Distribution Of Heterozygosity Research Articles

Extensive hybridization and past introgression between divergent lineages in a quasi-clonal hermaphroditic fish: Ramifications for species concepts and taxonomy.

Extreme inbreeding is expected to reduce the incidence of hybridization, serving as a prezygotic barrier. Mangrove rivulus is a small killifish that reproduces predominantly by self-fertilization, producing highly homozygous lines throughout its geographic range. The Bahamas and Caribbean are inhabited by two highly diverged phylogeographic lineages of mangrove rivulus, Kryptolebias marmoratus and a 'Central clade' closely related to K.hermaphroditus from Brazil. The two lineages are largely allopatric, but recently were found in syntopy on San Salvador, Bahamas, where a single hybrid was reported. To better characterize the degree of hybridization and the possibility of secondary introgression, here we conducted a detailed genetic analysis of the contact zone on San Salvador. Two mixed populations were identified, one of which contained sexually mature hybrids. The distribution of heterozygosity at diagnostic microsatellite loci in hybrids showed that one of these hybrids was an immediate offspring from the K.marmoratus x Central clade cross, whereas the remaining five hybrids were products of reproduction by self-fertilization for 1-3 generations following the initial cross. Two hybrids had mitochondrial haplotypes of K.marmoratus and the remaining four hybrids had a haplotype of the Central clade, indicating that crosses go in both directions. In hybrids, alleles of parental lineages were represented in equal proportions suggesting lack of recent backcrossing to either of the parental lineages. However, sympatric populations of two lineages were less diverged than allopatric populations, consistent with introgression. Results are discussed in terms of applicability of the biological species concept for isogenic, effectively clonal, organisms.

Analysis of the hybrid genomes of two field isolates of the soil-borne fungal species Verticillium longisporum

BackgroundBrassica plant species are attacked by a number of pathogens; among them, the ones with a soil-borne lifestyle have become increasingly important. Verticillium stem stripe caused by Verticillium longisporum is one example. This fungal species is thought to be of a hybrid origin, having a genome composed of combinations of lineages denominated A and D. In this study we report the draft genomes of 2 V. longisporum field isolates sequenced using the Illumina technology. Genomic characterization and lineage composition, followed by selected gene analysis to facilitate the comprehension of its genomic features and potential effector categories were performed.ResultsThe draft genomes of 2 Verticillium longisporum single spore isolates (VL1 and VL2) have an estimated ungapped size of about 70 Mb. The total number of protein encoding genes identified in VL1 was 20,793, whereas 21,072 gene models were predicted in VL2. The predicted genome size, gene contents, including the gene families coding for carbohydrate active enzymes were almost double the numbers found in V. dahliae and V. albo-atrum. Single nucleotide polymorphisms (SNPs) were frequently distributed in the two genomes but the distribution of heterozygosity and depth was not independent. Further analysis of potential parental lineages suggests that the V. longisporum genome is composed of two parts, A1 and D1, where A1 is more ancient than the parental lineage genome D1, the latter being more closer related to V. dahliae. Presence of the mating-type genes MAT1–1-1 and MAT1–2-1 in the V. longisporum genomes were confirmed. However, the MAT genes in V. dahliae, V. albo-atrum and V. longisporum have experienced extensive nucleotide changes at least partly explaining the present asexual nature of these fungal species.ConclusionsThe established draft genome of V. longisporum is comparatively large compared to other studied ascomycete fungi. Consequently, high numbers of genes were predicted in the two V. longisporum genomes, among them many secreted proteins and carbohydrate active enzyme (CAZy) encoding genes. The genome is composed of two parts, where one lineage is more ancient than the part being more closely related to V. dahliae. Dissimilar mating-type sequences were identified indicating possible ancient hybridization events.

Viability selection creates negative heterozygosity\u2013fitness correlations in female Black Grouse Lyrurus tetrix

There is widespread interest in the relationship between individual genetic diversity and fitness–related traits (heterozygosity–fitness correlations; HFCs). Most studies have found weak continuous increases of fitness with increasing heterozygosity, while negative HFCs have rarely been reported. Negative HFCs are expected in cases of outbreeding depression, but outbreeding is rare in natural populations. Negative HFCs may also arise through viability selection acting on low heterozygosity individuals at an early stage producing a skew in the heterozygosity distribution. We tested this idea using survival and clutch parameters (egg mass, egg volume, chick mass, clutch size) in female Black Grouse Lyrurus tetrix and carried out simulations to determine how survival selection may impact the HFCs measured using clutch parameters. We show that survival is positively related to both individual heterozygosity and female body mass. There was a positive effect of body mass on all clutch parameters, but the selective mortality of females with both low heterozygosity and low body mass led to overrepresentation of high heterozygosity-low body mass females and hence a negative relationship between egg volume and heterozygosity. Using simulated data, we show that survival selection acting on both low body mass and low heterozygosity leads to a skew in the quality of breeding females, resulting in negative HFCs with egg volume. Our results indicate that survival selection can strongly influence the strength and direction of any HFCs that occur later in life and that only an integration of all aspects of individual reproductive investment and reproductive success can enable us to fully understand how heterozygosity can shape individual fitness.

Detecting natural hybridization between two vulnerable Andean pupfishes (Orestias agassizii and O. luteus) representative of the Altiplano endemic fisheries

The detection of hybridization among freshwater fish species is of main concern for conservation programs and fish farming. We assessed the incidence of natural hybridization between two vulnerable species of Andean pupfishes (Cyprinodontidae; Orestias agassizii and O. luteus) that represent an important component of local fisheries. We combined mitochondrial and nuclear DNA sequencing, microsatellites genotyping and morphometrics to characterize hybridization patterns between the two species in lakes Titicaca and Uru Uru (N = 175). The clustering analysis of 10 microsatellite loci together with heterozygosity distribution at seven species-specific diagnostic sites in rhodopsin (nuclear DNA) proved to be a robust diagnostic tool to detect F1 and potential backcross hybrids. For the first time on a genetic basis, we confirmed the incidence of natural hybridization between the two Andean pupfishes, at frequency rates reaching almost 10 %. The morphological intermediacy criterion (relative to parental species) did not apply in hybrids, since the latter (i) deviated through their larger caudal peduncle height, and (ii) had greater, overlapping ranges in their morphometric ratios. Although viable F1 and F2 hybrids between O. agassizii and O. luteus had been reported under controlled conditions, the ecological and/or demographic factors facilitating interspecific gene flow in the wild remain speculative. We recommend that regional fish farming and restocking programs targeting O. agassizii and O. luteus call on the genetic diagnosis of hybrids to avoid the potentially deleterious impacts of releasing hybrid populations in the wild.

Analysis of distributions of single-locus heterozygosity as a test of neutral theory

SummaryThree tests of neutral theory were carried out using a large dataset of vertebrate allozyme studies. The first test considered the relationship between the mean and variance of single locus heterozygosity across a sample of enzymes and non-enzymatic proteins. The second test compared the distributions of heterozygosity between paired proteins in balanced datasets in which each protein is scored for the same sample of species. The third test compared the observed distribution of single locus heterozygosity with theoretical distributions predicted by neutral theory. The results show an excellent quantitative fit with the predictions of neutral theory, though some small deviations from neutrality were observed which are consistent with the action of natural selection.

The distribution of heterozygosity in template and tropical species of Drosophila.

SUMMARYElectrophoretic surveys for nine species ofDrosophilahave been summarized in terms of the relative contribution to heterozygosity of each of ten gene frequency classes, the mean frequency of heterozygotes within subpopulations, and the degree of genetic divergence between subpopulations. It has been shown that the neutral model proposed by Kimura, and modified by Ohta to include the accumulation of slightly disadvantageous mutations, is capable of explaining all features of the data. The consistent difference between group I and group II enzymes can be explained by a difference in the average intensity of selection against mutational variants in the two groups. A highly significant difference between the temperate and tropical species in the distribution of heterozygosity appears to be due to the smaller effective breeding population sizes in the case of the temperate species.

STATISTICAL STUDIES ON PROTEIN POLYMORPHISM IN NATURAL POPULATIONS II. GENE DIFFERENTIATION BETWEEN POPULATIONS

With the aim of testing the validity of the mutation-drift hypothesis, we examined the pattern of genetic differentiation between populations by using data from Drosophila, fishes, reptiles, and mammals. The observed relationship between genetic identity and correlation of heterozygosities of different populations or species was generally in good agreement with the theoretical expectations from the mutation-drift theory, when the variation in mutation rate among loci was taken into account. In some species of Drosophila, however, the correlation was unduly high. The relationship between the mean and variance of genetic distance was also in good agreement with the theoretical prediction in almost all organisms. We noted that both the distribution of heterozygosity within species and the pattern of genetic differentiation between species can be explained by the same set of genetic parameters in each group of organisms. Alternative hypotheses for explaining these observations are discussed.

Simulation results with stepwise mutation model and their interpretations.

Monte Carlo simulations are performed to compare the predictions based on the two presently used theoretical models for studying genetic variations in natural populations, the infinite allele model and the stepwise mutation model. Distribution of heterozygosity is noticed to be similar under these models until the product of population size and mutation rate is large. It is seen that electromorphs with high population frequency usually contain older allels (at the codon level) than an electromorph of low population frequency. The interpretations of these results in explaining the allelic variations at electrophoretic level is also discussed.

Genetic Variation and Cultural Evolution

The breakdown of isolation between groups is theoretically expected to increase the amount of variation within groups. One measure of the in-group variation is the frequency of heterozygosity; this should increase in accordance with the evolution of culture. Concurrently, the variation between groups should diminish. A survey of mean AB, MN, and Cc heterozygosity is undertaken on 252 ethnic groups. Each is classified by level of socio-cultural integration: band, tribe, chiefdom, and state. The geographical distribution of the variables is mapped. Individual ethnic groups are organized into thirteen regions (heterographic areas) which provide reasonably independent tests of the hypothesis in question. Mean blood group heterozygosity for the three loci investigated is 32.47%±0.59 among states as compared to 24.86%±0.49 among primitive societies. The difference (7.61%) is highly significant. Furthermore, in-group heterozygosity increases with each stage of social evolution. The variance between groups diminishes consecutively. It is concluded that the distribution of heterozygosity is strongly dependent upon cultural evolution. Primitive societies are genetically more homogeneous. Empiric evidence supports the Law of Biocultural Evolution. Multiple factor traits would be expected to show an analogous pattern. In contrast to man in general, human paleontologists should find primitive societies to provide closer models of the in-group and between-group variance of fossil hominids. The role of biocultural evolution toward maintaining and increasing human variation is discussed.

Letter to the editor: Analysis of heterozygosity in regard to the neutrality theory of protein polymorphism.

In conjunction with a theoretical calculation, a distribution of heterozygosity (more precisely, 2x(1 − x), where x is the allele frequency) was examined with special reference to the neutrality hypothesis of protein polymorphisms. Data of some 400 polymorphic proteins collectively are consistent with the theoretical expectation based on the neutrality hypothesis, although other possibilities are not ruled out.

The effects of heterozygosity changes on viability in Drosophila melanogaster.

The viability effects of chromosomes from an old and from a new laboratory strain of D. melanogaster were studied in eight factorial combinations and at two heterozygosity levels. The combinations were so constructed that heterozygosity level could be varied in the third chromosomes of the carriers of a homozygous lethal marker, in the third chromosomes of their wild-type segregants, and in the genetic backgrounds of both. Excluding the effect of the marker and the exceptional outcomes of two of the combinations, and taking into account both large and small deviations from theoretical expectation, the following summary is given as the simplest consistent explanation of the results: 1) If total heterozygosities of two segregant types tend toward equality their viabilities tend toward equality also, whether background heterozygosity is high or low; if background heterozygosities is higher the tendency toward equality is slightly greater. 2) If total heterozygosity of two segregant types are unequal the less heterozygous type has the lower viability; the difference is more pronounced when background heterozygosity is low, less when it is high. 3) Differences between segregant viabilities are correlated with differences between the total heterozygosities of the two segregants; genetic background is effective to the extent, and only to the extent, that it contributes to the magnitude of this difference. This in turn appears to underlie, at least partly, the expression of a pronounced interchromosomal epistasis. Thus in this study viability is seen to depend upon both the quantity and distribution of heterozygosity, not only among the chromosomes of an individual but among the individuals of a given combination as well.