Better Fitness in Captive Cuvier’s Gazelle despite Inbreeding Increase: Evidence of Purging?

Captive breeding of endangered species often aims at preserving genetic diversity and to avoid the harmful effects of inbreeding. However, deleterious alleles causing inbreeding depression can be purged when inbreeding persists over several generations. Despite its great importance both for evolutionary biology and for captive breeding programmes, few studies have addressed whether and to which extent purging may occur. Here we undertake a longitudinal study with the largest captive population of Cuvier''s gazelle managed under a European Endangered Species Programme since 1975. Previous results in this population have shown that highly inbred mothers tend to produce more daughters, and this fact was used in 2006 to reach a more appropriate sex-ratio in this polygynous species by changing the pairing strategy (i.e., pairing some inbred females instead of keeping them as surplus individuals in the population). Here, by using studbook data we explore whether purging has occurred in the population by investigating whether after the change in pairing strategy a) inbreeding and homozygosity increased at the population level, b) fitness (survival) increased, and c) the relationship between inbreeding and juvenile survival, was positive. Consistent with the existence of purging, we found an increase in inbreeding coefficients, homozygosity and juvenile survival. In addition, we showed that in the course of the breeding programme the relationship between inbreeding and juvenile survival was not uniform but rather changed over time: it was negative in the early years, flat in the middle years and positive after the change in pairing strategy. We highlight that by allowing inbred individuals to mate in captive stocks we may favour sex-ratio bias towards females, a desirable managing strategy to reduce the surplus of males that force most zoos to use ethical culling and euthanizing management tools. We discuss these possibilities but also acknowledge that many other effects should be considered before implementing inbreeding and purging as elements in management decisions.     

INBREEDING IN DARWIN'S MEDIUM GROUND FINCHES (GEOSPIZA FORTIS)

We studied the frequency and causes of inbreeding and its effect on reproductive success in a population of Darwin's Medium Ground Finches (Geospiza fortis) on Isla Daphne Major, Galápagos, during four breeding seasons (1981, 1983, 1984, and 1987). Pedigree analysis showed that levels of inbreeding were low but comparable with those observed in other passerine birds. For pairs with at least half of their grandparents known, approximately 20% of all pairings were between detectably related birds. The frequency of pairings between closely related birds (coefficient of kinship [φ] ≥ 0.250) among all pairs was 0.6%. We detected no effect of inbreeding on reproductive success, although sample sizes were small. The observed reproductive output of related pairs was not significantly different from the output of unrelated pairs, and there was no correlation between a pair's kinship coefficient and an estimate of the potential magnitude of inbreeding depression. Comparisons with a study of Great Tits (Parus major) by van Noordwijk and Scharloo (1981) suggest that, even if present, the fitness costs of inbreeding in this population of G. fortis would be low. Observed levels of inbreeding in each breeding episode were accurately predicted by simulations of random mating in which relatedness had no influence on pairing between individuals. This result suggests that levels of inbreeding in this population are determined more by demographic factors than by behavioral avoidance of mating with kin.     

Consequences of a One-male Harem Reproductive System and Inbreeding in a Captive Group of <Emphasis Type="BoldItalic">Cercopithecus solatus</Emphasis>

In closed captive populations, where dispersal is not possible, kin recognition and behavioral avoidance are the only mechanisms by which closely related individuals can avoid inbreeding. In the absence of avoidance, a loss of genetic diversity is inevitable in successive generations.In the 1980s, the CIRMF in Gabon established a small breeding group of sun-tailed monkeys (Cercopithecus solatus) with 4 individuals, and subsequently 17 births have been registered. We aimed to describe via microsatellite genotyping the reproductive system in the colony of Cercopithecus solatus, to evaluate the loss of genetic diversity with succeeding generations, and to evaluate consequences of inbreeding depression on a measure of the lifespan reproductive success of females giving birth to inbred vs. noninbred offspring. During the 11-yr period for which data are available, only alpha males sired offspring, confirming a one-male social organization. They reproduced only during their period of tenure. Two of the 3 alpha males were responsible for all the infants born. Genetic diversity decreased and inbreeding coefficients increased with successive generations. Interbirth interval was increased following the birth of an inbred infant, indicating possible increased maternal costs of rearing inbred infants. Loss of genetic variability in this captive group of sun-tailed monkeys has led to significant inbreeding depression and demonstrates the importance of male-mediated gene flow in restricted one-male harem breeding groups.     

Cryptic inbreeding depression in a growing population of a long‐lived species

Genetic effects are often overlooked in endangered species monitoring, and populations showing positive growth are often assumed to be secure. However, the continued reproductive success of a few individuals may mask issues such as inbreeding depression, especially in long‐lived species. Here, we test for inbreeding depression in little spotted kiwi (Apteryx owenii) by comparing a population founded with two birds to one founded with 40 birds, both from the same source population and both showing positive population growth. We used a combination of microsatellite genotypes, nest observations and modelling to examine the consequences of assessing population viability exclusively via population growth. We demonstrate (i) significantly lower hatching success despite significantly higher reproductive effort in the population with two founders; (ii) positive growth in the population with two founders is mainly driven by ongoing chick production of the founding pair; and (iii) a substantial genetic load in the population founded with two birds (10–15 diploid lethal equivalents). Our results illustrate that substantial, cryptic inbreeding depression may still be present when a population is growing, especially in long‐lived species with overlapping generations.     

Inbreeding depression in ring-tailed lemurs (<Emphasis Type="Italic">Lemur catta</Emphasis>): genetic diversity predicts parasitism,immunocompetence, and survivorship

The consequences of inbreeding have been well studied in a variety of taxa, revealing that inbreeding has major negative impacts in numerous species, both in captivity and in the wild; however, as trans-generational health data are difficult to obtain for long-lived, free-ranging species, similar analyses are generally lacking for nonhuman primates. Here, we examined the long-term effects of inbreeding on numerous health estimates in a captive colony of ring-tailed lemurs (Lemur catta), housed under semi-natural conditions. This vulnerable strepsirrhine primate is endemic to Madagascar, a threatened hotspot of biodiversity; consequently, this captive population represents an important surrogate. Despite significant attention to maintaining the genetic diversity of captive animals, breeding colonies invariably suffer from various degrees of inbreeding. We used neutral heterozygosity as an estimate of inbreeding and showed that our results reflect genome-wide inbreeding, rather than local genetic effects. In particular, we found that genetic diversity affects several fitness correlates, including the prevalence and burden of Cuterebra parasites and a third (N = 6) of the blood parameters analyzed, some of which reflect immunocompetence. As a final validation of inbreeding depression in this captive colony, we showed that, compared to outbred individuals, inbred lemurs were more likely to die earlier from diseases. Through these analyses, we highlight the importance of monitoring genetic variation in captive animals—a key objective for conservation geneticists—and provide insight into the potential negative consequences faced by small or isolated populations in the wild. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Molecular paternity determination in captive bonobos and the impact of inbreeding on infant mortality

Inbreeding and the loss of genetic diversity may lower fitness and reduce the potential for a population to adapt to changing environments. In small populations, for example in captive populations or populations of endangered species, this can have considerable consequences for their survival. We investigated the effects of inbreeding on infant mortality in the world captive population of bonobos Pan paniscus . Using a combination of studbook data and high-quality pedigree data from genotyped individuals, inbreeding information was available for 142 captive-born individuals. For the determination of paternities that were unresolved in the studbook, nuclear microsatellite DNA was amplified from hair and blood samples using the Great Ape Kit and PowerPlex^® 16 System. In total, 54 bonobos (17 offspring and their putative parents) were genotyped at eight tetranucleotide repeat microsatellite loci. Inbreeding coefficients were calculated for each individual for whom paternity was confirmed by either studbook data or DNA analysis. We found significantly higher infant mortality in inbred offspring compared with non-inbred offspring, suggesting that inbreeding reduces infant survival in captive bonobos. In addition, we argue that the total magnitude of inbreeding depression is probably underestimated in this captive population. In conclusion, even though the breeding programme of captive bonobos is aimed at avoiding inbreeding, closely related individuals do occasionally produce offspring that do show inbreeding depression. There is, however, no indication that this currently threatens the long-time survival of the captive population of bonobos.     

How many came home? Evaluating ex situ conservation of green turtles in the Cayman Islands

Ex situ management is an important conservation tool that allows the preservation of biological diversity outside natural habitats while supporting survival in the wild. Captive breeding followed by re‐introduction is a possible approach for endangered species conservation and preservation of genetic variability. The Cayman Turtle Centre Ltd was established in 1968 to market green turtle (Chelonia mydas) meat and other products and replenish wild populations, thought to be locally extirpated, through captive breeding. We evaluated the effects of this re‐introduction programmme using molecular markers (13 microsatellites, 800‐bp D‐loop and simple tandem repeat mitochondrial DNA sequences) from captive breeders (N = 257) and wild nesting females (N = 57) (sampling period: 2013–2015). We divided the captive breeders into three groups: founders (from the original stock), and then two subdivisions of F₁ individuals corresponding to two different management strategies, cohort 1995 (“C1995”) and multicohort F₁ (“MCF1”). Loss of genetic variability and increased relatedness was observed in the captive stock over time. We found no significant differences in diversity among captive and wild groups, and similar or higher levels of haplotype variability when compared to other natural populations. Using parentage and sibship assignment, we determined that 90% of the wild individuals were related to the captive stock. Our results suggest a strong impact of the re‐introduction programmme on the present recovery of the wild green turtle population nesting in the Cayman Islands. Moreover, genetic relatedness analyses of captive populations are necessary to improve future management actions to maintain genetic diversity in the long term and avoid inbreeding depression.     

An investigation of inbreeding depression and purging in captive pedigreed populations

We use regression models to investigate the effects of inbreeding in 119 zoo populations, encompassing 88 species of mammals, birds, reptiles and amphibians. Meta-analyses show that inbreeding depression for neonatal survival was significant across the 119 populations although the severity of inbreeding depression appears to vary among taxa. However, few predictors of a population's response to inbreeding are found reliable. The models are most likely to detect inbreeding depression in large populations, that is, in populations in which their statistical power is maximised. Purging was found to be significant in 14 populations and a significant trend of purging was found across populations. The change in inbreeding depression due to purging averaged across the 119 populations is <1%, however, suggesting that the fitness benefits of purging are rarely appreciable. The study re-emphasises the necessity to avoid inbreeding in captive breeding programmes and shows that purging cannot be relied upon to remove deleterious alleles from zoo populations.     

Inbreeding and disease avoidance in a free‐ranging koala population

Habitat destruction and fragmentation are increasing globally, forcing surviving species into small, isolated populations. Isolated populations typically experience heightened inbreeding risk and associated inbreeding depression and population decline; although individuals in these populations may mitigate these risks through inbreeding avoidance strategies. For koalas, as dietary specialists already under threat in the northern parts of their range, increased habitat fragmentation and associated inbreeding costs are of great conservation concern. Koalas are known to display passive inbreeding avoidance through sex‐biased dispersal, although population isolation will reduce dispersal pathways. We tested whether free‐ranging koalas display active inbreeding avoidance behaviours. We used VHF tracking data, parentage reconstruction, and veterinary examination results to test whether free‐ranging female koalas avoid mating with (a) more closely related males; and (b) males infected with sexually transmitted Chlamydia pecorum. We found no evidence that female koalas avoid mating with relatively more related available mates. In fact, as the relatedness of potential mates increases, so did inbreeding events. We also found no evidence that female koalas can avoid mating with males infected with C. pecorum. The absence of active inbreeding avoidance mechanisms in koalas is concerning from a conservation perspective, as small, isolated populations may be at even higher risk of inbreeding depression than expected. At risk koala populations may require urgent conservation interventions to augment gene flow and reduce inbreeding risks. Similarly, if koalas are not avoiding mating with individuals with chlamydial disease, populations may be at higher risk from disease than anticipated, further impacting population viability.     

Phenotype‐associated inbreeding biases estimates of inbreeding depression in a wild bird population

Inbreeding depression is usually quantified by regressing individual phenotypic values on inbreeding coefficients, implicitly assuming there is no correlation between an individual's phenotype and the kinship coefficient to its mate. If such an association between parental phenotype and parental kinship exists, and if the trait of interest is heritable, estimates of inbreeding depression can be biased. Here we first derive the expected bias as a function of the covariance between mean parental breeding value and parental kinship. Subsequently, we use simulated data to confirm the existence of this bias, and show that it can be accounted for in a quantitative genetic animal model. Finally, we use long‐term individual‐based data for white‐throated dippers (Cinclus cinclus), a bird species in which inbreeding is relatively common, to obtain an empirical estimate of this bias. We show that during part of the study period, parents of inbred birds had shorter wings than those of outbred birds, and as wing length is heritable, inbred individuals were smaller, independent of any inbreeding effects. This resulted in the overestimation of inbreeding effects. Similarly, during a period when parents of inbred birds had longer wings, we found that inbreeding effects were underestimated. We discuss how such associations may have arisen in this system, and why they are likely to occur in others, too. Overall, we demonstrate how less biased estimates of inbreeding depression can be obtained within a quantitative genetic framework, and suggest that inbreeding and additive genetic effects should be accounted for simultaneously whenever possible.     

Inbreeding depression of sperm traits in the zebra finch Taeniopygia guttata

Inbreeding depression, or the reduction in fitness due to mating between close relatives, is a key issue in biology today. Inbreeding negatively affects many fitness‐related traits, including survival and reproductive success. Despite this, very few studies have quantified the effects of inbreeding on vertebrate gamete traits under controlled breeding conditions using a full‐sib mating approach. Here, we provide comprehensive evidence for the negative effect of inbreeding on sperm traits in a bird, the zebra finch Taeniopygia guttata. We compared sperm characteristics of both inbred (pedigree F = 0.25) and outbred (pedigree F = 0) individuals from two captive populations, one domesticated and one recently wild‐derived, raised under standardized conditions. As normal spermatozoa morphology did not differ consistently between inbred and outbred individuals, our study confirms the hypothesis that sperm morphology is not particularly susceptible to inbreeding depression. Inbreeding did, however, lead to significantly lower sperm motility and a substantially higher percentage of abnormal spermatozoa in ejaculate. These results were consistent across both study populations, confirming the generality and reliability of our findings.     

Male vocalizations convey information on kinship and inbreeding in a lekking bird

Kinship and inbreeding are two major components involved in sexual selection and mating system evolution. However, the mechanisms underlying recognition and discrimination of genetically related or inbred individuals remain unclear. We investigated whether kinship and inbreeding information is related to low‐frequency vocalizations, “booms,” produced by males during their courtship in the lekking houbara bustard (Chlamydotis undulata undulata). Based on a captive breeding program where the pedigree of all males is known, we investigated the similarity of booms’ acoustic parameters among captive males more or less individually inbred and therefore genetically related with each other. In the wild, we investigated the relationship between the spatial distribution of males within leks and the similarity of acoustic parameters of their booms. In the captive population, we found (a) a relationship between the individual inbreeding level of captive males and their vocalization parameters; (b) that kin share similar frequency and temporal characteristics of their vocalizations. In the wild, we found no evidence for spatial structuring of males based on their acoustic parameters, in agreement with previous genetic findings on the absence of kin association within houbara bustard leks. Overall, our results indicate that genetic information potentially related to both the identity and quality of males is contained in their vocalizations.     

Ex situ conservation genetics: a review of molecular studies on the genetic consequences of captive breeding programmes for endangered animal species

Captive breeding has become an important tool in species conservation programmes. Current management strategies for ex situ populations are based on theoretical models, which have mainly been tested in model species or assessed using studbook data. During recent years an increasing number of molecular genetic studies have been published on captive populations of several endangered species. However, a comprehensive analysis of these studies is still outstanding. Here, we present a review of the published literature on ex situ conservation genetics with a focus on molecular studies. We analysed 188 publications which either presented empirical studies using molecular markers (105), studbook analyses (26), theoretical work (38), or tested the genetic effects of management strategies using model species (19). The results show that inbreeding can be minimized by a thorough management of captive populations. There seems to be a minimum number of founders (15) and a minimum size of a captive population (100) necessary in order to minimize a loss of genetic diversity. Optimally, the founders should be unrelated and new founders should be integrated into the captive population successively. We recommend that genetic analyses should generally precede and accompany ex situ conservation projects in order to avoid inbreeding and outbreeding depression. Furthermore, many of the published studies do not provide all the relevant parameters (founder size, captive population size, H_o, H_e, inbreeding coefficients). We, therefore, propose that a general standard for the presentation of genetic studies should be established, which would allow integration of the data into a global database.     

Lifetime inbreeding depression in a leaf beetle

Ongoing habitat loss and fragmentation result in rapid population size reductions, which can increase the levels of inbreeding. Consequently, many species are threatened by inbreeding depression, a loss of individual fitness following the mating of close relatives. Here, we investigated inbreeding effects on fitness‐related traits throughout the lifetime of the mustard leaf beetle (Phaedon cochleariae) and mechanisms for the avoidance of inbreeding. Previously, we found that these beetles have family‐specific cuticular hydrocarbon profiles, which are likely not used as recognition cue for precopulatory inbreeding avoidance. Thus, we examined whether adult beetles show postcopulatory inbreeding avoidance instead. For this purpose, we determined the larval hatching rate of eggs laid by females mated sequentially with two nonsiblings, two siblings, a nonsibling, and a sibling or vice versa. The beetles suffered from inbreeding depression throughout their entire ontogeny, as evinced by a prolonged larval development, a decreased larval and adult survival and a decreased reproductive output of inbred compared to outbred individuals. The highest larval hatching rates were detected when females were mated with two nonsiblings or first with a sibling and second with a nonsibling. Significantly lower hatching rates were measured in the treatments with a sibling as second male. Thus, the results do not support the existence of postcopulatory inbreeding avoidance in P. cochleariae, but revealed evidence for second male sperm precedence. Consequently, an alternative strategy to avoid inbreeding costs might exist in this beetle, such as a polyandrous mating system, potentially coupled with a specific dispersal behavior.     

Resolving the conundrum of inbreeding depression but no inbreeding avoidance: Estimating sex‐specific selection on inbreeding by song sparrows (Melospiza melodia)

Inbreeding avoidance among interacting females and males is not always observed despite inbreeding depression in offspring fitness, creating an apparent “inbreeding paradox.” This paradox could be resolved if selection against inbreeding was in fact weak, despite inbreeding depression. However, the net magnitude and direction of selection on the degree to which females and males inbreed by pairing with relatives has not been explicitly estimated. We used long‐term pedigree data to estimate phenotypic selection gradients on the degree of inbreeding that female and male song sparrows (Melospiza melodia) expressed by forming socially persistent breeding pairs with relatives. Fitness was measured as the total numbers of offspring and grand offspring contributed to the population, and as corresponding expected numbers of identical‐by‐descent allele copies, thereby accounting for variation in offspring survival, reproduction, and relatedness associated with variation in parental inbreeding. Estimated selection gradients on the degree to which individuals paired with relatives were weakly positive in females, but negative in males that formed at least one socially persistent pairing. However, males that paired had higher mean fitness than males that remained socially unpaired. These analyses suggest that net selection against inbreeding may be weak in both sexes despite strong inbreeding depression, thereby resolving the “inbreeding paradox.”     

A Test of Inbreeding Avoidance in the Zebra Finch

Optimal-outbreeding theory suggests that the genetic relatedness of individuals may be an important factor in mate choice. Several studies have demonstrated that matings between individuals of intermediate genetic relatedness tend to produce more offspring than those between more closely or distantly related mates. Inbreeding avoidance has been studied in captive zebra finches, Poephila guttata. Slater & Clements (1981) found a preference for closely related individuals, while Evans-Layng (1987), in a different design, found a preference for less related mates. Our study examines patterns of mate choice in small flocks of zebra finches of known genetic relatedness. 13 flocks of 9 birds (3 females and 6 males) were released into separate aviaries and left until pairs had formed. 6 of these flocks consisted of siblings and nonrelatives and 7 consisted of cousins and nonrelatives. The degree of genetic relatedness of the individuals used did not affect mate choice, while factors such as male age and experience were correlated with mating success. There was a marginally significant trend for sibling pairs to take longer to lay eggs, although no overall difference in clutch size among sibling pairs, cousin pairs and genetically unrelated pairs was detected. We conclude, then, that there is no evidence of inbreeding avoidance in captive zebra finches.     

Sustainability of the South China tiger: implications of inbreeding depression and introgression

The South China tiger (Panther tigris amoyensis) is critically endangered with 73 remaining individuals living in captivity, all derived from six wild founders since 1963. The population shows a low level of juvenile survivorship and reproductive difficulties, and faces a huge conservation challenge. In this study, inbreeding depression and genetic diversity decline were examined by using pedigree data and 17 microsatellites. The constant B, which is related to the number of lethal equivalents, was estimated to be 0 for the offspring of noninbred parents, but was >0 for the offspring of inbred parents and for all offspring. Percentage of successfully breeding tigers inversely correlated with inbreeding level (r = −0.626, α = 0.05). Taken together, these findings suggest the population is suffering from inbreeding depression in juvenile survivorship and fecundity. No significant correlation was detectable for the mean litter size with f of either dams (r = −0.305, α = 0.46) or kittens (r = 0.105, α = 0.71), indicating litter size was not strongly subject to inbreeding depression. The average number of alleles per locus was 4.24 ± 1.03 (SE), but effective number of alleles was only 2.53 ± 0.91. Twenty-one alleles carried by early breeders at 13 loci were absent in the present breeders and potential breeders. Multilocus heterozygosity was inversely correlated with inbreeding levels (r = −0.601, α = 0.004). These findings suggest rapid allelic diversity loss is occurring in this small captive population and that heterozygosity is being lost as it becomes more inbred. Our phylogenetic analysis supports past work indicating introgression from northern Indochinese tigers in the population. As no wild representatives of the South China tiger can be added to the captive population, we may consider the alternate scenario of further introgression in the interest of countering inbreeding depression and declining genetic diversity.     

Inbreeding depression in sperm quality in a critically endangered amphibian

Small, isolated populations often experience increased inbreeding and decreased heterozygosity, which increases the potential risk of inbreeding depression. The relationship between inbreeding and sperm health is well-documented in a variety of taxa, but has yet to be explored in amphibians. The dusky gopher frog, Lithobates sevosus, is a critically endangered species with years of documented inbreeding and low genetic variability as a consequence of isolation and population size reduction. This study investigated the effects of inbreeding on sperm quality in captive L. sevosus using an outbred, sister species (Lithobates pipiens) as a standard for comparison. We found L. sevosus to have severely reduced sperm quality in terms of total motility, forward progressive motility, concentration, and viability. Additionally, we observed a significant, negative relationship between total sperm motility and mean kinship within captive-bred individuals. These data serve to enhance our understanding of the role inbreeding plays in amphibians, and to provide valuable insight into new risk factors declining amphibian populations may face.     

Mating strategies in dominant meerkats: evidence for extra‐pair paternity in relation to genetic relatedness between pair mates

Rates of extra‐pair paternity (EPP) have frequently been associated with genetic relatedness between social mates in socially monogamous birds. However, evidence is limited in mammals. Here, we investigate whether dominant females use divorce or extra‐pair paternity as a strategy to avoid the negative effects of inbreeding when paired with a related male in meerkats Suricata suricatta, a species where inbreeding depression is evident for several traits. We show that dominant breeding pairs seldom divorce, but that rates of EPP are associated with genetic similarity between mates. Although extra‐pair males are no more distantly related to the female than social males, they are more heterozygous. Nevertheless, extra‐pair pups are not more heterozygous than within‐pair pups. Whether females benefit from EPP in terms of increased fitness of the offspring, such as enhanced survival or growth, requires further investigations.     

Inbreeding Depression and Inbreeding Avoidance in a Natural Population of Guppies (Poecilia reticulata)

Maintenance of genetic variation in the face of strong natural selection is a long‐standing problem in evolutionary biology. One of the most extreme examples of within‐population variation is the polymorphic, genetically determined color pattern of male Trinidad guppies (Poecilia reticulata). Female mating preference for rare or novel patterns has been implicated as a factor in maintaining this variation. The origin of this preference is not understood, although inbreeding avoidance has been proposed as a mechanism. Inbreeding avoidance is advantageous when populations exhibit inbreeding depression and the opportunity for mating between relatives exists. To determine whether these conditions are met in a natural guppy population, we assessed mating and reproductive patterns using polymorphic molecular markers. Females produced more offspring with less‐related males than with more‐related ones. In addition, females were more likely to have mated with less‐related males, but this trend was only marginally significant. Male heterozygosity was positively correlated with mating success and with the number of offspring sired, consistent with strong inbreeding depression for adult male fitness. These results provide substantial insight into mating patterns of a wild guppy population: strong inbreeding depression occurs, and individuals tend to avoid mating with relatives.