A high‐quality pedigree and genetic markers both reveal inbreeding depression for quality but not survival in a cooperative mammal

Inbreeding depression, the reduced fitness of offspring of closely related parents, is commonplace in both captive and wild populations and has important consequences for conservation and mating system evolution. However, because of the difficulty of collecting pedigree and life‐history data from wild populations, relatively few studies have been able to compare inbreeding depression for traits at different points in the life cycle. Moreover, pedigrees give the expected proportion of the genome that is identical by descent (IBD_g) whereas in theory with enough molecular markers realized IBD_g can be quantified directly. We therefore investigated inbreeding depression for multiple life‐history traits in a wild population of banded mongooses using pedigree‐based inbreeding coefficients (f_ped) and standardized multilocus heterozygosity (sMLH) measured at 35–43 microsatellites. Within an information theoretic framework, we evaluated support for either f_ped or sMLH as inbreeding terms and used sequential regression to determine whether the residuals of sMLH on f_ped explain fitness variation above and beyond f_ped. We found no evidence of inbreeding depression for survival, either before or after nutritional independence. By contrast, inbreeding was negatively associated with two quality‐related traits, yearling body mass and annual male reproductive success. Yearling body mass was associated with f_ped but not sMLH, while male annual reproductive success was best explained by both f_ped and residual sMLH. Thus, our study not only uncovers variation in the extent to which different traits show inbreeding depression, but also reveals trait‐specific differences in the ability of pedigrees and molecular markers to explain fitness variation and suggests that for certain traits, genetic markers may capture variation in realized IBD_g above and beyond the pedigree expectation.     

Heterozygosity-fitness correlations in zebra finches: microsatellite markers can be better than their reputation

Numerous studies have reported associations between heterozygosity in microsatellite markers and fitness-related traits (heterozygosity-fitness correlations, HFCs). However, it has often been questioned whether HFCs reflect general inbreeding depression, because a small panel of microsatellite markers does not reflect very well an individual's inbreeding coefficient (F) as calculated from a pedigree. Here, we challenge this prevailing view. Because of chance events during Mendelian segregation, an individual's realized proportion of the genome that is identical by descent (IBD) may substantially deviate from the pedigree-based expectation (i.e. F). This Mendelian noise may result in a weak correlation between F and multi-locus heterozygosity, but this does not imply that multi-locus heterozygosity is a bad estimator of realized IBD. We examined correlations between 11 fitness-related traits measured in up to 1192 captive zebra finches and three measures of inbreeding: (i) heterozygosity across 11 microsatellite markers, (ii) heterozygosity across 1359 single-nucleotide polymorphism (SNP) markers and (iii) F, based on a 5th-generation pedigree. All 11 phenotypic traits showed positive relationships with measures of heterozygosity, especially traits that are most closely related to fitness. Remarkably, the small panel of microsatellite markers produced equally strong HFCs as the large panel of SNP markers. Both marker-based approaches produced stronger correlations with phenotypes than the pedigree-based F, and this did not seem to result from the shortness of our pedigree. We argue that a small panel of microsatellites with high allelic richness may better reflect an individual's realized IBD than previously appreciated, especially in species like the zebra finch, where much of the genome is inherited in large blocks that rarely experience cross-over during meiosis.     

A comparison of pedigree‐ and DNA‐based measures for identifying inbreeding depression in the critically endangered Attwater's Prairie‐chicken

The primary goal of captive breeding programmes for endangered species is to prevent extinction, a component of which includes the preservation of genetic diversity and avoidance of inbreeding. This is typically accomplished by minimizing mean kinship in the population, thereby maintaining equal representation of the genetic founders used to initiate the captive population. If errors in the pedigree do exist, such an approach becomes less effective for minimizing inbreeding depression. In this study, both pedigree‐ and DNA‐based methods were used to assess whether inbreeding depression existed in the captive population of the critically endangered Attwater's Prairie‐chicken (Tympanuchus cupido attwateri), a subspecies of prairie grouse that has experienced a significant decline in abundance and concurrent reduction in neutral genetic diversity. When examining the captive population for signs of inbreeding, variation in pedigree‐based inbreeding coefficients (f_pedigree) was less than that obtained from DNA‐based methods (f_DNA). Mortality of chicks and adults in captivity were also positively correlated with parental relatedness (r_DNA) and f_DNA, respectively, while no correlation was observed with pedigree‐based measures when controlling for additional variables such as age, breeding facility, gender and captive/release status. Further, individual homozygosity by loci (HL) and parental r_DNA values were positively correlated with adult mortality in captivity and the occurrence of a lethal congenital defect in chicks, respectively, suggesting that inbreeding may be a contributing factor increasing the frequency of this condition among Attwater's Prairie‐chickens. This study highlights the importance of using DNA‐based methods to better inform management decisions when pedigrees are incomplete or errors may exist due to uncertainty in pairings.     

Gene survival in the Asian wild horse (Equus przewalskii): II. Gene survival in the whole population,in subgroups,and through history

In populations with a known pedigree, exact joint probability distributions of numbers of surviving of genes from each founder can now be calculated for moderately large complex pedigrees (1,000–2,000 individuals and much inbreeding). The usefulness of such calculations is shown by our analysis of gene survival in the Asian wild horse (Equus przewalskii), a species now extinet in the wild with a captive population with 1,516 individuals in the known pedigree (12 generations). We calculate the genetic diversity of subsets of the current population interesting to the North American Species Survival Plan, trace the loss of genetic diversity in this species through its history in captivity, and determine genetically important individuals in the North American population—those with relatively high probabilities of having unique copy genes (genes not found in any other living individual in North America).     

An evaluation of inbreeding measures using a whole-genome sequenced cattle pedigree

The estimation of the inbreeding coefficient (F) is essential for the study of inbreeding depression (ID) or for the management of populations under conservation. Several methods have been proposed to estimate the realized F using genetic markers, but it remains unclear which one should be used. Here we used whole-genome sequence data for 245 individuals from a Holstein cattle pedigree to empirically evaluate which estimators best capture homozygosity at variants causing ID, such as rare deleterious alleles or loci presenting heterozygote advantage and segregating at intermediate frequency. Estimators relying on the correlation between uniting gametes (F_UNI) or on the genomic relationships (F_GRM) presented the highest correlations with these variants. However, homozygosity at rare alleles remained poorly captured. A second group of estimators relying on excess homozygosity (F_HOM), homozygous-by-descent segments (F_HBD), runs-of-homozygosity (F_ROH) or on the known genealogy (F_PED) was better at capturing whole-genome homozygosity, reflecting the consequences of inbreeding on all variants, and for young alleles with low to moderate frequencies (0.10 < . < 0.25). The results indicate that F_UNI and F_GRM might present a stronger association with ID. However, the situation might be different when recessive deleterious alleles reach higher frequencies, such as in populations with a small effective population size. For locus-specific inbreeding measures or at low marker density, the ranking of the methods can also change as F_HBD makes better use of the information from neighboring markers. Finally, we confirmed that genomic measures are in general superior to pedigree-based estimates. In particular, F_PED was uncorrelated with locus-specific homozygosity.Subject terms: Conservation genomics, Animal breeding, Inbreeding     

Pedigrees, MHC and microsatellites: an integrated approach for genetic management of captive African wild dogs (Lycaon pictus)

Captive breeding programmes aim to provide an insurance against extinction in the wild and a source for re-introductions making it essential to minimise genetic threats, and maximise representation of wild adaptive genetic diversity. As such, genetic assessments of captive breeding programmes are increasingly common. However, these rarely include comprehensive comparisons with wild populations and typically neutral, rather than adaptive, genetic diversity is assayed. Moreover, genetic data are rarely integrated with studbook information, which enables the most robust assessments. Here we use the European captive African wild dog (Lycaon pictus) population to demonstrate the utility of this combined approach. Specifically, we combined studbook pedigree information with genetic assessments of captive and wild samples at both neutral markers and a locus thought to be important for adaptation (a gene at the Major Histocompatibility Complex, MHC). With these data we were able to evaluate founder origin and representation, as well as the distribution and origin of genetic variation within the captive population. We found discrepancies between diversity metrics derived from neutral and adaptive markers and pedigree versus genetic derived inbreeding estimates. Overall, however, we found a large proportion of genetic diversity from wild populations to be conserved in the captive population, much of which can be attributed to recent imports from outside of the European breeding programme. Nonetheless, we also found a high incidence of inbreeding and very skewed founder contributions. Based on these results, we proposed and implemented a genetic management plan to prevent further losses of diversity and reduce inbreeding.     

Molecular and pedigree measures of relatedness provide similar estimates of inbreeding depression in a bottlenecked population

Individual‐based estimates of the degree of inbreeding or parental relatedness from pedigrees provide a critical starting point for studies of inbreeding depression, but in practice wild pedigrees are difficult to obtain. Because inbreeding increases the proportion of genomewide loci that are identical by descent, inbreeding variation within populations has the potential to generate observable correlations between heterozygosity measured using molecular markers and a variety of fitness related traits. Termed heterozygosity‐fitness correlations (HFCs), these correlations have been observed in a wide variety of taxa. The difficulty of obtaining wild pedigree data, however, means that empirical investigations of how pedigree inbreeding influences HFCs are rare. Here, we assess evidence for inbreeding depression in three life‐history traits (hatching and fledging success and juvenile survival) in an isolated population of Stewart Island robins using both pedigree‐ and molecular‐derived measures of relatedness. We found results from the two measures were highly correlated and supported evidence for significant but weak inbreeding depression. However, standardized effect sizes for inbreeding depression based on the pedigree‐based kin coefficients (k) were greater and had smaller standard errors than those based on molecular genetic measures of relatedness (RI), particularly for hatching and fledging success. Nevertheless, the results presented here support the use of molecular‐based measures of relatedness in bottlenecked populations when information regarding inbreeding depression is desired but pedigree data on relatedness are unavailable.     

Quantifying and managing the loss of genetic variation in a free-ranging population of takahe through the use of pedigrees

Pedigree analysis has clear benefits for the genetic management of threatened populations through the evaluation of inbreeding, population structure and genetic diversity. The use of pedigrees is usually restricted to captive populations and few examples exist of their exclusive use in managing free-ranging populations. One such example is the management of the takahe (Porphyrio hochstetteri), a highly endangered, flightless New Zealand rail at risk from introduced mammalian predators and habitat loss. During the 1980’s and 90’s, as part of the takahe recovery programme, birds were translocated from the sole remnant population in Fiordland to four offshore islands from which introduced predators had been eradicated. The subsequent “island” population, now numbering 83 and thought to be at carrying capacity, has been closely monitored since founding. Detailed breeding records allow us to analyse the island pedigree, which is up to 7 generations deep. Gene-drop analysis indicated that 7.5% of genetic diversity has been lost over the relatively short timeframe since founding (2.1 generations on average; total genetic founders = 31) due to both a failure to equalise founder representation early on and subsequent disproportionate breeding success (founder equivalents = 12.5; founder genome equivalents = 6.6). A high prevalence of close inbreeding will have also impacted on genetic diversity. Predictions from pedigree modelling suggest that 90% genetic diversity will be maintained for only 12 years, but by introducing a low level of immigration from the Fiordland population and permitting the population to grow, 90% GD could be maintained over the next 100 years. More generally, the results demonstrate the value of maintaining pedigrees for wild populations, especially in the years immediately after a translocation event.     

Measuring individual inbreeding in the age of genomics: marker-based measures are better than pedigrees

Inbreeding (mating between relatives) can dramatically reduce the fitness of offspring by causing parts of the genome to be identical by descent. Thus, measuring individual inbreeding is crucial for ecology, evolution and conservation biology. We used computer simulations to test whether the realized proportion of the genome that is identical by descent (IBD_G) is predicted better by the pedigree inbreeding coefficient (F_P) or by genomic (marker-based) measures of inbreeding. Genomic estimators of IBD_G included the increase in individual homozygosity relative to mean Hardy–Weinberg expected homozygosity (F_H), and two measures (F_ROH and F_E) that use mapped genetic markers to estimate IBD_G. IBD_G was more strongly correlated with F_H, F_E and F_ROH than with F_P across a broad range of simulated scenarios when thousands of SNPs were used. For example, IBD_G was more strongly correlated with F_ROH, F_H and F_E (estimated with ⩾10 000 SNPs) than with F_P (estimated with 20 generations of complete pedigree) in populations with a recent reduction in the effective populations size (from N_e=500 to N_e=75). F_ROH, F_H and F_E generally explained >90% of the variance in IBD_G (among individuals) when 35 K or more SNPs were used. F_P explained <80% of the variation in IBD_G on average in all simulated scenarios, even when pedigrees included 20 generations. Our results demonstrate that IBD_G can be more precisely estimated with large numbers of genetic markers than with pedigrees. We encourage researchers to adopt genomic marker-based measures of IBD_G as thousands of loci can now be genotyped in any species.     

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.     

Genomic and phenotypic effects of inbreeding across two different hatchery management regimes in Chinook salmon

Genomic approaches permit direct estimation of inbreeding and its effect on fitness. We used genomic‐based estimates of inbreeding to investigate their relationship with eight adult traits in a captive‐reared Pacific salmonid that is released into the wild. Estimates were also used to determine whether alternative broodstock management approaches reduced risks of inbreeding. Specifically, 1,100 unlinked restriction‐site associated (RAD) loci were used to compare pairwise relatedness, derived from a relationship matrix, and individual inbreeding, estimated by comparing observed and expected homozygosity, across four generations in two hatchery lines of Chinook salmon that were derived from the same source. The lines are managed as “integrated” with the founding wild stock, with ongoing gene flow, and as “segregated” with no gene flow. While relatedness and inbreeding increased in the first generation of both lines, possibly due to population subdivision caused by hatchery initiation, the integrated line had significantly lower levels in some subsequent generations (relatedness: F₂–F₄; inbreeding F₂). Generally, inbreeding was similar between the lines despite large differences in effective numbers of breeders. Inbreeding did not affect fecundity, reproductive effort, return timing, fork length, weight, condition factor, and daily growth coefficient. However, it delayed spawn timing by 1.75 days per one standard deviation increase in F (~0.16). The results indicate that integrated management may reduce inbreeding but also suggest that it is relatively low in a small, segregated hatchery population that maximized number of breeders. Our findings demonstrate the utility of genomics to monitor inbreeding under alternative management strategies in captive breeding programs.     

Estimation of the inbreeding coefficient through use of genomic data

Many linkage studies are performed in inbred populations, either small isolated populations or large populations with a long tradition of marriages between relatives. In such populations, there exist very complex genealogies with unknown loops. Therefore, the true inbreeding coefficient of an individual is often unknown. Good estimators of the inbreeding coefficient (f) are important, since it has been shown that underestimation of f may lead to false linkage conclusions. When an individual is genotyped for markers spanning the whole genome, it should be possible to use this genomic information to estimate that individual's f. To do so, we propose a maximum-likelihood method that takes marker dependencies into account through a hidden Markov model. This methodology also allows us to infer the full probability distribution of the identity-by-descent (IBD) status of the two alleles of an individual at each marker along the genome (posterior IBD probabilities) and provides a variance for the estimates. We simulate a full genome scan mimicking the true autosomal genome for (1) a first-cousin pedigree and (2) a quadruple-second-cousin pedigree. In both cases, we find that our method accurately estimates f for different marker maps. We also find that the proportion of genome IBD in an individual with a given genealogy is very variable. The approach is illustrated with data from a study of demyelinating autosomal recessive Charcot-Marie-Tooth disease.     

Effective Population Size,Extended Linkage Disequilibrium and Signatures of Selection in the Rare Dog Breed Lundehund

The Lundehund is an old dog breed with remarkable anatomical features including polydactyly in all four limbs and extraordinary flexibility of the spine. We genotyped 28 Lundehund using the canine Illumina high density beadchip to estimate the effective population size (N_e) and inbreeding coefficients as well as to identify potential regions of positive selection. The decay of linkage disequilibrium was slow with r² = 0.95 in 50 kb distance. The last 7-200 generations ago, Ne was at 10-13. An increase of N_e was noted in the very recent generations with a peak value of 19 for N_e at generation 4. The FROH estimated for 50-, 65- and 358-SNP windows were 0.87, 087 and 0.81, respectively. The most likely estimates for F_ROH after removing identical-by-state segments due to linkage disequilibria were at 0.80-0.81. The extreme loss of heterozygosity has been accumulated through continued inbreeding over 200 generations within a probably closed population with a small effective population size. The mean inbreeding coefficient based on pedigree data for the last 11 generations (F_Ped = 0.10) was strongly biased downwards due to the unknown coancestry of the founders in this pedigree data. The long-range haplotype test identified regions with genes involved in processes of immunity, olfaction, woundhealing and neuronal development as potential targets of selection. The genes QSOX2, BMPR1B and PRRX2 as well as MYOM1 are candidates for selection on the Lundehund characteristics small body size, increased number of digits per paw and extraordinary mobility, respectively.     

Genetic structure analysis of a highly inbred captive population of the African antelope Addax nasomaculatus. Conservation and management implications

The African antelope Addax nasomaculatus is a rare mammal at high risk of extinction, with no more than 300 individuals in the wild and 1,700 captive animals distributed in zoos around the world. In this work, we combine genetic data and genealogical information to assess the structure and genetic diversity of a captive population located at Parque Lecocq Zoo (N=27), originated from only two founders. We amplified 39 microsatellites previously described in other Artiodactyls but new to this species. Seventeen markers were polymorphic, with 2–4 alleles per locus (mean=2.71). Mean expected heterozygosity (He) per locus was between 0.050 (marker ETH3) and 0.650 (marker D5S2), with a global He of 0.43. The mean inbreeding coefficient of the population computed from pedigree records of all registered individuals (N=53) was 0.222. The mean coancestry of the population was 0.298 and F_IS index was ?0.108. These results reflect the importance of an adequate breeding management on a severely bottlenecked captive population, which would benefit by the incorporation of unrelated individuals. Thanks to the successful amplification of a large number of microsatellites commonly used in domestic bovids, this study will provide useful information for the management of this population and serve as future reference for similar studies in other captive populations of this species. Zoo Biol 30:399–411, 2011. © 2010 Wiley‐Liss, Inc.     

Runs of homozygosity: current knowledge and applications in livestock

This review presents a broader approach to the implementation and study of runs of homozygosity (ROH) in animal populations, focusing on identifying and characterizing ROH and their practical implications. ROH are continuous homozygous segments that are common in individuals and populations. The ability of these homozygous segments to give insight into a population's genetic events makes them a useful tool that can provide information about the demographic evolution of a population over time. Furthermore, ROH provide useful information about the genetic relatedness among individuals, helping to minimize the inbreeding rate and also helping to expose deleterious variants in the genome. The frequency, size and distribution of ROH in the genome are influenced by factors such as natural and artificial selection, recombination, linkage disequilibrium, population structure, mutation rate and inbreeding level. Calculating the inbreeding coefficient from molecular information from ROH (F_ROH) is more accurate for estimating autozygosity and for detecting both past and more recent inbreeding effects than are estimates from pedigree data (F_PED). The better results of F_ROH suggest that F_ROH can be used to infer information about the history and inbreeding levels of a population in the absence of genealogical information. The selection of superior animals has produced large phenotypic changes and has reshaped the ROH patterns in various regions of the genome. Additionally, selection increases homozygosity around the target locus, and deleterious variants are seen to occur more frequently in ROH regions. Studies involving ROH are increasingly common and provide valuable information about how the genome's architecture can disclose a population's genetic background. By revealing the molecular changes in populations over time, genome‐wide information is crucial to understanding antecedent genome architecture and, therefore, to maintaining diversity and fitness in endangered livestock breeds.     

Pedigree reconstruction in wild cichlid fish populations

It is common practice to use microsatellites to detect parents and their offspring in wild and captive populations, in order to reconstruct a pedigree. However, correct inference is often constrained by a number of factors, including the absence of demographic data and ignorance regarding the completeness of parental sampling. Here we present a new Bayesian estimator that simultaneously estimates the pedigree and the size of the unsampled population. The method is robust to genotyping error, and can estimate pedigrees in the absence of demographic data. Using a large-scale microsatellite assay in four wild cichlid fish populations of Lake Tanganyika (1000 individuals in total), we assess the performance of the Bayesian estimator against the most popular assignment program, Cervus. We found small but significant pedigrees in each of the tested populations using the Bayesian procedure, but Cervus had very high type I error rates when the size of the unsampled population was assumed to be lower than what it was. The need of pedigree relationships to infer adaptive processes in natural populations places strong constraints on sampling design and identification of multigenerational pedigrees in natural populations.     

Male vocalizations convey information on kinship and inbreeding in a lekking bird

Kinship and inbreeding are two major components involved in sexual selection and mating system evolution. However, the mechanisms underlying recognition and discrimination of genetically related or inbred individuals remain unclear. We investigated whether kinship and inbreeding information is related to low‐frequency vocalizations, “booms,” produced by males during their courtship in the lekking houbara bustard (Chlamydotis undulata undulata). Based on a captive breeding program where the pedigree of all males is known, we investigated the similarity of booms’ acoustic parameters among captive males more or less individually inbred and therefore genetically related with each other. In the wild, we investigated the relationship between the spatial distribution of males within leks and the similarity of acoustic parameters of their booms. In the captive population, we found (a) a relationship between the individual inbreeding level of captive males and their vocalization parameters; (b) that kin share similar frequency and temporal characteristics of their vocalizations. In the wild, we found no evidence for spatial structuring of males based on their acoustic parameters, in agreement with previous genetic findings on the absence of kin association within houbara bustard leks. Overall, our results indicate that genetic information potentially related to both the identity and quality of males is contained in their vocalizations.     

Genetic variability,management, and conservation implications of the critically endangered Brazilian pitviper Bothrops insularis

Information on demographic, genetic, and environmental parameters of wild and captive animal populations has proven to be crucial to conservation programs and strategies. Genetic approaches in conservation programs of Brazilian snakes remain scarce despite their importance for critically endangered species, such as Bothrops insularis, the golden lancehead, which is endemic to Ilha da Queimada Grande, coast of São Paulo State, Brazil. This study aims to (a) characterize the genetic diversity of ex situ and in situ populations of B. insularis using heterologous microsatellites; (b) investigate genetic structure among and within these populations; and (c) provide data for the conservation program of the species. Twelve informative microsatellites obtained from three species of the B. neuwiedi group were used to access genetic diversity indexes of ex situ and in situ populations. Low‐to‐medium genetic diversity parameters were found. Both populations showed low—albeit significant—values of system of mating inbreeding coefficient, whereas only the in situ population showed a significant value of pedigree inbreeding coefficient. Significant values of genetic differentiation indexes suggest a small differentiation between the two populations. Discriminant analysis of principal components (DAPC) recovered five clusters. No geographic relationship was found in the island, suggesting the occurrence of gene flow. Also, our data allowed the establishment of six preferential breeding couples, aiming to minimize inbreeding and elucidate uncertain parental relationships in the captive population. In a conservation perspective, continuous monitoring of both populations is demanded: it involves the incorporation of new individuals from the island into the captive population to avoid inbreeding and to achieve the recommended allelic similarity between the two populations. At last, we recommend that the genetic data support researches as a base to maintain a viable and healthy captive population, highly genetically similar to the in situ one, which is crucial for considering a reintroduction process into the island.     

Severe inbreeding depression in a wild wolf (Canis lupus) population

The difficulty of obtaining pedigrees for wild populations has hampered the possibility of demonstrating inbreeding depression in nature. In a small, naturally restored, wild population of grey wolves in Scandinavia, founded in 1983, we constructed a pedigree for 24 of the 28 breeding pairs established in the period 1983-2002. Ancestry for the breeding animals was determined through a combination of field data (snow tracking and radio telemetry) and DNA microsatellite analysis. The population was founded by only three individuals. The inbreeding coefficient F varied between 0.00 and 0.41 for wolves born during the study period. The number of surviving pups per litter during their first winter after birth was strongly correlated with inbreeding coefficients of pups (R2=0.39, p<0.001). This inbreeding depression was recalculated to match standard estimates of lethal equivalents (2B), corresponding to 6.04 (2.58-9.48, 95% CI) litter-size-reducing equivalents in this wolf population.     

A Monte Carlo algorithm for computing the IBD matrices using incomplete marker information

Identity-By-Descent (IBD) is a general measurement of the relationship between two groups of genes. If the two groups consist of two homologous genes, one from each individual, the IBD is called the coancestry between the two individuals. Coancestry is an important concept in both population and quantitative genetics. It is the probability that both genes are copies of the same gene in the genealogy. The average coancestry value at a random locus in a population reflects the level of population diversity, effective population size, the level of inbreeding and other attributes. Coancestry is also the building block for the covariance structure used to estimate the additive genetic variance component for a quantitative trait. There are many other types of IBD matrices, depending on the natures of the genes included in each group, and these IBD matrices vary from locus to locus. Molecular markers distributed along the genome provide information that can be used to infer these locus-specific IBD matrices. As a result, we can estimate and test the variance components of a quantitative trait contributed by these loci using the inferred IBD matrices. In this study, we develop the concept of locus-specific epistatic IBD matrices and a Monte Carlo method to infer these IBD matrices. The method is suitable for large pedigrees with arbitrary complexity and various levels of missing marker information. With these locus-specific IBD matrices, we are ready to search for quantitative trait loci along the genome in complicated pedigrees.