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PubMed1994

HIV--Australasian experience. Current status of HIV infection in Australasia.

The HIV/AIDS pandemic continues to evolve in a volatile and heterogeneous fashion and is now best described as a series of different but related epidemics, all posing their own particular problems. The response to the first decade of the epidemic in Australasia has been effective in a number of ways, but much remains to be done. The problems raised by recent cases of transmission of HIV in a health care setting have yet to be resolved. The characteristics of the local epidemic are increasingly divergent from the overseas models used to date, necessitating a flexible and creative approach tailored to the particular characteristics and needs of the local communities.

Australia↗

PubMed1992

The evolution of the mitochondrial D-loop region and the origin of modern man.

The origin of modern man is a highly debated issue that has recently been tackled by using mitochondrial DNA sequences. The limited genetic variability of human mtDNA has been explained in terms of a recent common genetic ancestry, thus implying that all modern-population mtDNAs originated from a single woman who lived in Africa less than 0.2 Mya. This divergence time is based on both the estimation of the rate of mtDNA change and its calibration date. Because different estimates of the rate of mtDNA evolution can completely change the scenario of the origin of modern man, we have reanalyzed the available mitochondrial sequence data by using an improved version of the statistical model, the "Markov clock," devised in our laboratory. Our analysis supports the African origin of modern man, but we found that the ancestral female from which all extant human mtDNAs originated lived in a time span of 0.3-0.8 Mya. Pushing back the date of the deepest root of the human implies that the earliest divergence would have been in the Homo erectus population.

Animals↗

PubMed2004

Molecular population genetics of male accessory gland proteins in the Drosophila simulans complex.

Accessory gland proteins are a major component of Drosophila seminal fluid. These proteins have a variety of functions and may be subject to sexual selection and/or antagonistic evolution between the sexes. Most population genetic data from these proteins are from D. melanogaster and D. simulans. Here, we extend the population genetic analysis of Acp genes to the other simulans complex species, D. mauritiana and D. sechellia. We sequenced population samples of seven Acp's from D. mauritiana, D. sechellia, and D. simulans. We investigated the population genetics of these genes on individual simulans complex lineages and compared Acp polymorphism and divergence to polymorphism and divergence from a set of non-Acp loci in the same species. Polymorphism and divergence data from the simulans complex revealed little evidence for adaptive protein evolution at individual loci. However, we observed a dramatically inflated index of dispersion for amino acid substitutions in the simulans complex at Acp genes, but not at non-Acp genes. This pattern of episodic bursts of protein evolution in Acp's provides the strongest evidence to date that the population genetic mechanisms driving Acp divergence are different from the mechanisms driving evolution at most Drosophila genes.

Animals↗

PubMed1995

Evolution and the origins of man: clues from complete sequences of hominoid mitochondrial DNA.

Dating the origins of Homo sapiens sapiens is a central problem in human population genetics and anthropology. Do we descend from a single recent ancestral population in Africa, or from multiple ancestral populations in various regions of the world which one million years ago simultaneously began developing into H.s.sapiens? The high substitution rate of mitochondrial DNA (mtDNA) makes this molecule suitable for genealogical and chronological research on closely related hominoid species. We have analyzed the complete mtDNA sequences of three humans (African, European and Japanese) and two African apes (common chimpanzee and gorilla) in an attempt to estimate more accurately the substitution rates and divergence times of hominoid mtDNAs. Nonsynonymous substitutions and substitutions in RNA genes have accumulated at an approximately constant rate. Under the assumption, supported by the fossil record, that the orangutan and African apes diverged 13 million years ago, we have previously obtained 4.7 million years as the divergence time between humans and chimpanzees. Using this date, we calibrated the substitution rates at synonymous sites and in the displacement-loop region as 4.03 and 7.25 x 10(-8)/site/year, respectively. Based on these rates together with the observation that the African sequence presented here is most diverged from all other human sequences, we inferred the age of the last common ancestor of the human mtDNAs as 140,000 +/- 18,000 years. The result strongly supports the recent African origin of modern humans, H.s. sapiens.

Africa↗

PubMed2006

Paleontological evidence to date the tree of life.

The role of fossils in dating the tree of life has been misunderstood. Fossils can provide good "minimum" age estimates for branches in the tree, but "maximum" constraints on those ages are poorer. Current debates about which are the "best" fossil dates for calibration move to consideration of the most appropriate constraints on the ages of tree nodes. Because fossil-based dates are constraints, and because molecular evolution is not perfectly clock-like, analysts should use more rather than fewer dates, but there has to be a balance between many genes and few dates versus many dates and few genes. We provide "hard" minimum and "soft" maximum age constraints for 30 divergences among key genome model organisms; these should contribute to better understanding of the dating of the animal tree of life.

Animals↗

PubMed2002

Fossil calibration of molecular clocks and the divergence times of geminate species pairs separated by the isthmus of panama.

Calibration of nucleotide sequence divergence rates provides an important method by which to test many hypotheses of evolution. In the absence of an adequate fossil record, geological events, rather than the first appearances of sister taxa in the geological record, are often used to calibrate molecular clocks. The formation of the Isthmus of Panama, which isolated the tropical western Atlantic and eastern Pacific oceans, is one such event that is frequently used to infer rates of nucleotide sequence divergence. Isthmian calibrations assume that morphologically similar "geminate" species living now on either side of the isthmus were isolated geographically by the latest stages of seaway closure 3.1-3.5 MYA. Here, I have applied calibration dates from the fossil record to cytochrome c oxidase-1 (CO1) and nuclear histone-3 (H3) divergences among six pairs of geminates in the Arcidae to test this hypothesis. Analysis of CO1 first and third positions yield geminate divergences that predate final seaway closure, and on the basis of CO1 first positions, times for all six geminates are significantly greater than 3.5 Myr. H3 sequences produce much more recent geminate divergences, some that are younger than 3.1 Myr. But H3-derived estimates for all arcid geminates are not significantly different from both 0 and 15 Myr. According to CO1, one of the two most divergent pairs, Arca mutabilis and A. imbricata, split more than 30 MYA. This date is compatible with the fossil record, which indicates that these species were morphologically distinct at least 16-21 MYA. Across all CO1 nucleotide sites, divergence rates for arcids are slower than the rates reported for other taxa on the basis of isthmian calibrations, with the exception of rates determined from the least divergent species pair in larger surveys of multiple transisthmian pairs. Rate differences between arcids and some taxa may be real, but these data suggest that divergence rates can be greatly overestimated when dates corresponding to final closure of the Central American Seaway are used to calibrate the molecular clocks of marine organisms.

Animals↗

PubMed2002

Rostral horn evolution among agamid lizards of the genus Ceratophora endemic to Sri Lanka.

The first phylogenetic hypothesis for the Sri Lankan agamid lizard genus Ceratophora is presented based on 1670 aligned base positions (472 parsimony informative) of mitochondrial DNA sequences, representing coding regions for eight tRNAs, ND2, and portions of ND1 and COI. Phylogenetic analysis reveals multiple origins and possibly losses of rostral horns in the evolutionary history of Ceratophora. Our data suggest a middle Miocene origin of Ceratophora with the most recent branching of recognized species occurring at the Pliocene/Pleistocene boundary. Haplotype divergence suggests that an outgroup species, Lyriocephalus scutatus, dates at least to the Pliocene. These phylogenetic results provide a framework for comparative studies of the behavioral ecological importance of horn evolution in this group.

Animals↗

PubMed1988

The complete nucleotide sequence of the small-subunit ribosomal RNA coding region for the cycad Zamia pumila: phylogenetic implications.

The DNA sequence of the small-subunit ribosomal RNA coding region for the cycad Zamia pumila L. was determined. The Zamia small-subunit rRNA was found to be 1813 nucleotides in length and approximately 92% identical to published angiosperm small-subunit rRNA sequences. Conserved regions interspersed with variable regions are observed corresponding to those found in other eukaryotic small-subunit sequences. Using representatives from protist, fungal, plant, and animal groups, a distance matrix was constructed of average nucleotide substitution rates for pairs of organisms. Phylogenetic trees were inferred from similarities between sequences. The sequence of Zamia represents the earliest divergence from the higher plant lineage reported to date for small-subunit rRNA data. Inferred phylogenies also support a monophyletic origin for the angiosperms consistent with studies citing phenotypic characters.

Base Sequence↗

PubMed2003

The evolution of enzyme specificity in Fasciola spp.

Fasciola spp., commonly known as liver fluke, are significant trematode parasites of livestock and humans. They secrete several cathepsin L-like cysteine proteases, some of which differ in enzymatic properties and timing of expression in the parasite's life cycle. A detailed sequence and evolutionary analysis is presented, based on 18 cathepsin L-like enzymes isolated from Fasciola spp. (including a novel clone identified in this study). The enzymes form a monophyletic group which has experienced several gene duplication events over the last approximately 135 million years, giving rise to the present-day enzymatic repertoire of the parasite. This timing of these duplications appears to correlate with important points in the evolution of the mammalian hosts. Furthermore, the dates suggest that Fasciola hepatica and Fasciola gigantica diverged around 19 million years ago. A novel analysis, based on the pattern of amino acid diversity, was used to identify sites in the enzyme that are predicted to be subject to positive adaptive evolution. Many of these sites occur within the active site cleft of the enzymes, and hence would be expected to lead to differences in substrate specificity. Using homology modeling, with reference to previously obtained biochemical data, we are able to predict S2 subsite specificity for these enzymes: specifically those that can accommodate bulky hydrophobic residues in the P2 position and those that cannot. A number of other positions subject to evolutionary pressure and potentially significant for enzyme function are also identified, including sites anticipated to diminish cystatin binding affinity.

Amino Acid Sequence↗

PubMed2004

Molecular phylogeny of the tribe Bovini (Bovidae, Bovinae) and the taxonomic status of the Kouprey, Bos sauveli Urbain 1937.

The kouprey is a very rare bovid species of the Indochinese peninsula, and no living specimen has been described for a long time, suggesting that it is possibly extinct. Its systematic position within the tribe Bovini remains confused since the analyses of morphological characters have led to several conflicting hypotheses. Some authors have also suggested that it could be a hybrid species produced by the crossing of the banteng with gaur, zebu, or water buffalo. Here we performed a molecular phylogeny of the tribe Bovini to determine the taxonomic status of the kouprey. DNA was extracted from the holotype specimen preserved in the MNHN collections. Phylogenetic analyses were carried out on a matrix including all the taxonomic diversity described in the tribe Bovini, and 2065 nucleotide characters, representing three different markers, i.e., the promotor of the lactoferrin and two mitochondrial genes (cytochrome b and subunit II of the cytochrome c oxidase). The results show that the kouprey belongs to the subtribe Bovina, and that three different clades can be evidenced into this group: the first includes the domestic ox, zebu, and European bison; the second incorporates the yak and American bison; and the third contains the kouprey, banteng and gaur. All hypotheses involving hybridization for the origin of the kouprey can be rejected, confirming that it is a real wild species. Molecular datings and biogeographic inferences suggest that the kouprey diverged from banteng and gaur during the Plio-Pleistocene of Asia. In addition, several molecular signatures were detected in the cytochrome b gene, permitting a molecular identification of the kouprey. We propose a conservation project based on a molecular taxonomy approach for tracking the kouprey in Indochina in order to determine whether some populations still survive in the wild.

Animals↗

PubMed2006

Analysis of the complete mitochondrial DNA from Anopheles funestus: an improved dipteran mitochondrial genome annotation and a temporal dimension of mosquito evolution.

Virtually no information regarding timing of deep lineage divergences within mosquito family (Culicidae) exists, which poses an important problem in the postgenomic era. To address this issue, the complete 15,354 bp mitochondrial genome of Anopheles funestus was assembled from both mtDNA and cDNA sequences generated from transcripts of the mtDNA-encoded protein and rRNA genes. Analysis of the transcript information allowed an improved genome annotation, revealing that the translation initiation codon for the cox1 gene is TCG, rather than atypical, longer codons proposed in several other insects. The 5'ends of nad1 and nad5 transcripts begin with TTG and GTG triplets, respectively, which apparently serve as the translation initiators for those genes. We used all the A. funestus mtDNA gene sequences and three other publicly available mosquito mtDNA genomes for the estimation of divergence time points within Culicidae. The maximum likelihood date estimates for the splits between Anopheles and Aedes (approximately 145-200 Mya), between Anopheles subgenera Cellia and Anopheles (approximately 90-106 Mya), and between lineages within subgenus Anopheles (approximately 70-85 Mya) inferred from protein-coding genes are roughly twice as high as the dates based on RNA gene sequences. Although existing evidence does not unequivocally favor one of the alternatives, fossil-based predictions of the age of the family Culicidae are in better agreement with dates inferred from protein-coding genes.

Animals↗

PubMed1996

The complete mitochondrial DNA sequence of the greater Indian rhinoceros, Rhinoceros unicornis, and the Phylogenetic relationship among Carnivora, Perissodactyla, and Artiodactyla (+ Cetacea).

The sequence (16,829 nt) of the complete mitochondrial genome of the greater Indian rhinoceros, Rhinoceros unicornis, was determined. Like other perissodactyls studied (horse and donkey) the rhinoceros demonstrates length variation (heteroplasmy) associated with different numbers of repetitive motifs in the control region. The 16,829-nt variety of the molecule includes 36 identical control region motifs. The evolution of individual peptide-coding genes was examined by comparison with a distantly related perissodactyl, the horse, and the relationships among the orders Carnivora, Perissodactyla, and Artiodactyla (+ Cetacea) were examined on the basis of concatenated sequences of 12 mitochondrial peptide-coding genes. The phylogenetic analyses grouped Carnivora, Perissodactyla, and Artiodactyla (+ Cetacea) into a superordinal clade and within this clade a sister group relationship was recognized between Carnivora and Perissodactyla to the exclusion of Artiodactyla (+ Cetacea) . On the basis of the molecular difference between the rhinoceros and the horse and by applying as a reference to Artiodactyl/Cetacean divergence set at 60 million years ago (MYA), the evolutionary divergence between the families Rhinocerotidae and Equidae was dated to approximately 50 MYA.

Animals↗

PubMed2004

The phylogeography of salmonid proliferative kidney disease in Europe and North America.

Salmonid proliferative kidney disease (PKD) is caused by the myxozoan Tetracapsuloides bryosalmonae. Given the serious and apparently growing impact of PKD on farmed and wild salmonids, we undertook a phylogeographic study to gain insights into the history of genealogical lineages of T. bryosalmonae in Europe and North America, and to determine if the global expansion of rainbow trout farming has spread the disease. Phylogenetic analyses of internal transcribed spacer 1 sequences revealed a clade composed of all North American sequences plus a subset of Italian and French sequences. High genetic diversity in North America and the absence of genotypes diagnostic of the North American clade in the rest of Europe imply that southern Europe was colonized by immigration from North America; however, sequence divergence suggests that this colonization substantially pre-dated fisheries activities. Furthermore, the lack of southern European lineages in the rest of Europe, despite widespread rainbow trout farming, indicates that T. bryosalmonae is not transported through fisheries activities. This result strikingly contrasts with the commonness of fisheries-related introductions of other pathogens and parasites and indicates that fishes may be dead-end hosts. Our results also demonstrate that European strains of T. bryosalmonae infect and induce PKD in rainbow trout introduced to Europe.

Animals↗

PubMed1996

The mercury resistance operon of the IncJ plasmid pMERPH exhibits structural and regulatory divergence from other Gram-negative mer operons.

The bacterial mercury resistance determinant carried on the IncJ plasmid pMERPH has been characterized further by DNA sequence analysis. From the sequence of a 4097 bp Bg/II fragment which confers mercury resistance, it is predicted that the determinant consists of the genes merT, merP, merC and merA. The level of DNA sequence similarity between these genes and those of the mer determinant of Tn21 was between 56 center dot 4 and 62 center dot 4%. A neighbour-joining phylogenetic tree of merA gene sequences was constructed which suggested that pMERPH bears the most divergent Gram-negative mer determinant characterized to date. Although the determinant from pMERPH has been shown to be inducible, no regulatory genes have been found within the Bg/II fragment and it is suggested that a regulatory gene may be located elsewhere on the plasmid. The cloned determinant has been shown to express mercury resistance constitutively. Analysis of the pMERPH mer operator/promoter (O/P) region in vivo has shown constitutive expression from the mer PTCPA promoter, which could be partially repressed by the presence of a trans-acting MerR protein from a Tn21-like mer determinant. This incomplete repression of mer PTCPA promoter activity may be due to the presence of an extra base between the -35 and -10 sequences of the promoter and/or to variation in the MerR binding sites in the O/P region. Expression from the partially repressed mer PTCPA promoter could be restored by the addition of inducing levels of Hg2+ ions. Using the polymerase chain reaction with primers designed to amplify regions in the merP and merA genes, 1 center dot 37 kb pMERPH-like sequences have been amplified from the IncJ plasmid R391, the environmental isolate SE2 and from DNA isolated directly from non-cultivated bacteria in River Mersey sediment. This suggests that pMERPH-like sequences, although rare, are nevertheless persistent in natural environments.

Amino Acid Sequence↗

PubMed2002

Identification and analysis of over 2000 ribosomal protein pseudogenes in the human genome.

Mammals have 79 ribosomal proteins (RP). Using a systematic procedure based on sequence-homology, we have comprehensively identified pseudogenes of these proteins in the human genome. Our assignments are available at http://www.pseudogene.org or http://bioinfo.mbb.yale.edu/genome/pseudogene. In total, we found 2090 processed pseudogenes and 16 duplications of RP genes. In relation to the matching parent protein, each of the processed pseudogenes has an average relative sequence length of 97% and an average sequence identity of 76%. A small number (258) of them do not contain obvious disablements (stop codons or frameshifts) and, therefore, could be mistaken as functional genes, and 178 are disrupted by one or more repetitive elements. On average, processed pseudogenes have a longer truncation at the 5' end than the 3' end, consistent with the target-primed-reverse-transcription (TPRT) mechanism. Interestingly, on chromosome 16, an RPL26 processed pseudogene was found in the intron region of a functional RPS2 gene. The large-scale distribution of RP pseudogenes throughout the genome appears to result, chiefly, from random insertions with the numbers on each chromosome, consequently, proportional to its size. In contrast to RP genes, the RP pseudogenes have the highest density in GC-intermediate regions (41%-46%) of the genome, with the density pattern being between that of LINEs and Alus. This can be explained by a negative selection theory as we observed that GC-rich RP pseudogenes decay faster in GC-poor regions. Also, we observed a correlation between the number of processed pseudogenes and the GC content of the associated functional gene, i.e., relatively GC-poor RPs have more processed pseudogenes. This ranges from 145 pseudogenes for RPL21 down to 3 pseudogenes for RPL14. We were able to date the RP pseudogenes based on their sequence divergence from present-day RP genes, finding an age distribution similar to that for Alus. The distribution is consistent with a decline in retrotransposition activity in the hominid lineage during the last 40 Myr. We discuss the implications for retrotransposon stability and genome dynamics based on these new findings.

Amino Acid Sequence↗

PubMed1978

The amino-acid sequence of kangaroo pancreatic ribonuclease.

Red kangaroo (Macropus rufus) ribonuclease was isolated from pancreatic tissue by affinity chromatography. The amino acid sequence was determined by automatic sequencing of overlapping large fragments and by analysis of shorter peptides obtained by digestion with a number of proteolytic enzymes. The polypeptide chain consists of 122 amino acid residues. Compared to other ribonucleases, the N-terminal residue and residue 114 are deleted. In other pancreatic ribonucleases position 114 is occupied by a cis proline residue in an external loop at the surface of the molecule. Other remarkable substitutions are the presence of a tyrosine residue at position 123 instead of a serine which forms a hydrogen bond with the pyrimidine ring of a nucleotide substrate, and a number of hydrophobichydrophilic interchanges in the sequence 51-55, which forms part of an alpha-helix in bovine ribonuclease and exhibits few substitutions in the placental mammals. Kangaroo ribonuclease contains no carbohydrate, although the enzyme possesses a recognition site for carbohydrate attachment in the sequence Asn-Val-Thr (62-64). The enzyme differs at about 35-40% of the positions from all other mammalian pancreatic ribonucleases sequenced to date, which is in agreement with the early divergence between the marsupials and the placental mammals. From fragmentary data a tentative sequence of red-necked wallaby (Macropus rufogriseus) pancreatic ribonuclease has been derived. Eight differences with the kangaroo sequence were found.

Amino Acid Sequence↗

PubMed2006

Setting SNAREs in a different wood.

Vesicle traffic is essential for cell homeostasis, growth and development in plants, as it is in other eukaryotes, and is facilitated by a superfamily of proteins known as soluble N-ethylmaleimide-sensitive fusion protein attachment protein receptors (SNAREs). Although SNAREs are well-conserved across phylla, genomic analysis for two model angiosperm species available to date, rice and Arabidopsis, highlights common patterns of divergence from other eukaryotes. These patterns are associated with the expansion of some gene subfamilies of SNAREs, the absence of others and the appearance of new proteins that show no significant homologies to SNAREs of mammals, yeast or Drosophila. Recent findings indicate that the functions of these plant SNAREs also extend beyond the conventional 'housekeeping' activities associated with vesicle trafficking. A number of SNAREs have been implicated in environmental responses as diverse as stomata movements and gravisensing as well as sensitivity to salt and drought. These proteins are essential for signal transduction and response and, in most cases, appear also to maintain additional roles in membrane trafficking. One common theme to this added functionality lies in control of non-SNARE proteins, notably ion channels. Other examples include interactions between the SNAREs and scaffolding or other structural components within the plant cell.

Abscisic Acid↗

PubMed1999

Strong selective pressure for evolution of an Epstein-Barr virus LMP2B homologue in the rhesus lymphocryptovirus.

Latent membrane protein 2B (LMP2B) is expressed during latent Epstein-Barr virus (EBV) infection, but little is known about its role. The goal of this study was to determine whether an LMP2B homologue is conserved in the rhesus monkey lymphocryptovirus (LCV). Both rhesus LCV LMP2A and LMP2B genes were cloned and sequenced. The rhesus LCV LMP2B gene is positionally conserved, and the EBNA-2 responsiveness and the bidirectional nature of the LMP1-LMP2B promoter have also been functionally conserved. However, this region of the genome encoding the LMP1, LMP1-LMP2B promoter, and LMP2B first exon demonstrates the most dramatic nucleotide sequence divergence between human and nonhuman LCV observed to date. Evolution of the rhesus LCV LMP2B promoter and transcript despite the dynamic nature of this genomic region reflects strong selective pressure for a yet-to-be-identified LMP2B function.

Amino Acid Sequence↗