Inbreeding and fitness in captive populations: Lessons from Drosophila

The avoidance of inbreeding is a primary goal of endangered species population management. In order to fully understand the effects of inbreeding on the fitness of natural and captive populations, it is necessary to consider fitness components which span the entire life cycle of the organism. Using Drosophila melanogaster as a model organism for conservation genetics studies, we constructed 18 experimental lines derived from wild-type stocks which were homozygous for chromosome 2 (this chromosome constitutes 38% of the genome or is equivalent to F = 0.38). For six of these lines which exhibited a reduced homozygous fitness, we estimated the relative values of fitness components operating at both the juvenile stage (pre-adult viability) and adult stage (female fecundity and male-mating ability) of the life cycle. Males in these lines showed a markedly reduced mating ability, while viability and female fecundity were much less affected. Equilibrium values of the wild-type chromosomes in these lines were accurately predicted using a model that incorporated into it these independently estimated fitness components. These results emphasize the importance of studying all fitness components directly to determine overall fitness. A reduced mating ability among inbred males of a captive population can have serious consequences for its future sustainability, and can further jeopardize reintroduction efforts; consequently, a program to carefully monitor the reproductive success of individual males, as well as other fitness components, is recommended. © 1993 Wiley-Liss, Inc.     

Effect of temperature on the in vitro reproductive fitness of Pratylenchus coffeae populations from Vietnam

The in vitro reproductive fitness on carrot discs of 10 Pratylenchus coffeae populations collected from different agricultural crops in different agro-ecological regions in Vietnam was studied and compared with the reproductive fitness of a P. coffeae population from Ghana. Few major differences in in vitro reproductive fitness on carrot discs among the 10 P. coffeae populations from Vietnam examined (with the exception of one population originally isolated from the roots of an unidentified ornamental tree and one population originally isolated from banana), and between these populations and the P. coffeae population originally isolated from banana in Ghana were observed. Our observations indicate that although the optimum temperature for reproduction of three P. coffeae populations from Vietnam examined is 25?°C to, at least, 30?°C, these populations are also tolerant to low temperatures (15–20?°C) enabling them to survive the low temperatures which occur during the winter in the northern and central parts of Vietnam.     

Effects of population size and isolation on reproductive output in Aquilegia canadensis (Ranunculaceae)

It is generally expected that small, isolated populations will suffer reduced fitness due to inbreeding, yet few studies have investigated the relation between population characteristics, inbreeding and fitness. Among Ontario populations of the short‐lived, perennial plant Aquilegia canadensis, large populations (N>90 flowering plants) outcross twice as frequently as small populations (N=30–40), and inbreeding depression is extremely strong. We tested the prediction that reproductive output, a major component of population fitness, should be positively associated with population size. Data from a survey of 33 populations located on small islands in the St. Lawrence River, Canada and 23 populations on adjacent mainland areas supported this prediction. Population size correlated positively with reproductive output, measured as the number of seedlings produced per plant in 1995 (average r=+0.39 pooled P=0.019), and the number of fruits per plant in 1997 (r=+0.30, P=0.056). We also tested the prediction that fitness should decline with increasing spatial isolation between populations by measuring the distance separating all island populations. However, reproductive output did not correlate with isolation in either year. We compared island and mainland populations to test the prediction that reproductive output should be lower for populations on small islands than those occurring in more continuous mainland habitat. In contrast to our predictions, island populations exhibited, if anything, higher reproductive output than mainland populations. We also found no support for the prediction that the positive association between population size and reproductive output should be stronger for presumably isolated populations on small islands than for those on adjacent mainland areas. While the mechanisms underlying the association between population size and fitness are impossible to identify with correlations alone, our results are consistent with the hypothesis that inbreeding can significantly reduce the fitness of natural populations.     

Rapid genetic deterioration in captive populations: Causes and conservation implications

Many species require captive breeding to ensuretheir survival. The eventual aim of suchprograms is usually to reintroduce the speciesinto the wild. Populations in captivitydeteriorate due to inbreeding depression, lossof genetic diversity, accumulation of newdeleterious mutations and genetic adaptationsto captivity that are deleterious in the wild.However, there is little evidence on themagnitude of these problems. We evaluatedchanges in reproductive fitness in populationsof Drosophila maintained under benigncaptive conditions for 50 generations witheffective population sizes of 500 (2replicates), 250 (3), 100 (4), 50 (6) and 25(8). At generation 50, fitness in the benigncaptive conditions was reduced in smallpopulations due to inbreeding depression andincreased in some of the large populations dueto modest genetic adaptation. When thepopulations were moved to `wild' conditions,all 23 populations showed a marked decline(64–86%percnt;) in reproductive fitness compared tocontrols. Reproductive fitness showed acurvilinear relationship with population size,the largest and smallest population sizetreatments being the worst. Genetic analysesindicated that inbreeding depression andgenetic adaptation were responsible for thegenetic deterioration in `wild' fitness.Consequently, genetic deterioration incaptivity is likely to be a major problem whenlong-term captive bred populations ofendangered species are returned to the wild. Aregime involving fragmentation of captivepopulations of endangered species is suggestedto minimize the problems.     

Rapid spread of immigrant genomes into inbred populations

When local populations are genetically differentiated from one another and partially inbred, as typically occurs in subdivided populations, immigrant genomes are predicted to be at a frequency-dependent fitness advantage due to heterosis (hybrid vigour) in their descendants. We tested this prediction with pedigreed laboratory populations of the butterfly Bicyclus anynana and report here on a rapid increase over five generations in the contribution of an initially rare immigrant genome to the local population gene pool. The replicated experimental design, including immigrant controls, demonstrates that the mechanism underlying immigrant genome spread is heterosis, and that the advantage to the immigrant genes is sustained over several generations. Our result suggests that effective migration rates may often be much higher than the numbers of individual migrants assumed by classical population genetics models, with implications for the persistence and evolution of metapopulations.     

Conservation genetic management of a critically endangered New Zealand endemic bird: minimizing inbreeding in the Black Stilt Himantopus novaezelandiae

For threatened species with small captive populations, it is advisable to incorporate conservation management strategies that minimize inbreeding in an effort to avoid inbreeding depression. Using multilocus microsatellite genotype data, we found a significant negative relationship between genetic relatedness (inbreeding) and reproductive success (fitness) in a captive population of the critically endangered Black Stilt or KakīHimantopus novaezelandiae. In an effort to avoid inbreeding depression in this iconic New Zealand endemic, we recommend re‐pairing closely related captive birds with less related individuals and pairing new captive birds with distantly related individuals.     

Modeling problems in conservation genetics using captive Drosophila populations: Consequences of equalizing founder representation

Equalizing founder representation is a recommended practice for maintaining captive populations. However, this procedure has not been subject to controlled experimental evaluation. The effects on inbreeding, genetic variation, and reproductive fitness of maintaining small captive populations by equalizing founder representation (EFR) versus randomly choosing parents (RC) were compared. Ten replicate lines were created with unequal founder representations, split into EFR and RC lines, and maintained for a further eight generations. Founder representations computed from pedigrees were closer to equality in the EFR lines than in the RC lines or the base population, most of the changes being evident after one generation. Significant benefits of EFR were found in lowered inbreeding (mean inbreeding coefficients of 0.35 and 0.41, respectively, for EFR and RC lines) and average heterozygosity (0.141 for EFR, 0.084 for RC, compared with 0.216 in the base population). However, EFR was not significantly better than RC in moving allele frequencies towards equalized founder representation. No significant difference was found in reproductive fitness between EFR and RC (relative fitnesses compared to the base population were 0.179 for EFR and 0.182 for RC). The use of equalization of founder representation for a few generations can be recommended in the genetic management of captive populations derived from a small number of founders that contribute unequally. © 1992 Wiley-Liss, Inc.     

Modeling problems in conservation genetics using captive Drosophila populations: Rapid genetic adaptation to captivity

Long-term captive breeding programs for endangered species generally aim to preserve the option of release back into the wild. However, the success of re-release programs will be jeopardized if there is significant genetic adaptation to the captive environment. Since it is difficult to study this problem in rare and endangered species, a convenient laboratory animal model is required. The reproductive fitness of a large population of Drosophila melanogaster maintained in captivity for 12 months was compared with that of a recently caught wild population from the same locality. The competitive index measure of reproductive fitness for the captive population was twice that of the recently caught wild population, the difference being highly significant. Natural selection over approximately eight generations in captivity has caused rapid genetic adaptation. Captive breeding strategies for endangered species should minimize adaptation to captivity in populations destined for reintroduction into the wild. A framework for predicting the impact of factors on the rate of genetic adaptation to captivity is suggested. Equalization of family sizes is predicted to approximately halve the rate of genetic adaptation. Introduction of genes from the wild, increasing the generation interval, using captive environments close to those in the wild and achieving low mortality rates are all expected to slow genetic adaptation to captivity. Many of these procedures are already recommended for other reasons. © 1992 Wiley-Liss, Inc.     

Polymorphic microsatellite loci in peafowl (Pavo cristatus)

Understanding how the genetic characteristics of parents influence reproductive output is central to predicting the dynamics of small, endangered populations. We conducted a breeding experiment to look at the paternal genetic effects on offspring sex, fertility and growth in the peafowl (Pavo cristatus). Microsatellite loci were developed to allow maternity assignment and thus to allow us to separate maternal from paternal effects. We found 19 polymorphic loci in our inbred, captive population, six of which were only slightly polymorphic (H_E range: 0.04–0.70). The remaining 13 loci were polymorphic enough to determine maternity by exclusion in approximately 85% of offspring.     

Divergent levels of genetic variation and ploidy among populations of the rare shrub, Grevillea repens (Proteaceae)

Rare plant species are often restricted to small and/or isolated populations that can have reduced reproductive output and adaptive potential, resulting in an increased probability of extinction. Nevertheless, evolutionary changes might occur in such populations that increase their likelihood of persisting. In Australia, many threatened species from the ecologically important genus Grevillea (Proteaceae) are found in disjunct populations and these often display varied modes of reproduction from sexual to exclusively clonal. Here we use microsatellite markers to show that isolated populations across the entire range of G. repens have developed diverse patterns of genetic variation. The largest population has a relatively low level of genetic variation, one small population displays inbreeding, two populations show evidence of clonal reproduction and two contain both triploids and diploids. The global estimate of F _ST was moderately high (0.272) suggesting limited gene flow between populations and historical isolation. These findings indicate that the genetically distinct G. repens populations exhibit very different patterns of genetic variation and we propose that the development of clonality and polyploidy in small or isolated populations may allow persistence but also reduces the effective size of the sexual population. Grevillea repens populations from its eastern and western/western central centres of distribution should be viewed as separate units for conservation management.     

Immigrant inviability promotes reproductive isolation among host‐associated populations of the gall wasp Belonocnema treatae

Ecological speciation describes the evolutionary process whereby divergent natural selection between environments generates reproductive isolation. Studying the magnitude of sequential reproductive barriers between ecologically divergent populations improves our understanding of the way these barriers evolve and how each contributes to the speciation process. Immigrant inviability describes the lower fitness of immigrants in non‐native environments and is an important, but long underexplored, reproductive barrier. In this study, we test the role of immigrant inviability among host‐associated populations of the gall wasp Belonocnema treataeMayr (Hymenoptera: Cynipini: Cynipidae) by measuring the ability of gall wasps to initiate and complete gall formation, while avoiding host immune responses, on closely related native and non‐native live oaks, Quercus virginianaMill., Quercus fusiformisSmall, and Quercus geminataSmall (Fagaceae). In general, we found evidence for immigrant inviability when B. treatae populations colonized non‐native host species. However, patterns were variable among years, suggesting that episodic events may play an important role in connecting ecologically divergent populations.     

Source population characteristics affect heterosis following genetic rescue of fragmented plant populations

Understanding the relative importance of heterosis and outbreeding depression over multiple generations is a key question in evolutionary biology and is essential for identifying appropriate genetic sources for population and ecosystem restoration. Here we use 2455 experimental crosses between 12 population pairs of the rare perennial plant Rutidosis leptorrhynchoides (Asteraceae) to investigate the multi-generational (F₁, F₂, F₃) fitness outcomes of inter-population hybridization. We detected no evidence of outbreeding depression, with inter-population hybrids and backcrosses showing either similar fitness or significant heterosis for fitness components across the three generations. Variation in heterosis among population pairs was best explained by characteristics of the foreign source or home population, and was greatest when the source population was large, with high genetic diversity and low inbreeding, and the home population was small and inbred. Our results indicate that the primary consideration for maximizing progeny fitness following population augmentation or restoration is the use of seed from large, genetically diverse populations.     

The relative effects of mutation accumulation versus inbreeding depression on fitness in experimental populations of the housefly

Loss of fitness due to inbreeding depression in small captive populations of endangered species is widely appreciated. Populations of all sizes may also experience loss in fitness when environmental conditions are ameliorated because deleterious alleles may be rendered neutral and accumulate rapidly. Few data exist, however, to demonstrate loss in fitness due to relaxed selection. Loss of fitness in life‐history traits were compared between LARGE (N_e ≥ 500) and SMALL (N_e = 50) populations of the housefly Musca domestica L that were subjected to curtailed life span at 21 days to remove selection on late‐acting deleterious alleles. During the early part of the life history (≤21 days), the rate of decline in fecundity and progeny production over 24 generations was greater in the small (1.5%) than in the large populations <0.2%), but rate of loss in late‐life fecundity and progeny production (>21 days) was equivalent across populations, consistent with neutral theory, and amounted to 1.7% per generation. This rate of loss due to relaxed selection was equivalent to the rate of loss due to inbreeding in populations with an effective size of 50 individuals. Even if captive populations are kept large to avoid inbreeding, breeding them in benign environments where the forces of natural selection are curtailed may jeopardize the capability of these populations to exist in natural environments within few generations. Zoo Biol 20:145–156, 2001. © 2001 Wiley‐Liss, Inc.     

Fitness decline under osmotic stress in Caenorhabditis elegans populations subjected to spontaneous mutation accumulation at varying population sizes

The consequences of mutations for population fitness depends on their individual selection coefficients and the effective population size. An earlier study of Caenorhabditis elegans spontaneous mutation accumulation lines evolved for 409 generations at three population sizes found that N_e  = 1 populations declined significantly in fitness whereas the fitness of larger populations (N_e  = 5, 50) was indistinguishable from the ancestral control under benign conditions. To test if larger MA populations harbor a load of cryptic deleterious mutations that are obscured under benign laboratory conditions, we measured fitness under osmotic stress via exposure to hypersaline conditions. The fitness of N_e  = 1 lines exhibited a further decline under osmotic stress compared to benign conditions. However, the fitness of larger populations remained indistinguishable from that of the ancestral control. The average effects of deleterious mutations in N_e  = 1 lines were estimated to be 22% for productivity and 14% for survivorship, exceeding values previously detected under benign conditions. Our results suggest that fitness decline is due to large effect mutations that are rapidly removed via selection even in small populations, with implications for conservation practices. Genetic stochasticity may not be as potent and immediate a threat to the persistence of small populations as other demographic and environmental stochastic factors.     

Inbreeding depression and mating-distance dependent offspring fitness in large and small populations of Lychnis flos-cuculi (Caryophyllaceae)

The spatial structure of four Lychnis flos-cuculi populations, varying in size and degree of isolation, was studied by comparing the fitness of offspring resulting from self-pollination and pollinations by neighbouring plants, plants within the same population, and plants from other populations. Selfed offspring had the lowest fitness of the four offspring groups. No significant difference was found between the performance of offspring from pollinations by neighbouring plants and offspring pollinated by plants further apart but within the same population. A lower fitness of offspring from pollinations between neighbours would be expected if these matings, on average, yielded inbred offspring which suffered from inbreeding depression. These results imply that either a tight neighbourhood structuring is not present, or that the inbreeding depression for offspring by neighbours is too low to detect, although these are inbred. Crossings between populations produced offspring with a significantly higher fitness than offspring sired within populations. There were no significant differences in response to inbreeding among the populations, and differences in mean fitness among populations had no clear relation to the population size or degree of isolation. A reduced fitness of small populations due to inbreeding depression or a less severe response to experimental inbreeding due to purging of deleterious alleles is therefore not supported by our results.     

Rapid genetic and morphologic divergence between captive and wild populations of the endangered Leon Springs pupfish,Cyprinodon bovinus

The Leon Springs pupfish (Cyprinodon bovinus) is an endangered species currently restricted to a single desert spring and a separate captive habitat in southwestern North America. Following establishment of the captive population from wild stock in 1976, the wild population has undergone natural population size fluctuations, intentional culling to purge genetic contamination from an invasive congener (Cyprinodon variegatus) and augmentation/replacement of wild fish from the captive stock. A severe population decline following the most recent introduction of captive fish prompted us to examine whether the captive and wild populations have differentiated during the short time they have been isolated from one another. If so, the development of divergent genetic and/or morphologic traits between populations could contribute to a diminished ability of fish from one location to thrive in the other. Examination of genomewide single nucleotide polymorphisms and morphologic variation revealed no evidence of residual C. variegatus characteristics in contemporary C. bovinus samples. However, significant genetic and morphologic differentiation was detected between the wild and captive populations, some of which might reflect local adaptation. Our results indicate that genetic and physical characteristics can diverge rapidly between isolated subdivisions of managed populations, potentially compromising the value of captive stock for future supplementation efforts. In the case of C. bovinus, our findings underscore the need to periodically inoculate the captive population with wild genetic material to help mitigate genetic, and potentially morphologic, divergence between them and also highlight the utility of parallel morphologic and genomic evaluation to inform conservation management planning.     

Microsatellite analysis of the genetic structure of captive forest musk deer populations and its implication for conservation

Forest musk deer (Moschus berezovskii) are rare as a result of poaching for musk and habitat loss. Some captive populations of forest musk deer have been established for decades in China. However, little genetic information is available for conservation management. In this paper, genetic variations, population structures, and the genetic bottleneck hypothesis were examined using 11 microsatellite loci from captive populations in Miyalo, Jinfeng and Maerkang in Sichuan Province, China. Estimates of genetic variability revealed substantial genetic variation in the three populations. A total of 142 different alleles were observed in 121 forest musk deer and the effective number of alleles per locus varied from 6.76 to 12.95. The average values of observed heterozygosity, expected heterozygosity, and Nei's expected heterozygosity were 0.552, 0.899 and 0.894 respectively. The overall significant (P < 0.001) deficit of heterozygotes because of inbreeding within breeds amounted to 34.5%. The mean F_ST (P < 0.001) showed that approximately 90.2% of the genetic variation was within populations and 9.8% was across populations. The UPGMA diagram, based on Nei's unbiased genetic distance, indicated that the three populations were differentiated into two different groups and it agreed with their origin and history. Bottleneck tests indicated that all three populations have undergone a population bottleneck, suggesting a small effective population size. Acknowledging that the genetic structure of populations has crucial conservation implications, the present genetic information should be taken into account in management plans for the conservation of captive forest musk deer.     

Genetic structure of the critically endangered Red‐headed Wood Pigeon Columba janthina nitens and its implications for the management of threatened island populations

The Red‐headed Wood Pigeon Columba janthina nitens is endemic to the Ogasawara Islands, an oceanic island chain located 1000 km south of the main islands of Japan. The subspecies is at high risk of extinction because of its small population size and restricted habitat range. We undertook genetic analyses of this pigeon using sequences of a portion of the mitochondrial control region and five microsatellite markers to estimate the genetic characteristics of two wild populations from the Bonin and Volcano Islands, as well as one captive breeding population. The genetic diversity of the wild individuals was exceptionally low in both the mitochondria (nucleotide diversity = 0.00105) and at the microsatellite (3.2 alleles per locus and H_E = 0.12) loci. Higher numbers of microsatellite genotypes were observed in the Volcano Islands population than in the Bonin Islands population, which may be because of the relatively low impact of human disturbance. The most common mitochondrial haplotypes and microsatellite alleles observed in the two wild populations were completely fixed in the captive population. Our results suggest that the genetic diversity of the captive population needs to be increased. However, introduction of a wild individual into a captive population can lead to a decreased genetic diversity in the wild population and therefore should be done with caution. The genetic differentiation between the Bonin and the Volcano island groups was low, and the populations of the two island groups should be regarded as a single evolutionarily significant unit. However, special consideration is required for habitat conservation in the Volcano Islands, which may be functioning as a sanctuary for the Red‐headed Wood Pigeon. For the long‐term conservation of threatened bird species that live on remote oceanic islands, determination of management units considering gene flow caused by their flying capacity and maintenance of genetically suitable wild and captive populations are essential.     

Effects of Inbreeding on Skeletal Size and Fluctuating Asymmetry of Peromyscus polionotus Mice

Measurements of size and asymmetry in morphology might provide early indications of damaging effects of inbreeding or other genetic changes in conservation breeding programs. We examined the effects of inbreeding on size and fluctuating asymmetry (FA) in skull and limb bone measurements in experimental populations of three subspecies of Peromyscus polionotus mice that had previously been shown to suffer significant reductions in reproductive success when inbred. Inbreeding caused significant depression in mean size in two of the subspecies (P. p. rhoadsi and P. p. subgriseus), but the effects were smaller in the third (P. p. leucocephalus). Inbreeding caused an increase in FA of just one of eight bilateral traits in one subspecies (P. p. rhoadsi). Inbreeding depression in size was more easily detected than the effects of inbreeding on FA. FA may be much less sensitive to inbreeding and other stresses than are more direct measures of fitness such as reproductive output and body mass growth rate. Given the large sample sizes and statistical complexity required to assess changes to typically very small levels of FA in captive populations, FA will not likely provide a useful measure of inbreeding depression in captive populations. Zoo Biol. 32:125‐133, 2013. © 2012 Wiley Periodicals, Inc.     

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.