Genealogical Analysis of a Closed Herd of Black Hairless Iberian Pigs

Abstract: Livestock breeds are recognized as important components of world biodiversity. The Iberian pig is a swine breed well adapted to the Mediterranean forest ecosystem and provides cured products of high quality. The ancient population of Iberian pigs (  Sus scrofa meridionalis ) was differentiated in several local types, the black hairless pigs representing the fattest genetic type. The conservation program of the Guadyerbas strain has maintained this germplasm isolated since 1945 as a closed population in an experimental herd. The complete pedigree, with 1000 breeding animals descending from 24 founders, has been used to measure along the successive cohorts of breeding animals the effective number of founders, effective number of nonfounders, founder genome equivalents, and expected number of founders' surviving alleles. For the last cohort, the values were 10.34, 1.42, 1.25, and 4.06, respectively. The evolution of inbreeding and coancestry and its components attributable to each founder were also studied. The rate of increase in inbreeding and coancestry was 2.21% per cohort, or 0.906% per year. Finally, the effect of family structure and mating tactics on the evolution of coancestry was also analyzed. The greatest rates of coancestry per cohort were attributable to unbalanced family sizes, and the use of minimum coancestry matings effectively delayed the increase in inbreeding.     

Genetic Polymorphisms and Their Relationships with Inbreeding and Breed Structure in Rare British Sheep: The Portland, Manx Loghtan, and Hebridean

Abstract: 320 sheep of three rare British breeds were typed for blood group and biochemical polymorphism. Genetic distance was least between the Manx Loghtan and Hebridean (D = 0.1241, supporting historical evidence of a close relationship between the breeds. Distances to the Portland breed were 0.144 and 0.186, respectively. The claim that the Portland is related to the Dorset Horn was substantiated by the fact that both breeds possess the i blood group allele. Pedigree analysis showed that most rare or unusual alleles in the three bee could be traced to particular ancestors, which had been accepted for registration as foundation stocks, i. e., there was little evidence of genetic introgression from other breeh. Highly inbred sheep showed the predicted lack of heterozygosity.
When these sheep were first registered (1973), foundation stocks were defined comprising animals of correct breed type. Today, the pedigree of each sheep reveals the percentages of its ancestry attributable to each foundation stock Sheep were classified according to these percentages into subgroups, each of which, therefore corresponds to a strain within the breed Genetic distances were calculated among these subgroups within each breed For the Portland these distances were rather large (D up to 0.069), but distances were rather small for the other two breeds (D up to 0.027). The Manx Loghtan and Hebridean breeds are therefore relatively homogeneous while the genetic distances among Portland subgroups reveal the genetic consequences of the reproductive isolation of certain important flocks     

Estimates of Lethal Equivalents and the Cost of Inbreeding in Mammals

Abstract: The costs of inbreeding in natural populations of mammals are unknown despite their theoretical importance in genetic and sociobiological models and practical applications in conservation biology. A major cost of inbreeding is the reduced survival of inbred young. We estimate this cost from the regression of juvenile survival on the inbreeding coefficient using pedigrees of 40 captive mammalian populations belonging to 38 species.
The number of lethal equivalents ranged from –1.4 to 30.3, with a mean of 4.6 and a median of 3.1. There was no significant difference between populations founded with wild-caught individuals, a mixture of wild-caught and captive-born individuals, and individuals of unknown origin. The average cost of a parent-offspring or full sibling mating was 0.33, that is, mortality was 33% higher in offspring of such matings than in offspring of unrelated parents. This is likely to be an underestimate.     

野猪和几种家猪亲缘关系的RAPD分析

对二花脸猪、红灯笼猪、姜曲海猪、香猪、约克夏猪及华东地区野猪共２４个个体进行了随机扩增多态ＤＮＡ（ＲＡＰＤ）分析,以探讨家猪与野猪间的亲缘关系．实验从４０个引物中选用重复性较好的１３个引物对所有个体进行了随机扩增,共获得１９２个ＲＡＰＤ标记．ＲＡＰＤ研究结果表明：（１）长江下游江苏地区家猪品种或类群内遗传变异相对较小,群体的遗传趋异程度处于较低水平;（２）二花脸猪、红灯笼猪及姜曲海猪与华东地区的野猪可能起源于一个共同的祖先;（３）中国家猪各地方品种可能由分布于各地区的亚洲野猪经人们长期的定向选育而形成     

Inbreeding Depression in the Speke's Gazelle Captive Breeding Program

Abstract: The Speke's gazelle ( Gazella spekei ) captive breeding program has been presented as one of the few examples of selection reducing the genetic load of a population and as a potential model for the captive breeding of endangered species founded from a small number of individuals. In this breeding program, three generations of mate selection apparently increased the viability of inbred individuals. We reanalyzed the Speke's gazelle studbook and examined potential causes for the reduction of inbreeding depression. Our analysis indicates that the decrease in inbreeding depression is not consistent with any model of genetic improvement in the herd. Instead, we found that the effect of inbreeding decreased from severe to moderate during the first generation of inbreeding, and that this change is responsible for almost all of the decline in inbreeding depression observed during the breeding program. This eliminates selection as a potential explanation for the decrease in inbreeding depression and suggests that inbreeding depression may be more sensitive to environmental influences than is usually thought.     

Inbreeding-based bias in parental responsiveness to litters of oldfield mice

This study investigated variation in parental behavior in oldfield mice (Peromyscus polionotus). Specifically, I examined the possibility that parental behavior and probability of litter loss may differ depending on whether parents are related to one another and, therefore, whether offspring are inbred. When parents are related, they share more genes with their offspring and so may be predicted to invest more in inbred offspring if these offspring do not inherently have a greater risk of juvenile mortality. Survival of inbred pups did not differ from survival of outbred pups, and females tended to exhibit a preference, in the form of enhanced parental care, for inbred litters. Males did not display any consistent preferences. Inbred litters were left unattended more often during the immediate post-partum period than were outbred litters, but this inconsistent finding appeared to have a smaller effect than the overall improved maternal care provided to inbred litters. Females thus appeared to modulate their behavior to a greater degree than did males depending on characteristics of the litter. Patterns of litter loss indicated that complete death of litters was independent of litter inbreeding, whereas loss of selected pups in a litter occurred significantly more often when litters were inbred. Complete and partial loss of litters may be functionally different behaviors that are triggered by different cues. Received: 20 September 1996 / Accepted after revision: 28 April 1997     

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.     

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.     

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.     

Stress Resistance and Environmental Dependency of Inbreeding Depression in Drosophila melanogaster

Abstract: Both inbreeding and environmental stress can have adverse effects on fitness that affect the conservation of endangered species. Two important issues are whether stress and inbreeding effects are independent as opposed to synergistic, and whether inbreeding effects are general across stresses as opposed to stress-specific. We found that inbreeding reduced resistance to acetone and desiccation in adult Drosophila melanogaster , whereas resistance to knockdown heat stress was not affected. Inbred flies, however, experienced a greater proportional decrease in productivity than outbreds following heat stress. Correlations using line means indicated that all resistance traits were uncorrelated in the inbred as well as in the outbred flies. Recessive, deleterious alleles therefore did not appear to have any general deleterious effects on stress resistance. Inbreeding within a specific environment and selection for resistant genotypes may therefore purge a population of deleterious genes specific to only one environmental stress.     

Relative Contribution of Inbreeding Depression and Eroded Adaptive Diversity to Extinction Risk in Small Populations of Shore Campion

Abstract:  To study the relative importance of inbreeding depression and the loss of adaptive diversity in determining the extinction risk of small populations, we carried out an experiment in which we crossed and self-fertilized founder plants from a single, large population of shore campion ( Silene littorea Brot.). We used the seeds these plants produced to colonize 18 new locations within the distribution area of the species. The reintroduced populations were of three kinds: inbred and genetically homogeneous, each made up of selfed seed from a single plant; inbred and mixed, made up of a mixture of selfed seeds from all founder plants; and outbred and mixed, made up of a mixture of seeds obtained in outcrosses between the founders. We compared the inbred homogeneous populations with the inbred mixed to measure the effect of genetic diversity among individuals and the inbred mixed with the outbred mixed to measure the effect of inbreeding. Reintroduction success was seriously limited by inbreeding, whereas it was not affected by genetic diversity. This observation and the nonsignificant interaction between family and reintroduction location for individual plant characters suggest that the fixation of overall deleterious genes causing inbreeding depression posed a more serious threat to the short-term survival of the populations than the loss of genes involved in genotype and environment interactions. Thus, reintroduction success was related to adaptive diversity. Preventing such fixation might be the most important consideration in the genetic management and conservation of shore campion populations.     

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.     

运输应激对二花脸和皮特兰猪血浆应激和代谢相关激素水平的影响

比较二花脸和皮特兰猪在2h运输过程中血浆ACTH、皮质醇、胰岛素和T3、T4水平的动态变化模式,以分析内分泌激素变化的品种特征.选用雄性二花脸猪10头,皮特兰猪6头,体重达20kg时安装颈静脉瘘管,1wk后运输试验,运输过程中不同时间点采集血样,放射免疫分析法测定血浆激素水平.上车后两品种猪ACTH水平缓慢上升,60min后达到峰值,下车后15min恢复至基础水平,运输过程中ACTH水平及变化幅度均未表现显著的品种差异;运输前皮质醇水平二花脸显著高于皮特兰猪,上车后两品种皮质醇均迅速上升,出发后15min达到峰值,下车后15min均快速恢复至基础水平,运输过程中皮特兰皮质醇上升的幅度显著高于二花脸猪;两品种胰岛素水平上车后均呈下降趋势,二花脸胰岛素水平总体上显著高于皮特兰猪;T3水平在上车后也表现快速下降,无论是T3水平还是其变化幅度均不表现显著的品种差异;皮特兰猪上车后T4水平稍微下降而二花脸猪显著下降,皮特兰T4水平总体显著高于二花脸猪.运输应激伴随血浆ACTH和皮质醇水平升高,而胰岛素、T3和T4水平下降,皮质醇水平升高的幅度能够反映猪的应激敏感性.图1参25     

Population Viability Analysis for a Small Population of Red-Cockaded Woodpeckers and an Evaluation of Enhancement Strategies

We performed a series of population and pedigree analyses to examine the viability of a small Red-cockaded Woodpecker ( Picoides borealis ) population located at the Savannah River Site, in Barnwell and Aiken counties of South Carolina. The population's existence and future survival are precarious. As few as four individuals, including just one breeding pair, comprised this population in 1985. Now, primarily because of experimental transformation of birds from other areas, the population has increased to 25. As of 1990, genealogy pedigree analysis showed that the respective contribution of 14 founders to the extant population has not been equal. Founder gender equivalents are low (5.4) but could reach 9.2 if poorly-represented founders were to produce offspring. The fraction of founder gene diversity retained in the current population is 0.91. Successful recovery strategies would ensure 95% probability of population survival while maintaining 90% heterozygosity for 200 years. Viability analyses indicated that, depending on relative effects of inbreeding depression and stochastic environmental events, the Savannah River Site population has a 68–100% chance of extinction during this period. Annual translocation into the population of at least three females and two males for a 10-year period will achieve a 96% probability of survival for 200 years. Even with translocation of numerous males and females per year (up to 50 of each), the 90% heterozygosity goal may not be achieved. We discuss recommendations for choosing individuals for translocation logistical constraints on achieving recovery objectives, and limitations of our modeling approach.     

Genetic variation among trait groups and apparent absence of close inbreeding in grey-crowned babblers

Summary The grey-crowned babbler, Pomastostomus temporalis, is a non-migratory species with delayed breeding and prolonged association of young with siblings and parents. Since these conditions are conducive to incestuous matings, we have studied allozymic variation in a population in southeastern Queensland, to evaluate the possibility of close inbreeding. Eight of 20 loci tested were polymorphic, with an average proportion of heterozygous loci individual of 9.4%. No deficiency of heterozygotes was found, indicating the absence of detectable inbreeding. Some mechanism that prevents inbreeding seems to be present.     

Inbreeding and Extinction: A Threshold Effect

A fundamental assumption underlying the application of genetics within conservation biology is that inbreeding increases the risk of extinction. However, there is no information on the shape of the relationship, the available evidence has not distinguished genetic and nongenetic effects, and the issue is controversial. Methods were devised to separate genetic and nongenetic causes of extinction in inbred populations, and they were used to analyze data from Drosophila melanogaster, D. virilis and Mus musculus . Inbreeding markedly increased rates of extinction in all cases. All showed a threshold relationship between incremental extinction and inbreeding with low initial extinction, but they showed notably increased extinction beginning at intermediate levels of inbreeding. There was no difference in extinction levels at similar inbreeding coefficients in populations inbred at different rates (full sibling versus double first cousin). Endangered species may give little warning of impending extinction crises due to inbreeding.     

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.     

Shoaling decisions in three-spined sticklebacks (<Emphasis Type="Italic">Gasterosteus aculeatus</Emphasis>)—familiarity,kinship and inbreeding

Shoaling with familiar kin is a well-known phenomenon. It has been described both for adult and for fry of three-spined sticklebacks (Gasterosteus aculeatus). However, evidence of preference for kin independent of familiarity is scarce. Furthermore, inbreeding effects have not been studied for shoaling preferences and there is a lack of studies about changes in individuals’ ability to recognise kin during different phases of life history. We gave inbred and outbred, nonreproductive sticklebacks of different age the choice to shoal with a group of familiar siblings vs unfamiliar non-siblings and with unfamiliar siblings vs unfamiliar non-siblings. Subadult sticklebacks preferred to shoal with familiar kin over unfamiliar non-kin, but inbred and outbred individuals had similar preferences. When given the choice between unfamiliar siblings and unfamiliar non-sibs, adult outbred fish preferred the shoal of kin, while inbred fish behaved indifferently. Body characteristics of the group such as body mass, standard length and condition of its members did not significantly explain the shoaling preferences for kin. Thus, sticklebacks were capable of recognising familiar and unfamiliar kin. The latter capability was lost by inbreeding.     

Inbreeding and caste-specific variation in immune defence in the ant <Emphasis Type="Italic">Formica exsecta</Emphasis>

Social insects are a widespread and ecologically dominant group. Reproductive division of labour among the females in the colonies is a key trait for their success, but at the same time, it creates dense aggregations of relatives which may promote the spread of disease in the colonies. Hence, the appropriate regulation of immune defence is crucial for the well-being of a colony. Inbreeding may disturb this process through reduced resistance or by impairing the colony’s ability to regulate the responses. We tested the effect of inbreeding and the within-colony differences in the encapsulation response between the two female castes of the ant Formica exsecta. New reproductive females (gynes) born in more inbred colonies, and being more inbred themselves, showed an elevated immune response whereas inbreeding had no effect on worker response. Furthermore, the immune response exhibited by gynes was lower than that of workers and was not dependent on their body size whereas the worker response increased with body size. The elevated response is likely to reflect genetic stress caused by inbreeding, which in turn may compromise colony founding and longevity. Indeed, eliciting a high immune response in itself might not be adaptive. Our results show that the regulation of the expression of immunity differs between female castes despite their similar genetic make-up.