Modeling problems in conservation genetics using captive Drosophila populations: Rapid genetic adaptation to captivity

Long-term captive breeding programs for endangered species generally aim to preserve the option of release back into the wild. However, the success of re-release programs will be jeopardized if there is significant genetic adaptation to the captive environment. Since it is difficult to study this problem in rare and endangered species, a convenient laboratory animal model is required. The reproductive fitness of a large population of Drosophila melanogaster maintained in captivity for 12 months was compared with that of a recently caught wild population from the same locality. The competitive index measure of reproductive fitness for the captive population was twice that of the recently caught wild population, the difference being highly significant. Natural selection over approximately eight generations in captivity has caused rapid genetic adaptation. Captive breeding strategies for endangered species should minimize adaptation to captivity in populations destined for reintroduction into the wild. A framework for predicting the impact of factors on the rate of genetic adaptation to captivity is suggested. Equalization of family sizes is predicted to approximately halve the rate of genetic adaptation. Introduction of genes from the wild, increasing the generation interval, using captive environments close to those in the wild and achieving low mortality rates are all expected to slow genetic adaptation to captivity. Many of these procedures are already recommended for other reasons. © 1992 Wiley-Liss, Inc.     

Single large or several small? Population fragmentation in the captive management of endangered species

Captive populations of endangered species are typically maintained effectively as single random-mating populations by translocating individuals between institutions. Genetic, disease, and cost considerations, however, suggest that this may not be the optimal management strategy. Genetic theory predicts that a pooled population derived from several small isolated populations will have greater genetic diversity, less inbreeding, and less genetic adaptation to captivity than a single large population of equivalent total size, provided there are no population extinctions. These predictions were tested using populations of Drosophila with effective size comparisons of 50 vs. 2 × 25; 100 vs. 2 × 50 vs. 4 × 25, and 500 vs. 2 × 250 vs. 4 × 100 + 2 × 50 vs. 8 × 25 + 6 × 50. Populations were maintained at the indicated sizes as separate pedigreed populations for 50 generations. The several small treatments were subsequently pooled and maintained for eight to 10 generations prior to determination of fitness and evolutionary potential. Several small populations (pooled), when compared to single large populations of equivalent total size, were found to have lower average inbreeding coefficients, significantly higher reproductive fitness under competitive conditions, similar fitness under benign captive conditions, higher genetic diversity, and equivalent evolutionary potential. Trends favored the several small (pooled) populations in all comparisons at population sizes of 50 and 100. We recommend that endangered species in captivity be maintained as several small populations, with occasional exchange of genetic material. This has genetic benefits over current management both in captivity and especially for reintroductions, as well as reducing translocation costs and risks of disease transfer. Zoo Biol 17:467–480, 1998. © 1998 Wiley-Liss, Inc.     

Rapid genetic deterioration in captive populations: Causes and conservation implications

Many species require captive breeding to ensuretheir survival. The eventual aim of suchprograms is usually to reintroduce the speciesinto the wild. Populations in captivitydeteriorate due to inbreeding depression, lossof genetic diversity, accumulation of newdeleterious mutations and genetic adaptationsto captivity that are deleterious in the wild.However, there is little evidence on themagnitude of these problems. We evaluatedchanges in reproductive fitness in populationsof Drosophila maintained under benigncaptive conditions for 50 generations witheffective population sizes of 500 (2replicates), 250 (3), 100 (4), 50 (6) and 25(8). At generation 50, fitness in the benigncaptive conditions was reduced in smallpopulations due to inbreeding depression andincreased in some of the large populations dueto modest genetic adaptation. When thepopulations were moved to `wild' conditions,all 23 populations showed a marked decline(64–86%percnt;) in reproductive fitness compared tocontrols. Reproductive fitness showed acurvilinear relationship with population size,the largest and smallest population sizetreatments being the worst. Genetic analysesindicated that inbreeding depression andgenetic adaptation were responsible for thegenetic deterioration in `wild' fitness.Consequently, genetic deterioration incaptivity is likely to be a major problem whenlong-term captive bred populations ofendangered species are returned to the wild. Aregime involving fragmentation of captivepopulations of endangered species is suggestedto minimize the problems.     

The efficiency of close inbreeding to reduce genetic adaptation to captivity

Although ex situ conservation is indispensable for thousands of species, captive breeding is associated with negative genetic changes: loss of genetic variance and genetic adaptation to captivity that is deleterious in the wild. We used quantitative genetic individual-based simulations to model the effect of genetic management on the evolution of a quantitative trait and the associated fitness of wild-born individuals that are brought to captivity. We also examined the feasibility of the breeding strategies under a scenario of a large number of loci subject to deleterious mutations. We compared two breeding strategies: repeated half-sib mating and a method of minimizing mean coancestry (referred to as gc/mc). Our major finding was that half-sib mating is more effective in reducing genetic adaptation to captivity than the gc/mc method. Moreover, half-sib mating retains larger allelic and adaptive genetic variance. Relative to initial standing variation, the additive variance of the quantitative trait increased under half-sib mating during the sojourn in captivity. Although fragmentation into smaller populations improves the efficiency of the gc/mc method, half-sib mating still performs better in the scenarios tested. Half-sib mating shows two caveats that could mitigate its beneficial effects: low heterozygosity and high risk of extinction when populations are of low fecundity and size and one of the following conditions are met: (i) the strength of selection in captivity is comparable with that in the wild, (ii) deleterious mutations are numerous and only slightly deleterious. Experimental validation of half-sib mating is therefore needed for the advancement of captive breeding programs.     

Evolution of Peromyscus leucopus Mice in Response to a Captive Environment

Many wildlife species are propagated in captivity as models for behavioral, physiological, and genetic research or to provide assurance populations to protect threatened species. However, very little is known about how animals evolve in the novel environment of captivity. The histories of most laboratory strains are poorly documented, and protected populations of wildlife species are usually too small and too short-term to allow robust statistical analysis. To document the evolutionary change in captive breeding programs, we monitored reproduction and behavior across 18 generations in six experimental populations of Peromyscus leucopus mice started from a common set of 20 wild-caught founders. The mice were propagated under three breeding protocols: a strategy to retain maximal genetic diversity, artificial selection against stereotypic behaviors that were hypothesized to reflect poor adaptation to captivity, and random bred controls. Two replicates were maintained with each protocol, and inter-replicate crosses at generations 19 and 20 were used to reverse accumulated inbreeding. We found that one of the stereotypic behaviors (repetitive flipping) was positively associated with reproductive fitness, while the other (gnawing) was relatively invariant. Selection to reduce these stereotypic behaviors caused marked reduction in reproduction, and populations not under artificial selection to reduce these behaviors responded with large increases in flipping. In non-selected populations, there was rapid evolution toward much higher proportion of pairs breeding and more rapid conception. Litter size, pup survival, and weaning mass all declined slowly, to the extent that would be predicted based on inbreeding depression. Inter-crossing between replicate populations reversed these declines in fitness components but did not reverse the changes in behavior or the accelerated breeding. These findings indicate that adaptation to captivity can be rapid, affecting reproductive patterns and behaviors, even under breeding protocols designed to minimize the rate of genetic change due to random drift and inadvertent selection.     

Adaptations to Captivity in the Butterfly Pieris brassicae (L.) and the Implications for Ex situ Conservation

Captive breeding has been suggested as a method of conserving many threatened vertebrates, and is increasingly being proposed as a valuable conservation strategy for invertebrates. Potential genetic problems associated with ex situ conservation are widely recognized, but a further issue has received less attention: the possibility that populations will undergo adaptation to the captive environment, rendering them less well adapted to survival in the wild. We investigated six traits related to dispersal and reproduction in a culture of the large white butterfly Pieris brassicae (L.), that had been captive for c. 100–150 generations, and in recently wild stock reared simultaneously in a common environment. Individuals in the captive culture were heavier, with smaller wings and lower wing aspect ratios. Females from the captive culture laid many more eggs in cage experiments, and had higher ovary mass at the time of peak egg production. These differences are consistent with adaptation to captive conditions. Over time, similar evolutionary changes may affect invertebrates reared in ex situ conservation programmes, decreasing the likelihood that these species can be re-established in the wild. Although the timescale over which most vertebrates are likely to adapt to captivity is longer, and the traits involved will be different, invertebrates like P. brassicae may also provide a model of potential problems in long-term ex situ conservation programmes for both invertebrates and vertebrates. We suggest that measures to reduce or slow adaptation to captivity should be introduced alongside measures to reduce deleterious genetic effects in captive populations.     

Quantitative genetics in conservation biology

Most of the major genetic concerns in conservation biology, including inbreeding depression, loss of evolutionary potential, genetic adaptation to captivity and outbreeding depression, involve quantitative genetics. Small population size leads to inbreeding and loss of genetic diversity and so increases extinction risk. Captive populations of endangered species are managed to maximize the retention of genetic diversity by minimizing kinship, with subsidiary efforts to minimize inbreeding. There is growing evidence that genetic adaptation to captivity is a major issue in the genetic management of captive populations of endangered species as it reduces reproductive fitness when captive populations are reintroduced into the wild. This problem is not currently addressed, but it can be alleviated by deliberately fragmenting captive populations, with occasional exchange of immigrants to avoid excessive inbreeding. The extent and importance of outbreeding depression is a matter of controversy. Currently, an extremely cautious approach is taken to mixing populations. However, this cannot continue if fragmented populations are to be adequately managed to minimize extinctions. Most genetic management recommendations for endangered species arise directly, or indirectly, from quantitative genetic considerations.     

Minimizing kinship in captive breeding programs

Captive populations of endangered species are managed to preserve genetic diversity and retain reproductive fitness. Minimizing kinship (MK) has been predicted to maximize the retention of gene diversity in pedigreed populations with unequal founder representation. MK was compared with maximum avoidance of inbreeding (MAI) and random choice of parents (RAND) using Drosophila melanogaster. Forty replicate populations of each treatment were initiated with unequal founder representation and managed for four generations. MK retained significantly more gene diversity and allelic diversity based on six microsatellite loci and seven allozyme loci than MAI or RAND. Reproductive fitness under both benign and competitive conditions did not differ significantly among treatments. Of the methods considered, MK is currently the best available for the genetic management of captive populations. Zoo Biol 16:377–389, 1997. © 1997 Wiley-Liss, Inc.     

Captive Breeding Does Not Alter Brain Volume in a Marsupial Over a Few Generations

Captive breeding followed by reintroduction to the wild is a common component of conservation management plans for various taxa. Although it is commonly used, captive breeding can result in morphological changes, including brain size decrease. Brain size reduction has been associated with behavioral changes in domestic animals, and such changes may negatively influence reintroduction success of captive‐bred animals. Many marsupials are currently bred in captivity for reintroduction, yet the impacts of captive breeding on brain size have never been studied in this taxa. We investigated the impacts of a few generations (2–7) of captive breeding on brain volume in the stripe‐faced dunnart (Sminthopsis macroura), and found that captive breeding in a relatively enriched environment did not cause any changes in brain volume. Nonetheless, we advocate that great care be taken to provide suitable husbandry conditions and to minimize the number of captive generations if marsupial reintroduction programs are to be successful. Zoo Biol 31:82;–86, 2012. © 2011 Wiley Periodicals, Inc.     

Selection and genetic drift in captive versus wild populations: an assessment of neutral and adaptive (MHC-linked) genetic variation in wild and hatchery brown trout (<Emphasis Type="Italic">Salmo trutta</Emphasis>) populations

Captive bred individuals are often released into natural environments to supplement resident populations. Captive bred salmonid fishes often exhibit lower survival rates than their wild brethren and stocking measures may have a negative influence on the overall fitness of natural populations. Stocked fish often stem from a different evolutionary lineage than the resident population and thus may be maladapted for life in the wild, but this phenomenon has also been linked to genetic changes that occur in captivity. In addition to overall loss of genetic diversity via captive breeding, adaptation to captivity has become a major concern. Altered selection pressure in captivity may favour alleles at adaptive loci like the Major Histocompatibility Complex (MHC) that are maladaptive in natural environments. We investigated neutral and MHC-linked genetic variation in three autochthonous and three hatchery populations of Austrian brown trout (Salmo trutta). We confirm a positive selection pressure acting on the MHC II β locus, whereby the signal for positive selection was stronger in hatchery versus wild populations. Additionally, diversity at the MHC II β locus was higher, and more uniform among hatchery samples compared to wild populations, despite equal levels of diversity at neutral loci. We postulate that this stems from a combination of stronger genetic drift and a weakening of positive selection at this locus in wild populations that already have well adapted alleles for their specific environments.     

Genetic adaptation to captivity in species conservation programs

As wild environments are often inhospitable, many species have to be captive-bred to save them from extinction. In captivity, species adapt genetically to the captive environment and these genetic adaptations are overwhelmingly deleterious when populations are returned to wild environments. I review empirical evidence on (i) the genetic basis of adaptive changes in captivity, (ii) factors affecting the extent of genetic adaptation to captivity, and (iii) means for minimizing its deleterious impacts. Genetic adaptation to captivity is primarily due to rare alleles that in the wild were deleterious and partially recessive. The extent of adaptation to captivity depends upon selection intensity, genetic diversity, effective population size and number of generation in captivity, as predicted by quantitative genetic theory. Minimizing generations in captivity provides a highly effective means for minimizing genetic adaptation to captivity, but is not a practical option for most animal species. Population fragmentation and crossing replicate captive populations provide practical means for minimizing the deleterious effects of genetic adaptation to captivity upon populations reintroduced into the wild. Surprisingly, equalization of family sizes reduces the rate of genetic adaptation, but not the deleterious impacts upon reintroduced populations. Genetic adaptation to captivity is expected to have major effects on reintroduction success for species that have spent many generations in captivity. This issue deserves a much higher priority than it is currently receiving.     

Conservation Genetics of Threatened Hippocampus guttulatus in Vulnerable Habitats in NW Spain: Temporal and Spatial Stability of Wild Populations with Flexible Polygamous Mating System in Captivity

This study was focused on conservation genetics of threatened Hippocampus guttulatus on the Atlantic coast of NW Iberian Peninsula. Information about spatial structure and temporal stability of wild populations was obtained based on microsatellite markers, and used for monitoring a captive breeding program firstly initiated in this zone at the facilities of the Institute of Marine Research (Vigo, Spain). No significant major genetic structure was observed regarding the biogeographical barrier of Cape Finisterre. However, two management units under continuous gene flow are proposed based on the allelic differentiation between South-Atlantic and Cantabrian subpopulations, with small to moderate contemporary effective size based on single-sample methods. Temporal stability was observed in South-Atlantic population samples of H. guttulatus for the six-year period studied, suggesting large enough effective population size to buffer the effects of genetic drift within the time frame of three generations. Genetic analysis of wild breeders and offspring in captivity since 2009 allowed us to monitor the breeding program founded in 2006 in NW Spain for this species. Similar genetic diversity in the renewed and founder broodstock, regarding the wild population of origin, supports suitable renewal and rearing processes to maintain genetic variation in captivity. Genetic parentage proved single-brood monogamy in the wild and in captivity, but flexible short- and long-term mating system under captive conditions, from strict monogamy to polygamy within and/or among breeding seasons. Family analysis showed high reproductive success in captivity under genetic management assisted by molecular relatedness estimates to avoid inbreeding. This study provides genetic information about H. guttulatus in the wild and captivity within an uncovered geographical range for this data deficient species, to be taken into account for management and conservation purposes.     

Effects of a founder event and supplementary introductions on genetic variation in a captive breeding population of the endangered Spanish killifish

Twelve polymorphic allozyme loci were employed to assess the genetic change in a captive breeding population of the endangered killifish Aphanius baeticus in the Doñana National Park, south‐western Spain. The initial founder event did not significantly reduce the allelic richness or the expected heterozygosity. No genetic bottleneck signature was detected by tests for deviation from mutation‐drift equilibrium. The F _ST between the wild source and captive population, however, was relatively high (0·053 or 0·122 when excluding or including the locus IDHP‐1 * respectively), after just two to three generations in captivity. Two generations after the incorporation of 68 new wild specimens (greater than five generations after founding) decreased the genetic differences and the F _ST(0·041 excluding IDHP‐1 *). The restoration efforts appeared to be helpful and the study of 12 polymorphic loci and a sensitive parameter such as F _ST were useful for monitoring genetic changes in captivity. Nonetheless, future monitoring should include additional highly polymorphic loci (microsatellites) to achieve higher power to detect genetic change. Such restoration and monitoring efforts should help to avoid rapid inbreeding, adaptation to captivity, and to maintain the long‐term evolutionary potential in small isolated populations.     

Assortative mating among animals of captive and wild origin following experimental conservation releases

Captive breeding is a high profile management tool used for conserving threatened species. However, the inevitable consequence of generations in captivity is broad scale and often-rapid phenotypic divergence between captive and wild individuals, through environmental differences and genetic processes. Although poorly understood, mate choice preference is one of the changes that may occur in captivity that could have important implications for the reintroduction success of captive-bred animals. We bred wild-caught house mice for three generations to examine mating patterns and reproductive outcomes when these animals were simultaneously released into multiple outdoor enclosures with wild conspecifics. At release, there were significant differences in phenotypic (e.g. body mass) and genetic measures (e.g. G_st and F) between captive-bred and wild adult mice. Furthermore, 83% of offspring produced post-release were of same source parentage, inferring pronounced assortative mating. Our findings suggest that captive breeding may affect mating preferences, with potentially adverse implications for the success of threatened species reintroduction programmes.     

Assessment of microsatellite and SNP markers for parentage assignment in ex situ African Penguin (Spheniscus demersus) populations

Captive management of ex situ populations of endangered species is traditionally based on pedigree information derived from studbook data. However, molecular methods could provide a powerful set of complementary tools to verify studbook records and also contribute to improving the understanding of the genetic status of captive populations. Here, we compare the utility of single nucleotide polymorphisms (SNPs) and microsatellites (MS) and two analytical methods for assigning parentage in ten families of captive African penguins held in South African facilities. We found that SNPs performed better than microsatellites under both analytical frameworks, but a combination of all markers was most informative. A subset of combined SNP (n = 14) and MS loci (n = 10) provided robust assessments of parentage. Captive or supportive breeding programs will play an important role in future African penguin conservation efforts as a source of individuals for reintroduction. Cooperation among these captive facilities is essential to facilitate this process and improve management. This study provided us with a useful set of SNP and MS markers for parentage and relatedness testing among these captive populations. Further assessment of the utility of these markers over multiple (>3) generations and the incorporation of a larger variety of relationships among individuals (e.g., half‐siblings or cousins) is strongly suggested.     

The relative effects of mutation accumulation versus inbreeding depression on fitness in experimental populations of the housefly

Loss of fitness due to inbreeding depression in small captive populations of endangered species is widely appreciated. Populations of all sizes may also experience loss in fitness when environmental conditions are ameliorated because deleterious alleles may be rendered neutral and accumulate rapidly. Few data exist, however, to demonstrate loss in fitness due to relaxed selection. Loss of fitness in life‐history traits were compared between LARGE (N_e ≥ 500) and SMALL (N_e = 50) populations of the housefly Musca domestica L that were subjected to curtailed life span at 21 days to remove selection on late‐acting deleterious alleles. During the early part of the life history (≤21 days), the rate of decline in fecundity and progeny production over 24 generations was greater in the small (1.5%) than in the large populations <0.2%), but rate of loss in late‐life fecundity and progeny production (>21 days) was equivalent across populations, consistent with neutral theory, and amounted to 1.7% per generation. This rate of loss due to relaxed selection was equivalent to the rate of loss due to inbreeding in populations with an effective size of 50 individuals. Even if captive populations are kept large to avoid inbreeding, breeding them in benign environments where the forces of natural selection are curtailed may jeopardize the capability of these populations to exist in natural environments within few generations. Zoo Biol 20:145–156, 2001. © 2001 Wiley‐Liss, Inc.     

Effects of inbreeding on reproductive success,performance, litter size,and survival in captive red wolves (Canis rufus)

Captive‐breeding programs have been widely used in the conservation of imperiled species, but the effects of inbreeding, frequently expressed in traits related to fitness, are nearly unavoidable in small populations with few founders. Following its planned extirpation in the wild, the endangered red wolf (Canis rufus) was preserved in captivity with just 14 founders. In this study, we evaluated the captive red wolf population for relationships between inbreeding and reproductive performance and fitness. Over 30 years of managed breeding, the level of inbreeding in the captive population has increased, and litter size has declined. Inbreeding levels were lower in sire and dam wolves that reproduced than in those that did not reproduce. However, there was no difference in the inbreeding level of actual litters and predicted litters. Litter size was negatively affected by offspring and paternal levels of inbreeding, but the effect of inbreeding on offspring survival was restricted to a positive influence. There was no apparent relationship between inbreeding and method of rearing offspring. The observable effects of inbreeding in the captive red wolf population currently do not appear to be a limiting factor in the conservation of the red wolf population. Additional studies exploring the extent of the effects of inbreeding will be required as inbreeding levels increase in the captive population. Zoo Biol 29:36–49, 2010. © 2009 Wiley‐Liss, Inc.     

Testing alternative captive breeding strategies with the subsequent release into the wild

We used the housefly (Musca domestica L.) as an experimental model to compare two strategies for the captive breeding of an endangered species: a strategy to minimize inbreeding and balance founder contributions (termed “MAI” for “maximum avoidance of inbreeding”) versus a scheme to select against less fit individuals (disregarding relatedness). By balancing the initial founder contributions, the MAI protocol was analogous to methods for minimizing kinship. In both breeding strategies, the population growth rate was limited to a maximum increase of 50% per generation. Five replicate populations, each starting with five male–female pairs, were subjected to five generations of captive breeding. Six generations of simulated “release into the wild” allowed ad lib breeding with less restrictive population growth potential, in either a benign or stressful environment (i.e., constant or variable temperature). Population size, fecundity, and fertility were assayed throughout the experiment, with juvenile‐to‐adult survival assayed in the second phase of the project. Allozyme assays determined the resultant inbreeding coefficients from the captive breeding schemes. The MAI breeding scheme resulted in significantly lower inbreeding coefficients and higher fitness, with qualitatively reduced extinction potential, most notable in the stressful environment. Spontaneous fitness rebounds suggested that the MAI strategy facilitated some form of purging of inbreeding depression effects. Importantly, the advantages of the MAI strategy were difficult to detect during the captive breeding phase, suggesting that the long‐term advantages of the MAI approach could be underestimated in actual breeding programs. We concur with the common recommendation of maximum avoidance of inbreeding at least for systems with low reproductive potential. Zoo Biol 0:1–18, 2005. © 2005 Wiley‐Liss, Inc.     

The effects of sexual selection on life‐history traits: an experimental study on guppies

Sexual selection is often prevented during captive breeding in order to maximize effective population size and retain genetic diversity. However, enforcing monogamy and thereby preventing sexual selection may affect population fitness either negatively by preventing the purging of deleterious mutations or positively by reducing sexual conflicts. To better understand the effect of sexual selection on the fitness of small populations, we compared components of female fitness and the expression of male secondary sexual characters in 19 experimental populations of guppies (Poecilia reticulata) maintained under polygamous or monogamous mating regimes over nine generations. In order to generate treatments that solely differed by their level of sexual selection, the middle‐class neighbourhood breeding design was enforced in the monogamous populations, while in the polygamous populations, all females contributed similarly to the next generation with one male and one female offspring. This experimental design allowed potential sexual conflicts to increase in the polygamous populations because selection could not operate on adult‐female traits. Clutch size and offspring survival showed a weak decline from generation to generation but did not differ among treatments. Offspring size, however, declined across generations, but more in monogamous than polygamous populations. By generation eight, orange‐ and black‐spot areas were larger in males from the polygamous treatment, but these differences were not statistically significant. Overall, these results suggest that neither sexual conflict nor the purging of deleterious mutation had important effects on the fitness of our experimental populations. However, only few generations of enforced monogamy in a benign environment were sufficient to negatively affect offspring size, a trait potentially crucial for survival in the wild. Sexual selection may therefore, under certain circumstances, be beneficial over enforced monogamy during captive breeding.     

Altered wing phenotypes of captive-bred migratory birds lower post-release fitness

Captive breeding and release to the wild is a globally important conservation tool. However, captivity can result in phenotypic changes that incur post-release fitness costs, especially if they affect strenuous or risky behaviours. Bird wing shape is critical for migration success and suboptimal phenotypes are strongly selected against. In this study, I demonstrate surprising plasticity of bird wing phenotypes in captivity for 4/16 studied species. In a model species, captive-born juveniles with wild wing phenotypes (a 1-mm longer distal primary flight feather) survived post-release at 2.7 times the rate of those with captive phenotypes (i.e. a shorter distal feather). Subtle phenotypic changes and their fitness impacts are more common than widely realised because they are easily overlooked. To improve captive breeding for conservation, practitioners must surveil phenotypic changes and find ways to mitigate them.