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 (F_is) 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.     

Non‐timber Forest Product Harvest does not Affect the Genetic Diversity of a Tropical Tree Despite Negative Effects on Population Fitness

The level of genetic diversity in a population can affect ecological processes and plant responses to disturbance. In turn, disturbance can alter population genetic diversity and structure. Populations in fragmented and logged habitats often show reduced genetic diversity and increased inbreeding and differentiation. Long‐term harvesting of wild plants (for foliage, bark, and roots), can affect population genetic diversity by altering individual fitness and genetic contribution. Our understanding of these changes in genetic diversity due to the harvesting of plant organs is still limited. We used nine microsatellite markers to study the effect of long‐term bark and foliage harvest by Fulani people on the genetic diversity and structure of 12 populations of African mahogany (Khaya senegalensis) in Benin. We sampled 20 individuals in each population to test the effect of harvesting. For each population, we divided the samples equally between seedling and adults to test if the effects are stronger in seedlings. We found moderate genetic diversity (H_e = 0.53 ± 0.04) and weak but significant differentiation among local populations (F_ST = 0.043, P < 0.001). There was no significant effect of harvest on genetic diversity or structure, although previous work found significant negative effects of harvest on the reproduction of adults, offspring density, and population fitness. Our results suggest that demographic responses to disturbance precede a detectable genetic response. Future studies should focus on using parentage analysis to test if genotypes of harvested parents are directly represented in the offspring populations.     

The effects of sexual selection on life‐history traits: an experimental study on guppies

Sexual selection is often prevented during captive breeding in order to maximize effective population size and retain genetic diversity. However, enforcing monogamy and thereby preventing sexual selection may affect population fitness either negatively by preventing the purging of deleterious mutations or positively by reducing sexual conflicts. To better understand the effect of sexual selection on the fitness of small populations, we compared components of female fitness and the expression of male secondary sexual characters in 19 experimental populations of guppies (Poecilia reticulata) maintained under polygamous or monogamous mating regimes over nine generations. In order to generate treatments that solely differed by their level of sexual selection, the middle‐class neighbourhood breeding design was enforced in the monogamous populations, while in the polygamous populations, all females contributed similarly to the next generation with one male and one female offspring. This experimental design allowed potential sexual conflicts to increase in the polygamous populations because selection could not operate on adult‐female traits. Clutch size and offspring survival showed a weak decline from generation to generation but did not differ among treatments. Offspring size, however, declined across generations, but more in monogamous than polygamous populations. By generation eight, orange‐ and black‐spot areas were larger in males from the polygamous treatment, but these differences were not statistically significant. Overall, these results suggest that neither sexual conflict nor the purging of deleterious mutation had important effects on the fitness of our experimental populations. However, only few generations of enforced monogamy in a benign environment were sufficient to negatively affect offspring size, a trait potentially crucial for survival in the wild. Sexual selection may therefore, under certain circumstances, be beneficial over enforced monogamy during captive breeding.     

Heterozygosity at a single locus explains a large proportion of variation in two fitness‐related traits in great tits: a general or a local effect?

In natural populations, mating between relatives can have important fitness consequences due to the negative effects of reduced heterozygosity. Parental level of inbreeding or heterozygosity has been also found to influence the performance of offspring, via direct and indirect parental effects that are independent of the progeny own level of genetic diversity. In this study, we first analysed the effects of parental heterozygosity and relatedness (i.e. an estimate of offspring genetic diversity) on four traits related to offspring viability in great tits (Parus major) using 15 microsatellite markers. Second, we tested whether significant heterozygosity–fitness correlations (HFCs) were due to ‘local’ (i.e. linkage to genes influencing fitness) and/or ‘general’ (genome‐wide heterozygosity) effects. We found a significant negative relationship between parental genetic relatedness and hatching success, and maternal heterozygosity was positively associated with offspring body size. The characteristics of the studied populations (recent admixture, polygynous matings) together with the fact that we found evidence for identity disequilibrium across our set of neutral markers suggest that HFCs may have resulted from genome‐wide inbreeding depression. However, one locus (Ase18) had disproportionately large effects on the observed HFCs: heterozygosity at this locus had significant positive effects on hatching success and offspring size. It suggests that this marker may lie near to a functional locus under selection (i.e. a local effect) or, alternatively, heterozygosity at this locus might be correlated to heterozygosity across the genome due to the extensive ID found in our populations (i.e. a general effect). Collectively, our results lend support to both the general and local effect hypotheses and reinforce the view that HFCs lie on a continuum from inbreeding depression to those strictly due to linkage between marker loci and genes under selection.     

Experimental test of genetic rescue in isolated populations of brook trout

Genetic rescue is an increasingly considered conservation measure to address genetic erosion associated with habitat loss and fragmentation. The resulting gene flow from facilitating migration may improve fitness and adaptive potential, but is not without risks (e.g., outbreeding depression). Here, we conducted a test of genetic rescue by translocating ten (five of each sex) brook trout (Salvelinus fontinalis) from a single source to four nearby and isolated stream populations. To control for the demographic contribution of translocated individuals, ten resident individuals (five of each sex) were removed from each recipient population. Prior to the introduction of translocated individuals, the two smallest above‐barrier populations had substantially lower genetic diversity, and all populations had reduced effective number of breeders relative to adjacent below‐barrier populations. In the first reproductive bout following translocation, 31 of 40 (78%) translocated individuals reproduced successfully. Translocated individuals contributed to more families than expected under random mating and generally produced larger full‐sibling families. We observed relatively high (>20%) introgression in three of the four recipient populations. The translocations increased genetic diversity of recipient populations by 45% in allelic richness and 25% in expected heterozygosity. Additionally, strong evidence of hybrid vigour was observed through significantly larger body sizes of hybrid offspring relative to resident offspring in all recipient populations. Continued monitoring of these populations will test for negative fitness effects beyond the first generation. However, these results provide much‐needed experimental data to inform the potential effectiveness of genetic rescue‐motivated translocations.     

Diploid male production correlates with genetic diversity in the parasitoid wasp Venturia canescens: a genetic approach with new microsatellite markers

Sex determination is ruled by haplodiploidy in Hymenoptera, with haploid males arising from unfertilized eggs and diploid females from fertilized eggs. However, diploid males with null fitness are produced under complementary sex determination (CSD), when individuals are homozygous for this locus. Diploid males are expected to be more frequent in genetically eroded populations (such as islands and captive populations), as genetic diversity at the csd locus should be low. However, only a few studies have focused on the relation between population size, genetic diversity, and the proportion of diploid males in the field. Here, we developed new microsatellite markers in order to assess and compare genetic diversity and diploid male proportion (DMP) in populations from three distinct habitat types – mainland, island, or captive –, in the parasitoid wasp Venturia canescens. Eroded genetic diversity and higher DMP were found in island and captive populations, and habitat type had large effect on genetic diversity. Therefore, DMP reflects the decreasing genetic diversity in small and isolated populations. Thus, Hymenopteran populations can be at high extinction risk due to habitat destruction or fragmentation.     

DOES GENETIC DIVERSITY REDUCE SIBLING COMPETITION?

An enduring hypothesis for the proximal benefits of sex is that recombination increases the genetic variation among offspring and that this genetic variation increases offspring performance. A corollary of this hypothesis is that mothers that mate multiply increase genetic variation within a clutch and gain benefits due to genetic diversity alone. Many studies have demonstrated that multiple mating can increase offspring performance, but most attribute this increase to sexual selection and the role of genetic diversity has received less attention. Here, we used a breeding design to generate populations of full-siblings, half-siblings, and unrelated individuals of the solitary ascidian Ciona intestinalis. Importantly, we preclude the potentially confounding influences of maternal effects and sexual selection. We found that individuals in populations with greater genetic diversity had greater performance (metamorphic success, postmetamorphic survival, and postmetamorphic size) than individuals in populations with lower genetic diversity. Furthermore, we show that by mating with multiple males and thereby increasing genetic variation within a single clutch of offspring, females gain indirect fitness benefits in the absence of mate-choice. Our results show that when siblings are likely to interact, genetic variation among individuals can decrease competition for resources and generate substantial fitness benefits within a single generation.     

Genetic quality of the Miyaluo captive forest musk deer (Moschus berezovskii) population as assessed by microsatellite loci

The Miyaluo captive forest musk deer population (Sichuan Province, China) is one of the largest captive breeding populations in the world. In order to evaluate the genetic quality and provide available genetic management strategy, seven polymorphism microsatellite loci were applied to assess the genetic variation of the Miyaluo forest musk deer. The results indicated that a total of 168 alleles were detected from these seven microsatellite loci in 361 individuals, and the number of the alleles per locus ranged from 12 to 41 with a mean of 24. The average observed heterozygosity, expected heterozygosity, and PIC were 0.782, 0.854, and 0.837, respectively. Considering the results of the loci Hardy–Weinberg equilibrium test, the comparison of the common allele frequency as well as the private allele between the adults and juveniles, we concluded that the heterozygosity and the genetic diversity of the Miyaluo captive breeding population are increasing due to the input of new individuals from other populations. However, the frequency of some alleles declined sharply, and some were even lost indicating that there is a risk for diversity loss. Thus, we proposed an improved management and breeding strategy for the captive breeding population of the forest musk deer.     

Molecular paternity determination in captive bonobos and the impact of inbreeding on infant mortality

Inbreeding and the loss of genetic diversity may lower fitness and reduce the potential for a population to adapt to changing environments. In small populations, for example in captive populations or populations of endangered species, this can have considerable consequences for their survival. We investigated the effects of inbreeding on infant mortality in the world captive population of bonobos Pan paniscus . Using a combination of studbook data and high-quality pedigree data from genotyped individuals, inbreeding information was available for 142 captive-born individuals. For the determination of paternities that were unresolved in the studbook, nuclear microsatellite DNA was amplified from hair and blood samples using the Great Ape Kit and PowerPlex^® 16 System. In total, 54 bonobos (17 offspring and their putative parents) were genotyped at eight tetranucleotide repeat microsatellite loci. Inbreeding coefficients were calculated for each individual for whom paternity was confirmed by either studbook data or DNA analysis. We found significantly higher infant mortality in inbred offspring compared with non-inbred offspring, suggesting that inbreeding reduces infant survival in captive bonobos. In addition, we argue that the total magnitude of inbreeding depression is probably underestimated in this captive population. In conclusion, even though the breeding programme of captive bonobos is aimed at avoiding inbreeding, closely related individuals do occasionally produce offspring that do show inbreeding depression. There is, however, no indication that this currently threatens the long-time survival of the captive population of bonobos.     

Genetic rescue and inbreeding depression in Mexican wolves

Although inbreeding can reduce individual fitness and contribute to population extinction, gene flow between inbred but unrelated populations may overcome these effects. Among extant Mexican wolves (Canis lupus baileyi), inbreeding had reduced genetic diversity and potentially lowered fitness, and as a result, three unrelated captive wolf lineages were merged beginning in 1995. We examined the effect of inbreeding and the merging of the founding lineages on three fitness traits in the captive population and on litter size in the reintroduced population. We found little evidence of inbreeding depression among captive wolves of the founding lineages, but large fitness increases, genetic rescue, for all traits examined among F1 offspring of the founding lineages. In addition, we observed strong inbreeding depression among wolves descended from F1 wolves. These results suggest a high load of deleterious alleles in the McBride lineage, the largest of the founding lineages. In the wild, reintroduced population, there were large fitness differences between McBride wolves and wolves with ancestry from two or more lineages, again indicating a genetic rescue. The low litter and pack sizes observed in the wild population are consistent with this genetic load, but it appears that there is still potential to establish vigorous wild populations.     

Evaluation of the genetic management of the endangered black‐footed ferret (Mustela nigripes)

Empirical support for the genetic management strategies employed by captive breeding and reintroduction programs is scarce. We evaluated the genetic management plan for the highly endangered black‐footed ferret (Mustela nigripes) developed by the American Zoo and Aquarium Associations (AZA) as a part of the species survival plan (SSP). We contrasted data collected from five microsatellite loci to predictions from a pedigree‐based kinship matrix analysis of the captive black‐footed ferret population. We compared genetic diversity among captive populations managed for continued captive breeding or reintroduction, and among wild‐born individuals from two reintroduced populations. Microsatellite data gave an accurate but only moderately precise estimate of heterozygosity. Genetic diversity was similar in captive populations maintained for breeding and release, and it appears that the recovery program will achieve its goal of maintaining 80% of the genetic diversity of the founder population over 25 years. Wild‐born individuals from reintroduced populations maintained genetic diversity and avoided close inbreeding. We detected small but measurable genetic differentiation between the reintroduced populations. The model of random mating predicted only slightly lower levels of heterozygosity retention compared to the SSP strategy. The random mating strategy may be a viable alternative for managing large, stable, captive populations such as that of the black‐footed ferret. Zoo Biol 22:287–298, 2003. © 2003 Wiley‐Liss, Inc.     

Contrasting heterozygosity‐fitness correlations across life in a long‐lived seabird

Selection is a central force underlying evolutionary change and can vary in strength and direction, for example across time and space. The fitness consequences of individual genetic diversity have often been investigated by testing for multilocus heterozygosity‐fitness correlations (HFCs), but few studies have been able to assess HFCs across life stages and in both sexes. Here, we test for HFCs using a 26‐year longitudinal individual‐based data set from a large population of a long‐lived seabird (the common tern, Sterna hirundo), where 7,974 chicks and breeders of known age were genotyped at 15 microsatellite loci and sampled for life‐history traits over the complete life cycle. Heterozygosity was not correlated with fledging or post‐fledging prospecting probabilities, but was positively correlated with recruitment probability. For breeders, annual survival was not correlated with heterozygosity, but annual fledgling production was negatively correlated with heterozygosity in males and highest in intermediately heterozygous females. The contrasting HFCs among life stages and sexes indicate differential selective processes and emphasize the importance of assessing fitness consequences of traits over complete life histories.     

Nature versus nurture? Consequences of short captivity in early stages

Biological changes occurring as a consequence of domestication and/or captivity are not still deeply known. In Atlantic salmon (Salmo salar), endangered (Southern Europe) populations are enhanced by supportive breeding, which involves only 6 months of captive rearing following artificial spawning of wild‐collected adults. In this work, we assess whether several fitness‐correlated life‐history traits (migratory behavior, straying rate, age at maturity, and growth) are affected by early exposure to the captive environment within a generation, before reproduction thus before genetic selection. Results showed significant differences in growth and migratory behavior (including straying), associated with this very short period of captivity in natural fish populations, changing even genetic variability (decreased in hatchery‐reared adults) and the native population structure within and between rivers of the species. These changes appeared within a single generation, suggesting very short time of captivity is enough for initiating changes normally attributed to domestication. These results may have potential implications for the long‐term population stability/viability of species subjected to restoration and enhancement processes and could be also considered for the management of zoo populations.     

Multilocus heterozygosity, parental relatedness and individual fitness components in a wild mountain goat, Oreamnos americanus population

Matings between relatives lead to a decrease in offspring genetic diversity which can reduce fitness, a phenomenon known as inbreeding depression. Because alpine ungulates generally live in small structured populations and often exhibit a polygynous mating system, they are susceptible to inbreeding. Here, we used marker-based measures of pairwise genetic relatedness and inbreeding to investigate the fitness consequences of matings between relatives in a long-term study population of mountain goats ( Oreamnos americanus ) at Caw Ridge, Alberta, Canada. We first assessed whether individuals avoided mating with kin by comparing actual and random mating pairs according to their estimated genetic relatedness, which was derived from 25 unlinked polymorphic microsatellite markers and reflected pedigree relatedness. We then examined whether individual multilocus heterozygosity H , used as a measure of inbreeding, was predicted by parental relatedness and associated with yearling survival and the annual probability of giving birth to a kid in adult females. Breeding pairs identified by genetic parentage analyses of offspring that survived to 1 year of age were less genetically related than expected under random matings. Parental relatedness was negatively correlated with offspring H , and more heterozygous yearlings had higher survival to 2 years of age. The probability of giving birth was not affected by H in adult females. Because kids that survived to yearling age were mainly produced by less genetically related parents, our results suggest that some individuals experienced inbreeding depression in early life. Future research will be required to quantify the levels of gene flow between different herds, and evaluate their effects on population genetic diversity and dynamics.     

Specific alleles at immune genes,rather than genome‐wide heterozygosity,are related to immunity and survival in the critically endangered Attwater's prairie‐chicken

The negative effects of inbreeding on fitness are serious concerns for populations of endangered species. Reduced fitness has been associated with lower genome‐wide heterozygosity and immune gene diversity in the wild; however, it is rare that both types of genetic measures are included in the same study. Thus, it is often unclear whether the variation in fitness is due to the general effects of inbreeding, immunity‐related genes or both. Here, we tested whether genome‐wide heterozygosity (20 990 SNPs) and diversity at nine immune genes were better predictors of two measures of fitness (immune response and survival) in the endangered Attwater's prairie‐chicken (Tympanuchus cupido attwateri). We found that postrelease survival of captive‐bred birds was related to alleles of the innate (Toll‐like receptors, TLRs) and adaptive (major histocompatibility complex, MHC) immune systems, but not to genome‐wide heterozygosity. Likewise, we found that the immune response at the time of release was related to TLR and MHC alleles, and not to genome‐wide heterozygosity. Overall, this study demonstrates that immune genes may serve as important genetic markers when monitoring fitness in inbred populations and that in some populations specific functional genes may be better predictors of fitness than genome‐wide heterozygosity.     

中国圈养林麝微卫星DNA多样性研究

本文利用13对微卫星标记,对我国3个核心种源地（巴山、秦岭、川西高原）圈养林麝种群进行遗传多样性和遗传结构分析。在167份样品中共检测到142个等位基因（Na）,每个位点等位基因数介于7~16,均值为10.92,平均有效等位基因数（Ne）为6.3730,期望杂合度（He）和观测杂合度（Ho）均值分别为0.8302和0.3897。这些圈养林麝种群遗传多样性水平较高,但较低的观测杂合度表明圈养群体存在近交现象。两两群体间的Fst 值和AMOVA分析结果均表明种群之间分化程度不明显。群体遗传结构分析显示,全部样本聚为3个遗传簇（最佳K值=3）,其主体与3个地理来源相符,但种群间存在基因渗透现象。本研究中的秦岭种群遗传变异最为丰富,可以作为种质改良的基因池。     

Heterozygosity correlates with body size,nest site quality and productivity in a colonial waterbird,the whiskered tern (Chlidonias hybrida,Aves: Sternidae)

Positive effects of individual heterozygosity on naturally selected traits have been reported in wild populations of many animal taxa. The aim of this study was to test whether heterozygosity predicts the quality of acquired nest sites and productivity in a colonially breeding waterbird, the whiskered tern (Chlidonias hybrida). For this purpose, 40 adult terns from a small, recently established population in Central Poland were typed at eight microsatellite loci. We demonstrate that individual heterozygosity is positively related to hatching success. We hypothesize that this association could be mediated by direct effects of heterozygosity on the competitive abilities of individuals. We found that more heterozygous terns tended to breed in better protected central parts of the colony, suggesting that they had capabilities of outcompeting less heterozygous individuals and relegating them to the less attractive peripheries of the colony. It was also demonstrated that the link between heterozygosity and individual abilities to acquire more attractive nest site could be mediated by the larger size of heterozygous individuals. Although no correlations between heterozygosity and different components of condition were found, there was a positive association between female heterozygosity and both clutch size and egg size. We suggest that demonstrated heterozygosity‐fitness correlations could be primarily caused by inbreeding depression in the studied whiskered tern population.     

Captive rearing for Chinook salmon (Oncorhynchus tshawytscha) and Atlantic salmon (Salmo salar): the Idaho and Maine experiences

Captive rearing is a conservation strategy where juveniles are collected from the natural environment, reared to maturity in a hatchery environment, and then released back into the natural environment at maturity for volitional spawning. This strategy has been used to produce adult outplants for stock enhancement where natural escapement is poor or capture of adults is difficult. In both Idaho (Chinook salmon, Oncorhynchus tshawytscha) and Maine (Atlantic salmon, Salmo salar), captive rearing programs have been initiated as an experimental strategy to prevent cohort collapse and conserve genetic integrity of select depressed populations. In this paper, we provide an overview of these programs and describe some of the methods used to evaluate the effectiveness of this approach. Behaviors such as habitat selection, courting, and spawn timing were monitored. Data collected for both programs indicate that the captive fish display similar behaviors as their wild conspecifics in terms of habitat selection and spawning, although there were some differences in spawn timing. Evaluations of egg and fry production also indicate that captive-reared adults are successfully spawning and producing offspring. Each program is still waiting on final evaluations of reproductive success through genetic analyses of returning adults, but results so far indicate that this could be an additional captive propagation strategy for depressed populations.     

Multiple paternity in wild house mice (Mus musculus musculus): effects on offspring genetic diversity and body mass

Multiple mating is common in many species, but it is unclear whether multiple paternity enhances offspring genetic diversity or fitness. We conducted a survey on wild house mice (Mus musculus musculus), and we found that in 73 pregnant females, 29% of litters had multiple sires, which is remarkably similar to the 23–26% found in feral populations of Mus musculus domesticus in the USA and Australia, respectively. The question is: How has selection maintained multiple mating in these subspecies since the evolutionary divergence, ca. 2800–6000 years ago? We found no evidence that multiple paternity enhanced females’ litter size, contrary to the fertility assurance or genetic benefits hypotheses. Multiple paternity was associated with reduced mean and variance in offspring body mass, which suggests that females allocate fewer resources or that there is increased intrauterine conflict in multiple-versus single-sired litters. We found increased allelic diversity (though not heterozygosity) in multiple-sired litters, as predicted by the genetic diversity hypothesis. Finally, we found that the dams’ heterozygosity was correlated with the mean heterozygosity of their offspring in single-and multiple-sired litters, suggesting that outbred, heterozygous females were more likely to avoid inbreeding than inbred, homozygous females. Future studies are needed to examine how increased genetic diversity of litters and smaller mean (and variance) offspring body mass associated with multiple paternity affect offspring fitness.     

Are indirect genetic benefits associated with polyandry? Testing predictions in a natural population of lemon sharks

Multiple mating has clear fitness benefits for males, but uncertain benefits and costs for females. We tested for indirect genetic benefits of polyandry in a natural population, by using data from a long-term genetic and demographic study of lemon sharks ( Negaprion brevirostris ) at Bimini, Bahamas. To do so, we followed the fates of individuals from six cohorts (450 age-0 and 254 age-1 fish) in relation to their individual level of genetic variation, and whether they were from polyandrous or monoandrous litters. We find that offspring from polyandrous litters did not have a greater genetic diversity or greater survival than did the offspring of monoandrous litters. We also find no evidence of positive associations between individual offspring genetic diversity metrics and our surrogate measure of fitness (i.e. survival). In fact, age-1 individuals with fewer heterozygous microsatellite loci and more genetically similar parents were more likely to survive to age-2. Thus, polyandry in female lemon sharks does not appear to be adaptive from the perspective of indirect genetic benefits to offspring. It may instead be the result of convenience polyandry, whereby females mate multiply to avoid harassment by males. Our inability to find indirect genetic benefits of polyandry despite detailed pedigree and survival information suggests the need for similar assessments in other natural populations.