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.
Celotno besedilo
Dostopno za:
DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
The goal of captive breeding programmes is often to maintain genetic diversity until re‐introductions can occur. However, due in part to changes that occur in captive populations, approximately ...one‐third of re‐introductions fail. We evaluated genetic changes in captive populations using microsatellites and mtDNA. We analysed six populations of white‐footed mice that were propagated for 20 generations using two replicates of three protocols: random mating (RAN), minimizing mean kinship (MK) and selection for docility (DOC). We found that MK resulted in the slowest loss of microsatellite genetic diversity compared to RAN and DOC. However, the loss of mtDNA haplotypes was not consistent among replicate lines. We compared our empirical data to simulated data and found no evidence of selection. Our results suggest that although the effects of drift may not be fully mitigated, MK reduces the loss of alleles due to inbreeding more effectively than random mating or docility selection. Therefore, MK should be preferred for captive breeding. Furthermore, our simulations show that incorporating microsatellite data into the MK framework reduced the magnitude of drift, which may have applications in long‐term or extremely genetically depauperate captive populations.
Captive breeding programs aim to maintain populations that are demographically self-sustaining and genetically healthy. It has been well documented that the best way for managed breeding programs to ...retain gene diversity (GD) and limit inbreeding is to select breeding pairs that minimize a population's average kinship. We used a series of computer simulations to test 4 methods of minimizing average kinship across a variety of scenarios with varying generation lengths, mortality rates, reproductive rates, and rates of breeding pair success. "Static MK Selection" and "Dynamic MK Selection" are 2 methods for iteratively selecting genetically underrepresented individuals for breeding, whereas "Ranked MK Selection" and "Simultaneous MK Selection" are 2 methods for concurrently selecting the group of breeding individuals that produce offspring with the lowest average kinship. For populations with discrete generations (24 tested scenarios), we found that the Simultaneous and Ranked MK Selection methods were generally the best, nearly equivalent methods for selecting breeding pairs that retained GD and limited inbreeding. For populations with overlapping generations (198 tested scenarios), we found that Dynamic MK Selection was the most robust method for selecting breeding pairs. We used these results to provide guidelines for identifying which method of minimizing average kinship was most appropriate for various breeding program scenarios.
Abstract
The application of molecular tools to population management can improve the long-term genetic viability of ex situ populations. In this study, we aimed to understand the implications of ...integrating empirical kinships into the genetic management of an ex situ population of the endangered waterfowl, Baer’s pochard (Aythya baeri), in North America. Single nucleotide polymorphism data were generated for 141 Baer’s pochard using double digest restriction site-associated DNA sequencing and empirical kinships were derived and integrated into the population management software PMx. Analyses suggested 37.7% of pairwise relationships previously assumed to be unrelated were first, second, or third-order relatives. We determined that most genetic summary statistics were impacted through the calculation of the population’s mean kinship, which increased from MK¯=0.0772 to MK¯=0.2074 after empirical kinships were integrated into our analyses. Our results also revealed the importance of understanding how molecular kinships derived from a particular estimator are scaled, if the scale differs significantly from pedigree-based kinships. We describe the theory behind the genetic metrics impacted and provide general guidance on incorporating empirical kinships into ex situ population management as well as provide suggestions for sampling strategies to minimize the biases inherent in merging two types of kinship estimators.
The global zoo and aquarium community widely recognizes that its animal collections and cooperative breeding programs are facing a sustainability crisis. It has become commonly accepted that numerous ...priority species cannot be maintained unless new management strategies are adopted. While molecular data have the potential to greatly improve management across a range of scenarios, they have been generally underutilized by the zoo and aquarium community. This failure to effectively apply molecular data to collection management has been due, in part, to a paucity of resources within the community on which to base informed decisions about when the use of such data is appropriate and what steps are necessary to successfully integrate data into management. Here, we identify three broad areas of inquiry where molecular data can inform management: 1) taxonomic identification; 2) incomplete or unknown pedigrees; and 3) hereditary disease. Across these topics, we offer a discussion of the advantages, limitations, and considerations for applying molecular data to ex situ animal populations in a style accessible to zoo and aquarium professionals. Ultimately, we intend for this compiled information to serve as a resource for the community to help ensure that molecular projects directly and effectively benefit the long‐term persistence of ex situ populations.
Science‐based management confers a variety of benefits to wildlife populations that are cooperatively managed by zoos and aquariums, including those managed through the Association of Zoos and ...Aquariums. Briefly, when management strategies are successful, they result in reproductively robust populations that better retain genetic diversity and limit inbreeding than unmanaged populations. Although the benefits of demographic and genetic management have been well documented throughout both the scientific and popular literature, it has also been established that the majority of managed populations in zoos and aquariums are not meeting the minimum criteria believed to convey long‐term biological viability. For most of these populations, an inability to meet viability criteria is not an inherent failure of how cooperative management is implemented. Furthermore, in recent years, we have perceived that the need to meet specific viability goals sometimes has obscured the benefits that these populations receive from rigorous, science‐based management. To better clarify the conversation surrounding population viability in zoos and aquariums, we seek to decouple viability measures and how they predict population persistence from the benefits conferred to populations through science‐based management. A primary goal of population management is to facilitate the persistence of priority species for longer than would be expected if no such management were implemented. Although current viability measures and future projections of viability are important tools for assessing the likelihood of population persistence, they are not indicators of which populations may most benefit from science‐based management. Here, we review the history and purpose of applying science‐based management to zoo and aquarium populations, describe measures of population viability and caution against confusing those measures of viability with population management goals or long‐term population sustainability, and clearly articulate the benefits conferred to zoo and aquarium populations by science‐based management.
Slow rates of gene diversity loss in Association of Zoos and Aquariums Waldrapp ibis (Geronticus eremita) population highlight the benefits science‐based management confers to a population's viability beyond meeting specific genetic and demographic targets set by zoo associations.
Captive breeding programs for wildlife species typically rely on pedigrees to inform genetic management. Although pedigree-based breeding strategies are quite effective at retaining long-term genetic ...variation, management of zoo-based breeding programs continues to be hampered when pedigrees are poorly known. The objective of this study was to evaluate 2 options for generating single nucleotide polymorphism (SNP) data to resolve unknown relationships within captive breeding programs. We generated SNP data for a zoo-based population of addax (Addax nasomasculatus) using both the Illumina BovineHD BeadChip and double digest restriction site-associated DNA (ddRAD) sequencing. Our results demonstrated that estimates of allele sharing (AS) between pairs of individuals exhibited low variances. Average AS variances were highest when using 50 loci (SNPchipall = 0.00159; ddRADall = 0.0249), but fell below 0.0003 for the SNP chip dataset when sampling ≥250 loci and below 0.0025 for the ddRAD dataset when sampling ≥500 loci. Furthermore, the correlation between the SNPchipall and ddRADall AS datasets was 0.88 (95%CI = 0.84-0.91) when subsampling 500 loci. Collectively, our results indicated that both SNP genotyping methods produced sufficient data for accurately estimating relationships, even within an extremely bottlenecked population. Our results also suggested that analytic assumptions historically integrated into the addax pedigree are not adversely impacting long-term pedigree-based management; kinships calculated from the analytic pedigree were significantly correlated (P << 0.001) with AS estimates. Overall, our conclusions are intended to serve as both a proof of concept and a model for applying molecular data to the genetic management of captive breeding programs.
The study of the koala transcriptome has the potential to advance our understanding of its immunome—immunological reaction of a given host to foreign antigens—and to help combat infectious diseases ...(e.g., chlamydiosis) that impede ongoing conservation efforts. We used Illumina sequencing of cDNA to characterize genes expressed in two different koala tissues of immunological importance, blood and spleen. We generated nearly 600 million raw sequence reads, and about 285 million of these were subsequently assembled and condensed into ~70,000 subcomponents that represent putative transcripts. We annotated ~16 % of these subcomponents and identified those related to infection and the immune response, including Toll-like receptors (TLRs), RIG-I-like receptors (RLRs), major histocompatibility complex (MHC) genes, and koala retrovirus (KoRV). Using phylogenetic analyses, we identified 29 koala genes in these target categories and report their concordance with currently accepted gene groups. By mapping multiple sequencing reads to transcripts, we identified 56 putative SNPs in genes of interest. The distribution of these SNPs indicates that MHC genes (34 SNPs) are more diverse than KoRV (12 SNPs), TLRs (8 SNPs), or RLRs (2 SNPs). Our sequence data also indicate that KoRV sequences are highly expressed in the transcriptome. Our efforts have produced full-length sequences for potentially important immune genes in koala, which should serve as targets for future investigations that aim to conserve koala populations.
Genome resource banks (GRBs) have the potential to preserve the genetic diversity of a species over time, yet they are rarely utilized as effective components of conservation breeding programs. ...Advances have been made in reproductive biology, collection and storage techniques, and use of stored gametes for achieving successful reproduction, but there are few guidelines for integrating GRBs into established breeding programs. Here we present basic guidelines, focusing on strategies for the collection, maintenance, and use of semen GRBs for protecting genetic diversity. These guidelines should be applied in the context of the specific purposes and roles of a breeding program's GRB, which will differ among species depending on vulnerability to loss and the status of rescue and conservation efforts. We recommend establishing up to three types of collections: (1) a National Reserve to preserve a species' genetic diversity, to be used only as a last resort; (2) a Savings Account to be used periodically to invigorate a genetically depauperate population; and (3) a Checking Account to be used as a regular part of the breeding program. We present methods for identifying donors to maximize genetic diversity in a GRB, as well as strategies for maintaining and optimally using GRBs.
Three levels of gamete banks, each serving different roles, can enhance conservation breeding programs.
A “National Reserve” is a protected repository to be used only when population survival is at imminent risk.
A “Savings Account” serves to periodically reinvigorate populations.
A “Checking Account” contains semen to be considered as mate options each generation.
Highlights
The establishment and judicious use of three levels of gamete banks, each serving different roles, can enhance the protection of genetic diversity in conservation breeding programs.
A “National Reserve” serves as a protected repository holding to the fullest extent the genetic diversity of a species.
A “Savings Account” serves as a resource to periodically reinvigorate populations suffering from genetic erosion.
A “Checking Account” contains semen from both deceased and living males to be considered as mate options each generation.
We present quantitative methods for determining which males should be sampled to secure the desired genetic diversity in each type of bank.
An insurance population for the critically endangered Tasmanian devil was established in 2006. Due to successful captive breeding, the population has reached its carrying capacity of 600 devils and ...retains 99.95 % of founding gene diversity. Although reproduction has been quite successful, possible relatedness among founding individuals, influences of genetic provenance and pairing success on female productivity were evaluated to further refine insurance population management. Ten polymorphic microsatellite markers were used to assess the founders. Although the data were ultimately insufficient for determining specific founder relationships, a STRUCTURE analysis determined founders to be of eastern or western provenance. Western provenance animals had an observed heterozygosity of 0.38; while eastern provenance was 0.41. Allelic frequencies between the two provenances were similar. Although differences in pairing success of eastern and western provenance animals were noted, there was no difference in overall productivity (number of joeys/female). Cross-provenance pairings were not as successful as W–W but had similar productivity, and produced viable offspring. Birth origin (wild-born vs. zoo-born) had no influence on pairing success but wild-born females produce significantly more joeys/female. For zoo-born females, the number of joeys produced per female had a downward trend between respective generations in captivity. Current and future population managers should be aware of potential reductions in productivity across captive generations and adjust breeding recommendations accordingly. The ability to recruit founders from diseased females, along with a better understanding of the influence of genetic provenance and birth origin on productivity, has led to changes in acquisition of future founders for this insurance population.
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