Low Sequence Divergence Research Articles

A Variety of Bacterial Pili Involved in Horizontal Gene Transfer

Horizontal gene transfer (HGT) is central to microbial evolution. It contributes to the diversity of acquired traits, which are otherwise not available through gene transfer from parent to progeny. Occurrence of HGT is seen when comparing genomes of related bacteria, or of different isolates from the same species, in which homologous genes show low sequence divergence whereas gene content varies enormously. Those genes that are present or absent are mostly horizontally transferred. Pathogenicity islands are such mobile genetic elements that contribute to rapid changes in virulence potential in numerous bacterial pathogens.

Molecular phylogenetics and taxonomic reassessment of four Indian representatives of the genus Nymphaea

Because the classification of Nymphaea in India has been reported to be confusing, molecular taxonomic revision of four Indian representatives of the genus namely N. nouchali, N. pubescens, N. rubra and N. tetragona based on ITS, trnK intron and matK gene is presented and discussed. Molecular evidence provided here is in disagreement about the taxonomic identity of one specimen of N. nouchali and indicated a probable misidentification of N. tetragona. Interestingly, sequence analysis revealed lack of or low sequence divergence between N. pubescens and N. rubra. Phylogenetic relationship among members of Nymphaea subg. Lotos, represented by all known species viz. N. lotus, N. petersiana, N. pubescens and N. rubra was also conducted. Maximum parsimony analysis of the combined data matrix depicted two clades with N. petersiana and N. lotus forming one, N. pubescens and N. rubra representing the other. Bayesian inference showed N. petersiana as first branching, followed by N. lotus with N. pubescens and N. rubra emerging as a separate clade. The results indicated no close association between N. petersiana and N. nouchali, thereby, contradicting the morphology-based treatment of placing N. petersiana in synonymy under N. capensis and N. nouchali, respectively.

Light at the end of the tunnel: insights into the molecular systematics of East African puddle frogs (Anura: Phrynobatrachidae)

To investigate intra- and interspecific variability of ‘Little Brown Frogs’ (LBFs) from East Africa, we analysed molecular data from 23 species of Phrynobatrachus using 16S rRNA, a mitochondrial gene considered a universal DNA barcoding marker in amphibians. Conspecific populations, excluding P. natalensis, exhibited low (0–0.5%) sequence divergences, while conspecific populations of P. natalensis exhibited a wide range of differentiation (0.2–6.4%) with a distinct bimodal distribution, affirming that this may be a complex of cryptic species. Sister species yielded a range of differentiation from 1.5–8.3% with median of 2.3%. Results revealed that at least three non-sister populations of miniaturized puddle frogs are currently identified as P. mababiensis, and a new species from Ethiopia was identified. This first step into revising East African Phrynobatrachus systematics illustrates the necessity of rigorous taxonomic study, especially for groups with confusing or highly incomplete taxonomy.

Genome dynamics of Bartonella grahamii in micro-populations of woodland rodents

BackgroundRodents represent a high-risk reservoir for the emergence of new human pathogens. The recent completion of the 2.3 Mb genome of Bartonella grahamii, one of the most prevalent blood-borne bacteria in wild rodents, revealed a higher abundance of genes for host-cell interaction systems than in the genomes of closely related human pathogens. The sequence variability within the global B. grahamii population was recently investigated by multi locus sequence typing, but no study on the variability of putative host-cell interaction systems has been performed.ResultsTo study the population dynamics of B. grahamii, we analyzed the genomic diversity on a whole-genome scale of 27 B. grahamii strains isolated from four different species of wild rodents in three geographic locations separated by less than 30 km. Even using highly variable spacer regions, only 3 sequence types were identified. This low sequence diversity contrasted with a high variability in genome content. Microarray comparative genome hybridizations identified genes for outer surface proteins, including a repeated region containing the fha gene for filamentous hemaggluttinin and a plasmid that encodes a type IV secretion system, as the most variable. The estimated generation times in liquid culture medium for a subset of strains ranged from 5 to 22 hours, but did not correlate with sequence type or presence/absence patterns of the fha gene or the plasmid.ConclusionOur study has revealed a geographic microstructure of B. grahamii in wild rodents. Despite near-identity in nucleotide sequence, major differences were observed in gene presence/absence patterns that did not segregate with host species. This suggests that genetically similar strains can infect a range of different hosts.

Diversification and Taxonomy of the Liverwort Jubula Dumort. (Jungermanniopsida: Porellales) Inferred from Nuclear and Chloroplast DNA Sequences

Abstract Nucleotide sequence variation in the ITS1-5.8S-ITS2 region of nuclear ribosomal DNA and in the trnL-tmF region of cpDNA from 28 specimens of Jubula (Jubulaceae), and two outgroup species, was analyzed using maximum parsimony and maximum likelihood. The molecular topologies supported five to six allopatric taxa in Jubula. Relationships of most of these taxa remain unresolved due to lack of support of many deeper nodes. A principal component analysis indicated a broad overlap of morphological characters of these taxa. Based on the morphological similarities of the Jubula taxa and the observed low sequence variation, a subspecies concept is supported. This comprises the taxa J. hutchinsiae subsp. bogotensis, subsp. hutchinsiae, subsp. japonica, subsp. javanica, and subsp. pennsylvanica. With the exception of J. hutchinsiae subsp. javanica, all taxa are monophyletic. Multiple accessions of the temperate taxa J. hutchinsiae subsp. hutchinsiae and J. hutchinsiae subsp. pennsylvanica exhibit a lower seq...

Restricted Genetic Diversity of HIV-1 Subtype C Envelope Glycoprotein from Perinatally Infected Zambian Infants

BackgroundMother-to-child transmission of HIV-1 remains a significant problem in the resource-constrained settings where anti-retroviral therapy is still not widely available. Understanding the earliest events during HIV-1 transmission and characterizing the newly transmitted or founder virus is central to intervention efforts. In this study, we analyzed the viral env quasispecies of six mother-infant transmission pairs (MIPs) and characterized the genetic features of envelope glycoprotein that could influence HIV-1 subtype C perinatal transmission.Methodology and FindingsThe V1-V5 region of env was amplified from 6 MIPs baseline samples and 334 DNA sequences in total were analyzed. A comparison of the viral population derived from the mother and infant revealed a severe genetic bottleneck occurring during perinatal transmission, which was characterized by low sequence diversity in the infant. Phylogenetic analysis indicates that most likely in all our infant subjects a single founder virus was responsible for establishing infection. Furthermore, the newly transmitted viruses from the infant had significantly fewer potential N-linked glycosylation sites in Env V1-V5 region and showed a propensity to encode shorter variable loops compared to the nontransmitted viruses. In addition, a similar intensity of selection was seen between mothers and infants with a higher rate of synonymous (dS) compared to nonsynonymous (dN) substitutions evident (dN/dS<1).ConclusionsOur results indicate that a strong genetic bottleneck occurs during perinatal transmission of HIV-1 subtype C. This is evident through population diversity and phylogenetic patterns where a single viral variant appears to be responsible for infection in the infants. As a result the newly transmitted viruses are less diverse and harbored significantly less glycosylated envelope. This suggests that viruses with the restricted glycosylation in envelope glycoprotein appeared to be preferentially transmitted during HIV-1 subtype C perinatal transmission. In addition, our findings also indicated that purifying selection appears to predominate in shaping the early intrahost evolution of HIV-1 subtype C envelope sequences.

Molecular phylogeny of Menthinae (Lamiaceae, Nepetoideae, Mentheae) – Taxonomy, biogeography and conflicts

Although the subfamily Nepetoideae (Lamiaceae) is considered to be monophyletic, relationships between tribes, subtribes and genera within the subfamily are poorly understood as complex and possibly homoplasious morphological characters make taxa difficult to delimit. DNA sequence data from three regions (chloroplast: trnK intron; trnL-F; nuclear: ITS) in total including 278 accessions, representing 38 out of 40 genera of subtribe Menthinae and 11 outgroup genera, were used to reconstruct the evolutionary history, test previous hypotheses of classification, explain biogeographic patterns and elucidate character evolution. Using maximum parsimony (MP) and Bayesian analysis phylogenetic reconstructions based on nuclear and chloroplast sequence data were incongruent, consequently the data were analyzed separately. Both nuclear and chloroplast datasets provide strong support for three major lineages: the “ Satureja”, “ Micromeria” and “ Clinopodium” group. The first contains members of Satureja and Gontscharovia. In the second lineage Micromeria s.str. and Origanum were resolved as monophyletic, Pentapleura and Zataria indicated as sister groups. Thymbra includes two species of Satureja turning the latter genus polyphyletic. Thymus is revealed as paraphyletic with respect to Argantoniella and Saccocalyx in both and Origanum in the plastid dataset only. In the third lineage, the Clinopodium-group, branching pattern is highly incongruent among datasets and possibly influenced by recent and ancient hybridization, chloroplast capture and incomplete lineage sorting. However, identical terminal groups are inferred in both analyses. A Madagascan lineage of “ Micromeria”, sister to the recently described South African Killickia, is suggested to represent a new genus. The Himalayan Clinopodium nepalense group and the tropical African C. abyssinicum alliance are monophyletic but indicated in different positions. Both groups appear in the ITS phylogeny in a clade with Cyclotrichium and Mentha, relationships not suggested previously. The enigmatic Micromeria cymuligera is close to Mentha and possibly is a representative of this genus. Species of Acinos, now regarded as part of Clinopodium, are mixed up with species of Ziziphora, questioning either the inclusion of Acinos in Clinopodium or generic distinctness of Ziziphora. All data sets suggest a monophyly of the New World taxa and argue for long distance dispersal from the Old World, rather than a vicariance explanation. Bystropogon marks the split up between the two lineages. Inclusion of 22 genera intermixed with Clinopodium spp. in the New World clade provides evidence that the current circumscription of the genus is highly unnatural. Low sequence divergence resulting in low phylogenetic resolution especially at the base of the clade indicate a rapid radiation accompanied by considerable ecological diversification and speciation.

Generation of Diversity in Streptococcus mutans Genes Demonstrated by MLST

Streptococcus mutans, consisting of serotypes c, e, f and k, is an oral aciduric organism associated with the initiation and progression of dental caries. A total of 135 independent Streptococcus mutans strains from caries-free and caries-active subjects isolated from various geographical locations were examined in two versions of an MLST scheme consisting of either 6 housekeeping genes [accC (acetyl-CoA carboxylase biotin carboxylase subunit), gki (glucokinase), lepA (GTP-binding protein), recP (transketolase), sodA (superoxide dismutase), and tyrS (tyrosyl-tRNA synthetase)] or the housekeeping genes supplemented with 2 extracellular putative virulence genes [gtfB (glucosyltransferase B) and spaP (surface protein antigen I/II)] to increase sequence type diversity. The number of alleles found varied between 20 (lepA) and 37 (spaP). Overall, 121 sequence types (STs) were defined using the housekeeping genes alone and 122 with all genes. However π, nucleotide diversity per site, was low for all loci being in the range 0.019–0.007. The virulence genes exhibited the greatest nucleotide diversity and the recombination/mutation ratio was 0.67 [95% confidence interval 0.3–1.15] compared to 8.3 [95% confidence interval 5.0–14.5] for the 6 concatenated housekeeping genes alone. The ML trees generated for individual MLST loci were significantly incongruent and not significantly different from random trees. Analysis using ClonalFrame indicated that the majority of isolates were singletons and no evidence for a clonal structure or evidence to support serotype c strains as the ancestral S. mutans strain was apparent. There was also no evidence of a geographical distribution of individual isolates or that particular isolate clusters were associated with caries. The overall low sequence diversity suggests that S. mutans is a newly emerged species which has not accumulated large numbers of mutations but those that have occurred have been shuffled as a consequence of intra-species recombination generating genotypes which can be readily distinguished by sequence analysis.

Crystal Structure of a Mucus-binding Protein Repeat Reveals an Unexpected Functional Immunoglobulin Binding Activity

Lactobacillus reuteri mucus-binding protein (MUB) is a cell-surface protein that is involved in bacterial interaction with mucus and colonization of the digestive tract. The 353-kDa mature protein is representative of a broadly important class of adhesins that have remained relatively poorly characterized due to their large size and highly modular nature. MUB contains two different types of repeats (Mub1 and Mub2) present in six and eight copies, respectively, and shown to be responsible for the adherence to intestinal mucus. Here we report the 1.8-A resolution crystal structure of a type 2 Mub repeat (184 amino acids) comprising two structurally related domains resembling the functional repeat found in a family of immunoglobulin (Ig)-binding proteins. The N-terminal domain bears striking structural similarity to the repeat unit of Protein L (PpL) from Peptostreptococcus magnus, suggesting binding in a non-immune Fab-dependent manner. A distorted PpL-like fold is also seen in the C-terminal domain. As with PpL, Mub repeats were able to interact in vitro with a large repertoire of mammalian Igs, including secretory IgA. This hitherto undetected activity is consistent with the current model that antibody responses against commensal flora are of broad specificity and low affinity.

Genomic Diversity among Drug Sensitive and Multidrug Resistant Isolates of Mycobacterium tuberculosis with Identical DNA Fingerprints

Background Mycobacterium tuberculosis complex (MTBC), the causative agent of tuberculosis (TB), is characterized by low sequence diversity making this bacterium one of the classical examples of a genetically monomorphic pathogen. Because of this limited DNA sequence variation, routine genotyping of clinical MTBC isolates for epidemiological purposes relies on highly discriminatory DNA fingerprinting methods based on mobile and repetitive genetic elements. According to the standard view, isolates exhibiting the same fingerprinting pattern are considered direct progeny of the same bacterial clone, and most likely reflect ongoing transmission or disease relapse within individual patients.Methodology/Principal FindingsHere we further investigated this assumption and used massively parallel whole-genome sequencing to compare one drug-susceptible (K-1) and one multidrug resistant (MDR) isolate (K-2) of a rapidly spreading M. tuberculosis Beijing genotype clone from a high incidence region (Karakalpakstan, Uzbekistan). Both isolates shared the same IS6110 RFLP pattern and the same allele at 23 out of 24 MIRU-VNTR loci.We generated 23.9 million (K-1) and 33.0 million (K-2) paired 50 bp purity filtered reads corresponding to a mean coverage of 483.5 fold and 656.1 fold respectively. Compared with the laboratory strain H37Rv both Beijing isolates shared 1,209 SNPs. The two Beijing isolates differed by 130 SNPs and one large deletion. The susceptible isolate had 55 specific SNPs, while the MDR variant had 75 specific SNPs, including the five known resistance-conferring mutations.ConclusionsOur results suggest that M. tuberculosis isolates exhibiting identical DNA fingerprinting patterns can harbour substantial genomic diversity. Because this heterogeneity is not captured by traditional genotyping of MTBC, some aspects of the transmission dynamics of tuberculosis could be missed or misinterpreted. Furthermore, a valid differentiation between disease relapse and exogenous reinfection might be impossible using standard genotyping tools if the overall diversity of circulating clones is limited. These findings have important implications for clinical trials of new anti-tuberculosis drugs.

Post-Pleistocene radiation of the pea aphid complex revealed by rapidly evolving endosymbionts

Adaptation to different resources has the potential to cause rapid species diversification, but few studies have been able to quantify the time scale of recent adaptive radiations. The pea aphid, Acyrthosiphon pisum, a model of speciation for host-specialized parasites, consists of several biotypes (races or species) living on distinct legume hosts. To document this radiation, we used rapidly evolving sequences from Buchnera, the maternally transmitted bacterial endosymbiont of aphids. Analyses of Buchnera pseudogene sequences revealed that 11 host-associated biotypes sort mostly into distinct matrilines despite low sequence divergence. A calibration based on divergence times of 7 sequenced genomes of Buchnera allowed us to date the last maternal ancestor of these biotypes between 8,000 and 16,000 years, with a burst of diversification at an estimated 3,600-9,500 years. The recency of this diversification, which is supported by microsatellite data, implies that the pea aphid complex ranks among the most rapid adaptive radiations yet documented. This diversification coincides with post-Pleistocene warming and with the domestication and anthropogenic range expansion of several of the legume hosts of pea aphids. Thus, we hypothesize that the new availability or abundance of resources triggered a cascade of divergence events in this newly formed complex.

An SSU rDNA barcoding approach to the diversity of marine interstitial cercozoans, including descriptions of four novel genera and nine novel species

Environmental DNA surveys have revealed a great deal of hidden diversity within the Cercozoa. An investigation into the biodiversity of heterotrophic flagellates in marine benthic habitats of British Columbia, Canada, demonstrated the presence of several undescribed taxa with morphological features that resemble the cercozoan genera Cryothecomonas and Protaspis. Nine novel species of marine interstitial cercozoans are described that are distributed into five genera, four of which are new. Phylogenetic analyses of small subunit rDNA sequences derived from two uncultured isolates of Protaspis obliqua and nine novel cercozoan species (within four novel genera) provided organismal anchors that helped establish the cellular identities of several different environmental sequence clades. These data, however, also showed that the rarity of distinctive morphological features in cryomonads, and other groups of cercozoans, makes the identification and systematics of the group very difficult. Therefore, a DNA barcoding approach was applied as a diagnostic tool for species delimitation that used a 618 bp region at the 5' end of the SSU rDNA sequence. Nucleotide sequence analysis of this region showed high intergeneric sequence divergences of about 7% and very low intraspecific sequence divergences of 0-0.5%; phylogenetic analyses inferred from this barcoding region showed very similar tree topologies to those inferred from the full-length sequence of the gene. Overall, this study indicated that the 618 bp barcoding region of SSU rDNA sequences is a useful molecular signature for understanding the biodiversity and interrelationships of marine benthic cercozoans.

Mitochondrial DNA analysis reveals a low nucleotide diversity of Caligula japonica in China

Caligula japonica (Lepidoptera: Saturniidae), an endemic species in Eastern Asia, is not only an economically important pest to be controlled, but also a producer of expensive silk. We have demonstrated previously the presence of a higher genetic diversity and a certain degree of genetic differentiation related to geographical distribution in C. japonica based on RAPD and ISSR markers. In this paper, we determined the 574 bp segment of the mitochondrial cytochrome oxidase subunit I (COI) gene sequences of C. japonica in China to assess nucleotide sequence diversity (GenBank accession no. FJ358506-FJ358517). The pairwise COI sequence identity between these samples reached 99 - 100%, showing a low nucleotide sequence diversity (Pi = 0.0035). In NJ tree, these samples were divided well into Northern and Southern group, which was consistent with that previously reported based on RAPD and ISSR markers and suggested the genetic differentiation between them might have been occurred. Further work is needed to define the genetic structure of different populations of C. japonica.

Local genetic adaptation to grazing pressure of the green alga Desmodesmus armatus in a strongly connected pond system

Dispersal potentially homogenizes genetic variation among populations and thus may prevent local genetic adaptation. If selection gradients are strong and the selection response efficient, however, local genetic adaptation may persist in the face of high dispersal rates. We compared grazing‐resistance traits among populations of the green microalga Desmodesmus armatus, which inhabit ponds that are ecologically different but part of a strongly interconnected pond system. Desmodesmus clones were isolated from a clear‐water and a turbid pond. For 16 clones from an internal transcribed spacer 2 clade with low sequence variation (1.3%) corresponding morphologically to D. armatus, coenobial dimensions and the average number of cells per coenobium, in both the absence and the presence of water conditioned by their main grazer, the waterflea Daphnia, were determined. Clones from the clear‐water pond had four‐celled coenobia with a higher greatest axial linear dimension and an increased average number of cells per coenobium in response to Daphnia kairomone, contrary to clones from the turbid pond. Unexpectedly, they were also characterized by a lower average number of cells per coenobium. No differences among populations were detected for cell length. Genetic variation was present in both populations for all traits, except for the response to kairomone. Continuous dispersal through overflows and rivulets in this pond system is thus incapable of preventing strong among‐population genetic differentiation for ecological relevant traits, testifying both to the capacity of phytoplankton populations to adapt to local conditions and to the importance of grazing as a structuring factor in natural phytoplankton populations.

Genetic population structure of the swimming crab, Portunus trituberculatus in the East China Sea based on mtDNA 16S rRNA sequences

Portunus trituberculatus is a commercially important fishery species. In this study, intraspecific variation was examined by using mitochondrial DNA 16S rRNA gene in 213 individual crabs sampled from six localities along the coast of the East China Sea. Twenty-two polymorphic sites defined 25 distinct haplotypes, revealing a moderately high haplotype diversity and relatively low sequence divergence among the six localities. An excess of within population unique haplotypes at most sample locations were detected, which might influence genetic structure of the swimming crab populations. Neither neighbor-joining tree nor minimum spanning network (MSN) based on the haplotype data indicated distinct patterns of phylogeographic structure among the 25 haplotypes. Analyses of molecular variance (AMOVA) and F ST statistics supported the hypothesis that population samples from the East China Sea were genetically nonhomogenous, indicating that gene flow might be restricted across those regions, despite the high potential of dispersal. In addition, tests of neutral evolution and analysis of mismatch distribution suggested that P. trituberculatus might have undergone a population expansion, possibly within the last 127,000 and 429,000 years. Our study unraveled the extant population genetic structure of the P. trituberculatus, and addressed the related fishery management issues including artificial breeding, fishery stock identification and conservation.

Independent evolution of functional Pm3 resistance genes in wild tetraploid wheat and domesticated bread wheat

The Pm3 alleles of cultivated bread wheat confer gene for gene resistance to the powdery mildew fungus. They represent a particular case of plant disease resistance gene evolution, because of their recent origin and possible evolution after the formation of hexaploid wheat. The Pm3 locus is conserved in tetraploid wheat, thereby allowing the comparative evolutionary study of the same resistance locus in a domesticated species and in one of its wild ancestors. We have identified 61 Pm3 allelic sequences from wild and domesticated tetraploid wheat subspecies. The Pm3 sequences corresponded to 24 different haplotypes. They showed low sequence diversity, differing by only a few polymorphic sequence blocks that were further reshuffled between alleles by gene conversion and recombination. Polymorphic sequence blocks are different from the blocks found in functional Pm3 alleles of hexaploid wheat, indicating an independent evolution of the Pm3 loci in the two species. A new functional gene was identified in a wild wheat accession from Syria. This gene, Pm3k, conferred intermediate race-specific resistance to powdery mildew, and consists of a mosaic of gene segments derived from non-functional alleles. This demonstrates that Pm3-based resistance is not very frequent in wild tetraploid wheat, and that the evolution of functional resistance genes occurred independently in wild tetraploid and bread wheat. The Pm3 sequence variability and geographic distribution indicated that diversity was higher in wild emmer wheat from the Levant area, compared with the accessions from Turkey. Further screens for Pm3 functional genes in wild wheat should therefore focus on accessions from the Levant region.

Evolutionary Relationships of Araliaceae in the Malesian Region:a Preliminary Analysis

We employ the nuclear ribosomal ITS sequences to assess the evolutionary relationships of Araliaceae in the Malesian region. Malesian Araliaceae consist of 14 genera and about 500 species. Our analysis suggests a diffuse origin of Araliaceae taxa, with many genera belong to the Asian palmate clade or the tribe Hedereae. The Malesian endemic Harmsiopanax is morphologically unique and its phylogenetic position is not well resolved at present. Several morphologically diverse species of Brassaiopsis perhaps have a relatively recent origin in the Malay Peninsula and Sumatra, as suggested by their monophyly as well as their low ITS sequence divergence. Wardenia is not supported as W.simplex (=B.simplex) is nested within Brassaiopsis. The Malayan region is important for the development of Schefflera, and available evidence suggests that Schefflera in the region forms a clade with the Heptapleurum group. Dendropanax lancifolius does not form a clade with the core group of Dendropanax, and its status needs to be further analyzed. Macropanax maingayi was considered to be a highly distinct member comprising the monotypic genus Hederopsis. Our analysis clearly places it in Macropanax. Aralia merrillii was once considered to be the sole member of the genus Acanthophora because of its unusual climbing habit. The ITS data support its placement in Aralia. Our expanded sampling of Arthrophyllum continues to support its monophyly. Osmoxylon has a primary distribution in the Malesian region and it is a hylogenetically isolated member of Araliaceae.

Little population structuring and recent evolution of the Pacific saury ( Cololabis saira) as indicated by mitochondrial and nuclear DNA sequence data

Genetic population structure of the Pacific saury ( Cololabis saira) was investigated using nucleotide sequence analysis on the mitochondrial DNA control region (355-361 bp). Although the left domain of the control region is known to be highly variable in many species, extremely low nucleotide and haplotype diversities (π = 0.17% and h = 0.418, respectively) were observed in a total of 141 individuals collected from five distant locales (East China Sea, Sea of Okhotsk, northwest Pacific, central North Pacific and northeast Pacific). No significant haplotype frequency differences were detected among widely separated samples, therefore we were unable to reject the null hypothesis of no genetic structuring in the Pacific saury population. Moderate levels of nucleotide substitution ( p-distance) were observed between the Pacific saury and its Atlantic counterpart ( Scomberesox saurus) in the control region (7.44%), cytochrome b gene (4.64%), and internal transcribed spacer (ITS1) (11.49%), indicating that the low sequence diversity of the control region in the Pacific saury is not due to the slow mutation rate. The molecular data suggest the Pacific saury may be a relatively recent offshoot among the extant members in the family Scomberesocidae.

Frequent Toggling between Alternative Amino Acids Is Driven by Selection in HIV-1

Host immune responses against infectious pathogens exert strong selective pressures favouring the emergence of escape mutations that prevent immune recognition. Escape mutations within or flanking functionally conserved epitopes can occur at a significant cost to the pathogen in terms of its ability to replicate effectively. Such mutations come under selective pressure to revert to the wild type in hosts that do not mount an immune response against the epitope. Amino acid positions exhibiting this pattern of escape and reversion are of interest because they tend to coincide with immune responses that control pathogen replication effectively. We have used a probabilistic model of protein coding sequence evolution to detect sites in HIV-1 exhibiting a pattern of rapid escape and reversion. Our model is designed to detect sites that toggle between a wild type amino acid, which is susceptible to a specific immune response, and amino acids with lower replicative fitness that evade immune recognition. Through simulation, we show that this model has significantly greater power to detect selection involving immune escape and reversion than standard models of diversifying selection, which are sensitive to an overall increased rate of non-synonymous substitution. Applied to alignments of HIV-1 protein coding sequences, the model of immune escape and reversion detects a significantly greater number of adaptively evolving sites in env and nef. In all genes tested, the model provides a significantly better description of adaptively evolving sites than standard models of diversifying selection. Several of the sites detected are corroborated by association between Human Leukocyte Antigen (HLA) and viral sequence polymorphisms. Overall, there is evidence for a large number of sites in HIV-1 evolving under strong selective pressure, but exhibiting low sequence diversity. A phylogenetic model designed to detect rapid toggling between wild type and escape amino acids identifies a larger number of adaptively evolving sites in HIV-1, and can in some cases correctly identify the amino acid that is susceptible to the immune response.

Phylogeography and hybridization in Ctenosaura species (Sauria, Iguanidae) from Caribbean Honduras: insights from mitochondrial and nuclear DNA

In order to infer the phylogenetic relationships and biogeographical patterns in Honduran spiny-tailed iguanas (Ctenosaura), we analyzed partial sequences of the mitochondrial NADH dehydrogenase subunit 4 (ND4) gene. In addition, we used nuclear sequences of the internal transcribed spacer 2 of the large ribosomal subunit (ITS2) to test whether hybridization occurs in two Ctenosaura species on the Honduran Utila Island as reported in former morphology-based studies. The phylogenetic trees based on ND4 support the current classification of Ctenosaura and its subdivision into three subgenera. The low average interspecific sequence divergence of 1–2% within the clade Loganiosaura that comprises C. bakeri, C. oedirhina, and C. melanosterna indicates their rather recent evolutionary origin. Another clade of Ctenosaura is represented by C. similis, which occurs on Utila and Guanaja as well as across most of Central America. Low genetic differentiation among the Honduran populations of C. similis suggests recent gene flow between them. Comparison of the phylogeographic patterns with the geological history of Caribbean Honduras implies a mixture of dispersal and vicariance events as the most plausible explanation for the current distribution of Ctenosaura in coastal Honduras. Accordingly, Utila has been successively colonized by two species, C. bakeri and C. similis. The comparison of ND4 and ITS2 based trees revealed that both species hybridize. We suggest that hybridization between these originally allopatric species is the result of recent secondary contact due to successive island colonization. We are concerned that habitat destruction leads to increased contacts between the two species, and therefore may increase the rates of introgression. This phenomenon may potentially pose a serious conservation problem for C. bakeri. (© 2008 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim)