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PubMed2000

Evolution of genes and taxa: a primer.

The rapidly growing fields of molecular evolution and systematics have much to offer to molecular biology, but like any field have their own repertoire of terms and concepts. Homology, for example, is a central theme in evolutionary biology whose definition is complex and often controversial. Homology extends to multigene families, where the distinction between orthology and paralogy is key. Nucleotide sequence alignment is also a homology issue, and is a key stage in any evolutionary analysis of sequence data. Models based on our understanding of the processes of nucleotide substitution are used both in the estimation of the number of evolutionary changes between aligned sequences and in phylogeny reconstruction from sequence data. The three common methods of phylogeny reconstruction--parsimony, distance and maximum likelihood--differ in their use of these models. All three face similar problems in finding optimal--and reliable--solutions among the vast number of possible trees. Moreover, even optimal trees for a given gene may not reflect the relationships of the organisms from which the gene was sampled. Knowledge of how genes evolve and at what rate is critical for understanding gene function across species or within gene families. The Neutral Theory of Molecular Evolution serves as the null model of molecular evolution and plays a central role in data analysis. Three areas in which the Neutral Theory plays a vital role are: interpreting ratios of nonsynonymous to synonymous nucleotide substitutions, assessing the reliability of molecular clocks, and providing a foundation for molecular population genetics.

Base Sequence↗

PubMed1995

Molecular classification of living organisms.

Recent studies in molecular evolution have generated strong conflicts in opinion as to how world living organisms should be classified. The traditional classification of life into five kingdom has been challenged by the molecular analysis carried out mostly on rRNA sequences, which supported the division of the extant living organisms into three major groups: Archaebacteria, Eubacteria, and Eukaryota. As to the problem of placing the root of the tree of life, the analysis carried out on a few genes has provided discrepant results. In order to measure the genetic distances between species, we have carried out an evolutionary analysis of the glutamine synthetase genes, which previously have been revealed to be good molecular clocks, and of the small and large rRNA genes. All data demonstrate that archaebacteria are more closely related to eubacteria than to eukaryota, thus supporting the classical division of living organisms into two main superkingdoms, Prokaryota and Eukaryota.

Archaea↗

PubMed1989

Polymorphic DNA haplotypes at the LDL receptor locus.

Mutations in the low-density lipoprotein (LDL) receptor gene result in the autosomal dominant disorder familial hypercholesterolemia (FH). Many different LDL receptor mutations have been identified and characterized, demonstrating a high degree of allelic heterogeneity at this locus. The ability to identify mutant LDL receptor genes for prenatal diagnosis of homozygous FH or to study the role of the LDL receptor gene in polygenic hypercholesterolemia requires the use of closely linked RFLPs. In the present study we used 10 different RFLPs, including three newly described polymorphisms, to construct 123 independent haplotypes from 20 Caucasian American pedigrees. Our sample contained 31 different haplotypes varying in frequency from 0.8% to 29.3%; the five most common haplotypes account for 67.5% of the sample. The heterozygosity and PIC of each site were determined, and these values disclosed that eight of the RFLPs were substantially polymorphic. Linkage-disequilibrium analysis of the haplotype data revealed strong nonrandom associations among all 10 RFLPs, especially among those sites clustered in the 3' region of the gene. Evolutionary analysis suggests the occurrence of both mutational and recombinational events in the generation of the observed haplotypes. A strategy for haplotype analysis of the LDL receptor gene in individuals of Caucasian American descent is presented.

Computer Simulation↗

PubMed1994

An analysis of retroposition in plants based on a family of SINEs from Brassica napus.

The identification of a family of SINE retroposons dispersed in the genome of oilseed rape Brassica napus has provided the basis for an evolutionary analysis of retroposition in plants. The repetitive elements (called S1Bn) are 170 bp long and occupy roughly 500 loci by haploid genome. They present characteristic features of SINE retroposons such as a 3' terminal A-rich region, two conserved polymerase III motifs (box A and B), flanking direct repeats of variable sizes, and a primary and secondary sequence homology to several tRNA species. A consensus sequence was made from the alignment of 34 members of the family. The retroposon population was divided into five subfamilies based on several correlated sets of mutations from the consensus. These precise separations in subfamilies based on "diagnostic" mutations and the random distribution of mutations observed inside each subfamily are consistent with the master sequence model proposed for the dispersion of mammalian retroposons. An independent analysis of each subfamily provides strong evidence for the coexpression of at least three subfamily master sequences (SMS). In contrast to mammalian retroposition, diagnostic positions are not shared between SMS. We therefore propose that SMS were all derived from a general master sequence (GMS) and independently activated for retroposition after a variable period of random drift. Possible models for plant retroposition are discussed.

Base Sequence↗

PubMed1994

Human parainfluenza virus type 1 evolution combines cocirculation of strains and development of geographically restricted lineages.

The hemagglutinin neuraminidase (HN) glycoprotein of human parainfluenza virus type 1 (HPIV-1) mediates attachment to the host cell and is the target of protective antibody. Since the efficacy of a potential vaccine depends on antigenic constancy, the antigenic and genetic stability of the HPIV-1 HN glycoprotein was examined for 13 isolates obtained between 1981 and 1989. Antigenic analysis with a panel of 11 monoclonal antibodies demonstrated a single change among 3 isolates from 1989 that distinguished them from all other isolates. The HN genes from all 13 isolates and 13 previously published HN gene sequences shared > 95% homology. Evolutionary analysis demonstrated cocirculation of strains, without a dominant lineage. The 1989 isolates and the previously proposed subtype A isolates occupied distinct evolutionary branches, indicating geographically limited evolution. The slow rate of evolution and HN homogeneity may allow development of a single vaccine formulation for the prevention of disease.

Antigens, Viral↗

PubMed2000

Comparative sequence analysis of the VHL tumor suppressor gene.

Comparative genome analysis may provide novel insights into gene evolution and function. To investigate the von Hippel-Lindau (VHL) disease tumor suppressor gene, we sequenced the VHL gene in seven primate species. Comparative analysis was performed for human, primate, and rodent VHL genes and for a putative Caenorhabditis elegans VHL homologue identified by database analysis. The VHL gene has two translation initiation sites (at codons 1 and 54); however, the relative importance of the full-length translation product (pVHL30) and that translated from the second internal translation initiation site (pVHL19) is unclear. The N-terminal sequence of pVHL30 contains eight copies of a GXEEX acidic repeat motif in human and higher primates, but only three copies were present in the marmoset, and only one copy was present in rodent VHL genes. Evolutionary analysis suggested that the N-terminal repetitive sequence in pVHL30 was of less functional importance than those regions present in both pVHL30 and pVHL19. The VHL gene product is reported to form complexes with various proteins including elongin B, elongin C, VBP-1, fibronectin, Spl, CUL2, and HIF-1. Although most of the regions in pVHL that had been implicated in binding specific proteins demonstrated evolutionary conservation, the carboxy-terminal putative VBP-1 binding site was less well conserved, suggesting that VBP-1 binding may have less functional significance. Although an amino acid substitution (K171T) close to the pVHL elongin binding region was found in baboon, analysis of the structure of human pVHL suggested that this substitution would not interfere with pVHL/elongin C interaction. In general, there was a good correlation between the pVHL domains that demonstrated most evolutionary conservation and those that were most frequently mutated in tumors. Analysis of human/C. elegans conservation and human germline and somatic mutation patterns identified a highly conserved mutation cluster region between codons 74 and 90. However, this region is likely to be important for the structural integrity of pVHL rather than representing an additional protein binding domain.

Amino Acid Sequence↗

PubMed2003

Polymorphic membrane protein H has evolved in parallel with the three disease-causing groups of Chlamydia trachomatis.

Chlamydia trachomatis is a human pathogen causing trachoma, urogenital disease, and lymphogranuloma venereum (LGV). A family of nine polymorphic membrane protein genes (pmpA to pmpI), resembling autotransporter proteins, has recently been discovered in C. trachomatis. pmp genes are large and predicted to be outer membrane proteins. We hypothesized that they would contain useful nucleotide sequence variability for epidemiologic studies. Since sequence information is available only for serovars D and L2, we sought to determine the amount of diversity within an individual pmp gene among serovars. We used restriction fragment length polymorphism (RFLP) analysis as a primary screen to assess the amount of sequence divergence among the pmp genes for serovars A to L3 of C. trachomatis. RFLP analysis showed little variation for some of the genes, such as pmpA, but substantial variation in others, such as pmpI. pmpH and pmpE yielded RFLP patterns that clustered the 15 serovars into ocular, urogenital, and LGV groups, and both proteins have been localized to the outer membrane. Therefore, we chose to sequence pmpE, pmpH, and pmpI from each of the 15 serovars. Evolutionary analysis showed three distinct divergence patterns. PmpI was least variable, resulting in an ambiguous evolutionary pattern. PmpE showed a high degree of diversity in the ocular strains compared to the other strains. Finally, the evolution of PmpH shows three groups that reflect disease groups, suggesting this protein may play a role in pathogenesis.

Bacterial Outer Membrane Proteins↗

PubMed2025

Comparative genomic analysis of Artemisia argyi reveals asymmetric expansion of terpene synthases and conservation of artemisinin biosynthesis.

Artemisia argyi, a perennial herb of the Asteraceae family, possesses significant therapeutic and economic value. We present a 7.88 Gb chromosome-level haplotype-resolved genome assembly, revealing its unique evolutionary trajectory. The karyotype (2n = 34) of A. argyi is that of an autotetraploid, which underwent gametic chromosome fusion prior to species-specific whole-genome duplication (WGD-3). The genome exhibits pronounced multivalent chromosome pairing and frequent recombination among homologous groups. Asymmetrical evolution following WGD-3 is a hallmark feature, evidenced by imbalanced allelic gene loss and widespread neofunctionalization. The terpene synthase (TPS) gene family exemplifies this pattern, having expanded through four duplication events in A. argyi. Recent tandem duplications and allelic functional differentiation have generated substantial gene functional diversity. Notably, we identified a tandem-duplicated six-copy ADS homolog (AarADS)-a key TPS gene in the artemisinin biosynthetic pathway of Artemisia annua (AanADS)-localized exclusively to a single chromosome in A. argyi. Unlike AanADS, which converts farnesyl pyrophosphate (FPP) to amorpha-4,11-diene, AarADS catalyzes FPP to α-bisabolol. Evolutionary analysis suggested that AanADS acquired its specialized function via a derived mutation in the A. annua lineage. This study elucidates the genomic evolution underpinning A. argyi's distinctive medicinal properties.

Alkyl and Aryl Transferases↗

PubMed1995

A mitochondrial DNA clone is associated with increased risk for Alzheimer disease.

Severe mitochondrial genetic mutations lead to early degeneration of specific human tissues; milder mitochondrial mutations may cause degeneration at a later point in life. A mutation at position 4336 was reported to occur at increased frequency in individuals with Alzheimer disease (AD) and Parkinson disease [Shoffner, J. M., Brown, M. D., Torroni, A., Lott, M. T., Cabell, M. F., Mirra, S. S., Beal, M. F., Yang, C.-C., Gearing, M., Salvo, R., Watts, R. L., Juncos, J. L., Hansen, L. A., Crain, B. J., Fayad, M., Reckord, C. L. & Wallace, D. C. (1993) Genomics 17, 171-184]. We have investigated the notion that this mutation leads to excess risk of AD by using a case-control study design of 72 AD autopsies and 296 race- and age-matched controls. The 4336G mutation occurred at higher frequency in AD autopsies than age-matched controls, a statistically significant difference. Evolutionary analysis of mtDNAs bearing the 4336G mutation indicated they were more closely related to each other than to other mtDNAs, consistent with the model of a single origin for this mutation. The tight evolutionary relatedness and homoplasmy of mtDNAs that confer elevated risk for a late-onset disease contrast strikingly with the distant relatedness and heteroplasmy of mitochondrial genomes that cause early-onset disease. The dichotomy can be explained by a lack of selection against mutations that confer a phenotype at advanced age during most of the evolution of humans. We estimate that approximately 1.5 million Caucasians in the United States bear the 4336G mutation and are at significantly increased risk of developing mitochondrial AD in their lifetime. A mechanism for 4336G-mediated cell death is proposed.

Aged↗

PubMedDate not supplied

Comparison of protein structures reveals monophyletic origin of the AdoMet-dependent methyltransferase family and mechanistic convergence rather than recent differentiation of N4-cytosine and N6-adenine DNA methylation.

Phylogenetic analysis of the S-adenosyl-L-methionine-dependent methyltransferases was performed based on similarity of positions of main chain alpha-carbon atoms in published structures of members of this superfamily. The evolutionary tree was inferred and the problem of mono/polyphyletic origin of DNA methyltransferases from the Rossmann-fold enzymes was solved, bridging two seemingly antithetical hypotheses. The comparison of protein structures provides evidence for an evolutionary link between widely diverged subfamilies of RNA and DNA N6-adenine methyltransferases and argues against the close homology of N6-adenine and N4-cytosine methyltransferases, apparent from biochemical data and comparison of fragments of sequences. Such evolutionary analysis of methyltransferases has never been published yet in the literature and will guide further phylogenetical studies based on both sequence and structure comparison.

Adenine↗

PubMed2003

Aldehyde dehydrogenase gene superfamily: the 2002 update.

The aldehyde dehydrogenase (ALDH) superfamily represents a divergently related group of enzymes that metabolize a wide variety of endogenous and exogenous aldehydes. With the advent of megabase genome sequencing, the ALDH superfamily is continuously expanding on many fronts. The presence of ALDH encoding genes in the vast majority of archaeal, eubacterial and eukaryotic genomes supports the notion that these enzymes are important components of metabolic processes in living organisms and that the ALDH superfamily is ancient in origin. As of July 2002, the ALDH superfamily consists of 555 distinct genes: 32 in archaea, 351 in eubacteria, and 172 in eukaryota. Complete sequencing of individual genomes reveals the number of ALDH genes found per organism ranges from 1 to 5 in archaeal species, 1-26 genes in eubacterial species, and 8-17 genes in eukaryotic species. In the human genome, 17 functional genes and 3 pseudogenes have been identified to date. A standardized ALDH gene nomenclature system has been developed based on multiple alignment analysis of eukaryotic ALDH amino acid sequences. Both Human and Mouse Genome Projects have accepted this nomenclature system. In this report, we present a complete listing of all ALDH sequences known to date, along with the evolutionary analysis of the eukaryotic ALDHs. Thus far, the eukaryotic ALDHs comprise 20 gene families. Detailed information on ALDH gene superfamily is also available at http://www.uchsc.edu/sp/sp/alcdbase/aldhcov.html.

Aldehyde Dehydrogenase↗

PubMed1988

[A principle of maximum topological similarity in molecular systematics].

The paper deals with the problem of phylogenetic reconstruction on the basis of comparative analysis of features. Main attention is paid to comparison and classification of the biopolymer sequences. Different approaches to this task are critically reviewed. The novel principle of construction of tree-like classification schemes permitting subsequent evolutionary analysis is proposed. It concentrates on reconstruction of the tree with a topologic structure that is most close to topologic features, imprinted in the source distance matrix. Realization of this approach was made possible by development of the special formalism, enabling evaluation and comparison of topologic features of distance matrices and trees.

Animals↗

PubMed1994

The origins and evolutionary expansion of the Strongylida (Nematoda).

The Strongylida are thought to have arisen from free-living rhabditoid nematodes, but the relationships between the major groupings within the Strongylida, the Strongylina, the Metastrongylina, Trichostrongylina and the Ancylostomatina are far from clear in spite of the abundance of morphological data now available for analysis. Evolutionary mechanisms including co-evolution, host switching, host dispersal, use of intermediate hosts, various sites of localisation within the definitive host and modifications of life-cycle strategies appear to have been utilised in the expansion of the Strongylida, with different mechanisms predominating in different families or superfamilies. Co-evolution appears to have been a major mode of evolution in the Strongylina, in contrast to the Trichostrongylina, which have used host dispersal and host-switching to great advantage. The phylogeny of the Ancylostomatina shows little association with host evolution, but does match the feeding preferences of the hosts. The Metastrongylina have utilised intermediate hosts and life cycle modifications including a shift to extra-intestinal sites as major means of diversification, in contrast to the other sub-orders. The review, while indicating much progress in our understanding of the phylogeny of the Strongylida, also reveals that enormous gaps still exist, and emphasises the tentative nature of many of the phylogenetic hypotheses tendered to date.

Animals↗

PubMed1987

Accumulation pattern of amino acid substitutions in protein evolution.

A simple method for the evolutionary analysis of amino acid sequence data is presented and used to examine whether the number of variable sites (NVS) of a protein is constant during its evolution. The NVSs for hemoglobin and for mitochondrial cytochrome c are each found to be almost constant, and the ratio between the NVSs is close to the ratio between the unit evolutionary periods. This indicates that the substitution rate per variable site is almost uniform for these proteins, as the neutral theory claims. An advantage of the present analysis is that it can be done without knowledge of paleontological divergence times and can be extended to bacterial proteins such as bacterial c-type cytochromes. It is suggested that the NVS of cytochrome c has been almost constant even over the long period (ca. 3.0 billion years) of bacterial evolution but that at least two different substitution rates are necessary to describe the accumulated changes in the sequence. This "two clock" interpretation is consistent with fossil evidence for the appearance times of photosynthetic bacteria and eukaryotes.

Amino Acid Sequence↗

PubMed2001

A novel variant genotype C of hepatitis B virus identified in isolates from Australian Aborigines: complete genome sequence and phylogenetic relatedness.

There have been no reports of DNA sequences of hepatitis B virus (HBV) strains from Australian Aborigines, although the hepatitis B surface antigen (HBsAg) was discovered among them. To investigate the characteristics of DNA sequences of HBV strains from Australian Aborigines, the complete nucleotide sequences of HBV strains were determined and subjected to molecular evolutionary analysis. Serum samples positive for HBsAg were collected from five Australian Aborigines. Phylogenetic analysis of the five complete nucleotide sequences compared with DNA sequences of 54 global HBV isolates from international databases revealed that three of the five were classified into genotype D and were most closely related in terms of evolutionary distance to a strain isolated from a healthy blood donor in Papua New Guinea. Two of the five were classified into a novel variant genotype C, which has not been reported previously, and were closely related to a strain isolated from Polynesians, particularly in the X and Core genes. These two strains of variant genotype C differed from known genotype C strains by 5.9-7.4% over the complete nucleotide sequence and 4.0-5.6% in the small-S gene, and had residues Arg(122), Thr(127) and Lys(160), characteristic of serotype ayw3, which have not been reported previously in genotype C. In conclusion, this is the first report of the characteristics of complete nucleotide sequences of HBV from Australian Aborigines. These results contribute to the investigation of the worldwide spread of HBV, the relationship between serotype and genotype and the ancient common origin of Australian Aborigines.

Amino Acid Sequence↗

PubMed2002

Physical and genetic characterization reveals a pseudogene, an evolutionary junction, and unstable loci in distal Xq28.

A large portion of human Xq28 has been completely characterized but the interval between G6PD and Xqter has remained poorly understood. Because of a lack of stable, high-density clone coverage in this region, we constructed a 1.6-Mb bacterial and P1 artificial chromosome (BAC and PAC, respectively) contig to expedite mapping, structural and evolutionary analysis, and sequencing. The contig helped to reposition previously mismapped genes and to characterize the XAP135 pseudogene near the int22h-2 repeat. BAC clones containing the distal int22h repeats also demonstrated spontaneous rearrangements and sparse coverage, which suggested that they were unstable. Because the int22h repeats are involved in genetic diseases, we examined them in great apes to see if they have always been unstable. Differences in copy number among the apes, due to duplications and deletions, indicated that they have been unstable throughout their evolution. Taking another approach toward understanding the genomic nature of distal Xq28, we examined the homologous mouse region and found an evolutionary junction near the distal int22h loci that separated the human distal Xq28 region into two segments on the mouse X chromosome. Finally, haplotype analysis showed that a segment within Xq28 has resisted excessive interchromosomal exchange through great ape evolution, potentially accounting for the linkage disequilibrium recently reported in this region. Collectively, these data highlight some interesting features of the genomic sequence in Xq28 and will be useful for positional cloning efforts, mouse mutagenesis studies, and further evolutionary analyses.

Animals↗

PubMed2000

Phylogenetic analysis of the three polymerase genes (PB1, PB2 and PA) of influenza B virus.

Phylogenetic patterns of the three polymerase (PB2, PB1 and PA) genes of a total of 20 influenza B viruses isolated during a 58 year period, 1940-1998, were analysed in detail in a parallel manner. All three polymerase genes consistently showed evolutionary divergence into two major distinct lineages and their amino acid profiles demonstrated conserved lineage-specific substitutions. Dendrogram topologies of the PB2 and PB1 genes were very similar and contrasted with that of the PA gene. It was of particular interest to reveal that even though the PA gene evolved into two major lineages, that of three recent Asian Victoria/1/87-like strains formed a branch cluster located in the same lineage as that of recent Yamagata/16/88-like isolates. Differences in the phylogenetic pathways of three polymerase genes were not only a reflection of genetic reassortment between co-circulating influenza B viruses, but also an indication that the polymerase genes were not co-evolving as a unit. As a result, comparison of the phylogenetic patterns of the three polymerase genes with previously determined patterns of the HA, NP, M and NS genes of 18 viruses defined the existence of eight distinct genome constellations. Also, similar phylogenetic profiles among the PA, NP and M genes, as well as between the PB2 and PB1 genes, were observed, suggesting possible functional interactions among these proteins. Completion of evolutionary analysis of the six internal genes and the HA gene of influenza B viruses revealed frequent genetic reassortment among co-circulating variable strains and suggested co-dependent evolution of genes.

Amino Acid Sequence↗

PubMed2001

Evolutionary expansion of CRIB-containing Cdc42 effector proteins.

Cdc42, a small GTPase, regulates actin polymerization and other signaling pathways through interaction with many different downstream effector proteins. Most of these effector proteins contain a Cdc42-binding domain, called a CRIB domain. Here, we describe the evolutionary analysis of these CRIB-containing proteins in yeast, worms, flies and humans. The number of CRIB-containing effector proteins increases from yeast to humans, involving both an increase within families and the emergence of new families. These evolutionary changes correlate with the development of the more complex signaling pathways present in higher organisms.

Animals↗