Comparison Of Substitution Rates Research Articles

Section-level relationships of North American Agalinis (Orobanchaceae) based on DNA sequence analysis of three chloroplast gene regions

BackgroundThe North American Agalinis are representatives of a taxonomically difficult group that has been subject to extensive taxonomic revision from species level through higher sub-generic designations (e.g., subsections and sections). Previous presentations of relationships have been ambiguous and have not conformed to modern phylogenetic standards (e.g., were not presented as phylogenetic trees). Agalinis contains a large number of putatively rare taxa that have some degree of taxonomic uncertainty. We used DNA sequence data from three chloroplast genes to examine phylogenetic relationships among sections within the genus Agalinis Raf. (=Gerardia), and between Agalinis and closely related genera within Orobanchaceae.ResultsMaximum likelihood analysis of sequences data from rbcL, ndhF, and matK gene regions (total aligned length 7323 bp) yielded a phylogenetic tree with high bootstrap values for most branches. Likelihood ratio tests showed that all but a few branch lengths were significantly greater than zero, and an additional likelihood ratio test rejected the molecular clock hypothesis. Comparisons of substitution rates between gene regions based on linear models of pairwise distance estimates between taxa show both ndhF and matK evolve more rapidly than rbcL, although the there is substantial rate heterogeneity within gene regions due in part to rate differences among codon positions.ConclusionsPhylogenetic analysis supports the monophyly of Agalinis, including species formerly in Tomanthera, and this group is sister to a group formed by the genera Aureolaria, Brachystigma, Dasistoma, and Seymeria. Many of the previously described sections within Agalinis are polyphyletic, although many of the subsections appear to form natural groups. The analysis reveals a single evolutionary event leading to a reduction in chromosome number from n = 14 to n = 13 based on the sister group relationship of section Erectae and section Purpureae subsection Pedunculares. Our results establish the evolutionary distinctiveness of A. tenella from the more widespread and common A. obtusifolia. However, further data are required to clearly resolve the relationship between A. acuta and A. tenella.

Comparison of substitution rates in ZFX and ZFY introns of sheep and goat related species supports the hypothesis of male-biased mutation rates.

There is a growing body of evidence that males serve as the major generators of mutations, due to the larger number of cell divisions involved in sperm compared to egg production. In mammals, this hypothesis (referred to as "male-driven evolution") has been tested by comparison of nucleotide substitution rates on the X and Y sex chromosomes in a limited number of taxa, predominantly primates and rodents. This study asks whether male-driven evolution is a more general phenomenon among mammals, by comparison of paralogous ZFX and ZFY intron sequences in sheep and goat species (the tribe Caprini). The male-to-female mutation ratio, alpha(m), was estimated to be between 2.93 (95% CI, 1.51-8.61) and 3.94 (95% CI, 1.25-32.29) when calculated using pairwise distance and branch length, respectively, suggesting that the Caprini are subject to weak, male-driven evolution. Comparison to published values for primates, felids, and rodents implies that there may be some correlation with reproductive life span. However, this is difficult to test with current data because confidence intervals are large and overlapping. Nonindependent evolution of paralogous sequences and/or the presence of selective constraints could lead to inaccurate estimates of alpha(m). No evidence for gene conversion between the ZFX and the ZFY introns was found, and this suggests that they have evolved independently during the radiation of the Caprini. Finally, there was no apparent evidence that these introns are subject to selective constraints, although low levels of intraspecific polymorphism reduce the power of neutrality tests.

Evolution of heteroneuran Lepidoptera (Insecta) and the utility of dopa decarboxylase for Cretaceous-age phylogenetics

Abstract This study tests the utility of the nuclear gene encoding dopa decarboxylase ( DDC ) for recovering Cretaceous-age divergences within the lepidopteran clade Heteroneura, which contains 98% of lepidopteran species. A 709-bp fragment of DDC has been sequenced in 32 species, including representatives of all major lineages of Heteroneura plus outgroups from more basal lepidopteran groups and the related order Trichoptera. Pairwise divergences across the first and second codon positions and amino acids increase with depth throughout the taxonomic hierarchy, indicating that non-synonymous substitutions are not fully saturated; whereas, divergences across the third codon position level off at the family to superfamily level. Inclusion of non-neolepidopteran outgroups results in phylogeny estimates that contradict well established groups, almost surely due to sparse taxon sampling and high character divergence. When these taxa and an equivalently divergent basal ditrysian are excluded, DDC trees show nearly complete recovery of ten uncontroversial basal heteroneuran «test clades» of family rank and higher, about half with strong bootstrap support. Thus, DDC clearly carries phylogenetic signal at these levels. Bootstrap support for resolution of the controversial relationships among the five main heteroneuran groups (four monotrysian superfamilies plus Ditrysia) is individually low, but two of three previous hypotheses were statistically rejected overall by DDC. DDC trees within the primitive heteroneuran superfamily Incurvarioidea, though modestly supported, closely resemble a previous morphological hypothesis, while removing the requirement for reversal in a possible «key adaptation», the larval case. Taxon overlap with a previous mtDNA study of Prodoxidae (Incurvarioidea), which includes much-studied mutualist pollinators, permits a comparison of substitution rates with the conservative mitochondrial COI + COII region, as well as combined-data re-examination of generic reltionships. Non-synonymous substitution is about 25% slower in DDC than in COI + COII , though synonymous substitution is faster. With additional taxon sampling, and in combination with other genes, DDC promises to be a powerful tool for reconstructing among-superfamily relationships within Lepidoptera and probably other insect groups.