Bayesian Evolutionary Analysis Sampling Trees Research Articles

Molecular Identification and Evolutionary Divergence of the Sri Lankan Sambar Deer, Rusa unicolor (Kerr 1792).

The Sambar is one of the largest deer species distributed mainly in Asia, and it has been listed as a vulnerable species. Taxonomy based on morphological characterization has been the gold standard method used to identify the Sambar deer species. Yet, morphological identification is challenging and requires expertise. To conduct species identification and taxonomic decisions, we performed the molecular identification of R. unicolor found in Sri Lanka using DNA barcodes, COI, and Cyt b to compare the Sri Lankan R. unicolor with the Indian R. unicolor and other R. unicolor subspecies. We obtained mitochondrial DNA sequences from COI and Cyt b from blood samples collected from the wet zone in Sri Lanka. A phylogenetic tree was constructed based on the Bayesian analyses using MrBayes 3.2.7. Molecular dating was implemented in Bayesian Evolutionary Analysis Sampling Trees (BEAST v1.8.2) on the concatenated sequence using a log-normal relaxed clock and Yule species tree prior, with four categories. The results showed that the Sri Lankan R. unicolor is genetically different from the Indian R. unicolor and other R. unicolor subspecies. The divergence occurred approximately 1.1 MYA (million years ago) in the Pleistocene era. The results are essential for designing new conservation platforms for these Sambar deer species.

Phylodynamics of Highly Pathogenic Avian Influenza A(H5N1) Virus Circulating in Indonesian Poultry.

After its first detection in 1996, the highly pathogenic avian influenza A(H5Nx) virus has spread extensively worldwide. HPAIv A(H5N1) was first detected in Indonesia in 2003 and has been endemic in poultry in this country ever since. However, Indonesia has limited information related to the phylodynamics of HPAIv A(H5N1) in poultry. The present study aimed to increase the understanding of the evolution and temporal dynamics of HPAIv H5N1 in Indonesian poultry between 2003 and 2016. To this end, HPAIv A(H5N1) hemagglutinin sequences of viruses collected from 2003 to 2016 were analyzed using Bayesian evolutionary analysis sampling trees. Results indicated that the common ancestor of Indonesian poultry HPAIv H5N1 arose approximately five years after the common ancestor worldwide of HPAI A(H5Nx). In addition, this study indicated that only two introductions of HPAIv A(H5N1) occurred, after which these viruses continued to evolve due to extensive spread among poultry. Furthermore, this study revealed the divergence of H5N1 clade 2.3.2.1c from H5N1 clade 2.3.2.1b. Both clades 2.3.2.1c and 2.3.2.1b share a common ancestor, clade 1, suggesting that clade 2.3.2.1 originated and diverged from China and other Asian countries. Since there was limited sequence and surveillance data for the HPAIv A(H5N1) from wild birds in Indonesia, the exact role of wild birds in the spread of HPAIv in Indonesia is currently unknown. The evolutionary dynamics of the Indonesian HPAIv A(H5N1) highlight the importance of continuing and improved genomic surveillance and adequate control measures in the different regions of both the poultry and wild birds. Spatial genomic surveillance is useful to take adequate control measures. Therefore, it will help to prevent the future evolution of HPAI A(H5N1) and pandemic threats.

Molecular phylogeny and morphometric analyses in the genus Cousinia Cass. (Family Asteraceae), sections Cynaroideae Bunge and Platyacanthae Rech. f.

Taxonomy and molecular phylogeny of the genus Cousinia are complicated and unresolved mainly because of disagreement between morphological and molecular phylogenetic studies. The genus Cousinia has approximately 700 species, which makes it one of the most varied genera found in central and southwest Asia. Section Cynaroideae, containing 89 species, is considered the largest section of the genus. Identification and delineation as well as classifying the section and the species’ relationships within the genus Cousinia generally remain debatable. Therefore, the present study aims to: 1) identify and delineate the species within the two sections Cynaroideae and Platyacanthae; 2) study the species relationships based on both morphological and molecular features (Internal Transcribed Spacer (ITS) marker); 3) study the sectional delimitation and its monophyly; and 4) estimate the divergence time of the studied sections. To this end, 50 Cousinia species occurring in Iran were investigated for the first time. A maximum parsimony tree of the morphological features separated the species of the two sections from each other. However, the ITS-based phylogenetic tree did not delimit the two studied sections. The relationships among the studied Cousinia species in the genetic trees were generally not congruent with the obtained morphological tree. The divergence time of the studied species within the Cynaroideae and Platyacanthae sections determined using Bayesian Evolutionary Analysis Sampling Trees (BEAST) was estimated to be around 3.5 million years ago (Mya).

Evaluation of global evolutionary variations in the early stage of SARS-CoV-2 pandemic

To understand the origin of variants and their evolutionary history in the early stage of the COVID-19 pandemic, time-scaled phylogenetic and gene variation analyses were performed. The mutation patterns and evolution characteristics were examined using the Bayesian Evolutionary Analysis Sampling Trees (BEAST) with 349 whole-genome sequences available by March 2020. The results revealed five phylogenetic clusters (Groups A–E), with 408 nucleotide variants. The mutations including the deletion of three nucleotides underwent various and complicated changes in the whole genome over time, while some frequency or transient mutations were also observed. Phylogenetic analysis demonstrated that SARS-CoV-2 originated from China and was transmitted to other Asian countries, followed by North America and Europe. This study could help to comprehensively understand the evolutionary characteristics of SARS-CoV-2 with a special emphasis on its global variation patterns.

Snakes on an African plain: the radiation of Crotaphopeltis and Philothamnus into open habitat (Serpentes: Colubridae).

BackgroundThe African continent is comprised of several different biomes, although savanna is the most prevalent. The current heterogeneous landscape was formed through long-term vegetation shifts as a result of the global cooling trend since the Oligocene epoch. The overwhelming trend was a shift from primarily forest, to primarily savanna. As such, faunal groups that emerged during the Paleogene/Neogene period and have species distributed in both forest and savanna habitat should show a genetic signature of the possible evolutionary impact of these biome developments. Crotaphopeltis and Philothamnus (Colubridae) are excellent taxa to investigate the evolutionary impact of these biome developments on widespread African colubrid snakes, and whether timing and patterns of radiation are synchronous with biome reorganisation.MethodsA phylogenetic framework was used to investigate timing of lineage diversification. Phylogenetic analysis included both genera as well as other Colubridae to construct a temporal framework in order to estimate radiation times for Crotaphopeltis and Philothamnus. Lineage diversification was estimated in Bayesian Evolutionary Analysis Sampling Trees (BEAST), using two mitochondrial markers (cyt–b, ND4), one nuclear marker (c–mos), and incorporating one fossil and two biogeographical calibration points. Vegetation layers were used to classify and confirm species association with broad biome types (‘closed’ = forest, ‘open’ = savanna/other), and the ancestral habitat state for each genus was estimated.ResultsPhilothamnus showed an ancestral state of closed habitat, but the ancestral habitat type for Crotaphopeltis was equivocal. Both genera showed similar timing of lineage diversification diverging from their sister genera during the Oligocene/Miocene transition (ca. 25 Mya), with subsequent species radiation in the Mid-Miocene. Philothamnus appeared to have undergone allopatric speciation during Mid-Miocene forest fragmentation. Habitat generalist and open habitat specialist species emerged as savanna became more prevalent, while at least two forest associated lineages within Crotaphopeltis moved into Afromontane forest habitat secondarily and independently.DiscussionWith similar diversification times, but contrasting ancestral habitat reconstructions, we show that these genera have responded very differently to the same broad biome shifts. Differences in biogeographical patterns for the two African colubrid genera is likely an effect of distinct life-history traits, such as the arboreous habits of Philothamnus compared to the terrestrial lifestyle of Crotaphopeltis.

A closer look at the migration and diversification of the false foxgloves (genus: Agalinis; family: Orobanchaceae) in temperate North America

The genus Agalinis (commonly known as the “false foxgloves”) belonging to the family Orobanchaceae, is native to the Western Hemisphere. Approximately 40 species are distributed across temperate North America, and a large group is native to Missouri and the Midwestern United States. Twenty-one species of this genus warrant conservation measures. Our main aims were to understand the migration and diversification of temperate North American Agalinis, as well as focusing on the six species native to the state of Missouri. This study is the first to investigate the evolutionary diversification of this genus in temperate North America. Computer applications including BEAST (Bayesian evolutionary analysis sampling trees) and SDIVA (statistical dispersal vicariance analysis), and secondary calibrations from previous studies were implemented to understand the diversification timings and ancestral areas of this group. Our study points to southeastern United States as the center of diversity and place of origin of the Agalinis in temperate North America, from which they spread to the rest of the United States and even migrated to Canada, around the mid-late Miocene period. We were also able to trace the biogeography of the Missouri natives which diversified between the late Miocene and the Pleistocene period. It may be hypothesized that climatic shifts and increase in seasonality during the mid-late Miocene period was one of the primary causes leading to the migration and diversification of this genus throughout temperate North America.

Assessing the genomic relatedness and evolutionary rates of persistent verotoxigenic Escherichia coli serotypes within a closed beef herd in Canada.

Verotoxigenic Escherichia coli (VTEC) are food- and water-borne pathogens associated with both sporadic illness and outbreaks of enteric disease. While it is known that cattle are reservoirs of VTEC, little is known about the genomic variation of VTEC in cattle, and whether the variation in genomes reported for human outbreak strains is consistent with individual animal or group/herd sources of infection. A previous study of VTEC prevalence identified serotypes carried persistently by three consecutive cohorts of heifers within a closed herd of cattle. This present study aimed to: (i) determine whether the genomic relatedness of bovine isolates is similar to that reported for human strains associated with single source outbreaks, (ii) estimate the rates of genome change among dominant serotypes over time within a cattle herd, and (iii) identify genomic features of serotypes associated with persistence in cattle. Illumina MiSeq genome sequencing and genotyping based on allelic and single nucleotide variations were completed, while genome change over time was measured using Bayesian evolutionary analysis sampling trees. The accessory genome, including the non-protein-encoding intergenic regions (IGRs), virulence factors, antimicrobial-resistance genes and plasmid gene content of representative persistent and sporadic cattle strains were compared using Fisher’s exact test corrected for multiple comparisons. Herd strains from serotypes O6:H34 (n=22), O22:H8 (n=30), O108:H8 (n=39), O139:H19 (n=44) and O157:H7 (n=106) were readily distinguishable from epidemiologically unrelated strains of the same serotype using a similarity threshold of 10 or fewer allele differences between adjacent nodes. Temporal-cohort clustering within each serotype was supported by date randomization analysis. Substitutions per site per year were consistent with previously reported values for E. coli ; however, there was low branch support for these values. Acquisition of the phage-encoded Shiga toxin 2 gene in serotype O22:H8 was observed. Pan-genome analyses identified accessory regions that were more prevalent in persistent serotypes (P≤0.05) than in sporadic serotypes. These results suggest that VTEC serotypes from a specific cattle population are highly clonal with a similar level of relatedness as human single-source outbreak-associated strains, but changes in the genome occur gradually over time. Additionally, elements in the accessory genomes may provide a selective advantage for persistence of VTEC within cattle herds.

Phylogeny and Historical Biogeography of Paphiopedilum Pfitzer (Orchidaceae) Based on Nuclear and Plastid DNA.

The phylogeny and biogeography of the genus Paphiopedilum were evaluated by using phylogenetic trees derived from analysis of nuclear ribosomal internal transcribed spacer (ITS) sequences, the plastid trnL intron, the trnL-F spacer, and the atpB-rbcL spacer. This genus was divided into three subgenera: Parvisepalum, Brachypetalum, and Paphiopedilum. Each of them is monophyletic with high bootstrap supports according to the highly resolved phylogenetic tree reconstructed by combined sequences. There are five sections within the subgenus Paphiopedilum, including Coryopedilum, Pardalopetalum, Cochlopetalum, Paphiopedilum, and Barbata. The subgenus Parvisepalum is phylogenetic basal, which suggesting that Parvisepalum is comprising more ancestral characters than other subgenera. The evolutionary trend of genus Paphiopedilum was deduced based on the maximum likelihood (ML) tree and Bayesian Evolutionary Analysis Sampling Trees (BEAST). Reconstruct Ancestral State in Phylogenies (RASP) analyses based on the combined sequence data. The biogeographic analysis indicates that Paphiopedilum species were firstly derived in Southern China and Southeast Asia, subsequently dispersed into the Southeast Asian archipelagoes. The subgenera Paphiopedilum was likely derived after these historical dispersals and vicariance events. Our research reveals the relevance of the differentiation of Paphiopedilum in Southeast Asia and geological history. Moreover, the biogeographic analysis explains that the significant evolutionary hotspots of these orchids in the Sundaland and Wallacea might be attributed to repeated migration and isolation events between the south-eastern Asia mainland and the Sunda Super Islands.

Molecular investigation in few spices of Dacocephalum in Iran: Species relationship, reticulation and divergence time

It is believed that Lamiaceae or the Mint family has numerous paraphyletic genera and the relationship between the species has not been fully determined in several cases. The genus Dracocephalum is one of the genera, which has not been investigated thoroughly. In the family Lamiaceae, Dracocephalum is the second largest genus consisting of about 186 species. Eight Dracocephalum species were reported of Iran belonging to the Irano-Turanian phytogeographical region. The present study has attempted to investigate Dracocephalum in terms of the molecular phylogeny for the first time and gather data on their species relationship, divergence time, and show how they are distributed geographically. To report the results, Chloroplast DNA (ribosomal protein L16 (rpL16)) sequences and Inter Simple Sequence Repeat (ISSR) molecular markers have been used. According to the results, the genus Dracocephalum is paraphyletic and has close affinity with Lallemantia. The results of horizontal gene transfer (HGT) analysis confirmed the inter-specific hybridization in the genus. Chronogram obtained by Bayesian Evolutionary Analysis Sampling Trees (BEAST) date revealed Dracocephalum species divergence time back to 2–10 million years ago(MYA). These findings extend the knowledge on the evolution of Lamiaceae.

Genome epidemiology of Mycobacterium bovis infection in contemporaneous, sympatric badger and cattle populations in Northern Ireland

Introduction Bovine tuberculosis (bTB) is an epidemiologically complex disease affecting both cattle and badgers in the UK and Ireland. Traditional molecular typing schemes have been used to characterise the spatial structure of the pathogen and relationship of M. bovis derived from sympatric animals. However, these methods lack the resolution to describe transmission dynamics at the farm level or to inform on the extent to which the hosts contribute. Whole genome sequencing can improve resolution of molecular epidemiology investigations in this epi-system. Methods We collected 598 M. bovis isolates from contemporaneous badgers (n=119) and cattle (n =479), located in a 100 km2 area of Northern Ireland. Cultures were DNA extracted and genome sequenced. Bioinformatic analysis was undertaken using the reddog pipeline and maximum likelihood phylogenetic analyses were conducted using RAxML, with the major endemic clade in the region subjected to phylodynamic analysis using Bayesian Evolutionary Analysis Sampling Trees (BEAST) software. Results and Discussion All 598 isolates produced reads of good quality, aligning to >90 % of the M. bovis reference genome with coverage of at least x10. A total of 1598 SNPs were detected. Phylogenetic analysis indicated the presence of nine major lineages circulating in the region. Eight exhibited long branch-lengths suggesting they were not endemic in the area. One lineage was endemic, comprising isolates from 60 badgers and 363 cattle. From the substitution rate of 0.36 SNPs per annum, this lineage arose in the study area in the mid-1980s. Data were consistent with ongoing transmission within and between both hosts.

Phylogeny and diversification history of the large Neotropical genus Philodendron (Araceae): Accelerated speciation in a lineage dominated by epiphytes.

Philodendron is a large genus of ~560 species and among the most conspicuous epiphytic components of Neotropical forests, yet its phylogenetic relationships, timing of divergence, and diversification history have remained unclear. We present a comprehensive phylogenetic study for Philodendron and investigate its diversification, including divergence-time estimates and diversification rate shift analyses. We performed the largest phylogenetic reconstruction for Philodendron to date, including 125 taxa with a combined dataset of three plastid regions (petD, rpl16, and trnK/matK). We estimated divergence times using Bayesian evolutionary analysis sampling trees and inferred shifts in diversification rates using Bayesian analysis of macroevolutionary mixtures. We found that Philodendron, its three subgenera, and the closely related genus Adelonema are monophyletic. Within Philodendron subgenus Philodendron, 12 statistically well-supported clades are recognized. The genus Philodendron originated ~25 mya and a diversification rate upshift was detected at the origin of subgenus Philodendron ~12 mya. Philodendron is a species-rich Neotropical lineage that diverged from Adelonema during the late Oligocene. Within Philodendron, the three subgenera currently accepted are recovered in two lineages: one contains the subgenera Meconostigma and Pteromischum and the other contains subgenus Philodendron. The lineage containing subgenera Meconostigma and Pteromischum underwent a consistent diversification rate. By contrast, a diversification rate upshift occurred within subgenus Philodendron ~12 mya. This diversification rate upshift is associated with the species radiation of the most speciose subgenus within Philodendron. The sections accepted within subgenus Philodendron are not congruent with the clades recovered. Instead, the clades are geographically defined.

Evolutionary features of influenza A/H5N1 virus populations in Egypt: poultry and human health implications.

Since 2006, in Egypt, highly pathogenic avian influenza virus (HPAIV) H5N1 has established endemic status in poultry. Bayesian evolutionary analysis sampling trees suggested an introduction date in the third quarter of 2005. Evolutionary dynamics using Bayesian analysis showed that H5N1 viruses of clade 2.2.1.1 evolved at higher rates than those of clade 2.2.1.2. Bayesian skyline plot analysis of the HA gene of 840 and NA gene of 401 Egyptian H5N1 viruses from 2006-2015 identified two waves of viral population expansion correlating with the stepwise emergence of the 2.2.1.1 variant lineage in 2008 and with the newly emerging 2.2.1.2 cluster in late 2014. H5N1 infections in human hosts in 2014-2015 were statistically linked to a contemporary poultry outbreak.

Transmission of hepatitis C virus infection among younger and older people who inject drugs in Vancouver, Canada

Understanding HCV transmission among people who inject drugs (PWID) is important for designing prevention strategies. This study investigated whether HCV infection among younger injectors occurs from few or many transmission events from older injectors to younger injectors among PWID in Vancouver, Canada. HCV antibody positive participants at enrolment or follow-up (1996-2012) were tested for HCV RNA and sequenced (Core-E2). Time-stamped phylogenetic trees were inferred using Bayesian Evolutionary Analysis Sampling Trees (BEAST). Association of age with phylogeny was tested using statistics implemented in the software Bayesian Tip Significance (BaTS) testing. Factors associated with clustering (maximum cluster age: five years) were identified using logistic regression. Among 699 participants with HCV subtype 1a, 1b, 2b and 3a infection (26% female, 24% HIV+): 21% were younger (<27years), and 10% had recent HCV seroconversion. When inferred cluster age was limited to <5years, 15% (n=108) were in clusters/pairs. Although a moderate degree of segregation was observed between younger and older participants, there was also transmission between age groups. Younger age (<27 vs. >40, AOR: 3.14; 95% CI: 1.54, 6.39), HIV (AOR: 1.97; 95% CI: 1.22, 3.18) and subtype 3a (AOR: 2.12; 95% CI: 1.33, 3.38) were independently associated with clustering. In this population of PWID from Vancouver, HCV among young injectors was seeded from many transmission events between HCV-infected older and younger injectors. Phylogenetic clustering was associated with younger age and HIV. These data suggest that HCV transmission among PWID is complex, with transmission occurring between and among older and younger PWID.

Biogeography of the Phalaenopsis amabilis species complex inferred from nuclear and plastid DNAs.

BackgroundPhalaenopsis is one of the important commercial orchids in the world. Members of the P. amabilis species complex represent invaluable germplasm for the breeding program. However, the phylogeny of the P. amabilis species complex is still uncertain. The Phalaenopsis amabilis species complex (Orchidaceae) consists of subspecies amabilis, moluccana, and rosenstromii of P. amabilis, as well as P. aphrodite ssp. aphrodite, P. ap. ssp. formosana, and P. sanderiana. The aims of this study were to reconstruct the phylogeny and biogeographcial patterns of the species complex using Neighbor Joining (NJ), Maxinum Parsimony (MP), Bayesian Evolutionary Analysis Sampling Trees (BEAST) and Reconstruct Ancestral State in Phylogenies (RASP) analyses based on sequences of internal transcribed spacers 1 and 2 from the nuclear ribosomal DNA and the trnH-psbA spacer from the plastid DNA.ResultsA pattern of vicariance, dispersal, and vicariance + dispersal among disjunctly distributed taxa was uncovered based on RASP analysis. Although two subspecies of P. aphrodite could not be differentiated from each other in dispersal state, they were distinct from P. amabilis and P. sanderiana. Within P. amabilis, three subspecies were separated phylogenetically, in agreement with the vicariance or vicariance + dispersal scenario, with geographic subdivision along Huxley’s, Wallace’s and Lydekker’s Lines. Molecular dating revealed such subdivisions among taxa of P. amabilis complex dating back to the late Pleistocene. Population-dynamic analyses using a Bayesian skyline plot suggested that the species complex experienced an in situ range expansion and population concentration during the late Last Glacial Maximum (LGM).ConclusionsTaxa of the P. amabilis complex with disjunct distributions were differentiated due to vicariance or vicariance + dispersal, with events likely occurring in the late Pleistocene. Demographic growth associated with the climatic oscillations in the Würm glacial period followed the species splits. Nevertheless, a subsequent population slowdown occurred in the late LGM due to extinction of regional populations. The reduction of suitable habitats resulted in geographic fragmenttation of the remaining taxa.Electronic supplementary materialThe online version of this article (doi:10.1186/s12870-015-0560-z) contains supplementary material, which is available to authorized users.

Phylogeography of the arid shrub Atraphaxis frutescens (Polygonaceae) in northwestern China: evidence from cpDNA sequences.

Climatic fluctuations during the Pleistocene are usually considered as a significant factor in shaping intraspecific genetic variation and influencing demographic histories. To well-understand these processes in desert northwest China, we selected arid adapted Atraphaxis frutescens as the study species. Two cpDNA regions (psbK-psbI, psbB-psbH) were sequenced in 272 individuals from 33 natural populations across the range of this shrub, and 10 haplotypes were identified. It was found to contain high levels of total gene diversity (H T = 0.858), and low levels of within-population diversity (H S = 0.092). Analysis of molecular variance (AMOVA) indicates that genetic differentiation primarily occurs among groups of populations. Based on BEAST (Bayesian Evolutionary Analysis Sampling Trees) analysis, we suggest that intraspecific differentiation of the species, resulting from isolated populations, accompanied enhanced desertification during the middle and late Pleistocene. The expansion of the Gurbantunggut and Kumtag deserts in this area appears to have triggered divergence among populations of the western, central, and eastern portions of the region and shaped genetic differentiation among them. Two possible independent glacial refugia were predicted, the Ili Valley and the northern Junggar Basin. Extensive development of arid habitats (desert margin and arid piedmont grassland) coupled with a more equable climate because the early Holocene are factors likely to have generated recent expansion of A. frutescens.

Spatiotemporal Phylogenetic Analysis and Molecular Characterisation of Infectious Bursal Disease Viruses Based on the VP2 Hyper-Variable Region

BackgroundInfectious bursal disease is a highly contagious and acute viral disease caused by the infectious bursal disease virus (IBDV); it affects all major poultry producing areas of the world. The current study was designed to rigorously measure the global phylogeographic dynamics of IBDV strains to gain insight into viral population expansion as well as the emergence, spread and pattern of the geographical structure of very virulent IBDV (vvIBDV) strains.Methodology/Principal FindingsSequences of the hyper-variable region of the VP2 (HVR-VP2) gene from IBDV strains isolated from diverse geographic locations were obtained from the GenBank database; Cuban sequences were obtained in the current work. All sequences were analysed by Bayesian phylogeographic analysis, implemented in the Bayesian Evolutionary Analysis Sampling Trees (BEAST), Bayesian Tip-association Significance testing (BaTS) and Spatial Phylogenetic Reconstruction of Evolutionary Dynamics (SPREAD) software packages. Selection pressure on the HVR-VP2 was also assessed. The phylogeographic association-trait analysis showed that viruses sampled from individual countries tend to cluster together, suggesting a geographic pattern for IBDV strains. Spatial analysis from this study revealed that strains carrying sequences that were linked to increased virulence of IBDV appeared in Iran in 1981 and spread to Western Europe (Belgium) in 1987, Africa (Egypt) around 1990, East Asia (China and Japan) in 1993, the Caribbean Region (Cuba) by 1995 and South America (Brazil) around 2000. Selection pressure analysis showed that several codons in the HVR-VP2 region were under purifying selection.Conclusions/SignificanceTo our knowledge, this work is the first study applying the Bayesian phylogeographic reconstruction approach to analyse the emergence and spread of vvIBDV strains worldwide.

A novel empirical mutual information approach to identify co-evolving amino acid positions of influenza A viruses

Mutual information (MI) is an approach commonly used to estimate the evolutionary correlation of 2 amino acid sites. Although several MI methods exist, prior to our contribution no systematic method had been developed to assess their performance, or to establish numerical thresholds to detect co-evolving amino acid sites. The current study performed a Markov chain Monte Carlo (MCMC) algorithm on influenza viral sequences to capture their evolutionary characteristics. A consensus maximum clade credibility (MCC) tree was estimated from the samples, together with their amino acid substitution statistics, from which we generated synthetic sequences of known dependent and independent paired amino acid sites. A pair-to-pair and influenza-specific amino acid substitution matrix (P2PFLU) incorporated into Bayesian Evolutionary Analysis Sampling Trees (BEAST) enumerated these synthetic sequences. The sequences inherited evolutionary features and co-varying characteristics from the real viral sequences, rendering these synthetic data ideal for exploring their co-evolving features. For the MI measure, we proposed a novel metric called the empirical MI (MIEm), which outperformed other MI measures in analysis of receiver operating characteristics (ROC). We implemented our approach on 1086 all-time PB2 sequences of influenza A H5N1 viruses, in which we found 97 sites exhibiting co-evolutionary substitution of one or more amino acid sites. In particular, PB2 451, along with eight other PB2 sites of various MIEm scores, was found to co-evolve with PB2 627, a known species-associated amino acid residue which plays a critical role in influenza virus replication.

Multiple independent origins of a protease inhibitor resistance mutation in salvage therapy patients.

BackgroundCombination anti-viral therapies have reduced treatment failure rates by requiring multiple specific mutations to be selected on the same viral genome to impart high-level drug resistance. To determine if the common protease inhibitor resistance mutation L90M is only selected once or repeatedly on different HIV genetic backbones during the course of failed anti-viral therapies we analyzed a linked region of the viral genome during the evolution of multi-drug resistance.ResultsUsing L90M allele specific PCR we amplified and sequenced gag-pro regions linked to very early L90M containing HIV variants prior to their emergence and detection as dominant viruses in 15 failed salvage therapy patients. The early minority L90M linked sequences were then compared to those of the later L90M viruses that came to dominate the plasma quasispecies. Using Bayesian evolutionary analysis sampling trees the emergence of L90M containing viruses was seen to take place on multiple occasion in 5 patients, only once for 2 patients and an undetermined number of time for the remaining 8 patients.ConclusionThese results indicate that early L90M mutants can frequently be displaced by viruses carrying independently selected L90M mutations rather than by descendents of the earlier mutants.