Homoplasy corrected estimation of genetic similarity from AFLP bands, and the effect of the number of bands on the precision of estimation

AFLP is a DNA fingerprinting technique, resulting in binary band presence–absence patterns, called profiles, with known or unknown band positions. We model AFLP as a sampling procedure of fragments, with lengths sampled from a distribution. Bands represent fragments of specific lengths. We focus on estimation of pairwise genetic similarity, defined as average fraction of common fragments, by AFLP. Usual estimators are Dice (D) or Jaccard coefficients. D overestimates genetic similarity, since identical bands in profile pairs may correspond to different fragments (homoplasy). Another complicating factor is the occurrence of different fragments of equal length within a profile, appearing as a single band, which we call collision. The bias of D increases with larger numbers of bands, and lower genetic similarity. We propose two homoplasy- and collision-corrected estimators of genetic similarity. The first is a modification of D, replacing band counts by estimated fragment counts. The second is a maximum likelihood estimator, only applicable if band positions are available. Properties of the estimators are studied by simulation. Standard errors and confidence intervals for the first are obtained by bootstrapping, and for the second by likelihood theory. The estimators are nearly unbiased, and have for most practical cases smaller standard error than D. The likelihood-based estimator generally gives the highest precision. The relationship between fragment counts and precision is studied using simulation. The usual range of band counts (50–100) appears nearly optimal. The methodology is illustrated using data from a phylogenetic study on lettuce

Width of Gene Expression Profile Drives Alternative Splicing

Alternative splicing generates an enormous amount of functional and proteomic diversity in metazoan organisms. This process is probably central to the macromolecular and cellular complexity of higher eukaryotes. While most studies have focused on the molecular mechanism triggering and controlling alternative splicing, as well as on its incidence in different species, its maintenance and evolution within populations has been little investigated. Here, we propose to address these questions by comparing the structural characteristics as well as the functional and transcriptional profiles of genes with monomorphic or polymorphic splicing, referred to as MS and PS genes, respectively. We find that MS and PS genes differ particularly in the number of tissues and cell types where they are expressed.We find a striking deficit of PS genes on the sex chromosomes, particularly on the Y chromosome where it is shown not to be due to the observed lower breadth of expression of genes on that chromosome. The development of a simple model of evolution of cis-regulated alternative splicing leads to predictions in agreement with these observations. It further predicts the conditions for the emergence and the maintenance of cis-regulated alternative splicing, which are both favored by the tissue specific expression of splicing variants. We finally propose that the width of the gene expression profile is an essential factor for the acquisition of new transcript isoforms that could later be maintained by a new form of balancing selection

Divergência genética em germoplasma de aveias silvestres com base em caracteres multicategóricos e quantitativos

As aveias silvestres são importantes fontes de genes para programas de melhoramento e sua caracterização é fundamental para a efetiva conservação e uso. Por isso, o objetivo deste estudo foi avaliar a divergência genética em uma coleção de 71 subamostras de aveias silvestres, do Banco de Germoplasma da Embrapa Trigo, com base em caracteres multicategóricos e quantitativos. Procederam-se às análises de variância, para os caracteres quantitativos, e multivariada, para ambos os tipos de caracteres. Os métodos de agrupamento UPGMA, a partir da distância euclidiana média (caracteres multicategóricos), e de ligação completa, com base na distância de Mahalanobis (caracteres quantitativos), foram os mais adequados para ilustrar a relação entre as subamostras. A pilosidade da base dos grãos foi o caractere com maior contribuição relativa para divergência genética (32,16%) e a menor contribuição foi da pilosidade do nó superior (0,081%). As subamostras divergiram quanto a vinte caracteres: pilosidade da bainha da folha inferior, bordas da lâmina imediatamente abaixo da folha bandeira, nó superior, face externa do lema e base do grão; posição da folha bandeira e das ramificações na panícula; frequência de plantas com folha bandeira recurvada; intensidade da pilosidade do nó superior e da cerosidade do lema; orientação das ramificações na panícula; comprimento dos pelos basais do grão, ráquila, panícula, glumas e planta; cor do lema, tipo de arista, número de grãos por espigueta e ciclo. O germoplasma apresenta elevada variabilidade genética e genes de interesse para o melhoramento de aveias