Mean Kinship Research Articles

Characterization of genetic diversity in Turkish common bean gene pool using phenotypic and whole-genome DArTseq-generated silicoDArT marker information.

Turkey presents a great diversity of common bean landraces in farmers’ fields. We collected 183 common bean accessions from 19 different Turkish geographic regions and 5 scarlet runner bean accessions to investigate their genetic diversity and population structure using phenotypic information (growth habit, and seed weight, flower color, bracteole shape and size, pod shape and leaf shape and color), geographic provenance and 12,557 silicoDArT markers. A total of 24.14% markers were found novel. For the entire population (188 accessions), the expected heterozygosity was 0.078 and overall gene diversity, Fst and Fis were 0.14, 0.55 and 1, respectively. Using marker information, model-based structure, principal coordinate analysis (PCoA) and unweighted pair-group method with arithmetic means (UPGMA) algorithms clustered the 188 accessions into two main populations A (predominant) and B, and 5 unclassified genotypes, representing 3 meaningful heterotic groups for breeding purposes. Phenotypic information clearly distinguished these populations; population A and B, respectively, were bigger (>40g/100 seeds) and smaller (<40g/100 seeds) seed-sized. The unclassified population was pure and only contained climbing genotypes with 100 seed weight 2–3 times greater than populations A and B. Clustering was mainly based on A: seed weight, B: growth habit, C: geographical provinces and D: flower color. Mean kinship was generally low, but population B was more diverse than population A. Overall, a useful level of gene and genotypic diversity was observed in this work and can be used by the scientific community in breeding efforts to develop superior common bean strains.

The formation of marine kin structure: effects of dispersal, larval cohesion, and variable reproductive success

The spatial distribution of relatives has profound effects on kin interactions, inbreeding, and inclusive fitness. Yet, in the marine environment, the processes that generate patterns of kin structure remain understudied because larval dispersal on ocean currents was historically assumed to disrupt kin associations. Recent genetic evidence of co-occurring siblings challenges this assumption and raises the intriguing question of how siblings are found together after a (potentially) disruptive larval phase. Here, we develop individual-based models to explore how stochastic processes operating at the individual level affect expected kinship at equilibrium. Specifically, we predict how limited dispersal, sibling cohesion, and variability in reproductive success differentially affect patterns of kin structure. All three mechanisms increase mean kinship within populations, but their spatial effects are markedly different. We find that (1) when dispersal is limited, kinship declines monotonically as a function of the distance between individuals; (2) when siblings disperse cohesively, kinship increases within a site relative to between sites; and (3) when reproductive success varies, kinship increases equally at all distances. The differential effects of these processes therefore only become apparent when individuals are sampled at multiple spatial scales. Notably, our models suggest that aggregative larval behaviors, such as sibling cohesion, are not necessary to explain documented levels of relatedness within marine populations. Together, these findings establish a theoretical framework for disentangling the drivers of marine kin structure.

Pedigree‐based genetic management improves bison conservation

ABSTRACTOverhunting and widespread land use change nearly caused the extinction of North American bison (Bison bison) by the late 1800s. Recovery efforts focused on preserving the remaining individuals and establishing federally managed conservation herds to build more sustainable populations. Today, bison in conservation herds are maintained in small, isolated herds that are managed through an annual or biannual cull of individuals to maintain target population sizes. We assessed alternative culling strategies for maintaining genetic variation over the long term in managed wild bison herds. Our objective was to compare a strategy modeled after a United States Fish and Wildlife Service strategy (all‐allele conservation culling strategy [AAC]) to a pedigree‐based mean kinship strategy (MK) and to a Random strategy that does not incorporate genetic data and is used to manage some conservation herds. We built an individual‐based model, parameterized in accordance with bison biology, to compare these culling strategies in 2 federally managed conservation herds at the Fort Niobrara National Wildlife Refuge (FTN herd) and the National Bison Range (NBR herd). Our MK strategy retained more genetic variation and slowed the accumulation of inbreeding relative to the AAC or Random strategies, and these findings were consistent across wild bison herds with different founding sizes and current genetic diversity. These findings extend previous work demonstrating the utility of pedigree‐based management strategies in captive and wild population management, and show that such strategies maximize the retention of genome‐wide variation in contemporary bison herds. The modeling approach used in this study was useful for assessing outcomes prior to implementation, and the specific models developed for this study can be easily adapted to other managed wildlife species. © 2018 The Wildlife Society.

Genetic variability of some Italian and Polish duck breeds

This study is aimed to estimate and compare the inter- and within-breed variability of duck populations under genetic conservation programmes. The following four duck breeds were analysed: Germanata Veneta (AGV) and Mignon (AMG) from Italy, Pekin Krajowy (33P) and Pomniejszona (2K) from Poland. The characterisation of the four populations was carried out through a panel of 23 microsatellite markers. The analysis involved 180 individuals: 39 for AGV, 41 for AMG, 50 for 33P and 50 for 2K. An average of 11.36 alleles per locus was identified. Twenty-two loci showed high values of polymorphism information content from 0.575 to 0.912, while CAUD136 was monomorphic for the Italian breeds. The breeds showed relatively high heterozygosity: higher for the Polish populations (0.6920 for 33P and 0.6521 for 2K), and lower for the Italian (0.4497 and 0.3718 for AGV and AMG, respectively). The inbreeding coefficient was higher for the Italian breeds, AMG in particular (0.133, 0.097 and 0.121), as well as the differentiation index (0.253). The Nei’s minimum distances (DM) and Reynolds distances (DR) were low between the Polish populations (0.131 and 0.088, respectively); these were associated to AGV (DM = 0.191 and DR = 0.259 for 33P; DM = 0.174 and DR = 0.226 for 2K). Finally, AGV was distant from AMG (DM = 0.259 and DR = 0.317). The molecular coancestry, or mean kinship was higher for the Italian breeds compared to Polish populations. The Italian populations showed intermediate values. The obtained results can be perceived as an important tool for the applied genetic conservation programmes.

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.

Contrasting results from molecular and pedigree-based population diversity measures in captive zebra highlight challenges facing genetic management of zoo populations.

Zoo conservation breeding programs manage the retention of population genetic diversity through analysis of pedigree records. The range of demographic and genetic indices determined through pedigree analysis programs allows the conservation of diversity to be monitored relative to the particular founder population for a species. Such approaches are based on a number of well-documented founder assumptions, however without knowledge of actual molecular genetic diversity there is a risk that pedigree-based measures will be misinterpreted and population genetic diversity misunderstood. We examined the genetic diversity of the captive populations of Grevy's zebra, Hartmann's mountain zebra and plains zebra in Japan and the United Kingdom through analysis of mitochondrial DNA sequences. Very low nucleotide variability was observed in Grevy's zebra. The results were evaluated with respect to current and historic diversity in the wild, and indicate that low genetic diversity in the captive population is likely a result of low founder diversity, which in turn suggests relatively low wild genetic diversity prior to recent population declines. Comparison of molecular genetic diversity measures with analogous diversity indices generated from the studbook data for Grevy's zebra and Hartmann's mountain zebra show contrasting patterns, with Grevy's zebra displaying markedly less molecular diversity than mountain zebra, despite studbook analysis indicating that the Grevy's zebra population has substantially more founders, greater effective population size, lower mean kinship, and has suffered less loss of gene diversity. These findings emphasize the need to validate theoretical estimates of genetic diversity in captive breeding programs with empirical molecular genetic data. Zoo Biol. 36:87-94, 2017. © 2016 Wiley Periodicals, Inc.

Does cooperation mean kinship between spatially discrete ant nests?

Eusociality is one of the most complex forms of social organization, characterized by cooperative and reproductive units termed colonies. Altruistic behavior of workers within colonies is explained by inclusive fitness, with indirect fitness benefits accrued by helping kin. Members of a social insect colony are expected to be more closely related to one another than they are to other conspecifics. In many social insects, the colony can extend to multiple socially connected but spatially separate nests (polydomy). Social connections, such as trails between nests, promote cooperation and resource exchange, and we predict that workers from socially connected nests will have higher internest relatedness than those from socially unconnected, and noncooperating, nests. We measure social connections, resource exchange, and internest genetic relatedness in the polydomous wood ant Formica lugubris to test whether (1) socially connected but spatially separate nests cooperate, and (2) high internest relatedness is the underlying driver of this cooperation. Our results show that socially connected nests exhibit movement of workers and resources, which suggests they do cooperate, whereas unconnected nests do not. However, we find no difference in internest genetic relatedness between socially connected and unconnected nest pairs, both show high kinship. Our results suggest that neighboring pairs of connected nests show a social and cooperative distinction, but no genetic distinction. We hypothesize that the loss of a social connection may initiate ecological divergence within colonies. Genetic divergence between neighboring nests may build up only later, as a consequence rather than a cause of colony separation.

Fourteen tail feathers: An autosomal recessive trait in california condors (Gymnogyps californianus).

Eight pairs of California Condors (Gymnogyps californianus) have produced 12 chicks with 14 tail feathers instead of the normal 12. The 14 tail feather trait appears to follow an autosomal recessive pattern of inheritance and is not known to be deleterious. The putative allele for the trait was present in at least seven of the 13 founders of the population. The 14 tail feather allele is the second recessive allele discovered in the condor population. Due to the founder effect, which changes the frequency of many formerly rare recessive alleles, and genetic management to minimize mean kinship, which reduces the expression of recessive traits, it is likely that this population carries other recessive alleles that have not yet been detected. Zoo Biol. 36:1-4, 2017. © 2016 Wiley Periodicals, Inc.

Using Genetic Distance to Infer the Accuracy of Genomic Prediction.

The prediction of phenotypic traits using high-density genomic data has many applications such as the selection of plants and animals of commercial interest; and it is expected to play an increasing role in medical diagnostics. Statistical models used for this task are usually tested using cross-validation, which implicitly assumes that new individuals (whose phenotypes we would like to predict) originate from the same population the genomic prediction model is trained on. In this paper we propose an approach based on clustering and resampling to investigate the effect of increasing genetic distance between training and target populations when predicting quantitative traits. This is important for plant and animal genetics, where genomic selection programs rely on the precision of predictions in future rounds of breeding. Therefore, estimating how quickly predictive accuracy decays is important in deciding which training population to use and how often the model has to be recalibrated. We find that the correlation between true and predicted values decays approximately linearly with respect to either FST or mean kinship between the training and the target populations. We illustrate this relationship using simulations and a collection of data sets from mice, wheat and human genetics.

Use of animals with partially known ancestries in scientifically managed breeding programs.

Animals with only partially known ancestry present a problem for population managers because it can be difficult to determine their relative genetic value to the population. So long as their ancestry is not completely unknown, population management software such as PMx can calculate a mean kinship for these animals, but that mean kinship is calculated such that there is no decrease in relative genetic value or "penalty" for only partially known ancestry. However, there is a longer-term genetic cost to having animals with only partially known ancestry in the population, and thus it is appropriate to "penalize" animals with partially known ancestry to some extent. The challenge is determining the correct "penalty" which will serve to decrease the percent unknown ancestry in subsequent generations while not causing excessive selection against the known ancestry of the animal. A new parameter of relative genetic value is developed which takes into account both an animal's mean kinship as well as its percent known ancestry. The method used in PMx to calculate the mean kinships also in general overestimates the inbreeding coefficients of offspring of animals with partially known ancestry when the known parents share a common ancestor, but can underestimate inbreeding if common ancestors exist within the unknown portion of the pedigree. This may result in population managers selecting less suitable pairs for breeding in an attempt to avoid an apparent higher level of inbreeding. A parameter is developed that adjusts the inbreeding coefficient to more accurately reflect the likely inbreeding coefficient of potential offspring. Zoo Biol. 35:319-325, 2016. © 2016 Wiley Periodicals, Inc.

Reduced reproductive fitness of an endemic insular juniper population: An eco-genetic mediation hypothesis

The mutual reinforcement of multiple drivers of global change erodes ecosystem services and accelerates plant population decline worldwide. This is particularly the case for island ecosystems where anthropogenic activity has imperilled insular floras for centuries. Different hypotheses have put forward the combined effects of environmental shifts and genetic factors in driving fecundity decline in threatened populations. In this study, we combined population genetic tools and structural equation models to test the eco-genetic mediation hypothesis, that the environmental conditions influence genetic variation, which in turn affects plant fitness. Our study species is Juniperus cedrus, an endangered juniper species endemic to the Canary Islands. Juniper woodlands have been depleted since the arrival of human inhabitants confined extant populations to marginal lands. More recently, long-distance dispersers have been extirpated from the study area, potentially eliminating connectivity among fragmented populations. We expected strong intrapopulation subdivision and high levels of inbreeding and kinship that should negatively affect individual fitness. We found evidence of population subdivision into several mating neighbourhoods (K=13), some of them highly inbred. However, contrary to our expectations, neither inbreeding nor mean kinship mediated a population response to environmental factors. Our results suggest three remedial actions to reverse the declining demographic trends: (i) re-establish native vegetation to ameliorate local environmental conditions; (ii) restore dispersal services to increase connectivity; and (iii) monitor fitness decline to identify lagged effects associated with deforestation. Overall, this study shows that structural equation models combined with population genetic techniques are suitable tools to identify high-order effects among multiple drivers of global change that underlie forest decline.

Inbreeding and neighbouring vegetation drive drought‐induced die‐off within juniper populations

Summary Drought‐induced episodes of forest die‐off are being reported world‐wide, and recent evidence shows that increases in temperature due to climate change are contributing to this decline. Several ecological mechanisms have been invoked at the plant level to explain the vulnerability of trees to this widespread drought‐induced mortality. Apart from ecological factors, some genetic factors might also influence population responses to disturbances: it has been reported, for example, that genetic diversity enhances population resilience through genotypic complementarity, whereas genetic relatedness between conspecific individuals exerts a negative influence on variations in fecundity. However, we lack empirical data that prove any functional relationship between levels of individual inbreeding or kinship and patterns of drought‐induced forest die‐off resulting from field conditions. Here, we investigated the role of ecological, phenotypic and genetic factors in determining the response of trees to prolonged drought conditions. We focused on populations of the small tree Juniperus phoenicea L. that recently experienced severe drought‐induced die‐off in semi‐arid woodlands from central Spain. We correlated mean individual inbreeding (f) and mean kinship between individuals within a plot (fij) with remaining green plant canopy and crop size. We found that f was negatively correlated with plant performance, whereas fij was not. Healthier canopy also tended to correspond with large plants and neighbourhoods dominated by trees and shrubs, suggesting a role for facilitative interactions and microsite heterogeneity. Accordingly, the probability of severe damage increased linearly with f, and individuals growing in open habitats with f values &gt; 0·625 only had 15% chance of remaining unaffected after a period of prolonged drought. We show that both vegetative and reproductive responses to prolonged drought episodes are determined by multiple factors, including individual inbreeding. Therefore, any fuller understanding of phenomena such as drought‐induced forest die‐off needs to incorporate the contribution of individual genetic variations in conjunction with plant–plant interactions.

Evaluation of alternative management strategies for maintenance of genetic variation in wildlife populations

Wildlife management strategies are often designed around a population's demographic goals, but such strategies also can inadvertently impact genetic variation. For species like bison Bison bison, where management includes the regular removal of individuals to maintain restricted population sizes on constrained landscapes, management actions can be tailored to address genetic diversity retention in addition to simply maintaining a target population size. In this study, we provide an assessment of alternative culling strategies for maintenance of genetic variation in managed wildlife populations. Our primary goal was to compare the long-term retention of genetic variation and accumulation of inbreeding among three types of culling strategies, including one that considered genetic variation directly by measuring variation at a suite of variable loci [mean allele frequency (MAF) strategy], one that used genome-wide measures of variation [mean kinship (MK) strategy] and one that relied solely on demographic information (sex and age; RANDOM). To achieve this goal, we built an individual-based model, parameterized in accordance with bison biology, to project levels of genetic variation and inbreeding over time under each of the three management strategies. Our results suggest wildlife management strategies that incorporate goals for retaining genetic variation (MAF and MK strategies) are better suited to preserving the evolutionary potential of wildlife populations than those that focus solely on a target size and demographic stability (RANDOM). In particular, the MK culling strategy performed the best at maximizing the retention of genome-wide variation. These results extend previous work demonstrating the utility of pedigree-based mate selection strategies in captive population management, and show that such strategies maximize the retention of genome-wide variation under culling practices as well. These models will aid in the long-term management of bison, and can be adapted to other managed wildlife species.

Integrating Genomic Data Sets for Knowledge Discovery: An Informed Approach to Management of Captive Endangered Species.

Many endangered captive populations exhibit reduced genetic diversity resulting in health issues that impact reproductive fitness and quality of life. Numerous cost effective genomic sequencing and genotyping technologies provide unparalleled opportunity for incorporating genomics knowledge in management of endangered species. Genomic data, such as sequence data, transcriptome data, and genotyping data, provide critical information about a captive population that, when leveraged correctly, can be utilized to maximize population genetic variation while simultaneously reducing unintended introduction or propagation of undesirable phenotypes. Current approaches aimed at managing endangered captive populations utilize species survival plans (SSPs) that rely upon mean kinship estimates to maximize genetic diversity while simultaneously avoiding artificial selection in the breeding program. However, as genomic resources increase for each endangered species, the potential knowledge available for management also increases. Unlike model organisms in which considerable scientific resources are used to experimentally validate genotype-phenotype relationships, endangered species typically lack the necessary sample sizes and economic resources required for such studies. Even so, in the absence of experimentally verified genetic discoveries, genomics data still provides value. In fact, bioinformatics and comparative genomics approaches offer mechanisms for translating these raw genomics data sets into integrated knowledge that enable an informed approach to endangered species management.

A pedigree gone bad: increased offspring survival after using DNA‐based relatedness to minimize inbreeding in a captive population

AbstractCaptive breeding programs often use a pedigree to identify breeding pairs that maintain genetic diversity and limit inbreeding. However, unintentional breeding of closely related individuals can occur when errors exist in the pedigree and may subsequently result in inbreeding depression. In this study, a DNA‐based approach was used to identify parentage assignment errors in the captive pedigree of the critically endangered Attwater's prairie‐chicken Tympanuchus cupido attwateri, and tested whether clutch survival increased using DNA‐relatedness values for assigning breeding pairs instead of the pedigree and mean kinship. Parentage assignment error was observed in each year surveyed ranging from 2.4 to 7.3%. After correcting identified errors prior to the 2013 breeding season, 11 of 38 assigned pedigree‐based breeding pairs still possessed DNA‐based relatedness coefficients (rDNA) ≥0.125 suggesting that additional errors remained in the pedigree. Two approaches were used to prevent breeding among close relatives in 2013 and 2014. Assigned pedigree‐based breeding pairs in 2013 that possessed rDNA ≥0.125 were reassigned unrelated breeding partners, while all individuals in 2014 were used to identify the minimum overall rDNA for the breeding population without reference to the pedigree other than to verify founder representation. Both years resulted in a significant reduction in mean parental relatedness among chicks (P &lt; 0.001) and a significant increase in the proportion of the clutch surviving to 5 weeks post‐hatch (P ≤ 0.006) compared to 2012 when breeding pairs were assigned using only the pedigree. No significant difference in the proportion of the clutch surviving was observed between 2013 and 2014 (P &gt; 0.300). These results have important implications for the captive management of endangered species, and highlight the importance of periodically evaluating for pedigree errors. To what degree pedigree errors limit fitness in other endangered species captive populations deserves further attention.

Founded: Genetic Reconstruction of Lineage Diversity and Kinship InformsEx situConservation of Cuban Amazon Parrots (Amazona leucocephala)

Captive breeding is a widespread conservation strategy, yet such programs rarely include empirical genetic data for assessing management assumptions and meeting conservation goals. Cuban Amazon parrots (Amazona leucocephala) are considered vulnerable, and multiple on-island captive populations have been established from wild-caught and confiscated individuals of unknown ancestry. Here, we used mitochondrial haplotypic and nuclear genotypic data at 9 microsatellite loci to quantify the extent and distribution of genetic variation within and among captive populations in Zapata Swamp and Managua, Cuba, and to estimate kinship among breeders (n = 88). Using Bayesian clustering analysis, we detected 2 distinct clusters within the Zapata population, one of which was shared with Managua. Individuals from the cluster unique to Zapata possessed mitochondrial haplotypes with affinities to Cuban subspecies (A. l. leucocephala, A. l. palmarum); the shared cluster was similar, but also included haplotypes closely related to the subspecies restricted to Cayman Brac (A. l. hesterna). Overall mean kinship was low within each captive population (-0.026 to -0.012), with 19 and 11 recommended breeding pairs in Zapata and Managua, respectively, ranked according to mean kinship and informed by molecular sexing. Our results highlight the importance of understanding population history within ex situ management programs, while providing genetic information to directly inform Cuban parrot conservation.

Genetic Analyses in the Japanese Captive Population of Japanese Crested Ibis (Nipponia nippon) using Pedigree Information.

The Japanese captive population of Japanese crested ibis (Nipponia nippon) was established using 5 founders derived from the Chinese captive population. Its size has increased rapidly, and the maintenance phase is about to start. Thus, this study was designed to perform genetic analyses in this population with pedigree information, considering the adoption of mean kinship strategy as the breeding strategy suited to the maintenance phase. Because the relationships among the 5 founders were unknown, different assumptions were set up ranging from 0 to 0.25 of kinship coefficients between the 5 founders. Assuming that the 5 founders were non-inbred in all the assumptions, the results showed that the gene diversity and the mean inbreeding coefficient would fluctuate largely from ∼65% to ∼82% and from ∼0.07 to ∼0.29, respectively. Moreover, the genetic importance of individuals based on mean kinship shifted largely. This study suggested that the Japanese captive population had low gene diversity and high mean inbreeding coefficient even under the assumption that the 5 founders were unrelated and non-inbred. In addition, the study also suggested that it became more effective to analyze the genetic status and to introduce mean kinship strategy into this population with more credible molecular evaluation of the relationships among founders.

Captive management and the maintenance of genetic diversity in a vulnerable marsupial, the greater bilby

The endemic Australian greater bilby (Macrotis lagotis) is a vulnerable and iconic species. It has declined significantly due to habitat loss, as well as competition and predation from introduced species. Conservation measures include a National Recovery Plan that incorporates several captive breeding programs. Two of these programs were established within 12 months of one another (1997/98), with the same number and sex ratio of founding individuals, but executed different breeding strategies: (1) unmanipulated mating in semi–free range natural habitat versus (2) minimising mean kinship in large enclosures, with the supplementation of new individuals into both populations. This study evaluates the long-term genetic impact of these programs and examines the congruency between the pedigree studbook estimates of diversity and molecular data. Our data demonstrate that genetic diversity was maintained in both populations, with the supplementation of new individuals contributing to the gene pool. The studbook estimates of diversity and inbreeding are not consistent with the microsatellite data and should not solely be relied upon to evaluate the genetic health of captive populations. Our analyses suggest that captive breeding programs may not require costly and intensive management to effectively maintain long-term genetic diversity in a promiscuous species.

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

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

Genetic evidence of hybridization between the critically endangered Cuban crocodile and the American crocodile: implications for population history and in situ/ex situ conservation

Inter-specific hybridization may be especially detrimental when one species is extremely rare and the other is abundant owing to the potential for genetic swamping. The Cuban crocodile (Crocodylus rhombifer) is a critically endangered island endemic largely restricted to Zapata Swamp, where it is sympatric with the widespread American crocodile (C. acutus). An on-island, C. rhombifer captive breeding program is underway with the goals of maintaining taxonomic integrity and providing a source of individuals for reintroduction, but its conservation value is limited by lack of genetic information. Here we collected mtDNA haplotypic and nuclear genotypic data from wild and captive C. rhombifer and C. acutus in Cuba to: (1) investigate the degree of inter-specific hybridization in natural (in situ) and captive (ex situ) populations; (2) quantify the extent, distribution and in situ representation of genetic variation ex situ; and (3) reconstruct founder relatedness to inform management. We found high levels of hybridization in the wild (49.1%) and captivity (16.1%), and additional evidence for a cryptic lineage of C. acutus in the Antilles. We detected marginally higher observed heterozygosity and allelic diversity ex situ relative to the wild population, with captive C. rhombifer exhibiting over twice the frequency of private alleles. Although mean relatedness was high in captivity, we identified 37 genetically important individuals that possessed individual mean kinship (MK) values lower than the population MK. Overall, these results will guide long-term conservation management of Cuban crocodiles for maintaining the genetic integrity and viability of this species of high global conservation value.