MEGA2: molecular evolutionary genetics analysis software

We have developed a new software package, Molecular Evolutionary Genetics Analysis version 2 (MEGA2), for exploring and analyzing aligned DNA or protein sequences from an evolutionary perspective. MEGA2 vastly extends the capabilities of MEGA version 1 by: (1) facilitating analyses of large datasets; (2) enabling creation and analyses of groups of sequences; (3) enabling specification of domains and genes; (4) expanding the repertoire of statistical methods for molecular evolutionary studies; and (5) adding new modules for visual representation of input data and output results on the Microsoft Windows platform.

AVAILABILITY

http://www.megasoftware.net.

CONTACT

s.kumar@asu.edu

TreeGeneBrowser: phylogenetic data mining of gene sequences from public databases

MOTIVATION

Sequence databases represent an enormous resource of phylogenetic information, but there is a lack of tools for accessing that information in order to assess the amount of evolutionary information in these databases that may be suitable for phylogenetic reconstruction and for identifying areas of the taxonomy that are under-represented for specific gene sequences.

RESULTS

We have developed TreeGeneBrowser which allows inspection and evaluation of gene sequence data for phylogenetic reconstruction. This program improves the efficiency of identification of genes that may be useful for particular phylogenetic studies and identifies taxa and taxonomic branches that are under-represented in sequence databases.

How important is DNA replication for mutagenesis?

Rates of mutation and substitution in mammals are generally greater in the germ lines of males. This is usually explained as resulting from the larger number of germ cell divisions during spermatogenesis compared with oogenesis, with the assumption made that mutations occur primarily during DNA replication. However, the rate of cell division is not the only difference between male and female germ lines, and mechanisms are known that can give rise to mutations independently of DNA replication. We investigate the possibility that there are other causes of male-biased mutation. First, we show that patterns of variation at approximately 5,200 short tandem repeat (STR) loci indicate a higher mutation rate in males. We estimate a ratio of male-to-female mutation rates of approximately 1.9. This is significantly greater than 1 and supports a greater rate of mutation in males, affecting the evolution of these loci. Second, we show that there are chromosome-specific patterns of nucleotide and dinucleotide composition in mammals that have been shaped by mutation at CpG dinucleotides. Comparable patterns occur in birds. In mammals, male germ lines are more methylated than female germ lines, and these patterns indicate that differential methylation has played a role in male-biased vertebrate evolution. However, estimates of male mutation bias obtained from both classes of mutation are substantially lower than estimates of cell division bias from anatomical data. This discrepancy, along with published data indicating slipped-strand mispairing arising at STR loci in nonreplicating DNA, suggests that a substantial percentage of mutation may occur in nonreplicating DNA.

Patterns of reticulate evolution for the classical class I and II HLA loci

Some alleles of the major histocompatibility complex (MHC) genes have a reticulate pattern of evolution, probably resulting from the exchange of segments by gene conversion or recombination. Here we compare the extent and patterns of reticulate evolution among the classical class I and class II loci of the human MHC using the recently developed compatibility and partition matrix methods. A complex pattern is revealed with substantial differences among loci in the extent and pattern of reticulation. Extremely high levels of reticulation are observed at HLA-B and HLA-DPB1, high levels at HLA-A and HLA-DRB1, moderate levels at HLA-C and HLA-DQB1, and low levels at HLA-DQA1. The reticulate events are concentrated in the exons encoding the highly variable, peptide-binding domains, suggesting that the sequence combinations produced by these events are maintained by natural selection.

Correlating sequence variation with HLA-A allelic families: implications for T cell receptor binding specificities

Six families of HLA-A alleles have been previously proposed on the basis of nucleotide sequence and phylogenetic analysis. Here, sequence polymorphism has been examined at both the protein and DNA levels in a family specific manner and new minimal signatures for each of the families have been delineated. The DNA and protein sites that constitute these signatures are distributed throughout the length of the sequence and generally do not appear to act to promote structural or functional features of the molecules. This is explained by the fact that traditional signatures suffer biases where, for example, recombination products of low frequency can obscure one family's trend by introducing 'impurities' intrinsic to another family. In the absence of complete frequency data, a closer approximation of family signatures can be defined by sites that show strong correlation with the family groups. Using this description, the amino acid positions 62, 97 and 114, localized in the antigen-binding cleft are, in combination, sufficient to discriminate between the six families. Thus, while the composition of the whole cleft defines the details of antigen specificity, these sites in particular, play a key role in modulating supertype peptide specificity and T cell recognition.

The partition matrix: exploring variable phylogenetic signals along nucleotide sequence alignments

The partition matrix is a graphical tool for comparative analysis of nucleotide sequences following alignment. It is particularly useful for investigating the divergent phylogenies of sequence regions undergoing reticulate evolution. A partition matrix is generated by determining the consistency of the parsimoniously informative sites in a set of aligned sequences with the binary partitions inferred from the sequences. Since the linear order of sites is maintained, the matrix can be used to assess whether the distribution of sites either supporting or conflicting with particular partitions changes along the length of the alignment. The usefulness of the matrix in allowing visual identification of differences in evolutionary history among regions depends on the order in which partitions are shown; several suitable ordering schemes are proposed. We demonstrate the use of the partition matrix in interpreting the evolution of the pseudoautosomal boundary region on the sex chromosome of catarrhine primates. Its routine use should help to avoid attempts to derive single phylogenies from sequences whose evolution has been reticulate and to identify the gene conversion or recombination events underlying the reticulation. The method is relatively fast. It is exploratory, and it can form the basis for more formal analysis, which we discuss.

Structural comparison of major histocompatibility complex class I molecules and homology modelling of five distinct human leukocyte antigen-A alleles

The peptide complexes of 19 major histocompatibility complex class I alpha 1 and alpha 2 domains have been compared to identify similarities that can be interpreted as constraints necessary for the function or stability of the molecule. It was found that nearly half of the residues maintained their side-chain conformations (or had no side chain), with the remaining residues being highly solvent exposed and/or polymorphic. Seven hydrogen bonds between the molecule and peptide are conserved in all the structures and serve to orientate the ends of the peptide in the binding groove. Furthermore, the general orientations of most residue side chains in the peptide are similar. Based on these constraints, homology models for the distinct human leukocyte antigen-A alleles A*0302, A*2403, A*2603, A*3101 and A*8001 have been constructed and the implications for peptide binding discussed. The models provide a useful framework from which to engineer allele-specific peptides with a high binding affinity.

Evolution of mammalian X-linked and autosomal Pgk and Pdh E1 alpha subunit genes

The phylogeny and substitution rates of the mammalian X chromosome-located and autosomal phosphoglycerate kinase and pyruvate dehydrogenase genes were investigated. Compatibility analysis was used to show reticulate evolution in these genes. Analysis of the marsupial, mouse, and human phosphoglycerate kinase genes suggests that at least two recombination events have taken place, one occurring about the time of the placental-marsupial split involving exons 1-5 and the other before the primate-rodent split involving exons 9-10. Similar analysis of the pyruvate dehydrogenase genes indicates a recombination event involving exons 2-3 at a time before the primate-rodent split and a gene conversion between exons 3-4 in the human somatic and testis-specific pyruvate dehydrogenase genes after the primate-rodent split. This demonstrates that genetic exchange can occur between paralogous genes at widely separated chromosomal locations. Estimation of nucleotide substitution rates in these genes confirmed a higher substitution rate in the pyruvate dehydrogenase genes. In the phosphoglycerate kinase genes, there is no difference between the substitution rates in mice and humans and between the X chromosome- and autosome-located genes. A greater substitution rate was noted in the mouse autosomal pyruvate dehydrogenase gene when compared with the other mouse and human genes. This may be a result of either directional natural selection or a relaxation of functional constraint at this specific gene.

A program for calculating and displaying compatibility matrices as an aid in determining reticulate evolution in molecular sequences

Reticulate evolution in molecular sequences is caused by recombination or gene conversion, and may interfere with the reconstruction of evolutionary history. This paper presents a program which calculates compatibility matrices for detecting reticulate evolution. In addition to visual inspection of matrices, they can be analysed statistically for clustering. The method is demonstrated using human and chimpanzee gamma-globin sequences.

Characterization of the HLA-A polymorphism by locus-specific polymerase chain reaction amplification and oligonucleotide hybridization

This report describes a PCR-based typing protocol for the HLA-A polymorphism. Locus-specific primers selectively amplified HLA-A sequences from exon 1 to exon 3 in a single PCR that avoided co-amplification of other classical and nonclassical class I genes. The allelic variation in exons 2 and 3 of the HLA-A gene was examined with a set of 44 oligonucleotide probes. According to the recognized HLA-A sequences the protocol is potentially able to distinguish all known HLA-A alleles with unique nucleotide sequences in this gene region. The related HLA-A genotypes can also be identified in both homozygous and heterozygous individuals. Thus the protocol provides the highest resolution for HLA-A typing. The PCR-SSO typing technique is accurate, reliable, and particularly suitable for a large number of samples. The DNA typing results from 42 Tenth IHWS B-cell lines are compatible with the serologic and IEF definitions. Sixty-six unrelated donors from a northern Chinese population were also tested, with 16 HLA-A alleles detected. Four subtypes of HLA-A2 were found in this population. The distribution of HLA-A subtypes in the population indicated that 40% of donor-recipient pairs thought to be matched for HLA-A by serology would be mismatched. Two novel HLA-A alleles were identified by unusual oligonucleotide hybridization patterns.

HLA-DPB1 alleles correlate with risk for multiple sclerosis in Caucasoid and Cantonese patients lacking the high-risk DQB1*0602 allele

Multiple sclerosis (MS) is a demyelinating disease associated with the HLA-DR2-related haplotype DRB1*1501, DQB1*0602 in Caucasoids and with DQB1*0602 in DR2-positive Cantonese. However, many MS patients do not have the high-risk HLA-D determinants and alternative genes may contribute to the pathogenesis of MS. One candidate gene is HLA-DPB1. Our reanalysis of five earlier reports of HLA-DPB1 antigen distributions in Caucasoid MS patients shows a consistent and highly significant increase (p = 1.5 x 10(-5)) in frequency of HLA-DPw3 in the combined data set. This study tests whether HLA-DPw3 (DPB1*0301) is also increased in frequency in Australian and Cantonese MS patients and whether any distortion in DPB1 allelic distributions can be attributed to linkage disequilibrium with DQB1*0602. PCR-RFLPs were used to determine distributions of 20 HLA-DPB1 alleles in 41 Australian MS patients and 67 controls of known DQB1*0602 status and in 11 Cantonese MS patients and 33 controls positive for HLA-DR2. HLA-DP distributions in Australian MS patients and controls positive for DQB1*0602 did not differ, but in those MS patients lacking DQB1*0602, the DPB1*0301 antigen (phenotype) frequency was significantly (p = 0.006) increased (50.0%) when compared with DQB1*0602-negative controls (9.1%). DPB1*0301 was associated (p = 0.003) with DQB1*0402 (DR8) in Caucasoid MS patients.(ABSTRACT TRUNCATED AT 250 WORDS)