A Two-Locus Forensic Match Probability for Subdivided Populations

A two-locus match probability is presented that incorporates the effects of within-subpopulation inbreeding (consanguinity) in addition to population subdivision. The usual practice of calculating multi-locus match probabilities as the product of single-locus probabilities assumes independence between loci. There are a number of population genetics phenomena that can violate this assumption: in addition to consanguinity, which increases homozygosity at all loci simultaneously, gametic disequilibrium will introduce dependence into DNA profiles. However, in forensics the latter problem is usually addressed in part by the careful choice of unlinked loci. Hence, as is conventional, we assume gametic equilibrium here, and focus instead on between-locus dependence due to consanguinity. The resulting match probability formulae are an extension of existing methods in the literature, and are shown to be more conservative than these methods in the case of double homozygote matches. For two-locus profiles involving one or more heterozygous genotypes, results are similar to, or smaller than, the existing approaches. This revised version was published online in August 2006 with corrections to the Cover Date.     

Estimating sex-specific dispersal rates with autosomal markers in hierarchically structured populations

Abstract –A recent study suggests that sex-specific dispersal rates can be quantitatively estimated on the basis of sex- and state-specific (pre- vs. postdispersal) F -statistics. In the present paper, we extend this approach to account for the hierarchical structure of natural populations, and we validate it through individual-based simulations. The model is applied to an empirical data set consisting of 536 individuals (males, females, and predispersal juveniles) of greater white-toothed shrews ( Crocidura russula ), sampled according to a hierarchical design and typed for seven autosomal microsatellite loci. From this dataset, dispersal is significantly female biased at the local scale (breeding-group level), but not at the larger scale (among local populations). We argue that selective pressures on dispersal are likely to depend on the spatial scale considered, and that short-distance dispersal should mainly respond to kin interactions (inbreeding or kin competition avoidance), which exert differential pressure on males and females.     

Assessing priorities for conservation in Tuscan cattle breeds using microsatellites

Preservation of rare genetic stocks requires assessment of within-population genetic diversity and between-population differentiation to make inferences on their degree of uniqueness. A total of 194 Tuscan cattle (44 Calvana, 35 Chianina, 25 Garfagnina, 31 Maremmana, 31 Mucca Pisana and 28 Pontremolese) individuals were genotyped for 34 microsatellite markers. Moreover, 56 samples belonging to Argentinean Creole and Asturiana de la Montaña cattle breeds were used as an outgroup. Genetic diversity was quantified in terms of molecular coancestry and allelic richness. STRUCTURE analyses showed that the Tuscan breeds have well-differentiated genetic backgrounds, except for the Calvana and Chianina breeds, which share the same genetic ancestry. The between-breed Nei's minimum distance (D_m) matrices showed that the pair Calvana–Chianina was less differentiated (0.049 ± 0.006). The endangered Tuscan breeds (Calvana, Garfagnina, Mucca Pisana and Pontremolese) made null or negative contributions to diversity, except for the Mucca Pisana contribution to allelic richness (C_T = 1.8%). The Calvana breed made null or negative within-breed contributions (f¯_W = 0.0%; C_W = −0.4%). The Garfagnina and Pontremolese breeds made positive contributions to between-breed diversity but negative and high within-breed contributions, thus suggesting population bottleneck with allelic losses and increase of homozygosity in the population. Exclusion of the four endangered Tuscan cattle breeds did not result in losses in genetic diversity (f¯_T = −0.7%; C_T = −1.2%), whereas exclusion of the non-endangered breeds (Chianina and Maremmana) did (f¯_T = 2.1%; C_T = 3.9%); the simple exclusion of the Calvana breed from the former group led to losses in genetic diversity (f¯_T = 0.47%; C_T = 2.34%), indicating a diverse significance for this breed. We showed how quantifying both within-population diversity and between-population differentiation in terms of allelic frequencies and allelic richness provides different and complementary information on the genetic backgrounds assessed and may help to implement priorities and strategies for conservation in livestock.     

Estimation of coancestry in Iberian pigs using molecular markers

Genetic markers provide a useful tool toestimate pairwise coancestry betweenindividuals in the absence of a known pedigree. Inthe present work 62 pigs from two relatedstrains of Iberian breed, Guadyerbas andTorbiscal, belonging to a conservationprogramme with completely known pedigrees since1945, have been genotyped for 49microsatellites. Four coefficients thatsummarise molecular resemblance betweenindividuals together with eightestimators of coancestry have been calculatedfrom this information. Their values werecompared with the genealogical coancestry,calculated from the complete or partialpedigree. The eight estimations obtained usingmolecular information substantiallyunderestimate the coancestry calculated usingthe genealogical analysis. The correlationbetween the estimates and the genealogicalvalues was also calculated. This correlationwas high, between 0.78 and 0.93 for differentestimators, when all pairwise comparisons amongthe 62 animals were considered. However, thecorrelation decreases remarkably to 0.49–0.69and 0.37–0.47 for the Guadyerbas and Torbiscalpopulations respectively, when they wereanalysed separately. All the correlations weresimilar to those obtained when using simplecoefficients of molecular resemblance such asmolecular coancestry or similarity indexes.Finally, simulations were carried out tofurther explore the results obtained. It isconcluded that lack of information on theallele frequencies in the base population mayexplain the bias of these estimators inpopulations with complex pedigrees.     

广东省汉族人群的亚群分析

为调查广东地区汉族人群中是否存在着亚群结构,对来自广州、佛山、东莞、江门和中山-珠海5个不同地区的471随机个体血样本进行15个STR的基因分型,并作Hardy-Weinberg平衡检验,比较群体之间的等位基因频率,计算这个5个地区人群间的共祖系数。结果显示,广东汉族人群没有明显的Hardy-Weinberg不平衡,5个地区人群的等位基因分布均没有差异,他们之间的共祖系数小于0.01。因此,广东地区汉族人群中没有明显的亚群结构。 Abstract:To investigate the subpopulation structure within the Han Population in Guandong area,a total of 471 DNA samples from five populations in Guandong Province,including Guangzhou,Foshan,Dongguan,Jiangmen and Zhongshan-Zhuhai region,were genotyped at 15 STR(short tandem repeats) markers.Hardy-Weinberg tests were performed,allele frequencies were compared,and the genetic coancestry coefficient(FST ) was estimated.The results did not show significant departure from Hardy-Weinberg equilibrium in the total population.Difference of allele frequencies among these populations was not observed,and the coancestry coefficient(FST)was less than 0.01.Subpopulation structure within Han Population in Guandong Province could not be detected.     

Pedigree analysis and inbreeding effects over morphological traits in Campolina horse population

Genetic improvement, without control of inbreeding, can go to loss of genetic variability, reducing the potential for genetic gains in the domestic populations. The aim of this study was to analyze the population structure and the inbreeding depression in Campolina horses. Phenotype information from 43 465 individuals was analyzed, data provided by the Campolina Breeders Association. A pedigree file containing 107 951 horses was used to connected the phenotyped individuals. The inbreeding coefficient was performed by use of the diagonal of the relationship matrix and the genealogical parameters were computed using proper softwares. The effective population size was estimated based on the rate of inbreeding and census information, and the stratification of the population was verified by the average relationship coefficient between animals born in different regions of Brazil. The effects of inbreeding on morphological traits were made by the use of inbreeding coefficient as a covariate in the model of random regression. The inbreeding coefficient increased from 1990 on, impacting effective population size and, consequently, shrinking genetic variability. The paternal inbreeding was greater than maternal, which may be attributed to the preference for inbred animals in reproduction. The average genetic relationship coefficient of animals born in different states was lower than individuals born within the same state. The increase in the inbreeding coefficient was negatively associated with all studied traits, showing the importance to avoid genetic losses in the long term. Although results do not indicate a severe narrowing of the population until the present date, the average relationship coefficient shows signs of increase, which could cause a drastic reduction in genetic variability if inbred mating is not successfully controlled in the Campolina horse population.     

How Pronghorn Females Avoid Inbreeding Depression

After a bottleneck in a closed population of pronghorn (Antilocapra americana), some inbred matings occurred, and we detected significant inbreeding depression. But inbred matings occurred less frequently than would be expected by chance. Pronghorn females chose mates after a sampling period and had complete control of the mating decision. Therefore, to discover the behavioral mechanism by which females avoided mating with close kin, we studied female movements and courtship sequences. When females moved from one harem to another in the sampling process, they did not shift to harem males of lower coancestry as they approached estrus. Rather, females progressed more slowly through the later courtship stages when the harem male was related vs. unrelated. Also, the rates of male courtship acts were higher within unrelated vs. related pairs. Some females appeared to use multiple mating as an inbreeding avoidance strategy. Our results suggested that inbreeding avoidance by female pronghorn occurred primarily by reactions to the late stages of male courtship, rather than by spatial avoidance of related males.     

Molecular characterization and genetic structure of the Nero Siciliano pig breed

Nero Siciliano is an autochthonous pig breed that is reared mainly in semi-extensive systems in northeastern Sicily. Despite its economic importance and well-appreciated meat products, this breed is currently endangered. Consequently, an analysis of intra-breed variability is a fundamental step in preserving this genetic resource and its breeding system. In this work, we used 25 microsatellite markers to examine the genetic composition of 147 unrelated Nero Siciliano pigs. The total number of alleles detected (249, 9.96 per locus) and the expected heterozygosity (0.708) indicated that this breed had a high level of genetic variability. Bayesian cluster analysis showed that the most likely number of groups into which the sample could be partitioned was nine. Based on the proportion of each individuals genome derived from ancestry, pigs with at least 70% of their genome belonging to one cluster were assigned to that cluster. The cluster size ranged from 7 to 17 (n = 108). Genetic variability in this sub-population was slightly lower than in the whole sample, genetic differentiation among clusters was moderate (F(ST) 0.125) and the F(IS) value was 0.011. NeighborNet and correspondence analysis revealed two clusters as the most divergent. Molecular coancestry analysis confirmed the good within-breed variability and highlighted the clusters that retained the highest genetic diversity.     

Do surface plant and soil seed bank populations differ genetically? a multipopulation study of the desert mustard Lesquerella fendleri (Brassicaceae)

Seed banks are an important component of many plant populations, but few empirical studies have investigated the genetic relationship between soil seeds and surface plants. We compared the genetic structure of soil seeds and surface plants of the desert mustard Lesquerella fendleri within and among five ecologically diverse populations at the Sevilleta National Wildlife Refuge in Central New Mexico. At each site, 40 Lesquerella surface plants and 40 samples of soil seeds were mapped and genetically analyzed using starch gel electrophoresis. Overall allele frequencies of soil seeds and surface plants showed significant differences across the five populations and within three of the five individual populations. Surface plants had significantly greater amounts of single and multilocus heterozygosity, and mean surface plant heterozygosity was also greater at the total population level and in four of the five individual populations. Overall soil seed (bot not surface plant) homozygosity was significantly greater than predicted by Hardy-Weinberg expectations at the total and individual population levels. Although F-alpha estimates revealed similarly small but significant genetic divergence within each life-history stage, estimates of coancestry showed that fine-scale (0.5-2 m) genetic correlations among the surface plant genotypes were roughly twice those of soil seed genotypes. An unweighted pair group method with arithrnetic mean cluster analysis indicated that in the two geographically closest sites, the surface plants were slightly more genetically similar to each other than to their own respective seed banks. We also found weak and/or negative demographic associations between Lesquerella soil seed and surface plant densities within each of the five sites. We discuss the difficulties involved with sampling and genetically comparing these two life-history stages.     

Reduction of inbreeding in commercial females by rotational mating with several sire lines

A mating system to reduce the inbreeding of commercial females in the lower level was examined theoretically, assuming a hierarchical breed structure, in which favorable genes are accumulated in the upper level by artificial selection and the achieved genetic progress is transferred to the lower level through migration of males. The mating system examined was rotational mating with several closed sire lines in the upper level. Using the group coancestry theory, we derived recurrence equations for the inbreeding coefficient of the commercial females. The asymptotic inbreeding coefficient was also derived. Numerical computations showed that the critical factor for determining the inbreeding is the number of sire lines, and that the size of each sire line has a marginal effect. If four or five sire lines were available, rotational mating was found to be quite an effective system to reduce the short- and long-term inbreeding of the commercial females, irrespective of the effective size of each sire line. Oscillation of the inbreeding coefficient under rotational mating with initially related sire lines could be minimized by avoiding the consecutive use of highly related lines. Extensions and perspectives of the system are discussed in relation to practical application.