Allozyme evidence for genetic autopolyploidy and high genetic diversity in tetraploid cranberry, Vaccinium oxycoccos (Ericaceae)

Polyploidy has been important in the evolution of angiosperms and may significantly affect population genetic diversity and structure. Nineteen isoenzyme loci were studied in diploid and tetraploid populations of Vaccinium oxycoccos (Ericaceae), and the results are compared with data previously reported for the related V. macrocarpon. Diploid V. oxycoccos and V. macrocarpon were readily discriminated based on their allozymic variation. No evidence for fixed heterozygosity was found in tetraploid V. oxycoccos. In contrast, all polymorphic loci exhibited both balanced and unbalanced heterozygotes, with some individuals exhibiting a pattern consistent with the presence of three alleles. These results support an autopolyploid origin for tetraploid V. oxycoccos. However, tetraploid V. oxycoccos possessed a suite of alleles not found in diploid V. oxycoccos; half of these alleles were shared with V. macrocarpon. This suggests that autotetraploid V. oxycoccos may have undergone hybridization with V. macrocarpon or that the autotetraploid retained the genetic variation present in an ancestral diploid species. Following theoretical expectations, proportion of polymorphic loci, mean number of alleles, and observed heterozygosity were significantly higher for the autotetraploid than for the diploid. Mean inbreeding (F(IS)) was similar for diploid and tetraploid V. oxycoccos. The latter exhibited population differentiation (F(ST)) exceeding both diploid species.     

Vegetation gradients in Atlantic Europe: the use of existing phytosociological data in preliminary investigations on the potential effects of climate change on British vegetation

• 1 This paper aims to demonstrate the use of available vegetation data from the phytosociological literature in preliminary analyses to generate hypotheses regarding vegetation and climate change.
  • 2 Data for over 3000 samples of calcareous grassland, mesotrophic grassland, heath and woodland vegetation were taken from the literature for a region in the west of Atlantic Europe and subjected to ordination by detrended correspondence analysis in order to identify the main gradients present.
    • 3 Climate data were obtained at a resolution of 0.5° from an existing database. The relationship between vegetation composition and climate was investigated by the correlation of the mean scores for the first two ordination axes for each 0.5° cell with the climate and location variables.
      • 4 The ordinations resulted in clear geographical gradients for calcareous grasslands, heaths and woodlands but not for mesotrophic grasslands. Significant correlations were shown between some of the vegetation gradients and the climate variables, with the strongest relationships occurring between the calcareous grassland gradients and July temperature, latitude and oceanicity. Some of the vegetation gradients were also inferred to reflect edaphic factors, management and vegetation history.
        • 5 Those gradients that were related to temperature were hypothesized to reflect the influence of a progressively warmer climate on species composition, providing a baseline for further studies on the influence of climate change on species composition.
        • 6 The validity of the literature data was assessed by the collection of an original set of field data for calcareous grasslands and the subsequent ordination of a dataset containing samples from both the literature and the field. The considerable overlap between the samples from the literature and the field suggest that literature data can be used, despite certain limitations. Such preliminary analyses, using readily available data, can thus achieve useful results, thereby saving lengthy and costly field visits.

     

A diagnostic for Cox regression with discrete failure-time models

Changes in maximum likelihood parameter estimates due to deletion of individual observations are useful statistics, both for regression diagnostics and for computing robust estimates of covariance. For many likelihoods, including those in the exponential family, these delete-one statistics can be approximated analytically from a one-step Newton-Raphson iteration on the full maximum likelihood solution. But for general conditional likelihoods and the related Cox partial likelihood, the one-step method does not reduce to an analytic solution. For these likelihoods, an alternative analytic approximation that relies on an appropriately augmented design matrix has been proposed. In this paper, we extend the augmentation approach to explicitly deal with discrete failure-time models. In these models, an individual subject may contribute information at several time points, thereby appearing in multiple risk sets before eventually experiencing a failure or being censored. Our extension also allows the covariates to be time dependent. The new augmentation requires no additional computational resources while improving results.     

A Two-Locus Forensic Match Probability for Subdivided Populations

A two-locus match probability is presented that incorporates the effects of within-subpopulation inbreeding (consanguinity) in addition to population subdivision. The usual practice of calculating multi-locus match probabilities as the product of single-locus probabilities assumes independence between loci. There are a number of population genetics phenomena that can violate this assumption: in addition to consanguinity, which increases homozygosity at all loci simultaneously, gametic disequilibrium will introduce dependence into DNA profiles. However, in forensics the latter problem is usually addressed in part by the careful choice of unlinked loci. Hence, as is conventional, we assume gametic equilibrium here, and focus instead on between-locus dependence due to consanguinity. The resulting match probability formulae are an extension of existing methods in the literature, and are shown to be more conservative than these methods in the case of double homozygote matches. For two-locus profiles involving one or more heterozygous genotypes, results are similar to, or smaller than, the existing approaches. This revised version was published online in August 2006 with corrections to the Cover Date.     

Last judgment: the visionary biology of J.B.S. Haldane

This paper seeks to reinterpret the life and work of J. B. S. Haldane by focusing on an illuminating but largely ignored essay he published in1927, “The Last Judgment” – the sequel to his better known work, Daedalus (1924). This astonishing essay expresses a vision of the human future over the next 40,000,000 years, one that revises and updates Wellsian futurism with the long range implications of the “new biology” for human destiny. That vision served as a kind of lifelong credo, one that infused and informed his diverse scientific work, political activities, and popular writing, and that gave unity and coherence to his remarkable career. This revised version was published online in July 2006 with corrections to the Cover Date.     

Rapid Evaluation of Least-Squares and Minimum-Evolution Criteria on Phylogenetic Trees

We present fast new algorithms for evaluating trees with respectto least squares and minimum evolution (ME), the most commonlyused criteria for inferring phylogenetic trees from distancedata. The new algorithms include an optimal O(N2) time algorithmfor calculating the edge (branch or internode) lengths on atree according to ordinary or unweighted least squares (OLS);an O(N3) time algorithm for edge lengths under weighted leastsquares (WLS) including the Fitch-Margoliash method; and anoptimal O(N4) time algorithm for generalized least-squares (GLS)edge lengths (where N is the number of taxa in the tree). TheME criterion is based on the sum of edge lengths. Consequently,the edge lengths algorithms presented here lead directly toO(N2), O(N3), and O(N4) time algorithms for ME under OLS, WLS,and GLS, respectively. All of these algorithms are as fast asor faster than any of those previously published, and the algorithmsfor OLS and GLS are the fastest possible (with respect to orderof computational complexity). A major advantage of our new methodsis that they are as well adapted to multifurcating trees asthey are to binary trees. An optimal algorithm for determiningpath lengths from a tree with given edge lengths is also developed.This leads to an optimal O(N2) algorithm for OLS sums of squaresevaluation and corresponding O(N3) and O(N4) time algorithmsfor WLS and GLS sums of squares, respectively. The GLS algorithmis time-optimal if the covariance matrix is already inverted.The speed of each algorithm is assessed analytically—thespeed increases we calculate are confirmed by the dramatic speedincreases resulting from their implementation in PAUP* 4.0.The new algorithms enable far more extensive tree searches andstatistical evaluations (e.g., bootstrap, parametric bootstrap,or jackknife) in the same amount of time. Hopefully, the fastalgorithms for WLS and GLS will encourage the use of these criteriafor evaluating trees and their edge lengths (e.g., for approximatedivergence time estimates), since they should be more statisticallyefficient than OLS.     

The role of water chemistry in the distribution of Austropotamobius pallipes (Crustacea Decapoda Astacidae) in Piedmont (Italy)

Over the last decades, the populations of Austropotamobius pallipes have decreased markedly all over Europe. If we evaluate the ecological factors that determine its presence, we will have information that could guide conservation decisions. This study aims to investigate the chemical-physical demands of A. pallipes in NW Italy. To this end, we investigated 98 sites. We performed Principal Component Analysis using chemical-physical parameters, collected in both presence and absence sites. We then used principal components with eigenvalue > 1 to run Discriminant Function Analysis and Logistic Regression. The statistics on the concentration of Ca²⁺, water hardness, pH and BOD₅ were significantly different in the presence and in the absence sites. pH and BOD₅ played the most important role in separating the presence from the absence locations. These findings are further evidence that we should reduce dissolved organic matter and fine particles in order to contribute to species management and conservation.     

DnaSAM: Software to perform neutrality testing for large datasets with complex null models

Patterns of DNA sequence polymorphisms can be used to understand the processes of demography and adaptation within natural populations. High-throughput generation of DNA sequence data has historically been the bottleneck with respect to data processing and experimental inference. Advances in marker technologies have largely solved this problem. Currently, the limiting step is computational, with most molecular population genetic software allowing a gene-by-gene analysis through a graphical user interface. An easy-to-use analysis program that allows both high-throughput processing of multiple sequence alignments along with the flexibility to simulate data under complex demographic scenarios is currently lacking. We introduce a new program, named DnaSAM, which allows high-throughput estimation of DNA sequence diversity and neutrality statistics from experimental data along with the ability to test those statistics via Monte Carlo coalescent simulations. These simulations are conducted using the ms program, which is able to incorporate several genetic parameters (e.g. recombination) and demographic scenarios (e.g. population bottlenecks). The output is a set of diversity and neutrality statistics with associated probability values under a user-specified null model that are stored in easy to manipulate text file.