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PubMed1991

Influence of gene flow and breeding tactics on gene diversity within populations.

Expressions describing the accumulation of gene correlations within and among lineages and individuals of a population are derived. The model permits different migration rates by males and females and accounts for various breeding tactics within lineages. The resultant equations enable calculation of the probabilistic quantities for the fixation indices, rates of loss of genetic variation, accumulation of inbreeding, and coefficients of relationship for the population at any generation. All fixation indices were found to attain asymptotic values rapidly despite the consistent loss of genetic variation and accumulation of inbreeding within the population. The time required to attain asymptotic values, however, was prolonged when gene flow among lineages was relatively low (less than 20%). The degree of genetic differentiation among breeding groups, inbreeding coefficients, and gene correlations within lineages were found to be primarily functions of breeding tactics within groups rather than gene flow among groups. Thus, the asymptotic value of S. Wright's island model is not appropriate for describing genetic differences among groups within populations. An alternative solution is provided that under limited conditions will reduce to the original island model. The evolution of polygynous breeding tactics appears to be more favorable for promoting intragroup gene correlations than modification of migration rates. Inbreeding and variance effective sizes are derived for populations that are structured by different migration and breeding tactics. Processes that reduce the inbreeding effective population size result in a concomitant increase in variance effective population size.

Animals↗

PubMed1999

The effect of mating system differences on nucleotide diversity at the phosphoglucose isomerase locus in the plant genus Leavenworthia.

To test the theoretical prediction that highly inbreeding populations should have low neutral genetic diversity relative to closely related outcrossing populations, we sequenced portions of the cytosolic phosphoglucose isomerase (PgiC) gene in the plant genus Leavenworthia, which includes both self-incompatible and inbreeding taxa. On the basis of sequences of intron 12 of this gene, the expected low diversity was seen in both populations of the selfers Leavenworthia uniflora and L. torulosa and in three highly inbreeding populations of L. crassa, while high diversity was found in self-incompatible L. stylosa, and moderate diversity in L. crassa populations with partial or complete self-incompatibility. In L. stylosa, the nucleotide diversity was strongly structured into three haplotypic classes, differing by several insertion/deletion sequences, with linkage disequilibrium between sequences of the three types in intron 12, but not in the adjacent regions. Differences between the three kinds of haplotypes are larger than between sequences of this gene region from different species. The haplotype divergence suggests the presence of a balanced polymorphism at this locus, possibly predating the split between L. stylosa and its two inbreeding sister taxa, L. uniflora and L. torulosa. It is therefore difficult to distinguish between different potential causes of the much lower sequence diversity at this locus in inbreeding than outcrossing populations. Selective sweeps during the evolution of these populations are possible, or background selection, or merely loss of a balanced polymorphism maintained by overdominance in the populations that evolved high selfing rates.

Base Sequence↗

PubMed2006

Maternal sex and mate relatedness affect offspring quality in the gynodioecious Silene acaulis.

In gynodioecious species, females sacrifice fitness by not producing pollen, and hence must have a fitness advantage over hermaphrodites. Because females are obligately outcrossed, they may derive a fitness advantage by avoiding selfing and inbreeding depression. However, both sexes are capable of biparental inbreeding, and there are currently few estimates of the independent effects of maternal sex and multiple levels of inbreeding on female advantage. To test these hypotheses, females and hermaphrodites from six Alaskan populations of Silene acaulis were crossed with pollen from self (hermaphrodites only), a sibling, a random plant within the same population, and a plant from a different population. Germination, survivorship and early growth revealed inbreeding depression for selfs and higher germination but reduced growth in sib-crosses, relative to outcrosses. Independent of mate relatedness, females germinated more seeds that grew faster than offspring from hermaphrodites. This indicates that inbreeding depression as well as maternal sex can influence breeding system evolution. The effect of maternal sex may be explained by higher performance of female genotypes and a greater abundance of female genotypes among the offspring of female mothers.

Animals↗

PubMed1996

Factors influencing genetic evaluations of linebred Hereford cattle in diverse environments.

Data from four closely related Line 1 Hereford herds were used to estimate variance components and predict EPD for birth weight (BWT), weaning weight (WWT), and postweaning gain (PWG). Herds were located in diverse environments and differed in level of phenotypic performance. Within-herd BWT analyses considered effects of inbreeding of calf and dam, sex, age of dam (AOD), and contemporary group as fixed and direct and maternal additive genetic effects and permanent environmental effects due to dam as random. The model for WWT included these effects and age of calf. The model for PWG included inbreeding of calf, contemporary group, and direct additive genetic effects. Across-herd analyses were conducted with additional models. The first considered herd-specific inbreeding, sex, and AOD effects. A second model pooled these effects across herds, and a third included pooled sex and AOD effects but ignored inbreeding. Across-herd EPD, including and ignoring inbreeding, were predicted for WWT preadjusted with standard adjustments for Hereford cattle. Within-herd analyses indicated potential for heterogenous genetic and environmental variances across herds. Across-herd variance component estimates were consistent, regardless of the model. Estimates of genetic trends indicated potential for bias in genetic evaluations resulting from choice of model. Differences in magnitude of fixed effects between herds were observed. Genetic evaluations were different when pooled or herd-specific fixed effects were used. Allowance for individual herd differences in fixed effects in across-herd evaluations is suggested.

Aging↗

PubMed1981

Weaning trait comparisons among inbred lines and selected noninbred and randomly bred control groups of Rambouillet, Targhee and Columbia sheep.

A program of inbreeding with concurrent selection was followed in the development of 26 Rambouiller, 20 Targhee and 10 Columbia inbred lines for subsequent linecross and topcross performance evaluation. Inbreeding coefficients averaged 30.4, 28.5 and 29.8% for the three breeds, respectively, at the end of the study. Selected noninbred control and unselected randomly bred control groups were maintained for each breed. Weaning trait data were evaluated for 1,332 Rambouillet, 1,557 Targhee and 1,049 Columbia inbred line and control group lambs during the final 2 years of inbreeding. Results showed a slight response to selection within inbred lines for the more highly heritable traits and some degree of genetic divergence among lines at the current levels of inbreeding. In general, the traits most sensitive to inbreeding depression were those more closely associated with fitness and those of low to moderate heritability. Even though a fairly large number of lines was developed, only a few inbred lines were superior (P less than .05) to their respective selected control groups - and usually for only one trait. Significantly, not a single Rambouillet, Targhee or Columbia inbred line was superior (P less than .05) in overall merit to its appropriate selected control group. Unselected control group means tended to be slightly superior to means for most inbred lines for traits of low heritability (weaning weight, body type and body condition) and inferior for more highly heritable traits (staple length, face cover, and neck folds). Notably, only six of a total of 56 inbred lines were superior (P less than .05) in overall merit to their appropriate unselected control groups.

Animals↗

PubMed2006

Isonymic analysis of population structure in Gredos, Spain.

For the period 1875-1975 an isonymic analysis was made based on 41,696 marriages celebrated in three valleys (Tormes, Alberche and Tietar) from Gredos (Spain). Total inbreeding (Ft) was lower in the Tietar valley (0.0103- 0.0136), followed by the Tormes (0.0125-0.0255) and the Alberche (0.0153-0.0200). In the latter, random inbreeding (Fr) surpassed non random (Fn). Correlation coefficients were obtained to confirm an association of inbreeding from isonymy with valley and village endogamy rates, locality census, altitude, and alpha inbreeding. Fn correlated positively with average valley endogamy and village endogamy and with altitude, but inversely with census size. Contrarily, Fr related significantly to village endogamy. The non-random component from isonymy related positively to inbreeding from dispensations. Except for village endogamy, both variables show the same relationships to variables, such as altitude, which reflect limitations to mobility; or valley endogamy indicating the disposability of potential mates which in turn depends on the census size.

Altitude↗

PubMed1991

Genetics of subdivided populations and its relationships with certain measures of association.

Unlike inbreeding, population subdivision affects different genotypes differently for multiple alleles, so that the simple relationship between inbreeding and subdivision for two alleles no longer holds for all genotypes. In this communication, the detailed effects of subdivision have been studied for three alleles with results easily generalized to any number of alleles. Then an average effect of subdivision is proposed. This average effect of subdivision is found to play the same role as the inbreeding coefficient for multiple alleles, so that the overall relationship between inbreeding and subdivision may be reestablished again. In the final section, we discuss the relationship of the genetic result with measures of association of square contingency tables arising from epidemiological, social studies, educational and psychological studies.

Alleles↗

PubMed1997

Genetic and environmental stress, and the persistence of populations.

Many populations of endangered species have to cope both with stressful and deteriorating environmental conditions (mostly the primary cause of the endangerment) and with an increase in homozygosity due to genetic drift and/or inbreeding in small isolated populations. The latter will result in genetic stress often accompanied by a decrease in fitness (inbreeding depression). We have studied the consequences of genetic stress, under optimal as well as stressful environmental conditions, for the fitness and persistence of small populations using Drosophila melanogaster as a model system. The results show that, already under optimal environmental conditions, an increase in homozygosity or inbreeding both impairs fitness and increases the extinction risk of populations significantly. Under environmental stress, however, these effects become greatly enhanced. More important, the results show that the impact of environmental stress becomes significantly greater for higher inbreeding levels. This explicitly demonstrates that genetic and environmental stress are not independent but can act synergistically. This apparent interaction may have important consequences for the conservation of endangered species.

Animals↗

PubMed2003

A test for a metastable epigenetic component of heterosis using haploid induction in maize.

We conducted a test to detect if there is a heritable epigenetic component to hybrid vigor and/or inbreeding depression. The impetus for this work was a classical study of the effect of homozygosis on the expression of the maize red color ( r1) locus. It had been shown that maintaining R1 mottling alleles in the homozygous state over several generations produces a progressive decrease of their paternally imprinted expression. This effect is reversed by R1/r1 allele heterozygosity. If this behavior were characteristic of many regulatory genes, then such a phenomenon could contribute to inbreeding depression and heterosis. To examine this question, inbreds of Mo17 and B73 and the two reciprocally produced hybrids were crossed by Stock 6 to generate four classes of maternal haploids. The mature haploid plants were measured for several quantitative traits. If inbreeding depression results from an accumulating heritable effect that is reversed by the hybrid state, one would expect the haploids derived from the hybrids to perform better than those derived from the inbred lines. The hybrid-derived haploids did not exhibit greater average performance than the inbred-derived haploids. These data fail to support the hypothesis that inbreeding depression and heterosis have a metastable epigenetic component.

Epigenesis, Genetic↗

PubMed2006

Effects of self-fertilization, environmental stress and exposure to xenobiotics on fitness-related traits of the freshwater snail Lymnaea stagnalis.

Genetic and ecological factors may interact in their effects on fitness. Such interactions are thus to be expected between inbreeding and exposure of a population to a toxicant. The magnitude of inbreeding depression is thought to increase in stressful environments. To test this hypothesis, we investigated the combined effects of environmental conditions and inbreeding on fitness in the self-fertile snail Lymnaea stagnalis, using a stress gradient (0-2) applied to a 100 isolated and paired lineages: laboratory control (0), outdoor microcosm control (1) and pesticide exposure under outdoor microcosm conditions (2). Outdoor stress conditions were maintained for 28 days prior to measurements of fitness traits (fecundity, hatching success, and size at hatching) under laboratory conditions, so that delayed environmental effects could be estimated. Under laboratory control conditions, we found significant initial family level heterogeneity for most measured traits, including physiological performances as assessed through energetic biomarkers. Whatever the environmental conditions, inbreeding depression was very low for progeny performances. Negative values of self-fertilization depression (SFD) were obtained. Unexpectedly, SFD showed a negative relationship with the assumed stress intensity, reflecting a higher sensitivity under pairing than under selfing, mostly due to parental fecundity. This suggests that stressful conditions may favour selfing. Stress intensity increased the distribution limits of both depression indices, suggesting that changes in fitness are less predictable in a population under stress. Implications of such findings for environmental risk assessment of pesticides are discussed.

Animals↗

PubMedDate not supplied

Testing alternative methods for purging genetic load using the housefly (Musca domestica L.).

When a population faces long-term inbreeding, artificial selection, in principle, can enhance natural selection processes for purging the exposed genetic load. However, strong purge pressures might actually decrease fitness through the inadvertent fixation of deleterious alleles and allelic combinations. We tested lines of the housefly (Musca domestica L.) for the effectiveness of artificial selection to promote the adaptation to small population size. Specifically, replicate populations were held at average census sizes of 54 for nine generations or 30 for 14 generations while being subjected to artificial selection pressure for increased fitness in overall mating propensity (i.e., the proportion of virgin male-female pairs initiating copulation within 30 min), while also undergoing selection to create differences among lines in multivariate components of courtship performance. In the 14-generation experiment, a subset of the lines were derived from a founder-flush population (i.e., derived from three male-female pairs). In both experiments, we also maintained parallel non-selection lines to assess the potential for natural purging through serial inbreeding alone. Sub-populations derived from a stock newly derived from the wild responded to artificial selection for increased mating propensity, but only in the short-term, with eventual rebounds back to the original levels. Serial inbreeding in these lines simply reduced mating propensity. In sub-populations derived from the same base population, but 36 generations later, both artificial selection and serial inbreeding increased mating propensity, but mainly to restore the level found upon establishment in the laboratory. Founder-flush lines responded as well as the non-bottlenecked controls, so we base our major conclusions on the comparisons between fresh-caught and long-term laboratory stocks. We suggest that the effectiveness of the alternative purge protocols depended upon the amount of genetic load already exposed, such that prolonged periods of relaxed or altered selection pressures of the laboratory rendered a population more responsive to purging protocols.

Animals↗

PubMed1999

Quantitative genetics in conservation biology.

Most of the major genetic concerns in conservation biology, including inbreeding depression, loss of evolutionary potential, genetic adaptation to captivity and outbreeding depression, involve quantitative genetics. Small population size leads to inbreeding and loss of genetic diversity and so increases extinction risk. Captive populations of endangered species are managed to maximize the retention of genetic diversity by minimizing kinship, with subsidiary efforts to minimize inbreeding. There is growing evidence that genetic adaptation to captivity is a major issue in the genetic management of captive populations of endangered species as it reduces reproductive fitness when captive populations are reintroduced into the wild. This problem is not currently addressed, but it can be alleviated by deliberately fragmenting captive populations, with occasional exchange of immigrants to avoid excessive inbreeding. The extent and importance of outbreeding depression is a matter of controversy. Currently, an extremely cautious approach is taken to mixing populations. However, this cannot continue if fragmented populations are to be adequately managed to minimize extinctions. Most genetic management recommendations for endangered species arise directly, or indirectly, from quantitative genetic considerations.

Animals↗

PubMed1998

Characterization of deleterious mutations in outcrossing populations.

Deng and Lynch recently proposed estimating the rate and effects of deleterious genomic mutations from changes in the mean and genetic variance of fitness upon selfing/outcrossing in outcrossing/highly selfing populations. The utility of our original estimation approach is limited in outcrossing populations, since selfing may not always be feasible. Here we extend the approach to any form of inbreeding in outcrossing populations. By simulations, the statistical properties of the estimation under a common form of inbreeding (sib mating) are investigated under a range of biologically plausible situations. The efficiencies of different degrees of inbreeding and two different experimental designs of estimation are also investigated. We found that estimation using the total genetic variation in the inbred generation is generally more efficient than employing the genetic variation among the mean of inbred families, and that higher degree of inbreeding employed in experiments yields higher power for estimation. The simulation results of the magnitude and direction of estimation bias under variable or epistatic mutation effects may provide a basis for accurate inferences of deleterious mutations. Simulations accounting for environmental variance of fitness suggest that, under full-sib mating, our extension can achieve reasonably well an estimation with sample sizes of only approximately 2000-3000.

Analysis of Variance↗

PubMed1999

A quantitative model of the relationship between phenotypic variance and heterozygosity at marker loci under partial selfing.

Negative relationships between allozyme heterozygosity and morphological variance have often been observed and interpreted as evidence for increased developmental stability in heterozygotes. However, inbreeding can also generate such relationships by decreasing heterozygosity at neutral loci and redistributing genetic variance at the same time. I here provide a quantitative genetic model of this process by analogy with heterozygosity-fitness relationships. Inbreeding generates negative heterozygosity-variance relationships irrespective of the genetic architecture of the trait. This holds for fitness traits as well as neutral traits, the effect being stronger for fitness traits under directional dominance or overdominance. The order of magnitude of heterozygosity-variance regressions is compatible with empirical data even with very low inbreeding. Although developmental stability effects cannot be excluded, inbreeding is a parsimonious explanation that should be seriously considered to explain correlations between heterozygosity and both mean and variance of phenotypes in natural populations.

Animals↗

PubMed2003

The advantages of segregation and the evolution of sex.

In diploids, sexual reproduction promotes both the segregation of alleles at the same locus and the recombination of alleles at different loci. This article is the first to investigate the possibility that sex might have evolved and been maintained to promote segregation, using a model that incorporates both a general selection regime and modifier alleles that alter an individual's allocation to sexual vs. asexual reproduction. The fate of different modifier alleles was found to depend strongly on the strength of selection at fitness loci and on the presence of inbreeding among individuals undergoing sexual reproduction. When selection is weak and mating occurs randomly among sexually produced gametes, reductions in the occurrence of sex are favored, but the genome-wide strength of selection is extremely small. In contrast, when selection is weak and some inbreeding occurs among gametes, increased allocation to sexual reproduction is expected as long as deleterious mutations are partially recessive and/or beneficial mutations are partially dominant. Under strong selection, the conditions under which increased allocation to sex evolves are reversed. Because deleterious mutations are typically considered to be partially recessive and weakly selected and because most populations exhibit some degree of inbreeding, this model predicts that higher frequencies of sex would evolve and be maintained as a consequence of the effects of segregation. Even with low levels of inbreeding, selection is stronger on a modifier that promotes segregation than on a modifier that promotes recombination, suggesting that the benefits of segregation are more likely than the benefits of recombination to have driven the evolution of sexual reproduction in diploids.

Alleles↗

PubMed2001

Molecular characterization of the Smyth chicken sublines and their parental controls by RFLP and DNA fingerprint analysis.

The Smyth line (SL) chicken, a model for autoimmune human vitiligo, is characterized by a spontaneous posthatch epidermal pigment loss (vitiligo). Even though the immunological and morphological changes accompanying the vitiligo process have been well studied, the genetics of this phenomenon remains elusive. The SL lines have been maintained by nonpedigreed matings since their inception, and therefore, the inbreeding status is unknown. The present study was designed to provide an estimate of the inbreeding coefficients and the molecular genetic profiles of the SL sublines, each homozygous for a different MHC haplotype and their MHC-matched parental control (BL) sublines. The DNA fingerprint analysis revealed that there is a moderate level of inbreeding within the SL and BL parental sublines. Of the two SL sublines studied, SL101 had the highest level of inbreeding (0.948). Similarly, its parental control line (BL101) was more inbred than the parental subline of SL102 (BL102). The very high level of similarity between the SL sublines and their respective parental control lines is shown further by the similarity index (SI) estimates (SI between SL101 and BL101 was 0.949 and that between SL102 and BL102 was 0.932). Restriction fragment length polymorphism (RFLP) analysis of the endogenous viral genes (avian leukosis virus subgroup E, ALVE) showed that five ALVE-related BamH1 fragments were present in the SL101 and four in SL102 sublines, whereas the parental BL101 and BL102 sublines had five and six fragments, respectively. SL101 and SL102 shared two fragments, but the frequencies were different. Similarly, BL101 and BL102 shared two fragments. SL101 and BL101 shared three fragments, and SL102 and BL102 also shared three fragments.

Animals↗

PubMed2006

Disease ecology in the Galápagos Hawk (Buteo galapagoensis): host genetic diversity, parasite load and natural antibodies.

An increased susceptibility to disease is one hypothesis explaining how inbreeding hastens extinction in island endemics and threatened species. Experimental studies show that disease resistance declines as inbreeding increases, but data from in situ wildlife systems are scarce. Genetic diversity increases with island size across the entire range of an extremely inbred Galápagos endemic bird, providing the context for a natural experiment examining the effects of inbreeding on disease susceptibility. Extremely inbred populations of Galápagos hawks had higher parasite abundances than relatively outbred populations. We found a significant island effect on constitutively produced natural antibody (NAb) levels and inbred populations generally harboured lower average and less variable NAb levels than relatively outbred populations. Furthermore, NAb levels explained abundance of amblyceran lice, which encounter the host immune system. This is the first study linking inbreeding, innate immunity and parasite load in an endemic, in situ wildlife population and provides a clear framework for assessment of disease risk in a Galápagos endemic.

Animals↗

PubMed2002

A metapopulation perspective on genetic diversity and differentiation in partially self-fertilizing plants.

Partial self-fertilization is common in higher plants. Mating system variation is known to have important consequences for how genetic variation is distributed within and among populations. Selfing is known to reduce effective population size, and inbreeding species are therefore expected to have lower levels of genetic variation than comparable outcrossing taxa. However, several recent empirical studies have shown that reductions in genetic diversity within populations of inbreeding species are far greater than the expected reductions based on the reduced effective population size. Two different processes have been argued to cause these patterns, selective sweeps (or hitchhiking) and background selection. Both are expected to be most effective in reducing genetic variation in regions of low recombination rates. Selfing is known to reduce the effective recombination rate, and inbreeding taxa are thus thought to be particularly vulnerable to the effects of hitchhiking or background selection. Here I propose a third explanation for the lower-than-expected levels of genetic diversity within populations of selfing species; recurrent extinctions and recolonizations of local populations, also known as metapopulation dynamics. I show that selfing in a metapopulation setting can result in large reductions in genetic diversity within populations, far greater than expected based the lower effective population size inbreeding species is expected to have. The reason for this depends on an interaction between selfing and pollen migration.

Genetic Variation↗