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PubMed2005

Genetic variability and molecular evolution of the human respiratory syncytial virus subgroup B attachment G protein.

Human respiratory syncytial virus (HRSV) is the most important cause of acute respiratory disease in infants. Two major subgroups (A and B) have been identified based on antigenic differences in the attachment G protein. Antigenic variation between and within the subgroups may contribute to reinfections with these viruses by evading the host immune responses. To investigate the circulation patterns and mechanisms by which HRSV-B viruses evolve, we analyzed the G protein genetic variability of subgroup B sequences isolated over a 45-year period, including 196 Belgian strains obtained over 22 epidemic seasons (1982 to 2004). Our study revealed that the HRSV-B evolutionary rate (1.95 x 10(-3) nucleotide substitutions/site/year) is similar to that previously estimated for HRSV-A (1.83 x 10(-3) nucleotide substitutions/site/year). However, natural HRSV-B isolates appear to accommodate more drastic changes in their attachment G proteins. The most recent common ancestor of the currently circulating subgroup B strains was estimated to date back to around the year 1949. The divergence between the two major subgroups was calculated to have occurred approximately 350 years ago. Furthermore, we have identified 12 positively selected sites in the G protein ectodomain, suggesting that immune-driven selective pressure operates in certain codon positions. HRSV-A and -B strains have similar phylodynamic patterns: both subgroups are characterized by global spatiotemporal strain dynamics, where the high infectiousness of HRSV permits the rapid geographic spread of novel strain variants.

Amino Acid Sequence↗

PubMed2000

Evolution of air-breathing and central CO(2)/H(+) respiratory chemosensitivity: new insights from an old fish?

While little is known of the origin of air-breathing in vertebrates, primitive air breathers can be found among extant lobe-finned (Sarcopterygii) and ray-finned (Actinopterygii) fish. The descendents of Sarcopterygii, the tetrapods, generate lung ventilation using a central pattern generator, the activity of which is modulated by central and peripheral CO(2)/H(+) chemoreception. Air-breathing in Actinopterygii, in contrast, has been considered a 'reflexive' behaviour with little evidence for central CO(2)/H(+) respiratory chemoreceptors. Here, we describe experiments using an in vitro brainstem preparation of a primitive air-breathing actinopterygian, the longnose gar Lepisosteus osseus. Our data suggest (i) that gill and air-breathing motor patterns can be produced autonomously by the isolated brainstem, and (ii) that the frequency of the air-breathing motor pattern is increased by hypercarbia. These results are the first evidence consistent with the presence of an air-breathing central pattern generator with central CO(2)/H(+) respiratory chemosensitivity in any primitive actinopterygian fish. We speculate that the origin of the central neuronal controller for air-breathing preceded the divergence of the sarcopterygian and actinopterygian lineages and dates back to a common air-breathing ancestor.

Animals↗

PubMed2005

The Genomes of Oryza sativa: a history of duplications.

We report improved whole-genome shotgun sequences for the genomes of indica and japonica rice, both with multimegabase contiguity, or almost 1,000-fold improvement over the drafts of 2002. Tested against a nonredundant collection of 19,079 full-length cDNAs, 97.7% of the genes are aligned, without fragmentation, to the mapped super-scaffolds of one or the other genome. We introduce a gene identification procedure for plants that does not rely on similarity to known genes to remove erroneous predictions resulting from transposable elements. Using the available EST data to adjust for residual errors in the predictions, the estimated gene count is at least 38,000-40,000. Only 2%-3% of the genes are unique to any one subspecies, comparable to the amount of sequence that might still be missing. Despite this lack of variation in gene content, there is enormous variation in the intergenic regions. At least a quarter of the two sequences could not be aligned, and where they could be aligned, single nucleotide polymorphism (SNP) rates varied from as little as 3.0 SNP/kb in the coding regions to 27.6 SNP/kb in the transposable elements. A more inclusive new approach for analyzing duplication history is introduced here. It reveals an ancient whole-genome duplication, a recent segmental duplication on Chromosomes 11 and 12, and massive ongoing individual gene duplications. We find 18 distinct pairs of duplicated segments that cover 65.7% of the genome; 17 of these pairs date back to a common time before the divergence of the grasses. More important, ongoing individual gene duplications provide a never-ending source of raw material for gene genesis and are major contributors to the differences between members of the grass family.

Base Sequence↗

PubMed1998

Differences in reverse transcriptase activity versus p24 antigen detection in cell culture, when comparing a homogeneous group of HIV type 1 subtype B viruses with a heterogeneous group of divergent strains.

Failure to detect infection with HIV-1 non-B subtypes in some antibody screening assays has been shown. To date, however, no studies have been published evaluating the capacity of standard tests to quantify replication of divergent HIV-1 in cell culture. Reverse transcriptase (RT) activity and p24 antigen assays are the two methods most commonly used for this purpose. A homogeneous panel of HIV-1 subtype B viruses from northern Italy and a heterogeneous panel of diverse genetic subtypes (A to F and O) from different regions of the world were cultured under identical conditions. A new nonradioactive RT assay was used as a basis for comparison to evaluate the capacity of two p24 assays to quantify viral growth in both panels. Comparison of the p24 amount/RT activity (p24/RT) ratios showed that ratios in the subtype B panel tended to be markedly higher than in the diverse subtype panel. Greatest variation was seen with one of the subtype O isolates, where up to a 400 times lower ratio was obtained compared with the average ratio for the subtype B panel. In addition, one Thai subtype B virus also gave a markedly reduced ratio. Furthermore, comparison between the two p24 assays showed different abilities to detect p24 from different HIV-1 isolates. We discuss limitations for the use of anti-HIV-1 p24 antibodies produced by immunization with subtype B p24 in p24 assays.

AIDS Serodiagnosis↗

PubMed1983

Conservation and divergence of immunoglobulin VH pseudogenes.

The 12 immunoglobulin VH pseudogenes, that have been characterized to date, differ from most pseudogenes of other multigene families in two aspects: (i) they carry only one (11 cases) or at the most two (1 case) deleterious mutations and (ii) they show no evidence of increased divergence from intact VH genes. We describe here the first immunoglobulin VH pseudogene that does not have these characteristics. This pseudogene accumulated numerous deleterious mutations and diverged considerably from other genes of the VH gene family to which it belongs. In possible contrast to the other VH pseudogenes, this pseudogene seems to be selectively neutral. We discuss the implications of the characterization of this diverged VH pseudogene in relation to our understanding of the genetic mechanisms that generate diversity among germline immunoglobulin VH genes.

Animals↗

PubMed2004

DNA variability and divergence at the notch locus in Drosophila melanogaster and D. simulans: a case of accelerated synonymous site divergence.

DNA diversity in two segments of the Notch locus was surveyed in four populations of Drosophila melanogaster and two of D. simulans. In both species we observed evidence of non-steady-state evolution. In D. simulans we observed a significant excess of intermediate frequency variants in a non-African population. In D. melanogaster we observed a disparity between levels of sequence polymorphism and divergence between one of the Notch regions sequenced and other neutral X chromosome loci. The striking feature of the data is the high level of synonymous site divergence at Notch, which is the highest reported to date. To more thoroughly investigate the pattern of synonymous site evolution between these species, we developed a method for calibrating preferred, unpreferred, and equal synonymous substitutions by the effective (potential) number of such changes. In D. simulans, we find that preferred changes per "site" are evolving significantly faster than unpreferred changes at Notch. In contrast we observe a significantly faster per site substitution rate of unpreferred changes in D. melanogaster at this locus. These results suggest that positive selection, and not simply relaxation of constraint on codon bias, has contributed to the higher levels of unpreferred divergence along the D. melanogaster lineage at Notch.

Animals↗

PubMed1990

The fossil record and estimating divergence times between lineages: maximum divergence times and the importance of reliable phylogenies.

Bounded estimates on divergence times between lineages are crucial to the calculation of absolute rates of molecular evolution. Upper (minimum) bounds on divergence times are easily estimated based on earliest fossil finds. Lower (maximum) bounds are more difficult to estimate; the age of putative ancestors may be used, though in practice it is virtually impossible to distinguish ancestors from primitive sister groups, which do not, of logical necessity, constitute lower bounds on divergence times. Two relatively new approaches to estimating lower bounds directly assess the incompleteness of the fossil record. The first uses taphonomic control groups to distinguish real absences from nonpreservation, while the second, and probably more powerful, uses the quality of the fossil record to estimate confidence intervals on the bases of stratigraphic ranges. For some groups, especially vertebrates, the inclusion or exclusion of problematic fossils can dramatically affect estimated lower bounds on divergence times, often swamping the uncertainties due to the incompleteness of the fossil record and/or correlation and dating errors. When datable paleogeographic events reflect ancient divisions of faunas, a lower bound on the divergence time of species within a fauna can be established based on the geologic, rather than fossil, record. The fossil records of hominids, eutherian mammals, echinoids, and geese are used as examples.

Animals↗

PubMed2005

After the duplication: gene loss and adaptation in Saccharomyces genomes.

The ancient duplication of the Saccharomyces cerevisiae genome and subsequent massive loss of duplicated genes is apparent when it is compared to the genomes of related species that diverged before the duplication event. To learn more about the evolutionary effects of the duplication event, we compared the S. cerevisiae genome to other Saccharomyces genomes. We demonstrate that the whole genome duplication occurred before S. castellii diverged from S. cerevisiae. In addition to more accurately dating the duplication event, this finding allowed us to study the effects of the duplication on two separate lineages. Analyses of the duplication regions of the genomes indicate that most of the duplicated genes (approximately 85%) were lost before the speciation. Only a small amount of paralogous gene loss (4-6%) occurred after speciation. On the other hand, S. castellii appears to have lost several hundred genes that were not retained as duplicated paralogs. These losses could be related to genomic rearrangements that reduced the number of chromosomes from 16 to 9. In addition to S. castellii, other Saccharomyces sensu lato species likely diverged from S. cerevisiae after the duplication. A thorough analysis of these species will likely reveal other important outcomes of the whole genome duplication.

Adaptation, Physiological↗

PubMed1992

Mitochondrial DNA evolution at a turtle's pace: evidence for low genetic variability and reduced microevolutionary rate in the Testudines.

Evidence is compiled suggesting a slowdown in mean microevolutionary rate for turtle mitochondrial DNA (mtDNA). Within each of six species or species complexes of Testudines, representing six genera and three taxonomic families, sequence divergence estimates derived from restriction assays are consistently lower than expectations based on either (a) the dates of particular geographic barriers with which significant mtDNA genetic clades appear associated or (b) the magnitudes of sequence divergence between mtDNA clades in nonturtle species that otherwise exhibit striking phylogeographic concordance with the genetic partitions in turtles. Magnitudes of the inferred rate slowdowns average eightfold relative to the "conventional" mtDNA clock calibration of 2%/Myr sequence divergence between higher animal lineages. Reasons for the postulated deceleration remain unknown, but two intriguing correlates are (a) the exceptionally long generation length most turtles and (b) turtles' low metabolic rate. Both factors have been suspected of influencing evolutionary rates in the DNA sequences of some other vertebrate groups. Uncertainities about the dates of cladogenetic events in these Testudines leave room for alternatives to the slowdown interpretation, but consistency in the direction of the inferred pattern, across several turtle species and evolutionary settings, suggests the need for caution in acceptance of a universal mtDNA-clock calibration for higher animals.

Animals↗

PubMed1996

Molecular phylogeny of the extinct ground sloth Mylodon darwinii.

DNA was extracted from the remains of 35 ground sloths from various parts of North and South America. Two specimens of Mylodon darwinii, a species that went extinct at the end of the last glaciation, yielded amplifiable DNA. However, of the total DNA extracted, only approximately 1/1000 originated from the sloth, whereas a substantial part of the remainder was of bacterial and fungal origin. In spite of this, > 1100 bp of sloth mitochondrial rDNA sequences could be reconstructed from short amplification products. Phylogenetic analyses using homologous sequences from all extant edentate groups suggest that Mylodon darwinii was more closely related to the two-toed than the three-toed sloths and, thus, that an arboreal life-style has evolved at least twice among sloths. The divergence of Mylodon and the two-toed sloth furthermore allows a date for the radiation of armadillos, anteaters, and sloths to be estimated. This result shows that the edentates differ from other mammalian orders in that they contain lineages that diverged before the end of the Cretaceous Period.

Animals↗

PubMed2001

Phylogeography of the spotted sand bass, Paralabrax maculatofasciatus: divergence of Gulf of California and Pacific Coast populations.

Have the warm tropical waters and currents of the southern Gulf of California, Mexico (also known as the Sea of Cortez), formed a barrier to gene flow, resulting in disjunct populations in the upper gulf that are isolated from the outer Pacific Coast? Phylogeographic and genetic divergences of the spotted sand bass, Paralabrax maculatofasciatus, from three Gulf of California and two outer Pacific coastal locations were tested using mitochondrial DNA (mtDNA) control region sequences. Sequence data from two congeners that are sympatrically distributed along the outer Pacific Coast, the barred sand bass, P. nebulifer, and the kelp bass, P. clathratus, were used to gauge the levels of genetic divergences. Differences among the three species and between the northern gulf and outer Pacific coastal populations of P. maculatofasciatus also were analyzed using 40 allozymic presumptive gene loci. Allozyme and mtDNA analyses each revealed many fixed differences among the species. Three significant allozymic frequency differences and two fixed mtDNA substitutions differentiated the gulf and outer Pacific coastal populations of P. maculatofasciatus. Three unique mtDNA haplotypes and three unique allozyme alleles were identified from the outer Pacific coastal population. The gulf sites contained four unique mtDNA haplotypes and six unique allozyme alleles. Partitioning of the mtDNA variation revealed that 72% of the variance occurred between the gulf and outer Pacific Coast, 20% between sampling sites in the two regions, and 8% within the sites. There appears to be little gene flow across the waters of the southern Baja Penninsula, producing divergence estimated as 120,000 to 600,000 years between the outer Pacific coastal and the Gulf of California populations. This separation level may date to a hypothesized seaway closure near La Paz, Mexico, during the mid-Pleistocene, and characterizes other fish populations. A second pattern of deeper allopatric species-level divergences in some other fishes may date to a Pliocene closure of a mid Baja Penninsular seaway. Significant differences also were discerned in P. maculatofasciatus between the San Diego and central Baja California coastal sites and between the upper/central and the lower gulf locations. Variation between locations in the two regions may be indicative of larval retention and low adult migration, which needs to be tested further.

Animals↗

PubMed2001

Sponge homologs of vertebrate protein tyrosine kinases and frequent domain shufflings in the early evolution of animals before the parazoan-eumetazoan split.

The protein tyrosine kinases (PTKs) diverged specifically in animal lineages by gene duplications and domain shufflings to form a large protein family comprising diverse subfamilies with distinct domain organizations and functions. On the basis of a phylogenetic tree inferred from a comparison of the shared kinase domains, we previously showed that gene duplications that gave rise to diverse subfamilies predate the divergence of parazoans and eumetazoans. There is, however, still a possibility that, although the kinase domain duplications are ancient events, the domain shufflings that gave rise to different subfamilies with distinct domain organization are more recent event than the kinase domain duplications. To clarify this problem, we have determined the complete sequences of 15 sponge PTKs and have compared the domain organizations of these sponge PTKs and those of eumetazoans. For each of ten sponge PTKs out of 15 analyzed here, a possible eumetazoan (human and Drosophila) ortholog has been identified. The sponge and eumetazoan orthologs are virtually identical in domain organization and belong to the same subfamily in the PTK family tree for each of ten orthologous pairs, except for one subfamily in which a considerable deletions and/or insertions of domains are observed. This result suggests that most, if not all, of the domain shufflings, together with gene duplications, are very old, going back to dates before the parazoan-eumetazoan split, the earliest divergence among extant animal phyla.

Animals↗

PubMed2006

A genetic signature of interspecies variations in gene expression.

Phenotypic diversity is generated through changes in gene structure or gene regulation. The availability of full genomic sequences allows for the analysis of gene sequence evolution. In contrast, little is known about the principles driving the evolution of gene expression. Here we describe the differential transcriptional response of four closely related yeast species to a variety of environmental stresses. Genes containing a TATA box in their promoters show an increased interspecies variability in expression, independent of their functional association. Examining additional data sets, we find that this enhanced expression divergence of TATA-containing genes is consistent across all eukaryotes studied to date, including nematodes, fruit flies, plants and mammals. TATA-dependent regulation may enhance the sensitivity of gene expression to genetic perturbations, thus facilitating expression divergence at particular genetic loci.

DNA↗

PubMed2000

Divergent backward projections from the anterior part of the inferotemporal cortex (area TE) in the macaque.

The organization of backward projections from the anterior part of the inferotemporal cortex (area TE) to the posterior part of the inferotemporal cortex (area TEO) was studied in the macaque monkey by using the anterograde tracer Phaseolus vulgaris-leucoagglutinin (PHA-L). The objectives of the study were to investigate this backward projection and to compare it with 1) the backward projections that have been described previously in the early sensory areas and 2) the forward projection from area TEO to area TE. After a single iontophoretic injection of PHA-L into area TE in three monkeys, a dense distribution of labeled terminals was observed in area TEO and in the ventral bank of the superior temporal sulcus (area PITd) that adjoined area TEO. A less dense distribution was observed in areas V4, V2, and V1. Clusters of labeled terminals in areas TEO and PITd extended more than 4 mm along the cortical surface. The forward projections from area TEO to area TE also were studied for comparison by reanalyzing two previous cases (Saleem et al. ¿1993 Cerebral Cortex 3:454-464). These projections (from area TEO to area TE) were more focal than the terminations that occurred in area TEO after injections into area TE. Nine single axons projecting from area TE to areas TEO/PITd were reconstructed through serial sections. These showed variable, complex branching patterns with multiple arbors (1-12). Arbors were localized in layers 1-3 for four axons, in layer 1 for one axon, layers 5 and 6 for two axons, and in both layers 1-3 and layers 5-6 for two axons. Axons with horizontally elongated arbors confined to layer 1 were not predominant. The size of the individual arbors of these axons along their long axes tended to be larger (1.56 +/- 1.24 mm) than those of TEO-to-TE forward axons (<0.6 mm). Thus, the authors conclude that, like other backward systems described to date, those from area TE to areas TEO/PITd are divergent. However, single axons have more variable laminar patterns of terminal distribution than those in the other backward systems.

Animals↗

PubMed1991

Molecular distance and divergence time in carnivores and primates.

Numerous studies have used indices of genetic distance between species to reconstruct evolutionary relationships and to estimate divergence time. However, the empirical relationship between molecular-based indices of genetic divergence and divergence time based on the fossil record is poorly known. To date, the results of empirical studies conflict and are difficult to compare because they differ widely in their choice of taxa, genetic techniques, or methods for calibrating rates of molecular evolution. We use a single methodology to analyze the relationship of molecular distance and divergence time in 86 taxa (72 carnivores and 14 primates). These taxa have divergence times of 0.01-55 Myr and provide a graded series of phylogenetic divergences such that the shape of the curve relating genetic distance and divergence time is often well defined. The techniques used to obtain genetic distance estimates include one- and two-dimensional protein electrophoresis, DNA hybridization, and microcomplement fixation. Our results suggest that estimates of molecular distance and divergence time are highly correlated. However, rates of molecular evolution are not constant; rather, in general they decline with increasing divergence time in a linear fashion. The rate of decline may differ according to technique and taxa. Moreover, in some cases the variability in evolutionary rates changes with increasing divergence time such that the accuracy of nodes in a phylogenetic tree varies predictably with time.

Animals↗

PubMed2001

Genetic identification and characterization of limestone canyon virus, a unique Peromyscus-borne hantavirus.

Hantaviruses, family Bunyaviridae, are rodent-borne RNA viruses that can cause hantavirus pulmonary syndrome (HPS) in various regions of the Americas. A coevolutionary relationship exists between hantaviruses and their specific rodent reservoir hosts; the phylogeny of the viruses generally matches that of the rodents. There are several Peromyscus-borne hantaviruses, including Sin Nombre virus, the most common cause of HPS in North America. This report describes the genetic detection and characterization of a newly discovered Peromyscus boylii-borne virus, Limestone Canyon (LSC) virus, the most divergent member of the Peromyscus-borne hantaviruses to date. Analysis of a 1209-nucleotide region of the S segment of LSC virus showed it to be more closely related to hantaviruses found in harvest mice (Reithrodontomys megalotis and R. mexicanus) than to other Peromyscus-associated hantaviruses (Sin Nombre, New York, and Monongahela). Phylogenetic analysis of virtually the entire M genome segment (3489 nucleotides) of LSC virus revealed a similar picture in which LSC virus was found to be very distinct from other Peromyscus-associated viruses, but its exact relationship to the other Peromyscus-borne and the Reithrodontomys-borne viruses was not resolved. These results indicate that hantavirus host species-jumping events can occur by which a hantavirus may switch to, and become established in, a rodent host belonging to a different genus. P. boylii are present throughout the southwestern United States and central Mexico. More extensive screening of HPS patients by using RT-PCR assays will be necessary to determine if LSC virus can cause human disease.

Animals↗

PubMed2000

Evolution of introns and exons of class II major histocompatibility complex genes of vertebrates.

The phylogenetic relationships and patterns of nucleotide substitution were compared for introns and exons of class II major histocompatibility complex (MHC) genes in three datasets: human DRB1, human DQA1, and cyprinid fish DAB1. In both human DRB1 and cyprinid DAB1, there was strong evidence that recombination events between alleles have occurred in such a way that intron and exon sequences of a given allele do not necessarily share the same evolutionary history. In the case of human DRB1, recombination was found to have homogenized intron 1 and intron 2 sequences relative to exon 2 sequences within lineages of alleles but not between lineages. As a result, mean divergence times of intron sequences are much more recent than those of exonic sequences. Thus, the divergence time of DRB1 introns cannot be used to date that of exons in the same alleles, and the hypothesis that most human DRB1 polymorphism is of very recent origin is not supported.

Alleles↗

PubMed1993

Conserved secondary structures in the ITS2 of trematode pre-rRNA.

Biological functions of transcribed spacer regions in eucaryotic pre-rRNAs remain elusive so far. Utilization of the comparative approach to analyse their secondary structure has been impeded by the extensive sequence divergence observed among most of the specimens available to date. However, we have taken advantage of the recent derivation of a set of largely similar sequences for different schistosome species to look for the presence of constrained secondary structures within the internally transcribed spacer 2 (ITS2). We show that several common features of secondary structure are shared by these species despite sequence variation, with some of them supported by compensatory changes, suggesting a significant role of ITS2 as an RNA domain during ribosome biogenesis.

Animals↗