SEARCH · PubMed Health

Results for “Divergence dates”

Explore indexed PubMed citations for clinical trials, systematic reviews and public health research. Read source abstracts and follow each citation to its original PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 289 records · Page 16Linked to original sources

PubMed2005

The influence of Pleistocene glacial refugia on tawny owl genetic diversity and phylogeography in western Europe.

The glacial refugia hypothesis indicates that during the height of the Pleistocene glaciations the temperate species that are today widespread in western Europe must have survived in small and climatically favourable areas located in the southern peninsulas of Iberia, Italy and Balkans. One such species is the tawny owl, a relatively sedentary, nonmigratory bird presently distributed throughout Europe. It is a tree-nesting species closely associated with deciduous and mixed coniferous woodlands. In this study I used control region mtDNA sequences from 187 individuals distributed among 14 populations to determine whether current genetic patterns in tawny owl populations were consistent with postglacial expansion from peninsular refugia. European, North African and Asian tawny owls were found to represent three distinct lineages, where North Africa is the sister clade to all European owls. Within Europe, I found three well-supported clades that correspond to each of the three allopatric refugia. Expansion patterns indicate that owls from the Balkan refugium repopulated most of northern Europe, while expansion out of Iberia and Italy had only regional effects leading to admixture in France. Estimates of population divergence times between refugia populations are roughly similar, but one order of magnitude smaller between Greece and northern Europe. Based on a wide range of mutation rates and generation times, divergence between refugia appears to date to the Pleistocene.

Africa, Northern↗

PubMed1997

Mouse Dll3: a novel divergent Delta gene which may complement the function of other Delta homologues during early pattern formation in the mouse embryo.

Mouse delta-like 3 (Dll3), a novel vertebrate homologue of the Drosophila gene Delta was isolated by a subtracted library screen. In Drosphila, the Delta/Notch signalling pathway functions in many situations in both embryonic and adult life where cell fate specification occurs. In addition, a patterning role has been described in the establishment of the dorsoventral compartment boundary in the wing imaginal disc. Dll3 is the most divergent Delta homologue identified to date. We confirm that Dll3 can inhibit primary neurogenesis when ectopically expressed in Xenopus, suggesting that it can activate the Notch receptor and therefore is a functional Delta homologue. An extensive expression study during gastrulation and early organogenesis in the mouse reveals a diverse and dynamic pattern of expression. The three major sites of expression implicate Dll3 in somitogenesis and neurogenesis and in the production of tissue from the primitive streak and tailbud. A careful comparison of Dll3 and Dll1 expression by double RNA in situ hybridisation demonstrates that these genes have distinct patterns of expression, but implies that together they operate in many of the same processes. We postulate that during somitogenesis Dll3 and Dll1 coordinate in establishing the intersomitic boundaries. We confirm that, during neurogenesis in the spinal cord, Dll1 and Dll3 are expressed by postmitotic cells and suggest that expression is sequential such that cells express Dll1 first followed by Dll3. We hypothesise that Dll1 is involved in the release of cells from the precursor population and that Dll3 is required later to divert neurons along a specific differentiation pathway.

Amino Acid Sequence↗

PubMed2006

Heritable endosymbionts of Drosophila.

Although heritable microorganisms are increasingly recognized as widespread in insects, no systematic screens for such symbionts have been conducted in Drosophila species (the primary insect genetic models for studies of evolution, development, and innate immunity). Previous efforts screened relatively few Drosophila lineages, mainly for Wolbachia. We conducted an extensive survey of potentially heritable endosymbionts from any bacterial lineage via PCR screens of mature ovaries in 181 recently collected fly strains representing 35 species from 11 species groups. Due to our fly sampling methods, however, we are likely to have missed fly strains infected with sex ratio-distorting endosymbionts. Only Wolbachia and Spiroplasma, both widespread in insects, were confirmed as symbionts. These findings indicate that in contrast to some other insect groups, other heritable symbionts are uncommon in Drosophila species, possibly reflecting a robust innate immune response that eliminates many bacteria. A more extensive survey targeted these two symbiont types through diagnostic PCR in 1225 strains representing 225 species from 32 species groups. Of these, 19 species were infected by Wolbachia while only 3 species had Spiroplasma. Several new strains of Wolbachia and Spiroplasma were discovered, including ones divergent from any reported to date. The phylogenetic distribution of Wolbachia and Spiroplasma in Drosophila is discussed.

Animals↗

PubMed2002

Likelihood and Bayes estimation of ancestral population sizes in hominoids using data from multiple loci.

Polymorphisms in an ancestral population can cause conflicts between gene trees and the species tree. Such conflicts can be used to estimate ancestral population sizes when data from multiple loci are available. In this article I extend previous work for estimating ancestral population sizes to analyze sequence data from three species under a finite-site nucleotide substitution model. Both maximum-likelihood (ML) and Bayes methods are implemented for joint estimation of the two speciation dates and the two population size parameters. Both methods account for uncertainties in the gene tree due to few informative sites at each locus and make an efficient use of information in the data. The Bayes algorithm using Markov chain Monte Carlo (MCMC) enjoys a computational advantage over ML and also provides a framework for incorporating prior information about the parameters. The methods are applied to a data set of 53 nuclear noncoding contigs from human, chimpanzee, and gorilla published by Chen and Li. Estimates of the effective population size for the common ancestor of humans and chimpanzees by both ML and Bayes methods are approximately 12,000-21,000, comparable to estimates for modern humans, and do not support the notion of a dramatic size reduction in early human populations. Estimates published previously from the same data are several times larger and appear to be biased due to methodological deficiency. The divergence between humans and chimpanzees is dated at approximately 5.2 million years ago and the gorilla divergence 1.1-1.7 million years earlier. The analysis suggests that typical data sets contain useful information about the ancestral population sizes and that it is advantageous to analyze data of several species simultaneously.

Algorithms↗

PubMed2003

A molecular phylogeny of the Littorininae (Gastropoda: Littorinidae): unequal evolutionary rates, morphological parallelism, and biogeography of the Southern Ocean.

A molecular phylogeny is presented for the subfamily Littorininae (including representatives of all subgeneric taxa and all members of a group of southern-temperate species formerly classified as 'Nodilittorina'), based on sequence data from two nuclear (18S rRNA, 28S rRNA) and two mitochondrial (12S rRNA, CO1) genes. The phylogeny shows considerable disagreement with earlier hypotheses derived from morphological data. In particular, 'Nodilittorina' is polyphyletic and is here divided into four genera (Echinolittorina, Austrolittorina, Afrolittorina new genus, and the monotypic Nodilittorina s.s.). The phylogenetic relationships of 'Littorina' striata have been controversial and it is here transferred to the genus Tectarius, a surprising relationship for which there is little morphological support. The relationships of the enigmatic Mainwaringia remain poorly resolved, but it is not a basal member of the subfamily. The two living species of Mainwaringia are remarkable for a greatly elevated rate of evolution in all four genes examined; it is suggested that this may be connected with their protandrous hermaphroditism, which is unique in the family. The molecular phylogeny provides a new framework for the adaptive radiation of the Littorininae, showing more frequent shifts between habitats and climatic regimes than previously suspected, and striking parallelism of morphological characters. The fossil record of littorinids is poor, but ages of clades are estimated using a calibration based on a Lower Eocene age of the genus Littoraria. Using these estimates, the antitropical distribution of Littorina and Afrolittorina is an ancient pattern of possibly Cretaceous age. The five members of Austrolittorina show a Gondwanan distribution in Australia, New Zealand, and South America. Based on the morphological uniformity within this clade, relatively recent (Plio-Pleistocene) trans-Pacific dispersal events seemed a likely explanation, as proposed for numerous other congeneric marine taxa. However, molecular estimation of ages of divergence suggest an initial vicariance between Australian and South American lineages at 40-73Ma, contemporary with the later stages of fragmentation of the Gondwanan supercontinent, followed by more recent (but still mid-Cenozoic) dispersal events across the Tasman Sea and the Pacific Ocean. Afrolittorina is another Cretaceous clade, now restricted to southern Africa and southern Australia, but divergence between these lineages (29-55Ma) post-dates Gondwanan fragmentation. Within both Austrolittorina and Afrolittorina all sister-species divergences are estimated to fall in the range 10-47Ma, so that there is no evidence for speciation events in the Plio-Pleistocene.

Adaptation, Biological↗

PubMed1999

Atypically low rate of cytochrome b evolution in the scleractinian coral genus Acropora.

Unexpectedly low levels of mitochondrial DNA (mtDNA) cytochrome b sequence divergence are found between species of the scleractinian coral genus Acropora. Comparison of 964 positions of the cytochrome b gene of two out of the three Caribbean Acropora species with seven of their Pacific congeners shows only 0.3-0.8% sequence difference. Species in these biogeographic regions have been evolving independently for at least three million years (since the rise of the Isthmus of Panama) and this geological date is used to estimate nucleotide divergence rates. The results indicate that the Acropora cytochrome b gene is evolving at least 10-20 times slower than the 'standard' vertebrate mtDNA clock and is one of the most slowly evolving animal mitochondrial genes described to date. The possibility is discussed that, unlike higher animals, cnidarians may have a functional mtDNA mismatch repair system.

Animals↗

PubMed2004

Co-existence of recent and ancestral nucleotide sequences in viral quasispecies of human immunodeficiency virus type 1 patients.

In human immunodeficiency virus type 1 (HIV-1) infection, the presence of divergent nucleotide sequences within a quasispecies has been associated with double infections or samples from different times or from different tissue compartments. The authors analysed HIV-1 proviral quasispecies from PBMC of three untreated Spanish patients displaying highly divergent nucleotide sequences without evidence of double infection. The origin of these nucleotide sequences was determined by phylogenetic analysis and by dating of the different groups using a genetic divergence versus sampling year plot from a set of Spanish samples. By their short genetic distance to the node of the patient's HIV-1 phylogenetic tree and by their early date of origin, close to the seroconversion time, some groups of sequences were considered ancestral. The presence within HIV-1 quasispecies of ancestral sequences, dated up to 10 years earlier than present ones, has important consequences for in vivo viral evolution, in the pathogenesis and treatment of HIV-1 infection.

Amino Acid Sequence↗

PubMed1993

Evolution of the monotremes. The sequences of the protamine P1 genes of platypus and echidna.

The protamine P1 genes from two monotremes, platypus (Ornithorhynchus anatinus) and echidna (Tachyglossus aculeatus) were isolated after polymerase-chain-reaction amplification then cloned and sequenced. The two protamine P1 genes are of 290 bp and 311 bp for platypus and echidna, respectively, and are clearly orthologous to the published sequences of protamine P1 genes of eutherian mammals and birds. Both genes contain an intron, like the mammals and marsupials and unlike the bird P1 genes that are intronless. The deduced protein sequences from the coding areas of the platypus and echidna protamine P1 genes do not contain any cysteine residues. This absence of cysteine residues leaves the sperm nuclei susceptible to disruption in vitro by exposure to increasing ionic strength and is a characteristic of fish, birds and marsupials. In contrast, the P1 protamines of placental mammals invariably contain 6-9 cysteine residues that, as a result of the formation of intermolecular and intramolecular disulfide bridges, significantly increase the stability of the sperm nuclei that can only be disrupted following disulfide-bond cleavage. Phylogenetic analysis of the protamine P1 gene sequences indicates that the monotremes occupy a position half-way between the eutherian mammals and birds. From the DNA sequences we estimate the time of divergence of the platypus and the echidna to be around 22 million years ago. This date agrees very well with the published estimates of divergence based on other criteria.

Amino Acid Sequence↗

PubMed2002

Using the fossil record to estimate the age of the last common ancestor of extant primates.

Divergence times estimated from molecular data often considerably predate the earliest known fossil representatives of the groups studied. For the order Primates, molecular data calibrated with various external fossil dates uniformly suggest a mid-Cretaceous divergence from other placental mammals, some 90 million years (Myr) ago, whereas the oldest known fossil primates are from the basal Eocene epoch (54-55 Myr ago). The common ancestor of primates should be earlier than the oldest known fossils, but adequate quantification is needed to interpret possible discrepancies between molecular and palaeontological estimates. Here we present a new statistical method, based on an estimate of species preservation derived from a model of the diversification pattern, that suggests a Cretaceous last common ancestor of primates, approximately 81.5 Myr ago, close to the initial divergence time inferred from molecular data. It also suggests that no more than 7% of all primate species that have ever existed are known from fossils. The approach unites all the available palaeontological methods of timing evolutionary events: the fossil record, extant species and clade diversification models.

Animals↗

PubMed2005

Rapid divergence and postglacial colonization in western North American Steller's jays (Cyanocitta stelleri).

Post-Pleistocene avian colonization of deglaciated North America occurred from multiple refugia, including a coastal refugium in the northwest. The location of a Pacific Coastal refugium is controversial; however, multiple lines of evidence suggest that it was located near the Queen Charlotte Islands (also known as Haida Gwaii). The Queen Charlotte Islands contain a disproportionately large number of endemic plants and animals including the Steller's jay Cyanocitta stelleri carlottae. Using five highly variable microsatellite markers, we studied population structure among eight populations of Steller's jay (N = 150) from geographical areas representing three subspecies in western North America: C. s. carlottae, C. s. stelleri and C. s. annectens. Microsatellite analyses revealed genetic differentiation between each of the three subspecies, although more extensive sampling of additional C. s. annectens populations is needed to clarify the level of subspecies differentiation. High levels of population structure were found among C. s. stelleri populations with significant differences in all but two pairwise comparisons. A significant isolation by distance pattern was observed amongst populations in the Pacific Northwest and Alaska. In the C. s. carlottae population, there was evidence of reduced genetic variation, higher number of private alleles than northern C. s. stelleri populations and higher levels of divergence between Queen Charlotte Island and other populations. We were unable to reject the hypothesis that the Queen Charlotte Islands served as a refugium during the Pleistocene. Steller's jay may have colonized the Queen Charlotte Islands near the end of the last glaciation or persisted throughout the Pleistocene, and this subspecies may thus represent a glacial relic. The larger number of private alleles, despite reduced genetic variation, morphological distinctiveness and high divergence from other populations suggests that the Queen Charlotte Island colonization pre-dates that of the mainland. Furthermore, our results show rapid divergence in Steller's jay populations on the mainland following the retreat of the ice sheets.

Animals↗

PubMed1994

Evolution of the chAB4 multisequence family in primates.

Approximately 50 members of the primate-specific multisequence family chAB4 are located as clusters at eight different chromosomal loci within the human genome. The whole cloned region of chAB4 represents a single-copy or low-copy sequence in all nonhuman primates tested, with the exception of the chimpanzee, for which we found chAB4 copy numbers similar to those in the human. An Alu element was inserted into chAB4 after the divergence of the Old World monkeys from the hominoids but before chAB4 was amplified. The first amplification step could be dated after the great apes and the human diverged from the Old World monkeys. We have evidence that neither the copy numbers nor the chromosomal locations remained stable after this initial step and that gross alterations in the relative copy numbers of individual family members occurred even after the divergence of the human and the chimpanzee. Taken together, our data suggest that chAB4, in an evolutionary sense, is an unusually unstable sequence family.

Animals↗

PubMed2002

Complex patterns of colonization and refugia revealed for European grayling Thymallus thymallus, based on complete sequencing of the mitochondrial DNA control region.

The complete mitochondrial DNA (mtDNA) control region (1043 base pairs) and 162-bp of flanking transfer RNA genes were sequenced in 316 European grayling, Thymallus thymallus, from 44 populations throughout the Western European range of the species. A total of 58 haplotypes were revealed with pairwise divergence ranging from 0.001 to 0.038. An inferred intraspecific phylogenetic tree revealed two well-supported clades within the Danube basin, one highly divergent clade in the Adriatic basin, and one large, diverse group representing most other populations. A deeply divergent haplotype fixed in the Loire basin in central France, more groups of haplotypes from distinct Danubian tributaries, and a relatively ancestral haplotype fixed in former tributaries of the Elbe in Denmark all suggest a complex pattern of interglacial and postglacial expansions originating from disjunct refugia throughout central Europe. Despite some evidence of human-mediated stock transfers, parsimony-network-based nested-clade analysis (NCA) supported specific inferences relating to corridors of postglacial expansion such as the lower Rhine (Moselle) and Elbe systems (Danish populations) serving as sources for expansion into the Baltic to the north as well as the upper Rhine and Danube to the south; and specific Rhine populations (Doller, Orbe and Reuss) serving as sources for colonization of the Rhone. The multiple divergent clades representing populations in the upper Danube, as well as the deeply divergent haplotypes found in the Adriatic and Loire basins (> 5% divergence from Asian outgroups) support the theory that European grayling have had a long history in Western Europe, pre-dating Pleistocene glacial cycles. The patterns of mtDNA divergence shown here support a perspective of rich inter- and intrabasin genetic diversity that should be protected from current trends to translocate brood stocks for rearing and release in response to declining populations, especially in southern European basins.

Animals↗

PubMed2003

Integrated crop management of the lesser date moth Batrachedra amydraula Meyr. (Lepidoptera: Cosmopteridae) infesting some date-palm varieties in Egypt.

The present study was conducted during the two subsequent seasons of 2001 and 2002 in El-Beheira Governorate, Egypt, to evaluate the efficiency of some agricultural practices on the incidence of the lesser date-moth, Batrachedra amydraula Meyr. (Lepidoptera: Cosmopteridae) on some date-palm varieties, i.e. Sammany, Hayany and Halawy. The studied agricultural practices, were: covering clusters of flowers with paper craft, covering date bunches with porous plastic cloth, thinning of bunches and/or diverging strands of bunches using special metal rings. The infestation percentages of the lesser date moth for each of the evaluated varieties indicated that Sammany had the lowest value (22.68) as compared with Hayany (37.42) and Halawy (53.16), successively. So, Sammany variety was more tolerable to the infestation than the other two varieties. In an attempt to explain such variations in the infestation by Batrachedra amydraula, determination of wax contents as well as the histological studies of the green fruits of each variety were conducted. Results revealed that tolerance of Sammany to the infestation was due to relatively higher wax content (0.420 g/10 fruits) than that of either Hayany (0.220 g/10 fruits) or Halawy (0.320/10 fruits), respectively. Moreover, the lowest infestation percentage in Sammany variety was attributed to the structure of the outer and inner layers of fruits tissues, which could be considered as natural barriers against the insect pest, causing a considerable reduction in its infestation. To know the effect of the studied agricultural practices on the quality of dates, the physical parameters of ripened fruits (length, diameter, thickness and weight), in addition to the chemical properties of the same fruits (P.H, T.S.S, T.S. and E.C.) were also determined. There is a correlation between the studied chemicals, morphological and histological characteristics of the fruits on one hand and the calculated infestation rates on the other one. The tested varieties showed that Sammany variety had the lowest value of T.S.S (20.40) in comparison to Halawy (30.2) and Hayany (35.6). Also, the estimated sugar values were 23.60, 28.10 and 30.40 for the Sammany, Halawy and Hayany, consecutively.

Animals↗

PubMed1994

A molecular analysis of relationships and biogeography within a species complex of Holarctic fish (genus Osmerus).

Episodes of trans-Arctic faunal exchange and isolation between the north Pacific and Atlantic ocean basins have been implicated as important historic geological events contributing to extant patterns of genetic diversity and structure in Holarctic faunas. We made a further test of the significance of such biogeographic events by examining mitochondrial DNA (mtDNA) restriction fragment length and cytochrome b sequence polymorphism among north Pacific and Arctic, north-western Atlantic (north-eastern North American), and north-eastern Atlantic (European) regional forms of the boreal smelt, genus Osmerus. Our analyses also assessed whether the regional forms within this 'species complex': (i) represent a single widely distributed and polytypic species, or is composed of three geographically distinct species, and (ii) resulted from a single split from north Pacific ancestral Osmerus or two independent Pacific-Atlantic divergences. MtDNA sequence divergence estimates among forms ranged from 5.6-8.9% and from 6.1-8.5% based on restriction fragment and 300 base pairs of cytochrome b sequencing, respectively. Divergence within forms averaged less than 0.5% for fragment analysis and no differences were detected from sequence analysis. Provisional dating of lineage separations in Osmerus based on our sequence divergence estimates suggested a mid-Pliocene to early Pleistocene time frame for diversification among the forms. These estimated lineage separation dates support the idea that geological events in 'Beringia' and the surrounding trans-Arctic area (e.g. opening of the Bering Seaway, Pleistocene glacial advances), occurring over a similar time frame, have influenced radiation in Osmerus. Phenetic and parsimony analyses of the sequence divergence estimates and of sequence polymorphisms suggested that the north Pacific/Arctic form and the north-western Atlantic form shared a common ancestor more recently than either has with the north-eastern Atlantic form, thus supporting the hypothesis that the species complex has arisen from two independent Pacific-Atlantic divergences probably beginning during the mid-Pliocene.

Animals↗

PubMed2002

High genetic diversity revealed by the study of TLMV infection in French hemodialysis patients.

TT virus-like minivirus (TLMV) was recently discovered as a human circovirus. Little is known about its natural history and molecular epidemiology. A study of TLMV infection is described in a population of French hemodialysis patients. TLMV DNA was tested by seminested PCR system located in the noncoding region in 81 patients divided into seven groups according to the origin of their renal disease. Quantitation of TLMV DNA in serum was carried out. Sequences from 28 patients were compared with 40 sequences retrieved from databases and 53 TLMV sequences cloned from the serum of a single patient. The prevalence of TLMV DNA in hemodialysis patients was 95.1%. In this study, 24 samples (29.6%) presented viral loads of > 125 equivalents of plasmid (Ep)/ml, and only 6 (7.8%) had viral loads of > 125 x 10(2) Ep/ml. A significant correlation (P < 0.029) was found between viral loads of > 125 x 10(2) Ep/ml and the neoplastic origin of end-stage renal disease. Analysis of 53 sequences cloned from a single individual demonstrated high sequence variability, as shown by the genetic distance of 40.2%. This genetic distance is comparable to that between the most divergent sequences of TLMV reported to date (43.5%). These data suggest that TLMV viral load is possibly related to the level of immunocompetence of hemodialysis patients; the genetic diversity of TLMV is extremely high; and co-infection by different strains is possible.

Adult↗

PubMed1995

Comparative mapping of DNA probes derived from the V kappa immunoglobulin gene regions on human and great ape chromosomes by fluorescence in situ hybridization.

Fluorescence in situ hybridization (FISH) of cosmid clones of human V kappa gene regions to human and primate chromosomes contributed to the dating of chromosome reorganizations in evolution. A clone from the kappa locus at 2p11-p12 (cos 106) hybridized to the assumed homologous chromosome bands in the chimpanzees Pan troglodytes (PTR) and P. paniscus (PPA), the Gorilla gorilla (GGO), and the orangutan Pongo pygmaeus (PPY). Human and both chimpanzees differed from gorilla and orangutan by the mapping of cos 170, a clone derived from chromosome 2cen-q11.2; the transposition of this orphon to the other side of the centromere can, therefore, be dated after the human/chimpanzee and gorilla divergence. Hybridization to homologous bands was also found with a cosmid clone containing a V kappa I orphon located on chromosome 1 (cos 115, main signal at 1q31-q32), although the probe is not fully unique. Also, a clone derived from the orphon V kappa region on chromosome 22q11 (cos 121) hybridized to the homologous bands in the great apes. This indicates that the orphons on human chromosomes 1 and 22 had been translocated early in primate evolution.

Animals↗

PubMed2006

Critical appraisal of DNA microarrays in psychiatric genomics.

Transcriptome profiling using DNA microarrays are data-driven approaches with the potential to uncover unanticipated relationships between gene expression alterations and psychiatric disorders. Studies to date have yielded both convergent and divergent findings. Differences may be explained, at least in part, by the use of a variety of microarray platforms and analytical approaches. Consistent findings across studies suggest, however, that important relationships may exist between altered gene expression and genetic susceptibility to psychiatric disorders. For example, GAD67, RGS4, DTNBP1, NRG1, and GABRAB2 show expression alterations in the postmortem brain of subjects with schizophrenia, and these genes have been also implicated as putative, heritable schizophrenia susceptibility genes. Thus, we propose that for some genes, altered expression in the postmortem human brain may have a dual origin: polymorphisms in the candidate genes themselves or upstream genetic-environmental factors that converge to alter their expression level. We hypothesize that certain gene products, which function as "molecular hubs," commonly show altered expression in psychiatric disorders and confer genetic susceptibility for one or more diseases. Microarray gene expression studies are ideally suited to reveal these putative disease-associated molecular hubs and to identify promising candidates for genetic association studies.

DNA↗

PubMed2005

Characterization of a novel pestivirus originating from a pronghorn antelope.

A unique pestivirus, isolated from a pronghorn antelope (Antilocopra americana), was characterized. Serum neutralization studies suggested that this virus was antigenically related to pestiviruses. Genomic characteristics, unique to pestiviruses, indicated that this virus belongs to the Pestivirus genus. These characteristics included the organization of the 5' untranslated region (5'-UTR), the presence and length of a viral Npro coding region, conservation of cysteine residues in Npro, conservation of predicted amino acid sequences flanking the cleavage sites between viral polypeptides Npro and C and between C and Erns and conservation of predicted hydrophobicity plots of Npro protein. While this data indicated the virus belongs to the Pestivirus genus, phylogenetic analysis in 5'-UTR, Npro and E2 regions suggested that it is the most divergent of the pestiviruses identified to date. This conclusion was also supported by the amino acid identity in coding regions. The corresponding values were much lower for the comparison of pronghorn pestivirus to other pestivirus genotypes than only between previous recognized genotypes. These results suggest the virus isolated from pronghorn antelope represents a new pestivirus genotype. It also represents the only pestivirus genotype first isolated from New World wildlife.

5' Untranslated Regions↗