Genetic Diversity In Captive Populations Research Articles

The necessity of considering founder kinships in conservation breeding programs

AbstractConservation breeding programs pursue the double objective of preserving genetic diversity and producing individuals to support in situ conservation measures. Genetic management and monitoring are commonly based on pedigree analyses and are therefore dependent on the pedigree quality and the underlying assumption that founders of the captive population are neither inbred nor related to each other or to the captive population. Should founders be related, this assumption may lead to an overestimation of genetic diversity and an underestimation of inbreeding in captivity. In this study, we examined the effects of the founder assumption on estimates of genetic diversity by combining three approaches: (1) computer simulations of pedigrees of theoretical captive populations and their associated in situ source populations, (2) analysis of pedigrees of real conservation breeding programs and (3) microsatellite‐based computation of kinship among founders from a captive population of houbara bustard. The theoretical approach revealed that the captive population's average mean kinship Mk increases linearly with founder average Mk. The bias in Mk due to the founder assumption was strongly related to the effective size of the source population and to pedigree quality while remaining critical after 25 generations of captivity. Results based on real populations were consistent with theoretical ones and confirmed the overestimation of genetic diversity in captive populations. Overall, our results indicate that under situations classically encountered in conservation breeding programs (e.g. small and isolated source population, incomplete pedigrees), estimates of genetic diversity are potentially highly overestimated, challenging the genetic management of captive populations of species of conservation concern.

Low genetic diversity in captive populations of the critically endangered Blue-crowned Laughingthrush (Garrulax courtoisi) revealed by a panel of novel microsatellites.

BackgroundCaptive populations permit research and conservation of endangered species in which these efforts are hardly implemented in wild populations. Thus, analysing genetic diversity and structure of captive populations offers unique opportunities. One example is the critically endangered Blue-crowned Laughingthrush, Garrulax courtoisi, which has only two known wild populations in Wuyuan, Jiangxi and Simao, Yunnan, China. We carried out the first conservation genetic study, in order to provide useful implications that allow for successful ex situ conservation and management of the Blue-crowned Laughingthrush.MethodsUsing the novel microsatellite markers developed by whole-genome sequencing, we genotyped two captive populations, from the Ocean Park Hong Kong, which are of unknown origin, and the Nanchang Zoo, which were introduced from the Wuyuan wild population since the year 2010–2011, respectively. The genetic diversity of captive Blue-crowned Laughingthrush populations was estimated based on genetic polymorphisms revealed by a new microsatellite data set and mitochondrial sequences. Then, we characterised the population structure using STRUCTURE, principal coordinates analysis, population assignment test using the microsatellite data, and haplotype analysis of mitochondrial data. Additionally, we quantified genetic relatedness based on the microsatellite data with ML-Relate.ResultsOur results showed equally low levels of genetic diversity of the two captive Blue-crowned Laughingthrush populations. The population structure analysis, population assignment test using the microsatellite data, and haplotype analysis of the mitochondrial data showed weak population structuring between these two populations. The average pairwise relatedness coefficient was not significant, and their genetic relatedness was quantified.DiscussionThis study offers a genetic tool and consequently reveals a low level of genetic diversity within populations of a critically endangered bird species. Furthermore, our results indicate that we cannot exclude the probability that the origin of the Hong Kong captive population was the wild population from Wuyuan. These results provide valuable knowledge that can help improve conservation management and planning for both captive and wild Blue-crowned Laughingthrush populations.

Reintroduction of the European Capercaillie from the Capercaillie Breeding Centre in Wisła 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.

Mitochondrial DNA analysis reveals hidden genetic diversity in captive populations of the threatened American crocodile (Crocodylus acutus) in Colombia.

Identification of units within species worthy of separate management consideration is an important area within conservation. Mitochondrial DNA (mtDNA) surveys can potentially contribute to this by identifying phylogenetic and population structure below the species level. The American crocodile (Crocodylus acutus) is broadly distributed throughout the Neotropics. Its numbers have been reduced severely with the species threatened throughout much of its distribution. In Colombia, the release of individuals from commercial captive populations has emerged as a possible conservation strategy that could contribute to species recovery. However, no studies have addressed levels of genetic differentiation or diversity within C. acutus in Colombia, thus complicating conservation and management decisions. Here, sequence variation was studied in mtDNA cytochrome b and cytochrome oxidase I gene sequences in three Colombian captive populations of C. acutus. Two distinct lineages were identified: C. acutus-I, corresponding to haplotypes from Colombia and closely related Central American haplotypes; and C. acutus-II, corresponding to all remaining haplotypes from Colombia. Comparison with findings from other studies indicates the presence of a single “northern” lineage (corresponding to C. acutus-I) distributed from North America (southern Florida), through Central America and into northern South America. The absence of C. acutus-II haplotypes from North and Central America indicates that the C. acutus-II lineage probably represents a separate South American lineage. There appears to be sufficient divergence between lineages to suggest that they could represent two distinct evolutionary units. We suggest that this differentiation needs to be recognized for conservation purposes because it clearly contributes to the overall genetic diversity of the species. All Colombian captive populations included in this study contained a mixture of representatives of both lineages. As such, we recommend against the use of captive-bred individuals for conservation strategies until further genetic information is available.

Population genetics and the effects of a severe bottleneck in an ex situ population of critically endangered Hawaiian tree snails.

As wild populations decline, ex situ propagation provides a potential bank of genetic diversity and a hedge against extinction. These programs are unlikely to succeed if captive populations do not recover from the severe bottleneck imposed when they are founded with a limited number of individuals from remnant populations. In small captive populations allelic richness may be lost due to genetic drift, leading to a decline in fitness. Wild populations of the Hawaiian tree snail Achatinella lila, a hermaphroditic snail with a long life history, have declined precipitously due to introduced predators and other human impacts. A captive population initially thrived after its founding with seven snails, exceeding 600 captive individuals in 2009, but drastically declined in the last five years. Measures of fitness were examined from 2,018 captive snails that died between 1998 and 2012, and compared with genotypic data for six microsatellite loci from a subset of these deceased snails (N = 335), as well as live captive snails (N = 198) and wild snails (N = 92). Surprisingly, the inbreeding coefficient (Fis) declined over time in the captive population, and is now approaching values observed in the 2013 wild population, despite a significant decrease in allelic richness. However, adult annual survival and fecundity significantly declined in the second generation. These measures of fitness were positively correlated with heterozygosity. Snails with higher measures of heterozygosity had more offspring, and third generation offspring with higher measures of heterozygosity were more likely to reach maturity. These results highlight the importance of maintaining genetic diversity in captive populations, particularly those initiated with a small number of individuals from wild remnant populations. Genetic rescue may allow for an increase in genetic diversity in the captive population, as measures of heterozygosity and rarified allelic richness were higher in wild tree snails.

Shift in phenotypic variation coupled with rapid loss of genetic diversity in captive populations of Eristalis tenax (Diptera: Syrphidae): consequences for rearing and potential commercial use.

Because of its importance as a pollinator and its potential economic usefulness for the biodegradation of organic animal waste, the genetic and phenotypic diversity of the drone fly, Eristalis tenax L. (Diptera: Syrphidae), was studied in both wild and captive populations from southeastern Europe. Wild specimens from a natural protected habitat (with low human impact), field crop habitat (semisynanthropic condition), and intensive pig farming habitat (synanthropic condition) were compared with a laboratory colony reared on artificial media An integrative approach was applied based on allozyme loci, cytochrome c oxidase I mitochondrial DNA, wing traits (size and shape), and abdominal color patterns. Our results indicate that the fourth and eighth generations of the laboratory colony show a severe lack of genetic diversity compared with natural populations. Reduced genetic diversity in subsequent generations (F4 and F8) of the laboratory colony was found to be linked with phenotypic divergence. Loss of genetic variability associated with phenotypic differentiation in laboratory samples suggests a founder effect, followed by stochastic genetic processes and inbreeding. Hence, our results have implications for captive bred Eristalis flies, which have been used in crop pollination and biodegradation of organic waste under synanthropic conditions.

Decreasing genetic diversity in wild and captive populations of endangered Itasenpara bittering (Acheilognathus longipinnis) in the Himi region, central Japan, and recommendations for conservation

Biodiversity is increasingly declining as a result of direct human impact and structural alteration of ecosystems resulting from changes in human life styles. Itasenpara bittering (Acheilognathus longipinnis), which has been maintained in floodplain and paddy fields, is a threatened cyprinid fish endemic to central Japan. To aid in the preservation of this species, information on genetic diversity and demographic variables in wild and captive populations was obtained using microsatellite DNA analysis. Temporal changes in genetic diversity and effective population size (N e) tended to be relatively stable in the wild Moo River population, although lower values were detected in the wild Busshouji River population, suggesting an extremely high risk of extinction in the latter. Captive populations derived from the Busshouji River population demonstrated significant genetic divergence even among intrapopulational cohorts, suggesting the influence of genetic drift caused by geographic isolation and small population size. Active maintenance of genetic diversity in captive population is a necessary part of conservation programs, as are continuous addition of wild individuals and replacement of individuals among captive populations. In addition, increasing or maintaining suitable floodplain areas and artificial habitats such as paddy fields might contribute to the conservation of genetic diversity in the Itasenpara bittering.

Simultaneous polyandry and heteropaternity in tiger (Panthera tigris altaica): Implications for conservation of genetic diversity in captive populations of felids

Male tigers (Panthera tigris altaica) in captivity copulate alternatively with an estrous female, suggesting a potential for heteropaternity as an effective reproductive strategy to maximize genetic diversity of offspring. We analyzed microsatellites to test and compare the genetic output of multiple male mating (simultaneous polyandry) and single male mating (monogamy) with a female in a captive population. Simultaneous polyandry resulted in heteropaternity in 66.7% observed litters. No significant differences between parental populations and between offspring populations were detected in the number of alleles (A), expected heterozygosity (H e), number of effective alleles (N e) per locus and standard individual heterozygosity (SH) (P>0.05 for all 4 indexes). Comparisons showed no significant reduction of A, H o, H e and SH from parental population to offspring population for the two mating modes (P>0.05) except for SH in polyandrous families (P=0.029). However, such reduction was equivalent to single mating families when the influence of relatedness was eliminated using effective SH (E SH ) (P>0.05). These results highlight an alternative strategy for managing captive populations of tiger and other wild felids in which animals are combined at one location allowing for copulation by multiple males to encourage heteropaternity in favor of maintained genetic diversity among offspring.

Using molecular markers for pedigree reconstruction of the greater amberjack (Seriola dumerili) in the absence of parental information

Ensuring appropriate levels of genetic diversity in captive populations is essential to avoid inbreeding and loss of rare alleles by genetic drift. Pedigree reconstruction and parentage analysis in the absence of parental genotypes can be a challenging task that relies in the assignment of sibship relationships among the offspring. Here, we used eight highly variable microsatellite markers and three different assignment methods to reconstruct the most likely genotypes of a parental group of wild Seriola dumerili fish based on the genotypes of six cohorts of their offspring, to assess their relative contributions to the offspring. We found that a combination of the four most variable microsatellites was enough to identify the number of parents and their contribution to the offspring, suggesting that the variability of the markers can be more critical than the number of markers. Estimated effective population sizes were lower than the number of breeders and variable among years. The results suggest unequal parental contribution that should be accounted for breeding programs in the future.

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.

Phylogeography of the Endangered Otago Skink, Oligosoma otagense: Population Structure, Hybridisation and Genetic Diversity in Captive Populations

Climatic cooling and substantial tectonic activity since the late Miocene have had a pronounced influence on the evolutionary history of the fauna of New Zealand's South Island. However, many species have recently experienced dramatic range reductions due to habitat fragmentation and the introduction of mammalian predators and competitors. These anthropogenic impacts have been particularly severe in the tussock grasslands of the Otago region. The Otago skink (Oligosoma otagense), endemic to the region, is one of the most critically endangered vertebrates in New Zealand. We use mitochondrial DNA sequence data to investigate the evolutionary history of the Otago skink, examine its population genetic structure, and assess the level of genetic diversity in the individuals in the captive breeding program. Our data indicate that the Otago skink diverged from its closest relatives in the Miocene, consistent with the commencement of tectonic uplift of the Southern Alps. However, there is evidence for past introgression with the scree skink (O. waimatense) in the northern Otago-southern Canterbury region. The remnant populations in eastern Otago and western Otago are estimated to have diverged in the mid-Pliocene, with no haplotypes shared between these two regions. This divergence accounts for 95% of the genetic diversity in the species. Within both regions there is strong genetic structure among populations, although shared haplotypes are generally evident between adjacent localities. Although substantial genetic diversity is present in the captive population, all individuals originate from the eastern region and the majority had haplotypes that were not evident in the intensively managed populations at Macraes Flat. Our data indicate that eastern and western populations should continue to be regarded as separate management units. Knowledge of the genetic diversity of the breeding stock will act to inform the captive management of the Otago skink and contribute to a key recovery action for the species.

Frozen-thawed rhesus sperm retain normal morphology and highly progressive motility but exhibit sharply reduced efficiency in penetrating cervical mucus and hyaluronic acid gel

The preservation of the genetic diversity of captive populations of rhesus monkeys is critical to the future of biomedical research. Cryopreservation of rhesus macaque sperm is relatively simple to perform, yields high post-thaw motility, and theoretically, provides via artificial insemination (AI) a way to easily transfer genetics among colonies of animals. In the interest of optimizing semen cryopreservation methods for use with vaginal AI, we evaluated the ability of frozen-thawed rhesus sperm to penetrate periovulatory cervical mucus (CM). Motile sperm concentration of pre-freeze (“fresh”) and post-thawed (“thawed”) samples from five different males were normalized for both computer assisted sperm motion analysis and CM penetration experiments. Sperm samples were deposited into slide chambers containing CM or gel composed of hyaluronic acid (HA) as a surrogate for CM and numbers of sperm were recorded as they entered a video field a preset distance from the sperm suspension-CM (or HA) interface. Fresh and thawed sperm were dried on glass slides, “Pap”-stained, and assessed for changes in head dimensions and head and flagellar shape. While retaining better than 80% of fresh sperm progressive motility, thawed sperm from the same ejaculate retained on average only 18.6% of the CM penetration ability. Experiments using HA gel yielded similar results only with reduced experimental error and thus improved detection of treatment differences. Neither the percentage of abnormal forms nor head dimensions differed between fresh and thawed sperm. While findings suggests that sperm-CM interaction is a prominent factor in previous failures of vaginal AI with cryopreserved macaque sperm, neither sperm motility nor morphology appears to account for changes in the ability of cryopreserved sperm to penetrate CM. Our data points to a previously unidentified manifestation of cryodamage which may have implications for assessment of sperm function beyond the cervix and across mammalian species.

Paternity Determination of Captive Bottlenose Dolphins (Tursiops truncatus) Using Microsatellite DNA Analysis

We applied previously published PCR primer pairs to amplify alleles at three polymorphic microsatellite loci to determine the genetic relationship of 6 bottlenose dolphins (Tursiops truncatus) that were living together in a Japanese aquarium. The three microsatellite loci were sufficient to determine the haplotype relationships of the six dolphins, which represented three different generations. It was confirmed that this genotyping method is simple and economical for assessing, establishing and maintaining genetic diversity in captive populations and will become a very effective technique for ex situ conservation in aquariums and zoos.

Nuclear DNA microsatellite analysis of genetic diversity in captive populations of Chinese water deer

The Chinese water deer ( Hydropotes inermis inermis) is becoming rare as a result of poaching and habitat loss. In recent years, many captive populations of Chinese water deer have been established. However, little genetic information is available for management decision. In this study, we investigated the nuclear genetic diversity and population structure of two representative captive populations (different origin) with a Zhoushan archipelago wild population for control, using 7 microsatellite loci. There was a relatively high level of genetic diversity of Chinese water deer for the total samples, comparing to the other rare cervid species. The mean number of observed alleles per locus was 5.143. The average observed and expected heterozygosity values were 0.662 and 0.531, respectively. The diversity of Nanjing Hongshan Zoo populations (mainland originated) is higher than that of the other two (Zhoushan archipelago originated) populations. Furthermore, strong differentiation between them was detected. Finally, many management strategies were also put forward for the purpose of maintaining genetic diversity of the captive Chinese water deer populations.

Empty Nest: A Case Study of Maternal Response to Separation From a Juvenile Offspring in a Captive Sumatran Orangutan (Pongo pygmaeus abelii)

Improving the welfare of captive nonhuman primates requires evaluating the stressors created by the captive environment and reducing their negative effects. Social separation, although sometimes necessary for managing the genetic diversity of captive populations of animals, causes both psychological and physiological stress in human and primate monkey infants. Few studies have examined the maternal response of great ape mothers to separation from their offspring. This article describes the behavioral changes of a mother orangutan (Pongo pygmaeus abelii) after separation from her juvenile daughter. We collected data on measures of proximity and social behavior before the separation of the mother-infant dyad and of locomotion, arboreality, abnormal behavior, solitary behavior, and vocalization both before and after separation. We observed no behavioral indications of protest but observed some indications of despair after separation: decreased locomotion, increased inactivity, and increased self-directed behavior. In addition, we observed increases in arboreality and object-oriented behavior during morning sessions. These findings suggest that mother-juvenile separation in orangutans might be less stressful for mothers than might be expected. Such research has implications for the welfare and management of captive animals.

A ‘Checklist’ of Possible Items for Prosimian Husbandry Manuals and Research

Zoo populations of prosimians are usually so small that death or reproductive failure of a few individuals may lead to a considerable loss of genetic diversity. Losses due to inadequate captive conditions must be minimized. This paper provides ideas and literature references for practical improvements of captive conditions and could serve as a checklist for writers of husbandry manuals. Items for inclusion in husbandry manuals containing detailed information about prosimians are provided. The preservation of genetic diversity in captive populations and adaptations of wild populations to their habitats are discussed. A list of items proposed for husbandry research includes an identification key for subpopulations and subspecies, field data and a variety of other factors such as housing, climatic needs, behaviour, relation between animals and keepers, reproduction, health, animal welfare and stress. Care for individuals as well as the metapopulation is recommended. The list includes some items which are not generally regarded as husbandry matters, but which ought to be considered, especially when a species is held for conservation purposes within managed programmes which include both in situ and ex situ components. The paper was based on experience with Loris tardigradus, so the needs of some other species may be less well covered.

Strategies for maintaining genetic diversity in captive populations through reproductive technology

AbstractThe maintenance of genetic diversity in captive populations is a primary goal of captive breeding plans, and it is becoming increasingly apparent that reproductive technology has much to offer captive breeding programs in attaining this goal. Reproductive technology can best assist captive breeding programs in this task by developing strategies that effectively increase the genetic contribution of new wild founders to a population as well as increase the reproductive life span of existing founders and their close descendents. This will act to reduce genetic drift and inbreeding effects in the population and thereby minimize the loss of genetic diversity.Considering only one aspect of reproductive technology, semen collection, this paper examines some of the genetic considerations that might be used for choosing which males in a population to collect semen from, assuming the goal of the captive breeding program is the preservation of genetic diversity. It is shown that semen collection and preservation, with future intent of artificial insemination, can make significant contributions to the maintenance of genetic diversity if careful consideration is given to the selection of donor males. Finally, the pedigree of the captive population of Asian lions (Panthera leo persica) is used to illustrate some of these genetic concepts that might be important in selecting males as semen donors.