Dynamics of genetic rescue in inbred Drosophila melanogaster populations

The evolutionary dynamics of local adaptations under genetic rescue is determined by mutational load and polygenicity

Inbred populations often suffer from increased mutational load and reduced fitness due to lower efficacy of purifying selection in groups with small effective population sizes. Genetic rescue (GR) is a conservation tool that is studied and deployed with the aim of increasing the fitness of such inbred populations by assisted migration of individuals from closely related outbred populations. The success of GR depends on several factors-such as their demographic history and distribution of dominance effects of mutations-that may vary across populations. While we understand the impact of these factors on the dynamics of GR, their impact on local adaptations remains unclear. To this end, we conduct a population genetics simulation study to evaluate the impact of trait complexity (Mendelian vs. polygenic), dominance effects, and demographic history on the efficacy of GR. We find that the impact on local adaptations depends highly on the mutational load at the time of GR, which is in turn shaped dynamically by interactions between demographic history and dominance effects of deleterious variation. Over time local adaptations are generally restored post-GR, though in the short term they are often compromised in the process of purging deleterious variation. We also show that while local adaptations are almost always fully restored, the degree to which ancestral genetic variation affecting the trait is replaced by donor variation can vary drastically and is especially high for complex traits. Our results provide insights on the impact of GR on trait evolution and considerations for the practical implementation of GR.

Immigration allows population persistence and maintains genetic diversity despite an attempted experimental extinction

Widespread fragmentation and degradation of habitats make organisms increasingly vulnerable to declines in population size. Immigration is a key process potentially affecting the rescue and persistence of populations in the face of such pressures. Field research addressing severe demographic declines in the context of immigration among interconnected local populations is limited owing to difficulties in detecting such demographic events and the need for long-term monitoring of populations. In a 17-subpopulation metapopulation of the butterfly, Parnassius smintheus, all adults observed in two adjacent patches were removed over eight consecutive generations. Despite this severe and long-term reduction in survival and reproduction, the targeted populations did not go extinct. Here, we use genetic data to assess the role of immigration versus in situ reproduction in allowing the persistence of these populations. We genotyped 471 samples collected from the targeted populations throughout the removal experiment at 152 single nucleotide polymorphisms. We found no reduction in the genetic diversity of the targeted populations over time, but a decrease in the number of loci in Hardy-Weinberg equilibrium, consistent with a high level of immigration from multiple surrounding populations. Our results highlight the role of connectivity and movement in making metapopulations resilient to even severe and protracted localized population reductions.

Population demographic history and evolutionary rescue: Influence of a bottleneck event

Rapid environmental change presents a significant challenge to the persistence of natural populations. Rapid adaptation that increases population growth, enabling populations that declined following severe environmental change to grow and avoid extinction, is called evolutionary rescue. Numerous studies have shown that evolutionary rescue can indeed prevent extinction. Here, we extend those results by considering the demographic history of populations. To evaluate how demographic history influences evolutionary rescue, we created 80 populations of red flour beetle, Tribolium castaneum, with three classes of demographic history: diverse populations that did not experience a bottleneck, and populations that experienced either an intermediate or a strong bottleneck. We subjected these populations to a new and challenging environment for six discrete generations and tracked extinction and population size. Populations that did not experience a bottleneck in their demographic history avoided extinction entirely, while more than 20% of populations that experienced an intermediate or strong bottleneck went extinct. Similarly, among the extant populations at the end of the experiment, adaptation increased the growth rate in the novel environment the most for populations that had not experienced a bottleneck in their history. Taken together, these results highlight the importance of considering the demographic history of populations to make useful and effective conservation decisions and management strategies for populations experiencing environmental change that pushes them toward extinction.

Challenges in quantifying genome erosion for conservation

Massive defaunation and high extinction rates have become characteristic of the Anthropocene. Genetic effects of population decline can lead populations into an extinction vortex, where declining populations show lower genetic fitness, in turn leading to lower populations still. The lower genetic fitness in a declining population due to a shrinking gene pool is known as genetic erosion. Three different types of genetic erosion are highlighted in this review: overall homozygosity, genetic load and runs of homozygosity (ROH), which are indicative of inbreeding. The ability to quantify genetic erosion could be a very helpful tool for conservationists, as it can provide them with an objective, quantifiable measure to use in the assessment of species at risk of extinction. The link between conservation status and genetic erosion should become more apparent. Currently, no clear correlation can be observed between the current conservation status and genetic erosion. However, the high quantities of genetic erosion in wild populations, especially in those species dealing with habitat fragmentation and habitat decline, may be early signs of deteriorating populations. Whole genome sequencing data is the way forward to quantify genetic erosion. Extra screening steps for genetic load and hybridization can be included, since they could potentially have great impact on population fitness. This way, the information yielded from genetic sequence data can provide conservationists with an objective genetic method in the assessment of species at risk of extinction. However, the great complexity of genome erosion quantification asks for consensus and bridging science and its applications, which remains challenging.

Sustained positive consequences of genetic rescue of fitness and behavioural traits in inbred populations of Drosophila melanogaster

One solution to alleviate the detrimental genetic effects associated with reductions in population size and fragmentation is to introduce immigrants from other populations. While the effects of this genetic rescue on fitness traits are fairly well known, it is less clear to what extent inbreeding depression and subsequent genetic rescue affect behavioural traits. In this study, replicated crosses between inbred lines of Drosophila melanogaster were performed in order to investigate the effects of inbreeding and genetic rescue on egg-to-adult viability and negative geotaxis behaviour-a locomotor response used to measure, e.g. the effects of physiological ageing. Transgenerational effects of outcrossing were investigated by examining the fitness consequences in both the F₁ and F₄  generation. The majority of inbred lines showed evidence for inbreeding depression for both egg-to-adult viability and behavioural performance (95% and 66% of lines, respectively), with inbreeding depression being more pronounced for viability compared with the locomotor response. Subsequent outcrossing with immigrants led to an alleviation of the negative effects for both viability and geotaxis response resulting in inbred lines being similar to the outbred controls, with beneficial effects persisting from F₁ to F₄ . Overall, the results clearly show that genetic rescue can provide transgenerational rescue of small, inbred populations by rapidly improving population fitness components. Thus, we show that even the negative effects of inbreeding on behaviour, similar to that of neurodegeneration associated with physiological ageing, can be reversed by genetic rescue.

Reviewing the consequences of genetic purging on the success of rescue programs

Genetic rescue is increasingly considered a promising and underused conservation strategy to reduce inbreeding depression and restore genetic diversity in endangered populations, but the empirical evidence supporting its application is limited to a few generations. Here we discuss on the light of theory the role of inbreeding depression arising from partially recessive deleterious mutations and of genetic purging as main determinants of the medium to long-term success of rescue programs. This role depends on two main predictions: (1) The inbreeding load hidden in populations with a long stable demography increases with the effective population size; and (2) After a population shrinks, purging tends to remove its (partially) recessive deleterious alleles, a process that is slower but more efficient for large populations than for small ones. We also carry out computer simulations to investigate the impact of genetic purging on the medium to long term success of genetic rescue programs. For some scenarios, it is found that hybrid vigor followed by purging will lead to sustained successful rescue. However, there may be specific situations where the recipient population is so small that it cannot purge the inbreeding load introduced by migrants, which would lead to increased fitness inbreeding depression and extinction risk in the medium to long term. In such cases, the risk is expected to be higher if migrants came from a large non-purged population with high inbreeding load, particularly after the accumulation of the stochastic effects ascribed to repeated occasional migration events. Therefore, under the specific deleterious recessive mutation model considered, we conclude that additional caution should be taken in rescue programs. Unless the endangered population harbors some distinctive genetic singularity whose conservation is a main concern, restoration by continuous stable gene flow should be considered, whenever feasible, as it reduces the extinction risk compared to repeated occasional migration and can also allow recolonization events.

Effects of genetic distance on heterosis in a Drosophila melanogaster model system

Habitat fragmentation and small population sizes can lead to inbreeding and loss of genetic variation, which can potentially cause inbreeding depression and decrease the ability of populations to adapt to altered environmental conditions. One solution to these genetic problems is the implementation of genetic rescue, which re-establishes gene flow between separated populations. Similar techniques are being used in animal and plant breeding to produce superior production animals and plants. To optimize fitness benefits in genetic rescue programs and to secure high yielding domestic varieties in animal and plant breeding, knowledge on the genetic relatedness of populations being crossed is imperative. In this study, we conducted replicated crosses between isogenic Drosophila melanogaster lines from the Drosophila Genetic Reference Panel. We grouped lines in two genetic distance groups to study the effect of genetic divergence between populations on the expression of heterosis in two fitness components; starvation resistance and reproductive output. We further investigated the transgenerational effects of outcrossing by investigating the fitness consequences in both the F₁- and the F₃-generations. High fitness enhancements were observed in hybrid offspring compared to parental lines, especially for reproductive output. However, the level of heterosis declined from the F₁- to the F₃-generation. Generally, genetic distance did not have strong impact on the level of heterosis detected, although there were exceptions to this pattern. The best predictor of heterosis was performance of parental lines with poorly performing parental lines showing higher hybrid vigour when crossed, i.e. the potential for heterosis was proportional to the level of inbreeding depression. Overall, our results show that outcrossing can have very strong positive fitness consequences for genetically depauperate populations.

Locally adapted traits maintained in the face of high gene flow

Gene flow between phenotypically divergent populations can disrupt local adaptation or, alternatively, may stimulate adaptive evolution by increasing genetic variation. We capitalised on historical Trinidadian guppy transplant experiments to test the phenotypic effects of increased gene flow caused by replicated introductions of adaptively divergent guppies, which were translocated from high- to low-predation environments. We sampled two native populations prior to the onset of gene flow, six historic introduction sites, introduction sources and multiple downstream points in each basin. Extensive gene flow from introductions occurred in all streams, yet adaptive phenotypic divergence across a gradient in predation level was maintained. Descendants of guppies from a high-predation source site showed high phenotypic similarity with native low-predation guppies in as few as ~12 generations after gene flow, likely through a combination of adaptive evolution and phenotypic plasticity. Our results demonstrate that locally adapted phenotypes can be maintained despite extensive gene flow from divergent populations.

Effects of inbreeding on fitness-related traits in a small isolated moose population

Inbreeding can affect fitness-related traits at different life history stages and may interact with environmental variation to induce even larger effects. We used genetic parentage assignment based on 22 microsatellite loci to determine a 25 year long pedigree for a newly established island population of moose with 20–40 reproducing individuals annually. We used the pedigree to calculate individual inbreeding coefficients and examined for effects of individual inbreeding (f) and heterozygosity on fitness-related traits. We found negative effects of f on birth date, calf body mass and twinning rate. The relationship between f and calf body mass and twinning rate were found to be separate but weaker after accounting for birth date. We found no support for an inbreeding effect on the age-specific lifetime reproductive success of females. The influence of f on birth date was related to climatic conditions during the spring prior to birth, indicating that calves with a low f were born earlier after a cold spring than calves with high f. In years with a warm spring, calf f did not affect birth date. The results suggest that severe inbreeding in moose has both indirect effects on fitness through delayed birth and lower juvenile body mass, as well as separate direct effects, as there still was a significant relationship between f and twinning rate after accounting for birth date and body mass as calf. Consequently, severe inbreeding as found in the study population may have consequences for population growth and extinction risk.

Genomic and environmental selection patterns in two distinct lettuce crop-wild hybrid crosses

Genomic selection patterns and hybrid performance influence the chance that crop (trans)genes can spread to wild relatives. We measured fitness(-related) traits in two different field environments employing two different crop–wild crosses of lettuce. We performed quantitative trait loci (QTL) analyses and estimated the fitness distribution of early- and late-generation hybrids. We detected consistent results across field sites and crosses for a fitness QTL at linkage group 7, where a selective advantage was conferred by the wild allele. Two fitness QTL were detected on linkage group 5 and 6, which were unique to one of the crop–wild crosses. Average hybrid fitness was lower than the fitness of the wild parent, but several hybrid lineages outperformed the wild parent, especially in a novel habitat for the wild type. In early-generation hybrids, this may partly be due to heterosis effects, whereas in late-generation hybrids transgressive segregation played a major role. The study of genomic selection patterns can identify crop genomic regions under negative selection across multiple environments and cultivar–wild crosses that might be applicable in transgene mitigation strategies. At the same time, results were cultivar-specific, so that a case-by-case environmental risk assessment is still necessary, decreasing its general applicability.

The benefits of interpopulation hybridization diminish with increasing divergence of small populations

Interpopulation hybridization can increase the viability of small populations suffering from inbreeding and genetic drift, but it can also result in outbreeding depression. The outcome of hybridization can depend on various factors, including the level of genetic divergence between the populations, and the number of source populations. Furthermore, the effects of hybridization can change between generations following the hybridization. We studied the effects of population divergence (low vs. high level of divergence) and the number of source populations (two vs. four source populations) on the viability of hybrid populations using experimental Drosophila littoralis populations. Population viability was measured for seven generations after hybridization as proportion of populations facing extinction and as per capita offspring production. Hybrid populations established at the low level of population divergence were more viable than the inbred source populations and had higher offspring production than the large control population. The positive effects of hybridization lasted for the seven generations. In contrast, at the high level of divergence, the viability of the hybrid populations was not significantly different from the inbred source populations, and offspring production in the hybrid populations was lower than in the large control population. The number of source populations did not have a significant effect at either low or high level of population divergence. The study shows that the benefits of interpopulation hybridization may decrease with increasing divergence of the populations, even when the populations share identical environmental conditions. We discuss the possible genetic mechanisms explaining the results and address the implications for conservation of populations.

Genetic erosion impedes adaptive responses to stressful environments

Biodiversity is increasingly subjected to human-induced changes of the environment. To persist, populations continually have to adapt to these often stressful changes including pollution and climate change. Genetic erosion in small populations, owing to fragmentation of natural habitats, is expected to obstruct such adaptive responses: (i) genetic drift will cause a decrease in the level of adaptive genetic variation, thereby limiting evolutionary responses; (ii) inbreeding and the concomitant inbreeding depression will reduce individual fitness and, consequently, the tolerance of populations to environmental stress. Importantly, inbreeding generally increases the sensitivity of a population to stress, thereby increasing the amount of inbreeding depression. As adaptation to stress is most often accompanied by increased mortality (cost of selection), the increase in the ‘cost of inbreeding’ under stress is expected to severely hamper evolutionary adaptive processes. Inbreeding thus plays a pivotal role in this process and is expected to limit the probability of genetically eroded populations to successfully adapt to stressful environmental conditions. Consequently, the dynamics of small fragmented populations may differ considerably from large nonfragmented populations. The resilience of fragmented populations to changing and deteriorating environments is expected to be greatly decreased. Alleviating inbreeding depression, therefore, is crucial to ensure population persistence.

Analysis of the effects of early nutritional environment on inbreeding depression in Drosophila melanogaster

The impact of nutritional deficiencies early in life in determining life-history variation in organisms is well recognized. The negative effects of inbreeding on fitness are also well known. Contrary to studies on vertebrates, studies on invertebrates are not consistent with the observation that inbreeding compromises resistance to parasites and pathogens. In this study, we investigated the effect of early nutrition on the magnitude of inbreeding depression in development time, adult body size and adult resistance to the bacterium Serratia marcescens in Drosophila melanogaster. We found that early nutritional environment had no effect on the magnitude of inbreeding depression in development time or adult body size but may have played a small role in adult resistance to the bacterial infection. Estimates of heritabilities for development time under the poor nutritional environment were larger than those measured under the standard nutritional conditions.