Wiley

genalex is a user‐friendly cross‐platform package that runs within Microsoft Excel, enabling population genetic analyses of codominant, haploid and binary data. Allele frequency‐based analyses include heterozygosity, F statistics, Nei's genetic distance, population assignment, probabilities of identity and pairwise relatedness. Distance‐based calculations include amova, principal coordinates analysis (PCA), Mantel tests, multivariate and 2D spatial autocorrelation and twogener. More than 20 different graphs summarize data and aid exploration. Sequence and genotype data can be imported from automated sequencers, and exported to other software. Initially designed as tool for teaching, genalex 6 now offers features for researchers as well. Documentation and the program are available at http://www.anu.edu.au/BoZo/GenAlEx/

Phân hủy DNA, nồng độ DNA thấp và đột biến vị trí mồi có thể dẫn đến việc phân công sai kiểu hình gen microsatellite, gây sai lệch cho các phân tích di truyền học quần thể. micro‐checker là phần mềm dựa trên giao diện windows® để kiểm tra kiểu hình gen của microsatellite từ các quần thể lưỡng bội. Chương trình hỗ trợ nhận diện lỗi kiểu hình gen do các allele không khuếch đại (allele ẩn), hiện tượng ưu thế allele ngắn (rơi allele lớn), và việc ghi nhận các đỉnh kẻ. Chương trình cũng phát hiện lỗi đánh máy. micro‐checker ước tính tần số của allele ẩn và quan trọng hơn, có thể điều chỉnh tần số allele và kiểu hình gen của các allele đã được khuếch đại, cho phép sử dụng chúng trong các phân tích di truyền học quần thể tiếp theo. micro‐checker có thể được tải về miễn phí từ http://www.microchecker.hull.ac.uk/.

The Barcode of Life Data System (bold) is an informatics workbench aiding the acquisition, storage, analysis and publication of DNA barcode records. By assembling molecular, morphological and distributional data, it bridges a traditional bioinformatics chasm. bold is freely available to any researcher with interests in DNA barcoding. By providing specialized services, it aids the assembly of records that meet the standards needed to gain BARCODE designation in the global sequence databases. Because of its web‐based delivery and flexible data security model, it is also well positioned to support projects that involve broad research alliances. This paper provides a brief introduction to the key elements of bold, discusses their functional capabilities, and concludes by examining computational resources and future prospects.

In analysis of multilocus genotypes from structured populations, individual coefficients of membership in subpopulations are often estimated using programs such as structure. distruct provides a general method for visualizing these estimated membership coefficients. Subpopulations are represented as colours, and individuals are depicted as bars partitioned into coloured segments that correspond to membership coefficients in the subgroups. distruct, available at http://www.cmb.usc.edu/~noahr/distruct.html, can also be used to display subpopulation assignment probabilities when individuals are assumed to have ancestry in only one group.

spag e d i version 1.0 is a software primarily designed to characterize the spatial genetic structure of mapped individuals or populations using genotype data of codominant markers. It computes various statistics describing genetic relatedness or differentiation between individuals or populations by pairwise comparisons and tests their significance by appropriate numerical resampling. spag e d i is useful for: (i) detecting isolation by distance within or among populations and estimating gene dispersal parameters; (ii) assessing genetic relatedness between individuals and its actual variance, a parameter of interest for marker based inferences of quantitative inheritance; (iii) assessing genetic differentiation among populations, including the case of haploids or autopolyploids.

The package hierfstat for the statistical software r, created by the R Development Core Team, allows the estimate of hierarchical F‐statistics from a hierarchy with any numbers of levels. In addition, it allows testing the statistical significance of population differentiation for these different levels, using a generalized likelihood‐ratio test. The package hierfstat is available at http://www.unil.ch/popgen/softwares/hierfstat.htm.

Investigating diversity in asexual organisms using molecular markers involves the assignment of individuals to clonal lineages and the subsequent analysis of clonal diversity. Assignment is possible using a distance matrix in combination with a user‐specified threshold, defined as the maximum distance between two individuals that are considered to belong to the same clonal lineage. Analysis of clonal diversity requires tests for differences in diversity and clonal composition between populations. We developed two programs,genotypeandgenodivefor such analyses of clonal diversity in asexually reproducing organisms. Additionally,genotypecan be used for detecting genotyping errors in studies of sexual organisms.

In molecular ecology the analysis of large microsatellite data sets is becoming increasingly popular. Here we introduce a new software tool, which is specifically designed to facilitate the analysis of large microsatellite data sets. All common microsatellite summary statistics and distances can be calculated. Furthermore, the microsatellite analyser (msa) software offers an improved method to deal with inbred samples (such as Drosophila isofemale lines). Executables are available for Windows and Macintosh computers.

Linkage disequilibrium is an ubiquitous biological phenomenon. However a common metric for disequilibrium – the index of association or I_A– is dependent on sample size. In this paper we present a modification of I_A that removes this dependency. This method has been implemented in a software package.

On the basis of simulated data, this study compares the relative performances of the Bayesian clustering computer programs structure, geneland, geneclust and a new program named tess. While these four programs can detect population genetic structure from multilocus genotypes, only the last three ones include simultaneous analysis from geographical data. The programs are compared with respect to their abilities to infer the number of populations, to estimate membership probabilities, and to detect genetic discontinuities and clinal variation. The results suggest that combining analyses using tess and structure offers a convenient way to address inference of spatial population structure.