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PubMed2003

Genome duplication, subfunction partitioning, and lineage divergence: Sox9 in stickleback and zebrafish.

Teleosts are the most species-rich group of vertebrates, and a genome duplication (tetraploidization) event in ray-fin fish appears to have preceded this remarkable explosion of biodiversity. What is the relationship of the ray-fin genome duplication to the teleost radiation? Genome duplication may have facilitated lineage divergence by partitioning different ancestral gene subfunctions among co-orthologs of tetrapod genes in different teleost lineages. To test this hypothesis, we investigated gene expression patterns for Sox9 gene duplicates in stickleback and zebrafish, teleosts whose lineages diverged early in Euteleost evolution. Most expression domains appear to have been partitioned between Sox9a and Sox9b before the divergence of stickleback and zebrafish lineages, but some ancestral expression domains were distributed differentially in each lineage. We conclude that some gene subfunctions, as represented by lineage-specific expression domains, may have assorted differently in separate lineages and that these may have contributed to lineage diversification during teleost evolution.

Animals↗
PubMed1994

Identification of cholecystokinin from frog and turtle. Divergence of cholecystokinin and gastrin occurred before the evolution of amphibia.

Cholecystokinins from brain and small intestine of the bullfrog (Rana catesbeiana) and red-eared slider turtle (Pseudomys scripta) were isolated. The purifications were monitored by an antiserum specific for the common C-terminus of mammalian cholecystokinin and gastrin. The peptide structures were identified by sequence analysis of the intact peptides and proteolytic fragments, mass spectrometry, and amino acid analysis. Brain and small intestine of both species contained cholecystokinin-8 and substantial amounts of cholecystokinin-7. Furthermore, the small intestine of both frog and turtle contained a major fraction of the immunoreactive material as large peptides consisting of 69 residues and 70 residues, respectively. The structure for frog cholecystokinin-69 is ASSSAQLKPFQRIDGTSDQKAVIGAMLAKYLQTRKAGSSTGRYAVLPNRPVIDPTHRINDRDYMGWMDF .NH2 and the structure for turtle cholecystokinin-70 is VPSSAGQLKPIQRLDGNVDQKANIGALLAKYLQQARKGPTGRISMMGNRVQNIDPTHRINDRDYMGWMD F.NH2. All the isolated peptides were tyrosine sulfated at the seventh last residue. The peptides are highly similar to each other and to mammalian cholecystokinins (70% mutual identity and more than 50% identity with human cholecystokinin). Thus, they are clearly related to the known mammalian cholecystokinins. Both peptides include the monobasic and dibasic cleavage sites giving rise to cholecystokinins-33, -39, and -58 in mammals. However, only a small amount of turtle cholecystokinin-40 (corresponding to mammalian cholecystokinin-39) was isolated. This confirms that post-translational processing is highly species dependent. Recently, we isolated peptides from frog and turtle antrum. Following their origin they were named gastrins in spite of their C-terminal cholecystokinin-like structure. Thus, two different cholecystokinin/gastrin peptides exist in frog and turtle justifying the choice of two names. This finding of two members of the cholecystokinin/gastrin family in frog shows that the divergence of cholecystokinin and gastrin occurred simultaneously with or earlier than the appearance of amphibia during phylogenesis. Frog cholecystokinin and gastrin show sufficient similarity along the whole sequence to support the notion of a gene duplication of a common ancestor.

Amino Acid Sequence↗
PubMed2005

[Genomic structure of the autotetraploid oat species Avena macrostachya inferred from comparative analysis of the ITS1 and ITS2 sequences: on the oat karyotype evolution during the early stages of the Avena species divergence].

To examine the genomic structure of Avena macrostachya, internal transcribed spacers, ITS1 and ITS2, as well as nuclear 5.8S tRNA genes from three oat species with AsAs karyotype (A. wiestii, A. hirtula, and A. atlantica), and those from A. longiglumis (AlAl), A. canariensis (AcAc), A. ventricosa (CvCv), A. pilosa, and A. clauda (CpCp) were sequenced. All species of the genus Avena examined represented a monophyletic group (bootstrap index = 98), within which two branches, i.e., species with A- and C-genomes, were distinguished (bootstrap indices = 100). The subject of our study, A. macrostachya, albeit belonging to the phylogenetic branch of C-genome oat species (karyotype with submetacentic and subacrocentric chromosomes), has preserved an isobrachyal karyotype, (i.e., that containing metacentric chromosomes), probably typical of the common Avena ancestor. It was suggested to classify the A. macrostachya genome as a specific form of C-genome, Cm-genome. Among the species from other genera studied, Arrhenatherum elatius was found to be the closest to Avena in ITS1 and ITS structure. Phylogenetic relationships between Avena and Helictotrichon remain intriguingly uncertain. The HPR389153 sequence from H. pratense genome was closest to the ITS1 sequences specific to the Avena A-genomes (p-distance = 0.0237), while the differences of this sequence from the ITS1 of A. macrostachya reached 0.1221. On the other hand, HAD389117 from H. adsurgens was close to the ITS1 specific to Avena C-genomes (p-distance = 0.0189), while its differences from the A-genome specific ITS1 sequences reached 0.1221. It seems likely that the appearance of highly polyploid (2n = 12-21x) species of H. pratense and H. adsurgens could be associated with interspecific hybridization involving Mediterranean oat species carrying A- and C-genomes. A hypothesis on the pathways of Avena chromosomes evolution during the early stages the oat species divergence is proposed.

Avena↗
PubMed1990

Geomyid evolution: the historical, selective, and random basis for divergence patterns within and among species.

Patterns of variation in life history, ecological distribution, genetic and morphological differentiation, and speciation of pocket gophers, family Geomyidae, have been examined in the context of the genetic demography of local populations. Emphasis has been placed on the structure of local breeding populations, dispersal potential leading to effective gene flow, and the influence of patchy distributions due to the availability of suitable soils. The focus of this paper is on those factors contributing to differentiation among geographic segments of species, or among different species--that is, to those processes responsible for converting phenotypically expressed variation within populations to that differentiating among them.

Animals↗
PubMed1995

Divergence of the phytochrome gene family predates angiosperm evolution and suggests that Selaginella and Equisetum arose prior to Psilotum.

Thirty-two partial phytochrome sequences from algae, mosses, ferns, gymnosperms, and angiosperms (11 of them newly released ones from our laboratory) were analyzed by distance and character-state approaches (PHYLIP, TREECON, PAUP). In addition, 12 full-length sequences were analyzed. Despite low bootstrap values at individual internal nodes, the inferred trees (neighbor-joining, Fitch, maximum parsimony) generally showed similar branching orders consistent with other molecular data. Lower plants formed two distinct groups. One basal group consisted of Selaginella, Equisetum, and mosses; the other consisted of a monophyletic cluster of frond-bearing pteridophytes. Psilotum was a member of the latter group and hence perhaps was not, as sometimes suggested, a close relative of the first vascular plants. The results further suggest that phytochrome gene duplication giving rise to a- and b- and later to c-types may have taken place within seedfern genomes. Distance matrices dated the separation of mono- and dicotyledons back to about 260 million years before the present (Myr B.P.) and the separation of Metasequoia and Picea to a fossil record-compatible value of 230 Myr B.P. The Ephedra sequence clustered with the c- or a-type and Metasequoia and Picea sequences clustered with the b-type lineage. The "paleoherb" Nymphaea branched off from the c-type lineage prior to the divergence of mono- and dicotyledons on the a- and b-type branches. Sequences of Piper (another "paleoherb") created problems in that they branched off from different phytochrome lineages at nodes contradicting distance from the inferred trees' origin.

Base Sequence↗
PubMed2003

Evolution of R5 and X4 human immunodeficiency virus type 1 gag sequences in vivo: evidence for recombination.

Human immunodeficiency virus type 1 (HIV-1) infection is in general established by CCR5-utilizing (R5) virus variants, which persist throughout the course of infection. R5 HIV-1 variants evolve into CXCR4-utilizing (X4) HIV-1 variants in approximately half of the infected individuals. We have previously observed an ongoing genetic evolution with a continuous divergence of envelope gp120 sequences of coexisting R5 and X4 virus variants over time. Here, we studied evolution of gag p17 sequences in two patients who developed X4 variants in the course of infection. In contrast to the envelope gp120 sequences, gag p17 sequences of R5 and X4 virus populations intermingled in phylogenetic trees and did not diverge from each other over time. Statistical evaluation using the Shimodaira-Hasegawa test indicated that the different genomic regions evolved along different topologies, supporting the hypothesis of recombination. Therefore, our data imply that recombination between R5 and X4 HIV-1 variants occurs in vivo.

Cell Line↗
PubMed2006

Evolution of arylalkylamine N-acetyltransferase: emergence and divergence.

The melatonin rhythm-generating enzyme, arylalkylamine N-acetyltransferase (AANAT) is known to have recognizable ancient homologs in bacteria and fungi, but not in other eukaryotes. Analysis of new cDNA and genomic sequences has identified several additional homologs in other groupings. First, an AANAT homolog has been found in the genome of the cephalochordate amphioxus, representing the oldest homolog in chordates. Second, two AANAT homologs have been identified in unicellular green algae. The homologs in amphioxus, unicellular green algae, fungi and bacteria are similarly primitive in that they lack sequences found in vertebrate AANATs that are involved in regulation and that facilitate binding and catalysis. In addition, all these sequences are intronless. These features are consistent with horizontal transfer of the AANAT ancestor from bacteria to green algae, fungi and chordates. Lastly, a third AANAT gene has been found in teleost fish, suggesting that AANAT genes serve multiple functions in addition to melatonin synthesis.

Amino Acid Sequence↗
PubMed2002

Host-plant adaptation drives the parallel evolution of reproductive isolation.

Parallel evolution of similar traits in independent populations that inhabit ecologically similar environments strongly implicates natural selection as the cause of evolution. Parallel speciation is a special form of parallel evolution where traits that determine reproductive isolation evolve repeatedly, in closely related populations, as by-products of adaptation to ecological conditions. The outcome of such parallel evolution is that ecologically divergent pairs of populations exhibit greater levels of reproductive isolation than ecologically similar pairs of populations of a similar or younger age. The parallel evolution of reproductive isolation provides strong evidence for natural selection in the process of speciation, but only one conclusive example from nature is known. Populations of the walking-stick insect Timema cristinae that use different host-plant species have diverged in body size and shape, host preference, behaviour and the relative frequency of two highly cryptic colour-pattern morphs. Here we report that divergent selection for host adaptation, and not genetic drift, has promoted the parallel evolution of sexual isolation in this species. Our findings represent a clear demonstration that host-plant adaptation can play a crucial and repeatable role in the early stages of speciation.

Adaptation, Physiological↗
PubMed1997

Long-term experimental evolution in Escherichia coli. VI. Environmental constraints on adaptation and divergence.

The effect of environment on adaptation and divergence was examined in two sets of populations of Escherichia coli selected for 1000 generations in either maltose-or glucose-limited media. Twelve replicate populations selected in maltose-limited medium improved in fitness in the selected environment, by an average of 22.5%. Statistically significant among-population genetic variation for fitness was observed during the course of the propagation, but this variation was small relative to the fitness improvement. Mean fitness in a novel nutrient environment, glucose-limited medium, improved to the same extent as in the selected environment, with no statistically significant among-population genetic variation. In contrast, 12 replicate populations previously selected for 1000 generations in glucose-limited medium showed no improvement, as a group, in fitness in maltose-limited medium and substantial genetic variation. This asymmetric pattern of correlated responses suggests that small changes in the environment can have profound effects on adaptation and divergence.

Adaptation, Physiological↗
PubMed1985

Evolution of an instinct under long-term divergent selection for geotaxis in domesticated populations of Drosophila melanogaster.

Long-term divergent selection for geotaxis in lines of Drosophila melanogaster (the fruit fly) is described. After 26 years (600+ generations) of intermittent selection, the mean geotactic scores now remain stable upon relaxed selection, a result suggesting that evolutionary changes have occurred in these lines. Because the stability is not due to genetic fixation (homozygosity) of the lines, it must be due to either close linkage of genes associated with geotaxis (which would not result in enduring change) or the development of new coadapted gene complexes utilizing genes associated with extreme geotaxis expression (which should result in enduring change). Better evidence for the latter hypothesis is obtained from the low, than from the high, line. The notions of coadaptation and genetic homeostasis are considered, as well as the prospective use of the geotaxis lines to study such concepts experimentally. The geotactic behavior expressed in each line is defined as "instinctive": It increases reproductive success and is characteristic of a population.

Animals↗
PubMed2006

Evolutionary radiation of "stone plants" in the genus Argyroderma (Aizoaceae): unraveling the effects of landscape, habitat, and flowering time.

Recent phylogenetic evidence suggests that the extraordinary diversity of the Cape Floristic Kingdom in South Africa may be the result of widespread evolutionary radiation. Our understanding of the role of adaptive versus neutral processes in these radiations remains largely speculative. In this study we investigated factors involved in the diversification of Argyroderma, a genus within the most spectacular of the Cape radiations, that of the Ruschioid subfamily of the Aizoaceae. We used amplified fragment length polymorphisms and a suite of morphological traits to elucidate patterns of differentiation within and between species of Argyroderma across the range of the genus. We then used a matrix correlation approach to assess the influence of landscape structure, edaphic gradients, and flowering phenology on phenotypic and neutral genetic divergence in the system. We found evidence for strong spatial genetic isolation at all taxonomic levels. In addition, genetic differentiation occurs along a temporal axis, between sympatric species with divergent flowering times. Morphological differentiation, which previous studies suggest is adaptive, occurs along a habitat axis, between populations occupying different edaphic microenvironments. Morphological differentiation is in turn significantly associated with flowering time shifts. Thus we propose that diversification within Argyroderma has occurred through a process of adaptive speciation in allopatry. Spatially isolated populations diverge phenotypically in response to divergent habitat selection, which in turn leads to the evolution of reproductive isolation through divergence of flowering phenologies, perhaps as a correlated response to morphological divergence. Evidence suggests that diversification of the group has proceeded in two phases: the first involving divergence of allopatric taxa on varied microhabitats within a novel habitat type (the quartz gravel plains), and the second involving range expansion of an early flowering phenotype on the most extreme edaphic habitat and subsequent incomplete differentiation of allopatric populations of the early flowering group. These results point to adaptive speciation in allopatry as a likely model for the spectacular diversification of the ice-plant family in the dissected landscapes of the southern African winter rainfall deserts.

Aizoaceae↗
PubMed2004

Isolation, characterization, and evolutionary divergence of mouse RNase 6: evidence for unusual evolution in rodents.

The evolution of the ribonuclease A (RNase A) vertebrate-specific enzyme family is interesting in that specific gene lineages appear to be responding to unique selective pressures in wildly diverse manners to generate proteins that are capable of reducing the infectivity of viruses, killing systemic pathogens, and inducing the growth of blood vessels all while maintaining the signature motifs of a ribonuclease. In this paper, we present the DNA sequence and gene structure of Mus musculus RNase 6 and examine the expression pattern and enzymatic activity of the recombinant protein. M. musculus RNase 6 has a limited expression pattern compared to human RNase 6 and is an efficient ribonuclease, with a catalytic efficiency 17-fold higher than that of human protein. Evolutionary analysis reveals that RNase 6 was subject to unusual evolutionary forces (dN/dS = 1.2) in an ancestral rodent lineage before the separation of Mus and Rattus. However, more recent evolution of rodent RNase 6 has been relatively conserved, with an average dN/dS of 0.66. These data suggest that the ancestral rodent RNase 6 was subject to accelerated evolution, resulting in the conserved modern gene, which most likely plays an important role in mouse physiology.

Amino Acid Sequence↗
PubMed1985

Nucleotide sequence divergence and functional constraint in VIP precursor mRNA evolution between human and rat.

The nucleotide sequence analysis of cloned cDNA for VIP precursor from rat cerebral cortex reveals that the precursor contains both rat VIP and PHI-27. The deduced primary structure of rat VIP is identical with human VIP. The amino acid sequence of rat PHI-27 differs by 4 amino acids from human PHM-27. When each VIP precursor is divided functionally into 6 domains, the amino acid sequence homology between rat and human precursors ranges from 69 to 100%. In contrast, any domain exhibits an essentially equal degree of nucleotide sequence homology.

Amino Acid Sequence↗
PubMed1988

Mosaic evolution of prepropancreatic polypeptide. II. Structural conservation and divergence in pancreatic polypeptide gene.

We demonstrated that nucleotide and amino acid sequences in the carboxyl-terminal regions of rat, mouse, and human prepropancreatic polypeptide exhibit a high degree of divergence, whereas the amino-terminal domains are highly conserved. To understand the molecular basis of this divergence and conservation, we determined the nucleotide sequence of the rat pancreatic polypeptide gene from an islet genomic library and compared it with that of the human gene. Exon 2 of the rat gene encodes the signal peptide and pancreatic polypeptide, exon 3 encodes the carboxyl-terminal region, and exons 1 and 4 encode the 5'- and 3'- untranslated regions of the mRNA, respectively. Exons 1 and 2 of rat and human genes are well conserved. The rat and human genes, however, have exons 3 and 4 of different lengths and heterologous nucleotide sequences. Mutational accumulation in exons 3 and 4 and intron 3 of the rat gene appears to have caused splice junction sliding and translational frameshift, resulting in a structural divergence in the carboxyl-terminal region. Available evidence indicates that the mosaicism of structural conservation and divergence in pancreatic polypeptide genes may have been caused by a difference in the evolutionary rates of the genomic regions.

Amino Acid Sequence↗
PubMed2003

Gene loss, protein sequence divergence, gene dispensability, expression level, and interactivity are correlated in eukaryotic evolution.

Lineage-specific gene loss, to a large extent, accounts for the differences in gene repertoires between genomes, particularly among eukaryotes. We derived a parsimonious scenario of gene losses for eukaryotic orthologous groups (KOGs) from seven complete eukaryotic genomes. The scenario involves substantial gene loss in fungi, nematodes, and insects. Based on this evolutionary scenario and estimates of the divergence times between major eukaryotic phyla, we introduce a numerical measure, the propensity for gene loss (PGL). We explore the connection among the propensity of a gene to be lost in evolution (PGL value), protein sequence divergence, the effect of gene knockout on fitness, the number of protein-protein interactions, and expression level for the genes in KOGs. Significant correlations between PGL and each of these variables were detected. Genes that have a lower propensity to be lost in eukaryotic evolution accumulate fewer substitutions in their protein sequences and tend to be essential for the organism viability, tend to be highly expressed, and have many interaction partners. The dependence between PGL and gene dispensability and interactivity is much stronger than that for sequence evolution rate. Thus, propensity of a gene to be lost during evolution seems to be a direct reflection of its biological importance.

Amino Acid Substitution↗
PubMed1997

A cottontail rabbit papillomavirus strain (CRPVb) with strikingly divergent E6 and E7 oncoproteins: An insight in the evolution of papillomaviruses.

We previously observed that warts induced by an isolate of cottontail rabbit papillomavirus (CRPV) showed incomplete instead of systemic regression in some domestic rabbits. We report that the viral isolate contained, as a major component, a CRPV strain (CRPVb) showing an unexpectedly high divergence in the E6 and E7 open reading frames (ORFs), compared to the prototype CRPVa present in the isolate as a minor component. The E6 and E7 oncoproteins of CRPVa and -b disclosed only 87.5% identical amino acids and differed in size by three and two amino acids, respectively. This divergence involved (i) a great number (4.4%) of nucleotide substitutions and a high rate (83.3%) of nonsynonymous mutations; (ii) mutations changing the E6 and E7 stop codons; and (iii) in-frame sequence insertions in the E6 ORF (18 nucleotides) and downstream of the mutated E7 stop codon (6 nucleotides), both likely to result from a duplication of adjacent sequences. These extensive differences could account for distinct biological and antigenic properties. Strikingly, only four (0.8%) amino acids of the L1 major capsid protein were variable. Thus, it seems likely that sequence duplications and mutations affecting stop codons exert a strong selection pressure on the fixation of nonsynonymous mutations and that phylogenetic calculations based only on point mutations may misevaluate the time scale of the evolution of papillomaviruses.

Amino Acid Sequence↗
PubMed1996

The emergence of major cellular processes in evolution.

The phylogenetic distribution of divergently related protein families into the three domains of life (archaea, bacteria and eukaryotes) can signify the presence or absence of entire cellular processes in these domains and their ancestors. We can thus study the emergence of the major transitions during cellular evolution, and resolve some of the controversies surrounding the evolutionary status of archaea and the origins of the eukaryotic cell. In view of the ongoing projects that sequence the complete genomes of several Archaea, this work forms a testable prediction when the genome sequences become available. Using the presence of the protein families as taxonomic traits, and linking them to biochemical pathways, we are able to reason about the presence of the corresponding cellular processes in the last universal ancestor of contemporary cells. The analysis shows that metabolism was already a complex network of reactions which included amino acid, nucleotide, fatty acid, sugar and coenzyme metabolism. In addition, genetic processes such as translation are conserved and close to the original form. However, other processes such as DNA replication and repair or transcription are exceptional and seem to be associated with the structural changes that drove eukaryotes and bacteria away from their common ancestor. There are two major hypotheses in the present work: first, that archaea are probably closer to the last universal ancestor than any other extant life form, and second, that the major cellular processes were in place before the major splitting. The last universal ancestor had metabolism and translation very similar to the contemporary ones, while having an operonic genome organization and archaean-like transcription. Evidently, all cells today contain remnants of the primordial genome of the last universal ancestor.

Archaea↗
PubMed2000

Protein tyrosine phosphatases from amphioxus, hagfish, and ray: divergence of tissue-specific isoform genes in the early evolution of vertebrates.

Since separation from fungi and plants, multicellular animals evolved a variety of gene families involved in cell-cell communication from a limited number of ancestral precursors by gene duplications in two separate periods of animal evolution. In the very early evolution of animals before the separation of parazoans and eumetazoans, animals underwent extensive gene duplications by which different subtypes (subfamilies) with distinct functions diverged. The multiplicity of members (isoforms) in the same subtype increased by further gene duplications (isoform duplications) in the first half of chordate evolution before the fish-tetrapod split; different isoforms are virtually identical in structure and function but differ in tissue distribution. From cloning and phylogenetic analyses of four subfamilies of the protein tyrosine kinase (PTK) family, we recently showed extensive isoform duplications in a limited period around or just before the cyclostome-gnathostome split. To obtain a reliable estimate for the divergence time of vertebrate isoforms, we have conducted isolation of cDNAs encoding the protein tyrosine phosphatases (PTPs) from Branchiostoma belcheri, an amphioxus, Eptatretus burgeri, a hagfish, and Potamotrygon motoro, a ray. We obtained 33 different cDNAs in total, most of which belong to known PTP subfamilies. The phylogenetic analyses of five subfamilies based on the maximum likelihood method revealed frequent isoform duplications in a period around or just before the gnathostome-cyclostome split. An evolutionary implication was discussed in relation to the Cambrian explosion.

Animals↗