Captive-born Individuals Research Articles

Evaluating the performance of conservation translocations in large carnivores across the world

Globally, fragmented landscapes and other anthropogenic pressures are causing declines in large carnivore populations. Conservation organizations are working to counteract these trends through the translocations of large carnivores, for example by reintroducing them to their historic ranges or by reinforcing existing populations to promote gene flow and resilience. This study analyses a dataset gathered from 33 translocation projects involving 297 individual animals across 22 countries in five continents, with 18 different large carnivore (>15 kg) species surveyed. An overall success rate (survival > six months) of 66 % for all individuals was shown for large carnivores, indicating an above average success rate when compared to the translocation of other terrestrial vertebrates. While captive-born individuals still fared worse than wild-born individuals, a 32 % increase in success rates was observed for releases of captive-born individuals within the last 14 years compared to a 17 % increase in success for releases of wild-born individuals. Despite the encouraging trends in metrics of success, only 37 % of study individuals were observed engaging in reproductive behavior. While this is likely an under-count, we caution against the conflation of translocation success with population establishment. We also identified key choices in the decision tree facing those implementing translocations, and analyzed associated metrics of success. Critical decisions include whether or not to use soft-releases, choosing younger animals, selecting unfenced release locations, and sourcing wild-born individuals – all of which can lead to a higher likelihood of success. As the UN Decade of Ecosystem Restoration gets underway, we hope this information can assist decision makers and practitioners in achieving more desirable outcomes for conservation translocation of large carnivores.

Demography and epidemiology of captive former biomedical research chimpanzees (Pan troglodytes) 1: Survival and mortality.

Accurate and up-to-date data on longevity and mortality are essential for describing, analyzing, and managing animal populations in captivity. We assembled a comprehensive demography data set and analyzed survival and mortality patterns in a population of captive former biomedical research chimpanzees. The study synthesized over 51,000 life-years of demographic data collected on 2349 individuals between 1923 and 2014. Our goal was to assess the population's current age-sex composition, estimate rates of survivorship, mortalityand life expectancy, and compare findings withother chimpanzee populations of interest. Results indicated an increasingly geriatric contemporary population declining in size. The median life expectancy (MLE) of the entire population was 32.6 years (males 29.1, females 36.1). For chimpanzees who reached 1year of age, the MLE increased to 34.9 years (males 31.0, females 38.8). Survival probability was influenced by both sex and birth type. Females exhibited greater survivorship than males (β1 = -0.34, z = -5.74, p < 0.001) and wild-born individuals exhibited greater survivorship than captive-born individuals (β2 = -0.55, z = -5.89, p < 0.001). There was also a seasonal trend in mortality, wherein more individuals died during the winter months (December-February) compared withother seasons. Analyses of life expectancy over time showed continual increases in both median age of living individuals and median age at death, suggesting that these chimpanzees have yet to reach their full aging potential in a postresearch environment. As they continue to age, ongoing monitoring and analysis of demographic changes will be necessary for science-based population and program management until extinction occurs some decades in the future.

04. Segmental muscle twitching behaviour in the flanks of lancehead vipers Bothrops spp in response to human approach

ABSTRACT - Bothrops species are known to have a wide range of defensive behaviours against potential threats. Herein we show a frequently observed, but to date undocumented, behaviour in male and female Bothrops spp of varying sizes in newly arrived specimens from the wild, short-or long-term captives as well as in captive born individuals. The behaviour consists of irregular, synchronous or asynchronous muscular twitches in segments of the body flanks in otherwise motionless snakes. We named this ‘Segmental Muscle Twitching Behaviour’ (SMTB). We observed fifteen Bothrops spp from six species groups for incidence of this behaviour and made videos of snakes during the ‘alertness’ and ‘threatening’ phases of response to human approach. We found the behaviour in only five species, these belong to the monophyletic Bothrops jararacussu and Bothrops atrox species groups, suggesting a single evolutionary origin of this behaviour. Macroscopically, SMTB varied in the number of segments involved and the twitches had uneven intensities. Although recurrent and often replicable in similar situations during human approach, the behaviour was not displayed consistently. In addition, SMTB can be interrupted, stay inactive for quite some time and then restart. Hypotheses to explain this behaviour are suggested.

Assessment of Eurasian lynx reintroduction success and mortality risk in north-west Poland

Despite recent local reintroductions of the Eurasian lynx Lynx lynx in central and north-eastern Poland, the increase in its population was not followed by its westward expansion. To address this problem and restore the lynx population in north-western Poland, 61 captive-born individuals of Baltic population origin were released in the province of Western Pomerania in 2019–2021. Prior to their release, all the animals underwent an adaptation training phase. They were then set free according to a hard-release protocol and subsequently monitored by means of GPS telemetry. In order to assess the short-term reintroduction success, the survival and causes of death of the released individuals were studied as a function of sex, age, training time, and release time and place. The overall survival rate was 71.15%, the median survival time 202 days. Most mortality, due to environmental factors, i.e. scabies (> 200 days) or traffic collisions (< 200 days), was recorded during the first 300 days following release. Age, year of release and training time were significantly related to survival, indicating that the older the lynx was when released, the better its survival changes. In contrast, the longer the training time, the poorer were the chances of survival. There was no evidence of any effect of sex, month of release or place of release. Based on these results, recommendations were made for the planning of further releases and measures to manage the restored population.

Body condition, skin bacterial communities and disease status: insights from the first release trial of the limosa harlequin frog, Atelopus limosus.

Many endangered amphibian species survive in captive breeding facilities, but there have been few attempts to reintroduce captive-born individuals to rebuild wild populations. We conducted a soft-release trial of limosa harlequin frogs, Atelopus limosus, which are highly susceptible to the amphibian chytrid fungus Batrachochytrium dendrobatidis (Bd), to understand changes associated with the transition from captivity to the wild. Specifically, we assessed changes in body condition, skin-associated bacterial communities and disease status after release. Frogs were housed individually in field mesocosms and monitored for 27 days. Body condition did not significantly change in the mesocosms, and was similar to, or higher than, that of wild conspecifics at day 27. The skin bacteria of captive-born frogs, based on 16S rRNA gene amplicons, became similar to that of wild conspecifics after 27 days in mesocosms. Prevalence of Bd in wild conspecifics was 13-27%, and 15% of the A. limosus in mesocosms became infected with Bd, but no mortality of infected frogs was observed. We conclude that mesocosms are suitable for systematically and repeatedly monitoring amphibians during release trials, and that body condition, the skin microbiome, and Bd status can all change within one month of placement of captive-born individuals back into the wild.

You can go your own way: No evidence for social behavior based on kinship or familiarity in captive juvenile box turtles

Behavioral interactions between conspecific animals can be influenced by relatedness and familiarity. Compared to other vertebrate taxa, considering such aspects of social behavior when housing captive reptiles has received less attention, despite the implications this could have for informing husbandry practices, enhancing welfare, and influencing outcomes of conservation translocations. To test how kinship and familiarity influenced social behavior in juvenile Eastern Box Turtles (Terrapene carolina), we reared 16 captive-born individuals under semi-natural conditions in four equally sized groups, where each group comprised pairs of siblings and non-siblings. Using separation distance between pairs of turtles in rearing enclosures as a measure of gregariousness, we found no evidence suggesting siblings more frequently interacted with one another compared to non-relatives over the first five months of life (β = −0.016, 95% CI: −0.117 to 0.084). Average pair separation distance decreased during this time (β = −0.146, 95% CI: −0.228 to −0.063) but may have been due to turtles aggregating around concentrated resources like heat and moist retreat areas as cold winter temperatures approached. When subjects were eight months old, we measured repeated separation distances between unique pair combinations in an experimental environment and similarly found no support for gregariousness (associations) being influenced by kinship or familiarity (β = −1.554, 95% CI: −9.956 to 6.848). Additionally, neither differences in body size between pairs of turtles (β = −22.289, 95% CI: −68.448 to 23.870) nor the five-minute time interval during the 90-minute trial (P ≥ 0.18) had any apparent effect on associations. Agonistic interactions between individuals were never observed. Encouragingly, based on our results, group housing and rearing of juvenile box turtles did not appear to negatively impact their welfare. Unlike findings for other taxa, including some reptiles, our results suggest strategically housing groups of juvenile T. carolina to maintain social stability may not be an important husbandry consideration or necessary when planning releases of captive-reared individuals for conservation purposes.

Loss of Predator Discrimination by Critically Endangered Vancouver Island Marmots Within Five Generations of Breeding for Release

Conservation translocations, which involve the intentional movement and release of organisms for conservation benefit, are increasingly required to recover species of conservation concern. In order to maximize post-release survival, and to accomplish conservation translocation objectives, animals must exhibit behaviors that facilitate survival in the wild. The Vancouver Island marmot (Marmota vancouverensis) is a critically endangered endemic in Canada which has been captive-bred for 24 years for reintroductions and reinforcements that have increased the wild population from ~30 to more than 200 individuals. Despite this success many marmots are killed by predators after release and predation represents a major hurdle to full marmot recovery. To better understand if captive-bred marmots are prepared for the novel environment into which they will be released, and to determine whether such suitability changes over time, we presented taxidermy mounts of mammalian predators and non-predators to marmots that were wild-caught, and captive born for between one and five generations. We also examined mortality of offspring from marmots we tested that had been released to the wild. A minimum of 43% of offspring were killed by predators in the wild over 17 years, most by cougars. Marmots in captivity generally responded to taxidermy mounts by decreasing foraging and increasing vigilance, and overall responded more strongly to predators than non-predators, especially wolves. However, marmots in captivity for more than two generations lacked discrimination between cougars, non-predators, and controls, suggesting a rapid loss of predator recognition. This study was only possible because predator-recognition trials were initiated early in the conservation translocation program, and could then be repeated after a number of generations. The finding that changes occurred relatively rapidly (within five generations during which changes in genetic diversity were negligible) suggests that behavioral suitability may deteriorate more rapidly than genetics would suggest. Strategies addressing potential behavior loss should be considered, including sourcing additional wild individuals or pre-release training of captive-born individuals. Subsequently, post-release survival should be monitored to determine the efficacy of behavior-optimization strategies.

Personality and plasticity of defensive behavior in collared peccary (Dicotyles tajacu)

Inter-individual differences in behavior, together with phenotypic plasticity, may play a key role in the reintroduction success of captive-born individuals. Therefore, we aimed to investigate whether and how personality traits affect the plasticity of defensive behavior in collared peccary (Dicotyles tajacu). Twenty-six adult captive-born collared peccaries (12 males and 14 females) were submitted to three short-term challenges for personality assessment. Thereafter, each individual was submitted to four sequential tests, with different degrees of risk, allowing us to assess temporal/context consistencies in personality traits as well as the plasticity of defensive behavior. We noted a pronounced variability among the individuals’ boldness trait, while males and females did not differ in their behavioral responses in all tests. Additionally, collared peccaries show behavioral plasticity of defensive behavior across risk conditions. We also verified an association between boldness and defensive behavior in this species: the higher the boldness score, the less time collared peccaries spent on wariness behaviors in the higher risk condition. The link between personality traits and behavioral plasticity of collared peccaries across risk conditions warrants further investigation to understand the impact of this association on the post-release success of this and other species.

Captivity-induced metabolic programming in an endangered felid: implications for species conservation

Reintroduction of captive-bred individuals into the wild is an important conservation activity. However, environmental conditions can influence developmental programming, potentially causing metabolic disorders in adults. These effects are investigated here for the first time in an endangered species. Using body weight and feed intake data for Iberian lynx (Lynx pardinus) (n = 22), we compared the growth of captive versus wild born and/or reared individuals. Captive-born individuals gained weight as a function of calorie intake, unlike wild-born individuals. When compared with females reared in the wild, captive-reared females achieved a larger body size, without evidence of obesity. Captivity-associated changes to metabolic programming may compromise survival in the wild if an increased body size incurs a greater energy requirement. Large body size may also confer a competitive advantage over smaller, wild-born individuals, disrupting the social organisation of existing wild populations, and inferring long-term implications for the phenotypic composition of wild populations.

Erysipelas vaccination protocols in dolphins Tursiops truncatus evaluated by antibody responses over twenty continuous years.

Erysipelas is an infection caused by Erysipelothrix rhusiopathiae that affects many different species around the world, including cetaceans. The acute septicemic form can rapidly cause death in bottlenose dolphins Tursiops truncatus. The ultimate goals of this long-term study were the development and identification of the most effective vaccination protocol against clinical erysipelas in T. truncatus using a commercially available swine vaccine, and to determine whether there is a need for a semi-annual vaccination versus an annual vaccination. The present study concentrated on the immunization of a dolphin population (7 wild-born and 22 captive-born individuals) with 2 swine vaccines, the European 'Eurovac Ery®' vaccine and the American 'ER Bac Plus®' vaccine, and immunological profile results over a 20-yr time period. The general protocol was a primo-vaccination (between 3 and 7 mo of age for calves) with or without a booster 1 mo post primo-vaccination and either annual or semi-annual vaccination thereafter. Sera were collected prior to vaccination, 2 wk post-vaccination and monthly. A dolphin-specific ELISA was developed to analyze the erysipelas-specific antibody response of vaccinated animals. The final ELISA results (n = 1362 samples from 29 animals at pre- and post-vaccination time) suggest that (1) there is a significant difference in antibody levels at the start of the vaccination between older and younger animals; (2) at least 3 vaccinations are necessary to obtain antibody levels above the levels at pre-vaccination; (3) thereafter, annual vaccinations seem sufficient to keep antibody levels above the levels at pre-vaccination; and (4) both vaccines induced similar responses. No case of erysipelas infection was observed in this population during the study.

To breed or not to breed? Maintaining genetic diversity in white sturgeon supplementation programs

Conservation-focused reintroduction or supplementation programs using wild-born individuals tend to be more successful than those based on release of captive-born individuals. Negative genetic consequences of captive breeding, such as genetic diversity loss, domestication selection, and inbreeding, may contribute to this lowered success. In this study, we compare genetic consequences of repatriation, or collection of wild-born juveniles for captive rearing and release, and broodstock-based breeding, where wild adults are bred in captivity, in a conservation program for white sturgeon, Acipenser transmontanus. Specifically, we use microsatellite markers to compare the genetic diversity and number of spawners, Ns, represented by each captive breeding strategy. We present a novel method to estimate Ns in which simulated known family configurations of varying complexity are used to identify appropriate inclusive and exclusive probability thresholds in the maximum likelihood-based pedigree reconstruction program Colony. These probability thresholds are then applied to reconstruct progeny arrays and estimate Ns in empirical datasets of two repatriation cohorts and a naturally produced year class. We find that a repatriation approach preserves more genetic diversity and represents more spawners than broodstock-based captive breeding. Furthermore, a repatriation approach represents levels of genetic diversity similar to those found in a wild cohort. These results are the first comparison of Ns between broodstock and repatriation-based methods with respect to a hatchery program, and provide evidence that when possible, repatriation can be a more effective strategy for conserving genetic diversity than broodstock-based breeding for supplementation and reintroduction.

Long-term demographic and genetic effects of releasing captive-born individuals into the wild.

Because of continued habitat destruction and species extirpations, the need to use captive breeding for conservation purposes has been increasing steadily. However, the long-term demographic and genetic effects associated with releasing captive-born individuals with varied life histories into the wild remain largely unknown. To address this question, we developed forward-time, agent-based models for 4 species with long-running captive-breeding and release programs: coho salmon (Oncorhynchus kisutch), golden lion tamarin (Leontopithecus rosalia), western toad (Anaxyrus boreas), and Whooping Crane (Grus americana). We measured the effects of supplementation by comparing population size and neutral genetic diversity in supplemented populations to the same characteristics in unaltered populations 100 years after supplementation ended. Releasing even slightly less fit captive-born individuals to supplement wild populations typically resulted in reductions in population sizes and genetic diversity over the long term when the fitness reductions were heritable (i.e., due to genetic adaptation to captivity) and populations continued to be regulated by density-dependent mechanisms over time. Negative effects for species with longer life spans and lower rates of population replacement were smaller than for species with shorter life spans and higher rates of population replacement. Programs that released captive-born individuals over fewer years or that avoided breeding individuals with captive ancestry had smaller reductions in population size and genetic diversity over the long term. Relying on selection in the wild to remove individuals with reduced fitness mitigated some negative demographic effects, but at a substantial cost to neutral genetic diversity. Our results suggest that conservation-focused captive-breeding programs should take measures to prevent even small amounts of genetic adaptation to captivity, quantitatively determine the minimum number of captive-born individuals to release each year, and fully account for the interactions among genetic adaptation to captivity, population regulation, and life-history variation.

INVESTIGATION OF FACTORS POTENTIALLY ASSOCIATED WITH SERUM FERRITIN CONCENTRATIONS IN THE BLACK RHINOCEROS ( DICEROS BICORNIS) USING A VALIDATED RHINOCEROS-SPECIFIC ASSAY.

Iron overload disorder (IOD) can lead to organ dysfunction and may exacerbate other diseases in the critically endangered black rhinoceros ( Diceros bicornis). It is important to develop methods for monitoring the progression of iron storage (hemosiderosis), diagnosing the disease, and evaluating treatments in this species. Traditionally, an equine enzyme immunoassay (EIA) was used to measure rhinoceros ferritin, a serum protein correlated to iron stores. The goal of this study was to validate a rhinoceros-specific assay and investigate factors potentially associated with ferritin concentrations in black rhinoceros. A ferritin EIA developed for Sumatran rhinoceros was validated for black rhinoceros via Western blot analysis of liver ferritin and confirmed parallelism of serum samples to the EIA standard curve and used to analyze serum samples ( n = 943) collected from 36 black rhinoceros (<1-33 yr) at 14 U.S. institutions. Mean (±SEM) serum ferritin concentration was 6,738 ± 518 ng/ml (range: 85-168,451 ng/ml). Concentrations differed among individuals with eastern black rhinoceros (7,444 ± 1,130 ng/ml) having a higher mean ferritin than southern black rhinoceros (6,317 ± 505 ng/ml; P < 0.05) and higher mean values in wild-born (11,110 ± 1,111 ng/ml) than captive-born individuals (3,487 ± 293 ng/ml; P < 0.05). Ferritin concentrations did not differ between young rhinoceros (<5 yr old; 2,163 ± 254 ng/ml) and adults (7,623 ± 610 ng/ml) and were not correlated with age ( r = 0.143) or time in captivity ( r = 0.146, wild born; r = 0.104, all animals). Ferritin concentration was not impacted by sex (female: 2,086 ± 190 ng/ml; male: 8,684 ± 717 ng/ml), date, month, or season of collection ( P > 0.05). Data indicate ferritin concentrations are variable and not necessarily associated with IOD; ferritin is not recommended for diagnosing or monitoring IOD in black rhinoceros.

Reintroduction of the giant panda into the wild: A good start suggests a bright future

Reintroduction is an important approach in the conservation of endangered species and in recent decades a number of reintroduction programs have been conducted for conservation purposes. Generally, the success rate of reintroduction is low, but long-term monitoring of most reintroduction programs remains uncommon and this may influence the evaluation of reintroduction. The giant panda is a flagship species of biodiversity conservation. The Chinese government runs a giant panda reintroduction program and here we present reintroduction monitoring data from 2009 to 2015 for three giant pandas released into a small isolated wild population in western Sichuan, China. The results indicate that all three giant pandas display similar activity patterns to wild giant pandas, however, the wild-caught female demonstrated better adaptive ability to the wild environment than the two captive-born individuals in that she established a stable home range in the quickest time and gave birth to a cub. Genetic analysis indicates that new genetic material has been introduced into the local population. Our study provides the latest update on the giant panda introduction program and indicates that it is progressing well.

Captive Ancestry Upwardly Biases Estimates of Relative Reproductive Success.

Supplementation programs, which release captive-born individuals into the wild, are commonly used to demographically bolster declining populations. In order to evaluate the effectiveness of these programs, the reproductive success of captive-born individuals released into the wild is often compared to the reproductive success of wild-born individuals in the recipient population (relative reproductive success, RRS). However, if there are heritable reductions in fitness associated with captive breeding, gene flow from captive-born individuals into the wild population can reduce the fitness of the wild population. Here, we show that when captive ancestry in the wild population reduces mean population fitness, estimates of RRS are upwardly biased, meaning that the relative fitness of captive-born individuals is over-estimated. Furthermore, the magnitude of this bias increases with the length of time that a supplementation program has been releasing captive-born individuals. This phenomenon has long-term conservation impacts since management decisions regarding the design of a supplementation program and the number of individuals to release can be based, at least in part, on RRS estimates. Therefore, we urge caution in the interpretation of relative fitness measures when the captive ancestry of the wild population cannot be precisely measured.

Inbreeding and selection shape genomic diversity in captive populations: Implications for the conservation of endangered species

Captive breeding programs are often initiated to prevent species extinction until reintroduction into the wild can occur. However, the evolution of captive populations via inbreeding, drift, and selection can impair fitness, compromising reintroduction programs. To better understand the evolutionary response of species bred in captivity, we used nearly 5500 single nucleotide polymorphisms (SNPs) in populations of white-footed mice (Peromyscus leucopus) to measure the impact of breeding regimes on genomic diversity. We bred mice in captivity for 20 generations using two replicates of three protocols: random mating (RAN), selection for docile behaviors (DOC), and minimizing mean kinship (MK). The MK protocol most effectively retained genomic diversity and reduced the effects of selection. Additionally, genomic diversity was significantly related to fitness, as assessed with pedigrees and SNPs supported with genomic sequence data. Because captive-born individuals are often less fit in wild settings compared to wild-born individuals, captive-estimated fitness correlations likely underestimate the effects in wild populations. Therefore, minimizing inbreeding and selection in captive populations is critical to increasing the probability of releasing fit individuals into the wild.

Giant panda reintroduction: factors affecting public support

Reintroducing captive-born individuals of some extirpated flagship animal species is a helpful and remedy measure for promoting biodiversity conservation, and a successful reintroduction relies heavily on public support. However, little information is available on the factors affecting the public support for reintroduction of large carnivore species. In order to evaluate public support and willingness to pay for the Giant Panda Reintroduction Project (GPRP), we conducted 1100 interviews in August 2014 at Huaying city, Sichuan, China, close to where captive-born giant pandas (Ailuropoda melanoleuca) will be reintroduced. The results showed that local people strongly support this project and that 78.5 % of them are willing to pay an annual contribution. Per capita annual payments averaged USD31, and the potential value of donations to the GPRP in Huaying is about 11 million USD per year. Factors like interviewees’ residential area, occupation, education level, liking of wildlife, level of concern for wildlife conservation, the degree of familiarity with giant pandas, and the frequency of visiting captive giant pandas significantly affected their attitudes and willingness to pay for the project. The notion of “because I love pandas” was the main reason why respondents were willing to pay for the project; respondents’ doubts about the appropriate use of donated funds made them be unwilling to pay for the project. The results suggest that the GPRP is highly and socially acceptable amongst locals due to perceived social, economic and ecological benefits of the reintroduction. These findings clearly indicate, for the chances of reintroduction to be most socially accepted, governments should improve management and accountability when using donated funds, and create more opportunities for the public to engage with giant pandas, thereby encouraging people to become involved in conservation work benefiting conservation for the giant pandas and other endangered species.

Island survivors: population genetic structure and demography of the critically endangered giant lizard of La Gomera, Gallotia bravoana.

BackgroundThe giant lizard of La Gomera (Gallotia bravoana), is an endemic lacertid of this Canary Island that lives confined to a very restricted area of occupancy in a steep cliff, and is catalogued as Critically Endangered by IUCN. We present the first population genetic analysis of the wild population as well as of captive-born individuals (for which paternity data are available) from a recovery center. Current genetic variability, and inferred past demographic changes were determined in order to discern the relative contribution of natural versus human-mediated effects on the observed decline in population size.ResultsGenetic analyses indicate that the only known natural population of the species shows low genetic diversity and acts as a single evolutionary unit. Demographic analyses inferred a prolonged decline of the species for at least 230 generations. Depending on the assumed generation time, the onset of the decline was dated between 1200–13000 years ago. Pedigree analyses of captive individuals suggest that reproductive behavior of the giant lizard of La Gomera may include polyandry, multiple paternity and female long-term sperm retention.ConclusionsThe current low genetic diversity of G. bravoana is the result of a long-term gradual decline. Because generation time is unknown in this lizard and estimates had large credibility intervals, it is not possible to determine the relative contribution of humans in the collapse of the population. Shorter generation times would favor a stronger influence of human pressure whereas longer generation times would favor a climate-induced origin of the decline. In any case, our analyses show that the wild population has survived for a long period of time with low levels of genetic diversity and a small effective population size. Reproductive behavior may have acted as an important inbreeding avoidance mechanism allowing the species to elude extinction. Overall, our results suggest that the species retains its adaptive potential and could restore its ancient genetic diversity under favorable conditions. Therefore, management of the giant lizard of La Gomera should concentrate efforts on enhancing population growth rates through captive breeding of the species as well as on restoring the carrying capacity of its natural habitat.Electronic supplementary materialThe online version of this article (doi:10.1186/s12863-014-0121-8) contains supplementary material, which is available to authorized users.

How Much Does Inbreeding Contribute to the Reduced Fitness of Hatchery-Born Steelhead (Oncorhynchus mykiss) in the Wild?

Many declining populations are supplemented with captive-born individuals that are released directly into the wild. Because captive-born individuals can have lower fitness in the wild than their wild-born counterparts, a comprehensive understanding of the mechanisms responsible for the reduced fitness of these individuals is required for appropriate conservation and management decisions. Inbreeding among captive-born individuals is one plausible mechanism because captive breeding programs frequently use small numbers of breeders to create large numbers of siblings that are subsequently released together into the wild. We tested this hypothesis in a supplementation program for steelhead (Oncorhynchus mykiss) from the Hood River, Oregon, for which first-generation hatchery fish were demonstrated to have lower fitness in the wild than their wild-born counterparts. To determine the contribution of inbreeding to this fitness decline, we first assigned 11 run-years of hatchery steelhead (3005 fish) back to their broodstock parents (462 fish) using 8 polymorphic microsatellite loci. By combining pedigree analyses with species-specific estimates of genetic load, we found that inbreeding could at most account for a 1-4% reduction in the fitness of hatchery fish relative to wild fish. Thus, inbreeding alone cannot adequately explain the 15% average fitness decline observed in first-generation hatchery fish from this population.

Great ape genetic diversity and population history

Most great ape genetic variation remains uncharacterized; however, its study is critical for understanding population history, recombination, selection and susceptibility to disease. Here we sequence to high coverage a total of 79 wild- and captive-born individuals representing all six great ape species and seven subspecies and report 88.8 million single nucleotide polymorphisms. Our analysis provides support for genetically distinct populations within each species, signals of gene flow, and the split of common chimpanzees into two distinct groups: Nigeria-Cameroon/western and central/eastern populations. We find extensive inbreeding in almost all wild populations, with eastern gorillas being the most extreme. Inferred effective population sizes have varied radically over time in different lineages and this appears to have a profound effect on the genetic diversity at, or close to, genes in almost all species. We discover and assign 1,982 loss-of-function variants throughout the human and great ape lineages, determining that the rate of gene loss has not been different in the human branch compared to other internal branches in the great ape phylogeny. This comprehensive catalogue of great ape genome diversity provides a framework for understanding evolution and a resource for more effective management of wild and captive great ape populations.