Masatoshi Nei

MEGA5: Molecular Evolutionary Genetics Analysis Using Maximum Likelihood, Evolutionary Distance, and Maximum Parsimony Methods

Comparative analysis of molecular sequence data is essential for reconstructing the evolutionary histories of species and inferring the nature and extent of selective forces shaping the evolution of genes and species. Here, we announce the release of Molecular Evolutionary Genetics Analysis version 5 (MEGA5), which is a user-friendly software for mining online databases, building sequence alignments and phylogenetic trees, and using methods of evolutionary bioinformatics in basic biology, biomedicine, and evolution. The newest addition in MEGA5 is a collection of maximum likelihood (ML) analyses for inferring evolutionary trees, selecting best-fit substitution models (nucleotide or amino acid), inferring ancestral states and sequences (along with probabilities), and estimating evolutionary rates site-by-site. In computer simulation analyses, ML tree inference algorithms in MEGA5 compared favorably with other software packages in terms of computational efficiency and the accuracy of the estimates of phylogenetic trees, substitution parameters, and rate variation among sites. The MEGA user interface has now been enhanced to be activity driven to make it easier for the use of both beginners and experienced scientists. This version of MEGA is intended for the Windows platform, and it has been configured for effective use on Mac OS X and Linux desktops. It is available free of charge from http://www.megasoftware.net.

GENETIC DISTANCE BETWEEN POPULATIONS

A measure of genetic distance (D) based on the identity of genes between populations is formulated. It is defined as D = -logeI, where I is the normalized identity of genes between two populations. This genetic distance measures the accumulated allele differences per locus. If the rate of gene substitution per year is constant, it is linearly related to the divergence time between populations under sexual isolation. It is also linearly related to geographical distance or area in some migration models. Since D is a measure of the accumulated number of codon differences per locus, it can also be estimated from data on amino acid sequences in proteins even for a distantly related species. Thus, if enough data are available, genetic distance between any pair of organisms can be measured in terms of D. This measure is applicable to any kind of organism without regard to ploidy or mating scheme.

THE BOTTLENECK EFFECT AND GENETIC VARIABILITY IN POPULATIONS

In a population of constant size the expected heterozygosity for a neutral locus when mutation and genetic drift are balanced is given by 4 Nv/(4Nv + 1) under the assumption that new mutations are always different from the pre-existing alleles in the population, where N is the effective population size and v the mutation rate per locus per generation (Kimura, 1968). The size of a natural population, however, often changes drastically in the evolutionary process. In an extreme case a single inseminated female from a large population may migrate to an unoccupied geographical or ecological territory and establish a new colony, followed by rapid population growth to form a new species. This process seems to have occurred repeatedly in the evolution of Hawaiian Drosophila species (Carson, 1970; 1971) and also in the establishment of the Bogota, Colombia, population of Drosophila pseudoobscura (Prakash, 1972). When population size is suddenly reduced, the average heterozygosity per locus is expected to decline, the rate of decline depending on the effective population size, while if population size increases the aver-

MEGA: A biologist-centric software for evolutionary analysis of DNA and protein sequences

The Molecular Evolutionary Genetics Analysis (MEGA) software is a desktop application designed for comparative analysis of homologous gene sequences either from multigene families or from different species with a special emphasis on inferring evolutionary relationships and patterns of DNA and protein evolution. In addition to the tools for statistical analysis of data, MEGA provides many convenient facilities for the assembly of sequence data sets from files or web-based repositories, and it includes tools for visual presentation of the results obtained in the form of interactive phylogenetic trees and evolutionary distance matrices. Here we discuss the motivation, design principles and priorities that have shaped the development of MEGA. We also discuss how MEGA might evolve in the future to assist researchers in their growing need to analyze large data set using new computational methods.

F-statistics and analysis of gene diversity in subdivided populations.

It is shown that Wrights F‐statistics can be defined as ratios of gene diversities of heterozygosities rather than as the correlations of uniting gametes. This definition is applicable irrespective of the number of alleles involved or whether there is selection or not. The relationship between F‐statistics and Neis gene diversity analysis is discussed.

Estimation of fixation indices and gene diversities

Considering the multinomial sampling of genotypes, unbiased estimators of various gene diversity measures in subdivided populations are presented. Using these quantities, formulae for estimating Wrights fixation indices (FIS, FIT, and FST) from a finite sample are developed.

Overcredibility of molecular phylogenies obtained by Bayesian phylogenetics

Bayesian phylogenetics has recently been proposed as a powerful method for inferring molecular phylogenies, and it has been reported that the mammalian and some plant phylogenies were resolved by using this method. The statistical confidence of interior branches as judged by posterior probabilities in Bayesian analysis is generally higher than that as judged by bootstrap probabilities in maximum likelihood analysis, and this difference has been interpreted as an indication that bootstrap support may be too conservative. However, it is possible that the posterior probabilities are too high or too liberal instead. Here, we show by computer simulation that posterior probabilities in Bayesian analysis can be excessively liberal when concatenated gene sequences are used, whereas bootstrap probabilities in neighbor-joining and maximum likelihood analyses are generally slightly conservative. These results indicate that bootstrap probabilities are more suitable for assessing the reliability of phylogenetic trees than posterior probabilities and that the mammalian and plant phylogenies may not have been fully resolved.

BOTTLENECK EFFECTS ON AVERAGE HETEROZYGOSITY AND GENETIC DISTANCE WITH THE STEPWISE MUTATION MODEL

When a population goes through a small bottleneck, the genetic variability of the population is expected to decline rapidly, but as soon as population size becomes large, it starts to increase owing to new mutations (Wright, 1931; Mayr, 1954). Recently, Nei et al. (1975) studied this problem mathematically and showed that the pattern of change in genetic variability largely depends on the size of bottleneck, rate of population growth, and mutation rate. They provided a general formula for computing the average heterozygosity per locus in a population of changing size. This study is based on the assumption that new mutations occurring in a population are always different from the preexisting ones (Kimura and Crows (1964) infinite allele model). This assumption seems to be roughly correct if allelic differences are studied at the nucleotide or codon level. In practice, however, the genetic variability of natural populations is usually studied by electrophoretic mobility of proteins. Electrophoretic mobility of a protein is determined mainly by the net charge of the protein, and a positive or negative change in the net charge due to an amino acid substitution may be canceled by the second opposite charge change. Therefore, strictly speaking, the infinite allele model is not appropriate for the study of protein variation detected by electrophoresis. In view of this circumstance, Ohta and Kimura (1973) introduced the so-called stepwise mutation model. In this model each allele is represented as one of the infinite sequence of allelic states and mutation is assumed to produce a one-step change in either the positive or the negative direction. They derived a formula for average heterozygosity in an equilibrium population. Later, Wehrhahn (1975) and Li (1976) extended Ohta and Kimuras work to the case of nonequilibrium populations. On the other hand, Nei and Chakraborty (1973) studied the expected genetic distance between two populations when these are separated for an arbitrary number of generations, using a similar genetic model. The purpose of the present paper is to study the bottleneck effects on average heterozygosity and genetic distance by using the stepwise mutation model. Some studies on the bottleneck effect (the effect of reduction in population size) on genetic distance have been made by Chakraborty and Nei (1974) and Nei (1976), using the infinite allele model. These authors have shown that the reduction in population size results in an accelerated increase in genetic distance in the early generations. In the present paper we shall employ the method of generating function first used by Nei and Chakraborty (1973) in the study of protein variation and extended considerably by Wehrhahn ( 19 7 5).

The evolution of animal chemosensory receptor gene repertoires: roles of chance and necessity.

Chemosensory receptors are essential for the survival of organisms that range from bacteria to mammals. Recent studies have shown that the numbers of functional chemosensory receptor genes and pseudogenes vary enormously among the genomes of different animal species. Although much of the variation can be explained by the adaptation of organisms to different environments, it has become clear that a substantial portion is generated by genomic drift, a random process of gene duplication and deletion. Genomic drift also generates a substantial amount of copy-number variation in chemosensory receptor genes within species. It seems that mutation by gene duplication and inactivation has important roles in both the adaptive and non-adaptive evolution of chemosensation.

POPTREE2: Software for Constructing Population Trees from Allele Frequency Data and Computing Other Population Statistics with Windows Interface

Currently, there is a demand for software to analyze polymorphism data such as microsatellite DNA and single nucleotide polymorphism with easily accessible interface in many fields of research. In this article, we would like to make an announcement of POPTREE2, a computer program package, that can perform evolutionary analyses of allele frequency data. The original version (POPTREE) was a command-line program that runs on the Command Prompt of Windows and Unix. In POPTREE2 genetic distances (measures of the extent of genetic differentiation between populations) for constructing phylogenetic trees, average heterozygosities (H) (a measure of genetic variation within populations) and G(ST) (a measure of genetic differentiation of subdivided populations) are computed through a simple and intuitive Windows interface. It will facilitate statistical analyses of polymorphism data for researchers in many different fields. POPTREE2 is available at http://www.med.kagawa-u.ac.jp/ approximately genomelb/takezaki/poptree2/index.html.