Forest inventory and the genetic diversity of the remaining fragment of Hymenaea courbaril L.

ABSTRACT Hymenaea courbaril is a rare species in the riparian areas of the state of Sergipe, Brazil. This species is known as Brazilian cherry or Brazilian copal and it occurs in fragments of the Rainy Forest and in the transition zones between the Rainy Forest and the Caatinga Biomes. This work was carried out, in order to quantify the genetic diversity of the remaining population of Brazilian cherry, by RAPD markers. In a studied area of 100 ha in the low course of the São Francisco River, only 15 individuals were observed. The analyzed parameters were as follows: Jaccard’s genetic similarity, the number of observed alleles, the number of effective alleles, the genetic diversities of Nei, the percentages of the polymorphic loci, the genetic diversities when using the Shannon index and the coancestry coefficient. There was no correlation between the genetic distances and the geographical distances. Despite the low number of individuals, high genetic diversity was observed, a fact that contributes to the development of strategies for the conservation of the species.

Diversidad haplotípica del exón XII del gen dopamina β-hidroxilasa en tres razas bovinas

Polymorphisms in the dopamine β-hydroxylase gene (DBH) have been associated with temperament in cattle. In 16 animals of Colombian creole breed Blanco Orejinegro (BON), 20 Brahman (BRA) and 16 fighting bulls (GLI), polymorphisms of exon XII of the DBH gene were evaluated by sequencing. 13 haplotypes were found, 6 in BON, 9 and 2 in BRA and GLI respectively. Haplotype H2 was the most frequent in the whole population (0,615) and it was found in all breeds. Haplotypes H6 and H9 were shared between BON-BRA and BRA-GLI, respectively. The greatest value of genetic(DG: 0.915 ± 0.04) and nucleotide (DN: 0.011 ± 0.006) diversity, was found in BRA, followed by BON (DG: 0.700 ± 0.12; DN: 0.008 ± 0.004) and GLI (DG: 0.350 ± 0.14;DN: 0.0011 ± 0.001). The D-Tajima test was greater than zero, but not significant (P> 0.05) in BON and BRA, GLI presented a value of −1.92 (P < 0.05). The analysis of molecular variance showed a variation between the breeds of 23.9% and a poblacional structure (FST) of 0.23 (P < 0.001). The highest values of the coancestry coefficient were presented between GLI and BRA (0.52) and between GLI and BON (0.22). It is concluded that the GLI race has low diversity in the DBH gene compared to BON and BRA, that there are effects of neutral selection in BON and BRA breeds, whereas, in the GLI and not in favor of temperament.

Individual, fruit, and annual variation in correlated mating in a Genipa americana population

In this paper, we use six microsatellite loci to examine a spatially isolated population of Genipa americana in relation to mating system variation at the level of individual and among and within fruits, over two reproductive events. For our analysis, we sampled hierarchically among and within fruits open-pollinated seeds collected from 13 seed trees during the reproductive event in 2010 and 12 seed trees in 2011. The rate of mating among relatives (1-ts) was significantly greater than zero and different between the investigated reproductive events, indicating that some seeds are inbred. The estimate of fixation index (Fo) was significantly higher than zero for seeds from both reproductive events (2010: Fo = 0.258; 2011: Fo = 0.294), confirming that seeds present inbreeding, probably originated from mating among full-sibs. The multilocus paternity correlation within fruits (rp(w)) and among fruits (rp(a)) varied among seed trees and reproductive events. The rp(w) was significantly higher than rp(a) in both reproductive events, suggesting that it is more likely to find full-sibs within fruits (2010: 36.4%; 2011: 72.4%), than among fruits (2010: 18.9%; 2011: 12.8%). Due to the presence of inbreeding, mating among relatives and correlated mating, the within families coancestry coefficient (Θ) was higher and the variance effective size (Ne) lower than expected in open-pollinated families from panmictic populations (Θ = 0.125, Ne = 4). In practical terms for conservation programs, our results show the need to collect seeds from at least 60 seed trees to retain progeny arrays with a total effective size of 150.

Estimating coancestry within open-pollinated progenies of a dioecious species: the case study of Myracrodruon urundeuva

Understanding the coancestry coefficient within openpollinated progenies has long been an area of interest because of the implications of coancestry on estimates of additive genetic variation, variance effective size and the number of seed trees required for seed collection for ex situ conservation, tree breeding and environmental restoration. This study compares three methods to calculate the coancestry coefficient within open-pollinated progenies of the dioecious tree species, Myracrodruon urundeuva, using six microsatellite loci. The methods compared were: i) correlated mating model (CMM) (RITLAND, 1989); ii) TWOGENER method (SMOUSE et al., 2001) to estimate the differentiation among pollen pools (TGM); and iii) HARDY et al.’s 2004 method using the estimate of coancestry from LOISELLE et al. (1995) (HLM) and from RITLAND (1996) (HRM). The data analysis was based on four data sets: two populations were composed of 12 progenies, two of 24 progenies, and all progenies consisted of 15 plants. The coancestry estimated using CMM ranged among populations from 0.145 to 0.158, using TGM it ranged from 0.153 to 0.181, using HLM from 0.153 to 0.162, and HRM from 0.144 to 0.147. To investigate the bias of the estimates of true relatedness within progenies we simulated two half-sib and two full-sib populations. The most accurate method found in the study was CMM because the estimated values presented no bias for true half- or full-sib progenies and these values were very similar to those expected (0.125 and 0.25, respectively). These results have significant implications for breeding and conservation programs because coancestry-within-progenies is a key parameter in assessing the variance effective size.

Analyse der Populationsstruktur des Bunten Bentheimer Schweins

Title of the paper: Analysis of the population structure of the Black and White Bentheim pig The assessment of the present state of the Black-and-White Bentheim pig (Buntes Bentheimer Schwein) is based on an analysis of the inbreeding and coancestry coefficients of 112 breeding animals registered in the year 2003. Pedigree data included 575 individuals from five generations. Pedigrees reached a completeness of about 76%. The average inbreeding coefficient in the actual population was 8.01%. The mean coancestry coefficient was 14.54%. The mean coancestry coefficient within boar and sow lines was higher.

Effects of identity disequilibrium and linkage on quantitative variation in finite populations

SummaryIdentity disequilibrium, ID, is the difference between joint identity by descent and the product of the separate probabilities of identity by descent for two loci. The effects of ID on the additive by additive (a * a) epistatic variance and joint dominance component between populations and in the additive, dominance and a * a variance within populations, including the effects on covariances of relatives within populations, were studied for finite monoecious populations. The effects are formulated in terms of three additive partitions, ηb, ηa and ηd of the total ID, each of which increases from zero to a maximum at some generation dependent upon linkage and population size and decreases thereafter. ηd is about four times the magnitude of the other two but none is of any consequence except for tight linkage and very small populations. For single-generation bottleneck populations only d is not zero. With random mating of expanded populations ηb remains constant and ηa and ηd go to zero at a rate dependent upon linkage, very fast with free recombination. The contributions of joint dominance to the genetic components of variance within and between populations are entirely a function of the η's while those of a * a variance to the components are functions mainly of the coancestry coefficient and only modified by the η's. The contributions of both to the covariances of half-sibs, full-sibs and parent-offspring follow the pattern expected from their contributions to the genetic components of variance within populations except for minor terms which most likely are of little importance.

JOINT FREQUENCIES OF ALLELES DETERMINED BY SEPARATE FORMULATIONS FOR THE MATING AND MUTATION SYSTEMS

ABSTRACT A method to calculate joint gene frequencies, which are the probabilities that two neutral genes taken at random from a population have certain allelic states, is developed taking into account the effects of the mating system and the mutation scheme. We assume that the mutation rates are constant in the population and that the mating system does not depend on allelic states. Under either–the condition that mutation rates are symmetric or that the mating unit is large and the mutation rate is small–the general formula is represented by two terms, one for the mating system and the other for the mutation scheme. The term for the mating system is expressed using the coancestry coefficient in the infinite allele model, and the term for the mutation scheme is a function of the eigenvalues and the eigenvectors of the mutation matrix. Several examples are presented as applications of the method, including homozygosity in a stepping-stone model with a symmetric mutation scheme.

ESTIMATION OF THE COANCESTRY COEFFICIENT: BASIS FOR A SHORT-TERM GENETIC DISTANCE

ABSTRACT A distance measure for populations diverging by drift only is based on the coancestry coefficient θ, and three estimators of the distance D = -ln(1 - θ) are constructed for multiallelic, multilocus data. Simulations of a monoecious population mating at random showed that a weighted ratio of single-locus estimators performed better than an unweighted average or a least squares estimator. Jackknifing over loci provided satisfactory variance estimates of distance values. In the drift situation, in which mutation is excluded, the weighted estimator of D appears to be a better measure of distance than others that have appeared in the literature.