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PubMed2004

Multiple genotypes of influenza B virus circulated between 1979 and 2003.

The segmented genome of influenza B virus allows exchange of gene segments between cocirculating strains. Through this process of reassortment, diversity is generated by the mixing of genes between viruses that differ in one or more gene segments. Phylogenetic and evolutionary analyses of all 11 genes of 31 influenza B viruses isolated from 1979 to 2003 were used to study the evolution of whole genomes. All 11 genes diverged into two new lineages prior to 1987. All genes except the NS1 gene were undergoing linear evolution, although the rate of evolution and the degree to which nucleotide changes translated into amino acid changes varied between lineages and by gene. Frequent reassortment generated 14 different genotypes distinct from the gene constellation of viruses circulating prior to 1979. Multiple genotypes cocirculated in some locations, and a sequence of reassortment events over time could not be established. The surprising diversity of the viruses, unrestricted mixing of lineages, and lack of evidence for coevolution of gene segments do not support the hypothesis that the reassortment process is driven by selection for functional differences.

Biological Evolution↗

PubMed2006

Large punctuational contribution of speciation to evolutionary divergence at the molecular level.

A long-standing debate in evolutionary biology concerns whether species diverge gradually through time or by punctuational episodes at the time of speciation. We found that approximately 22% of substitutional changes at the DNA level can be attributed to punctuational evolution, and the remainder accumulates from background gradual divergence. Punctuational effects occur at more than twice the rate in plants and fungi than in animals, but the proportion of total divergence attributable to punctuational change does not vary among these groups. Punctuational changes cause departures from a clock-like tempo of evolution, suggesting that they should be accounted for in deriving dates from phylogenies. Punctuational episodes of evolution may play a larger role in promoting evolutionary divergence than has previously been appreciated.

Animals↗

PubMed2001

The Adaptive Evolution Database (TAED).

BACKGROUND: Developing an understanding of the molecular basis for the divergence of species lies at the heart of biology. The Adaptive Evolution Database (TAED) serves as a starting point to link events that occur at the same time in the evolutionary history (tree of life) of species, based upon coding sequence evolution analyzed with the Master Catalog. The Master Catalog is a collection of evolutionary models, including multiple sequence alignments, phylogenetic trees, and reconstructed ancestral sequences, for all independently evolving protein sequence modules encoded by genes in GenBank [1]. RESULTS: We have estimated from these models the ratio of nonsynonymous to synonymous nucleotide substitution (Ka/Ks), for each branch in their respective evolutionary trees of every subtree containing only chordata or only embryophyta proteins. Branches with high Ka/Ks values represent candidate episodes in the history of the family where the protein may have undergone positive selection, a phenomenon in molecular evolution where the mutant form of a gene must have conferred more fitness than the ancestral form. Such episodes are frequently associated with change in function. We have found that an unexpectedly large number of families (between 10 and 20% of those families examined) have at least one branch with a notably high Ka/Ks value (putative adaptive evolution). As a resource for biologists wishing to understand the interaction between protein sequences and the Darwinian processes that shape these sequences, we have collected these into The Adaptive Evolution Database (TAED). CONCLUSIONS: Placed in a phylogenetic perspective, candidate genes that are undergoing evolution at the same time in the same lineage can be viewed together. This framework based upon coding sequence evolution can be readily expanded to include other types of evolution. In its present form, TAED provides a resource for bioinformaticists interested in data mining and for experimental evolutionists seeking candidate examples of adaptive evolution for further experimental study.

Animals↗

PubMed2026

Genome Wide Analysis Reveals Divergence and Ancestral Origins of Min Pigs.

The Min pig, a representative northern Chinese indigenous breed, carries a unique ancestral background shaped by the historical phylogeography of Northeast Asia. This study aimed to dissect the population structure, temporal genetic divergence, and ancestral composition of Min pigs, trace their evolutionary origin, and identify trait-linked functional genes, providing information regarding their evolutionary history and conservation. We analyzed 61 Min pigs sampled across nearly 20 years and 701 reference pigs comprising other Chinese indigenous breeds, Western commercial lines, and Chinese wild boars, using PCA, NJ phylogenetic analysis, Admixture, TreeMix, D-statistic, f4-ratio, and combined selection signature scans (sliding-window FST, XP-EHH, and π-ratio). Clear genetic stratification was observed among Min pig subpopulations, reflecting long-term divergence under natural and artificial selection. PCA and Admixture (K = 2-4) separated East Asian indigenous and Western ancestral components, verifying an admixed Northeast Asian origin with a dominant ancient East Asian component and a Western component. Compared with early-2000s Min pigs, contemporary individuals are genetically closer to Western breeds and exhibit a more scattered structure due to shifted ancestral component proportions, further confirmed by D-statistic and f4-ratio values. We identified 321 differentiated SNP loci based on the Animal QTL database, corresponding to core candidate genes (AKT3, ACACA, MAP3K5, FGFR4, C3, and SERPINC1) enriched for meat quality, growth, reproduction, immunity, energy metabolism, and MAPK/PI3K-Akt/AMPK pathways. This study reveals Min pigs' admixed origin and temporal divergence, clarifying their Northeast Asian evolution and providing molecular markers for genetic monitoring and conservation.

Animals↗

PubMed1997

Cloning and origin of the two forms of chicken vitamin D receptor.

The cDNA for the chicken vitamin D receptor (VDR) has been cloned in full length by screening cDNA libraries from chicken intestine and chicken kidney. The chicken kidney cDNA library constructed by both oligo(dT) and random primer methods yielded several full-length clones. These contained a 66-bp additional coding sequence at the 5' end in comparison to the cDNAs of human, rat, and mouse VDR. The Japanese quail VDR cDNA was also cloned in full length. We found that the 5' coding sequence reported previously had been artifactually inverted. Both chicken and quail cDNAs have three conserved ATG sites for translation initiation with the 3' one corresponding to the only ATG site found in the mammalian cDNAs. Northern blot analysis showed that the VDR gene is expressed as a single 2.69-kb transcript in chicken intestine and kidney. An analysis of the avian multiple ATG sites revealed that the first ATG is in a suboptimal context of TCCATGT, while the second ATG is in AGC-ATGG, matching the optimal context: R-3NNATGG+4. As a result, the two forms of chicken VDR (cVDR) (form A, 60.3 kDa; form B, 58.6 kDa) likely arise from the first and second ATG sites of a single mRNA during translation. Mutational analysis confirmed this belief. The wild-type construct starting from the first ATG site with its original context was subcloned into pCMV5 expression vector and expressed in COS-1 cells. Two receptor proteins, exactly comigrating with the form A and form B cVDRs isolated from chicken intestine, were detected by immunoblotting. Point mutations optimizing the first ATG context led to exclusive production of form A, while knocking out the first ATG site resulted in the sole generation of form B. Form A translated from the first ATG site has 451 amino acids, and form B from the second ATG has 437 amino acids. Comparison between avian and mammalian VDRs indicated that VDR is essentially conserved in DNA binding and ligand binding domains. The significant difference especially at the N-terminus demonstrates divergence of this receptor during evolution of these species.

Amino Acid Sequence↗

PubMed2000

Reactivity of the cysteine residues in the protein splicing active center of the Mycobacterium tuberculosis RecA intein.

Protein splicing involves the self-catalyzed excision of an intervening polypeptide segment, an intein, from a precursor protein. The first two steps in the protein splicing process lead to the formation of ester intermediates through nucleophilic attacks by the side chains of cysteine, serine, or threonine residues adjacent to the splice junctions. Since both nucleophilic residues in the Mycobacterium tuberculosis RecA intein are cysteine, their reactivities could be compared by sulfhydryl group titration. This was accomplished by using fusion proteins containing a truncated RecA intein modified by mutation to prevent protein splicing, in which the cysteines at the splice junctions were the only sulfhydryl groups. The ability to undergo hydroxylamine-induced cleavage at the upstream splice junction showed that the modified intein was not impaired in the ability to form ester intermediates. Sulfhydryl titration with iodoacetamide, monitored by quantitating the residual thiols after reaction with a maleimide derivative of biotin, revealed a striking difference in the apparent pK(a) values of the cysteines at the two splice junctions. The apparent pK(a) of the cysteine at the upstream splice junction, which initiates the N-S acyl rearrangement leading to the linear ester intermediate, was approximately 8.2, whereas that of the cysteine residue at the downstream splice junction, which initiates the transesterification reaction converting the linear ester to the branched ester intermediate, was about 5.8. This suggests that the transesterification step is facilitated by an unusually low pK(a) of the attacking thiol group. Comparison of the rates of cleavage of the linear ester intermediates derived from the M. tuberculosis RecA and the Saccharomyces cerevisiae VMA inteins by dithiothreitol and hydroxylamine revealed that the former reacted relatively more slowly with dithiothreitol, suggesting that the RecA intein has diverged in the course of evolution to react preferentially with thiolate anions and thus lacks the basic groups that may facilitate nucleophilic attack by thiols in other inteins.

Amino Acid Substitution↗

PubMed2000

Ancestral lineages of arbuscular mycorrhizal fungi (Glomales).

Using new and existing 18S rRNA sequence data, we show that at least five species of glomalean fungi lie outside the previously defined families and diverged very early in the evolution of that group. These five fungi would have been missed by many previous ecological studies because their sequences are not well matched to available taxon-specific primers and they do not stain well with the standard reagents used for morphological analysis. Based upon spore morphology, these species are currently assigned to Glomus and Acaulospora, and two of the species are dimorphic, exhibiting spore stages of both genera. This suggests that dimorphic spores are the ancestral state for the order and that one or the other morphology was lost in various lineages. Our analyses also show that Geosiphon pyriforme, a symbiont with cyanobacteria, is not necessarily a sister group of the Glomales; instead, it may be derived from mycorrhizal ancestors.

DNA, Fungal↗

PubMed1995

Enzymes: chemistry and biochemistry.

Basic principles underlying enzyme action are considered. Catalytic antibodies (abzymes), catalytic RNA (ribozymes), and non-biological counterparts of enzyme-catalyzed reactions are mentioned. Enzyme evolution is considered in terms of divergence, convergence, and lateral gene transfer.

Amino Acid Sequence↗

PubMed1990

A new Igk-V gene family in the mouse.

We have identified and characterized a novel mouse Igk-V gene family, which we have designated Igk-V34. Southern hybridization and nucleotide sequence analysis indicate that this family is comprised of either one or two members in mice of different Igk haplotypes. The gene family members share between 95% and 98% sequence similarity, indicating that they diverged only recently during the evolution of the Igk locus. Sequence relationships between members of this family are discussed.

Amino Acid Sequence↗

PubMed1993

Rapid divergence of Agrobacterium vitis octopine-cucumopine Ti plasmids from a recent common ancestor.

The octopine/cucumopine (o/c) Ti plasmids of the grapevine-associated Agrobacterium vitis strains constitute a family of related DNA molecules. Restriction maps were established of two limited-host-range o/c Ti plasmids, pTiAg57 and pTiAB3, and of the wide-host-range o/c Ti plasmid pTiHm1. Together with the previously obtained map of the wide-host-range o/c Ti plasmid pTiTm4, about 1000 kb were mapped with a resolution of 0.2 kb, allowing a detailed comparison of the various structures. One region of the o/c Ti plasmids is highly conserved and differs mainly by the presence or absence of relatively small DNA fragments (0.9-2.7 kb); the other region has been modified more extensively and carries large sequences specific for each Ti plasmid type. The sequence similarity within large conserved regions shows that these plasmids have diverged recently and that their evolution was driven by large-scale genetic events rather than single nucleotide changes. These results have important implications for studies on bacterial evolution.

Arginine↗

PubMed1984

Catalytic properties of alcohol dehydrogenase isozymes specified by duplicate genes in the diploid plant Stephanomeria exigua.

The alcohol dehydrogenase (ADH) isozymes induced in flooded roots of the diploid plant Stephanomeria exigua are specified by tightly linked genes comprising a complex locus, Adh1. Individuals homozygous for a complex with two active genes which specify electrophoretically different subunits have three ADH-1 isozymes, two intragenic homodimers and an intergenic heterodimer. Individual isozymes were partially purified from plants homozygous for several different Adh1 complexes and apparent Km values for acetaldehyde, ethanol, NAD, and NADH and responses to temperature, pH, and two different alcohols were determined. The two homodimeric enzymes specified by a particular Adh1 complex generally differed in one or more of the properties studied, and in three of four cases, intergenic heterodimers differed significantly from intermediacy, often having lower Km values than either homodimer. None of the isozymes studied could be considered greatly divergent or defective. Constraints on evolution of duplicate genes which form intergenic heterodimers are considered.

Alcohol Dehydrogenase↗

PubMed1984

Characterization of reiterated human DNA with respect to mammalian X chromosome homology.

Recombinants containing human repetitive DNA sequences were identified by dot hybridization and classified with respect to presence on the X chromosome and homology to mouse DNA. Using genomic probes that differ in number of X chromosomes, we observed extensive homology between human autosomal and X sequences. Hybridization to genomic probes that differ in species of origin indicate that these reiterated sequences have diverged between mouse and man. Eleven recombinants, each containing a different reiterated sequence(s), were hybridized in situ to metaphase chromosomes of mouse and man. These studies indicate that reiterated DNA which is homologous to the human X chromosome is more similar to DNA of human autosomes than to any murine chromosome. Therefore, it seems that reiterated DNA sequences on the human X chromosome have diverged as much during mammalian evolution as sequences on human autosomes. Moreover, the extensive modification of the original mammalian X has not interferred with the X inactivation process.

Animals↗

PubMed1996

Roles of the conserved serines of metallothionein in cadmium binding.

The sequence of six amino acid residues -Ser-Cys-Cys-Ser-Cys-Cys- is present in all mammalian metallothionein sequences and has been highly conserved during evolution, although the metallothioneins have divergent primary sequences. To determine whether two serines in the sequence play a crucial role in metal-binding of metallothioneins, a mutant metallothionein with these two serines replaced by leucines was obtained using an Escherichia coli expression system. The expressed protein was analyzed for its chemical and spectroscopic properties. It was confirmed that the mutant metallothionein (MT) bound cadmium through a metal-thiolate complex and that there was no strong difference between the mutant and the wild-type MTs in retaining the metal-binding cluster. However, the metal-binding cluster of the mutant metallothionein was more unstable than that of the wild-type metallothionein. The two conservative serines could play a role in the stability of metal-binding ligands.

Amino Acid Sequence↗

PubMed2003

Comparative genetic linkage maps of Eucalyptus grandis, Eucalyptus globulus and their F1 hybrid based on a double pseudo-backcross mapping approach.

Comparative genetic mapping in interspecific pedigrees presents a powerful approach to study genetic differentiation, genome evolution and reproductive isolation in diverging species. We used this approach for genetic analysis of an F(1) hybrid of two Eucalyptus tree species, Eucalyptus grandis (W. Hill ex Maiden.) and Eucalyptus globulus (Labill.). This wide interspecific cross is characterized by hybrid inviability and hybrid abnormality. Approximately 20% of loci in the genome of the F(1) hybrid are expected to be hemizygous due to a difference in genome size between E. grandis (640 Mbp) and E. globulus (530 Mbp). We investigated the extent of colinearity between the two genomes and the distribution of hemizygous loci in the F(1) hybrid using high-throughput, semi-automated AFLP marker analysis. Two pseudo-backcross families (backcrosses of an F(1) individual to non-parental individuals of the parental species) were each genotyped with more than 800 AFLP markers. This allowed construction of de novo comparative genetic linkage maps of the F(1) hybrid and the two backcross parents. All shared AFLP marker loci in the three single-tree parental maps were found to be colinear and little evidence was found for gross chromosomal rearrangements. Our results suggest that hemizygous AFLP loci are dispersed throughout the E. grandis chromosomes of the F(1) hybrid.

Chromosome Mapping↗

PubMed2002

Sequence polymorphism of dotA and mip alleles mediating invasion and intracellular replication of Legionella pneumophila.

Legionella pneumophila inhabit a variety of natural and man-made aquatic environments, where they live primarily as intracellular parasites of protozoans. Given the proper exposure, however, they can cause opportunistic pneumonic infections in humans. The products of two L. pneumophila genes, dotA and mip, are part of the mechanism mediating the initial invasion of eukaryotic cells, and subsequent intracellular survival and multiplication. In this study, DNA polymorphism of the dotA and mip genes was assessed for 17 clinical and environmental isolates by nucleotide sequencing to determine the level of sequence variation, rates of molecular evolution, and history of gene divergence. The mip gene is highly conserved, whereas dotA is extremely variable, with an average level of nucleotide diversity four times greater than that of mip. Gene trees for each locus support a division of the L. pneumophila isolates into two clonal lineages. There are several disagreements between the gene trees suggesting that although L. pneumophila has a clonal population structure, genetic exchange has contributed to genotypic variation among strains in nature.

Alleles↗

PubMed2006

Mitochondrial cytochrome c oxidase subunit 1 gene and nuclear rDNA regions of Enterobius vermicularis parasitic in captive chimpanzees with special reference to its relationship with pinworms in humans.

Sequences of mitochondrial cytochrome c oxidase subunit 1 (CO1) gene, nuclear internal transcribed spacer 2 (ITS2) region of ribosomal DNA (rDNA), and 5S rDNA of Enterobius vermicularis from captive chimpanzees in five zoos/institutions in Japan were analyzed and compared with those of pinworm eggs from humans in Japan. Three major types of variants appearing in both CO1 and ITS2 sequences, but showing no apparent connection, were observed among materials collected from the chimpanzees. Each one of them was also observed in pinworms in humans. Sequences of 5S rDNA were identical in the materials from chimpanzees and humans. Phylogenetic analysis of CO1 gene revealed three clusters with high bootstrap value, suggesting considerable divergence, presumably correlated with human evolution, has occurred in the human pinworms. The synonymy of E. gregorii with E. vermicularis is supported by the molecular evidence.

Animals↗

PubMed2000

Universal Primers for Amplification of Mitochondrial Small Subunit Ribosomal RNA-Encoding Gene in Scleractinian Corals.

We describe the construction of polymerase chain reaction primers designed to amplify a portion of the mitochondrial (mt) small subunit ribosomal (SSU) RNA-encoding genes in scleractinian corals. Combinations of cloning and sequencing show that the amplified fragments are between 694 and 896 bp in length. Alignment of the amplified DNA sequences to the published mt SSU rRNA genes of Metridium senile and Sarcophyton glaucum indicates several conserved regions among actiniarian, corallimorpharian, octocorallian, and scleractinians, suggesting this primer set can successfully amplify over 80% of the mt SSU rDNA region of scleractinian corals. Surveys of sequence variation and estimation of the rate of evolution show an extremely slow divergence of the SSU rRNA gene in the family Acroporidae.

Journal Article↗

PubMed1988

Sequence of the 3386 3' nucleotides of the genome of the AVO1 strain rabies virus: structural similarities in the protein regions involved in transcription.

DNA fragments complementary to the genome of an avirulent strain (AVO1) of the rabies virus were cloned and sequenced. The sequence of the 3386 nucleotides from the 3' end covers the genes encoding the leader RNA, the nucleoprotein N, the phosphoprotein M1 and the matrix protein M2, as well as the intergenic regions. Comparison of the AVO1 sequence with those of other rabies strains reveals a very high conservation at both the nucleotide and the amino acid levels. The non-protein coding regions of the genome (leader gene, untranslated regions flanking mRNAs, untranscribed intergenic regions) are discussed in terms of their possible involvement in the rabies virus biology. Comparison of the rabies genome with those of other unsegmented negative strand RNA viruses (rhabdoviruses and paramyxoviruses) indicates that the start and stop transcription signals, located at the border of each gene encoding a protein, and the regions of the phosphoprotein and matrix proteins that could be implicated in the transcription process, retain a similar overall structure. Thus, it appears that during evolution, these virus genomes have diverged while keeping the protein structures and regulatory sequence important in transcription. These results prompt us to propose that the major distinctive feature of the rabies transcription may arise from the highly variable intergenic regions where the attenuation of transcription is assumed to take place.

Base Sequence↗