The population growth consequences of variation in individual heterozygosity

Heterozygosity has been associated with components of fitness in numerous studies across a wide range of taxa. Because heterozygosity is associated with individual performance it is also expected to be associated with population dynamics. However, investigations into the association between heterozygosity and population dynamics have been rare because of difficulties in linking evolutionary and ecological processes. The choice of heterozygosity measure is a further issue confounding such studies as it can be biased by individual differences in the frequencies of the alleles studied, the number of alleles at each locus as well as the total number of loci typed. In this study, we first examine the differences between the principal metrics used to calculate heterozygosity using long-term data from a marked population of Soay sheep (Ovis aries). Next, by means of statistical transformation of the homozygosity weighted by loci index, we determine how heterozygosity contributes to population growth in Soay sheep by modelling individual contributions to population growth (p(t(i))) as a function of several covariates, including sex, weight and faecal egg count--a surrogate of parasitic nematode burden in the gut. We demonstrate that although heterozygosity is associated with some components of fitness, most notably adult male reproductive success, in general it is only weakly associated with population growth.     

Variation of short tandem repeats within and between species belonging to the Canidae family

Frequency distribution and allele size in 20 canine microsatellite loci were analyzed in 33 flat-coated retrievers, 32 dachshunds, 10 red foxes, and 10 Arctic foxes. Overall, the major difference between the two dog breeds was the relative allele frequencies rather than the size ranges of alleles at the individual locus. The average heterozygosity within the two dog breeds was not significantly different. Since the average heterozygosity at several polymorphic loci is a relative measure of heterogeneity within the population, analysis of heterozygosity within microsatellite loci is suggested as a measure for the diversity of populations. Eighty percent (16 of 20) of the canine microsatellite primer pairs amplified corresponding loci in the two fox species. This reflects a very high sequence conservation within the Canidae family relative to findings in, for instance, the Muridae family. This indicates that it will be possible to utilize the well-characterized fox karyotype instead of the dog karyotype as a step towards physical mapping of the dog genome. Analysis of exclusion power and probabilities of genetic identity between unrelated animals by use of the seven most informative loci demonstrated that it will be possible to assemble a panel of microsatellite loci that is effective for parentage analysis in all breeds.     

Age‐dependent,negative heterozygosity–fitness correlations and local effects in an endangered Caribbean reptile,Iguana delicatissima

Inbreeding depression can have alarming impacts on threatened species with small population sizes. Assessing inbreeding has therefore become an important focus of conservation research. In this study, heterozygosity–fitness correlations (HFCs) were measured by genotyping 7 loci in 83 adult and 184 hatchling Lesser Antillean Iguanas, Iguana delicatissima, at a communal nesting site in Dominica to assess the role of inbreeding depression on hatchling fitness and recruitment to the adult population in this endangered species. We found insignificant correlations between multilocus heterozygosity and multiple fitness proxies in hatchlings and adults. Further, multilocus heterozygosity did not differ significantly between hatchlings and adults, which suggests that the survivorship of homozygous hatchlings does not differ markedly from that of their heterozygous counterparts. However, genotypes at two individual loci were correlated with hatching date, a finding consistent with the linkage between specific marker loci and segregating deleterious recessive alleles. These results provide only modest evidence that inbreeding depression influences the population dynamics of I. delicatissima on Dominica.     

Analysis of the relationship between allozyme heterozygosity and fitness in the rare Gentiana pneumonanthe L.

Especially for rare species occurring in small populations, which are prone to loss of genetic variation and inbreeding, detailed knowledge of the relationship between heterozygosity and fitness is generally lacking. After reporting on allozyme variation and fitness in relation to population size in the rare plant Gentiana pneumonanthe, we present a more detailed analysis of the association between heterozygosity and individual fitness. The aim of this study was to test whether increased fitness of more heterozygous individuals is explained best by the ‘inbreeding’ hypothesis or by the ‘overdominance’ hypothesis. Individual fitness was measured during 8 months of growth in the greenhouse as the performance for six life-history parameters. PCA reduced these parameters to four main Fitness Components. Individual heterozygosity was scored for seven polymorphic allozyme loci. For some of these loci (e.g. Aat3, Pgm1 and 6Pgdh2) heterozygotes showed a significantly higher relative fitness than homozygotes. To test the inbreeding model, regression analyses were performed between each Fitness Component and the number of heterozygous loci per individual. Multiple regressions with the adaptive distance of five loci as independent variables were used to test the overdominance model. Only the inbreeding model was a statistically significant explanation for the relationship between heterozygosity and fitness in G. pneumonanthe. The number of heterozygous loci was significantly negatively correlated with the coefficients of variation of three of the six initially measured fitness parameters. This suggests a lower developmental stability among more homozygous plants and may explain the higher phenotypic variation in small populations of the species observed earlier. The importance of the results for conservation biology is discussed.     

Strikingly high levels of heterozygosity despite 20 years of inbreeding in a clonal honey bee

Inbreeding (the mating between closely related individuals) often has detrimental effects that are associated with loss of heterozygosity at overdominant loci, and the expression of deleterious recessive alleles. However, determining which loci are detrimental when homozygous, and the extent of their phenotypic effects, remains poorly understood. Here, we utilize a unique inbred population of clonal (thelytokous) honey bees, Apis mellifera capensis, to determine which loci reduce individual fitness when homozygous. This asexual population arose from a single worker ancestor approximately 20 years ago and has persisted for at least 100 generations. Thelytokous parthenogenesis results in a 1/3 of loss of heterozygosity with each generation. Yet, this population retains heterozygosity throughout its genome due to selection against homozygotes. Deep sequencing of one bee from each of the three known sub‐lineages of the population revealed that 3,766 of 10,884 genes (34%) have retained heterozygosity across all sub‐lineages, suggesting that these genes have heterozygote advantage. The maintenance of heterozygosity in the same genes and genomic regions in all three sub‐lineages suggests that nearly every chromosome carries genes that show sufficient heterozygote advantage to be selectively detrimental when homozygous.     

Heterozygosity at neutral and immune loci is not associated with neonatal mortality due to microbial infection in Antarctic fur seals

Numerous studies have reported correlations between the heterozygosity of genetic markers and fitness. These heterozygosity–fitness correlations (HFCs) play a central role in evolutionary and conservation biology, yet their mechanistic basis remains open to debate. For example, fitness associations have been widely reported at both neutral and functional loci, yet few studies have directly compared the two, making it difficult to gauge the relative contributions of genome‐wide inbreeding and specific functional genes to fitness. Here, we compared the effects of neutral and immune gene heterozygosity on death from bacterial infection in Antarctic fur seal (Arctocephalus gazella) pups. We specifically developed a panel of 13 microsatellites from expressed immune genes and genotyped these together with 48 neutral loci in 234 individuals, comprising 39 pups that were classified at necropsy as having most likely died of bacterial infection together with a five times larger matched sample of healthy surviving pups. Identity disequilibrium quantified from the neutral markers was positive and significant, indicative of variance in inbreeding within the study population. However, multilocus heterozygosity did not differ significantly between healthy and infected pups at either class of marker, and little evidence was found for fitness associations at individual loci. These results support a previous study of Antarctic fur seals that found no effects of heterozygosity at nine neutral microsatellites on neonatal survival and thereby help to refine our understanding of how HFCs vary across the life cycle. Given that nonsignificant HFCs are underreported in the literature, we also hope that our study will contribute toward a more balanced understanding of the wider importance of this phenomenon.     

Microsatellite DNA markers for the Chinese wood frog (Rana chensinensis) and tests for their cross-utility in 15 ranid frog species

We developed 22 microsatellite markers for the Chinese wood frog (Rana chensinensis) to study the impact of landscape features on its population structure. Thirty‐four individuals from one breeding site were examined and 14 loci were polymorphic. The number of alleles, expected heterozygosity and observed heterozygosity varied from two to 14, from 0.0833 to 0.9118, and from 0.1376 to 0.8667, respectively. Cross‐species amplification was tested for 15 ranid frog species. The Plateau brown frog, Rana kukunoris (n = 23), was successfully amplified at 18 loci, and 15 were polymorphic with number of alleles varying from two to 18. Ten other species were also amplified at a limited number of loci.     

Loss of genetic diversity and fitness in Common Toad (Bufo bufo) populations isolated by inimical habitat

Measures of genetic diversity (including heterozygosity), survival and developmental homeostasis were found to be significantly lower in small, urban populations of the Common Toad (Bufo bufo) than in larger, rural populations of the same region. The autecology and genetic analysis of this relatively sedentary species suggested that the causal mechanism was genetic drift, arising from barriers to migration created by urban development. The pre-metamorphic survival of larvae cultured in identical conditions increased positively with the mean number of alleles at a locus and the percentage of polymorphic loci. Observed heterozygosity in urban garden and rural populations was correlated inversely with the number of observed physical abnormalities (used as a measure of developmental homeostasis) in the developing tadpoles. Genetic distances between town sites of mean 2.2 km separation were significantly higher than those between rural sites of mean 37 km separation. Genetic data were based on allozyme analysis of 27 loci in 8 urban and 4 rural populations. A subset of these sites (3 urban, 2 rural) were also assessed at 3 minisatellite loci and a positive correlation found between the average number of alleles per locus detected by the two methods. Estimates of Nei's 1972 genetic distance, derived separately from the DNA and protein data, were not, however, correlated. The reduction in genetic diversity and fitness observed in these urban toads provides an example of the effect on population persistence that longer term depletion in numbers and habitat fragmentation can have in the wider environment.     

Polymorphism of bovine microsatellite DNA sequences in the lowland European bison

Investigations of genetic polymorphism of microsatellite DNA sequences were conducted in 22 individuals of the European bisonBison bonasus (Linneaus, 1758) from Bia?owie?a Primeval Forest. For this purpose 27 cattle microsatellite primer pairs were used. Among the 27 microsatellite markers examined, an amplification product was obtained for 21 loci. This rendered it possible to identify total of 40 alleles in the bison population tested. In addition, eight loci were proved to be monomorphic. A majority of the 40 alleles identified was identical with the alleles identified at the corresponding loci in cattle. Only two alleles seem to be specific for the European bison. The value of heterozygosity for the examined loci in bison population from Bia?owie?a was low and ranged from 0.13 to 0.53. Hence, the polymorphism information content was low as well. Based on our results the microsatellite DNA markers identified in cattle may be used to analyse the genetic structure of the population of European bison.     

Homozygosity at a class II MHC locus depresses female reproductive ability in European brown hares

The link between adaptive genetic variation, individual fitness and wildlife population dynamics is fundamental to the study of ecology and evolutionary biology. In this study, a Bayesian modelling approach was employed to examine whether individual variability at two major histocompatibility complex (MHC) class II loci (DQA and DRB) and eight neutral microsatellite loci explained variation in female reproductive success for wild populations of European brown hare (Lepus europaeus). We examined two aspects of reproduction: the ability to reproduce (sterility) and the number of offspring produced (fecundity). Samples were collected from eastern Austria, experiencing a sub‐continental climatic regime, and from Belgium with a more Atlantic‐influenced climate. As expected, reproductive success (both sterility and fecundity) was significantly influenced by age regardless of sampling locality. For Belgium, there was also a significant effect of DQA heterozygosity in determining whether females were able to reproduce (95% highest posterior density interval of the regression parameter [−3.64, −0.52]), but no corresponding effect was found for Austria. In neither region was reproduction significantly associated with heterozygosity at the DRB locus. DQA heterozygotes from both regions also showed a clear tendency, but not significantly so, to produce a larger number of offspring. Predictive simulations showed that, in Belgium, sub‐populations of homozygotes will have higher rates of sterile individuals and lower average offspring numbers than heterozygotes. No similar effect is predicted for Austria. The mechanism for the spatial MHC effect is likely to be connected to mate choice for increased heterozygosity or to the linkage of certain MHC alleles with lethal recessives at other loci.     

Isolation and characterization of DNA microsatellite from cotton bollworm (Helicoverpa armigera,Hübner)

Five microsatellite loci of Helicoverpa armigera were isolated from a partial genomic library screened by oligonucleotide probes. Primers were designed to detect allelic variability and heterozygosity in 60 individuals collected from different host species. All loci were found to be polymorphic, have 8–11 alleles with expected heterozygosity ranging from 0.81 to 0.88. Our results indicate that the five microsatellite loci could provide valuable markers for population genetic and ecological studies of the cotton bollworm.     

HETEROZYGOSITY AND DEVELOPMENTAL STABILITY UNDER INBREEDING AND CROSSBREEDING IN PINUS ATTENUATA

The relationship between stability of annual trunk growth and heterozygosity at 24 polymorphic isozyme loci was studied in 10-year-old trees of knobcone pine (Pinus attenuata Lemm.) that were the products of contrasting systems of mating, self-, and interpopulation cross-pollination. Heterozygosity and variability of trunk growth were strongly related only when inbreds and crossbreds were compared; the crossbreds showed greater residual variability on an absolute scale, and greater responsiveness to climate on both absolute and relative scales. Within the inbreds there was no evidence of a relationship between heterozygosity and variability. Within the crossbreds, only one trait, a measure of relative trunk growth rate, showed a relationship with heterozygosity, and indicated greater variability of the more heterozygous trees. These results, and others in the literature, suggest that the relationship of heterozygosity to homeostasis for fitness components is neither simple nor monotonic; it varies between scales of measurement, genetic backgrounds, and environments.     

Genic heterozygosity, chromosomal interchanges and fitness in rye: any relationship?

Relationship between heterozygosity at allozyme loci, chromosomal interchanges and fitness was analyzed in a rye cultivar showing a polymorphism for such rearrangements. Nine allozyme systems (ACO, ACPH, GOT, GPI, LAP, MDH, PER, PGD and PGM) and five components of fitness (number of fertile tillers, total offspring, egg cell fertility, flowers/ear and seeds/ear) were studied. The estimated selection coefficients against interchange heterozygotes ranged from s = 0.12 to s = 0.34. A significant effect of the genic heterozygosity on some fitness components was observed in interchange heterozygotes (tillering and total offspring), in their standard homozygous sibs (flowers/ear and seeds/ear) and in the descendants of the crosses between standard karyotypes (flowers/ear, seeds/ear and egg cell fertility). However, the main effect was linked to genetic background associated to different crosses. Significant differences for Acph-1, Gpi-1, Lap-1, Mdh-1, Mdh-4, Pgd-2 and Pgm-1 loci were also found in some of these crosses although these differences were inconsistent. This suggests that probably the allozyme loci analyzed were not directly contributing to the fitness and that they are linked, in some cases, to different deleterious alleles depending on both cross and locus. This fact could support the local effect hypothesis as explanation although we do not discard the existence of some inbreeding level (general effect hypothesis) since all crosses and loci studied show a overall consistent trend of increased fitness with increased heterozygosity.     

Ten new microsatellite loci for analysis of genetic diversity in isolated populations of the Alpine land snail <Emphasis Type="Italic">Cylindrus obtusus</Emphasis>

In this study we characterized 10 polymorphic microsatellite markers for the land snail Cylindrus obtusus, an endemism of the Austrian Alps with a distribution in isolated populations above approximately 1,600 m. The microsatellite loci were analyzed in 44 individuals from two populations. Number of alleles per locus ranged between two and eight. Observed heterozygosity ranged between 0.00 and 1.00, and expected heterozygosity between 0.09 and 0.72. No significant linkage disequilibrium was found between pairs of loci. One of the sampled populations (Dachstein) showed no deviation from Hardy–Weinberg equilibrium and no presence of null alleles, whereas the other one (Schneeberg) did. These diverging results probably reflect differences in population structure rather than characteristics of the microsatellite loci and underline the usefulness of these markers for studying genetic diversity, population structure and differentiation in C. obtusus.     

Short tandem repeat based analysis of genetic variability in Kanarese buffalo of South India

The goal of the present study was assessing genetic diversity within Kanarese buffalo, the dual purpose breed of South India. A total of 48 unrelated animals were genotyped at 23 short tandem repeat (STR markers)loci. The total number of observed alleles was 180 with a mean of 7.83 per locus, which varied from 3 to 12 across different loci. The mean observed and expected heterozygosity in South Kanara buffaloes was estimated to be 0.518 and 0.712 respectively. Within population inbreeding estimate (F _IS) was significantly positive in most of the investigated loci which resulted in significant deviation from Hardy-Weinberg equilibrium at 19 of 23 loci analyzed. Evaluation of South Kanara buffalo population for mutation drift equilibrium revealed no significant heterozygosity excess under three different models of evolution viz. infinite alleles model (IAM), step-wise mutation model (SMM) and two phase model (TPM), thus indicating the absence of any recent genetic bottleneck. The results of the present study will help in formulating rational breeding strategies as well as conservation of this important germplasm.     

Characterization of 42 polymorphic microsatellite loci in Mimulus ringens (Phrymaceae) using Illumina sequencing

• Premise of the study: Microsatellite markers were isolated and characterized in Mimulus ringens (Phrymaceae), a herbaceous wetland perennial, to facilitate studies of mating patterns and population genetic structure. • Methods and Results: A total of 42 polymorphic loci were identified from a sample of 24 individuals from a single population in Ohio, USA. The number of alleles per locus ranged from two to nine, and median observed heterozygosity was 0.435. • Conclusions: This large number of polymorphic loci will enable researchers to quantify male fitness, patterns of multiple paternity, selfing, and biparental inbreeding in large natural populations of this species. These markers will also permit detailed study of fine-scale patterns of genetic structure.     

Genetic diversity and bottleneck analysis of Indian bellary sheep by microsatellite markers

Bellary sheep population variability and structure was investigated genetically utilizing FAO recommended microsatellite markers. Genetic variation at 20 microsatellite loci, population structure, and genetic bottleneck hypothesis were examined. Estimates of genetic variability such as effective number of alleles and gene diversities revealed substantial genetic variation frequently displayed by microsatellite markers. A total of 133 alleles were detected. Average polymorphism across the studied loci and expected gene diversity in the population were 1.419 ± 0.405 and 0.684 ± 0.140, respectively. No significant genotypic linkage disequilibrium was detected across population, suggesting no evidence of linkage between loci. The population was observed to be significantly differentiated into different groups, showed fairly high level of inbreeding (f = 0.253 ± 0.050) and global heterozygote deficit. Population structure analysis indicated the intermixing/introduction of unique/rare alleles in these migrating flocks. A normal L-shaped distribution of mode-shift test, non-significant heterozygosity excess on the basis of different models, as revealed from sign, standardized differences and Wilcoxon sign rank tests suggested that there was no recent bottleneck. The study revealed that even a breed with increasing population trend needs genetic management for the conservation and improvement. The text was submitted by the authors in English.     

Estimating genome-wide heterozygosity: effects of demographic history and marker type

Heterozygosity–fitness correlations (HFCs) are often used to link individual genetic variation to differences in fitness. However, most studies examining HFCs find weak or no correlations. Here, we derive broad theoretical predictions about how many loci are needed to adequately measure genomic heterozygosity assuming different levels of identity disequilibrium (ID), a proxy for inbreeding. We then evaluate the expected ability to detect HFCs using an empirical data set of 200 microsatellites and 412 single nucleotide polymorphisms (SNPs) genotyped in two populations of bighorn sheep (Ovis canadensis), with different demographic histories. In both populations, heterozygosity was significantly correlated across marker types, although the strength of the correlation was weaker in a native population compared with one founded via translocation and later supplemented with additional individuals. Despite being bi-allelic, SNPs had similar correlations to genome-wide heterozygosity as microsatellites in both populations. For both marker types, this association became stronger and less variable as more markers were considered. Both populations had significant levels of ID; however, estimates were an order of magnitude lower in the native population. As with heterozygosity, SNPs performed similarly to microsatellites, and precision and accuracy of the estimates of ID increased as more loci were considered. Although dependent on the demographic history of the population considered, these results illustrate that genome-wide heterozygosity, and therefore HFCs, are best measured by a large number of markers, a feat now more realistically accomplished with SNPs than microsatellites.     

Isolation and characterization of microsatellite loci for the jack mackerel (<Emphasis Type="Italic">Trachurus murphyi</Emphasis> Nichols, 1920)

Eight microsatellite loci were developed for the jack mackerel (Trachurus murphyi), a fish of significant commercial importance in the Southeast Pacific. Genetic variation at these loci was examined in 15 samples from the locality of Talcahuano (Chile). All eight were highly polymorphic, with a number of alleles per locus ranging from 4 to 22 and an observed heterozygosity from 0.429 to 1. These markers will be useful to address issues of population genetics, ecology, conservation and fisheries management related to that species.     

Heterozygosity–fitness correlations in a wild mammal population: accounting for parental and environmental effects

HFCs (heterozygosity–fitness correlations) measure the direct relationship between an individual's genetic diversity and fitness. The effects of parental heterozygosity and the environment on HFCs are currently under‐researched. We investigated these in a high‐density U.K. population of European badgers (Meles meles), using a multimodel capture–mark–recapture framework and 35 microsatellite loci. We detected interannual variation in first‐year, but not adult, survival probability. Adult females had higher annual survival probabilities than adult males. Cubs with more heterozygous fathers had higher first‐year survival, but only in wetter summers; there was no relationship with individual or maternal heterozygosity. Moist soil conditions enhance badger food supply (earthworms), improving survival. In dryer years, higher indiscriminate mortality rates appear to mask differential heterozygosity‐related survival effects. This paternal interaction was significant in the most supported model; however, the model‐averaged estimate had a relative importance of 0.50 and overlapped zero slightly. First‐year survival probabilities were not correlated with the inbreeding coefficient (f); however, small sample sizes limited the power to detect inbreeding depression. Correlations between individual heterozygosity and inbreeding were weak, in line with published meta‐analyses showing that HFCs tend to be weak. We found support for general rather than local heterozygosity effects on first‐year survival probability, and g2 indicated that our markers had power to detect inbreeding. We emphasize the importance of assessing how environmental stressors can influence the magnitude and direction of HFCs and of considering how parental genetic diversity can affect fitness‐related traits, which could play an important role in the evolution of mate choice.