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PubMed1992

Evolution of thymidine and thymidylate kinases: the possibility of independent capture of TK genes by different groups of viruses.

Phylogenetic analysis of viral and cellular thymidine and thymidylate kinases was performed using computer-assisted methods. Multiple alignments and tentative phylogenetic trees were generated for the two families of these enzymes, which include a) thymidine kinases (TK) of mammals, poxviruses, African swine fever virus, E. coli, and bacteriophage T4; and b) thymidylate kinases (ThyK) of yeast and poxviruses and distantly related herpesvirus proteins with both enzymatic activities. Analysis of the alignment of the TKs of the first family highlighted three strongly conserved segments. Two of these corresponded to the A and B motifs of the purine NTP-binding pattern. The third, C-terminal segment, showing the highest conservation, encompassed a modified Zn finger motif. It is speculated that this motif might be involved in TK oligomerization. Phylogenetic trees constructed by three different methods suggested that cellular TK genes could be captured independently by T4 bacteriophage, African swine fever virus, fowlpox virus, and the other poxviruses. The observed tree topologies appear to contradict the popular virus-host coevolution schemes and to imply that different subdivisions of poxviruses diverged at earlier stages of evolution than their hosts did. It was shown that deoxynucleoside monophosphate kinase of bacteriophage T4 is related to the ThyK family. Phylogenetic analysis suggested that ThyK genes probably have been acquired independently by phage T4, poxviruses, and herpes-viruses.

Amino Acid Sequence↗
PubMed2006

The biology and evolution of music: a comparative perspective.

Studies of the biology of music (as of language) are highly interdisciplinary and demand the integration of diverse strands of evidence. In this paper, I present a comparative perspective on the biology and evolution of music, stressing the value of comparisons both with human language, and with those animal communication systems traditionally termed "song". A comparison of the "design features" of music with those of language reveals substantial overlap, along with some important differences. Most of these differences appear to stem from semantic, rather than structural, factors, suggesting a shared formal core of music and language. I next review various animal communication systems that appear related to human music, either by analogy (bird and whale "song") or potential homology (great ape bimanual drumming). A crucial comparative distinction is between learned, complex signals (like language, music and birdsong) and unlearned signals (like laughter, ape calls, or bird calls). While human vocalizations clearly build upon an acoustic and emotional foundation shared with other primates and mammals, vocal learning has evolved independently in our species since our divergence with chimpanzees. The convergent evolution of vocal learning in other species offers a powerful window into psychological and neural constraints influencing the evolution of complex signaling systems (including both song and speech), while ape drumming presents a fascinating potential homology with human instrumental music. I next discuss the archeological data relevant to music evolution, concluding on the basis of prehistoric bone flutes that instrumental music is at least 40,000 years old, and perhaps much older. I end with a brief review of adaptive functions proposed for music, concluding that no one selective force (e.g., sexual selection) is adequate to explaining all aspects of human music. I suggest that questions about the past function of music are unlikely to be answered definitively and are thus a poor choice as a research focus for biomusicology. In contrast, a comparative approach to music promises rich dividends for our future understanding of the biology and evolution of music.

Animal Communication↗
PubMed2005

Gene conversion and evolution of Xq28 duplicons involved in recurring inversions causing severe hemophilia A.

Inversions breaking the 1041 bp int1h-1 or the 9.5-kb int22h-1 sequence of the F8 gene cause hemophilia A in 1/30,000 males. These inversions are due to homologous recombination between the above sequences and their inverted copies on the same DNA molecule, respectively, int1h-2 and int22h-2 or int22h-3. We find that (1) int1h and int22h duplicated more than 25 million years ago; (2) the identity of the copies (>99%) of these sequences in humans and other primates is due to gene conversion; (3) gene conversion is most frequent in the internal regions of int22h; (4) breakpoints of int22h-related inversions also tend to involve the internal regions of int22h; (5) sequence variations in a sample of human X chromosomes defined eight haplotypes of int22h-1 and 27 of int22h-2 plus int22h-3; (6) the latter two sequences, which lie, respectively, 500 and 600 kb telomeric to int22h-1 are five-fold more identical when in cis than when in trans, thus suggesting that gene conversion may be predominantly intrachromosomal; (7) int1h, int22h, and flanking sequences evolved at a rate of about 0.1% substitutions per million years during the divergence between humans and other primates, except for int1h during the human-chimpanzee divergence, when its rate of evolution was significantly lower. This is reminiscent of the slower evolution of palindrome arms in the male specific regions of the Y chromosome and we propose, as an explanation, that intrachromosomal gene conversion and cosegregation of the duplicated regions favors retention of the ancestral sequence and thus reduces the evolution rate.

Animals↗
PubMed2002

Nested evolution of a tRNA(Leu)(UAA) group I intron by both horizontal intron transfer and recombination of the entire tRNA locus.

The origin and evolution of bacterial introns are still controversial issues. Here we present data on the distribution and evolution of a recently discovered divergent tRNA(Leu)(UAA) intron. The intron shows a higher sequence affiliation with introns in tRNA(Ile)(CAU) and tRNA(Arg)(CCU) genes in alpha- and beta-proteobacteria, respectively, than with other cyanobacterial tRNA(Leu)(UAA) group I introns. The divergent tRNA(Leu)(UAA) intron is sporadically distributed both within the Nostoc and the Microcystis radiations. The complete tRNA gene, including flanking regions and intron from Microcystis aeruginosa strain NIVA-CYA 57, was sequenced in order to elucidate the evolutionary pattern of this intron. Phylogenetic reconstruction gave statistical evidence for different phylogenies for the intron and exon sequences, supporting an evolutionary model involving horizontal intron transfer. The distribution of the tRNA gene, its flanking regions, and the introns were addressed by Southern hybridization and PCR amplification. The tRNA gene, including the flanking regions, were absent in the intronless stains but present in the intron-containing strains. This suggests that the sporadic distribution of this intron within the Microcystis genus cannot be attributed to intron mobility but rather to an instability of the entire tRNA(Leu)(UAA) intron-containing genome region. Taken together, the complete data set for the evolution of this intron can best be explained by a model involving a nested evolution of the intron, i.e., wherein the intron has been transferred horizontally (probably through a single or a few events) to a tRNA(Leu)(UAA) gene which is located within a unstable genome region.

Base Sequence↗
PubMed2002

Role of a locus control region in the mutually exclusive expression of human red and green cone pigment genes.

Trichromacy in humans and other Old World primates evolved from a dichromatic color vision system approximately 30-40 million years ago. One essential part of this evolution was the duplication and divergence of sequences on the X chromosome to create the present-day red and green cone pigment genes. Earlier work demonstrated that a locus control region (LCR) located upstream of these genes is essential for their expression. In the present work, we have generated a variety of modified human red and green pigment gene arrays that direct the expression of distinguishable histochemical reporters from each gene promoter. Transgenic mice carrying a single copy of each modified array were studied to define the role of three variables in producing mutually exclusive expression of red and green pigment transgenes: the distance between the promoter and the LCR, the identity of the visual pigment promoter, and LCR copy number. The results support a model in which the mutually exclusive expression of these genes in their respective cone types is controlled by competition between visual pigment promoters for pairing with the LCR, and they suggest a facile mechanism for the evolution of trichromacy after visual pigment gene duplication.

Animals↗
PubMed1996

A novel endogenous mouse mammary tumor virus locus in Asian wild mice and its evolutionary divergency.

The divergency of endogenous mouse mammary tumor virus (MMTV) in European mouse strains indicates acquisition of exogenous MMTV into their genomes during evolution. In the present study, we selected two strains of Asian wild mice, Cas-Hmi (Mus musculus castaneus) and Sub-Kjr (M. m. subspecies) to investigate a possible divergency of endogenous MMTVs among Asian mouse strains. Southern blot analysis and polymerase chain reaction (PCR) demonstrated that Cas-Hmi and Sub-Kjr have the full structure of integrated endogenous MMTVs, suggesting that these mice were diverged during evolution after MMTV endemics.

Animals↗
PubMed2001

Divergence of function in sequence-related groups of Escherichia coli proteins.

The most prominent mechanism of molecular evolution is believed to have been duplication and divergence of genes. Proteins that belong to sequence-related groups in any one organism are candidates to have emerged from such a process and to share a common ancestor. Groups of proteins in Escherichia coli having sequence similarity are mostly composed of proteins with closely related function, but some groups comprise proteins with unrelated functions. In order to understand how function can change while sequences remain similar, we have examined some of these groups in detail. The enzymes analyzed in this work include representatives of amidotransferases, phosphotransferases, decarboxylases, and others. Most sequence-related groups contain enzymes that are in the same classes of Enzyme Commission (EC) numbers. We have concentrated on groups that are heterogeneous in that respect, and also on groups containing more than one enzyme of any pathway. We find that although the EC number may differ, the reaction chemistry of these sequence-related proteins is the same or very similar. Some of these families illustrate how diversification has taken place in evolution, using common features of either reaction chemistry or ligand specificity, or both, to create catalysts for different kinds of biochemical reactions. This information has relevance to the area of functional genomics in which the activities of gene products of unknown reading frames are attributed by analogy to the functions of sequence-related proteins of known function.

Bacterial Proteins↗
PubMed2000

Phylogenetic analyses indicate that the 19'Hexanoyloxy-fucoxanthin-containing dinoflagellates have tertiary plastids of haptophyte origin.

The three anomalously pigmented dinoflagellates Gymnodinium galatheanum, Gyrodinium aureolum, and Gymnodinium breve have plastids possessing 19'-hexanoyloxy-fucoxanthin as the major carotenoid rather than peridinin, which is characteristic of the majority of the dinoflagellates. Analyses of SSU rDNA from the plastid and the nuclear genome of these dinoflagellate species indicate that they have acquired their plastids via endosymbiosis of a haptophyte. The dinoflagellate plastid sequences appear to have undergone rapid sequence evolution, and there is considerable divergence between the three species. However, distance, parsimony, and maximum-likelihood phylogenetic analyses of plastid SSU rRNA gene sequences place the three species within the haptophyte clade. Pavlova gyrans is the most basal branching haptophyte and is the outgroup to a clade comprising the dinoflagellate sequences and those of other haptophytes. The haptophytes themselves are thought to have plastids of a secondary origin; hence, these dinoflagellates appear to have tertiary plastids. Both molecular and morphological data divide the plastids into two groups, where G. aureolum and G. breve have similar plastid morphology and G. galatheanum has plastids with distinctive features.

Animals↗
PubMed2005

Duplication-divergence model of protein interaction network.

We investigate a very simple model describing the evolution of protein-protein interaction networks via duplication and divergence. The model exhibits a remarkably rich behavior depending on a single parameter, the probability to retain a duplicated link during divergence. When this parameter is large, the network growth is not self-averaging and an average node degree increases algebraically. The lack of self-averaging results in a great diversity of networks grown out of the same initial condition. When less than a half of links are (on average) preserved after divergence, the growth is self-averaging, the average degree increases very slowly or tends to a constant, and a degree distribution has a power-law tail. The predicted degree distributions are in a very good agreement with the distributions observed in real protein networks.

Computer Simulation↗
PubMed1989

The evolution of lysozyme and alpha-lactalbumin.

From the analysis of phylogenetic trees constructed from the amino acid sequences and metal-binding properties of various lysozymes c and alpha-lactalbumins, it was found that before the divergence of the lineages of birds and mammals, calcium-binding lysozyme diverged from non-calcium-binding lysozyme. alpha-Lactalbumin evolved from the calcium-binding lysozyme along the mammalian lineage after the divergence of birds and mammals. Rapid evolution took place, not in the process of acquisition of the activity of alpha-lactalbumin, but after the loss of lysozyme activity, due to the change in the distribution of selective pressure on each amino acid site. A general process for the change in function of a protein during evolution is suggested to be as follows: after duplication of the gene, one of their protein products acquires a new function, besides that already present; the old function is eventually lost.

Amino Acid Sequence↗
PubMed1998

Estimation of evolutionary distances under stationary and nonstationary models of nucleotide substitution.

Estimation of evolutionary distances has always been a major issue in the study of molecular evolution because evolutionary distances are required for estimating the rate of evolution in a gene, the divergence dates between genes or organisms, and the relationships among genes or organisms. Other closely related issues are the estimation of the pattern of nucleotide substitution, the estimation of the degree of rate variation among sites in a DNA sequence, and statistical testing of the molecular clock hypothesis. Mathematical treatments of these problems are considerably simplified by the assumption of a stationary process in which the nucleotide compositions of the sequences under study have remained approximately constant over time, and there now exist fairly extensive studies of stationary models of nucleotide substitution, although some problems remain to be solved. Nonstationary models are much more complex, but significant progress has been recently made by the development of the paralinear and LogDet distances. This paper reviews recent studies on the above issues and reports results on correcting the estimation bias of evolutionary distances, the estimation of the pattern of nucleotide substitution, and the estimation of rate variation among the sites in a sequence.

Animals↗
PubMed1991

Homeobox genes in mouse development.

Following the discovery of the homeobox as a conserved sequence in developmentally important genes of Drosophila, a plethora of such sequences have been identified in evolutionarily distant organisms. Among mammals, the mouse homeobox genes have been studied most intensively with a hope of deciphering basic mechanisms of embryonic development. The genomic arrangement of many mouse homeobox genes is similar to the organization of the Drosophila genes, suggesting that they arose as a consequence of gene duplication and divergence from a primordial cluster during evolution. Homeobox genes encode proteins that may form a part of the autoregulatory and transregulatory network specifying positional value in the embryo. Supporting this view, the more diverged members of this growing family function as transcription factors, some of which regulate the expression of tissue-specific genes. Mouse homeobox genes are expressed during embryonic development in a spatially restricted manner and alterations in their expression pattern can disrupt embryonic development. The implications of these findings will be discussed in the context of the role of homeobox genes in the embryonic development of Drosophila and other organisms.

Amino Acid Sequence↗
PubMed2003

Recent duplication of the common carp (Cyprinus carpio L.) genome as revealed by analyses of microsatellite loci.

Genome duplications may have played a role in the early stages of vertebrate evolution, near the time of divergence of the lamprey lineage. Additional genome duplication, specifically in ray-finned fish, may have occurred before the divergence of the teleosts. The common carp (Cyprinus carpio) has been considered tetraploid because of its chromosome number (2n = 100) and its high DNA content. We studied variation using 59 microsatellite primer pairs to better understand the ploidy level of the common carp. Based on the number of PCR amplicons per individual, about 60% of these primer pairs are estimated to amplify duplicates. Segregation patterns in families suggested a partially duplicated genome structure and disomic inheritance. This could suggest that the common carp is tetraploid and that polyploidy occurred by hybridization (allotetraploidy). From sequences of microsatellite flanking regions, we estimated the difference per base between pairs of alleles and between pairs of paralogs. The distribution of differences between paralogs had two distinct modes suggesting one whole-genome duplication and a more recent wave of segmental duplications. The genome duplication was estimated to have occurred about 12 MYA, with the segmental duplications occurring between 2.3 and 6.8 MYA. At 12 MYA, this would be one of the most recent genome duplications among vertebrates. Phylogenetic analysis of several cyprinid species suggests an evolutionary model for this tetraploidization, with a role for polyploidization in speciation and diversification.

Animals↗
PubMed1980

Repetitions in the NH2-terminal amino acid sequence of beta-ketoadipate enol-lactone hydrolase from Pseudomonas putida.

Muconolactone delta-isomerase (EC 5.3.3.4) and beta-ketoadipate enol-lactone hydrolase (EC 3.1.1.24) mediate consecutive reactions in the beta-ketoadipate pathway of bacteria. An earlier investigation (Yeh, W.K., Davis, G., Fletcher, P., and Ornston, L.N. (1978) J. Biol. Chem. 253, 4920-4923) revealed that the respective NH2-terminal amino acid sequences of Pseudomonas putida muconolactone isomerase and Acinetobacter calcoaceticus beta-ketoadipate enol-lactone hydrolase II are evolutionarily homologous. In this report, we describe the purification of Pseudomonas beta-ketoadipate enol-lactone hydrolase and present evidence indicating that the protein is a trimer composed of identical 11,000-dalton subunits. The NH2-terminal amino acid sequences of Pseudomonas muconolactone isomerase and Pseudomonas enol-lactone hydrolase have diverged widely from each other, yet the two sequences contain different fragments of an ancestral sequence which is represented in Acinetobacter enol-lactone hydrolase II. The widely divergent Pseudomonas muconolactone isomerase and Pseudomonas enol-lactone hydrolase sequences each contain unique sets of repeated peptides. In principle, the repetitive sequences might have been introduced by elongation mutations which occurred early in the evolution of the proteins. However, the divergence of Pseudomonas muconolactone isomerase and Pseudomonas enol-lactone hydrolase is so extreme that the observed sequence repetitions cannot have been conserved from ancestral duplication mutations. Rather, the data favor the interpretation that copies of DNA were substituted into structural genes for the enzymes as they diverged.

Adipates↗
PubMed2006

Evolution of cis elements in the differential expression of two Hoxa2 coparalogous genes in pufferfish (Takifugu rubripes).

Sequence divergence in cis-regulatory elements is an important mechanism contributing to functional diversity of genes during evolution. Gene duplication and divergence provide an opportunity for selectively preserving initial functions and evolving new activities. Many vertebrates have 39 Hox genes organized into four clusters (Hoxa-Hoxd); however, some ray-finned fishes have extra Hox clusters. There is a single Hoxa2 gene in most vertebrates, whereas fugu (Takifugu rubripes) and medaka (Oryzias latipes) have two coparalogous genes [Hoxa2(a) and Hoxa2(b)]. In the hindbrain, both genes are expressed in rhombomere (r) 2, but only Hoxa2(b) is expressed in r3, r4, and r5. Multiple regulatory modules directing segmental expression of chicken and mouse Hoxa2 genes have been identified, and each module is composed of a series of discrete elements. We used these modules to investigate the basis of differential expression of duplicated Hoxa2 genes, as a model for understanding the divergence of cis-regulatory elements. Therefore, we cloned putative regulatory regions of the fugu and medaka Hoxa2(a) and -(b) genes and assayed their activity. We found that these modules direct reporter expression in a chicken assay, in a manner corresponding to their endogenous expression pattern in fugu. Although sequence comparisons reveal many differences between the two coparalogous genes, specific subtle changes in seven cis elements of the Hoxa2(a) gene restore segmental regulatory activity. Therefore, drift in subsets of the elements in the regulatory modules is responsible for the differential expression of the two coparalogous genes, thus providing insight into the evolution of cis elements.

Animals↗
PubMed1999

Mosaic evolution of ruminant stomach lysozyme genes.

The genomes of ruminant artiodactyls, such as cow and sheep, have approximately 10 lysozyme genes, 4 of which are expressed in the stomach. Most of the duplications of the lysozyme genes occurred 40-50 million years ago, before the divergence of cow and sheep. Despite this, the coding regions of stomach lysozyme genes within a species (e.g., cow, sheep, or deer) are more similar to each other than to lysozyme genes in other ruminants. This observation suggests that the coding regions of the stomach lysozyme genes have evolved in a concerted fashion. Our previous characterization of 3 cow stomach lysozyme genes suggested that it was only the coding exons that had participated in concerted evolution. To determine whether the introns and flanking regions of ruminant stomach lysozyme genes are evolving in a concerted or a divergent fashion, we have isolated and characterized 2 sheep stomach lysozyme genes. Comparison of the sequences of the sheep and cow stomach lysozyme genes clearly shows that the introns and flanking regions have evolved, like the 3' untranslated region of the mRNAs, in a divergent manner. Thus, if the four coding exons are evolving by concerted evolution, then a mosaic pattern of concerted and divergent evolution is occurring in these genes. The independent concerted evolution of coding exons of the ruminant stomach lysozyme gene may have assisted in the accelerated adaptive evolution of the lysozyme to new function in the early ruminant.

3' Untranslated Regions↗
PubMed1996

A molecular and evolutionary study of the beta-globin gene family of the Australian marsupial Sminthopsis crassicaudata.

Beta-globin gene families in eutherians (placental mammals) consist of a set of four or more developmentally regulated genes which are closely linked and, in general, arranged in the order 5'-embryonic/fetal genes-adult genes-3'. This cluster of genes is proposed to have arisen by tandem duplication of ancestral beta-globin genes, with the first duplication occurring 200 to 155 MYBP just prior to a period in mammalian evolution when eutherians and marsupials diverged from a common ancestor. In this paper we trace the evolutionary history of the beta-globin gene family back to the origins of these mammals by molecular characterization of the beta-globin gene family of the Australian marsupial Sminthopsis crassicaudata. Using Southern and restriction analysis of total genomic DNA and bacteriophage clones of beta-like globin genes, we provide evidence that just two functional beta-like globin genes exist in this marsupial, including one embryonic-expressed gene (S.c-epsilon) and one adult-expressed gene (S.c-beta), linked in the order 5'-epsilon-beta-3'. The entire DNA sequence of the adult beta-globin gene is reported and shown to be orthologous to the adult beta-globin genes of the North American marsupial Didelphis virginiana and eutherian mammals. These results, together with results from a phylogenetic analysis of mammalian beta-like globin genes, confirm the hypothesis that a two-gene cluster, containing an embryonic- and an adult-expressed beta-like globin gene, existed in the most recent common ancester of marsupials and eutherians. Northern analysis of total RNA isolated from embryos and neonatals indicates that a switch from embryonic to adult gene expression occurs at the time of birth, coinciding with the transfer of the marsupial from a uterus to a pouch environment.

Age Factors↗
PubMed2006

Drosophila flies in "Evolution Canyon" as a model for incipient sympatric speciation.

The genetic basis of population divergence leading to adaptive radiation and speciation is a major unresolved problem of evolutionary biology. Molecular elucidation of "speciation genes" advanced recently, yet it remains without clear identification of the gene complexes participating in reproductive isolation between natural populations, particularly, in sympatry. Genetic divergence was discovered between Drosophila melanogaster populations inhabiting ecologically contrasting, opposite slopes in "Evolution Canyon" (EC), Mt. Carmel, Israel. Interslope migration of flies is easy and verified. Nevertheless, significant interslope D. melanogaster population divergence was established at EC involving habitat choice, mate choice, thermal and drought tolerances, adaptive genes, and mobile elements. Parallel patterns of stress tolerance, habitat choice, and mate choice were demonstrated in Drosophila simulans at EC, although on a smaller scale. However, some tests for interslope genetic differentiation in Drosophila, derived from the opposite EC slopes, gave somewhat controversial results. Here we present new empirical data on interslope genetic divergence of Drosophila at EC, and summarize previous supporting and controversial results. We suggest that Drosophila populations at EC represent a rare example, demonstrating how selection overrides migration, and propose an ad hoc ecological model of incipient sympatric divergence.

Adaptation, Biological↗