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PubMed1999

Molecular evolution of the COX7A gene family in primates.

COX VIIa is one of 10 nuclear-encoded subunits of the COX holoenzyme, and one of three that have isoforms with tissue-specific differences in expression. Analysis of nucleotide substitution rates revealed an accelerated rate of nonsynonymous substitutions relative to that of synonymous substitutions for the heart isoform gene (COX7AH) in six primate lineages. Rate accelerations have been noted for four other COX-related genes in this time period, suggesting that the COX holoenzyme has experienced an episode of adaptive evolution. A third member of the gene family, COX7AR, has recently been described. Although its function is currently unknown, low nonsynonymous substitution/synonymous substitution (N/S) ratios in mammalian evolution suggest that COX7AR is of functional importance. When the COX7A isoforms were divided into domains, examination of nucleotide substitution rates suggested that mitochondrial targeting residues experienced an accelerated nonsynonymous substitution rate in the period following gene duplication. In contrast, paralogous comparisons of the targeting residues of each isoform show they have been relatively conserved in mammalian evolution. This pattern is consistent with the evolution of tissue-specific function.

Amino Acid Sequence↗
PubMed1996

Inhibitory glutamate receptor channels.

Inhibitory glutamate receptors (IGluRs) are a family of ion channel proteins closely related to ionotropic glycine and gamma-aminobutyric acid (GABA) receptors; They are gated directly by glutamate; the open channel is permeable to chloride and sometimes potassium. Physiologically and pharmacologically, IGluRs most closely resemble GABA receptors; they are picrotoxin-sensitive and sometimes crossdesensitized by GABA. However, the amino acid sequences of cloned IGluRs are most similar to those of glycine receptors. Ibotenic acid, a conformationally restricted glutamate analog closely related to muscimol, activates all IGluRs. Quisqualate is not an IGluR agonist except among pulmonate molluscs and for a unique multiagonist receptor in the crayfish Austropotamobius torrentium. Other excitatory amino acid agonists are generally ineffective. Avermectins have several effects on IGluRs, depending on concentration: potentiation, direct gating, and blockade, both reversible and irreversible. Since IGluRs have only been clearly described in protostomes and pseudocoelomates, these effects may mediate the powerful antihelminthic and insecticidal action of avermectins, while explaining their low toxicity to mammals. IGluRs mediate synaptic inhibition in neurons and are expressed extrajunctionally in striated muscles. The presence of IGluRs in a neuron or muscle is independent of the presence or absence of excitatory glutamate receptors or GABA receptors in the cell. Generally, extrajunctional IGluRs in muscle have a higher sensitivity to glutamate than do neuronal synaptic receptors. Some extrajunctional receptors are sensitive in the range of circulating plasma glutamate levels, suggesting a role for IGluRs in regulating muscle excitability The divergence of the IGlu/GABA/Gly/ACh receptor superfamily in protostomes could become a powerful model system for adaptive molecular evolution. Physiologically and pharmacologically, protostome receptors are considerably more diverse than their vertebrate counterparts. Antagonist profiles are only loosely correlated with agonist profiles (e.g., curare-sensitive GABA receptors, bicuculline-sensitive AChRs), and pharmacologically identical receptors may be either excitatory or inhibitory, and permeable to different ions. The assumption that agonist sensitivity reliably connotes discrete, homologous receptor families is contraindicated. Protostome ionotropic receptors are highly diverse and straightforward to assay; they provide an excellent system in which to study and integrate fundamental questions in molecular evolution and adaptation.

Amino Acid Sequence↗
PubMed2006

Hybridization and the colonization of novel habitats by annual sunflowers.

Although invasive plant species often have a hybrid ancestry, unambiguous evidence that hybridization has stimulated the evolution of invasive behaviors has been difficult to come by. Here, we briefly review how hybridization might contribute to the colonization of novel habitats, range expansions, and invasiveness and then describe work on hybrid sunflowers that forges a direct link between hybridization and ecological divergence. We first discuss the invasion of Texas by the common sunflower and show that the introgression of chromosomal segments from a locally adapted species may have facilitated range expansion. We then present evidence that the colonization of sand dune, desert floor, and salt marsh habitats by three hybrid sunflower species was made possible by selection on extreme or "transgressive" phenotypes generated by hybridization. This body of work corroborates earlier claims regarding the role of hybridization in adaptive evolution and provides an experimental and conceptual framework for ongoing studies in this area.

Biological Evolution↗
PubMed2003

Selection-driven evolution of emergent dengue virus.

In the last four decades the incidence of dengue fever has increased 30-fold worldwide, and over half the world's population is now threatened with infection from one or more of four co-circulating viral serotypes (DEN-1 through DEN-4). To determine the role of viral molecular evolution in emergent disease dynamics, we sequenced 40% of the genome of 82 DEN-4 isolates collected from Puerto Rico over the 20 years since the onset of endemic dengue on the island. Isolates were derived from years with varying levels of DEN-4 prevalence. Over our sampling period there were marked evolutionary shifts in DEN-4 viral populations circulating in Puerto Rico; viral lineages were temporally clustered and the most common genotype at a particular sampling time often arose from a previously rare lineage. Expressed changes in structural genes did not appear to drive this lineage turnover, even though these regions include primary determinants of viral antigenic properties. Instead, recent dengue evolution can be attributed in part to positive selection on the nonstructural gene 2A (NS2A), whose functions may include replication efficiency and antigenicity. During the latest and most severe DEN-4 epidemic in Puerto Rico, in 1998, viruses were distinguished by three amino acid changes in NS2A that were fixed far faster than expected by drift alone. Our study therefore demonstrates viral genetic turnover within a focal population and the potential importance of adaptive evolution in viral epidemic expansion.

Communicable Diseases, Emerging↗
PubMed1999

Patterns of evolutionary rate variation among genes of the anthocyanin biosynthetic pathway.

The anthocyanin biosynthetic pathway is responsible for the production of anthocyanin pigments in plant tissues and shares a number of enzymes with other biochemical pathways. The six core structural genes of this pathway have been cloned and characterized in two taxonomically diverse plant species (maize and snapdragon). We have recently cloned these genes for a third species, the common morning glory, Ipomoea purpurea. This additional information provides an opportunity to examine patterns of evolution among genes within a single biochemical pathway. We report here that upstream genes in the anthocyanin pathway have evolved substantially more slowly than downstream genes and suggest that this difference in evolutionary rates may be explained by upstream genes being more constrained because they participate in several different biochemical pathways. In addition, regulatory genes associated with the anthocyanin pathway tend to evolve more rapidly than the structural genes they regulate, suggesting that adaptive evolution of flower color may be mediated more by regulatory than by structural genes. Finally, for individual anthocyanin genes, we found an absence of rate heterogeneity among three major angiosperm lineages. This rate constancy contrasts with an accelerated rate of evolution of three CHS-like genes in the Ipomoea lineage, indicating that these three genes have diverged without coordinated adjustment by other pathway genes.

Acyltransferases↗
PubMed2002

Speciation despite gene flow when developmental pathways evolve.

Evolutionary biologists assume that species formation requires a drastic reduction in gene exchange between populations, but the rate sufficient to prevent speciation is unknown. To study speciation, we use a new class of population genetic models that incorporate simple developmental genetic rules, likely present in all organisms, to construct the phenotype. When we allow replicate populations to evolve in parallel to a new, shared optimal phenotype, often their hybrids acquire poorly regulated phenotypes: Dobzhansky-Muller incompatibilities arise and postzygotic reproductive isolation evolves. Here we show that, although gene exchange does inhibit this process, it is the proportion of migrants exchanged (m) rather than the number of migrants (Nm) that is critical, and rates as high as 16 individuals exchanged per generation still permit the evolution of postzygotic isolation. Stronger directional selection counters the inhibitory effect of gene flow, increasing the speciation probability. We see similar results when populations in a standard two-locus, two-allele Dobzhansky-Muller model are subject to simultaneous directional selection and gene flow. However, in developmental pathway models with more than two loci, gene flow is more able to impede speciation. Genetic incompatibilities arise as frequent by-products of adaptive evolution of traits determined by regulatory pathways, something that does not occur when phenotypes are modeled using the standard, additive genetic framework. Development therefore not only constrains the microevolutionary process, it also facilitates the interactions among genes and gene products that make speciation more likely-even in the face of strong gene flow.

Animals↗
PubMed2001

Evidence for positive selection driving the evolution of HIV-1 env under potent antiviral therapy.

In HIV-infected individuals treated with potent antiretroviral therapy, viable virus can be isolated from latently infected cells several years into therapy, due to the long life of these cells, ongoing replication replenishing this population, or both. We have analysed the V3 region of the HIV-1 env gene isolated from six patients who have undergone 2 years of potent antiretroviral therapy without frank failure of viral suppression. We show that in two (and possibly three) patients, the sequence changes between baseline virus and virus isolated from infected cells persisting 2 years into infection result from positive selection driving adaptive evolution, occurring either prior to or during therapy. Our analyses suggest low-level replication despite absence of drug resistance due to drug sanctuary sites, or to low-level ongoing replication in the presence of alterations in the selective environment during therapy, perhaps due to a decline in HIV-specific immune responsiveness or changes in target cell pools. In one patient, genetic divergence between baseline plasma and infected cells isolated during therapy may reflect the long half-life of some of these persistent cell populations and the divergence of viral subpopulations that occurred prior to therapy.

Amino Acid Sequence↗
PubMed2006

Simple sequence repeats as advantageous mutators in evolution.

Simple sequence repeats (SSRs) often serve to modify genes with which they are associated. The influence of SSRs on gene regulation, transcription and protein function typically depends on the number of repeats, while mutations that add or subtract repeat units are both frequent and reversible. SSRs thus provide a prolific source of quantitative and qualitative variation. Over the past decade, researchers have found that this spontaneous variation has been tapped by natural and artificial selection to adjust almost every aspect of gene function. These studies support the hypothesis that SSRs, by virtue of their special mutational and functional qualities, have a major role in generating the genetic variation underlying adaptive evolution.

Animals↗
PubMed2001

Rapid, local adaptation of zooplankton behavior to changes in predation pressure in the absence of neutral genetic changes.

Organisms producing resting stages provide unique opportunities for reconstructing the genetic history of natural populations. Diapausing seeds and eggs often are preserved in large numbers, representing entire populations captured in an evolutionary inert state for decades and even centuries. Starting from a natural resting egg bank of the waterflea Daphnia, we compare the evolutionary rates of change in an adaptive quantitative trait with those in selectively neutral DNA markers, thus effectively testing whether the observed genetic changes in the quantitative trait are driven by natural selection. The population studied experienced variable and well documented levels of fish predation over the past 30 years and shows correlated genetic changes in phototactic behavior, a predator-avoidance trait that is related to diel vertical migration. The changes mainly involve an increased plasticity response upon exposure to predator kairomone, the direction of the changes being in agreement with the hypothesis of adaptive evolution. Genetic differentiation through time was an order of magnitude higher for the studied behavioral trait than for neutral markers (DNA microsatellites), providing strong evidence that natural selection was the driving force behind the observed, rapid, evolutionary changes.

Adaptation, Physiological↗
PubMed2003

Sequence divergence, functional constraint, and selection in protein evolution.

The genome sequences of multiple species has enabled functional inferences from comparative genomics. A primary objective is to infer biological functions from the conservation of homologous DNA sequences between species. A second, more difficult, objective is to understand what functional DNA sequences have changed over time and are responsible for species' phenotypic differences. The neutral theory of molecular evolution provides a theoretical framework in which both objectives can be explicitly tested. Development of statistical tests within this framework has provided insight into the evolutionary forces that constrain and in some cases change DNA sequences and the resulting patterns that emerge. In this article, we review recent work on how functional constraint and changes in protein function are inferred from protein polymorphism and divergence data. We relate these studies to our understanding of the neutral theory and adaptive evolution.

DNA↗
PubMed2002

Modularity, individuality, and evo-devo in butterfly wings.

Modularity in animal development is thought to have facilitated morphological diversification, but independent change of those traits integrated within a module might be restricted. Correlations among traits describe potential developmental constraints on evolution. These have often been postulated to explain patterns of morphological variation and have been examined theoretically but seldom analyzed experimentally. Here, we use artificial selection to explore the modular organization of butterfly wing patterns and the extent to which their evolution is constrained by the genetic correlations among repeated pattern elements. We show that, in Bicyclus anynana butterflies, despite the evidence that all eyespots are developmentally coupled, the response to selection for increased size of one individual eyespot can proceed in a manner largely independent from selection imposed on another eyespot. We argue that among-eyespot correlations are unlikely to have constrained the evolutionary diversification of butterfly wing patterns but might be important when only limited time is available for adaptive evolution to occur. The ease with which we have been able to produce independent responses to artificial selection on different eyespots may be linked to a legacy of natural selection favoring individuality. Our results are discussed within the context of the evolution of modularity and individuality of serially repeated morphological traits.

Animals↗
PubMed2007

Rapid evolution of flowering time by an annual plant in response to a climate fluctuation.

Ongoing climate change has affected the ecological dynamics of many species and is expected to impose natural selection on ecologically important traits. Droughts and other anticipated changes in precipitation may be particularly potent selective factors, especially in arid regions. Here we demonstrate the evolutionary response of an annual plant, Brassica rapa, to a recent climate fluctuation resulting in a multiyear drought. Ancestral (predrought) genotypes were recovered from stored seed and raised under a set of common environments with descendant (postdrought) genotypes and with ancestorxdescendant hybrids. As predicted, the abbreviated growing seasons caused by drought led to the evolution of earlier onset of flowering. Descendants bloomed earlier than ancestors, advancing first flowering by 1.9 days in one study population and 8.6 days in another. The intermediate flowering time of ancestorxdescendant hybrids supports an additive genetic basis for divergence. Experiments confirmed that summer drought selected for early flowering, that flowering time was heritable, and that selection intensities in the field were more than sufficient to account for the observed evolutionary change. Natural selection for drought escape thus appears to have caused adaptive evolution in just a few generations. A systematic effort to collect and store propagules from suitable species would provide biologists with materials to detect and elucidate the genetic basis of further evolutionary shifts driven by climate change.

Biological Evolution↗
PubMed2006

Was Australopithecus anamensis ancestral to A. afarensis? A case of anagenesis in the hominin fossil record.

We tested the hypothesis that early Pliocene Australopithecus anamensis was ancestral to A. afarensis by conducting a phylogenetic analysis of four temporally successive fossil samples assigned to these species (from earliest to latest: Kanapoi, Allia Bay, Laetoli, Hadar) using polarized character-state data from 20 morphological characters of the dentition and jaws. If the hypothesis that A. anamensis is ancestral to A. afarensis is true, then character-state changes between the temporally ordered site-samples should be congruent with hypothesized polarity transformations based on outgroup (African great ape) conditions. The most parsimonious reconstruction of character-state evolution suggests that each of the hominin OTUs shares apomorphies only with geologically younger OTUs, as predicted by the hypothesis of ancestry (tree length=31; Consistency Index=0.903). This concordance of stratigraphic and character-state data supports the idea that the A. anamensis and A. afarensis samples represent parts of an anagenetically evolving lineage, or evolutionary species. Each site-sample appears to capture a different point along this evolutionary trajectory. We discuss the implications of this conclusion for the taxonomy and adaptive evolution of these early-middle Pliocene hominins.

Animals↗
PubMed2005

Elevated evolutionary rates in the laboratory strain of Saccharomyces cerevisiae.

By using the maximum likelihood method, we made a genome-wide comparison of the evolutionary rates in the lineages leading to the laboratory strain (S288c) and a wild strain (YJM789) of Saccharomyces cerevisiae and found that genes in the laboratory strain tend to evolve faster than in the wild strain. The pattern of elevated evolution suggests that relaxation of selection intensity is the dominant underlying reason, which is consistent with recurrent bottlenecks in the S. cerevisiae laboratory strain population. Supporting this conclusion are the following observations: (i) the increases in nonsynonymous evolutionary rate occur for genes in all functional categories; (ii) most of the synonymous evolutionary rate increases in S288c occur in genes with strong codon usage bias; (iii) genes under stronger negative selection have a larger increase in nonsynonymous evolutionary rate; and (iv) more genes with adaptive evolution were detected in the laboratory strain, but they do not account for the majority of the increased evolution. The present discoveries suggest that experimental and possible industrial manipulations of the laboratory strain of yeast could have had a strong effect on the genetic makeup of this model organism. Furthermore, they imply an evolution of laboratory model organisms away from their wild counterparts, questioning the relevancy of the models especially when extensive laboratory cultivation has occurred. In addition, these results shed light on the evolution of livestock and crop species that have been under human domestication for years.

Biological Evolution↗
PubMed2000

Structure and phylogeny of the venom group I phospholipase A(2) gene.

Phospholipases A(2) (PLA(2)s) catalyzing the hydrolysis of phospholipids form a family of proteins with diverse physiological and pharmacological properties. While there have been several reports on the cloning of PLA(2) cDNAs, very few studies have been carried out on the PLA(2) genes and, most importantly, no information has been available on the gene structure and function of group I venom PLA(2). This study, on the PLA(2) gene from a spitting cobra, besides being the very first report on any venom group I PLA(2) gene, constitutes the missing link in the biology and evolution of phospholipases. The 4-kb gene consists of four exons and three introns and resembles the human pancreatic PLA(2) gene. However, the size of intron 3 in particular is much smaller than that in the pancreatic gene. Interestingly, the information for the toxic and most of the pharmacological properties of the venom PLA(2) can be attributed to the end of exon 3 and the whole of exon 4 of the gene. This functional delineation fits in well with the theory of adaptive evolution exhibited by the venom PLA(2)s. We also show that the mammalian pancreatic and elapid PLA(2)s have similar paths of evolution (probably following gene duplication) from a common ancestral gene. Venom group II phospholipases, although evolved from the same ancestor, diverged early in evolution from the group I PLA(2) genes. Intriguingly, CAT reporter gene assays and DNase 1 footprinting studies on the promoter and its deletion constructs using CHO and HepG2 cell lines identified the possible involvement of cis elements such as Sp1, AP2, gamma-IRE, and (TG)(12) repeats in the expression of the gene in a tissue-specific manner.

Animals↗
PubMed2000

Comparative physiology of body fluid regulation in vertebrates with special reference to thirst regulation.

The origin of life took place in the ancient sea where the ionic concentration is thought to have been somewhat lower than that of the present day seas. This may partly explain why most vertebrate species have plasma ionic concentrations roughly one-third of seawater. Exceptions are primitive marine cyclostomes whose plasma is almost identical to seawater, and marine cartilaginous fishes that accumulate urea in plasma to increase osmolarity to a seawater level. The mechanisms for regulation of water and electrolyte balance should have evolved from these animals into those of more advanced ones in which plasma ions are regulated to one-third of seawater irrespective of the habitat. Although most extant terrestrial and aquatic animals maintain similar plasma osmolarity and ionic concentrations, the mechanisms of regulation differ greatly among different groups of animals according to their habitat. An outstanding difference is that while plasma Na(+) concentration is a primary factor of regulation in terrestrial mammals and birds, blood volume is most strictly regulated in aquatic teleost fishes. Consistently, while an increase in plasma osmolarity (cellular dehydration) is a major dipsogenic stimulus for birds and mammals, hypovolemia (extracellular dehydration) is a much stronger stimulus for elicitation of drinking in teleost fishes. Furthermore, fish cells in culture are tolerant to changes in environmental osmolarity compared with mammalian cells, further suggesting a secondary role of plasma osmolarity as a target of regulation in fishes. A secondary role of blood volume for body fluid regulation in birds is further assessed by the fact that volume receptors for thirst, salt gland secretion, and vasotocin secretion are localized in the extravascular, interstitial space in some species of birds. All terrestrial animals including mammals have derived from the fishes in phylogeny, during which the mechanisms for body fluid regulation underwent adaptive evolution in the course of transition from aquatic to terrestrial life. Therefore, much can be learned from comparative studies of body fluid regulation that reveals the diversity and uniformity of the mechanisms. In this review, important comparative studies that may contribute to an understanding of body fluid regulation throughout vertebrate species will be summarized.

Adaptation, Biological↗
PubMed2005

Phylogenomic approaches to common problems encountered in the analysis of low copy repeats: the sulfotransferase 1A gene family example.

BACKGROUND: Blocks of duplicated genomic DNA sequence longer than 1000 base pairs are known as low copy repeats (LCRs). Identified by their sequence similarity, LCRs are abundant in the human genome, and are interesting because they may represent recent adaptive events, or potential future adaptive opportunities within the human lineage. Sequence analysis tools are needed, however, to decide whether these interpretations are likely, whether a particular set of LCRs represents nearly neutral drift creating junk DNA, or whether the appearance of LCRs reflects assembly error. Here we investigate an LCR family containing the sulfotransferase (SULT) 1A genes involved in drug metabolism, cancer, hormone regulation, and neurotransmitter biology as a first step for defining the problems that those tools must manage. RESULTS: Sequence analysis here identified a fourth sulfotransferase gene, which may be transcriptionally active, located on human chromosome 16. Four regions of genomic sequence containing the four human SULT1A paralogs defined a new LCR family. The stem hominoid SULT1A progenitor locus was identified by comparative genomics involving complete human and rodent genomes, and a draft chimpanzee genome. SULT1A expansion in hominoid genomes was followed by positive selection acting on specific protein sites. This episode of adaptive evolution appears to be responsible for the dopamine sulfonation function of some SULT enzymes. Each of the conclusions that this bioinformatic analysis generated using data that has uncertain reliability (such as that from the chimpanzee genome sequencing project) has been confirmed experimentally or by a "finished" chromosome 16 assembly, both of which were published after the submission of this manuscript. CONCLUSION: SULT1A genes expanded from one to four copies in hominoids during intra-chromosomal LCR duplications, including (apparently) one after the divergence of chimpanzees and humans. Thus, LCRs may provide a means for amplifying genes (and other genetic elements) that are adaptively useful. Being located on and among LCRs, however, could make the human SULT1A genes susceptible to further duplications or deletions resulting in 'genomic diseases' for some individuals. Pharmacogenomic studies of SULT1Asingle nucleotide polymorphisms, therefore, should also consider examining SULT1A copy number variability when searching for genotype-phenotype associations. The latest duplication is, however, only a substantiated hypothesis; an alternative explanation, disfavored by the majority of evidence, is that the duplication is an artifact of incorrect genome assembly.

Animals↗
PubMed2005

Positive correlation between evolutionary rate and recombination rate in Drosophila genes with male-biased expression.

Previous studies have shown that genes that are expressed predominantly or exclusively in males tend to evolve rapidly in comparison to other genes. In most cases, however, it is unknown whether this rapid evolution is the result of increased positive (or sexual) selection on male-expressed traits or if it is due to a relaxation of selective constraints. To distinguish between these two possibilities, we analyzed the relationship between the nonsynonymous substitution rate (dN) and local recombination rate for 343 Drosophila genes that were classified as male, female, or nonsex biased in their expression. For the male-biased genes, a positive correlation between dN and recombination rate was observed. This can be explained by an increased rate of adaptive evolution in regions of higher recombination due to a reduction of Hill-Robertson interference. In contrast, the correlation between dN and recombination rate was negative for both female- and nonsex-biased genes, suggesting that these genes are primarily subject to purifying selection, which is expected to be less effective in regions of reduced recombination.

Animals↗