Widespread selective sweeps affecting microsatellites in Drosophila populations adapting to captivity: Implications for captive breeding programs

Many threatened species are being maintained in captivity to save them from extinction, often with the eventual aim of reintroduction. The objective of genetic management in captivity is to ‘freeze’ evolution i.e. to avoid genetic adaptation to captivity and to retain genetic diversity. Most current genetic management of threatened species addresses the latter, but does not explicitly address the former. The theory underlying current genetic management and its practical implementation assumes neutrality of loci. However, genetic adaptation in captive populations may cause non-neutral behavior at neutral loci due to selective sweeps (hitchhiking) caused by rapid allele frequency changes at linked fitness loci. We compared changes in microsatellite genetic diversity at eight non-coding loci with neutral predictions in 23 pedigreed captive populations of Drosophila melanogaster maintained with effective sizes of 25 (eight replicates), 50 (6), 100 (4), 250 (3) and 500 (2) for 48 generations. Loss of microsatellite heterozygosity was significantly faster (by 12%) than predicted by neutral theory, as assessed by regressing proportion of heterozygosity retained on pedigree inbreeding coefficients. Further, greater than neutral changes were observed for both variances in allele frequencies across replicates (by 25%), and for temporal changes in allele frequencies (by 33%). All eight microsatellite loci showed signals of selectively-driven changes. Rather than having their evolution ‘frozen’, captive populations are undergoing major genome-wide selective sweeps that affect not only fitness loci but linked neutral loci. Captive genetic management for threatened species destined for reintroduction requires modification to explicitly minimize genetic adaptation to captivity.     

Generations in captivity increases behavioral variance: considerations for captive breeding and reintroduction programs

Long-term maintenance of captive populations followed by release of captive animals into the wild is one of many approaches to endangered species conservation. To assess captivity's effects on behavior, a simulated predator was presented and response behaviors measured in oldfield mice, Peromyscus polionotus subgriseus. The animals tested were from four populations collected from Ocala National Forest, Florida, and held in captivity for varying numbers of generations: 35, 14, 2, and 0 (wild caught). Results show (1) that the more generations a population has been in captivity, the less likely an individual is to take cover after seeing a predator and (2) variance in predator-response behaviors increases with generations in captivity. These results point to two ways in which captivity can compromise animal behavior and, in turn, the success of reintroduction programs. First, because individuals from populations that have been in captivity for multiple generations seek refuge less often than their wild counterparts, they might experience increased mortality in the wild due to predation. Second, increased behavioral variance could translate into decreased survivorship upon reintroduction. Therefore, more individuals will need to be released to reach the targeted wild population size.     

Minimizing genetic adaptation in captive breeding programs: A review

Captive breeding for species of conservation concern is the act of bringing rare or endangered animals into captivity with the hope of rearing sustained captive populations for eventual reintroduction into the wild. Within captivity, genetic changes can occur that may reduce a species’ ability to persist once a population is reintroduced back into its natural habitat. We sought to determine the efficacy of recommendations made to minimize genetic adaptation to captivity by addressing the following questions: (i) Are these recommendations already being carried out in captive programs? (ii) How practical is each recommendation? and (iii) Which recommendations call for future investigation? We performed an extensive search of the published literature for studies of non-domestic, non-model, captive animals in which the investigators used and reported a strategy that can minimize genetic adaptation to the captive environment. We found different forms of each recommendation already being executed in captive programs to varying degrees. In all, we reviewed 90 articles covering four broad categories of strategies. We conclude that the best approach to minimize genetic adaptation is to reduce the number of generations that a species spends in captivity. If this is not possible, then we suggest attempting to minimize generations first by delaying reproduction and then by cryopreservation of germplasm. Other strategies are effective to varying degrees depending on the species’ natural history. A large gap in the current literature is the interactive effects of multiple strategies being implemented simultaneously, future research should focus on this issue.     

Captive breeding genetics and reintroduction success

Since threatened species are generally incapable of surviving in their current, altered natural environments, many conservation programs require to preserve them through ex situ conservation techniques prior to their reintroduction into the wild. Captive breeding provides species with a benign and stable environment but has the side effect to induce significant evolutionary changes in ways that compromise fitness in natural environments. I developed a model integrating both demographic and genetic processes to simulate a captive-wild population system. The model was used to examine the effect of the relaxation of selection in captivity on the viability of the reintroduced population, in interaction with the reintroduction method and various species characteristics. Results indicate that the duration of the reintroduction project (i.e., time from the foundation of the captive population to the last release event) is the most important determinant of reintroduction success. Success is generally maximized for intermediate project duration allowing to release a sufficient number of individuals, while maintaining the number of generations of relaxed selection to an acceptable level. In cases where a long residence time in captivity cannot be avoided, the use of distinct, genetically independent captive breeding units allows more efficient purging of the genetic load in the reintroduced population, and substantially improves its viability. Overall, the study allows to identify situations in which the genetic cost associated with selection relaxation may overwhelm the demographic benefits of programs.     

Population management of threatened taxa in captivity within their natural ranges: Lessons from Andean bears (Tremarctos ornatus) in Venezuela

Populations of threatened taxa in captivity within their natural ranges can make important contributions to conservation, but these may be compromised by the inappropriate application of population management goals developed in other contexts. We conducted demographic, genetic, and population viability analyses on the captive population of Andean bears (Tremarctos ornatus) in Venezuela to investigate the management of within-range captive populations in general, and to better integrate this population into the conservation of Andean bears in particular. We found that although the present population is very small and not internally self-sustaining, incorporation of confiscated wild individuals has resulted in a low average number of generations in captivity and low inbreeding, with moderate gene diversity and a high probability of future population persistence. However, past imports from extra-range populations have been from over-represented lineages of unknown origin, which have mixed with under-represented Venezuelan ones, reducing the future value of the Venezuelan population as a source for founder stock. Our analyses indicate that the rate of incorporation of wild recruits is a major factor influencing proxy measures of conservation value, and distinguishing within- from extra-range populations. This implies that, contrary to conventional wisdom, internal self-sustainability can be a misguided goal in within-range populations, which furthermore may not be suitable destinations for surplus animals from captive populations elsewhere.     

The importance of chemical communication studies to mammalian conservation biology: A review

The relevance of chemical communication to mammalian conservation is not often the focus of scientific investigation. Our review identifies and discusses ten key areas in which the study of chemical communication aids conservation behaviour. Articles (n = 140) were revealed, most were concerned with population monitoring (22.50%), reducing human-wildlife conflicts (18.93), influencing habitat selection (18.57%), increasing welfare of captive animals (12.86%), encouraging captive breeding (12.86%), reducing predation (5.71%), and increasing the success of release programmes (5.00%). Few articles (<4%) were found relating olfactory studies to health status of wild populations, reducing hybridization or as indication of pollution. A growing number of articles are addressing how olfactory studies may aid conservation, but more rigorous experimental testing and manipulations are required. The vast majority of studies linking olfaction with conservation involved the population monitoring of wild carnivores. We suggest that animal behavioural studies and manipulations of chemical communication can have significant impacts on conservation in these areas, which should be further developed to generate practical applications. Areas of future study include chemical communication of aquatic mammalian species, the transfer of olfactory cues under water, and the identification of genetic markers that may link ‘personality’ with olfactory responses. Linking olfactory studies to fitness, either on an individual or population scale, particularly in a wider ecological context is more likely to increase conservation value. Animal translocations and reintroduction programmes may offer a means to do this and could be an important area to direct future studies.     

An assessment of the contribution of captive breeding to the conservation of rare mammals

There have been few attempts to examine the success of zoos in the establishment and maintenance of captive populations of rare animals. Annual census data for population size and births of species in zoos are now available for a 15-year period. Sixty-one of 274 rare mammal species were considered to have bred frequently enough in captivity to warrant investigation. By comparing these species with each other and with a theoretical model it proved possible to identify five consecutive stages in the development of a successful population in captivity. Species were then assigned to each stage to determine the success of breeding programmes in zoos. Twenty-six species can be considered self-sustaining. With some idea of their contribution to date, the role of zoos in conservation is discussed. It is concluded that captive-breeding for reintroduction is a much less significant role for zoos than the maintenance and development of captive populations of all species for educational and research purposes, and as insurance for the future.     

Risks of a late start to captive management for conservation: Phenotypic differences between wild and captive individuals of a viviparous endangered skink (Oligosoma otagense)

Maintenance of demographically and genetically self-sustaining populations in captivity can assist conservation of threatened species. Captivity can, however, lead to changes in phenotype, though to date this issue has received little attention in reptiles. We compared phenotypic differences in the now critically-endangered Otago skink (Oligosoma otagense) between wild specimens (Otago, southern New Zealand) and in captivity (North Island). Individuals of this long-lived, viviparous species have been maintained up to three generations in captivity, primarily by private herpetoculturists, but increasingly there is interest in integrating management of captive stocks with conservation in situ. For the same snout-vent length, captive skinks pooled across three colonies had a significantly heavier body mass, wider tail base, longer tail (juveniles only), faster growth rate and much slower sprint speed than in the wild. Captive skinks also lacked ectoparasitic mites and haemogregarine parasites, and experienced warmer temperatures with probably greater access to food. Our study demonstrates the importance of not treating captive management for conservation as a tool of last resort. Important questions, if captive-raised animals are to be released to the wild, are is it better for released skinks to run swiftly or to be heavy-bodied, and what role does reinfestation with native parasites have in determining this balance? We also recommend genetic analysis and studbook management of captive stocks, research to determine implications of heavy body mass for reproduction in captivity, and production of at least some offspring for release inside larger enclosures within the local climate.     

The effects of captive experience on reintroduction survival in carnivores: A review and analysis

This review focuses on the success and survivorship of captive-born versus wild-caught carnivores used in reintroductions. Previous reviews have suggested that reintroduction projects using captive-born animals are less likely to be successful than projects translocating wild-caught animals. The purpose of this paper is to examine this statistically and investigate how captivity may affect the survival of reintroduced carnivores. We examined results published in previous reviews, and found evidence to support that reintroduction projects using wild-caught animals are significantly more likely to succeed than projects using captive-born animals. We further compiled our own review of 45 case studies in carnivore reintroduction projects (in 17 species across 5 families) to investigate survival rates rather than overall project ‘success’. We found that (1) wild-caught carnivores are significantly more likely to survive than captive-born carnivores in reintroductions; (2) that humans were the direct cause of death in over 50% of all fatalities and (3) that reintroduced captive-born carnivores are particularly susceptible to starvation, unsuccessful predator/competitor avoidance and disease.     

Population viability analysis of European bison populations in Polish and Belarusian parts of Bia?owie?a Forest with and without gene exchange

European bison (Bison bonasus) became extinct in the wild at the beginning of the 20th century. The contemporary Lowland line of bison was founded by seven individuals that survived in captivity. The largest population of Lowland bison live in the Bia?owie?a Forest, but the forest and the population are divided by a border fence between Poland and Belarus. This fence is a barrier to the movement of ungulates. In this study, we used population genetic models to predict the future viability of the Polish and Belarusian bison populations. We determined the founder contribution, founder equivalent, mean inbreeding coefficient, mean kinship, and the proportion of genetic diversity retained in the Belarusian bison population. Although the founding group of the Belarusian population was larger than that of the Polish population, the latter had more favourable genetic parameters. We assessed inbreeding depression for fecundity in free-ranging European bison compared to captive individuals. Using population viability analysis (PVA) we modelled both bison populations with or without gene exchange, and with or without incorporating the kinship of the founders. When founder kinship was included, in both populations the mean number of alleles and the gene diversity retained within extant populations decreased substantially compared to PVA models in which founders were not related. The worst genetic parameters were obtained for the Belarusian population under a scenario in which the founders are related and gene exchange is lacking, which is the closest to the real situation. Creation of passages for animals by partial removal of the border fence would have a favourable effect on the genetic variation and viability of both bison populations, especially the Belarusian.     

An integrated comparison of captive-bred and wild Atlantic salmon (Salmo salar): Implications for supportive breeding programs

Supportive breeding is a strategy consisting in maintaining a pool of locally-adapted wild genitors in captivity whose offspring are released in the wild at an early developmental stage. In this study, we tested the utility of this strategy in preventing phenotypic and genetic divergences between captive-bred and wild animals that could be detrimental for wild populations. Combining microsatellite analyses, morphological measurements and behavioural trials in the laboratory, we compared the progeny of Atlantic salmon (Salmo salar) born in captivity with individuals born in the wild. At all these levels, we found significant differences between the progeny of the two groups. Specifically, allelic frequencies significantly differed between groups, with captive-bred fish tending to be less variable with lower heterozygosity and allelic richness values. The shape of wild-born fish was also different from that of the captive-group, particularly in the depth of the head and the length of the pectoral fins. Finally, captive-bred individuals were, on average, more aggressive than wild-born fish. We demonstrated that this difference was strongly dependent upon the environment as captive-bred fish were more aggressive only when together with their wild conspecifics or with an exotic competitor, the rainbow trout (Oncorhynchus mykiss). Overall, our results showed that both phenotypic and genetic changes can arise even if genitors share a common brood-stock and after only a few months of rearing in a controlled environment. We conclude that the progeny produced in such supportive breeding programs does not meet the criteria necessary to ensure preserving the genetic and ecological integrity of wild populations.     

Genetic consequences of intensive management in game birds

Introduction of wildlife for game restocking is one major pathway of genetic homogenization. The red-legged partridge (Alectoris rufa, Phasianidae), a small game bird native to south-western Europe, is in high demand by hunters and natural populations are constantly supplemented by commercial stocks of captive-bred individuals. Also, in recent years human-mediated hybridization with congeneric chukar partridges (Alectoris chukar: Greece, Cyprus, from Middle East to East Asia) has been frequently documented in the wild and in captivity. This study attempts to evaluate the genetic consequences of intensive captive breeding and restocking in the A. rufa species. We investigated A. rufa genetic diversity by making comparisons in both a spatial (across the entire species’ range) and a temporal framework. We accomplished this latter by comparing modern vs. ancient partridges resident in museums and collected 1856-1934, well before supplemental stocking became common. Using mtDNA we found significant changes in the haplotype profile of modern vs. ancient A. rufa, and widespread introgression with chukar genes across the entire species range only in modern representatives, with the relevant exception of Corsican populations. However, Random Amplified Polymorphic DNA (RAPD), as opposed to microsatellite DNA markers, showed also modern Corsican populations to harbour many A. rufa × A. chukar hybrids. We conclude that captive breeding programs should make strict use of time-saving and comparatively low cost DNA barcodes to minimize genetic pollution, such as those provided by diagnostic RAPD markers. We also recommend that the active ban on import of exotics and/or hybrids be extended to non-local populations. Altogether this would represent a substantial step forward to preserve A. rufa as well as other game species subjected to similar intensive management.     

Captive breeding promotes aggression in an endangered Mexican fish

We compared the behaviour of wild and captive-bred butterfly splitfins (Ameca splendens), an endangered freshwater fish, to investigate whether captive breeding results in the behavioural divergence of wild and captive individuals. In a first experiment, we examined whether the captive environment allows for the similar expression of behaviours observed in wild fish. The foraging, courtship and aggressive behaviour of fish in their natural habitat (in Mexico) was compared with that of their counterparts that have been bred at London Zoo, UK, for 40 years. These in situ observations revealed that wild fish were preoccupied with searching for food whereas captive fish engaged more in aggressive interactions. In a subsequent laboratory experiment we compared the behaviour of wild-caught and captive-bred fish under standard conditions in two novel habitats: structured (enriched) and unstructured (bare) aquaria. Overall, captive-bred butterfly splitfins displayed higher levels of aggression than wild-caught fish. The relationship between aggression and habitat structure was influenced by density; captive-bred males were more aggressive when observed in structured habitats than unstructured ones, but only when they were stocked at a high density. We also found an effect of tank structure on foraging behaviour, with individuals spending more time foraging in unstructured tanks than structured tanks. There was no effect of captive breeding or habitat structure on courtship behaviour.Our findings suggest that captive environments can promote the development of aggressive behaviour which may affect the suitability of captive-bred fishes for reintroduction into the wild.     

Challenges and opportunities of genetic approaches to biological conservation

I discuss future challenges and opportunities in genetic approaches to biodiversity conservation. Resolving taxonomy uncertainties and identifying diverged evolutionary units within species are both bedevilled by a plethora of definitions: the challenge for the conservation community is to come to an agreed definition of species and for a unit within species for conservation purposes. For genetic management in the wild, the main challenge is to apply well-established genetic principles to management, especially of fragmented populations. Fears about outbreeding depression are preventing rational use of gene flow for genetic rescue; predicting the risk of outbreeding depression is the most important unmet scientific challenge in the field. The major challenge in genetic management of captive populations of threatened animal species is to institute explicit management to minimize genetic adaptation to captivity, so that reintroduction success is maximized. The development of low cost genome sequencing offers many research opportunities and challenges. For example, there are opportunities to identify genes involved in speciation and a major challenge is to devise molecular tests to predict reproductive isolation between populations. Genomics offers opportunities to provide higher precision estimate for many parameters of importance to conservation. A major challenge is to devise means to assess, on a genome-wide basis, genetic diversity that is important to adaptive evolution. There is a challenge to develop simple inexpensive means to monitor genetic diversity of species on a global scale. Many of the most important practical challenges concern application of current genetic knowledge to the management of threatened species.     

Survival, interactions with conspecifics and reproduction in 37 chimpanzees released into the wild

We report the results of eight years of post-release monitoring of 37 wild-born, captive chimpanzees released into the Conkouati-Douli National Park, Republic of Congo. Overall survival was high, with 23 (62%) individuals remaining in the release zone, and only 5 (14%) confirmed dead. Released females regularly interacted with wild chimpanzees. Several females appeared to have integrated into wild groups for extended periods of time, and four released females gave birth to a total of five offspring. However, encounters with wild chimpanzees were a major cause of mortality in released males, and 40-50% of released males would have died without veterinary intervention. These sex differences are in accordance with knowledge of chimpanzee behavioural ecology. Our results demonstrate that wild-born, captive chimpanzees can be released into the wild successfully, under certain specific conditions. Most importantly, careful planning and preparation is critical at all stages; a suitable release area must be identified; potential risks to existing wild populations, including the possibility of disease transmission, must be minimised; and post-release monitoring is essential. Adolescent females are the most suitable candidates for release, as they appear to be able to integrate successfully into wild communities. However, males should not be released where wild chimpanzees occur, as they are likely to be attacked and killed. Release into the wild addresses the welfare of certain individual animals, although it clearly cannot address the fate of all captive, wild-born chimpanzees. Knowledge of how to successfully release chimpanzees into the wild also has both current and potential future benefits for the conservation of wild chimpanzee populations.     

Monitoring the performance of wild-born and introduced lizards in a fragmented landscape: Implications for ex situ conservation programmes

Ex situ conservation of animal populations may benefit from captive-breeding programmes, but these are criticised because they are assumed to be difficult, time-consuming and expensive, while they do not guarantee success. However, such assumptions remain untested in most organisms; for example, introductions could be very useful for recovering populations of small-sized species with short generation time, no learned behaviours, and ease to rear in captivity. Here, we document an easy, cheap and successful reintroduction programme of the lacertid lizard Psammodromus algirus. Two captive-bred cohorts (178 juveniles in 2001 and 187 in 2002) were released in four woodland fragments (0.9-5.2 ha) at two localities (B and V); B housed a stable lizard population whereas V apparently lacked a viable population of lizards. We monitored introduced and native lizards during 2002 and 2003, and carried out a corroborative searching in 2006 which confirmed the existence of a lizard population at site V. Introduced lizards had higher activity and dispersed more frequently among woodland fragments than native ones. Survivorship and growth rates were similar for both groups, but introduced juveniles were about 25% larger than native ones, due to both early hatching and better rearing conditions. The whole procedure was easily implemented in our Faculty facilities (mean hatching and hatchling survival rates of 0.90 and 0.87), and cost less than 20,000 € (excluding salaries). Therefore, similar programmes may be of wide application in small animals and of practical importance for species with a meta-population structure living in fragmented landscapes.     

Minimum viable population and conservation status of the Atlantic Forest spiny rat Trinomys eliasi

A population viability analysis (PVA) was conducted to assess the minimum viable population (MVP) of the Atlantic Forest spiny rat Trinomys eliasi, a species threatened by habitat loss and restricted geographical distribution. Objectives were to suggest quasi-extinction thresholds, estimate minimum areas of suitable habitat (MASH) and MVPs, and compare results with the species’ current status. The computer package VORTEX was used. The model predicted sizes of 200 animals to achieve demographic stability, but buffering declines in genetic variability required populations of 2000 animals. Estimated MASHs were approximately 250 and 2500 ha for demographic and genetic stability, respectively. Mortality rate and mean litter size were the most sensitive parameters to changes in model assumptions. The protection of known populations and the search for extant populations are the first steps in conservation. T. eliasi's issue could help protecting the coastal shrubland ecosystem of Rio de Janeiro state. Observing IUCN's criteria for listing threatened species, it is suggested that T. eliasi should be ranked as vulnerable in red lists.     

The unappreciated ecology of landrace populations: Conservation consequences of soil seed banks in Cassava

Failure to take into account the ecological complexity of landrace populations of crop plants limits our ability to conserve their genetic resources in situ. Soil seed banks are a central feature of the ecology of landrace populations of cassava; their existence has consequences for conservation. Seedlings recruited from seed banks are incorporated by farmers into their stocks of clones of this vegetatively propagated crop, transforming pure clonality into a mixed clonal/sexual reproductive system. Soil seed banks, and farmers’ responses to them, play an important role in maintaining diversity in populations of cassava landraces. In a study combining genetic and ethnobiological approaches, we showed the following: (i) Recruitment from soil seed banks increased diversity of populations at the local scale. At the level of a field, the presence of plants issued from seeds resulted in significantly greater diversity of genotypes and phenotypes than if only individuals planted by farmers had been present. (ii) Farmers’ use of seed banks has enabled indirect ‘exchange’ of locally adapted cassava germplasm between cultural groups, without requiring that groups actually encountered one another and engaged in social exchange of cultivars. (iii) Farmers have responded to catastrophic crop failure by using seed banks to regenerate stocks of clones. This use of seed banks should enable cassava populations to respond to disasters by an increase of genetic diversity, rather than by a narrowing of the genetic base, often feared in such situations.     

Genetic differences between the two remaining wild populations of the endangered Indian rhinoceros (Rhinoceros unicornis)

The management of rare and endangered species in the wild and in captivity requires an understanding of the characterization of the genetic units within each species and their relationships to each other. The Indian rhinoceros (Rhinoceros unicornis) is an endangered species with a current population size of c. 2800 individuals. We analyzed 26 individuals of known origin kept in captivity and 21 wild ranging individuals of the two remnant large wild populations in Assam (India) and Nepal employing mitochondrial and microsatellite markers to determine whether the two geographically isolated populations show distinct patterns of genetic diversity, and whether the genetic diversity of the populations is influenced by past demographic bottlenecks. We identified 10 different mitochondrial D-loop haplotypes, of which 4 were specific to the Assam population (10 sequences examined) and 6 specific to the Nepal population (19 sequences). Similarly, the microsatellite analysis demonstrated a strong genetic differentiation between the Assam and Nepal populations and allowed to assign each individual to its origin with high confidence. Furthermore, our analyses revealed the occurrence of a bottleneck in the Assam population long before the reported bottleneck in 1908, and it revealed that the Nepal population is a recent (probably post-glacial) colonization. In summary, the extent of genetic divergence between the two remnant R. unicornis populations suggests separate conservation programs (even for captive individuals) as long as the persistence of the entire species is not severely threatened. The microsatellite markers can also be used to determine the origin of confiscated material such as horns.