The crucial role of genome-wide genetic variation in conservation.

The unprecedented rate of extinction calls for efficient use of genetics to help conserve biodiversity. Several recent genomic and simulation-based studies have argued that the field of conservation biology has placed too much focus on conserving genome-wide genetic variation, and that the field should instead focus on managing the subset of functional genetic variation that is thought to affect fitness. Here, we critically evaluate the feasibility and likely benefits of this approach in conservation. We find that population genetics theory and empirical results show that conserving genome-wide genetic variation is generally the best approach to prevent inbreeding depression and loss of adaptive potential from driving populations toward extinction. Focusing conservation efforts on presumably functional genetic variation will only be feasible occasionally, often misleading, and counterproductive when prioritized over genome-wide genetic variation. Given the increasing rate of habitat loss and other environmental changes, failure to recognize the detrimental effects of lost genome-wide genetic variation on long-term population viability will only worsen the biodiversity crisis.

Genetic rescue remains underused for aiding recovery of federally listed vertebrates in the United States.

Restoring gene flow among fragmented populations is discussed as a potentially powerful management strategy that could reduce inbreeding depression and cause genetic rescue. Yet, examples of assisted migration for genetic rescue remain sparse in conservation, prompting several outspoken calls for its increased use in genetic management of fragmented populations. We set out to evaluate the extent to which this strategy is underused and to determine how many imperiled species would realistically stand to benefit from genetic rescue, focusing on federally threatened or endangered vertebrate species in the United States. We developed a "genetic rescue suitability index (GR index)" based on concerns about small population problems relative to risks associated with outbreeding depression and surveyed the literature for 222 species. We found that two-thirds of these species were good candidates for consideration of assisted migration for the purpose of genetic rescue according to our suitability index. Good candidate species spanned all taxonomic groups and geographic regions, though species with more missing data tended to score lower on the suitability index. While we do not recommend a prescriptive interpretation of our GR index, we used it here to establish that assisted migration for genetic rescue is an underused strategy. For example, we found in total, "genetic rescue" was only mentioned in 11 recovery plans and has only been implemented in 3 of the species we surveyed. A potential way forward for implementation of this strategy is incorporating genetic rescue as a priority in USFWS recovery documentation. In general, our results suggest that although not appropriate for all imperiled species, many more species stand to benefit from a conservation strategy of assisted migration for genetic rescue than those for which it has previously been considered or implemented.

Reproductive benefits associated with dispersal in headwater populations of Trinidadian guppies (Poecilia reticulata).

Theory suggests that the evolution of dispersal is balanced by its fitness costs and benefits, yet empirical evidence is sparse due to the difficulties of measuring dispersal and fitness in natural populations. Here, we use spatially explicit data from a multi-generational capture-mark-recapture study of two populations of Trinidadian guppies (Poecilia reticulata) along with pedigrees to test whether there are fitness benefits correlated with dispersal. Combining these ecological and molecular data sets allows us to directly measure the relationship between movement and reproduction. Individual dispersal was measured as the total distance moved by a fish during its lifetime. We analysed the effects of dispersal propensity and distance on a variety of reproductive metrics. We found that number of mates and number of offspring were positively correlated to dispersal, especially for males. Our results also reveal individual and environmental variation in dispersal, with sex, size, season, and stream acting as determining factors.

An experimental test of alternative population augmentation scenarios.

Human land use is fragmenting habitats worldwide and inhibiting dispersal among previously connected populations of organisms, often leading to inbreeding depression and reduced evolutionary potential in the face of rapid environmental change. To combat this augmentation of isolated populations with immigrants is sometimes used to facilitate demographic and genetic rescue. Augmentation with immigrants that are genetically and adaptively similar to the target population effectively increases population fitness, but if immigrants are very genetically or adaptively divergent, augmentation can lead to outbreeding depression. Despite well-cited guidelines for the best practice selection of immigrant sources, often only highly divergent populations remain, and experimental tests of these riskier augmentation scenarios are essentially nonexistent. We conducted a mesocosm experiment with Trinidadian guppies (Poecilia reticulata) to test the multigenerational demographic and genetic effects of augmenting 2 target populations with 3 types of divergent immigrants. We found no evidence of demographic rescue, but we did observe genetic rescue in one population. Divergent immigrant treatments tended to maintain greater genetic diversity, abundance, and hybrid fitness than controls that received immigrants from the source used to seed the mesocosms. In the second population, divergent immigrants had a slightly negative effect in one treatment, and the benefits of augmentation were less apparent overall, likely because this population started with higher genetic diversity and a lower reproductive rate that limited genetic admixture. Our results add to a growing consensus that gene flow can increase population fitness even when immigrants are more highly divergent and may help reduce uncertainty about the use of augmentation in conservation.

Fire Does Not Strongly Affect Genetic Diversity or Structure of a Common Treefrog in the Endangered Florida Scrub.

Fire regimes influence natural populations of organisms in diverse ways, via direct effects on population dynamics as well as indirect effects on habitat and ecosystem processes. Although many amphibian species have evolved to persist in fire-dependent ecosystems, the effects of fire on the genetic diversity of amphibian populations remain relatively unexplored. We examined how different aspects of fire history relate to population genetic diversity and structure of an abundant anuran, Hyla femoralis, in a large, intact area of Florida scrub containing hundreds of seasonally inundated ponds. Specifically, we assessed the overall population genetic structure and examined whether variation in time since fire, fire intensity, or historical fire frequency at breeding sites explained spatial variation in genetic diversity. Based on our sampling of 17 breeding aggregations within the 2,100-ha study area, neither recent nor frequent fire reduce genetic diversity or restrict connectivity among ponds for H. femoralis. Overall, mean effective population sizes were large (average range = 68-572). We detected a positive trend between effective population size (Ne) and average intensity of the most-recent fire, with this factor explaining 42% of the variation in Ne. Our results contrast with previous studies that consistently demonstrate strong relationships between fire history and population genetic structure of scrub-associated lizard species, suggesting that H. femoralis is resilient to a wide range of fire regimes. More generally, our study contributes to understanding the roles of life-history characteristics and environmental unpredictability in shaping organisms' responses to fire.

Adaptive divergence despite strong genetic drift: genomic analysis of the evolutionary mechanisms causing genetic differentiation in the island fox (Urocyon littoralis).

The evolutionary mechanisms generating the tremendous biodiversity of islands have long fascinated evolutionary biologists. Genetic drift and divergent selection are predicted to be strong on islands and both could drive population divergence and speciation. Alternatively, strong genetic drift may preclude adaptation. We conducted a genomic analysis to test the roles of genetic drift and divergent selection in causing genetic differentiation among populations of the island fox (Urocyon littoralis). This species consists of six subspecies, each of which occupies a different California Channel Island. Analysis of 5293 SNP loci generated using Restriction-site Associated DNA (RAD) sequencing found support for genetic drift as the dominant evolutionary mechanism driving population divergence among island fox populations. In particular, populations had exceptionally low genetic variation, small Ne (range = 2.1-89.7; median = 19.4), and significant genetic signatures of bottlenecks. Moreover, islands with the lowest genetic variation (and, by inference, the strongest historical genetic drift) were most genetically differentiated from mainland grey foxes, and vice versa, indicating genetic drift drives genome-wide divergence. Nonetheless, outlier tests identified 3.6-6.6% of loci as high FST outliers, suggesting that despite strong genetic drift, divergent selection contributes to population divergence. Patterns of similarity among populations based on high FST outliers mirrored patterns based on morphology, providing additional evidence that outliers reflect adaptive divergence. Extremely low genetic variation and small Ne in some island fox populations, particularly on San Nicolas Island, suggest that they may be vulnerable to fixation of deleterious alleles, decreased fitness and reduced adaptive potential.

Parallelism isn't perfect: could disease and flooding drive a life-history anomaly in Trinidadian guppies?

Nonparallel evolution, where independent populations occupy similar environments but show phenotypic differences, can uncover previously ignored selective factors. We investigated a nonparallelism in the life-history strategy of a Trinidadian guppy population, a system famous for parallel adaptation to differences in predation risk. We tested the hypothesis that high mortality drives an observed fast life-history pattern (i.e., earlier maturation and more frequent reproductive events) that is atypical for a low-predation environment. Using mark-recapture techniques, we compared neighboring low-predation populations, finding significantly higher mortality rates in the population with atypical life-history traits. Mortality was elevated during the wet season, when flooding was common. Moreover, individuals from the anomalous population were more likely to transition from healthy to infected disease states. Our results stand out against previous patterns observed in this system, indicating that higher mortality caused by disease and flooding may have selected for a faster life history. Thus, we highlight that even in systems famous for parallel adaptation, variation in selective pressures can result in nonparallel phenotypic evolution.

Pitfalls and windfalls of detecting demographic declines using population genetics in long-lived species.

Detecting recent demographic changes is a crucial component of species conservation and management, as many natural populations face declines due to anthropogenic habitat alteration and climate change. Genetic methods allow researchers to detect changes in effective population size (N e ) from sampling at a single timepoint. However, in species with long lifespans, there is a lag between the start of a decline in a population and the resulting decrease in genetic diversity. This lag slows the rate at which diversity is lost, and therefore makes it difficult to detect recent declines using genetic data. However, the genomes of old individuals can provide a window into the past, and can be compared to those of younger individuals, a contrast that may help reveal recent demographic declines. To test whether comparing the genomes of young and old individuals can help infer recent demographic bottlenecks, we use forward-time, individual-based simulations with varying mean individual lifespans and extents of generational overlap. We find that age information can be used to aid in the detection of demographic declines when the decline has been severe. When average lifespan is long, comparing young and old individuals from a single timepoint has greater power to detect a recent (within the last 50 years) bottleneck event than comparing individuals sampled at different points in time. Our results demonstrate how longevity and generational overlap can be both a hindrance and a boon to detecting recent demographic declines from population genomic data.

Pitfalls and windfalls of detecting demographic declines using population genetics in long-lived species.

Detecting recent demographic changes is a crucial component of species conservation and management, as many natural populations face declines due to anthropogenic habitat alteration and climate change. Genetic methods allow researchers to detect changes in effective population size (Ne) from sampling at a single timepoint. However, in species with long lifespans, there is a lag between the start of a decline in a population and the resulting decrease in genetic diversity. This lag slows the rate at which diversity is lost, and therefore makes it difficult to detect recent declines using genetic data. However, the genomes of old individuals can provide a window into the past, and can be compared to those of younger individuals, a contrast that may help reveal recent demographic declines. To test whether comparing the genomes of young and old individuals can help infer recent demographic bottlenecks, we use forward-time, individual-based simulations with varying mean individual lifespans and extents of generational overlap. We find that age information can be used to aid in the detection of demographic declines when the decline has been severe. When average lifespan is long, comparing young and old individuals from a single timepoint has greater power to detect a recent (within the last 50 years) bottleneck event than comparing individuals sampled at different points in time. Our results demonstrate how longevity and generational overlap can be both a hindrance and a boon to detecting recent demographic declines from population genomic data.

Population origin and heritable effects mediate road salt toxicity and thermal stress in an amphibian.

Human impacts on wild populations are numerous and extensive, degrading habitats and causing population declines across taxa. Though these impacts are often studied individually, wild populations typically face suites of stressors acting concomitantly, compromising the fitness of individuals and populations in ways poorly understood and not easily predicted by the effects of any single stressor. Developing understanding of the effects of multiple stressors and their potential interactions remains a critical challenge in environmental biology. Here, we focus on assessing the impacts of two prominent stressors associated with anthropogenic activities that affect many organisms across the planet - elevated salinity (e.g., from road de-icing salt) and temperature (e.g. from climate change). We examined a suite of physiological traits and components of fitness across populations of wood frogs originating from ponds that differ in their proximity to roads and thus their legacy of exposure to pollution from road salt. When experimentally exposed to road salt, wood frogs showed reduced survival (especially those from ponds adjacent to roads), divergent developmental rates, and reduced longevity. Family-level effects mediated these outcomes, but high salinity generally eroded family-level variance. When combined, exposure to both temperature and salt resulted in very low survival, and this effect was strongest in roadside populations. Taken together, these results suggest that temperature is an important stressor capable of exacerbating impacts from a prominent contaminant confronting many freshwater organisms in salinized habitats. More broadly, it appears likely that toxicity might often be underestimated in the absence of multi-stressor approaches.

Genome-wide diversity and habitat underlie fine-scale phenotypic differentiation in the rainbow darter (Etheostoma caeruleum).

Adaptation to environmental change requires that populations harbor the necessary genetic variation to respond to selection. However, dispersal-limited species with fragmented populations and reduced genetic diversity may lack this variation and are at an increased risk of local extinction. In freshwater fish species, environmental change in the form of increased stream temperatures places many cold-water species at-risk. We present a study of rainbow darters (Etheostoma caeruleum) in which we evaluated the importance of genetic variation on adaptive potential and determined responses to extreme thermal stress. We compared fine-scale patterns of morphological and thermal tolerance differentiation across eight sites, including a unique lake habitat. We also inferred contemporary population structure using genomic data and characterized the relationship between individual genetic diversity and stress tolerance. We found site-specific variation in thermal tolerance that generally matched local conditions and morphological differences associated with lake-stream divergence. We detected patterns of population structure on a highly local spatial scale that could not be explained by isolation by distance or stream connectivity. Finally, we showed that individual thermal tolerance was positively correlated with genetic variation, suggesting that sites with increased genetic diversity may be better at tolerating novel stress. Our results highlight the importance of considering intraspecific variation in understanding population vulnerability and stress response.

Rapture-ready darters: Choice of reference genome and genotyping method (whole-genome or sequence capture) influence population genomic inference in Etheostoma.

Researchers studying nonmodel organisms have an increasing number of methods available for generating genomic data. However, the applicability of different methods across species, as well as the effect of reference genome choice on population genomic inference, remain difficult to predict in many cases. We evaluated the impact of data type (whole-genome vs. reduced representation) and reference genome choice on data quality and on population genomic and phylogenomic inference across several species of darters (subfamily Etheostomatinae), a highly diverse radiation of freshwater fish. We generated a high-quality reference genome and developed a hybrid RADseq/sequence capture (Rapture) protocol for the Arkansas darter (Etheostoma cragini). Rapture data from 1,900 individuals spanning four darter species showed recovery of most loci across darter species at high depth and consistent estimates of heterozygosity regardless of reference genome choice. Loci with baits spanning both sides of the restriction enzyme cut site performed especially well across species. For low-coverage whole-genome data, choice of reference genome affected read depth and inferred heterozygosity. For similar amounts of sequence data, Rapture performed better at identifying fine-scale genetic structure compared to whole-genome sequencing. Rapture loci also recovered an accurate phylogeny for the study species and demonstrated high phylogenetic informativeness across the evolutionary history of the genus Etheostoma. Low cost and high cross-species effectiveness regardless of reference genome suggest that Rapture and similar sequence capture methods may be worthwhile choices for studies of diverse species radiations.

Genomic and Fitness Consequences of Genetic Rescue in Wild Populations.

Gene flow is an enigmatic evolutionary force because it can limit adaptation but may also rescue small populations from inbreeding depression [1-3]. Several iconic examples of genetic rescue-increased population growth caused by gene flow [4, 5]-have reversed population declines [6, 7]. However, concerns about outbreeding depression and maladaptive gene flow limit the use of human-mediated gene flow in conservation [8, 9]. Rescue effects of immigration through demographic and/or genetic mechanisms have received theoretical and empirical support, but studies that monitor initial and long-term effects of gene flow on individuals and populations in the wild are lacking. Here, we used individual-based mark-recapture, multigenerational pedigrees, and genomics to test the demographic and evolutionary consequences of manipulating gene flow in two isolated, wild Trinidadian guppy populations. Recipient and source populations originated from environments with different predation, flow, and resource regimes [10]. We documented 10-fold increases in population size following gene flow and found that, on average, hybrids lived longer and reproduced more than residents and immigrants. Despite overall genomic homogenization, alleles potentially associated with local adaptation were not entirely swamped by gene flow. Our results suggest that genetic rescue was caused not just by increasing individual genetic diversity, rather new genomic variation from immigrants combined with alleles from the recipient population resulted in highly fit hybrids and subsequent increases in population size. Contrary to the classic view of maladaptive gene flow, our study reveals conditions under which immigration can produce long-term fitness benefits in small populations without entirely swamping adaptive variation.

Geographical variation in genetic structure of an Atlantic Coastal Forest frog reveals regional differences in habitat stability.

Climatic oscillations throughout the Pleistocene combined with geological and topographic complexity resulted in extreme habitat heterogeneity along the Atlantic coast of Brazil. Inferring how these historic landscape patterns have structured the current diversity of the region's biota is important both for our understanding of the factors promoting diversification, as well as the conservation of this biodiversity hotspot. Here we evaluate potential historical scenarios of diversification in the Atlantic Coastal Forest of Brazil by investigating the population genetic structure of a frog endemic to the region. Using mitochondrial and nuclear sequences, we generated a Bayesian population-level phylogeny of the Thoropa miliaris species complex. We found deep genetic divergences among five geographically distinct clades. Southern clades were monophyletic and nested within paraphyletic northern clades. Analyses of historical demographic patterns suggest an overall north to south population expansion, likely associated with regional differences in habitat stability during the Pliocene and early Pleistocene. However, genetic structure among southern populations is less pronounced and likely represents more recent vicariant events resulting from Holocenic sea-level oscillations. Our analyses corroborate that the Atlantic Coastal Forest has been a biogeographically dynamic landscape and suggest that the high diversity of its fauna and flora resulted from a combination of climatic and geologic events from the Pliocene to the present.

Does gene flow aggravate or alleviate maladaptation to environmental stress in small populations?

Environmental change can expose populations to unfamiliar stressors, and maladaptive responses to those stressors may result in population declines or extirpation. Although gene flow is classically viewed as a cause of maladaptation, small and isolated populations experiencing high levels of drift and little gene flow may be constrained in their evolutionary response to environmental change. We provide a case study using the model Trinidadian guppy system that illustrates the importance of considering gene flow and genetic drift when predicting (mal)adaptive response to acute stress. We compared population genomic patterns and acute stress responses of inbred guppy populations from headwater streams either with or without a recent history of gene flow from a more diverse mainstem population. Compared to "no-gene flow" analogues, we found that populations with recent gene flow showed higher genomic variation and increased stress tolerance-but only when exposed to a stress familiar to the mainstem population (heat shock). All headwater populations showed similar responses to a familiar stress in headwater environments (starvation) regardless of gene flow history, whereas exposure to an entirely unfamiliar stress (copper sulfate) showed population-level variation unrelated to environment or recent evolutionary history. Our results suggest that (mal)adaptive responses to acutely stressful environments are determined in part by recent evolutionary history and in part by previous exposure. In some cases, gene flow may provide the variation needed to persist, and eventually adapt, in the face of novel stress.

Recent evolutionary history predicts population but not ecosystem-level patterns.

In the face of rapid anthropogenic environmental change, it is increasingly important to understand how ecological and evolutionary interactions affect the persistence of natural populations. Augmented gene flow has emerged as a potentially effective management strategy to counteract negative consequences of genetic drift and inbreeding depression in small and isolated populations. However, questions remain about the long-term impacts of augmented gene flow and whether changes in individual and population fitness are reflected in ecosystem structure, potentiating eco-evolutionary feedbacks. In this study, we used Trinidadian guppies (Poecilia reticulata) in experimental outdoor mesocosms to assess how populations with different recent evolutionary histories responded to a scenario of severe population size reduction followed by expansion in a high-quality environment. We also investigated how variation in evolutionary history of the focal species affected ecosystem dynamics. We found that evolutionary history (i.e., gene flow vs. no gene flow) consistently predicted variation in individual growth. In addition, gene flow led to faster population growth in populations from one of the two drainages, but did not have measurable impacts on the ecosystem variables we measured: zooplankton density, algal growth, and decomposition rates. Our results suggest that benefits of gene flow may be long-term and environment-dependent. Although small in replication and duration, our study highlights the importance of eco-evolutionary interactions in determining population persistence and sets the stage for future work in this area.

The Exciting Potential and Remaining Uncertainties of Genetic Rescue.

Restoring gene flow into small, isolated populations can alleviate genetic load and decrease extinction risk (i.e., genetic rescue), yet gene flow is rarely augmented as a conservation strategy. Due to this discrepancy between opportunity and action, a recent call was made for widespread genetic rescue attempts. However, several aspects of augmenting gene flow are poorly understood, including the magnitude and duration of beneficial effects and when deleterious effects are likely to occur. We discuss the remaining uncertainties of genetic rescue in order to promote and direct future research and to hasten progress toward implementing this potentially powerful conservation strategy on a broader scale.

Sex, Mitochondria, and Genetic Rescue.

Genetic rescue is a potentially effective management tool to offset the effects of reduced genetic diversity in imperiled populations. However, implementation requires complex choices. Here we address the consequences of introducing males versus females, highlighting the possibility that introduced females might lead to maladapted mitonuclear genomes and reduced offspring fitness.

Gene flow from an adaptively divergent source causes rescue through genetic and demographic factors in two wild populations of Trinidadian guppies.

Genetic rescue, an increase in population growth owing to the infusion of new alleles, can aid the persistence of small populations. Its use as a management tool is limited by a lack of empirical data geared toward predicting effects of gene flow on local adaptation and demography. Experimental translocations provide an ideal opportunity to monitor the demographic consequences of gene flow. In this study we take advantage of two experimental introductions of Trinidadian guppies to test the effects of gene flow on downstream native populations. We individually marked guppies from the native populations to monitor population dynamics for 3 months before and 26 months after gene flow. We genotyped all individuals caught during the first 17 months at microsatellite loci to classify individuals by their genetic ancestry: native, immigrant, F1 hybrid, F2 hybrid, or backcross. Our study documents a combination of demographic and genetic rescue over multiple generations under fully natural conditions. Within both recipient populations, we found substantial and long-term increases in population size that could be attributed to high survival and recruitment caused by immigration and gene flow from the introduction sites. Our results suggest that low levels of gene flow, even from a divergent ecotype, can provide a substantial demographic boost to small populations, which may allow them to withstand environmental stochasticity.