Many studies have quantified the distribution of heterozygosity and relatedness in natural populations, but few have examined the demographic processes driving these patterns. In this study, we take a novel approach by studying how population structure affects both pairwise identity and the distribution of heterozygosity in a natural population of the self-incompatible plant Antirrhinum majus. Excess variance in heterozygosity between individuals is due to identity disequilibrium, which reflects the variance in inbreeding between individuals; it is measured by the statistic g2. We calculated g2 together with FST and pairwise relatedness (Fij) using 91 SNPs in 22,353 individuals collected over 11 years. We find that pairwise Fij declines rapidly over short spatial scales, and the excess variance in heterozygosity between individuals reflects significant variation in inbreeding. Additionally, we detect an excess of individuals with around half the average heterozygosity, indicating either selfing or matings between close relatives. We use 2 types of simulation to ask whether variation in heterozygosity is consistent with fine-scale spatial population structure. First, by simulating offspring using parents drawn from a range of spatial scales, we show that the known pollen dispersal kernel explains g2. Second, we simulate a 1,000-generation pedigree using the known dispersal and spatial distribution and find that the resulting g2 is consistent with that observed from the field data. In contrast, a simulated population with uniform density underestimates g2, indicating that heterogeneous density promotes identity disequilibrium. Our study shows that heterogeneous density and leptokurtic dispersal can together explain the distribution of heterozygosity.

OBJECTIVE: This study was planned to evaluate the genetic diversity in the admixed and Teli (a Hindu caste) populations of Maharashtra, India using 20 autosomal Short Tandem Repeat (STR) genetic markers. We further investigated the genetic relatedness of the studied populations with other Indian populations.
RESULTS: The studied populations showed a wide range of observed heterozygosity viz. 0.690 to 0.918 for the admixed population and 0.696 to 0.942 for the Teli population. This might be due to the multi-directional gene flow. The admixed and Teli populations also showed a high degree polymorphism which ranged from 0.652 to 0.903 and 0.644 to 0.902, respectively. Their combined value of matching probability for all the studied loci was 4.29 × 10-25 and 5.01 × 10-24, respectively. The results of Neighbor-Joining tree and Principal Component Analysis showed that the studied populations clustered with the general populations of Jharkhand, UttarPradesh, Rajasthan and Central Indian States, as well as with the specific populations of Maharashtra (Konkanastha Brahmins) and Tamil Nadu (Kurmans). Overall, the obtained data showed a high degree of forensic efficacy and would be useful for forensic applications as well as genealogical studies.

High levels of genetic variation are often observed in natural populations, suggesting the action of processes such as frequency-dependent selection, heterozygote advantage and variable selection. However, the maintenance of genetic variation in fitness-related traits remains incompletely explained. The extent of genetic variation in obligately self-fertilizing populations of Lobelia inflata (Campanulaceae L.) strongly implies balancing selection. Lobelia inflata thus offers an exceptional opportunity for an empirical test of genotype-environment interaction (G × E) as a variance-maintaining mechanism under fluctuating selection: L. inflata is monocarpic and reproduces only by seed, facilitating assessment of lifetime fitness; genome-wide homozygosity precludes some mechanisms of balancing selection, and microsatellites are, in effect, genotypic lineage markers. Here, we find support for the temporal G × E hypothesis using a manipulated space-for-time approach across four environments: a field environment, an outdoor experimental plot and two differing growth-chamber environments. High genetic variance was confirmed: 83 field-collected individuals consisted of 45 distinct microsatellite lineages with, on average, 4.5 alleles per locus. Rank-order fitness, measured as lifetime fruit production in 16 replicated multilocus genotypes, changed significantly across environments. Phenotypic differences among microsatellite lineages were detected. Results thus support the G × E hypothesis in principle. However, the evaluation of the effect size of this mechanism and fitness effects of life-history traits will require a long-term study of fluctuating selection on labelled genotypes in the field.

To enhance their conservation value, several hundred islands worldwide have been cleared of invasive alien rats, Rattus spp. One of the largest projects yet undertaken was on 43 km(2) Henderson Island in the Pitcairn group, South Pacific, in August 2011. Following massive immediate mortality, a single R. exulans was observed in March 2012 and, subsequently, rat numbers have recovered. The survivors show no sign of resistance to the toxicant used, brodifacoum. Using pre- and post-operation rat tissue samples from Henderson, plus samples from around the Pacific, we exclude re-introduction as the source of continued rat presence. Microsatellite analysis of 18 loci enabled comparison of genetic diversity of Henderson rats before and after the bait drop. The fall in diversity measured by allele frequency change indicated that the bottleneck (N e) through which the breeding population passed was probably around 50 individuals, representing a census population of about 60-80 animals. This is the first failed project that has estimated how close it was to success.

A heterozygosity-fitness correlations (HFCs) may reflect inbreeding depression, but the extent to which they do so is debated. HFCs are particularly likely to occur after demographic disturbances such as population bottleneck or admixture. We here study HFC in an introduced and isolated ungulate population of white-tailed deer Odocoileus virginianus in Finland founded in 1934 by four individuals. A total of 422 ≥ 1-year-old white-tailed deer were collected in the 2012 hunting season in southern Finland and genotyped for 14 microsatellite loci. We find significant identity disequilibrium as estimated by g 2. Heterozygosity was positively associated with size- and age-corrected body mass, but not with jaw size or (in males) antler score. Because of the relatively high identity disequilibrium, heterozygosity of the marker panel explained 51% of variation in inbreeding. Inbreeding explained approximately 4% of the variation in body mass and is thus a minor, although significant source of variation in body mass in this population. The study of HFC is attractive for game- and conservation-oriented wildlife management because it presents an affordable and readily used approach for genetic monitoring that allowing identification of fitness costs associated with genetic substructuring in what may seem like a homogeneous population.

Most single-locus molecular approaches to species delimitation available to date have been designed and tested on data sets comprising at least tens of species, whereas the opposite case (species-poor data sets for which the hypothesis that all individuals are conspecific cannot by rejected beforehand) has rarely been the focus of such attempts. Here we compare the performance of barcode gap detection, haplowebs and generalized mixed Yule-coalescent (GMYC) models to delineate chimpanzees and bonobos using nuclear sequence markers, then apply these single-locus species delimitation methods to data sets of one, three, or six species simulated under a wide range of population sizes, speciation rates, mutation rates and sampling efforts. Our results show that barcode gap detection and GMYC models are unable to delineate species properly in data sets composed of one or two species, two situations in which haplowebs outperform them. For data sets composed of three or six species, bGMYC and haplowebs outperform the single-threshold and multiple-threshold versions of GMYC, whereas a clear barcode gap is only observed when population sizes and speciation rates are both small. The latter conditions represent a \"sweet spot\" for molecular taxonomy where all the single-locus approaches tested work well; however, the performance of these methods decreases strongly when population sizes and speciation rates are high, suggesting that multilocus approaches may be necessary to tackle such cases.

Insertion/deletion (INDELs) marker sets can serve as a useful supplementary tool for human identification. A commercial kit, the Qiagen DIPplex(®) Investigator kit, multiplexes 30 biallelic autosomal INDELs and Amelogenin for forensic use. We performed a validation study based on the DIPplex(®) kit in four Chinese populations: Han, Tibetan, Uyghur, and Kazakh. There were no significant departures from Hardy-Weinberg equilibrium or significant linkage disequilibrium (pair-wised r(2)<0.2) between the 30 INDELs. The random match probabilities were in the range of 3.84 × 10(-11) to 1.20 × 10(-12), and the power of exclusion was >0.99. The multiplex PCR was optimized for a 5-μL volume, full profiles were obtained with 0.062 ng/μL of template DNA, and excellent performance was obtained with degraded casework samples. This study demonstrates that the multiplex INDEL assay can be used as a supplementary method for degraded DNA detection in the studied Chinese populations.