Single nucleotide polymorphisms (SNPs) represent the most widespread type of sequence variation in genomes, yet they have only emerged recently as valuable genetic markers for revealing the evolutionary history of populations. Their occurrence throughout the genome also makes them ideal for analyses of speciation and historical demography, especially in light of recent theory suggesting that many unlinked nuclear loci are needed to estimate population genetic parameters with statistical confidence. In spite of having lower variation compared with microsatellites, SNPs should make the comparison of genomic diversities and histories of different species (the core goal of comparative biogeography) more straightforward than has been possible with microsatellites. The most pervasive, but correctable, complication to SNP analysis is a bias towards analyzing only the most variable loci, an artifact that is usually introduced by the limited number of individuals used to screen initially for polymorphisms. Although the use of SNPs as markers in population studies is still new, innovative methods for SNP identification, automated screening, haplotype inference and statistical analysis might quickly make SNPs the marker of choice.
Molecular clocks have profoundly influenced modern views on the timing of important events in evolutionary history. We review recent advances in estimating divergence times from molecular data, emphasizing the continuum between processes at the phylogenetic and population genetic scales. On the phylogenetic scale, we address the complexities of DNA sequence evolution as they relate to estimating divergences, focusing on models of nucleotide substitution and problems associated with among-site and among-lineage rate variation. On the population genetic scale, we review advances in the incorporation of ancestral population processes into the estimation of divergence times between recently separated species. Throughout the review we emphasize new statistical methods and the importance of model testing during the process of divergence time estimation.
The molecular systematics of vertebrates has been based entirely on alignments of primary structures of macromolecules; however, higher order features of DNA sequences not used in traditional studies also contain valuable phylogenetic information. Recent molecular data sets conflict over the phylogenetic placement of flightless birds (ratites - paleognaths), but placement of this clade critically influences interpretation of character change in birds. To help resolve this issue, we applied a new bioinformatics approach to the largest molecular data set currently available. We distilled nearly one megabase (1 million base pairs) of heterogeneous avian genomic DNA from 20 birds and an alligator into genomic signatures, defined as the complete set of frequencies of short sequence motifs (strings), thereby providing a way to directly compare higher order features of nonhomologous DNA sequences. Phylogenetic analysis and principal component analysis of the signatures strongly support the traditional hypothesis of basal ratites and monophyly of the nonratite birds (neognaths) and imply that ratite genomes are linguistically primitive within birds, despite their base compositional similarity to neognath genomes. Our analyses show further that the phylogenetic signal of genomic signatures are strongest among deep splits within vertebrates. Despite clear problems with phylogenetic analysis of genomic signatures, our study raises intriguing issues about the biological and genomic differences that fundamentally differentiate paleognaths and neognaths. [Bioinformatics; CpG island; genomics; isochore; ratite.]
The major histocompatibility complex (Mhc) has been identified as a locus influencing disease resistance, mate choice, and kin recognition in mammals and fish. However, it is unclear whether the mechanisms by which Mhc genes influence behavior in mammals are applicable to other nonmammalian vertebrates such as birds. We review the biology of Mhc genes with particular reference to their relevance to avian mating and social systems. New genomics ap-proaches recently have been applied to the Mhcs of chickens, quail, and several icons of avian behavioral ecology, including red-winged blackbirds (Agelaius phoeniceus) and house finches (Carpodacus mex-icanus). The predominance of concerted evolution at avian Mhc loci makes such methods attractive for providing access to this compli-cated multigene family. Although some biological processes influ-enced by Mhc in mammals are physiologically implausible for birds, Mhc could influence cues that form well-known bases for mate choice in birds by influencing the health and vigor of individuals. The tight associations of Mhc variation and disease resistance in chickens raise hope that finding associations of Mhc genes, disease, and mate choice in natural populations of birds will be as fruitful as in mammalian systems.
Two recent papers analysing nuclear DNA sequence data shed new light on the origin of perching birds (Passeriformes) and the structure of their radiation. Both papers find that the New Zealand wrens Acanthisitta fall at the base of the passerine radiation, implying an origin of this clade in Gondwana. Additionally, among oscine passerines (songbirds), both papers fail to support a sister group relationship between the largely Australo–Papuan Corvida and the Afro–Eurasian Passerida, as outlined in Sibley and Ahlquist’s tapestry. Rather, they converge on a phylogeny in which the Passerida is nested within the Corvida, suggesting an origin of songbirds in eastern Gondwana (Australia plus New Guinea). Finally, a Cretaceous origin of passerine birds is supported by the new data, albeit more on grounds of biogeography than of molecular clocks. The new papers solidify a synthesis of paleontological, phylogenetic and molecular data that has been growing over the past decade, and pave the way for a new generation of comparative studies of passerines.
DNA sequences from the first intron of the nuclear gene rhodopsin (RDP1) and from the mitochondrial gene ND2 were used to construct a phylogeny of the avian family Megapodiidae. RDP1 sequences evolved about six times more slowly than ND2 and showed less homoplasy, substitution bias, and rate heterogeneity across sites. Analysis of RDP1 produced a phylogeny that was well resolved at the genus level, but RDP1 did not evolve rapidly enough for intrageneric comparisons. The ND2 phylogeny resolved intrageneric relationships and was congruent with the RDP1 phylogeny except for a single node: this node was the only aspect of tree topology sensitive to weighting in parsimony analyses. Despite differences in sequence evolution, RDP1 and ND2 contained congruent phylogenetic signal and were combined to produce a phylogeny that reflects the resolving power of both genes. This phylogeny shows an early split within the megapodes, leading to two major clades: (1) Macrocephalon and the mound-building genera Talegalla, Leipoa, Aepypodius, and Alectura, and (2) Eulipoa and Megapodius. It differs significantly from previous hy-potheses based on morphology but is consistent with affiliations suggested by a recent study of parasitic chewing lice.
Here we present the sequence of a 45 kb cosmid containing a previously characterized poly-morphic Mhc class II B gene (Agph-DAB1) from the red-winged blackbird (Agelaius phoeniceus). We compared it with a previously sequenced cosmid from this species, revealing two regions of 7.5 kb and 13.0 kb that averaged greater than 97% similarity to each another, indicating a very recent shared duplication. We found 12 retroelements, including two chicken repeat 1 (CR1) elements, constituting 6.4% of the sequence and indicating a lower frequency of retroelements than that found in mammalian genomic DNA. Agph-DAB3, a new class II B gene discovered in the cosmid, showed a low rate of polymorphism and may be functional. In addi-tion, we found a Mhc class II B gene fragment and three genes likely to be functional (encod-ing activin receptor type II, a zinc finger, and a putativeγ-filamin). Phylogenetic analysis of exon 2 alleles of all three known blackbird Mhc genes indicated strong clustering of alleles by locus, implying that large amounts of interlocus gene conversion have not occurred since these genes have been diverging. Despite this, interspecific comparisons indicate that all three black-bird Mhc genes diverged from one another less than 35 million years ago and are subject to con-certed evolution in the long term. Comparison of blackbird and chicken Mhc promoter regions revealed songbird promoter elements for the first time. The high gene density of this cosmid confirms similar findings for the chicken Mhc, but the segment duplications and diversity of retroelements resembles mammalian sequences.