Patterns Of Inbreeding Research Articles

Runs of homozygosity reveal contrasting histories of inbreeding across global lineages of the edible porcini mushroom, Boletus edulis.

Inbreeding, the mating of individuals that are related through common ancestry, is of central importance in evolutionary and conservation biology due to its impacts on individual fitness and population dynamics. However, while advanced genomic approaches have revolutionised the study of inbreeding in animals, genomic studies of inbreeding are rare in plants and lacking in fungi. We investigated global patterns of inbreeding in the prized edible porcini mushroom Boletus edulis using 225 whole genomes from seven lineages distributed across the northern hemisphere. Genomic inbreeding was quantified using runs of homozygosity (ROHs). We found appreciable variation both among and within lineages, with some individuals having over 20% of their genomes in ROHs. Much of this variation could be explained by a combination of elevation and latitude, and to a lesser extent by predicted habitat suitability during the last glacial maximum. In line with this, the majority of ROHs were short, reflecting ancient common ancestry dating back approximately 200-1700 generations ago, while longer ROHs indicative of recent common ancestry (less than approximately 50 generations ago) were infrequent. Our study reveals the inbreeding legacy of major climatic events in a widely distributed forest mutualist, aligning with prevailing theories and empirical studies of the impacts of historical glaciation events on the dominant forest tree species of the northern hemisphere.

Differences in the genomic diversity, structure and inbreeding patterns in wild and managed populations of Agave potatorum used in the production of Tobalá mezcal in Southern México.

Differences in the genomic diversity, structure and inbreeding patterns in wild and managed populations of Agave potatorum used in the production of Tobalá mezcal in Southern México.

Unraveling inbreeding patterns and selection signals in Alpine Grey cattle

Inbreeding plays a crucial role in livestock breeding, influencing genetic diversity and phenotypic traits. Genomic data have helped address limitations posed by incomplete pedigrees, providing deeper insights into breed genetic diversity. This study assesses inbreeding levels via pedigree and genomic approaches and analyzes old and recent inbreeding using runs of homozygosity (ROH), and selection signals in Alpine Grey cattle. Pedigree data from 165 575 individuals, analyzed with INBUPGF90 software, computed inbreeding coefficients. Genomic-based coefficients derived from PLINK v1.9. or DetectRUNS R package analyses of 1 180 individuals’ genotypes. Common single nucleotide polymorphisms within ROH pinpointed genomic regions, aggregating into “ROH islands” indicative of selection pressure. Overlaps with USCS Genome Browser unveiled gene presence. Moderate correlations (0.20–0.54) existed between pedigree and genomic coefficients, with most genomic estimators having higher (>0.8) correlation values. Inbreeding averaged 0.04 in < 8 Mb ROH segments, and 0.03 in > 16 Mb segments; > 90% of ROHs were < 8 Mb, indicating ancient inbreeding prevalence. Recent inbreeding proved less detrimental than in cosmopolitan breeds. Two major ROH islands on chromosomes 6 and 7 harbored genes linked to immune response, disease resistance (PYURF, HERC3), and fertility (EIF4EBP3, SRA1). This study underscores the need for detailed inbreeding analyses to understand genetic characteristics and historical changes in local breeds like Alpine Grey cattle. Genomic insights, especially from ROH, facilitated overcoming pedigree limitations, illuminating breed genetic diversity. Our findings reveal ancient inbreeding's enduring genetic impact and ROH islands potential for selective sweeps, elucidating traits in Alpine Grey cattle.

Population genomic data reveal low genetic diversity, divergence and local adaptation among threatened Reeves's Pheasant (Syrmaticus reevesii)

Population genomic data could provide valuable information for conservation efforts; however, limited studies have been conducted to investigate the genetic status of threatened pheasants. Reeves's Pheasant (Syrmaticus reevesii) is facing population decline, attributed to increases in habitat loss. There is a knowledge gap in understanding the genomic status and genetic basis underlying the local adaptation of this threatened bird. Here, we used population genomic data to assess population structure, genetic diversity, inbreeding patterns, and genetic divergence. Furthermore, we identified candidate genes linked with adaptation across the current distribution of Reeves's Pheasant. The present study assembled the first de novo genome sequence of Reeves's Pheasant and annotated 19,458 genes. We also sequenced 30 individuals from three populations (Dabie Mountain, Shennongjia, Qinling Mountain) and found that there was clear population structure among those populations. By comparing with other threatened species, we found that Reeves's Pheasants have low genetic diversity. Runs of homozygosity suggest that the Shennongjia population has experienced serious inbreeding. The demographic history results indicated that three populations experienced several declines during the glacial period. Local adaptative analysis among the populations identified 241 candidate genes under directional selection. They are involved in a large variety of processes, including the immune response and pigmentation. Our results suggest that the three populations should be considered as three different conservation units. The current study provides genetic evidence for conserving the threatened Reeves's Pheasant and provides genomic resources for global biodiversity management.

Differences in the genomic diversity, structure, and inbreeding patterns in wild and managed populations of Agave potatorum Zucc. used in the production of Tobalá mezcal in Southern Mexico.

Agave potatorum Zucc. locally known as Tobalá, is an important species for mezcal production. It is a perennial species that takes 10 to 15 years to reach reproductive age. Because of high demand of Tobalá mezcal and the slow maturation of the plants, its wild populations have been under intense anthropogenic pressure. The main objective of this study was to estimate the genome-wide diversity in A. potatorum and determine if the type of management has had any effect on its diversity, inbreeding and structure. We analyzed 174 individuals (105 wild, 42 cultivated and 27 from nurseries) from 34 sites with a reduced representation genomic method (ddRADseq), using 14,875 SNPs. The diversity measured as expected heterozygosity was higher in the nursery and wild plants than in cultivated samples. We did not find private alleles in the cultivated and nursery plants, which indicates that the individuals under management recently derived from wild populations, which was supported by higher gene flow estimated from wild populations to the managed plants. We found low but positive levels of inbreeding (FIS = 0.082), probably related to isolation of the populations. We detected low genetic differentiation among populations (FST = 0.0796), with positive and significant isolation by distance. The population genetic structure in the species seems to be related to elevation and ecology, with higher gene flow among populations in less fragmented areas. We detected an outlier locus related to the recognition of pollen, which is also relevant to self-incompatibility protein (SI). Due to seed harvest and long generation time, the loss of diversity in A. potatorum has been gradual and artificial selection and incipient management have not yet caused drastic differences between cultivated and wild plants. Also, we described an agroecological alternative to the uncontrolled extraction of wild individuals.

Outlining inbreeding in the Brazilian higher education system

AbstractThis study describes characteristics of academic inbreeding in the Brazilian higher education system. Results show the rate of inbreeding significantly differs among distinct types of institutions, fields of knowledge, states and university ranking tiers. According to this study, inbreeding is most likely to be found in established elite research institutions, concentrated in the Southeast of Brazil, in the STEM fields. These also happen to be the main providers and most prestigious consumers of the well‐trained local academic workforce, supporting the conclusion that both internal and external factors could be influencing the high concentration of inbred scholars at prominent alma maters. It contributes to international literature by evaluating the role of individual characteristics and by showing how the expansion of higher education to more geographically distant areas may establish different patterns of inbreeding.

Non-random mating within an Island rookery of Hawaiian hawksbill turtles: demographic discontinuity at a small coastline scale.

Hawksbill sea turtles (Eretmochelys imbricata) from the Hawaiian archipelago form a small and genetically isolated population, consisting of only a few tens of individuals breeding annually. Most females nest on the island of Hawai'i, but little is known about the demographics of this rookery. This study used genetic relatedness, inferred from 135 microhaplotype markers, to determine breeding sex-ratios, estimate female nesting frequency and assess relationships between individuals nesting on different beaches. Samples were collected during the 2017 nesting season and final data included 13 nesting females and 1002 unhatched embryos, salvaged from 41 nests, of which 13 had no observed mother. Results show that most females used a single nesting beach laying 1-5 nests each. From female and offspring alleles, the paternal genotypes of 12 breeding males were reconstructed and many showed high relatedness to their mates. Pairwise relatedness of offspring revealed one instance of polygyny but otherwise suggested a 1 : 1 breeding-sex ratio. Relatedness analysis and spatial-autocorrelation of genotypes indicate that turtles from different nesting areas do not regularly interbreed, suggesting that strong natal homing tendencies in both sexes result in non-random mating across the study area. Complexes of nearby nesting beaches also showed unique patterns of inbreeding across loci, further indicating that Hawaiian hawksbill turtles have demographically discontinuous nesting populations separated by only tens of km.

Genomic signatures of inbreeding depression for a threatened Aotearoa New Zealand passerine.

For small and isolated populations, the increased chance of mating between related individuals can result in a substantial reduction in individual and population fitness. Despite the increasing availability of genomic data to measure inbreeding accurately across the genome, inbreeding depression studies for threatened species are still scarce due to the difficulty of measuring fitness in the wild. Here, we investigate inbreeding and inbreeding depression for the extensively monitored Tiritiri Mātangi island population of a threatened Aotearoa New Zealand passerine, the hihi (Notiomystis cincta). First, using a custom 45 k single nucleotide polymorphism (SNP) array, we explore genomic inbreeding patterns by inferring homozygous segments across the genome. Although all individuals have similar levels of ancient inbreeding, highly inbred individuals are affected by recent inbreeding, which can probably be explained by bottleneck effects such as habitat loss after European arrival and their translocation to the island in the 1990s. Second, we investigate genomic inbreeding effects on fitness, measured as lifetime reproductive success, and its three components, juvenile survival, adult annual survival and annual reproductive success, in 363 hihi. We find that global inbreeding significantly affects juvenile survival but none of the remaining fitness traits. Finally, we employ a genome-wide association approach to test the locus-specific effects of inbreeding on fitness, and identify 13 SNPs significantly associated with lifetime reproductive success. Our findings suggest that inbreeding depression does impact hihi, but at different genomic scales for different traits, and that purging has therefore failed to remove all variants with deleterious effects from this population of conservation concern.

Using non-destructive sampling to evaluate the population genomic status of captive Brown Eared Pheasants

Evaluating the genetic status of threatened species is an essential task in conservation genetics. However, the genetic status of threatened species has been mostly evaluated through techniques that fail to estimate genetic diversity at the whole genomic level. Next generation sequencing can meet this demand, but high quality samples such as blood or muscle tissues are required. However, it is difficult to collect such samples from threatened species because sampling work may impact their health. Therefore, it is essential to design a workflow to evaluate the whole genomic status of threatened species using non-destructive sampling. Even though non-destructive sampling has been used in traditional barcoding technique, the barcoding technique cannot evaluate the whole genomic status. Brown Eared Pheasant (Crossoptilon mantchuricum) is an endangered species, with captive populations maintained in Taiyuan Zoo, China, and Europe. However, the genetic diversity, inbreeding pattern, and mutation load of these two populations are unclear. To uncover the genetic status of these two captive populations, we applied 2b-RAD technology to evaluate the genomic status of these populations using feathers as samples. The feathers could be collected by non-destructive sampling. The results indicate that the Taiyuan Zoo population has a lower genetic diversity and higher inbreeding coefficient than the European population. The Taiyuan Zoo population has lethal mutations when homozygous. The current project uses a non-destructive sampling technique to evaluate the whole genomic status of the two captive populations, providing a paradigm for conservation genetics, which will facilitate the development of conservation biology.

Genomic consequences of colonisation, migration and genetic drift in barn owl insular populations of the eastern Mediterranean.

The study of insular populations was key in the development of evolutionary theory. The successful colonisation of an island depends on the geographic context, and specific characteristics of the organism and the island, but also on stochastic processes. As a result, apparently identical islands may harbour populations with contrasting histories. Here, we use whole genome sequences of 65 barn owls to investigate the patterns of inbreeding and genetic diversity of insular populations in the eastern Mediterranean Sea. We focus on Crete and Cyprus, islands with similar size, climate and distance to mainland, that provide natural replicates for a comparative analysis of the impacts of microevolutionary processes on isolated populations. We show that barn owl populations from each island have a separate origin, Crete being genetically more similar to other Greek islands and mainland Greece, and Cyprus more similar to the Levant. Further, our data show that their respective demographic histories following colonisation were also distinct. On the one hand, Crete harbours a small population and maintains very low levels of gene flow with neighbouring populations. This has resulted in low genetic diversity, strong genetic drift, increased relatedness in the population and remote inbreeding. Cyprus, on the other hand, appears to maintain enough gene flow with the mainland to avoid such an outcome. Our study provides a comparative population genomic analysis of the effects of neutral processes on a classical island‐mainland model system. It provides empirical evidence for the role of stochastic processes in determining the fate of diverging isolated populations.

Body size, inbreeding, and lifespan in domestic dogs.

Inbreeding poses a real or potential threat to nearly every species of conservation concern. Inbreeding leads to loss of diversity at the individual level, which can cause inbreeding depression, and at the population level, which can hinder ability to respond to a changing environment. In closed populations such as endangered species and ex situ breeding programs, some degree of inbreeding is inevitable. It is therefore vital to understand how different patterns of breeding and inbreeding can affect fitness in real animals. Domestic dogs provide an excellent model, showing dramatic variation in degree of inbreeding and in lifespan, an important aspect of fitness that is known to be impacted by inbreeding in other species. There is a strong negative correlation between body size and lifespan in dogs, but it is unknown whether the higher rate of aging in large dogs is due to body size per se or some other factor associated with large size. We used dense genome-wide SNP array data to calculate average inbreeding for over 100 dog breeds based on autozygous segment length and found that large breeds tend to have higher coefficients of inbreeding than small breeds. We then used data from the Veterinary medical Database and other published sources to estimate life expectancies for pure and mixed breed dogs. When controlling for size, variation in inbreeding was not associated with life expectancy across breeds. When comparing mixed versus purebred dogs, however, mixed breed dogs lived about 1.2 years longer on average than size-matched purebred dogs. Furthermore, individual pedigree coefficients of inbreeding and lifespans for over 9000 golden retrievers showed that inbreeding does negatively impact lifespan at the individual level. Registration data from the American Kennel Club suggest that the molecular inbreeding patterns observed in purebred dogs result from specific breeding practices and/or founder effects and not the current population size. Our results suggest that recent inbreeding, as reflected in variation within a breed, is more likely to affect fitness than historic inbreeding, as reflected in variation among breeds. Our results also indicate that occasional outcrosses, as in mixed breed dogs, can have a substantial positive effect on fitness.

Demographic history and spatial genetic structure in a remnant population of the subtropical tree Anadenanthera colubrina var. cebil (Griseb.) Altschul (Fabaceae)

A remnant population of Anadenanthera colubrina var. cebil in Northern Argentina showed a mixed mating system, high genetic diversity, and moderate spatial genetic structure, which was stronger in saplings than in adults. Demographic history analyses revealed an ancient population expansion. Despite high genetic diversity, high inbreeding suggests caution in the use of this stand as seed source. Information on fine-scale spatial genetic structure (FSGS) and demographic history is essential to determine which mechanisms are responsible for population persistence and evolution. This is particularly important in fragmented biomes, such as the seasonally dry tropical forests. To assess the level of genetic diversity and population genetic structure in a remnant population of A. colubrina var. cebil, and to evaluate the influence of historical and contemporary environmental change on the genetic constitution of this population. Eight microsatellites were typed in 60 adults and 59 saplings. The existence of (non-spatial) genetic clusters was evaluated using STRUCTURE and PCAs. FSGS was evaluated by kinship analyses and sPCA. MCMCglmm models were used to provide insights into factors underlying FSGS. Demographic history was studied using bottleneck statistics and approximate Bayesian computation. We found high levels of genetic diversity and high inbreeding. Genetic structure was stronger in saplings than in adult trees, probably due to assortative mating, and was not explained by altitude or DBH. Demographic analyses suggested an ancient population expansion. Patterns of inbreeding and relatedness suggest a mixed mating system. High genetic diversity and moderate genetic structure suggest long-term population viability. High inbreeding suggests caution when using this stand as a source of material for reforestation.

Fine-Scale Resolution of Runs of Homozygosity Reveal Patterns of Inbreeding and Substantial Overlap with Recessive Disease Genotypes in Domestic Dogs

Inbreeding leaves distinct genomic traces, most notably long genomic tracts that are identical by descent and completely homozygous. These runs of homozygosity (ROH) can contribute to inbreeding depression if they contain deleterious variants that are fully or partially recessive. Several lines of evidence have been used to show that long (> 5 megabase) ROH are disproportionately likely to harbor deleterious variation, but the extent to which long vs. short tracts contribute to autozygosity at loci known to be deleterious and recessive has not been studied. In domestic dogs, nearly 200 mutations are known to cause recessive diseases, most of which can be efficiently assayed using SNP arrays. By examining genome-wide data from over 200,000 markers, including 150 recessive disease variants, we built high-resolution ROH density maps for nearly 2,500 dogs, recording ROH down to 500 kilobases. We observed over 678 homozygous deleterious recessive genotypes in the panel across 29 loci, 90% of which overlapped with ROH inferred by GERMLINE. Although most of these genotypes were contained in ROH over 5 Mb in length, 14% were contained in short (0.5 - 2.5 megabase) tracts, a significant enrichment compared to the genetic background, suggesting that even short tracts are useful for computing inbreeding metrics like the coefficient of inbreeding estimated from ROH (FROH). In our dataset, FROH differed significantly both within and among dog breeds. All breeds harbored some regions of reduced genetic diversity due to drift or selective sweeps, but the degree of inbreeding and the proportion of inbreeding caused by short vs. long tracts differed between breeds, reflecting their different population histories. Although only available for a few species, large genome-wide datasets including recessive disease variants hold particular promise not only for disentangling the genetic architecture of inbreeding depression, but also evaluating and improving upon current approaches for detecting ROH.

Pattern of inbreeding in thalassemia affected families resident in Tuman Leghari district Dera ghazi khan

The inbred marriages are highly acceptable in many populations of human beings but their prevalence and configuration vary depending on ethnicity, religious conviction, learning and socioeconomic circumstances of relevant population. Such social contracts are reported as the most important cause of enhancing the occurrence of the hereditary disorders by recessive autosomal, especially Thalassemia. The challenges of hereditary diseases trouble in the population calls for the progress of anticipation programs. But the implementations of different means require the information about types and prevalence of hereditary diseases and family system in population. This study focuses on inbred marriages and genetic diseases in the general population of Tuman Leghari resident in district D.G. Khan, Punjab, Pakistan. Ethnically the highest positive response was found in Saraiki (other than Baloch) 47.30% than Leghari (32.26%) or Khosa (20.44%). The Saraiki other than Baloch, Khosa and Leghari families were 47.30%, 32.26%, and 20.44% respectively. There was many differences found between the frequency of inbred and out bred marriages of total sample as well as within the ethnic groups, Leghari, and Khosa (X2=10.87 P

The Evolution of Consanguineous Marriages in the Archdiocese of Granada, Spain (1900-1979).

In the 20th century Spain maintained some of the highest rates of consanguineous marriage in Europe. In many regions these rates were still high in the 1950s and 1960s but then decreased rapidly, and by the 1970s a generalized transformation in mating patterns was under way. In the following decades the marriage of persons closely related by birth became rare. Consanguinity and inbreeding have been much studied in Spain but almost exclusively in the central and northern regions of the country. This is the first study of a whole large diocese in the southern region of Andalusia. This article is based on the analysis of 15,440 records of consanguineous unions registered between 1900 and 1979 in the Archbishopric of Granada in Andalusia. In this period, the rate of consanguinity up to second cousins was 5.51%, and the mean coefficient of inbreeding, α, was 2.04 × 10-3. There is a high range of variability within the research area: the rate of consanguinity was more than three times higher in rural areas (6.74%; α = 2.44 × 10-3) than in the capital city (2.03%; α = 0.93 × 10-3). There was a high frequency of unions between first cousins and first cousins once removed. These amounted to 35.3% and 13% of all consanguineous marriages, respectively, and contributed to 70% of α-values. Consanguinity here has been strongly related to local endogamy. Thus, 76% of all consanguineous couples were born in the same locality, and 89% resided in the same locality at marriage. By the end of the 1960s premarital migration increased and local endogamy started to decrease. On the other hand, inbreeding is inversely related to spatial endogamy. The more inbred couples, such as uncles-nieces (C12) or first cousins (C22), show significantly higher exogamy rates than second cousins (C33) and third cousins (C44), and higher rates of premarital migration. Neither males nor females in intrafamily unions seem to be significantly younger than those in nonconsanguineous unions. Considering their temporal evolution, consanguinity rates increased in the first third of the century, reaching a maximum in the late 1920s, when over 7.4% of all marriages were consanguineous (8.3% for the rural areas), and the resulting α-value was the highest of the century (α = 2.71 × 10-3 for the whole diocese; α = 3.00 × 10-3 for the rural areas). Rates of inbreeding remained high until the 1950s and decreased thereafter in a period of accelerated emigration to cities, urbanization, industrialization, and social modernization. Overall, levels of inbreeding are similar and sometimes larger than those found in dioceses in the northwest of Spain, although marriages between uncle and niece were less common. Some of the counties in the diocese had very high consanguinity levels, not only the isolated area of La Alpujarra, previously studied, but also other ecological and historical microregions (comarcas). These results indicate that the widely accepted north-south divisions of the Iberian Peninsula in terms of consanguinity and inbreeding patterns require considerable reevaluation.

Inbreeding in Southeastern Spain : The Impact of Geography and Demography on Marital Mobility and Marital Distance Patterns (1900-1969).

In this paper, the structure of a southeastern Spanish population was studied for the first time with respect to its inbreeding patterns and its relationship with demographic and geographic factors. Data on consanguineous marriages (up to second cousins) from 1900 to 1969 were taken from ecclesiastic dispensations. Our results confirm that the patterns and trends of inbreeding in the study area are consistent with those previously observed in most non-Cantabrian Spanish populations. The rate of consanguineous marriages was apparently stable between 1900 and 1935 and then sharply decreased since 1940, which coincides with industrialization in Spain. A marked departure from Hardy-Weinberg expectations (0.25) in the ratio of first cousin (M22) to second cousin (M33) marriages in the study population (0.88) was observed. The high levels of endogamy (>80%) and its significant steadiness throughout the twentieth century is noteworthy. Accordingly, our results show that exogamous marriages were not only poorly represented but also that this reduced mobility (<6km) suggests that the choice of a mate was preferentially local. We found higher mobility in M22 with respect to M33 cousin mating. The relationships between population size and consanguinity rates and inbreeding fit power-law distributions. A significant positive correlation was observed between inbreeding and elevation. Many Spanish populations have experienced a prolonged and considerable isolation across generations, which has led to high proportions of historical and local endogamy that is associated, in general, with high [Formula: see text] values. Thus, assessing genomic inbreeding using runs of homozygosity (ROH) in current Spanish populations could be an additional pertinent strategy for obtaining a more refined perspective regarding the population history inferred from the extent and frequency of ROH regions.

Intra-chromosomal estimates of inbreeding and coancestry in the Spanish Holstein cattle population

In recent years, inbreeding and coancestry are being estimated from genome-wide molecular information using a large number of SNPs. Molecular inbreeding and coancestry can be calculated for the whole genome or for particular regions of the genome. In this study, genome-based inbreeding and coancestry were estimated per chromosome and at intra-chromosomal level in a group of Holstein animals genotyped with the Illumina BovineSNP50 BeadChip. After applying filtering criteria, the genomic dataset included 36,693 autosomal SNPs and 10,569 animals. Genome-based inbreeding and coancestry at intra-chromosomal level were calculated using sliding windows of approximately 5Mb. The results showed differential patterns of inbreeding and coancestry on specific chromosome regions. These patterns provide a more detailed picture of genetic diversity that could be used, for example, for the detection of regions with low levels of genetic diversity that require a specific genetic management in conservation programmes.

Genetic diversity, sexual condition, and microhabitat preference determine mating patterns inSphagnum(Sphagnaceae) peat-mosses

In bryophytes, the possibility of intragametophytic selfing creates complex mating patterns that are not possible in seed plants, although relatively little is known about patterns of inbreeding in natural populations. In the peat-moss genus Sphagnum, taxa are generally bisexual (gametophytes produce both sperm and egg) or unisexual (gametes produced by separate male and female plants). We sampled populations of 14 species, aiming to assess inbreeding variation and inbreeding depression in sporophytes, and to evaluate correlations between sexual expression, mating systems, and microhabitat preferences. We sampled maternal gametophytes and their attached sporophytes at 12–19 microsatellite loci. Bisexual species exhibited higher levels of inbreeding than unisexual species but did generally engage in some outcrossing. Inbreeding depression did not appear to be common in either unisexual or bisexual species. Genetic diversity was higher in populations of unisexual species compared to populations of bisexual species. We found a significant association between species microhabitat preference and population genetic diversity: species preferring hummocks (high above water table) had populations with lower diversity than species inhabiting hollows (at the water table). We also found a significant interaction between sexual condition, microhabitat preference, and inbreeding coefficients, suggesting a vital role for species ecology in determining mating patterns in Sphagnum populations. © 2015 The Linnean Society of London, Biological Journal of the Linnean Society, 2015, 115, 96–113.

Genomic Patterns of Homozygosity in Worldwide Human Populations

Genome-wide patterns of homozygosity runs and their variation across individuals provide a valuable and often untapped resource for studying human genetic diversity and evolutionary history. Using genotype data at 577,489 autosomal SNPs, we employed a likelihood-based approach to identify runs of homozygosity (ROH) in 1,839 individuals representing 64 worldwide populations, classifying them by length into three classes-short, intermediate, and long-with a model-based clustering algorithm. For each class, the number and total length of ROH per individual show considerable variation across individuals and populations. The total lengths of short and intermediate ROH per individual increase with the distance of a population from East Africa, in agreement with similar patterns previously observed for locus-wise homozygosity and linkage disequilibrium. By contrast, total lengths of long ROH show large interindividual variations that probably reflect recent inbreeding patterns, with higher values occurring more often in populations with known high frequencies of consanguineous unions. Across the genome, distributions of ROH are not uniform, and they have distinctive continental patterns. ROH frequencies across the genome are correlated with local genomic variables such as recombination rate, as well as with signals ofrecent positive selection. In addition, long ROH are more frequent in genomic regions harboring genes associated with autosomal-dominant diseases than in regions not implicated in Mendelian diseases. These results provide insight into the way in which homozygosity patterns are produced, and they generate baseline homozygosity patterns that can be used to aid homozygosity mapping of genes associated with recessive diseases.

Temporal variation of allele frequencies in a natural population of wild Vigna unguiculata

Temporal variation in allele frequencies in a natural population of wild Vigna unguiculata was studied by making monthly collections of seeds over a two-year period. Using starch gel electrophoresis, four out of seven loci analysed were shown to be polymorphic (Enp, Fdh, Fle3 and Pgd2 ). These four loci showed significant variation in allele frequencies over time. Changes in population structure over time were analysed using F-statistic estimators. Although heterogeneity was evident between loci, the analysis showed significant differentiation among months within a year for all polymorphic loci. Fixation indexes were all positive and statistically different from zero, highlighting a significant departure from random mating. Using analysis of variance (ANOVA), the pattern of inbreeding (f) showed significant changes over time (season); among the polymorphic loci, Enp most strongly contributed to this significance. Significant correlations were found between allele frequencies at different loci. The monthly average gene diversity (He) and allele frequencies at the Enp locus were found to be significantly correlated with weather conditions (temperature and rainfall distribution). These allele frequency deviations over time can be attributed to changes in pollinator behaviour, and frequent genetic bottlenecks that are associated with changes in environmental conditions.