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

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

Patterns of genetic diversity of mitochondrial DNA within captive populations of the endangered itasenpara bitterling: implications for a reintroduction program

In this study, the level of genetic diversity of captive populations of the itasenpara bitterling (Acheilognathus longipinnis) was assessed to obtain information useful for successful captive breeding and reintroduction; this analysis was performed using mitochondrial DNA (mtDNA) sequence data. Comparison of the captive and wild populations showed low levels of genetic diversity within the captive population and significant genetic differentiation among the captive populations and also between the wild and captive populations, suggesting at chance effect during the founding process for the captive population and a subsequent genetic drift. Therefore, for successful reintroduction, it is important that the reintroduced population reflects all the genetic diversity available from the captive populations, and that releasing a large number of individuals that consist of all captive populations.     

Patterns of ancestry and genetic diversity in reintroduced populations of the slimy sculpin: implications for conservation

Reintroductions are a common approach for preserving intraspecific biodiversity in fragmented landscapes. However, they may exacerbate the reduction in genetic diversity initially caused by population fragmentation because the effective population size of reintroduced populations is often smaller and reintroduced populations also tend to be more geographically isolated than native populations. Mixing genetically divergent sources for reintroduction purposes is a practice intended to increase genetic diversity. We documented the outcome of reintroductions from three mixed sources on the ancestral composition and genetic variation of a North American fish, the slimy sculpin (Cottus cognatus). We used microsatellite markers to evaluate allelic richness and heterozygosity in the reintroduced populations relative to computer simulated expectations. Sculpins in reintroduced populations exhibited higher levels of heterozygosity and allelic richness than any single source, but only slightly higher than the single most genetically diverse source population. Simulations intended to mimic an ideal scenario for maximizing genetic variation in the reintroduced populations also predicted increases, but they were only moderately greater than the most variable source population. We found that a single source contributed more than the other two sources at most reintroduction sites. We urge caution when choosing whether to mix source populations in reintroduction programs. Genetic characteristics of candidate source populations should be evaluated prior to reintroduction if feasible. When combined with knowledge of the degree of genetic distinction among sources, simulations may allow the genetic diversity benefits of mixing populations to be weighed against the risks of outbreeding depression in reintroduced and nearby populations.     

Genotypic and phenotypic consequences of reintroduction history in the black-footed ferret (<Emphasis Type="Italic">Mustela nigripes</Emphasis>)

Population augmentation with translocated individuals has been shown to alleviate the effects of bottlenecks and drift. The first step to determine whether restoration for genetic considerations is warranted is to genetically monitor reintroduced populations and compare results to those from the source. To assess the need for genetic restoration, we evaluated genetic diversity and structure of reintroduced (n = 3) and captive populations of the endangered black-footed ferret (Mustela nigripes). We measured genotypic changes among populations using seven microsatellite markers and compared phenotypic changes with eight morphometric characters. Results indicated that for the population which rapidly grew post-reintroduction, genetic diversity was equivalent to the captive, source population. When growth languished, only the population that was augmented yearly maintained diversity. Without augmentation, allelic diversity declined precipitously and phenotypic changes were apparent. Ferrets from the genetically depaupertate population had smaller limbs and smaller overall body size than ferrets from the two populations with greater diversity. Population divergence (F _ST = 0.10 ± 0.01) was surprisingly high given the common source of populations. Thus, it appears that 5–10 years of isolation resulted in both genotypic divergence and phenotypic changes to populations. We recommend translocation of 30–40 captive individuals per annum to reintroduction sites which have not become established quickly. This approach will maximize the retention of genetic diversity, yet maintain the beneficial effects of local adaptation without being swamped by immigration.     

Genetic variation in a network of natural and reintroduced populations of Griffon vulture (Gyps fulvus) in Europe

It is generally considered that limiting the loss of genetic diversity in reintroduced populations is essential to optimize the chances of success of population restoration. Indeed, to counter founder effect in a reintroduced population we should maximize the genetic variability within the founding group but also take into account networks of natural populations in the choice of the reintroduction area. However, assessment of relevant reintroduction strategies requires long-term post-release genetic monitoring. In this study, we analyzed genetic data from a network of native and reintroduced Griffon vulture (Gyps fulvus) populations successfully restored in Southern Europe. Using microsatellite markers, we characterized the level of genetic diversity and degree of genetic structure within and among three native colonies, four captive founding groups and one long-term monitored reintroduced population. We also used Bayesian assignment analysis to examine recent genetic connections between the reintroduced population and the other populations. We aimed to assess the level of fragmentation among native populations, the effectiveness of random choice of founders to retain genetic variability of the species, the loss of genetic diversity in the reintroduced population and the effect of gene flow on this founder effect. Our results indicate that genetic diversity was similar in all populations but we detected signs of recent isolation for one native population. The reintroduced population showed a high immigration rate that limited loss of genetic diversity. Genetic investigations performed in native populations and post-released genetic monitoring have direct implications for founder choice and release design.     

Genetic management of the red squirrel,Sciurus vulgaris: a practical approach to regional conservation

The progressive decline in red squirrel (Sciurus vulgaris) numbers in Wales has led to conservation and reintroduction projects being established on the island of Anglesey. The recovery of the island’s remnant wild population was initially successful, however concern remained over potential loss of genetic diversity resulting from an observed demographic bottleneck. We used mitochondrial DNA (mtDNA) control region sequences and six microsatellite loci to assess current levels of genetic variation in the population. Samples were monomorphic for control region sequences and a historic specimen from the same area carrying a different haplotype demonstrated a loss of mtDNA diversity during the last 20 years. Inclusion of other Welsh haplotypes indicated phylogeographic structure in the region, in contrast to previous UK studies. Genotyping results showed allelic diversity and heterozygosity to be less than 50% of that recorded in other UK populations, with strong evidence for a recent genetic bottleneck. A parallel reintroduction programme on Anglesey included genetic analysis of individuals during the selection of captive breeding pairs. We present analysis of sequence and microsatellite data, and subsequent management decisions taken to maximise diversity in the founder and F1 generations. Population and Habitat Viability Analysis applied to both populations modelled future levels of heterozygosity and allelic diversity. Supplementation of the remnant and reintroduced populations with translocated squirrels was simulated as a potential management tool; results support use of this strategy to reduce loss of diversity and increase survival. The limitations of applying conservation genetic theory within small-scale management projects are discussed.     

Genetic management of captive populations: the advantages of circular mating

We performed computer simulations to evaluate the effectiveness of circular mating as a genetic management option for captive populations. As a benchmark, we used the method proposed by Fernández and Caballero according to which parental contributions are set to produce minimum coancestry among the offspring and matings are performed so as to minimize mean pairwise coancestry (referred to as the Gc/mc method). In contrast to other methods, fitness does not vary with population size in the case of circular mating, and can be higher than under random mating. Whether circular mating is an effective method in conserving captive populations depends on the trade-off between different considerations. On the one hand, circular mating shows the highest allelic diversity and the lowest mean pairwise coancestry for all population sizes. It also shows a relatively higher efficiency of purging deleterious alleles. More importantly, circular mating can significantly increase the success probability of populations released to the wild relative to the Gc/mc method. On the other hand, circular mating has the drawback of showing high inbreeding rates and low fitness in early generations, which can result to an increase in the extinction probability of the captive populations. However, this increase is slight unless population size and litter size are both very low. Overall, if the slight increase in extinction probability can be tolerated then circular mating fulfils the primary goals of a captive breeding program, i.e., it maintains high levels of genetic diversity and increases the success probability of reintroduced populations.     

Multi-generational evaluation of genetic diversity and parentage in captive southern pygmy perch (<Emphasis Type="Italic">Nannoperca australis</Emphasis>)

Maintaining genetic diversity within captive breeding populations is a key challenge for conservation managers. We applied a multi-generational genetic approach to the captive breeding program of an endangered Australian freshwater fish, the southern pygmy perch (Nannoperca australis). During previous work, fish from the lower Murray-Darling Basin were rescued before drought exacerbated by irrigation resulted in local extinction. This endemic lineage of the species was captive-bred in genetically designed groups, and equal numbers of F1 individuals were reintroduced to the wild with the return of favourable habitat. Here, we implemented a contingency plan by continuing the genetic-based captive breeding in the event that a self-sustaining wild population was not established. F1 individuals were available as putative breeders from the subset of groups that produced an excess of fish in the original restoration program. We used microsatellite-based parentage analyses of these F1 fish to form breeding groups that minimized inbreeding. We assessed their subsequent parental contribution to F2 individuals and the maintenance of genetic diversity. We found skewed parental contribution to F2 individuals, yet minimal loss of genetic diversity from their parents. However, the diversity was substantially less than that of the original rescued population. We attribute this to the unavoidable use of F1 individuals from a limited number of the original breeding groups. Alternative genetic sources for supplementation or reintroduction should be assessed to determine their suitability. The genetic fate of the captive-bred population highlights the strong need to integrate DNA-based tools for monitoring and adaptive management of captive breeding programs.     

Photoperiod manipulation to increase the productivity of black‐footed ferrets (Mustela nigripes) and Siberian polecats (M. eversmanii)

The endangered black‐footed ferret (Mustela nigripes) reproduces naturally in the spring. The Black‐Footed Ferret Recovery Program would benefit from increased productivity in the captive population by manipulating photoperiod and temperature to create three artificial cycles in 1½ years. In the present study the photoperiod was set at 8 hr light:16 hr dark for 1–2 months, then switched to 16 hr light:8 hr dark for 4–5 months. The males' light was switched 1 month before the females' light. Three cycles were performed in 2 years. During the first cycle, 0% of the males bred, 17% of the females came into estrus and were bred through artificial insemination, and 0% of the females whelped. In the second cycle, 100% of the females came into estrus and were bred naturally, and 77% whelped. In the third cycle, all males showed testicular recrudescence but none bred; all females showed signs of estrus, 40% were bred using artificial insemination, and 0% whelped. Siberian polecats (Mustela eversmanii), the black‐footed ferrets' closest living relative, also were put on an artificial photoperiod, coinciding with the black‐footed ferrets' third cycle. All female polecats came into estrus and were bred naturally, and 33% whelped. All males showed testicular recrudescence, and 22% produced sperm and bred. The low rate of success in breeding and whelping suggests that multiple cues may be needed to induce estrus in ferrets and polecats. Zoo Biol 22:1–14, 2003. © 2003 Wiley‐Liss, Inc.     

One year later: evaluation of PMC‐recommended births and transfers

To meet their exhibition, conservation, education, and scientific goals, members of the American Zoo and Aquarium Association (AZA) collaborate to manage their living collections as single species populations. These cooperative population management programs, Species Survival Plans^® (SSP) and Population Management Plans (PMP), issue specimen‐by‐specimen recommendations aimed at perpetuating captive populations by maintaining genetic diversity and demographic stability. Species Survival Plans and PMPs differ in that SSP participants agree to complete recommendations, whereas PMP participants need only take recommendations under advisement. We evaluated the effect of program type and the number of participating institutions on the success of actions recommended by the Population Management Center (PMC): transfers of specimens between institutions, breeding, and target number of offspring. We analyzed AZA studbook databases for the occurrence of recommended or unrecommended transfers and births during the 1‐year period after the distribution of standard AZA Breeding‐and‐Transfer Plans. We had three major findings: 1) on average, both SSPs and PMPs fell about 25% short of their target; however, as the number of participating institutions increased so too did the likelihood that programs met or exceeded their target; 2) SSPs exhibited significantly greater transfer success than PMPs, although transfer success for both program types was below 50%; and 3) SSPs exhibited significantly greater breeding success than PMPs, although breeding success for both program types was below 20%. Together, these results indicate that the science and sophistication behind genetic and demographic management of captive populations may be compromised by the challenges of implementation. Zoo Biol 0:1–11, 2006. © 2006 Wiley‐Liss, Inc.     

How do reproductive skew and founder group size affect genetic diversity in reintroduced populations?

Reduced genetic diversity can result in short-term decreases in fitness and reduced adaptive potential, which may lead to an increased extinction risk. Therefore, maintaining genetic variation is important for the short- and long-term success of reintroduced populations. Here, we evaluate how founder group size and variance in male reproductive success influence the long-term maintenance of genetic diversity after reintroduction. We used microsatellite data to quantify the loss of heterozygosity and allelic diversity in the founder groups from three reintroductions of tuatara ( Sphenodon ), the sole living representatives of the reptilian order Rhynchocephalia. We then estimated the maintenance of genetic diversity over 400 years (∼10 generations) using population viability analyses. Reproduction of tuatara is highly skewed, with as few as 30% of males mating across years. Predicted losses of heterozygosity over 10 generations were low (1–14%), and populations founded with more animals retained a greater proportion of the heterozygosity and allelic diversity of their source populations and founder groups. Greater male reproductive skew led to greater predicted losses of genetic diversity over 10 generations, but only accelerated the loss of genetic diversity at small population size (<250 animals). A reduction in reproductive skew at low density may facilitate the maintenance of genetic diversity in small reintroduced populations. If reproductive skew is high and density-independent, larger founder groups could be released to achieve genetic goals for management.     

The Influence of Translocation Strategy and Management Practices on the Genetic Variability of a Reestablished Elk (Cervus elaphus) Population

Reintroduction of terrestrial vertebrates with the goal of ecosystem restoration typically establishes small and isolated populations that may experience reduced genetic variability due to founder effects and genetic drift. Understanding the genetic structure of these populations and maintaining adequate genetic diversity is important for long‐term restoration success. We quantified genetic variability at six microsatellite loci for a reintroduced population of Cervus elaphus (elk) restored to the tallgrass prairie ecosystem of northeastern Kansas. Allelic richness, observed and expected heterozygosity were intermediate to levels reported in other North American elk populations. Current levels of genetic variability in restored North American elk populations were not well explained by founding population size, number of founding populations, or number of years since the last translocation. Simulation results suggest that the retention of genetic variability in isolated populations is strongly influenced by mating system while also being impacted by temporal variability in population size and population growth rate. Our results have implications for understanding how translocation strategies and post‐reintroduction management may influence genetic variability in restored populations.     

Reintroduction of the European Capercaillie from the Capercaillie Breeding Centre in Wis?a Forest District: Genetic Assessments of Captive and Reintroduced Populations

The Western capercaillie (Tetrao urogallus) is a specific bird species, which, despite its very broad distribution and large global population size, is highly endangered in many Western and Central European countries. According to the species situation, in many countries (including Poland), breeding and reintroduction programmes have been started. One of the most complex and large-scale reintroduction programmes was started in Bory Dolnośląskie Forest, and the Capercaillie Breeding Centre in Wisła Forest District was used as one of the sources of individuals for reintroduction. As genetic tools provide essential knowledge about species biodiversity, which is crucially important during the breeding process and reintroduction, both captive and reintroduced grouse populations were genetically analysed. We were particularly interested in genetic diversity of the individuals in both populations and the genetic relationship between them, as well as between them and other capercaillie representatives from their current range. To fulfil these goals we determined nine microsatellite loci along with a fragment of the mitochondrial control region. Genetic diversity parameters were moderate to high compared to populations from other Central and Western European countries. Both populations were clustered into three distinct genetic clades based on microsatellites. Phylogenetic analysis placed all mitochondrial haplotypes we revealed in the Eurasian clade. The present results will play an important role as they will help to preserve and maximize genetic diversity in captive populations, and will provide a basis for future monitoring of the reintroduction process.     

Evidence for African origins of founders of the asiatic lion species survival plan

The Asiatic lion (Panthera leo persica) exists in the wild as a single relict population of approximately 250 individuals in the protected Gir Forest Sanctuary in western India. In 1981, a species survival plan (SSP) for the Asiatic lion was established by the American Association of Zoological Parks and Aquariums to manage the 200 + descendants of Asiatic lions in captivity in western zoological facilities. This captive population was derived from seven founders. In order to compare the genetic structure of the Gir Forest population with that of the captive SSP population, a genetic survey of 46 electrophoretic allozyme systems resolved from extracts of lion blood was undertaken by using 29 SSP Asiatic lions and 28 wild-caught or captive-bred lions maintained at the Sakkarbaug Zoo in India but originally derived from the Gir Forest. The Gir lion population was found to be genetically monomorphic at each of 46 allozyme loci. This was in contrast to several African lion (Panthera leo leo) populations, which show moderate levels of allozyme variation at the same loci. The SSP lion population was polymorphic at three allozyme loci (IDHI, TF, and PTI) for alleles that were previously found only in African lion populations. Pedigree analysis of the genetic transmission of these three biochemical loci demonstrated that two of the five primary founder animals of the SSP Asiatic lion population (a breeding pair originally imported from the Trivandrum Zoo in southern India) were descendants of the African subspecies. Three other founder animals were pure Asian. A retrospective SSP pedigree analysis of two morphologic characters (prominent abdominal fold and pairing of infraorbital foramen) that are partially diagnostic for persica vs leo was consistent with this conclusion as well. The implications for the management of small captive populations of threatened species and of the Asiatic lion SSP population are discussed.     

Captive breeding and reintroduction of the lesser kestrel Falco naumanni: a genetic analysis using microsatellites

We used microsatellites to assess ongoing captive breeding and reintroduction programs of the lesser kestrel. The extent of genetic variation within the captive populations analysed did not differ significantly from that reported in wild populations. Thus, the application of widely recommended management practices, such as the registration of crosses between individuals in proper stud books and the introduction of new individuals into the genetic pools, has proven satisfactory to maintain high levels of genetic variation. The high rates of hatching failure occasionally documented in captivity can therefore not be attributed to depressed genetic variation. Even though genetic diversity in reintroduced populations did not differ significantly when compared to wild populations either, average observed heterozygosities and inbreeding coefficients were significantly lower and higher, respectively, when compared to the captive demes where released birds came. Monitoring of reproductive parameters during single-pairing breeding and paternity inference within colonial facilities revealed large variations in breeding success between reproductive adults. The relative number of breeding pairs that contributed to a large part of captive-born birds (50–56%) was similar in both cases (28.6 and 26.9%, respectively). Thus, the chances for polygyny (rarely in this study), extra-pair paternity (not found in this study) and/or social stimulation of breeding parameters do not seem to greatly affect the genetically effective population size. Independently of breeding strategies, the release of unrelated fledglings into the same area and the promotion of immigration should be mandatory to counteract founder effects and avoid inbreeding in reintroduced populations of lesser kestrels.     

Isolation and characterization of 23 polymorphic microsatellite loci for a West Indian iguana (Cyclura pinguis) from the British Virgin Islands

Twenty-three polymorphic microsatellite markers were identified and characterized for Cyclura pinguis, a critically endangered species of lizard (Sauria: Iguanidae) native to Anegada Island in the British Virgin Islands. We examined variation at these loci for 39 C. pinguis, finding up to five alleles per locus and an average expected heterozygosity of 0.55. Allele frequency estimates for these microsatellite loci will be used to characterize genetic diversity of captive and wild C. pinguis populations and to estimate relatedness among adult iguanas at the San Diego Zoo that form the nucleus of a captive breeding programme for this critically endangered species.     

Captive breeding and reintroduction of the oriental pied hornbill (Anthracoceros albirostris) in Khao Kheow Open Zoo,Thailand

This article discusses two related issues of the captive breeding and reintroduction of the Oriental pied hornbill (Anthracoceros albirostris) in order to increase its population in the natural habitats. Oriental pied hornbills were bred in Khao Kheow Open Zoo. Three pairs were separated and kept in breeding cages. Females occupied artificial nests between February and April 2005–2007. Eggs were laid and incubated between February and March each year from 2005 to 2007. Nestlings hatched in late March and left the nest in late April 2005–2007. Each breeding pair was fed with approximately 400 g of food each day. All three pairs reproduced resulting in mature offspring of seven in 2005, six in 2006, and five in 2007. Four of sixteen 3‐year‐old birds were randomly selected and equipped with a GPS receiver on their backs. Activities of the birds attached and unattached with GPS were not significantly different. The first two birds (one female, one male with GPS) were reintroduced on August 5, 2006, and another nine birds (four birds with GPS) were reintroduced on December 26, 2006. The average home range of these reintroduced birds was 0.13 km². Their foods consisted of wild plants and animals in the home range. The first reintroduced pair was able to breed naturally by laying and hatching eggs in an artificial nest. Two juveniles left the nest in April 2008. These results indicate that both captive breeding and reintroduction are potentially important ways to increase the population of the Oriental pied hornbill in natural habitats. Zoo Biol 31:683‐693, 2012. © 2011 Wiley Periodicals, Inc.     

Looking back to go forward: genetics informs future management of captive and reintroduced populations of the black-footed rock-wallaby <Emphasis Type="Italic">Petrogale lateralis</Emphasis>

Active management is essential to the survival of many threatened species globally. Captive breeding programmes can play an important role in facilitating the supplementation, translocation and reintroduction of wild populations. However, understanding the genetic dynamics within and among wild and captive populations is crucial to the planning and implementation of ex situ management, as adaptive potential is, in part, driven by genetic diversity. Here, we use 14 microsatellite loci and mitochondrial Control Region sequence to examine the population genetics of both wild populations and captive colonies of the endangered warru (the MacDonnell Ranges race of the black-footed rock-wallaby Petrogale lateralis) in central Australia, to understand how historical evolutionary processes have shaped current diversity and ensure effective ex situ management. Whilst microsatellite data reveal significant contemporary differentiation amongst remnant warru populations, evidence of contemporary dispersal and relatively weak isolation by distance, as well as a lack of phylogeographic structure suggests historical connectivity. Genetic diversity within current captive populations is lower than in the wild source populations. Based on our genetic data and ecological observations, we predict outbreeding depression is unlikely and hence make the recommendation that captive populations be managed as one genetic group. This will increase genetic diversity within the captive population and as a result increase the adaptive potential of reintroduced populations. We also identify a new site in the Musgrave Ranges which contains unique alleles but also connectivity with a population 6 km away. This novel genetic diversity could be used as a future source for supplementation.     

Parentage assignment reveals multiple paternity in the critically-endangered Guatemalan beaded lizard (Heloderma charlesbogerti)

Within captive management programs for species of conservation concern, understanding the genetic mating system is of fundamental importance, given its role in generating and maintaining genetic diversity and promoting opportunities for sperm competition. If a goal of a conservation program is reintroduction, knowledge of the mating system may also inform prediction models aimed at understanding how genetic diversity may be spatially organized, thus informing decisions regarding where and which individuals should be released to maximize genetic diversity in the wild population. Within captive populations, such information may also influence how animals are maintained in order to promote natural behaviors. Here we investigate the genetic mating system of the Guatemalan beaded lizard, Heloderma charlesbogerti, a member of an entire clade lacking such information. A group of adult male and female H. charlesbogerti co-habited a large outdoor enclosure for five years during the species’ perceived breeding season. Through genomic parentage analysis, 50% of clutches comprising multiple offspring were found to result from multiple paternity, with up to three males siring offspring within single clutches. Both males and females were observed to produce offspring with multiple partners within a given year. As such, within this captive environment, where opportunities existed for mating with multiple partners, the genetic mating system was found to be highly polygamous, with multiple paternity common within clutches. These findings are novel for the family Helodermatidae, and the results have broader implications about how reproductive opportunities should be managed within captive conservation programs.