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PubMed2005

Vestige: maximum likelihood phylogenetic footprinting.

BACKGROUND: Phylogenetic footprinting is the identification of functional regions of DNA by their evolutionary conservation. This is achieved by comparing orthologous regions from multiple species and identifying the DNA regions that have diverged less than neutral DNA. Vestige is a phylogenetic footprinting package built on the PyEvolve toolkit that uses probabilistic molecular evolutionary modelling to represent aspects of sequence evolution, including the conventional divergence measure employed by other footprinting approaches. In addition to measuring the divergence, Vestige allows the expansion of the definition of a phylogenetic footprint to include variation in the distribution of any molecular evolutionary processes. This is achieved by displaying the distribution of model parameters that represent partitions of molecular evolutionary substitutions. Examination of the spatial incidence of these effects across regions of the genome can identify DNA segments that differ in the nature of the evolutionary process. RESULTS: Vestige was applied to a reference dataset of the SCL locus from four species and provided clear identification of the known conserved regions in this dataset. To demonstrate the flexibility to use diverse models of molecular evolution and dissect the nature of the evolutionary process Vestige was used to footprint the Ka/Ks ratio in primate BRCA1 with a codon model of evolution. Two regions of putative adaptive evolution were identified illustrating the ability of Vestige to represent the spatial distribution of distinct molecular evolutionary processes. CONCLUSION: Vestige provides a flexible, open platform for phylogenetic footprinting. Underpinned by the PyEvolve toolkit, Vestige provides a framework for visualising the signatures of evolutionary processes across the genome of numerous organisms simultaneously. By exploiting the maximum-likelihood statistical framework, the complex interplay between mutational processes, DNA repair and selection can be evaluated both spatially (along a sequence alignment) and temporally (for each branch of the tree) providing visual indicators to the attributes and functions of DNA sequences.

Algorithms↗
PubMed2006

Evolution of the CD4 family: teleost fish possess two divergent forms of CD4 in addition to lymphocyte activation gene-3.

The T cell coreceptor CD4 is a transmembrane glycoprotein belonging to the Ig superfamily and is essential for cell-mediated immunity. Two different genes were identified in rainbow trout that resemble mammalian CD4. One (trout CD4) encodes four extracellular Ig domains reminiscent of mammalian CD4, whereas the other (CD4REL) codes for two Ig domains. Structural motifs within the amino acid sequences suggest that the two Ig domains of CD4REL duplicated to generate the four-domain molecule of CD4 and the related gene, lymphocyte activation gene-3. Here we present evidence that both of these molecules in trout are homologous to mammalian CD4 and that teleosts encode an additional CD4 family member, lymphocyte activation gene-3, which is a marker for activated T cells. The syntenic relationships of similar genes in other teleost and non-fish genomes provide evidence for the likely evolution of CD4-related molecules in vertebrates, with CD4REL likely representing the primordial form in fish. Expression of both CD4 genes is highest in the thymus and spleen, and mRNA expression of these genes is limited to surface IgM- lymphocytes. consistent with a role for T cell functionality. Finally, the intracellular regions of both CD4 and CD4REL possess the canonical CXC motif involved in the interaction of CD4 with p56LCK, implying that similar mechanisms for CD4+ T cell activation are present in all vertebrates. Our results therefore raise new questions about T cell development and functionality in lower vertebrates that cannot be answered by current mammalian models and, thus, is of fundamental importance for understanding the evolution of cell-mediated immunity in gnathosomes.

Amino Acid Sequence↗
PubMed1994

A good eye for arthropod evolution.

Insect and crustacean lineages diverged over 500 Myr ago, and there are continuing uncertainties about whether they evolved from a common arthropod ancestor or, alternatively, they evolved independently from annelid worms. Despite the diversity of their limbs and lifestyles, the nervous systems of insects and crustaceans share many common features both in development and in function. Cellular and molecular embryology techniques reveal good evidence for homologies in the developing segmental ganglia. In the visual system, this seemingly common programme of insect and crustacean CNS development culminates in common adult neural function. Comparisons of the cellular anatomy and physiology of animals as diverse as flies and crayfishes indicate that the neural circuits in the lamina of their optic lobe have been inherited largely unchanged from a common ancestor with good compound eyes.

Animals↗
PubMed2004

Estimating absolute rates of synonymous and nonsynonymous nucleotide substitution in order to characterize natural selection and date species divergences.

The rate of molecular evolution can vary among lineages. Sources of this variation have differential effects on synonymous and nonsynonymous substitution rates. Changes in effective population size or patterns of natural selection will mainly alter nonsynonymous substitution rates. Changes in generation length or mutation rates are likely to have an impact on both synonymous and nonsynonymous substitution rates. By comparing changes in synonymous and nonsynonymous rates, the relative contributions of the driving forces of evolution can be better characterized. Here, we introduce a procedure for estimating the chronological rates of synonymous and nonsynonymous substitutions on the branches of an evolutionary tree. Because the widely used ratio of nonsynonymous and synonymous rates is not designed to detect simultaneous increases or simultaneous decreases in synonymous and nonsynonymous rates, the estimation of these rates rather than their ratio can improve characterization of the evolutionary process. With our Bayesian approach, we analyze cytochrome oxidase subunit I evolution in primates and infer that nonsynonymous rates have a greater tendency to change over time than do synonymous rates. Our analysis of these data also suggests that rates have been positively correlated.

Animals↗
PubMed2003

Globin and linker sequences of the giant extracellular hemoglobin from the leech Macrobdella decora.

A detailed electrospray ionization mass spectrometric study of the approximately 3.5-MDa hexagonal bilayer hemoglobin (HBL Hb) from the pond leech Macrobdella decora has shown it to consist of at least six approximately 17-kDa globin chains, of which two are monomeric and the remaining four occur as disulfide-bonded heterodimers, and three approximately 24-kDa nonglobin linker chains (Weber et al., J. Mol. Biol. 251: 703-720, 1995). The cDNA sequences of the five major constituent chains, globin chains IIA, IIB, B, and C and linker chain L1, are reported here. The globins and linkers share 30%-50% and 20%-30% identity, respectively, with other annelid sequences. Furthermore, IIB and C align with strain A of annelid sequences, whereas IIA and B align with the strain B sequences. Although chains B and C are monomeric, chains IIA and IIB form the main disulfide-bonded dimer. They also have some unusual features: the distal His (E7) is replaced by Phe in IIA, and the highly conserved CD1Phe is replaced by Leu in IIB. In spite of these unusual features, the functional properties of Macrobdella Hb are comparable to those of other HBL Hbs. A phylogenetic analysis of the globin sequences from Macrobdella, the polychaete Tylorrhynchus, the oligochaete Lumbricus, and the vestimentiferan Lamellibrachia, indicates that the two strains originated by gene duplication followed by additional duplication of each of the two strains. The mutation rate of the linkers appeared to be faster than that of the globin chains. The phylogenetic trees constructed using the Maximum Likelihood, Neighbor-Joining and Fitch methods showed the Macrobdella globin sequences to be closest to Lumbricus, in agreement with a view of annelid evolution in which the divergence of the polychaetes occurred before the divergence of the leeches from oligochaetes.

Amino Acid Sequence↗
PubMed2000

Tests of pleistocene speciation in montane grasshoppers (genus Melanoplus) from the sky islands of western North America.

There has a been a resurgence of debate on whether the Pleistocene glaciations inhibited speciation. This study tests a model of Pleistocene speciation, estimating the phylogenetic relationships and divergence times of 10 species of montane grasshoppers, genus Melanoplus, using 1300 bp of the mitochondrial gene cytochrome oxidase I (COI). Based on average pairwise distances (corrected for multiple substitutions using Kimura's two-parameter model), all species appear to have originated within the Pleistocene. Sequence divergences between species are less than 4%, corresponding to divergence times less than 1.7 million years ago. Branching patterns among the species suggest that speciation was associated with more than one glacial-interglacial cycle. A likelihood-ratio test rejected a model of simultaneous species origins, the predicted branching pattern if species arose from the fragmentation of a widespread ancestor. These grasshoppers live in an area that was previously glaciated and, as inhabitants of the northern Rocky Mountain sky islands, underwent latitudinal and probably altitudinal shifts in distribution in response to climatic fluctuations. Given the repeated distributional shifts and range overlap of the taxa, there most likely has been ample opportunity for population mixing. However, despite periodic glacial cycles, with more than 10 major glaciations over the past million years and climatic fluctuations over as short a time scale as 10(3) to 10(4) years, the dynamic history of the Pleistocene did not preclude speciation. Although relationships among some taxa remain unresolved, these grasshopper species, even with their recent origins, exhibit genetic coherence and monophyletic or paraphyletic gene trees. The frequency of glacial cycles suggests that the speciation process must have been extremely rapid. These species of grasshoppers are morphologically very similar, differing primarily in the shape of the male genitalia. These characters are posited to be under sexual selection, may play an important role in reproductive isolation, and are known to diverge rapidly. This suggests the rapidity of evolution of reproductive isolation may determine whether species divergences occurred during the Pleistocene glaciations.

Animals↗
PubMed2025

Comparative Phylogenetics Reveal Clade-specific Drivers of Recombination Rate Evolution Across Vertebrates.

Meiotic recombination is an integral cellular process, required for the production of viable gametes. Recombination rate is a fundamental genomic parameter, modulating genomic responses to selection. Our increasingly detailed understanding of its molecular underpinnings raises the prospect that we can gain insight into trait divergence by examining the molecular evolution of recombination genes from a pathway perspective, as in mammals, where protein-coding changes in later stages of the recombination pathway are connected to divergence in intra-clade recombination rate. Here, we leverage increased availability of avian and teleost genomes to reconstruct the evolution of the recombination pathway across two additional vertebrate clades: birds, which have higher and more variable rates of recombination and similar divergence times to mammals, and teleost fish, which have much deeper divergence times. Rates of molecular evolution of recombination genes are highly correlated between vertebrate clades and significantly elevated compared to control panels, suggesting that they experience similar selective pressures. Avian recombination genes are significantly more likely to exhibit signatures of positive selection than other clades, unrestricted to later stages of the pathway. Signatures of positive selection in genes linked to recombination rate variation in mammalian populations and those with signatures of positive selection across the avian phylogeny are highly correlated. In contrast, teleost fish recombination genes have significantly less evidence of positive selection despite high intra-clade recombination rate variability. Gaining clade-specific understanding of patterns of variation in recombination genes can elucidate drivers of recombination rate and thus, factors influencing genetic diversity, selection efficacy, and species divergence.

Animals↗
PubMed2006

Screening for rapidly evolving genes in the ectomycorrhizal fungus Paxillus involutus using cDNA microarrays.

We have examined the variations in gene content and sequence divergence that could be associated with symbiotic adaptations in the ectomycorrhizal fungus Paxillus involutus and the closely related species Paxillus filamentosus. Strains with various abilities to form mycorrhizae were analysed by comparative genomic hybridizations using a cDNA microarray containing 1076 putative unique genes of P. involutus. To screen for genes diverging at an enhanced and presumably non-neutral rate, we implemented a simple rate test using information from both the variations in hybridizations signal and data on sequence divergence of the arrayed genes relative to the genome of Coprinus cinereus. C. cinereus is a free-living saprophyte and is the closest evolutionary relative to P. involutus that has been fully sequenced. Approximately 17% of the genes investigated were detected as rapidly diverging within Paxillus. Furthermore, 6% of the genes varied in copy numbers between the analysed strains. Genome rearrangements associated with this variation including duplications and deletions may also play a role in adaptive evolution. The cohort of divergent and duplicated genes showed an over-representation of either orphans, genes whose products are located at membranes, or genes encoding for components of stress/defence reactions. Some of the identified genomic changes may be associated with the variation in host specificity of ectomycorrhizal fungi. The proposed procedure could be generally applicable to screen for rapidly evolving genes in closely related strains or species where at least one has been sequenced or characterized by expressed sequence tag analysis.

Analysis of Variance↗
PubMed2003

Molecular systematics of dormice (Rodentia: Gliridae) and the radiation of Graphiurus in Africa.

The phylogenetic relationships among the Gliridae (order Rodentia) were assessed using 3430 nucleotides derived from three nuclear fragments (beta-spectrin non-erythrocytic 1, thyrotropin and lecithin cholesterol acyl transferase) and one mitochondrial gene (12S rRNA). We included 14 glirid species, representative of seven genera of the three recognized subfamilies (Graphiurinae, Glirinae and Leithiinae) in our analysis. The molecular data identified three evolutionary lineages that broadly correspond to the three extant subfamilies. However, the data suggest that the genus Muscardinus, previously regarded as falling within the Glirinae, should be included in the Leithiinae. Molecular dating using local molecular clocks and partitioned datasets allowed an estimate of the timing of cladogenesis within the glirids. Graphiurus probably diverged early in the group's evolution (40-50 Myr ago) and the three subfamilies diverged contemporaneously, probably in Europe. The radiation within Graphiurus is more recent, with the colonization of Africa by this lineage estimated at ca. 8-10 Myr ago.

Africa↗
PubMed2006

Molecular evolution at the cytochrome oxidase subunit 2 gene among divergent populations of the intertidal copepod, Tigriopus californicus.

The cytochrome c oxidase subunit 2 gene (COII) encodes a highly conserved protein that is directly responsible for the initial transfer of electrons from cytochrome c to cytochrome c oxidase (COX) crucial to the production of ATP during cellular respiration. Despite its integral role in electron transport, we have observed extensive intraspecific nucleotide and amino acid variation among 26 full-length COII sequences sampled from seven populations of the marine copepod, Tigriopus californicus. Although intrapopulation divergence was virtually nonexistent, interpopulation divergence at the COII locus was nearly 20% at the nucleotide level, including 38 nonsynonymous substitutions. Given the high degree of interaction between the cytochrome c oxidase subunit 2 protein (COX2) and the nuclear-encoded subunits of COX and cytochrome c (CYC), we hypothesized that some codons in the COII gene are likely to be under positive selection in order to compensate for amino acid substitutions in other subunits. Estimates of the ratio of nonsynonymous to synonymous substitution (omega), obtained using a series of maximum likelihood models of codon substitution, indicated that the majority of codons in T. californicus COII are under strong purifying selection (omega << 1), while approximately 4% of the sites in this gene appear to evolve under relaxed selective constraint (omega = 1). A branch-site maximum likelihood model identified three sites that may have experienced positive selection within the central California sequence clade in our COII phylogeny; these results are consistent with previous studies showing functional and fitness consequences among interpopulation hybrids between central and northern California populations.

Amino Acid Sequence↗
PubMed2006

Molecular evolution of prolactin gene family in rodents.

In this study, we identified two novel members of prolactin gene family in rat by blast searches against the published genomic database. A further analysis showed that gene duplications leading to PRL gene family in rodents occurred after rodents diverged from other mammals. Major reorganization of the gene loci in rodents was largely completed before the split of rat and mouse. But PL-I and PL-II genes are the exceptions, which have clustered in a species-specific manner in the phylogenetic tree. By combining results from gene conversion testing, relative chromosomal location comparison and estimated time for gene duplication, we believe that rodent PL-1 and PL-II genes are species-specific and are the results of serial duplications which occurred after the divergence of mouse and rat. Our analysis also reveals that continual gene duplication and divergence occurred during the evolution of rodent PRL gene family.

Amino Acid Sequence↗
PubMed2004

Biomechanical evidence for convergent evolution of the invasive growth process among fungi and oomycete water molds.

Diverse microorganisms traditionally called fungi are recognized as members of two kingdoms: mushroom-forming species and their relatives in the Fungi, and oomycete water molds in the Stramenopila. Phylogenetic analysis suggests that these kingdoms diverged early in the evolution of eukaryotes. The phylogenetic detachment of the fungi and oomycetes is reflected in radical differences in their biochemistry, cell structure, and development. In terms of their biological activities, however, they show great similarity, because both groups form colonies of filamentous hyphae that invade and decompose solid food sources. Here we present biomechanical evidence of the convergent evolution of the invasive growth process in these microorganisms. Using miniature strain gauges to measure the forces exerted by single hyphae, we show that the hyphae of species in both kingdoms exert up to 2 atmospheres of hydrostatic pressure as they extend at their tips. No other eukaryotes have adopted this process for meeting their nutritional needs.

Biological Evolution↗
PubMed1998

Aminoacylation of tRNA in the evolution of an aminoacyl-tRNA synthetase.

Aminoacyl-tRNA synthetases catalyze aminoacylation of tRNAs by joining an amino acid to its cognate tRNA. The selection of the cognate tRNA is jointly determined by separate structural domains that examine different regions of the tRNA. The cysteine-tRNA synthetase of Escherichia coli has domains that select for tRNAs containing U73, the GCA anticodon, and a specific tertiary structure at the corner of the tRNA L shape. The E. coli enzyme does not efficiently recognize the yeast or human tRNACys, indicating the evolution of determinants for tRNA aminoacylation from E. coli to yeast to human and the coevolution of synthetase domains that interact with these determinants. By successively modifying the yeast and human tRNACys to ones that are efficiently aminoacylated by the E. coli enzyme, we have identified determinants of the tRNA that are important for aminoacylation but that have diverged in the course of evolution. These determinants provide clues to the divergence of synthetase domains. We propose that the domain for selecting U73 is conserved in evolution. In contrast, we propose that the domain for selecting the corner of the tRNA L shape diverged early, after the separation between E. coli and yeast, while that for selecting the GCA-containing anticodon loop diverged late, after the separation between yeast and human.

Acylation↗
PubMed2006

Divergence from a dedicated cellular suicide mechanism: exploring the evolution of cell death.

The developmental cell death in the nematode C. elegans is controlled by a simple and dedicated genetic program. This genetic program is evolutionarily conserved in higher organisms, including mammals. However, although mammalian homologs of C. elegans cell death gene products continue to regulate apoptosis, they are no longer dedicated regulators of cell death. On the other hand, multiple cellular noncell death-related mechanisms have been recruited to regulate cell death under different conditions. Such evidence suggests that evolution has led to an extensive integration of mammalian apoptosis machinery with multiple cellular physiological processes.

Animals↗
PubMed1996

Duplication and functional divergence in the chalcone synthase gene family of Asteraceae: evolution with substrate change and catalytic simplification.

Plant-specific polyketide synthase genes constitute a gene superfamily, including universal chalcone synthase [CHS; malonyl-CoA:4-coumaroyl-CoA malonyltransferase (cyclizing) (EC 2.3.1.74)] genes, sporadically distributed stilbene synthase (SS) genes, and atypical, as-yet-uncharacterized CHS-like genes. We have recently isolated from Gerbera hybrida (Asteraceae) an unusual CHS-like gene, GCHS2, which codes for an enzyme with structural and enzymatic properties as well as ontogenetic distribution distinct from both CHS and SS. Here, we show that the GCHS2-like function is encoded in the Gerbera genome by a family of at least three transcriptionally active genes. Conservation within the GCHS2 family was exploited with selective PCR to study the occurrence of GCHS2-like genes in other Asteraceae. Parsimony analysis of the amplified sequences together with CHS-like genes isolated from other taxa of angiosperm subclass Asteridae suggests that GCHS2 has evolved from CHS via a gene duplication event that occurred before the diversification of the Asteraceae. Enzyme activity analysis of proteins produced in vitro indicates that the GCHS2 reaction is a non-SS variant of the CHS reaction, with both different substrate specificity (to benzoyl-CoA) and a truncated catalytic profile. Together with the recent results of Durbin et al. [Durbin, M. L., Learn, G. H., Jr., Huttley, G. A. & Clegg, M. T. (1995) Proc. Natl. Acad. Sci. USA 92, 3338-3342], our study confirms a gene duplication-based model that explains how various related functions have arisen from CHS during plant evolution.

Acyl Coenzyme A↗
PubMed2004

Fractal characterization of bpn weights evolution.

Training methodology of the Back Propagation Network (BPN) is well documented. One aspect of BPN that requires investigation is whether or not the BPN would get trained for a given training data set and architecture. In this paper the behavior of the BPN is analyzed during its training phase considering convergent and divergent training data sets. Evolution of the weights during the training phase was monitored for the purpose of analysis. The evolution of weights was plotted as return map and was characterized by means of fractal dimension. This fractal dimensional analysis of the weight evolution trajectories is used to provide a new insight to understand the behavior of BPN and dynamics in the evolution of weights.

Algorithms↗
PubMed2005

Compensatory evolution of interacting gene products through multifunctional intermediates.

When two mutations are singly deleterious but neutral or beneficial together, compensatory evolution can occur. The accumulation of derived, compensated genotypes contributes to the evolution of genetic incompatibilities between diverging populations or species. Previous two locus/two allele models have shown that compensatory evolution is appreciable only with tight linkage, the possibility of nearly simultaneous mutations, and/or a way to overcome negative selection against the singly mutated genotype. These conditions are often not met. Even when they are met, compensatory evolution is still predicted to be extremely slow, and in many scenarios selective advantage of the compensated genotype does little to accelerate it. Despite these obstacles, empirical studies suggest that it occurs readily. We describe here a set of related two locus/three allele models that invoke plausible neutral intermediates capable of productive interaction with both ancestral and compensated products of the interacting locus. These models are explored with analytical and computer simulation methods. The effect of these stepping-stone alleles on the evolution of ancestor-descendant incompatibilities is often profound, making the difference between evolution and stasis in several situations, including in small populations, when codominance or haploidy prevents shielding of mismatched genotypes, and in the absence of positive selection on the derived genotype. However, in large populations these intermediates can either speed or slow the evolution of incompatible genotypes relative to the two-allele case, depending on the specific fitness model. These results suggest that population size, the source of adaptive benefit, and the structural details of heteromeric gene product complexes interact to influence the path by which intergenic incompatibility evolves.

Computer Simulation↗