Birth weight and neonatal survival of harbour seal pups are positively correlated with genetic variation measured by microsatellites.

We examined the relations between fitness-related traits of wild harbour seal (Phoca vitulina) pups with microsatellite heterozygosity, and with a measure of genomic diversity based on the mean squared distance between microsatellite alleles within an individual, mean d2. Birth weight was positively influenced by maternal age, pup sex, and either mean d2 or individual heterozygosity in separate multiple regression models. The association of birth weight with mean d2 was stronger than that with heterozygosity, however. The factors maternal age, pup sex, and mean d2 combined to account for 36.8% of the variation in birth weight, with mean d2 accounting for the greatest explanatory power (52.3% of the variance explained). Pups which survived until weaning had significantly higher mean d2 than pups which died, independent of birth weight. These effects are consistent with heterosis resulting from recent population mixing, and/or inbreeding depression in this population. Mean d2 thus provides (i) a better measure of individual genetic variability than heterozygosity for microsatellite data; and (ii) a convenient tool for assessing the effects of inbreeding and outbreeding in natural populations.     

HETEROZYGOSITY-FITNESS CORRELATIONS REVEALED BY NEUTRAL AND CANDIDATE GENE MARKERS IN ROE DEER FROM A LONG-TERM STUDY

Heterozygosity-fitness correlations (HFCs) are increasingly reported but the underlying mechanisms causing HFCs are generally poorly understood. Here, we test for HFCs in roe deer ( Capreolus capreolus ) using 22 neutral microsatellites widely distributed in the genome and four microsatellites in genes that are potentially under selection. Juvenile survival was used as a proxy for individual fitness in a population that has been intensively studied for 30 years in northeastern France. For 222 juveniles, we computed two measures of genetic diversity: individual heterozygosity ( H ), and mean d ² (relatedness of parental genomes). We found a relationship between genetic diversity and fitness both for the 22 neutral markers and two candidate genes: IGF1 (Insulin-like Growth Factor I) and NRAMP (natural resistance-associated macrophage protein). Statistical evidence and the size of genetic effects on juvenile survival were comparable to those reported for early development and cohort variation, suggesting a substantial influence of genetic components on fitness in this roe deer population. For the 22 neutral microsatellites, a correlation with fitness was revealed for mean d ², but not for H , suggesting a possible outbreeding advantage. This heterosis effect could have been favored by introduction of genetically distant (Hungarian) roe deer to the population in recent times and, possibly, by the structuring of the population into distinct clans. The locus-specific correlations with fitness may be driven by growth rate advantages and resistance to diseases known to exist in the studied population. Our analyses of neutral and candidate gene markers both suggest that the observed HFCs are likely mainly due to linkage with dominant or overdominant loci that affect fitness ("local" effect) rather than to a genome-wide relationship with homozygosity due to inbreeding ("general" effect).     

MICROSATELLITE LOCI REVEAL SEX-DEPENDENT RESPONSES TO INBREEDING AND OUTBREEDING IN RED DEER CALVES

Mean d² is a recently devised microsatellite-based measure that is hypothesised to allow the detection of inbreeding depression and heterosis in free-living populations. Two studies that have investigated the measure have both demonstrated an association between mean d² and traits related to fitness. Here we present an association between mean d¹ and an important component of fitness, first-year overwinter survival, in a population of red deer on the Isle of Rum, Scotland. The association between survival and mean d² differed between males and females. As predicted, outbred female calves (high mean d²) survived better than those that were inbred (low mean d²). However, the association was in the opposite direction in male calves. We suggest that this difference is due to different early growth strategies between the sexes. The association between mean d² and survival was not significantly influenced by any single locus. Decomposition of mean d² into a recent inbreeding component and an outbreeding component showed that it was the degree of outbreeding that influenced survival in males and both the degree of outbreeding and recent inbreeding that influenced survival in females. Our analyses suggest that mean d² is an easy-to-calculate measure of inbreeding and degree of outbreeding that can reveal interesting interactions between genetics and ecology.     

Heterozygosity, inbreeding and neonatal traits in Soay sheep on St Kilda

We investigated whether birth weight and neonatal survival, a period within which 24% of all mortalities occur, were correlated with levels of inbreeding in St Kilda Soay sheep, using pedigree inbreeding coefficients and four marker-based estimators of inbreeding. None of the inbreeding estimators, either of the offspring, or of their mothers, explained significant variation in a lamb's birth weight or probability of surviving the neonatal period, suggesting low inbreeding depression for these traits. We evaluated the correlation between the marker-based measures of inbreeding and inbreeding coefficients obtained from the Soay pedigree, where paternal links were inferred using the same panel of microsatellite markers. Even when using a relatively complete portion of the pedigree, in which all individuals had known maternal and paternal grandparents, the correlation was found to be weak (r = -0.207, where mean f = 0.0168). These results add support to the recent prediction that when the mean and variance in inbreeding are low in a population, heterozygosity-fitness correlations can be very weak or even undetectable. The pursuit of more detailed pedigrees offers the best prospect for identifying inbreeding depression within this study population.     

Effects of experimental inbreeding on herbivore resistance and plant fitness: the role of history of inbreeding, herbivory and abiotic factors

Inbreeding is common in plant populations and can affect plant fitness and resistance against herbivores. These effects are likely to depend on population history. In a greenhouse experiment with plants from 17 populations of Lychnis flos-cuculi, we studied the effects of experimental inbreeding on resistance and plant fitness. Depending on the levels of past herbivory and abiotic factors at the site of plant origin, we found either inbreeding or outbreeding depression in herbivore resistance. Furthermore, when not damaged experimentally by snail herbivores, plants from populations with higher heterozygosity suffered from inbreeding depression and those from populations with lower heterozygosity suffered from outbreeding depression. These effects of inbreeding and outbreeding were not apparent under experimental snail herbivory. We conclude that inbreeding effects on resistance and plant fitness depend on population history. Moreover, herbivory can mask inbreeding effects on plant fitness. Thus, understanding inbreeding effects on plant fitness requires studying multiple populations and considering population history and biotic interactions.     

Outbreeding increases offspring survival in wild greater horseshoe bats (Rhinolophus ferrumequinum)

The factors influencing the survival of greater horseshoe bat (Rhinolophus ferrumequinum) offspring born over seven years at a maternity colony in south-west Britain were studied. The effects of a range of phenotypic and maternal variables were analysed using a historical data set. In addition, the influence of two genetic measures on mortality, individual heterozygosity and a new measure of outbreeding, termed mean d(2), was assessed. Logistic regressions were undertaken with survival modelled as a binary response variable. Survival to two life stages was studied for each variable and all models were developed for both sexes separately and together. Only one variable, mean d(2), was significantly associated with survival. Male offspring with high mean d(2) scores were more likely to survive to their first and second summers. The influence of mean d(2) was not due to a single locus under selection but a wider multilocus effect and probably represents heterosis as opposed to solely inbreeding depression. Therefore, the extent to which an individual is outbred may determine survival more than widely used phenotypic characteristics such as size and mass. Mean d(2) may reflect immunocompetence, which influences mortality. Protection of mating sites in order to facilitate gene flow and, therefore, outbreeding may help to promote population stability and growth.     

Inbreeding, outbreeding and environmental effects on genetic diversity in 46 walleye (Sander vitreus) populations

Genetic diversity is recognized as an important population attribute for both conservation and evolutionary purposes; however, the functional relationships between the environment, genetic diversity, and fitness-related traits are poorly understood. We examined relationships between selected lake parameters and population genetic diversity measures in 46 walleye (Sander vitreus) populations across the province of Ontario, Canada, and then tested for relationships between six life history traits (in three categories: growth, reproductive investment, and mortality) that are closely related to fitness, and genetic diversity measures (heterozygosity, d2, and Wright's inbreeding coefficient). Positive relationships were observed between lake surface area, growing degree days, number of species, and hatchery supplementation versus genetic diversity. Walleye early growth rate was the only life history trait significantly correlated with population heterozygosity in both males and females. The relationship between FIS and male early growth rate was negative and significant (P < 0.01) and marginally nonsignificant for females (P = 0.06), consistent with inbreeding depression effects. Only one significant relationship was observed for d2: female early growth rate (P < 0.05). Stepwise regression models showed that surface area and heterozygosity had a significant effect on female early growth rate, while hatchery supplementation, surface area and heterozygosity had a significant effect on male early growth rate. The strong relationship between lake parameters, such as surface area, and hatchery supplementation, versus genetic diversity suggests inbreeding and outbreeding in some of the populations; however, the weak relationships between genetic diversity and life history traits indicate that inbreeding and outbreeding depression are not yet seriously impacting Ontario walleye populations.     

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.     

Measuring inbreeding depression in the wild: the old ways are the best

Measuring inbreeding depression in normally outbreeding natural populations is an uphill task, because it requires inbreeding coefficients that are calculated from pedigrees. Instead of calculating inbreeding coefficients directly, several studies have reported the use of microsatellite-derived metrics, such as heterozygosity, to infer relative inbreeding among individuals. In two new papers, Slate et al. and Balloux et al. show that these molecular metrics are often only weakly correlated with inbreeding coefficients, and that correlations between heterozygosity and fitness require a new interpretation.     

Comparing molecular measures for detecting inbreeding depression

Correlations between heterozygosity and components of fitness have been investigated in natural populations for over 20 years. Positive correlations between a trait of interest and heterozygosity (usually measured at allozyme loci) are generally recognized as evidence of inbreeding depression. More recently, molecular markers such as microsatellites have been employed for the same purpose. A typical study might use around five to ten markers. In this paper we use a panel of 71 microsatellite loci to: (1) Compare the efficacy of heterozygosity and a related microsatellite‐specific variable, mean d², in detecting inbreeding depression; (2) Examine the statistical power of heterozygosity to detect such associations. We performed our analyses in a wild population of red deer (Cervus elaphus) in which inbreeding depression in juvenile traits had previously been detected using a panel of nine markers. We conclude that heterozygosity‐based measures outperform mean d²‐based measures, but that power to detect heterozygosity‐fitness associations is nonetheless low when ten or fewer markers are typed.     

Effects of inbreeding on fitness‐related traits in a small isolated moose population

Inbreeding can affect fitness‐related traits at different life history stages and may interact with environmental variation to induce even larger effects. We used genetic parentage assignment based on 22 microsatellite loci to determine a 25 year long pedigree for a newly established island population of moose with 20–40 reproducing individuals annually. We used the pedigree to calculate individual inbreeding coefficients and examined for effects of individual inbreeding (f) and heterozygosity on fitness‐related traits. We found negative effects of f on birth date, calf body mass and twinning rate. The relationship between f and calf body mass and twinning rate were found to be separate but weaker after accounting for birth date. We found no support for an inbreeding effect on the age‐specific lifetime reproductive success of females. The influence of f on birth date was related to climatic conditions during the spring prior to birth, indicating that calves with a low f were born earlier after a cold spring than calves with high f. In years with a warm spring, calf f did not affect birth date. The results suggest that severe inbreeding in moose has both indirect effects on fitness through delayed birth and lower juvenile body mass, as well as separate direct effects, as there still was a significant relationship between f and twinning rate after accounting for birth date and body mass as calf. Consequently, severe inbreeding as found in the study population may have consequences for population growth and extinction risk.     

Inbreeding depression influences lifetime breeding success in a wild population of red deer (Cervus elaphus)

Evolutionary and conservation biologists have a long-standing interest in the consequences of inbreeding. It is generally recognized that inbred individuals may experience reduced fitness or inbreeding depression. By the same token, relatively outbred individuals can have greater than average fitness, i.e. heterosis. However, nearly all of the empirical evidence for inbreeding depression comes from laboratory or domestic species. Inbreeding depression and heterosis are difficult to detect in natural populations due to the difficulties in establishing pedigrees. An alternative method is to correlate heterozygosity, which is measured using genetic markers, with a trait related to fitness. The typically studied traits, such as juvenile survival and growth rates, either cover only early life or are weakly correlated with lifetime breeding success (LBS). In this paper we show that heterozygosity is positively associated with male and female adult LBS in a wild population of red deer (Cervus elaphus) on the Isle of Rum, Scotland. To the authors' knowledge, this is the first time that inbreeding depression and/or heterosis have been detected for a trait highly correlated with overall fitness in both sexes in a wild population.     

Adult survival and microsatellite diversity in possums: effects of major histocompatibility complex-linked microsatellite diversity but not multilocus inbreeding estimators

Adult survival is perhaps the fitness parameter most important to population growth in long-lived species. Intrinsic and extrinsic covariates of survival are therefore likely to be important drivers of population dynamics. We used long-term mark-recapture data to identify genetic, individual and environmental covariates of local survival in a natural population of mountain brushtail possums (Trichosurus cunninghami). Rainfall and intra-individual diversity at microsatellite DNA markers were associated with increased local survival of adults and juveniles. We contrasted the performance of several microsatellite heterozygosity measures, including internal relatedness (IR), homozygosity by loci (HL) and the mean multilocus estimate of the squared difference in microsatellite allele sizes within an individual (mean d ²). However, the strongest effect on survival was not associated with multilocus microsatellite diversity (which would indicate a genome-wide inbreeding effect), but a subset of two loci. This included a major histocompatibility complex (MHC)-linked marker and a putatively neutral microsatellite locus. For both loci, diversity measures incorporating allele size information had stronger associations with survival than measures based on heterozygosity, whether or not allele frequency information was included (such as IR). Increased survival was apparent among heterozygotes at the MHC-linked locus, but the benefits of heterozygosity to survival were reduced in heterozygotes with larger differences in allele size. The effect of heterozygosity on fitness-related traits was supported by data on endoparasites in a subset of the individuals studied in this population. There was no apparent density dependence in survival, nor an effect of sex, age or immigrant status. Our findings suggest that in the apparent absence of inbreeding, variation at specific loci can generate strong associations between fitness and diversity at linked markers.     

Outbreeding depression and breeding system evolution in small,remnant populations of <Emphasis Type="Italic">Primula vulgaris</Emphasis>: consequences for genetic rescue

Many species suffer from anthropogenic habitat fragmentation. The resulting small and isolated populations are more prone to extinction due to, amongst others, genetic erosion, inbreeding depression and Allee-effects. Genetic rescue can help mitigate such problems, but might result in outbreeding depression. We evaluated offspring fitness after selfing and outcrossing within and among three very small and isolated remnant populations of the heterostylous plant Primula vulgaris. We used greenhouse-grown offspring from these populations to test several fitness components. One population was fixed for the pin-morph, and was outcrossed with another population in the field to obtain seeds. Genetic diversity of parent and offspring populations was studied using microsatellites. Morph and population-specific heterosis, inbreeding and outbreeding depression were observed for fruit and seed set, seed weight and cumulative fitness. Highest fitness was observed in the field-outcrossed F1-population, which also showed outbreeding depression following subsequent between-population (back)crossing. Despite outbreeding depression, fitness was still relatively high. Inbreeding coefficients indicated that the offspring were more inbred than their parent populations. Offspring heterozygosity and inbreeding coefficients correlated with observed fitness. One population is evolving homostyly, showing a thrum morph with an elongated style and high autonomous fruit and seed set. This has important implications for conservation strategies such as genetic rescue, as the mating system will be altered by the introduction of homostyles.     

Inbreeding coefficient and heterozygosity–fitness correlations in unhatched and hatched song sparrow nestmates

Heterozygosity–fitness correlations use molecular measures of heterozygosity as proxy estimates of individual inbreeding coefficients (f) to examine relationships between inbreeding and fitness traits. Heterozygosity–fitness correlations partly depend on the assumption that individual heterozygosity and f are strongly and negatively correlated. Although theory predicts that this relationship will be strongest when mean f and variance in f are high, few studies of heterozygosity–fitness correlations include estimates of f based on pedigrees, which allow for more thorough examinations of the relationship between f, heterozygosity and fitness in nature. We examined relationships between pedigree‐based estimates of f, multilocus heterozygosity (MLH) and the probability of survival to hatch in song sparrow nestmates. f and MLH were weakly, but significantly negatively correlated. Inbreeding coefficient predicted the probability of survival to hatch. In contrast, MLH did not predict the probability of survival to hatch nor did it account for residual variation in survival to hatch after statistically controlling for the effects of f. These results are consistent with the expectation that heterozygosity–f correlations will be weak when mean and variance in f are low. Our results also provide empirical support for recent simulation studies, which show that variation in MLH among siblings with equal f can be large and may obscure MLH–fitness relationships.     

Genomic analysis reveals depression due to both individual and maternal inbreeding in a free‐living mammal population

There is ample evidence for inbreeding depression manifested as a reduction in fitness or fitness‐related traits in the focal individual. In many organisms, fitness is not only affected by genes carried by the individual, but also by genes carried by their parents, for example if receiving parental care. While maternal effects have been described in many systems, the extent to which inbreeding affects fitness directly through the focal individual, or indirectly through the inbreeding coefficients of its parents, has rarely been examined jointly. The Soay sheep study population is an excellent system in which to test for both effects, as lambs receive extended maternal care. Here, we tested for both maternal and individual inbreeding depression in three fitness‐related traits (birthweight and weight and hindleg length at 4 months of age) and three fitness components (first‐year survival, adult annual survival and annual breeding success), using either pedigree‐derived inbreeding or genomic estimators calculated using ~37 000 SNP markers. We found evidence for inbreeding depression in 4‐month hindleg and weight, first‐year survival in males, and annual survival and breeding success in adults. Maternal inbreeding was found to depress both birthweight and 4‐month weight. We detected more instances of significant inbreeding depression using genomic estimators than the pedigree, which is partly explained through the increased sample sizes available. In conclusion, our results highlight that cross‐generational inbreeding effects warrant further exploration in species with parental care and that modern genomic tools can be used successfully instead of, or alongside, pedigrees in natural populations.     

Evaluation of d2, a microsatellite measure of inbreeding and outbreeding, in wolves with a known pedigree

We have evaluated a microsatellite measure proposed as an indicator of inbreeding and outbreeding using a captive wolf population with known inbreeding levels and founder sources. The measure, which is based on the difference in the repeat number for microsatellite alleles within an individual, was not more predictive of the known inbreeding coefficient than microsatellite heterozygosity (it was actually less predictive). We also found no support that the measure was predictive of the level of outbreeding. However, we could not determine if the measure was predictive of very low levels of inbreeding due to matings between remote relatives. Overall, it appears that the usefulness of this measure to identify individuals on the inbred-outbred continuum beyond that of heterozygosity and identify biologically important associations with fitness-related traits may be limited. We suggest that the measure be examined theoretically to determine when (and how much) the predictive value of the measure is different from that of heterozygosity for inbreeding or outbreeding levels in a variety of different scenarios.     

Mean d(2) and divergence time: transformations and standardizations

The fitness consequences of inbreeding and outbreeding have intrigued biologists for a long time. Recently a measure of relatedness of parental haplotypes has been proposed called mean d(2). This measure is based on a stepwise mutational process and therefore is tailored to microsatellite genetic markers. Theoretical work suggests that mean d(2) typically is less suited for measuring fitness consequences due to close inbreeding rather than heterozygosity. However, mean d(2) may be more appropriate than heterozygosity for measuring divergence times over longer time scales and thus for detecting outbreeding depression. Here, simulations are used to (1). identify appropriate standardization coefficients and transformations for mean d(2), and (2). evaluate mean d(2) as a measure of divergence time of parental lineages over time scales up to 10000 generations. Results show that mean d(2) is a linear predictor of divergence time. The coefficient of variation of mean d(2) approaches a constant value with increasing divergence time and therefore logarithm transformation is appropriate to restore homoscedasticity. When mutation rates and sizes are known for each locus they can be incorporated into a standardization coefficient to increase the precision of mean d(2). As few as 10 loci can explain more than 70% of the variation in divergence time between lineages. While heterozygosity outperforms mean d(2) at detecting differences in divergence time over relative short time periods (or=1000 generations). However, gene flow of as little as 1% per generation can significantly reduce the ability of either mean d(2) or heterozygosity to estimate divergence time.     

How inbreeding and outbreeding influence the risk of extinction--a genetically explicit model

We have developed a stochastic model to explore the common effect which genetics and demography have on the extinction risk of endangered populations. The dynamics is formulated as a MARKOVian birth and death process (in continuous time), whereby selection acts through different mortalities of each genotype. With the help of this model we are able to show how inbreeding and outbreeding can influence the genetic variability and the survival of a population. Whether inbreeding or outbreeding takes place depends on the specific mating system. In our model we consider positive assortative as well as disassortative mating. In the case of additive fitness we show that inbreeding reduces the extinction risk and the genetic variability.     

Outbreeding effects in an inbreeding insect,Cimex lectularius

In some species, populations with few founding individuals can be resilient to extreme inbreeding. Inbreeding seems to be the norm in the common bed bug, Cimex lectularius, a flightless insect that, nevertheless, can reach large deme sizes and persist successfully. However, bed bugs can also be dispersed passively by humans, exposing inbred populations to gene flow from genetically distant populations. The introduction of genetic variation through this outbreeding could lead to increased fitness (heterosis) or be costly by causing a loss of local adaptation or exposing genetic incompatibility between populations (outbreeding depression). Here, we addressed how inbreeding within demes and outbreeding between distant populations impact fitness over two generations in this re‐emerging public health pest. We compared fitness traits of families that were inbred (mimicking reproduction following a founder event) or outbred (mimicking reproduction following a gene flow event). We found that outbreeding led to increased starvation resistance compared to inbred families, but this benefit was lost after two generations of outbreeding. No other fitness benefits of outbreeding were observed in either generation, including no differences in fecundity between the two treatments. Resilience to inbreeding is likely to result from the history of small founder events in the bed bug. Outbreeding benefits may only be detectable under stress and when heterozygosity is maximized without disruption of coadaptation. We discuss the consequences of these results both in terms of inbreeding and outbreeding in populations with genetic and spatial structuring, as well as for the recent resurgence of bed bug populations.