Allele frequency spectra in structured populations: Novel-allele probabilities under the labelled coalescent

ABSTRACTWe address the effect of population structure on key properties of the Ewens sampling formula. We use our previously-introduced inductive method for determining exact allele frequency spectrum (AFS) probabilities under the infinite-allele model of mutation and population structure for samples of arbitrary size. Fundamental to the sampling distribution is the novel-allele probability, the probability that given the pattern of variation in the present sample, the next gene sampled belongs to an as-yet-unobserved allelic class. Unlike the case for panmictic populations, the novel-allele probability depends on the AFS of the present sample. We derive a recursion that directly provides the marginal novel-allele probability across AFSs, obviating the need first to determine the probability of each AFS. Our explorations suggest that the marginal novel-allele probability tends to be greater for initial samples comprising fewer alleles and for sampling configurations in which the next-observed gene derives from a deme different from that of the majority of the present sample. Comparison to the efficient importance sampling proposals developed by De Iorio and Griffiths and colleagues indicates that their approximation for the novel-allele probability generally agrees with the true marginal, although it may tend to overestimate the marginal in cases in which the novel-allele probability is high and migration rates are low.

BOTTLENECK ANALYSIS OF ANATOLIAN BLACK CATTLE (BOS TAURUS) USING MICROSATELLITE MARKERS

The present study was conducted in order to reveal the genetic diversity andbottleneck in Anatolian Black Cattle (Bos Taurus). Animal material of the studyconsisted of 75 cattle raised in International Center for Livestock Research andTraining. The bottleneck in the cattle breed studied was checked with 10microsatellites markers, amplified in a multiplex polymerase chain reaction (PCR)were used according to recommendation of FAO (2011). A total of 116 alleles wasobserved from microsatellites studied. Overall value belongs to average number ofalleles (Na), effective number of alleles (Ne), observed heterozygosity (Ho),expected heterozygosity (He), the polymorphic information content (PIC), averageheterozygosity (Ĥ), and FIS, known as the inbreeding coefficient, were 11.60, 5.35,0.80, 0.78, 0.80 and 0.012, respectively. All microsatellite markers except INRA23and ETH3 deviated from Hardy Weinberg equilibrium (HWE). Bottleneck wasanalyzed with Bottleneck software according to three different mutation modelsincluding the infinite allele model (IAM), two-phase mutation model (TPM) andstepwise mutation model (SMM). It can be said that there is not any ultimate risk interms of bottleneck considering L–shaped curve showing normal distributionobtained from the analysis.

Genetic diversity of migratory fish populations of the Rio Grande Reservoir (São Paulo, Brazil)

In recent years, anthropogenic factors such as pollution, overfishing, and construction of hydroelectric plants have significantly impacted natural fish populations. Research focusing on genetically evaluation of these impacts is necessary to objectively target conservation programs. The aim of this study was to evaluate the genetic diversity of Curimba (Prochilodus lineatus), Pacu (Piaractus mesopotamicus), and Piracanjuba (Brycon orbignyanus) populations from the Água Vermelha Reservoir, Rio Grande-SP. Microsatellite loci were amplified, producing 56, 24, and 26 alleles for the populations of the three species, respectively. The number of alleles per locus ranged from three to ten for P. lineatus, two to five for P. mesopotamicus, and two to four for B. orbignyanus. The observed heterozygosity (Ho) was higher in the P. lineatus population (0.547), relative to the P. mesopotamicus and B. orbignyanus populations (0.473 and 0.527, respectively). The mean values of Ho were lower than the average expected heterozygosity (He) in the three species, being corroborated by the positive inbreeding coefficient (Fis). Deviations from the Hardy-Weinberg equilibrium (HWE) were found in five, three, and two loci for P. lineatus, P. mesopotamicus, and B. orbignyanus, respectively. Wilcoxon tests revealed recent bottlenecks in the three species, evidenced by a significant excess of heterozygotes (p < 0.05) detected only in the Infinite Allele Model (IAM). In conclusion, adequate genetic variability was observed in the three populations with the presence of heterozygous deficits.

Genetic diversity of long-established populations of Elaeis guineensis jacquin (Arecaceae)

This study aimed to estimate the genetic diversity of three Elaeis guineensis populations in Rio Grande do Norte state, as well as to verify the decreases in effective population size. The population with the highest polymorphism was MAT (Mata) with+ 57 loci (72%), followed by RIA (Riacho) with 54 loci (68%) and HOR (Horta) with 34 loci (43.03%). The RIA population was shown to be the most genetically diverse, with Nei (h = 0.28) and Shannon (I = 0.41) diversity indices. There was high genetic differentiation among populations (AMOVA, analysis of molecular variance = 42%), which was separated into three distinct genetic groups according to a Bayesian analysis. There was a significant population decrease (P < 0.05) for the HOR population in the IAM (infinite allele model) and SMM (stepwise mutation model), and for the RIA population in the IAM. The data obtained in this study may support ex-situ conservation projects for Elaeis guineensis, contributing to the selection of genotypes and their sustainable use.

Genetic diversity in natural populations of Hancornia speciosa Gomes: Implications for conservation of genetic resources

ABSTRACT The continuing fragmentation of forests has been a threat to the maintenance of genetic resources. Genetic diversity is fundamental to the survival of species in natural environments in the long term, as well as being the basis for genetic improvement. The objective of this study was to evaluate the genetic diversity in natural populations of Hancornia speciosa and to contribute to the development of conservation strategies. We sampled 105 individuals of H. speciosa, distributed in seven populations. The ISSR (Inter-Simple Sequence Repeat) markers provided 70 loci, of which 81% were polymorphic. The mean genetic diversity of Nei (h) was 0.19, and the Shannon index (I) was 0.27. The h and I diversity indices ranged respectively from 0.16 to 0.24 in the PAD (Parque das Dunas) population and from 0.21 to 0.29 in MAC (Macaíba) population. Resulting from a Bayesian analysis, the genotypes were divided into four groups (K = 4). The allelic diversity patterns observed indicated the occurrence of the genetic bottleneck in all populations, according to the stepwise mutation model (SMM). The infinite allele model (IAM) revealed an imbalance between mutation and genetic drift only in the PAD population. Genetic conservation strategies for H. speciosa should cover each genetic group that was differentially structured. We recommend in situ conservation and the creation of germplasm banks, especially with the PAD population which demonstrated the lower genetic diversity and decreased effective population size according to the two mutational models.

Inductive determination of allele frequency spectrum probabilities in structured populations

ABSTRACTWe present a method for inductively determining exact allele frequency spectrum (AFS) probabilities for samples derived from a population comprising two demes under the infinite-allele model of mutation. This method builds on a labeled coalescent argument to extend the Ewens sampling formula (ESF) to structured populations. A key departure from the panmictic case is that the AFS conditioned on the number of alleles in the sample is no longer independent of the scaled mutation rate (θ). In particular, biallelic site frequency spectra, widely-used in explorations of genome-wide patterns of variation, depend on the mutation rate in structured populations. Variation in the rate of substitution across loci and through time may contribute to apparent distortions of site frequency spectra exhibited by samples derived from structured populations.

Genetic polymorphism of the Landrace pig based on microsatellite markers

The aim of this study was to analyze the genetic variability and population structure of the Landrace population by using 12 microsatellite markers. A total of 90 pigs representing one commercial breed (Landrace) were sampled. Twelve microsatellite loci (SW24, S0155, SW72, SW951, S0386, S0355, SW240, SW857, S0101, SW936 SW911 and S0228) were selected and belong to the list of microsatellite markers recommended by FAO/ISAG. GenAIEx software was used to calculate the allele frequencies, effective number of alleles (Ae), observed (Ho) and expected (He) heterozygosity, within-population inbreeding estimate (Fis), Shannon’s information index (ISh). Overall allele frequency values ranged from 0.006 to 0.9333 (at allele SW951120). The number of observed alleles (Na) detected ranged from 5 (S0155 and SW911) to 13 (SW72), with an overall mean of 9.00 ± 0.80 and a total of 108 alleles were observed at these loci. However, the effective number of alleles (Ae) ranged from 1.57 (SW951) to 5.49 (SW240) with a mean of 3.29 ± 0.33. Shannon’s information index (ISh) which measures the level of diversity, was sufficiently high – from 0.79 (for SW951) to 2.01 (for SW240) – with a mean of 1.43 ± 0.09. The overall means for observed (Ho) and expected (He) heterozygosities were 0.578 ± 0.009 and 0.662 ± 0.004, respectively, which ranged from 0.307 (SW951) to 0.814 (SW857) and 0.361 (SW951) to 0.818 (SW240), respectively. Of the 12 microsatellites analyzed using Fisher’s exact test, 50% were in Hardy-Weinberg equilibrium, and 6 were out of equilibrium (P < 0.05). Three mutation models namely, infinite allele model (I.A.M.), two phase model (T.P.M.), stepwise mutation model (S.M.M.) were estimated using the BOTTLENECK software. The results are indicated that the Landrace pig population is non-bottlenecked and remained at mutation-drift equilibrium. The study stands first in genetic characterization of the Ukrainian Landrace pig population through microsatellite markers. The various parameters and values used to quantify genetic variability, such as the high mean (and effective) number of alleles and the expected and observed heterozygosities, indicated high genetic variability in the Ukrainian Landrace pigs. The population has not undergone any recent and/or sudden reduction in the effective population size and remained at mutation-drift equilibrium.

Mutation at the Human D1S80 Minisatellite Locus

Little is known about the general biology of minisatellites. The purpose of this study is to examine repeat mutations from the D1S80 minisatellite locus by sequence analysis to elucidate the mutational process at this locus. This is a highly polymorphic minisatellite locus, located in the subtelomeric region of chromosome 1. We have analyzed 90,000 human germline transmission events and found seven (7) mutations at this locus. The D1S80 alleles of the parentage trio, the child, mother, and the alleged father were sequenced and the origin of the mutation was determined. Using American Association of Blood Banks (AABB) guidelines, we found a male mutation rate of1.04×10-4and a female mutation rate of5.18×10-5with an overall mutation rate of approximately7.77×10-5. Also, in this study, we found that the identified mutations are in close proximity to the center of the repeat array rather than at the ends of the repeat array. Several studies have examined the mutational mechanisms of the minisatellites according to infinite allele model (IAM) and the one-step stepwise mutation model (SMM). In this study, we found that this locus fits into the one-step mutation model (SMM) mechanism in six out of seven instances similar to STR loci.

Microsatellite analysis of genetic diversity in four populations of Populus tremuloides in Quebec

To determine overall genetic variability in aspen (Populus tremuloides Michx.) along the clay belt of northwestern Quebec, four populations were sampled at the transition zone between mixed-wood and conifer-dominated forests using a hierarchical strategy. Our objectives were (i) to estimate gene diversity among and within populations using microsatellite markers and (ii) to examine whether clonal structuring in aspen could be detected. For each population, three stands at least 1 km apart were sampled. Within each stand, five putative clones were sampled with a distance of 50 m between each clone. To examine potential genetic diversity within clones, for three of the putative clones sampled per stand, the three trees closest to this individual (potential ramets) were also sampled. All samples were analysed at four microsatellite loci. Measures of genetic variation all indicated that most of the variation occurred within rather than among the populations. Rst, based on a stepwise mutation model, was 0.0409, slightly higher than Fst, which was based on infinite allele model (0.0323). Within each stand, DNA fingerprint of five putative clones allowed the differentiation of genetically distinct individuals within these putative clones, and from 1.62 to 2.2 times more genetically distinct individuals were identified than by morphological identification. In the present study there was no correlation between the mean distance of the potential ramet to the central trunk (potential ramets were often within 2–3 m of the central trunk) and the possibility of the central trunk and ramet sharing the same genotype. The number of unique genotypes for the three putative clones sampled per stand varied from 11 genotypes per 15 samples to 14 per 15 samples. Consequently, it was not possible to identify clones by either distance from a given central trunk or morphological characteristics. Thus, after stand disturbance, suckers from different genotypes are likely to be closely mixed.Key words: genetic diversity, Populus tremuloides, microsatellites, clone size.