Estimating levels of inbreeding using AFLP markers.

In the absence of detailed pedigree records, researchers have attempted to estimate individuals' levels of inbreeding using molecular markers, generally making use of heterozygosity measures based on microsatellite markers. Here we report and validate a method for estimating an individual's inbreeding coefficient, f, using amplified fragment length polymorphism (AFLP) markers. We use simulations to confirm that our measure scales appropriately with f when allele frequencies can be estimated from a subset of outbred individuals. We also present an approach for obtaining satisfactory estimates even in the absence of an independent set of known outbred individuals from which to estimate allele frequencies. We then test our method against empirical data from 179 wild and captive-bred old-field mice, Peromyscus polionotus subgriseus, comprising pedigree-based estimates of f, along with genetic data from 94 AFLP markers and 12 microsatellites. Inbreeding estimates based on both AFLP and microsatellite markers were found to correlate strongly with pedigree-based inbreeding coefficients. Owing to their ease of amplification in any species, AFLP markers may prove to be a valuable new tool for estimating f in natural populations and for examining correlations between heterozygosity and fitness.

Effects of inbreeding on skeletal development of Rattus villosissimus.

In a species of Australian native rat, Rattus villosissimus, which experiences extreme population fluctuations and possibly episodes of local inbreeding in the wild, generations of inbreeding in a laboratory colony led to altered skull shape and increased fluctuating asymmetry in some skeletal characters. Although inbreeding was closely associated with the number of generations in captivity, the effect of inbreeding after controlling statistically for the generation number was to decrease skull length and width. The effect of generations in captivity after controlling for inbreeding was to increase skull length and width. The joint effect of these confounded determinants was to produce rats with increasingly broad and short skulls through generations of inbreeding. Developmental anomalies of the incisors and feet appeared in the population. The average effects of inbreeding on fluctuating asymmetry were not strong, as most inbred and noninbred rats were not detectably asymmetric. Asymmetry appeared to be a threshold phenomenon, as significantly asymmetric animals were more prevalent among the more highly inbred rats of later generations. We detected no trend for a lessening impact of inbreeding after many generations, as would have been expected if selection had been purging the population of its genetic load. Individual heterozygosity across five polymorphic allozyme loci was correlated with size and asymmetry metrics, but only in so far as could be accounted for by the correlation of sample heterozygosity with the level of inbreeding and the effect of inbreeding on size and asymmetry.

Behavior predicts genes structure in a wild primate group.

The predictability of genetic structure from social structure and differential mating success was tested in wild baboons. Baboon populations are subdivided into cohesive social groups that include multiple adults of both sexes. As in many mammals, males are the dispersing sex. Social structure and behavior successfully predicted molecular genetic measures of relatedness and variance in reproductive success. In the first quantitative test of the priority-of-access model among wild primates, the reproductive priority of dominant males was confirmed by molecular genetic analysis. However, the resultant high short-term variance in reproductive success did not translate into equally high long-term variance because male dominance status was unstable. An important consequence of high but unstable short-term variance is that age cohorts will tend to be paternal sibships and social groups will be genetically substructured by age.

Genome resource banking for species conservation: selection of sperm donors.

The systematic banking of genome resources using cryopreserved germ plasm offers the opportunity to further conservation strategies of endangered species by assisting in the effective genetic management of captive populations. Cryopreserved germ plasm will allow indefinite preservation of the presently available gene diversity represented in either captive or wild populations. If properly utilized, genome resource banks have the potential to decelerate the loss of gene and allelic diversity in captive populations through reintroducing "original" genetic material through time to counter genetic drift. However, in order for any genome resource bank to be effective, strategies need to be developed to identify genetically valuable individuals to bank which will represent optimal gene diversity of the specific population. Four selection strategies were evaluated to identify individual donors from four North American captive populations representing differently structured pedigrees. The strategies consisted of selecting: (1) all males in the population ("All Male Bank"); (2) only living founders and early generation descendents ("Founder Method Bank," FMB); (3) males remaining after culling to minimize mean kinship ("Culled Male Bank 1"); and (4) males remaining after culling to minimize mean kinship, with the males reduced to the number in the FMB ("Culled Male Bank 2"). The effectiveness of each strategy was based on the comparison of genetic variation metrics in each bank with the genetic variation in the present living managed population. Although maximal retention of allelic diversity was achieved by banking genes from all living animals, nearly optimal retention of allelic and gene diversity was obtained by utilizing the selection strategy based on minimizing mean kinships. As a consequence, properly designed and utilized, genome resource banks can become effective tools for preserving gene diversity in future generations of living populations.

An experimental study of inbreeding depression in a natural habitat.

Inbreeding is known to lead to decreased survival and reproduction in captive populations of animals. It is also important to know whether inbreeding has deleterious effects in natural habitats. An estimate was made of the effects of inbreeding in white-footed mice, Peromyscus leucopus noveboracensis, derived from a wild population. This study demonstrates that inbreeding had a significant detrimental effect on the survivorship of mice reintroduced into a natural habitat. This effect was more severe than the effect observed in laboratory studies of the population.

Inbreeding depression in insular and central populations of Peromyscus mice.

We tested the hypothesis that small, isolated populations would show less depression in fitness when inbred than would large, central populations. Laboratory stocks of Peromyscus leucopus and P. polionotus were established from insular, peninsular, and central populations. The isolated populations had one-third to one-half the genic diversity of central populations. Responses to inbreeding were highly varied: some populations had smaller litters, others experienced higher mortality, some showed slower growth rates, and one displayed no measurable effects when inbred. These results suggest that inbreeding depression is controlled by a small number of genes and that the size of the genetic load depends on which alleles are present in the founders of a population. The severity of fitness depression in inbred litters did not correlate with initial genic diversity of the stocks nor, therefore, with the size of the wild populations. Fitness measures appeared linearly related to the inbreeding coefficient of the liters, with no diminution of deleterious effects through subsequent generations of inbreeding. Thus overdominance of fitness traits probably contributed as much to the genetic load as did deleterious recessive alleles. The inbreeding level of the dam negatively affected the size, growth, and survival of litters only in genetically diverse populations, indicating that the load of recessive alleles negatively impacting maternal care may have been reduced by selection in the more peripheral populations during past bottlenecks.

Basal metabolic rates in mammals: taxonomic differences in the allometry of BMR and body mass.

No single equation adequately describes the allometric relation between body mass and BMR for mammals. Least squares regression of log-transformed data for 248 eutherian species results in a line with a slope (-0.30) significantly different from that of Kleiber's line (-0.25). Interordinal comparisons of least squares regressions of log-transformed BMR and mass suggest that the Insectivora have a significantly steeper slope to their allometric relationship than do most other orders, while the non-insectivore orders are statistically homogeneous with respect to slope. With respect to elevation, Edentata have the lowest BMRs; Marsupialia, Primates and Chiroptera are indistinguishable from each other but above the edentates; Primates, Chiroptera, Rodentia, Lagomorpha and Carnivora form the next highest homogeneous grouping; and Artiodactyla have the highest BMRs, significantly greater than all but Lagomorpha and Carnivora. Analysis of intraordinal variation within the Rodentia suggests significant heterogeneity among families in BMR-mass allometry.

Structure of Genetic Variation within and between Populations of Mycophagous Drosophila.

Patterns of genetic variation within and between populations of five species of mycophagous Drosophila were examined by gel electrophoresis of several polymorphic loci. Populations of the five species could not be shown to be subdivided into sympatric host-adapted races. Statistically significant, but small, between-host differences in gene frequencies were observed at three of 15 loci. Mean gene frequencies at all loci were similar in New York and Tennessee, and, with one exception, relatively little genetic differentiation was observed among study sites within those two regions. Gene frequencies generally were stable over several years of collecting as well. The unpredictable nature of the fungal hosts may preclude the site fidelity and continuity of diversifying selection necessary for adaptive divergence of populations.

Quantitative Genetic Analysis of Temperature Regulation in MUS MUSCULUS. I. Partitioning of Variance.

Heritabilities (from parent-offspring regression) and intraclass correlations of full sibs for a variety of traits were estimated from 225 litters of a heterogeneous stock (HS/Ibg) of laboratory mice. Initial variance partitioning suggested different adaptive functions for physiological, morphological and behavioral adjustments with respect to their thermoregulatory significance. Metabolic heat-production mechanisms appear to have reached their genetic limits, with little additive genetic variance remaining. This study provided no genetic evidence that body size has a close directional association with fitness in cold environments, since heritability estimates for weight gain and adult weight were similar and high, whether or not the animals were exposed to cold. Behavioral heat conservation mechanisms also displayed considerable amounts of genetic variability. However, due to strong evidence from numerous other studies that behavior serves an important adaptive role for temperature regulation in small mammals, we suggest that fluctuating selection pressures may have acted to maintain heritable variation in these traits.