A quantitative review of heterozygosity–fitness correlations in animal populations

The ease of obtaining genotypic data from wild populations has renewed interest in the relationship between individual genetic diversity and fitness-related traits (heterozygosity–fitness correlations, or HFC). Here we present a comprehensive meta-analysis of HFC studies using powerful multivariate techniques which account for nonindependence of data. We compare these findings with those from univariate techniques, and test the influence of a range of factors hypothesized to influence the strength of HFCs. We found small but significantly positive effect sizes for life-history, morphological, and physiological traits; while theory predicts higher mean effect sizes for life-history traits, effect size did not differ consistently with trait type. Newly proposed measures of variation were no more powerful at detecting relationships than multilocus heterozygosity, and populations predicted to have elevated inbreeding variance did not exhibit higher mean effect sizes. Finally, we found evidence for publication bias, with studies reporting weak, nonsignificant effects being under-represented in the literature. In general, our review shows that HFC studies do not generally reveal patterns predicted by population genetic theory, and are of small effect (less than 1% of the variance in phenotypic characters explained). Future studies should use more genetic marker data and utilize sampling designs that shed more light on the biological mechanisms that may modulate the strength of association, for example by contrasting the strength of HFCs in mainland and island populations of the same species, investigating the role of environmental stress, or by considering how selection has shaped the traits under investigation.     

Genome‐wide population structure and admixture analysis reveals weak differentiation among Ugandan goat breeds

Uganda has a large population of goats, predominantly from indigenous breeds reared in diverse production systems, whose existence is threatened by crossbreeding with exotic Boer goats. Knowledge about the genetic characteristics and relationships among these Ugandan goat breeds and the potential admixture with Boer goats is still limited. Using a medium‐density single nucleotide polymorphism (SNP) panel, we assessed the genetic diversity, population structure and admixture in six goat breeds in Uganda: Boer, Karamojong, Kigezi, Mubende, Small East African and Sebei. All the animals had genotypes for about 46 105 SNPs after quality control. We found high proportions of polymorphic SNPs ranging from 0.885 (Kigezi) to 0.928 (Sebei). The overall mean observed (H_O) and expected (H_E) heterozygosity across breeds was 0.355 ± 0.147 and 0.384 ± 0.143 respectively. Principal components, genetic distances and admixture analyses revealed weak population sub‐structuring among the breeds. Principal components separated Kigezi and weakly Small East African from other indigenous goats. Sebei and Karamojong were tightly entangled together, whereas Mubende occupied a more central position with high admixture from all other local breeds. The Boer breed showed a unique cluster from the Ugandan indigenous goat breeds. The results reflect common ancestry but also some level of geographical differentiation. admixture and f₄ statistics revealed gene flow from Boer and varying levels of genetic admixture among the breeds. Generally, moderate to high levels of genetic variability were observed. Our findings provide useful insights into maintaining genetic diversity and designing appropriate breeding programs to exploit within‐breed diversity and heterozygote advantage in crossbreeding schemes.     

Identification of a hTid-1 mutation which sensitizes gliomas to apoptosis

Human Tid-1 (hTid-1) is a DnaJ chaperone protein with homology to the Drosophila tumor suppressor Tid56. We report the first case of a tumor-associated mutation at the human TID1 locus, which was identified in the SF767 glioma cell line giving rise to aberrantly high levels of a hTid-1(L) mutant variant. In this study, we set out to determine whether this change in hTid-1 status influences the response of glioma cells to adenoviral (Ad)-mediated delivery of the two major isoforms of TID1, hTid-1(L) and hTid-1(S). Ad-hTid-1(S) induced apoptosis in hTid-1 mutant SF767 cells, while causing growth arrest in wild-type hTid-1-expressing U373 and U87 cells. By contrast, Ad-hTid-1(L) infection had no apparent effect on glioma cell growth. The apoptosis induced by hTid-1(S) was accompanied by mitochondrial cytochrome C release and caspase activation and blocked by stable overexpression of Bcl-X(L). Our findings suggest that the status of hTid-1 in gliomas may contribute to their susceptibility to cell death triggers.     

Exploring the relationship between parental relatedness and male reproductive success in the Antarctic fur seal Arctocephalus gazella

Recent genetic studies of natural populations have shown that heterozygosity and other genetic estimates of parental relatedness correlate with a wide variety of fitness traits, from juvenile survival and parasite resistance to male reproductive success. Many of these traits involve health and survival, where the underlying mechanism may involve changes in the effectiveness of the immune system. However, for traits such as reproductive success, the likely mechanisms remain less obvious. In this paper, we examine the relationship between heterozygosity and a range of traits that contribute to male reproductive success, including time spent on territories and competitiveness. Our analysis is based on observational and genetic data from eight consecutive breeding seasons at a colony of the Antarctic fur seal, Arctocephalus gazella. Overall, male reproductive success was found to correlate strongly with internal relatedness (IR, a form of heterozygosity). When different components of success were analyzed, we found that IR correlates independently with reproductive longevity, time spent ashore, and competitive ability per unit mating opportunity on the study beach, with more heterozygous males being more successful. Behavioral observations were sufficiently detailed to allow examination of how daily mean IR values for males present on the beach varied within seasons and from year to year. Again, significant variation was found both among and within seasons, with more homozygous males appearing less able to hold territories in poor seasons when pup production is low and, within a season, at both the start of the season and to some extent around the peak of female estrus. Finally, we tested whether the benefits of high heterozygosity are due mainly to a genomewide effect (e.g. inbreeding depression) or to single locus heterosis by asking whether the relationship between IR and male success was robust to the removal of any single locus or to any pair of loci. Since the relationship remained significant in all cases, we favor a multilocus explanation for the effects we report.     

A River Metapopulation Structure of a Japanese Freshwater Goby, Odontobutis Obscura, Deduced from Allozyme Genetic Indices

Gene products of 18 allozyme loci from 1268 individuals of a Japanese freshwater goby called donko, Odontobutis obscura (Odontobutidae; Gobioidei), from 33 localities in the Koya River, Yamaguchi Prefecture, Japan, were investigated to determine the extent of genetic divergence and gene flow within a river metapopulation. Genetic indices including GST(mean FST 0.182), FIT(mean 0.192) and D(mean 0.015) indicated a considerable divergence of local populations in the river. The genetic distance (D) and channel distance between pairs of populations did not show a good correlation, and geographical neighbors were not always genetic neighbors. Therefore, the genetic divergence of populations is attributable to independent genetic drift with restricted gene flow among populations. The agricultural dams and weirs constructed across the river must be responsible for the restricted gene flow. The metapopulation structure of O. obscura in the Koya River may be barely sustained by one-way gene flow only from the upper to the lower populations. An occasional artificial transplantation of some individuals from the lower to the upper populations may be one alternative to maintain a river metapopulation structure safely.     

Clonality disguises the vulnerability of a threatened arid zone Acacia

Long‐lived, widespread plant species are expected to be genetically diverse, reflecting the interaction between large population sizes, overlapping generations, and gene flow. Such species are thought to be resilient to disturbance, but may carry an extinction debt due to reproductive failure. Genetic studies of Australian arid zone plant species suggest an unusually high frequency of asexuality, polyploidy, or both. A preliminary AFLP genetic study implied that the naturally fragmented arid zone tree, Acacia carneorum, is almost entirely dependent on asexual reproduction through suckering, and stands may have lacked genetic diversity and interconnection even prior to the onset of European pastoralism. Here we surveyed microsatellite genetic variation in 20 stands to test for variation in life histories and further assessed the conservation status of the species by comparing genetic diversity within protected stands in National Parks and disturbed range lands. Using herbarium records, we estimate that 219 stands are extant, all of which occur in the arid zone, west of the Darling River in southeastern Australia. With two exceptions, all surveyed stands comprised only one multilocus genet and at least eight were putatively polyploid. Although some stands comprise thousands of stems, our findings imply that the species as a whole may represent ~240 distinct genetic individuals, many of which are polyploid, and most are separated by >10 km of unsuitable habitat. With only 34% of stands (and therefore genets) occurring within conservation reserves, A. carneorum may be at much greater risk of extinction than inferred from on‐ground census data. Land managers should prioritize on‐ground preservation of the genotypes within existing reserves, protecting both vegetative suckers and seedlings from herbivory. Importantly, three stands are known to set viable seed and should be used to generate genetically diverse germ‐plasm for ex situ conservation, population augmentation, or translocation.     

A STRUCTURED COALESCENT PROCESS FOR SEASONALLY FLUCTUATING POPULATIONS

Many short‐lived organisms pass through several generations during favorable growing seasons, separated by inhospitable periods during which only small hibernating or estivating refugia remain. This induces pronounced seasonal fluctuations in population size and metapopulation structure. The first generations in the growing season will be characterized by small, relatively isolated demes whereas the later generations will experience larger deme sizes with more extensive gene flow. Fluctuations of this sort can induce changes in the amount of genetic variation in early season samples compared to late season samples, a classical example being the observations of seasonal variation in allelism in New England Drosophila populations by P.T. Ives. In this article, we study the properties of a structured coalescent process under seasonal fluctuations using numerical analysis of exact state equations, analytical approximations that rely on a separation of timescales between intrademic versus interdemic processes, and individual‐based simulations. We show that although an increase in genetic variation during each favorable growing season is observed, it is not as pronounced as in the empirical observations. This suggests that some of the temporal patterns of variation seen by Ives may be due to selection against deleterious lethals rather than neutral processes.     

云南文山黄牛和迪庆黄牛遗传多样性的蛋白电泳研究

采用水平淀粉胶蛋白电泳技术分析了云南文山黄牛和迪庆黄牛的３３种血液蛋白及同工酶,共计３７个遗传座位,其中６个座位检测到多态性。文山黄牛的多态座位百分比Ｐ＝０．１３８９,平均杂合度Ｈ＝０．０６１０,迪庆黄牛Ｐ＝０．１６６７,Ｈ＝０．０６９１。通过Ｎｅｉ氏遗传距离计算,运用ＰＨＹＬＩＰ３．５Ｃ软件包中的“ＵＰＧＭＡ”,“ＣＯＮＴＭＬ”和“ＮＥＩＧＨＢＯＲ”法,结合前人报道的数据对１０个黄牛品种进行聚类分析。结果得出：文山黄牛可能主要起源于瘤牛（Ｂｏｓｉｎｄｉｃｕｓ）,迪庆黄牛可能主要起源于普通黄牛（Ｂｏｓｔａｕｒｕｓ）。我们的结果提示,云南黄牛可能是由当地人驯化的野生牛群与外来的驯化牛群相结合并适应当地气候和环境逐渐形成的,因而在蛋白水平上具有较为丰富的多样性。