirrels (Sciurus carolinensis), and measured the time and distance travelled by squirrels that consumed or cached each seed. We estimated 11 physical and chemical seed traits for each species, and the phylogenetic relationships between the 23 hardwood trees. Variance partitioning revealed that considerable variation in foraging investment was attributable to seed traits alone (27–73%), and combined effects of seed traits and phylogeny of hardwood trees (5–55%). A phylogenetic PCA (pPCA) on seed traits and tree phylogeny resulted in 2 “global” axes of traits that were phylogenetically autocorrelated at the family and genus level and a third “local” axis in which traits were not phylogenetically autocorrelated. Collectively, these axes explained 30–76% of the variation in squirrel foraging investments. The first global pPCA axis, which produced large scores for seed species with thin shells, low lipid and high carbohydrate content, was negatively related to time to consume and cache seeds and travel distance to cache. The second global pPCA axis, which produced large scores for seeds with high protein, low tannin and low dormancy levels, was an important predictor of consumption time only. The local pPCA axis primarily reflected kernel mass. Although it explained only 12% of the variation in trait space and was not autocorrelated among phylogenetic clades, the local axis was related to all four squirrel foraging investments. Squirrel foraging behaviors are influenced by a combination of phylogenetically conserved and more evolutionarily labile seed traits that is consistent with a weak or more diffuse coevolutionary relationship between rodents and hardwood trees rather than a direct coevolutionary relationship.

Inbreeding and selection shape genomic diversity in captive populations: Implications for the conservation of endangered species

Captive breeding programs are often initiated to prevent species extinction until reintroduction into the wild can occur. However, the evolution of captive populations via inbreeding, drift, and selection can impair fitness, compromising reintroduction programs. To better understand the evolutionary response of species bred in captivity, we used nearly 5500 single nucleotide polymorphisms (SNPs) in populations of white-footed mice (Peromyscus leucopus) to measure the impact of breeding regimes on genomic diversity. We bred mice in captivity for 20 generations using two replicates of three protocols: random mating (RAN), selection for docile behaviors (DOC), and minimizing mean kinship (MK). The MK protocol most effectively retained genomic diversity and reduced the effects of selection. Additionally, genomic diversity was significantly related to fitness, as assessed with pedigrees and SNPs supported with genomic sequence data. Because captive-born individuals are often less fit in wild settings compared to wild-born individuals, captive-estimated fitness correlations likely underestimate the effects in wild populations. Therefore, minimizing inbreeding and selection in captive populations is critical to increasing the probability of releasing fit individuals into the wild.

The importance of including imperfect detection models in eDNA experimental design

Environmental DNA (eDNA) is DNA that has been isolated from field samples, and it is increasingly used to infer the presence or absence of particular species in an ecosystem. However, the combination of sampling procedures and subsequent molecular amplification of eDNA can lead to spurious results. As such, it is imperative that eDNA studies include a statistical framework for interpreting eDNA presence/absence data. We reviewed published literature for studies that utilized eDNA where the species density was known and compared the probability of detecting the focal species to the sampling and analysis protocols. Although biomass of the target species and the volume per sample did not impact detectability, the number of field replicates and number of samples from each replicate were positively related to detection. Additionally, increased number of PCR replicates and increased primer specificity significantly increased detectability. Accordingly, we advocate for increased use of occupancy modelling as a method to incorporate effects of sampling effort and PCR sensitivity in eDNA study design. Based on simulation results and the hierarchical nature of occupancy models, we suggest that field replicates, as opposed to molecular replicates, result in better detection probabilities of target species.

Population Decline in a Long-Lived Species: The Wood Turtle in Michigan

Abstract: Populations of Wood Turtles, Glyptemys insculpta, have steadily decreased over the past 30 yr because of habitat destruction and degradation. We sampled Wood Turtles from three areas in Michigan, USA, to characterize populations, quantify demographic trends, and measure the effect of declining population size on genetic diversity. Wood Turtle samples (n = 68) were collected from three rivers in the Lower Peninsula of Michigan and analyzed at nine microsatellite loci. Bayesian clustering programs identified two populations that split the three sampling sites into North and South populations. In both populations, analysis of genealogies estimated r < 0, indicating population decline. However, no evidence of a bottleneck was detected (P = 0.30 North, P = 0.29 South), and little evidence of inbreeding was observed (average North FIS = 0.25, average South FIS = 0.23), relative to other Emydidae populations. The high genetic diversity observed in the North and South populations is likely due to immigration between the two populations (FST = 0.04), coupled with the long life span of the Wood Turtle. The conflicting signals suggested from the genealogy models compared to the FIS and bottleneck analysis suggests that coalescent models may be better suited to detect population decline than other measures of genetic diversity in long-lived species such as the Wood Turtle.

Rapid genetic adaptation to a novel environment despite a genome‐wide reduction in genetic diversity

Introduced species often colonize regions that have vastly different ecological and environmental conditions than those found in their native range. As such, species introductions can provide a deeper understanding into the process of adaptive evolution. In the 1880s, steelhead trout (Oncorhynchus mykiss) from California were introduced into Lake Michigan (Laurentian Great Lakes, North America) where they established naturally reproducing populations. In their native range, steelhead hatch in rivers, migrate to the ocean and return to freshwater to spawn. Steelhead in Lake Michigan continue to swim up rivers to spawn, but now treat the freshwater environment of the Great Lakes as a surrogate ocean. To examine the effects of this introduction, we sequenced the genomes of 264 fish. By comparing steelhead from Lake Michigan to steelhead from their ancestral range, we determined that the introduction led to consistent reductions in genetic diversity across all 29 chromosomes. Despite this reduction in genetic diversity, three chromosomal regions were associated with rapid genetic adaptation to the novel environment. The first region contained functional changes to ceramide kinase, which likely altered metabolic and wound‐healing rates in Lake Michigan steelhead. The second and third regions encoded carbonic anhydrases and a solute carrier protein, both of which are critical for osmoregulation, and demonstrate how steelhead physiologically adapted to freshwater. Furthermore, the contemporary release of diverse hatchery strains into the lake increased genetic diversity but reduced the signature of genetic adaptation. This study illustrates that species can rapidly adapt to novel environments despite genome‐wide reductions in genetic diversity.

Indirect evidence of prey-switching in minks: empirical evidence, theoretical modeling, and spatial drivers

Abstract A spatial gradient in the interactions between American minks (Neovison vison) and muskrats (Ondatra zibethicus) occurs in the Hudsons Bay Company fur harvest returns of Canada. Evidence for strong dependence of minks on muskrats exists in northwestern Canada, whereas evidence for weaker interactions exists in central and eastern Canada. We tested the hypothesis that minks consume fewer muskrats and more alternative prey in some areas, using fur records from 56 Hudsons Bay posts. Both muskrats and small microtines were found to explain mink dynamics, with small microtines and other alternative prey gaining importance in the eastern portion of our study area. Mink fur returns exhibited a range of cycle lengths from 2.6 to 13 years encompassing typical small microtine periodicities of 3–5 years and typical muskrat periodicities of 8–13 years. A time lag of 0 years occurred between mink and muskrat harvest data frequently in the eastern portion of our study area, hypothesized to be a result of minks consuming alternative prey. To biologically verify small microtines as a potential prey source, we modeled mink and muskrat population dynamics assuming small microtines were an alternative prey by modifying the Turchin and Hanski (1997) model. Simulated mink and muskrat time series replicated observed periodicity and time-lag range, suggesting that minks can be generalist predators and consume alternative prey. Finally, we examined species richness and land cover as potential drivers of mink prey-switching, but were unable to find support for either hypothesis, suggesting that additional environmental- or competition-related interactions influence mink population dynamics.

Detection of barriers to dispersal is masked by long lifespans and large population sizes

Abstract Population genetic analyses of species inhabiting fragmented landscapes are essential tools for conservation. Occasionally, analyses of fragmented populations find no evidence of isolation, even though a barrier to dispersal is apparent. In some cases, not enough time may have passed to observe divergence due to genetic drift, a problem particularly relevant for long‐lived species with overlapping generations. Failing to consider this quality during population structure analyses could result in incorrect conclusions about the impact of fragmentation on the species. We designed a model to explore how lifespan and population size influence perceived population structure of isolated populations over time. This iterative model tracked how simulated populations of variable lifespan and population size were affected by drift alone, using a freshwater mussel, Quadrula quadrula (mapleleaf), as a model system. In addition to exhibiting dramatic lifespan variability among species, mussels are also highly imperiled and exhibit fragmentation by dams throughout the range of many species. Results indicated that, unless population size was small (<50 individuals) or lifespan short (<22 years), observing genetic divergence among populations was unlikely. Even if wild populations are isolated, observing population structure in long‐lived mussels from modern damming practices is unlikely because it takes longer for population structure to develop in these species than most North American dams have existed. Larger population sizes and longer lifespans increase the time needed for significant divergence to occur. This study helps illuminate the factors that influence genetic responses by populations to isolation and provides a useful model for conservation‐oriented research.