Inbreeding Depression Accumulation across Life‐History Stages of the Endangered Takahe

Abstract: Studies evaluating the impact of inbreeding depression on population viability of threatened species tend to focus on the effects of inbreeding at a single life‐history stage (e.g., juvenile survival). We examined the effects of inbreeding across the full life‐history continuum, from survival up to adulthood, to subsequent reproductive success, and to the recruitment of second‐generation offspring, in wild Takahe ( Porphyrio hochstetteri ) by analyzing pedigree and fitness data collected over 21 breeding seasons. Although the effect size of inbreeding at individual life‐history stages was small, inbreeding depression accumulated across multiple life‐history stages and ultimately reduced long‐term fitness (i.e., successful recruitment of second‐generation offspring). The estimated total lethal equivalents (2B) summed across all life‐history stages were substantial (16.05, 95% CI 0.08–90.8) and equivalent to an 88% reduction in recruitment of second‐generation offspring for closely related pairs (e.g., sib–sib pairings) relative to unrelated pairs (according to the pedigree). A history of small population size in the Takahe could have contributed to partial purging of the genetic load and the low level of inbreeding depression detected at each single life‐history stage. Nevertheless, our results indicate that such “purged” populations can still exhibit substantial inbreeding depression, especially when small but negative fitness effects accumulate across the species’ life history. Because inbreeding depression can ultimately affect population viability of small, isolated populations, our results illustrate the importance of measuring the effects of inbreeding across the full life‐history continuum.     

Heterozygosity‐Fitness Correlations and Inbreeding Depression in Two Critically Endangered Mammals

The relation among inbreeding, heterozygosity, and fitness has been studied primarily among outbred populations, and little is known about these phenomena in endangered populations. Most researchers conclude that the relation between coefficient of inbreeding estimated from pedigrees and fitness traits (inbreeding‐fitness correlations) better reflects inbreeding depression than the relation between marker heterozygosity and fitness traits (heterozygosity‐fitness correlations). However, it has been suggested recently that heterozygosity‐fitness correlations should only be expected when inbreeding generates extensive identity disequilibrium (correlations in heterozygosity and homozygosity across loci throughout the genome). We tested this hypothesis in Mohor gazelle (Gazella dama mhorr) and Iberian lynx (Lynx pardinus). For Mohor gazelle, we calculated the inbreeding coefficient and measured heterozygosity at 17 microsatellite loci. For Iberian lynx, we measured heterozygosity at 36 microsatellite loci. In both species we estimated semen quality, a phenotypic trait directly related to fitness that is controlled by many loci and is affected by inbreeding depression. Both species showed evidence of extensive identity disequilibrium, and in both species heterozygosity was associated with semen quality. In the Iberian lynx the low proportion of normal sperm associated with low levels of heterozygosity was so extreme that it is likely to limit the fertility of males. In Mohor gazelle, although heterozygosity was associated with semen quality, inbreeding coefficient was not. This result suggests that when coefficient of inbreeding is calculated on the basis of a genealogy that begins after a long history of inbreeding, the coefficient of inbreeding fails to capture previous demographic information because it is a poor estimator of accumulated individual inbreeding. We conclude that among highly endangered species with extensive identity disequilibrium, examination of heterozygosity‐fitness correlations may be an effective way to detect inbreeding depression, whereas inbreeding‐fitness correlations may be poor indicators of inbreeding depression if the pedigree does not accurately reflect the history of inbreeding. Correlaciones Heterocigosidad‐ Adaptabilidad y Depresión Endogámica en Dos Especies de Mamíferos Críticamente en Peligro     

New Approaches Toward a Better Understanding of the Decline of Takahe (Porphyrio mantelli) in New Zealand

Island populations of endemic birds are known to be particularly susceptible to extinction. This paper focuses on factors behind past and present declines of the highly endangered Takahe ( Porphyrio mantelli ), a flightless rail endemic to New Zealand. Subfossil evidence indicates that Takahe were once found throughout this island nation, being most abundant along forest margins and streams in lowland regions. Their numbers have declined dramatically since human colonization about 800–1000 years ago, probably due to a combination of habitat destruction and hunting by early Polynesian settlers. Today, the wild Takahe population consists of about 100 adult birds in an isolated alpine habitat and approximately 30 individuals recently released on several small offshore islands. Despite protection and intensive management, including removal of an introduced competitor (red deer, Cervus elaphus ), the alpine population has continued to decline. In contrast, the Takahe's nearest relative, the Pukeko ( Porphyrio porphyrio ) has expanded its range across New Zealand despite heavy hunting pressure since its colonization from Australia less than 1000 years ago. We suggest that, unlike Pukeko, Takahe lack appropriate behavioral responses to cope with mammalian predators such as stoats ( Mustela erminea ), which have been introduced relatively recently by European colonists. A study comparing predator defense behavior between these two closely related species is currently underway.     

Founder Effects,Inbreeding, and Loss of Genetic Diversity in Four Avian Reintroduction Programs

Abstract: The number of individuals translocated and released as part of a reintroduction is often small, as is the final established population, because the reintroduction site is typically small. Small founder and small resulting populations can result in population bottlenecks, which are associated with increased rates of inbreeding and loss of genetic diversity, both of which can affect the long‐term viability of reintroduced populations. I used information derived from pedigrees of four monogamous bird species reintroduced onto two different islands (220 and 259 ha) in New Zealand to compare the pattern of inbreeding and loss of genetic diversity among the reintroduced populations. Although reintroduced populations founded with few individuals had higher levels of inbreeding, as predicted, other factors, including biased sex ratio and skewed breeding success, contributed to high levels of inbreeding and loss of genetic diversity. Of the 10–58 individuals released, 4–25 genetic founders contributed at least one living descendent and yielded approximately 3–11 founder–genome equivalents (number of genetic founders assuming an equal contribution of offspring and no random loss of alleles across generations) after seven breeding seasons. This range is much lower than the 20 founder–genome equivalents recommended for captive‐bred populations. Although the level of inbreeding in one reintroduced population initially reached three times that of a closely related species, the long‐term estimated rate of inbreeding of this one population was approximately one‐third that of the other species due to differences in carrying capacities of the respective reintroduction sites. The increasing number of reintroductions to suitable areas that are smaller than those I examined here suggests that it might be useful to develop long‐term strategies and guidelines for reintroduction programs, which would minimize inbreeding and maintain genetic diversity.     

Estimates of outcrossing rates and of inbreeding depression in a population of the marine angiosperm Zostera marina

Despite the great diversity of pollination and fertilization mechanisms observed in marine plants, little is known about the causes or maintenance of this variation. In this study, I estimated outcrossing rates and levels of inbreeding depression in Zostera marina L. (eelgrass), providing the first empirical test of hypotheses about the evolution of breeding systems in plants with submerged flowers. This study also addressed temporal separation of female and male flowering (dichogamy) in eelgrass as a mechanism promoting an outcrossing mating system, and whether the mating system in eelgrass is related to the degree of dichogamy in the field. Outcrossing rates (0<t<1) estimated from two polymorphic allozyme loci indicate that the Z. marina population in intertidal and subtidal habitats in False Bay, Washington, USA, was highly outcrossing in both 1991 (intertidal t=0.905, subtidal t=1.0) and 1992 (intertidal t=0.775, subtidal t=0.611). The outcrossing rates were positively associated with the degree of dichogamy in 1992; intertidal plants exhibited a greater temporal separation of female and male flowering and a higher outcrossing rate than did subtidal plants. Inbreeding depression at seed set was estimated from hand pollinations (self- and outcross) on 20 reproductive individuals from the False Bay population. Averaged across all maternal parents, a greater proportion of outcrossed flowers set seed than selfed flowers; i.e., inbreeding depression was detected. Plants exhibited genetic variation for inbreeding depression, detected as a significant pollination treatment × maternal family interaction in a log-likelihood analysis. By the end of the seed-maturation period (7 mo after intial seed set) some families showed outbreeding depression, i.e., greater fitness in progeny derived from selfing than in progeny from outcrossing. The inbreeding depression in the False Bay population may be an important selective factor contributing to the maintenance of dichogamy and an outcrossing mating system, as proposed for aquatic plants.     

Risk Assessment of Inbreeding and Outbreeding Depression in a Captive‐Breeding Program

Captive‐breeding programs can be implemented to preserve the genetic diversity of endangered populations such that the controlled release of captive‐bred individuals into the wild may promote recovery. A common difficulty, however, is that programs are founded with limited wild broodstock, and inbreeding can become increasingly difficult to avoid with successive generations in captivity. Program managers must choose between maintaining the genetic purity of populations, at the risk of inbreeding depression, or interbreeding populations, at the risk of outbreeding depression. We evaluate these relative risks in a captive‐breeding program for 3 endangered populations of Atlantic salmon (Salmo salar). In each of 2 years, we released juvenile F₁ and F₂ interpopulation hybrids, backcrosses, as well as inbred and noninbred within‐population crosstypes into 9 wild streams. Juvenile size and survival was quantified in each year. Few crosstype effects were observed, but interestingly, the relative fitness consequences of inbreeding and outbreeding varied from year to year. Temporal variation in environmental quality might have driven some of these annual differences, by exacerbating the importance of maternal effects on juvenile fitness in a year of low environmental quality and by affecting the severity of inbreeding depression differently in different years. Nonetheless, inbreeding was more consistently associated with a negative effect on fitness, whereas the consequences of outbreeding were less predictable. Considering the challenges associated with a sound risk assessment in the wild and given that the effect of inbreeding on fitness is relatively predictable, we suggest that risk can be weighted more strongly in terms of the probable outcome of outbreeding. Factors such as genetic similarities between populations and the number of generations in isolation can sometimes be used to assess outbreeding risk, in lieu of experimentation. Evaluación del Riesgo de Depresión por Endogamia y Exogamia en un Programa de Reproducción en Cautiverio     

Mate choice in the face of both inbreeding and outbreeding depression in the intertidal copepod Tigriopus californicus

 In species vulnerable to both inbreeding and outbreeding depression, individuals might be expected to choose mates at intermediate levels of genetic relatedness. Previous work on the intertidal copepod Tigriopus californicus has repeatedly shown that crosses between populations result in either no effect or hybrid vigor in the first generation, and hybrid breakdown in the second generation. Previous work also shows that mating between full siblings results in inbreeding depression. The present study again found inbreeding depression, with full sibling mating causing significant fitness declines in two of the three populations assayed. In the mate choice assays, a single female was combined with two males. Despite the costs of both inbreeding and outbreeding, mate choice showed clear inbreeding avoidance but no clear pattern of outbreeding avoidance. This lack of outbreeding avoidance may be attributed either to the temporary increase in fitness in the F₁ generation or to the absence of selection for premating isolation in wholly allopatric populations with infrequent migration. If this inability to avoid unwise matings is common to other taxa, it may contribute to the problem of outbreeding depression when allopatric populations are mixed together. Received: 18 May 1999 / Accepted: 25 January 2000     

Inbreeding avoidance or tolerance? Comparison of mating behavior between mass-reared and wild strains of the sweet potato weevil

Inadvertent selection is an important genetic process that frequently occurs during laboratory culture. The mass-reared strain of the sweet potato weevil Cylas formicarius exhibits stronger inbreeding depression than the wild strain does. When inbreeding depression occurs in a population, mating with a close relative is often considered maladaptive; however, in some contexts, the inclusive fitness benefits of inbreeding may outweigh the costs, favoring individuals that tolerate a low level of inbreeding depression. Theory predicts that mass-reared strain weevils will avoid inbreeding while wild strain weevils will tolerate inbreeding. To examine this prediction, we compared the effect of relatedness on the mating and insemination successes in mass-reared and wild strains of C. formicarius. While close relative pairs of the wild strain copulated less frequently than non-kin pairs, almost all mass-reared strain pairs copulated irrespective of relatedness. The results showed that the strain with weak inbreeding depression (wild strain) avoided inbreeding, whereas the strain with strong inbreeding depression (mass-reared strain) tolerated inbreeding. The contradiction between the theoretical prediction and our results is discussed from the perspective of laboratory adaptation, mating systems, and life history of C. formicarius.     

Using a common commensal bacterium in endangered Takahe as a model to explore pathogen dynamics in isolated wildlife populations

Predicting and preventing outbreaks of infectious disease in endangered wildlife is problematic without an understanding of the biotic and abiotic factors that influence pathogen transmission and the genetic variation of microorganisms within and between these highly modified host communities. We used a common commensal bacterium, Campylobacter spp., in endangered Takahe (Porphyrio hochstetteri) populations to develop a model with which to study pathogen dynamics in isolated wildlife populations connected through ongoing translocations. Takahe are endemic to New Zealand, where their total population is approximately 230 individuals. Takahe were translocated from a single remnant wild population to multiple offshore and mainland reserves. Several fragmented subpopulations are maintained and connected through regular translocations. We tested 118 Takahe from 8 locations for fecal Campylobacter spp. via culture and DNA extraction and used PCR for species assignment. Factors relating to population connectivity and host life history were explored using multivariate analytical methods to determine associations between host variables and bacterial prevalence. The apparent prevalence of Campylobacter spp. in Takahe was 99%, one of the highest reported in avian populations. Variation in prevalence was evident among Campylobacter species identified. C. sp. nova 1 (90%) colonized the majority of Takahe tested. Prevalence of C. jejuni (38%) and C. coli (24%) was different between Takahe subpopulations, and this difference was associated with factors related to population management, captivity, rearing environment, and the presence of agricultural practices in the location in which birds were sampled. Modeling results of Campylobacter spp. in Takahe metapopulations suggest that anthropogenic management of endangered species within altered environments may have unforeseen effects on microbial exposure, carriage, and disease risk. Translocation of wildlife between locations could have unpredictable consequences including the spread of novel microbes between isolated populations.     

The effects of age and relatedness on mating patterns in thornbug treehoppers: inbreeding avoidance or inbreeding tolerance?

The social environment of many species includes synchronous maturation of siblings in family groups, followed by limited dispersal of adults from their natal site. Under these conditions, females may experience high encounter rates with same-age siblings during mate searching, increasing their risk of inbreeding. If inbreeding depression occurs, mating with a sibling is often considered maladaptive; however, in some contexts, the inclusive fitness benefits of inbreeding may outweigh the costs, favoring females that tolerate some level of inbreeding depression. We evaluated mating patterns in the treehopper Umbonia crassicornis, a semelparous species in which females encounter same-age siblings during mate searching. A female U. crassicornis that mates with a brother suffers from inbreeding depression. We used a free-choice mating design that offered females simultaneous mating opportunities with three groups of males: siblings, same-age nonsiblings, and older nonsiblings. These groups represent the types of males typically encountered by females during mate searching. Our goal was to assess whether mating patterns were influenced by inbreeding avoidance by evaluating two hypotheses: kin discrimination and age-based mating (older males cannot be siblings in this species). There was no difference in the proportions of females mating with siblings vs nonsiblings, suggesting an absence of kin discrimination. However, females mated with a greater proportion of older vs younger males. Given that females do not avoid siblings as mates despite a cost to inbreeding, our results provide a possible example of inbreeding tolerance. We also discuss some factors that may have contributed to the mating advantage of older males.     

Environmental Dependency of Inbreeding Depression: Implications for Conservation Biology

Inbreeding depression is environmentally dependent, such that a population may suffer from inbreeding depression in one environment but not another. We examined the phenotypic responses of 35 inbred ( F = 0.672) lineages of the red flour beetle Tribolium castaneum in two different climatic environments. We found a significant environmental effect on males but not females. More important, we found that the rank fitness order of lineages differs between environments; lineages of high fitness in one environment may have low fitness in another environment. This change in rank is evident in a significant genotype-by-environment interaction for inbreeding depression for both females and males. These results suggest that even if we know the average environmental effect of inbreeding depression in a population, for any particular lineage measurements of inbreeding depression in one environment may not predict the level of inbreeding depression in another environment. Conservation biologists need to be aware of the environmental dependency of inbreeding depression when planning wildlife refuges or captive propagation programs for small populations. Ideally, captive propagation programs should maintain separate lineages for release efforts. Refuge design programs should consider maintaining a range of habitat types.     

Moving from trends to benchmarks by using regression tree analysis to find inbreeding thresholds in a critically endangered bird

Understanding how inbreeding affects endangered species in conservation breeding programs is essential for their recovery. The Hawaiian Crow (‘Alalā) (Corvus hawaiiensis) is one of the world's most endangered birds. It went extinct in the wild in 2002, and, until recent release efforts starting in 2016, nearly all of the population remained under human care for conservation breeding. Using pedigree inbreeding coefficients (F), we evaluated the effects of inbreeding on Hawaiian Crow offspring survival and reproductive success. We used regression tree analysis to identify the level of inbreeding (i.e., inbreeding threshold) that explains a substantial decrease in ‘Alalā offspring survival to recruitment. Similar to a previous study of inbreeding in ‘Alalā, we found that inbreeding had a negative impact on offspring survival but that parental (vs. artificial) egg incubation improved offspring survival to recruitment. Furthermore, we found that inbreeding did not substantially affect offspring reproductive success, based on the assumption that offspring that survive to adulthood breed with distantly related mates. Our novel application of regression tree analysis showed that offspring with inbreeding levels exceeding F = 0.098 were 69% less likely to survive to recruitment than more outbred offspring, providing a specific threshold value for ongoing population management. Our results emphasize the importance of assessing inbreeding depression across all life history stages, confirm the importance of prioritizing parental over artificial egg incubation in avian conservation breeding programs, and demonstrate the utility of regression tree analysis as a tool for identifying inbreeding thresholds, if present, in any pedigree-managed population.     

Translating effects of inbreeding depression on component vital rates to overall population growth in endangered bighorn sheep

Evidence of inbreeding depression is commonly detected from the fitness traits of animals, yet its effects on population growth rates of endangered species are rarely assessed. We examined whether inbreeding depression was affecting Sierra Nevada bighorn sheep (Ovis canadensis sierrae), a subspecies listed as endangered under the U.S. Endangered Species Act. Our objectives were to characterize genetic variation in this subspecies; test whether inbreeding depression affects bighorn sheep vital rates (adult survival and female fecundity); evaluate whether inbreeding depression may limit subspecies recovery; and examine the potential for genetic management to increase population growth rates. Genetic variation in 4 populations of Sierra Nevada bighorn sheep was among the lowest reported for any wild bighorn sheep population, and our results suggest that inbreeding depression has reduced adult female fecundity. Despite this population sizes and growth rates predicted from matrix-based projection models demonstrated that inbreeding depression would not substantially inhibit the recovery of Sierra Nevada bighorn sheep populations in the next approximately 8 bighorn sheep generations (48 years). Furthermore, simulations of genetic rescue within the subspecies did not suggest that such activities would appreciably increase population sizes or growth rates during the period we modeled (10 bighorn sheep generations, 60 years). Only simulations that augmented the Mono Basin population with genetic variation from other subspecies, which is not currently a management option, predicted significant increases in population size. Although we recommend that recovery activities should minimize future losses of genetic variation, genetic effects within these endangered populations-either negative (inbreeding depression) or positive (within subspecies genetic rescue)-appear unlikely to dramatically compromise or stimulate short-term conservation efforts. The distinction between detecting the effects of inbreeding depression on a component vital rate (e.g., fecundity) and the effects of inbreeding depression on population growth underscores the importance of quantifying inbreeding costs relative to population dynamics to effectively manage endangered populations.     

Inbreeding and competitive ability in the common shrew (<Emphasis Type="Italic">Sorex araneus</Emphasis>)

Common shrews (Sorex araneus) maintain a foraging territory for most of their immature life. Possessing a high-quality territory is vital for overwinter survival in the harsh boreal climate, and hence, competitive ability in territorial disputes is expected to be an important component of individual fitness. To test possible association between individual inbreeding and fitness, we used neutral arena trials to assess the competitive performance of young common shrews. The experiment involved pairs of individuals originating from small island populations, where breeding must often occur between related individuals, and from large outbred mainland populations. The percentage of neutral arena tests that an individual won was highly significantly explained by internal relatedness, a surrogate measure of individual inbreeding, measured using ten microsatellite markers. Body size, sex, learning, and population type (mainland vs island) made no significant contributions. Even a low level of individual inbreeding may lead to significant adverse consequences in multiple territorial contests, which may represent a significant cause of inbreeding depression in many wild vertebrate populations.     

Survival and Recruitment of Captive-Reared and Wild-Reared Takahe in Fiordland, New Zealand

Captive rearing for release back into the wild is considered a useful management tool for endangered species because it can potentially increase the rate of recruitment by bypassing the early, high-risk stages in an individual's life history. In evaluating the benefits of captive rearing to conservation, it is important to monitor the survival rate of animals after release, to be sure that they have the skills necessary for survival in the wild. Using radio telemetry, we compared the movement and survival of captive-reared Takahe (  Porphyrio mantelli), a large flightless rail endemic to New Zealand, to wild-reared Takahe in the rugged mountains of Fiordland over a 5–year period. The results indicated that captive-reared birds survived at least as well as wild-reared birds. Survival of wild-reared Takahe up to 1 year of age, which is prior to the release of captive-reared birds, was poor over two winters marked by particularly cold temperatures, which made the benefits of captive rearing more pronounced. Differences in post-release movements and habitat selection of the two groups did not have a detrimental effect on survival rate of captive-reared birds. Although there was no difference in the survival rate of captive-reared females versus males, eight out of nine (89%) surviving females have formed pairs since their release compared with only two of eight (25%) males. This unexpected result suggests there may be a shortage of females in the wild population. We conclude that captive rearing for release back into the wild increases the adult Takahe population in Fiordland.     

Mating with a kin decreases female remating interval: a possible example of inbreeding avoidance

Inbreeding depression is a relative decline in fitness in offspring of related parents. The magnitude of inbreeding costs varies among taxa and may increase under stressful conditions. Inbreeding tolerance is expected to be low and selection for inbreeding avoidance intense when both sexes invest substantially in shared offspring like in nuptial gift-giving butterflies. This is especially true for increasing mating rate for inbreeding avoidance as nuptial feeding decreases net costs of mating for females. We explored implications of inbreeding in the nuptial gift-giving green-veined white butterfly, Pieris napi. Compared to outbred ones, partially inbred (F = 0.25) eggs and neonate larvae had 25% lower hatching success and 30% lower survival until adult eclosion, respectively. Inbreeding was also associated with small size. Yet, the magnitude of inbreeding depression was independent of larval conditions. A lack of assortative mating and mating durations independent of mating type suggest that neither females nor males discriminate close relatives (r = 0.5) as mates. Indicative of a postcopulatory mechanism to avoid inbreeding, female remating intervals decreased following incestuous matings. Such a plastic response may affect the level of postcopulatory sexual selection as female remating interval (time between successive matings) is necessarily negatively correlated with mating rate (matings per unit time) and mating frequency (lifetime number of matings), and precopulatory mate choice appeared insignificant. Moreover, incest-induced shift in the phenotype towards the adaptive peak may contribute to the evolution of female mating rates, although alternative explanations for polyandry besides material benefits have rarely been invoked when nuptial feeding is involved.     

Population Bottlenecks and Increased Hatching Failure in Endangered Birds

Abstract: Severe population bottlenecks are expected to lead to increases in inbreeding depression and to reduce the long‐term viability of populations. We compared hatching failure across 51 threatened bird species to test the relation between the size of population bottleneck and population viability. Bottleneck size was defined as the lowest population size recorded in a species. Hatching failure was estimated as the proportion of eggs that failed to hatch due to infertility and embryonic death, both of which increase with inbreeding. The size of the bottleneck varied from 4 to 20,000 individuals across species and had a significant negative effect on hatching failure, a pattern that was consistent when we controlled for the confounding effects of phylogeny, body size, clutch size, time since the bottleneck occurred, and latitude. Hatching failure varied from 3 to 64% across species and was more than 10% in all populations passing through bottlenecks below 100–150 individuals. Our results show that the negative consequences of bottlenecks on hatching success are widespread in the populations of species we examined, and emphasize the conservation benefit of preventing bottlenecks below 150 individuals.     

Marine biogeographic disjunction in central New Zealand

We present a phylogeographic analysis of an abundant New Zealand endemic sea-star, Patiriella regularis, to help pinpoint the location of an important biogeographic disjunction in central New Zealand. The analysis incorporates 284 mtDNA control region sequences (approximately 800 bp) of P. regularis from 22 coastal locations around New Zealand. We detected 132 haplotypes, with a mean divergence of 0.96%. AMOVA analysis of New Zealand samples is consistent with a north-south biogeographic disjunction across central New Zealand (among-group genetic variance=6.10%; P=0.0005). Cook Strait, the shallow marine strait separating the main islands, is not correlated with the disjunction: samples from northern South Island are genetically indistinguishable from North Island samples (variance=1.69%; P=0.073). These results are consistent with the hypothesis that upwelling zones south of Cook Strait constitute a significant barrier to larval dispersal.Communicated by M.S. Johnson, Crawley