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Molecular biology and evolution [journal]
- Enigmatic orthology relationships between Hox clusters of the African butterfly fish and other teleosts following ancient whole genome duplication. [JOURNAL ARTICLE]
- Mol Biol Evol 2014 Jun 27.
Numerous ancient whole genome duplications (WGD) have occurred during eukaryote evolution. In vertebrates, duplicated developmental genes and their functional divergence have had important consequences for morphological evolution. While two vertebrate WGD events (1R/2R) occurred over 525 Myr ago, we have focussed on the more recent 3R or TGD (teleost genome duplication) event which occurred ~350 Myr ago in a common ancestor of over 26,000 species of teleost fishes. Through a combination of whole genome and BAC clone sequencing we characterized all Hox gene clusters of Pantodon buchholzi, a member of the early branching teleost subdivision Osteoglossomorpha. We find 45 Hox genes organized in only five clusters indicating that Pantodon has suffered more Hox cluster loss than other known species. Despite strong evidence for homology of the five Pantodon clusters to the four canonical pre-TGD vertebrate clusters (one HoxA, two HoxB, one HoxC and one HoxD), we were unable to confidently resolve 1:1 orthology relationships between four of the Pantodon clusters and the eight post-TGD clusters of other teleosts. Phylogenetic analysis revealed that many Pantodon genes segregate outside the conventional 'a' and 'b' post-TGD orthology groups, that extensive topological incongruence exists between genes physically linked on a single cluster, and that signal divergence causes ambivalence in assigning 1:1 orthology in concatenated Hox cluster analyses. Out of several possible explanations for this phenomenon we favour a model which keeps with the prevailing view of a single TGD prior to teleost radiation, but which also considers the timing of diploidization after duplication, relative to speciation events. We suggest that while the duplicated hoxa clusters diploidized prior to divergence of osteoglossomorphs, the duplicated hoxb, hoxc, and hoxd clusters concluded diploidization independently in osteoglossomorphs and other teleosts. We use the term 'tetralogy' to describe the homology relationship which exists between duplicated sequences which originate via a shared WGD, but which diploidize into distinct paralogs from a common allelic pool independently in two lineages following speciation.
- Prospects for building large timetrees using molecular data with incomplete gene coverage among species. [JOURNAL ARTICLE]
- Mol Biol Evol 2014 Jun 27.
Scientists are assembling sequence data sets from increasing numbers of species and genes to build comprehensive timetrees. However, data are often unavailable for some species and gene combinations, and the proportion of missing data is often large for data sets containing many genes and species. Surprisingly, there has not been a systematic analysis of the effect of the degree of sparseness of the species-gene matrix on the accuracy of divergence time estimates. Here, we present results from computer simulations and empirical data analyses to quantify the impact of missing gene data on divergence time estimation in large phylogenies. We found that estimates of divergence times were robust even when sequences from a majority of genes for most of the species were absent. From the analysis of such extremely sparse data sets, we found that the most egregious errors occurred for nodes in the tree that had no common genes for any pair of species in the immediate descendant clades of the node in question. These problematic nodes can be easily detected prior to computational analyses based only on the input sequence alignment and the tree topology. We conclude that it is best to use larger alignments, since adding both genes and species to the alignment augments the number of genes available for estimating divergence events deep in the tree, and improves their time estimates.
- Positive and purifying selection on the Drosophila Y chromosome. [JOURNAL ARTICLE]
- Mol Biol Evol 2014 Jun 27.
Y chromosomes, with their reduced effective population size, lack of recombination and male-limited transmission, present a unique collection of constraints for the operation of natural selection. Male-limited transmission may greatly increase the efficacy of selection for male-beneficial mutations, but the reduced effective size also inflates the role of random drift. Together, these defining features of the Y chromosome are expected to influence rates and patterns of molecular evolution on the Y as compared with X-linked or autosomal loci. Here we use sequence data from eleven genes in nine Drosophila species to gain insight into the efficacy of natural selection on the Drosophila Y relative to the rest of the genome. Drosophila is an ideal system for assessing the consequences of Y-linkage for molecular evolution in part because the gene content of Drosophila Y chromosomes is highly dynamic, with orthologous genes being Y-linked in some species while autosomal in others. Our results confirm the expectation that the efficacy of natural selection at weakly selected sites is reduced on the Y chromosome. In contrast, purifying selection on the Y chromosome for strongly deleterious mutations does not appear to be compromised. Finally, we find evidence of recurrent positive selection for four of the 11 genes studied here. Our results thus highlight the variable nature of the mode and impact of natural selection on the Drosophila Y chromosome.
- Evolution in an ancient detoxification pathway is coupled with a transition to herbivory in the Drosophilidae. [JOURNAL ARTICLE]
- Mol Biol Evol 2014 Jun 27.
Chemically-defended plant tissues present formidable barriers to herbivores. While mechanisms to resist plant defenses have been identified in ancient herbivorous lineages, adaptations to overcome plant defenses during transitions to herbivory remain relatively unexplored. The fly genus Scaptomyza is nested within the genus Drosophila and includes species that feed on living tissue of mustard plants (Brassicaceae), yet this lineage is derived from microbe-feeding ancestors. We found that mustard-feeding Scaptomyza species and microbe-feeding Drosophila melanogaster detoxify mustard oils, the primary chemical defenses in the Brassicaceae, using the widely conserved mercapturic acid pathway. This detoxification strategy differs from other specialist herbivores of mustards plants, which possess derived mechanisms to obviate mustard oil formation. To investigate if mustard feeding is coupled with evolution in the mercapturic acid pathway, we profiled functional and molecular evolutionary changes in the enzyme glutathione S-transferase D1 (GSTD1), which catalyzes the first step of the mercapturic acid pathway and is induced by mustard defense products in Scaptomyza. GSTD1 acquired elevated activity against mustard oils in one mustard-feeding Scaptomyza species in which GstD1 was duplicated. Structural analysis and mutagenesis revealed that substitutions at conserved residues within and near the substrate binding cleft account for most of this increase in activity against mustard oils. Functional evolution of GSTD1 was coupled with signatures of episodic positive selection in GstD1 after the evolution of herbivory. Overall, we found that pre-existing functions of generalized detoxification systems, and their refinement by natural selection, could play a central role in the evolution of herbivory.
- Subscription page. [Journal Article]
- Mol Biol Evol 2014 Jul; 31(7):i4.
- SMBE Editors and Council. [Journal Article]
- Mol Biol Evol 2014 Jul; 31(7):i3.
- Associate editors. [Journal Article]
- Mol Biol Evol 2014 Jul; 31(7):i2.
- Cover. [Journal Article]
- Mol Biol Evol 2014 Jul; 31(7):i1.
- Strength of selection pressure is an important parameter contributing to the complexity of antibiotic resistance evolution. [JOURNAL ARTICLE]
- Mol Biol Evol 2014 Jun 24.
Revealing the genetic changes responsible for antibiotic resistance can be critical for developing novel antibiotic therapies. However, systematic studies correlating genotype to phenotype in the context of antibiotic resistance have been missing. In order to fill in this gap, we evolved 88 isogenic Escherichia coli populations against 22 antibiotics for three weeks. For every drug, two populations were evolved under strong selection and two populations were evolved under mild selection. By quantifying evolved populations' resistances against all 22 drugs, we constructed two separate cross-resistance networks for strongly and mildly selected populations. Subsequently, we sequenced representative colonies isolated from evolved populations for revealing the genetic basis for novel phenotypes. Bacterial populations that evolved resistance against antibiotics under strong selection acquired high levels of cross-resistance against several antibiotics while other bacterial populations evolved under milder selection acquired relatively weaker cross-resistance. In addition, we found that strongly selected strains against aminoglycosides became more susceptible to five other drug classes compared to their wild type ancestor as a result of a point mutation on TrkH, an ion transporter protein. Our findings suggest that selection strength is an important parameter contributing to the complexity of antibiotic resistance problem and use of high doses of antibiotics to clear infections has the potential to promote increase of cross-resistance in clinics.
- A Generalized Mechanistic Codon Model. [JOURNAL ARTICLE]
- Mol Biol Evol 2014 Jun 23.
Models of codon evolution have attracted particular interest because of their unique capabilities to detect selection forces and their high fit when applied to sequence evolution. We described here a novel approach for modeling codon evolution, which is based on Kronecker product of matrices. The 61 × 61 codon substitution rate matrix is created using Kronecker product of three 4 × 4 nucleotide substitution matrices, the equilibrium frequency of codons and the selection rate parameter. The entities of the nucleotide substitution matrices and selection rate are considered as parameters of the model, which are optimized by maximum likelihood. Our fully mechanistic model allows the instantaneous substitution matrix between codons to be fully estimated with only 19 parameters instead of 3,721, by using the biological interdepence existing between positions within codons. We illustrate the properties of our models using computer simulations and assessed its relevance by comparing the AICc measures of our model and other models of codon evolution on simulations and a large range of empirical data sets. We show that our model fits biological data better compared to the current codon models. Furthermore, the parameters in our model can be interpreted in a similar way as the exchangeability rates found in empirical codon models.