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.     

Relationship of Breeding System to Rarity in the Lakeside Daisy (Hymenoxys acaulis var. glabra)

The breeding system of a rare Great Lakes endemic, the lakeside daisy ( Hymenoxys acaulis var. glabra ), was investigated when plants from a remnant Illinois population produced no seeds for over 15 years. To determine if the Lakeside daisy was self-incompatible, 20 plants from two populations, Illinois and Ohio, were selfed and outcrossed. Seed/ovule ratios were compared among the different treatments and the location of the incompatibility reaction was identified. Lakeside daisy was found to be self-incompatible (sporophytic). The last Illinois population was effectively extinct because the remaining plants belonged to the same mating type ( N _e = 1) and only produced seeds when outcrossed to the Ohio plants. Cross-incompatibility was also observed among Ohio plants, suggesting that within large populations, compatible mating types may be rare locally. In addition, inbreeding depression (lower seed/ovule ratios in inbred than in outcrosses) was observed after one generation of inbreeding. Small populations of self-incompatible species are vulnerable to extinction if the number of self-incompatibility alleles, either as a result of a bottleneck or of genetic drift, falls below tbe number needed for the breeding system to function. Recovery protocols based on these genetic considerations were developed and implemented in 1988 when Lakeside daisy populations were established at three Illinois nature preserves.     

Erosion of Heterozygosity in Fluctuating Populations

Abstract: Demographic, environmental, and genetic stochasticity threaten the persistence of isolated populations. The relative importance of these intertwining factors remains unresolved, but a common view is that random demographic and environmental events will usually drive small populations to the brink of extinction before genetic deterioration poses a serious threat. To evaluate the potential importance of genetic factors, we analyzed a model linking demographic and environmental conditions to the loss of genetic diversity in isolated populations undergoing natural levels of fluctuation. Nongenetic processes—environmental stochasticity and population demography—were modeled according to a bounded diffusion process. Genetic processes were modeled by quantifying the rate of drift according to the effective population size, which was predicted from the same parameters used to describe the nongenetic processes. We combined these models to predict the heterozygosity remaining at the time of extinction, as predicted by the nongenetic portion of the model. Our model predicts that many populations will lose most or all of their neutral genetic diversity before nongenetic random events lead to extinction. Given the abundant evidence for inbreeding depression and recent evidence for elevated extinction rates of inbred populations, our findings suggest that inbreeding may be a greater general threat to population persistence than is generally recognized. Therefore, conservation biologists should not ignore the genetic component of extinction risk when assessing species endangerment and developing recovery plans.     

Urban Plants as Genetic Reservoirs or Threats to the Integrity of Bushland Plant Populations

Abstract:  Remnant plants in urban fringes and native plants in gardens have the potential to contribute to the conservation of threatened plants by increasing genetic diversity, effective size of populations, and levels of genetic connectedness. But they also pose a threat through the disruption of locally adapted gene pools. At Hyams Beach, New South Wales, Australia, four bushland stands of the rare shrub, Grevillea macleayana McGillivray, surround an urban area containing remnant and cultivated specimens of this species. Numbers of inflorescences per plant, fruits per plant, and visits by pollinators were similar for plants in urban gardens and bushland. Urban plants represented a substantial but complex genetic resource, displaying more genetic diversity than bushland plants judged by H_e , numbers of alleles per locus, and number of private alleles. Of 27 private alleles in urban plants, 17 occurred in a set of 19 exotic plants. Excluding the exotic plants, all five stands displayed a moderate differentiation ( F_ST = 0.14 ± 0.02), although the urban remnants clustered with two of the bushland stands. These patterns may be explained by high levels of selfing and inbreeding in this species and by long-distance dispersal (several seeds in the urban stand were fathered by plants in other stands). Genetic leakage (gene flow) from exotic plants to 321 seeds on surrounding remnant or bushland plants has not occurred. Our results demonstrate the conservation value of this group of urban plants, which are viable, productive, genetically diverse, and interconnected with bushland plants. Gene flow has apparently not yet led to genetic contamination of bushland populations, but high levels of inbreeding would make this a rare event and difficult to detect. Remnant plants in urban gardens could successfully contribute to recovery plans for endangered and vulnerable species.     

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     

Inbreeding and Loss of Genetic Variation in a Reintroduced Population of Mauritius Kestrel

Abstract:  Many populations have recovered from severe bottlenecks either naturally or through intensive conservation management. In the past, however, few conservation programs have monitored the genetic health of recovering populations. We conducted a conservation genetic assessment of a small, reintroduced population of Mauritius Kestrel ( Falco punctatus ) to determine whether genetic deterioration has occurred since its reintroduction. We used pedigree analysis that partially accounted for individuals of unknown origin to document that (1) inbreeding occurred frequently (2.6% increase per generation; N _eI= 18.9), (2) 25% of breeding pairs were composed of either closely or moderately related individuals, (3) genetic diversity has been lost from the population (1.6% loss per generation; N _eV= 32.1) less rapidly than the corresponding increase in inbreeding, and (4) ignoring the contribution of unknown individuals to a pedigree will bias the metrics derived from that pedigree, ultimately obscuring the prevailing genetic dynamics. The rates of inbreeding and loss of genetic variation in the subpopulation of Mauritius Kestrel we examined were extreme and among the highest yet documented in a wild vertebrate population. Thus, genetic deterioration may affect this population's long-term viability. Remedial conservation strategies are needed to reduce the impact of inbreeding and loss of genetic variation in this species. We suggest that schemes to monitor genetic variation after reintroduction should be an integral component of endangered species recovery programs.     

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.     

Predicted Genetic Consequences of Strong Fertility Selection Due to Pollinator Loss in an Isolated Population of Primula sieboldii

Previous studies demonstrated strong fertility selection for a self-fertile, homostyle morph due to pollinator loss in an isolated population of Primula sieboldii , an endangered heterostylous species. To predict genetic consequences of the selection we developed a deterministic genetic model based on a classical "supergene" model, and we studied the effects of pollinator availability and inbreeding depression on temporal changes of morph frequencies through model simulation. Because of the severe pollinator limitation experienced by the population, fast, irreversible loss of the thrum morph from the population was predicted, even if high inbreeding depression was assumed. To prevent the breakdown of the normal breeding system of the species, morph frequency monitoring for timely active management should be implemented. Active management should include hand pollinations and pollinator therapy—reintroduction and reestablishment of suitable pollinator populations. The method we adopted in this study to parametrize pollinator availability can be used widely in conservation modeling for a range of plant species that have multiple mating types with different degrees of self-incompatibility.     

Genetic Structure of Fragmented Populations of the Endangered Daisy Rutidosis leptorrhynchoides

Abstract: The endangered grassland daisy Rutidosis leptorrhynchoides has been subject to severe habitat destruction and fragmentation over the past century. Using allozyme markers, we examined the genetic diversity and structure of 16 fragmented populations. The species had high genetic variation compared to other plant species, and both polymorphism and allelic richness showed strong positive relationships with log reproductive population size, reflecting a loss of rare alleles (frequency of q < 0.1) in smaller populations. Fixation coefficients were positively related to size, due either to a lack of rare homozygotes in small populations or to Wahlund effects (owing to spatial genetic structure) in large ones. Neither gene diversity nor heterozygosity was related to population size, and other population parameters such as density, spatial contagion, and isolation had no apparent effect on genetic variation. Genetic divergence among populations was low , despite a large north-to-south break in the species' current distribution. To preserve maximum genetic variation, conservation strategies should aim to maintain the five populations larger than 5000 reproductive plants, all of which occur in the north of the range, as well as the largest southern population of 626 plants at Truganina. Only one of these is currently under formal protection. High heterozygosity in smaller populations suggests that they are unlikely to be suffering from inbreeding depression and so are also valuable for conservation. Erosion of allelic richness at self-incompatibility loci, however, may limit the reproductive capacity of populations numbering less than 20 flowering plants.     

Inbreeding Depression, Environmental Stress, and Population Size Variation in Scarlet Gilia (Ipomopsis aggregata)

Despite a large body of theory, few studies have directly assessed the effects of variation in population size on fitness components in natural populations of plants. We conducted studies on 10 populations of scarlet gilia, Ipomopsis aggregata , to assess the effects of population size and year-to-year variation in size on the relative fitness of plants. We showed that seed size and germination success are significantly reduced in small populations (those 100 flowering plants) of scarlet gilia. Plants from small populations are also more susceptible to environmental stress. When plants from small and large populations were subjected to an imposed stress (combined effects of transplanting and experimental clipping, simulating ungulate herbivory) in a common garden experiment, plants from small populations suffered higher mortality and were ultimately of smaller size than plants from large populations. In addition, experimental evidence indicates that observed fitness reductions are genetic, due to the effects of genetic drift and/or inbreeding depression. When pollen was introduced from distant populations into two small populations, seed mass and percentage of germination were bolstered, while pollen transferred into a large population had no significant effect. Year-to-year variation in population size and its effects on plant fitness are also discussed. In one small population, for example, a substantial increase in size from within did not introduce sufficient new (archived) genetic material to fully overcome the effects of inbreeding depression.     

Mutation and Conservation

Mutation can critically affect the viability of small populations by causing inbreeding depression, by maintaining potentially adaptive genetic variation in quantitative characters, and through the erosion of fitness by accumulation of mildly detrimental mutations. I review and integrate recent empirical and theoretical work on spontaneous mutation and its role in population viability and conservation planning. I analyze both the maintenance of potentially adaptive genetic variation in quantitative characters and the role of detrimental mutations in increasing the extinction risk of small populations. Recent experiments indicate that the rate of production of quasineutral, potentially adaptive genetic variance in quantitative characters is an order of magnitude smaller than the total mutational variance because mutations with large phenotypic effects tend to be strongly detrimental. This implies that, to maintain normal adaptive potential in quantitative characters under a balance between mutation and random genetic drift (or among mutation, drift, and stabilizing natural selection), the effective population size should be about 5000 rather than 500 (the Franklin-Soulé number). Recent theoretical results suggest that the risk of extinction due to the fixation of mildly detrimental mutations may be comparable in importance to environmental stochasticity and could substantially decrease the long-term viability of populations with effective sizes as large as a few thousand. These findings suggest that current recovery goals for many threatened and endangered species are inadequate to ensure long-term population viability.     

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.     

Longitudinal monitoring of neutral and adaptive genomic diversity in a reintroduction

Restoration programs in the form of ex-situ breeding combined with reintroductions are becoming critical to counteract demographic declines and species losses. Such programs are increasingly using genetic management to improve conservation outcomes. However, the lack of long-term monitoring of genetic indicators following reintroduction prevents assessments of the trajectory and persistence of reintroduced populations. We carried out an extensive monitoring program in the wild for a threatened small-bodied fish (southern pygmy perch, Nannoperca australis) to assess the long-term genomic effects of its captive breeding and reintroduction. The species was rescued prior to its extirpation from the terminal lakes of Australia's Murray-Darling Basin, and then used for genetically informed captive breeding and reintroductions. Subsequent annual or biannual monitoring of abundance, fitness, and occupancy over a period of 11 years, combined with postreintroduction genetic sampling, revealed survival and recruitment of reintroduced fish. Genomic analyses based on data from the original wild rescued, captive born, and reintroduced cohorts revealed low inbreeding and strong maintenance of neutral and candidate adaptive genomic diversity across multiple generations. An increasing trend in the effective population size of the reintroduced population was consistent with field monitoring data in demonstrating successful re-establishment of the species. This provides a rare empirical example that the adaptive potential of a locally extinct population can be maintained during genetically informed ex-situ conservation breeding and reintroduction into the wild. Strategies to improve biodiversity restoration via ex-situ conservation should include genetic-based captive breeding and longitudinal monitoring of standing genomic variation in reintroduced populations.     

The Paradox of Forest Fragmentation Genetics

Abstract:  Theory predicts widespread loss of genetic diversity from drift and inbreeding in trees subjected to habitat fragmentation, yet empirical support of this theory is scarce. We argue that population genetics theory may be misapplied in light of ecological realities that, when recognized, require scrutiny of underlying evolutionary assumptions. One ecological reality is that fragment boundaries often do not represent boundaries for mating populations of trees that benefit from long-distance pollination, sometimes abetted by long-distance seed dispersal. Where fragments do not delineate populations, genetic theory of small populations does not apply. Even in spatially isolated populations, where genetic theory may eventually apply, evolutionary arguments assume that samples from fragmented populations represent trees that have had sufficient time to experience drift, inbreeding, and ultimately inbreeding depression, an unwarranted assumption where stands in fragments are living relicts of largely unrelated predisturbance populations. Genetic degradation may not be as important as ecological degradation for many decades following habitat fragmentation.     

Inbreeding Depression in a Captive Wolf (Canis lupus) Population

Abstract. Uncertainty currently exists regarding the extent to which mammalian carnivores suffer from inbreeding depression. In particular, it has been proposed that wolves and species with a similar social structure are adapted to close inbreeding. Empirical data, however, are scarce. This paper provides strong evidence against the contention that natural populations of wolves are resistant to inbreeding depression. We analyzed studbook data of a captive wolf population bred in Scandinavian zoos and found negative effects of inbreeding expressed as reductions in juvenile weight, reproduction, and longevity. The occurrence of an apparently bereditary form of blindness is also associated with inbreeding. Different effects of inbreeding can be attributed to genes originating from different founder pairs, thus indicating that alleles that are deleterious in the homozygous state are fairly common in natural wolf populations.     

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.     

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 and hermaphroditism in the sessile-brooding bryozoan Celleporella hyalina

This study examined the occurrence and effects of inbreeding in the sessile, colonial hermaphrodite Celleporella hyalina. The results are discussed with regard to theoretical explanations for the prevalence of hermaphroditism in sessile clonal organisms. C. hyalina exhibited inbreeding depression at all stages, including the pre-zygotic. Outcrossing, sib and half-sib matings produced offspring but selfing did not. There was inbreeding depression in embryo production and survival. Inbred colonies showed slower growth and later maturation, with fewer reproductive zooids. The relative numbers of male and female zooids were affected by inbreeding; increased production of males is a sign of stress in C. hyalina. When mated with an outbred non-relative, inbred colonies had lower success both as males and as females in embryo production and offspring survivorship. The low survivorship of embryos fathered by inbred colonies is a clear effect of inbreeding on the F2 generation. These results indicate that C. hyalina is unlikely to inbreed in the wild, supporting the "space-limited" model of hermaphroditism for this species. This study indicates that hermaphroditism, by avoiding much of the cost of sex, can confer optimal reproductive fitness for sessile brooding animals in a space-limited habitat even in the absence of inbreeding.     

Genetic Diversity, Population Size, and Fitness in Central and Peripheral Populations of a Rare Plant Lychnis viscaria

Abstract: Genetic diversity is expected to decrease in small and isolated populations as a consequence of bottlenecks, founder effects, inbreeding, and genetic drift. The genetics and ecology of the rare perennial plant Lychnis viscaria (Caryophyllaceae) were studied in both peripheral and central populations within its distribution area. We aimed to investigate the overall level of genetic diversity, its spatial distribution, and possible differences between peripheral and central populations by examining several populations with electrophoresis. Our results showed that the level of genetic diversity varied substantially among populations (  H _exp = 0.000–0.116) and that the total level of genetic diversity (mean H _exp = 0.056) was low compared to that of other species with similar life-history attributes. The peripheral populations of L. viscaria had less genetic variation (mean H _exp = 0.034) than the central ones (0.114). Analysis of genetic structure suggested limited gene flow (mean F _ST = 0.430) and high differentiation among populations, emphasizing the role of genetic drift (  N _e m = 0.33). Isolation was even higher than expected based on the physical distance among populations. We also focused on the association between population size and genetic diversity and possible effects on fitness of these factors. Population size was positively correlated with genetic diversity. Population size and genetic diversity, however, were not associated with fitness components such as germination rate, seedling mass, or seed yield. There were no differences in the measured fitness components between peripheral and central populations. Even though small and peripheral populations had lower levels of genetic variation, they were as viable as larger populations, which emphasizes their potential value for conservation.