Bayesian Phylogenetic Approach Research Articles

Whole genome sequencing of outbreak strains from 2017 to 2018 reveals an endemic clade of dengue 1 virus in Cameroon

ABSTRACT Dengue fever is expanding as a global public health threat including countries within Africa. For the past few decades, Cameroon has experienced sporadic cases of arboviral infections including dengue fever. Here, we conducted genomic analyses to investigate the origin and phylogenetic profile of Cameroon DENV-1 outbreak strains and predict the impact of emerging therapeutics on these strains. Bayesian and maximum-likelihood phylogenetic inference approaches were employed in virus evolutionary analyses. An in silico analysis was performed to assess the divergence in immunotherapeutic and vaccine targets in the new genomes. Six complete DENV-1 genomes were generated from 50 samples that met a clinical definition for DENV infection. Phylogenetic analyses revealed that the strains from the current study belong to a sub-lineage of DENV-1 genotype V and form a monophyletic taxon with a 2012 strain from Gabon. The most recent common ancestor (TMRCA) of the Cameroon and Gabon strains was estimated to have existed around 2008. Comparing our sequences to the vaccine strains, 19 and 15 amino acid (aa) substitutions were observed in the immuno-protective prM-E protein segments of the Dengvaxia® and TetraVax-DV-TV003 vaccines, respectively. Epitope mapping revealed mismatches in aa residues at positions E155 and E161 located in the epitope of the human anti-DENV-1 monoclonal antibody HMAb 1F4. The new DENV strains constitute a conserved genomic pool of viruses endemic to the Central African region that needs prospective monitoring to track local viral evolution. Further work is needed to ascertain the performance of emerging therapeutics in DENV strains from the African region.

Detecting Episodic Evolution through Bayesian Inference of Molecular Clock Models.

Molecular evolutionary rate variation is a key aspect of the evolution of many organisms that can be modeled using molecular clock models. For example, fixed local clocks revealed the role of episodic evolution in the emergence of SARS-CoV-2 variants of concern. Like all statistical models, however, the reliability of such inferences is contingent on an assessment of statistical evidence. We present a novel Bayesian phylogenetic approach for detecting episodic evolution. It consists of computing Bayes factors, as the ratio of posterior and prior odds of evolutionary rate increases, effectively quantifying support for the effect size. We conducted an extensive simulation study to illustrate the power of this method and benchmarked it to formal model comparison of a range of molecular clock models using (log) marginal likelihood estimation, and to inference under a random local clock model. Quantifying support for the effect size has higher sensitivity than formal model testing and is straight-forward to compute, because it only needs samples from the posterior and prior distribution. However, formal model testing has the advantage of accommodating a wide range molecular clock models. We also assessed the ability of an automated approach, known as the random local clock, where branches under episodic evolution may be detected without their a priori definition. In an empirical analysis of a data set of SARS-CoV-2 genomes, we find "very strong" evidence for episodic evolution. Our results provide guidelines and practical methods for Bayesian detection of episodic evolution, as well as avenues for further research into this phenomenon.

Novel Deletion in Exon 7 of Betaine Aldehyde Dehydrogenase 2 (BADH2)

The fragrance of rice is one of the premium characteristics that breeders want to include in rice varieties due to the higher market value. Nucleotide deletions in exons 2 (7 bp) and 7 (8 bp) of Betaine Aldehyde Dehydrogenase 2 (BADH2) are associated with fragrance in rice. In this study, a new 13 bp deletion in exon 7 of the BADH2 gene was discovered in the Nang Thom Cho Dao (NTCD) variety, and the mutation has been closely related to the genetic background of indica subspecies through the Bayesian phylogenetic approach and haplotype network analysis of the 3 000 Rice Genomes Project. In addition, a set of functional markers (EX07-13F, EX07-13RN, and EX07-13RM) identified the 13 bp deletion only within NTCD (no amplified band) compared with both non-aromatic and other aromatic rice varieties (110 bp band). The deletion of 13 bases instead of 8 bases in exon 7 of BADH2 caused a premature stop codon, which down-regulated the expression of the BADH2 transcript while associated with up-regulation of OsP5CS and the high amount of 2-acetyl-1-pyrroline. It is potential to use the deletion in exon 7 of the BADH2 gene as a novel marker for adulteration and breeding of fragrant rice varieties, particularly for NTCD.

Phasing Gene Copies into Polyploid Subgenomes Using a Bayesian Phylogenetic Approach.

This chapter describes the usage of homologizer to phase gene copies into polyploid subgenomes. Allopolyploids contain multiple copies of each genetic locus, where each copy potentially belongs to a different subgenome with its own distinct evolutionary history. If gene copies across different loci are incorrectly phased (i.e., assigned to the wrong subgenome), then the bifurcating tree assumption underlying multilocus phylogenetic inference and related analyses will be violated, leading to unsound results. homologizer is a highly flexible Bayesian method that uses a phylogenetic framework to infer the posterior probabilities of the phasing of gene copies into subgenomes. We describe how to prepare input data and other considerations needed to perform homologizer analyses and demonstrate how to visualize and interpret the results. We first walk through a basic example using homologizer to phase gene copies into polyploid subgenomes and then demonstrate how homologizer can be used as a hypothesis-testing tool to detect non-homeologous sequences such as hidden paralogs or allelic variation through the tools of Bayesian model comparison.

Relative performance of Bayesian morphological clock and parsimony methods for phylogenetic reconstructions: Insights from the case of Myomiminae and Dryomyinae glirid rodents.

Extinct organisms provide crucial information about the origin and time of origination of extant groups. The importance of morphological phylogenetics for rigorously dating the tree of life is now widely recognized and has been revitalized by methodological developments such as the application of tip-dating Bayesian approaches. Traditionally, molecular clocks have been node calibrated. However, node calibrations are often unsatisfactory because they do not allow the fossil age to inform about phylogenetic hypothesis. The introduction of tip calibrations allow fossil species to be included alongside their living relatives, and the absence of molecular sequence data for these taxa to be remedied by supplementing the sequence alignments for living taxa with phenotype character matrices for both living and fossil taxa. Therefore, only phylogenetic analyses that take into account morphological characters can incorporate both fossil and extant species. Herein we present an unprecedented morphological dataset for a vast group of glirid rodents, to which different phylogenetic methodologies have been applied. We have compared the tree topologies resulting from traditional parsimony and Bayesian phylogenetic approaches and calculate stratigraphic congruence indices for each. Bayesian tip-dated clock methods seem to outperform parsimony with our dataset. The strict consensus tree recovered by tip dating invalidates the classic classification and allows dates to be proposed for the divergence and origin of the different clades.

Generalizing Bayesian phylogenetics to infer shared evolutionary events

Many processes of biological diversification can simultaneously affect multiple evolutionary lineages. Examples include multiple members of a gene family diverging when a region of a chromosome is duplicated, multiple viral strains diverging at a "super-spreading" event, and a geological event fragmenting whole communities of species. It is difficult to test for patterns of shared divergences predicted by such processes because all phylogenetic methods assume that lineages diverge independently. We introduce a Bayesian phylogenetic approach to relax the assumption of independent, bifurcating divergences by expanding the space of topologies to include trees with shared and multifurcating divergences. This allows us to jointly infer phylogenetic relationships, divergence times, and patterns of divergences predicted by processes of diversification that affect multiple evolutionary lineages simultaneously or lead to more than two descendant lineages. Using simulations, we find that the method accurately infers shared and multifurcating divergence events when they occur and performs as well as current phylogenetic methods when divergences are independent and bifurcating. We apply our approach to genomic data from two genera of geckos from across the Philippines to test if past changes to the islands' landscape caused bursts of speciation. Unlike previous analyses restricted to only pairs of gecko populations, we find evidence for patterns of shared divergences. By generalizing the space of phylogenetic trees in a way that is independent from the likelihood model, our approach opens many avenues for future research into processes of diversification across the life sciences.

The phylogenetic position of ridley's worm lizard reveals the complex biogeographic history of New World insular amphisbaenids

The archipelago of Fernando de Noronha (FN) is located in the Equatorial South Atlantic Ocean, at 375 km off the northeastern coast of Brazil. Its endemic vertebrate land fauna is restricted to only six species, and three main hypotheses have been proposed to explain their presence in the archipelago. These hypotheses suggest FN had alternative biogeographic connections with: 1) the West Indies; 2) the South America mainland; or 3) Africa. Here, we evaluate for the first time the phylogenetic position of Amphisbaena ridleyi within the diversity of Amphisbaenia, and we infer the biogeographic processes that explain its presence in FN and its relationship with amphisbaenids from the West Indies. We analyzed a comprehensive multilocus dataset for Amphisbaenidae using maximum likelihood and time-calibrated Bayesian phylogenetic approaches. Based on our time-calibrated tree, we tested different biogeographic scenarios through historical biogeographic analyses. Our phylogenetic results for the high-level relationships of Amphisbaenia can be parenthetically summarized as (Rhineuridae, (Blanidae, (Bipedidae, (Cadeidae, (Trogonophidae, (Amphisbaenidae))))). Nine highly supported groups of species were recovered among the mainland South American amphisbaenids (SAA), whereas two phylogenetically distant groups of species were inferred for the West Indies: 1) WIC01, an Oligocene lineage present in Cuba and Hispaniola, which is the sister group of all other SAA groups; and 2) WIC02, a Miocene lineage that is restricted to southern Hispaniola and is closely related to Am. ridleyi. We estimated two events of transatlantic dispersal of amphisbaenians from Africa to West Indies: the dispersal of Cadeidae during the Middle Eocene, and the dispersal of the ancestor of Amphisbaena during the transition Eocene/Oligocene. These events were likely affected by the North Equatorial and South Equatorial currents, respectively, which have been flowing westwards since the Paleocene. The ancestral cladogenesis of Amphisbaena during the Late Oligocene is likely related to overwater dispersal events, or alternatively can be associated with the fragmentation of GAARlandia, when WIC01 was isolated in the West Indies, while the remaining groups of Amphisbaena diversified throughout the South American continent. During the Late Miocene, the ancestor of WIC02 dispersed from northern South America to the West Indies, while Am. ridleyi dispersed from the same region to FN. The overwater dispersal of WIC02 was driven by the North Brazilian Current and the dispersal of Am. ridleyi was likely influenced by the periodic shifts in direction and strength estimated for the North Equatorial Counter-Current during the Late Miocene.

High-level taxonomic splitting in allopatric taxa causes confusion downstream: a revision of the nudibranch family Сoryphellidae

Abstract Conformity of trans-Arctic Coryphellidae genera with the most recent revised taxonomy for the group was tested. Both morphological and molecular data were used to compare more than 200 specimens from various localities in the North Pacific, North Atlantic and Arctic Oceans. The molecular study included four markers (COI, 16S, H3 and 28S) and implemented Bayesian and maximum likelihood phylogenetic approaches. Species delimitation was investigated with automatic barcode gap discovery (ABGD), Poisson tree processes (PTP) and generalized mixed Yule coalescent (GMYC) methods. The inter- and intraspecific divergence were studied using the TCS-based haplotype analysis and calculation of p-distances. Morphological analysis included standard anatomical techniques and scanning electron microscopy. Based on integrative analysis, we conclude that Coryphella verrucosa and C. pseudoverrucosa represent a single species (C. verrucosa), which is highly heterogeneous at morphological and molecular levels. For Microchlamylla gracilis and M. amabilis, their synonymization under the name M. gracilis is suggested, but increased sample size is needed for further clarification of their identities. Finally, the amphiboreal species Borealea nobilis and the North Pacific B. sanamyanae are distinct species displaying secondary sympatry in the north-west Pacific. Based on these results, we propose a new classification system for the family Coryphellidae uniting all currently considered genera in the single genus Coryphella, and suggest a new approach for further revision of Flabellinidae s.l. taxa.

A Computational Protocol for Dating the Evolution of Cyanobacteria.

Cyanobacteria are known to play important roles in driving biological and geochemical innovations in ancient Earth. The origin of Cyanobacteria is the key to understanding these evolutionary events and thus has gained much interest to biologists and geobiologists. Recent development of the molecular dating approaches provides us an opportunity to assess the timeline of Cyanobacteria evolution based on relaxed clock models. The implementation of Bayesian phylogenetic approaches accommodates the uncertainties from different sources, such as fossil calibrations and topological structure of the phylogenomic tree, and provides us converged estimates of posterior mean ages. In this chapter, by taking Cyanobacteria as an example, we introduce a refined strategy to perform molecular dating analysis, as well as a practical method to evaluate the precision of dating analysis.

Global spatiotemporal transmission patterns of human enterovirus 71 from 1963 to 2019.

Enterovirus 71 (EV71) can cause large outbreaks of hand, foot, and mouth disease (HFMD) and severe neurological diseases, which is regarded as a major threat to public health, especially in Asia-Pacific regions. However, the global spatiotemporal spread of this virus has not been identified. In this study, we used large sequence datasets and a Bayesian phylogenetic approach to compare the molecular epidemiology and geographical spread patterns of different EV71 subgroups globally. The study found that subgroups of HFMD presented global spatiotemporal variation, subgroups B0, B1, and B2 have caused early infections in Europe and America, and then subgroups C1, C2, C3, and C4 replaced B0-B2 as the predominant genotypes, especially in Asia-Pacific countries. The dispersal patterns of genotype B and subgroup C4 showed the complicated routes in Asia and the source might in some Asian countries, while subgroups C1 and C2 displayed more strongly supported pathways globally, especially in Europe. This study found the predominant subgroup of EV71 and its global spatiotemporal transmission patterns, which may be beneficial to reveal the long-term global spatiotemporal transmission patterns of human EV71 and carry out the HFMD vaccine development.

Bayesian Morphological Clock versus Parsimony: An Insight into the Relationships and Dispersal Events of Postvacuum Cricetidae (Rodentia, Mammalia).

Establishing an evolutionary timeline is fundamental for tackling a great variety of topics in evolutionary biology, including the reconstruction of patterns of historical biogeography, coevolution, and diversification. However, the tree of life is pruned by extinction and molecular data cannot be gathered for extinct lineages. Until recently methodological challenges have prevented the application of tip-dating Bayesian approaches in morphology-based fossil-only data sets. Herein, we present a morphological data set for a group of cricetid rodents to which we apply an array of methods fairly new in paleontology that can be used by paleontologists for the analysis of entirely extinct clades. We compare the tree topologies obtained by traditional parsimony, time-calibrated, and noncalibrated Bayesian inference phylogenetic approaches and calculate stratigraphic congruence indices for each. Bayesian tip-dated clock methods outperform parsimony in the case of our data set, which includes highly homoplastic morphological characters. Regardless, all three topologies support the monophyly of Megacricetodontinae, Democricetodontinae, and Cricetodontinae. Dispersal and speciation events inferred through Bayesian Binary Markov chain Monte Carlo and biodiversity analyses provide evidence for a correlation between biogeographic events, climatic changes, and diversification in cricetids. [Bayesian tip-dating; Cricetidae; Miocene; morphological clock; paleobiodiversity; paleobiogeography; paleoecology; parsimony; STRAP.].

A new genus of frenulates (Annelida: Siboglinidae) from shallow waters of the Yenisey River estuary, Kara Sea

Only seven frenulate species are currently known along the Eurasian coast of the Arctic Ocean. We describe a new genus and a new species of frenulates Crispabrachia yenisey, gen. nov. et sp. nov. The morphological analysis involved standard anatomical techniques, semithin sections and scanning electron microscopy (SEM). The molecular study included four markers (partial COI, 16S, 18S and 28S) and implemented Bayesian and Maximum likelihood phylogenetic approaches. The description of Crispabrachia gen. nov. is the first documented finding of frenulates in the Kara Sea at the estuary of the Yenisey River in rather shallow water (28 m). The establishment of a new genus is warranted based on the composition of morphological characters and several specific features including free, comparatively short curly tentacles, a triangular cephalic lobe with amplate base, the valvate extension of the posterior part of the forepart and prominent papillae on the nonmetameric region. The tube structure with prominent frills and the worm’s numerous tentacles, metameric papillae with cuticular plaques and segmental furrow on the forepart indicate that the new genus belongs to the polybrachiid group. Although the type locality in the Yenisey River estuary is unusual for siboglinids in general, the physical conditions here are common for other frenulates habitats, i.e. salinity ~30–33, bottom water temperature –1.5°C. This finding was made in the Yenisey Gulf in the region with the highest methane concentrations in the southern part of the Kara Sea that reflects permafrost degradation under the influence of river flow. Further study of the region would help to understand the factors influencing frenulate distributions and improve our knowledge of their biodiversity.

Ignoring Fossil Age Uncertainty Leads to Inaccurate Topology and Divergence Time Estimates in Time Calibrated Tree Inference

Time calibrated trees are challenging to estimate for many extinct groups of species due to the incompleteness of the rock and fossil records. Additionally, the precise age of a sample is typically not known as it may have occurred at any time during the time interval spanned by the rock layer. Bayesian phylogenetic approaches provide a coherent framework for incorporating multiple sources of evidence and uncertainty. In this study, we simulate datasets with characteristics typical of Palaeozoic marine invertebrates, in terms of character and taxon sampling. We use these datasets to examine the impact of different age handling methods on estimated topologies and divergence times obtained using the fossilized birth-death process. Our results reiterate the importance of modeling fossil age uncertainty, although we find that the relative impact of fossil age uncertainty depends on both fossil taxon sampling and character sampling. Sampling the fossil ages as part of the inference gives topology and divergence time estimates that are as good as those obtained by fixing ages to the truth, whereas fixing fossil ages to incorrect values results in higher error and lower coverage. The relative effect increases with increased fossil and character sampling. Modeling fossil age uncertainty is thus critical, as fixing incorrect fossil ages will negate the benefits of improved fossil and character sampling.

Combining genomics and epidemiology to analyse bi-directional transmission of Mycobacterium bovis in a multi-host system.

Quantifying pathogen transmission in multi-host systems is difficult, as exemplified in bovine tuberculosis (bTB) systems, but is crucial for control. The agent of bTB, Mycobacterium bovis, persists in cattle populations worldwide, often where potential wildlife reservoirs exist. However, the relative contribution of different host species to bTB persistence is generally unknown. In Britain, the role of badgers in infection persistence in cattle is highly contentious, despite decades of research and control efforts. We applied Bayesian phylogenetic and machine-learning approaches to bacterial genome data to quantify the roles of badgers and cattle in M. bovis infection dynamics in the presence of data biases. Our results suggest that transmission occurs more frequently from badgers to cattle than vice versa (10.4x in the most likely model) and that within-species transmission occurs at higher rates than between-species transmission for both. If representative, our results suggest that control operations should target both cattle and badgers.

Molecular characteristic of HIV-1 CRF01_AE in Nanjing from 2015 to 2017

ObjectiveTo investigate the evolutionary dynamics and characteristic of the molecular transmission networks of HIV-1 CRF01_AE in Nanjing. MethodsViral samples were collected from 580 newly diagnosed HIV-1-infected patients. HIV-1 pol sequences were obtained and used for for molecular evolutionary analyses. The ML trees were constructed by MEGA 6.0 using under GTR+ G + I model with 1000 bootstrap replicates. The emergence and estimation of tMRCA and the evolutionary rate of the different CRF01_AE clusters were inferred using Bayesian phylogenetic analysis approaches implemented in the BEAST package. Pairwise genetic distances were calculated under the Tamura-Nei 93 model, a genetic distance threshold of ≤1.2% was used to identify potential transmission clusters. Network diagrams were plotted using Cytoscape 3.3.0. ResultsOf these HIV-1-infected patients, 551 (91.5%) were males. The largest number of infections were attributed to homosexual (462, 79.7%). A total of 518 full-length pol genes were successfully amplified, based on the phylogenetic analysis CRF01_AE was the most predominantly circulating strain (45.0%, 233/518). As shown in the ML tree, three distinct clusters were observed. The ‘Nanjing lineage’ 1, 2, 3 has an estimated tMRCA around1996.61, 1993.61, 1984.61 respectively. Of 233 Nanjing sequences, 123 (55.2%) distributed in 30 molecular clusters, average Links/node was 7.8 with range (1−33), most of Nanjing strains shared links with local strains. ConclusionHIV-1 CRF01_AE was the most predominantly circulating strain, the epidemic of CRF01_AE in Nanjing was driven by multiple clusters of HIV-1 strains, and most CRF01_AE stains in our study were estimated to have originated in China in the 1990s.

Transitions between foot postures are associated with elevated rates of body size evolution in mammals

Terrestrial mammals have evolved various foot postures: flat-footed (plantigrady), tiptoed (digitigrady), and hooved (unguligrady) postures. Although the importance of foot posture on ecology and body size of mammalian species has been widely recognized, its evolutionary trajectory and influence on body size evolution across mammalian phylogeny remain untested. Taking a Bayesian phylogenetic approach combined with a comprehensive dataset of foot postures in 880 extant mammalian species, we investigated the evolutionary history of foot postures and rates of body size evolution, within the same posture and at transitions between postures. Our results show that the common ancestor of mammals was plantigrade, and transitions predominantly occurred only between plantigrady and digitigrady and between digitigrady and unguligrady. At the transitions between plantigrady and digitigrady and between digitigrady and unguligrady, rates of body size evolution are significantly elevated leading to the larger body masses of digitigrade species (∼1 kg) and unguligrade species (∼78 kg) compared with their respective ancestral postures [plantigrady (∼0.75 kg) and digitigrady]. Our results demonstrate the importance of foot postures on mammalian body size evolution and have implications for mammalian body size increase through time. In addition, we highlight a way forward for future studies that seek to integrate morphofunctional and macroevolutionary approaches.

Insights from genome-wide approaches to identify variants associated to phenotypes at pan-genome scale: Application to L. monocytogenes' ability to grow in cold conditions

Intraspecific variability of the behavior of most foodborne pathogens is well described and taken into account in Quantitative Microbial Risk Assessment (QMRA), but factors (strain origin, serotype, …) explaining these differences are scarce or contradictory between studies. Nowadays, Whole Genome Sequencing (WGS) offers new opportunities to explain intraspecific variability of food pathogens, based on various recently published bioinformatics tools.The objective of this study is to get a better insight into different existing bioinformatics approaches to associate bacterial phenotype(s) and genotype(s). Therefore, a dataset of 51 L. monocytogenes strains, isolated from multiple sources (i.e. different food matrices and environments) and belonging to 17 clonal complexes (CC), were selected to represent large population diversity. Furthermore, the phenotypic variability of growth at low temperature was determined (i.e. qualitative phenotype), and the whole genomes of selected strains were sequenced. The almost exhaustive gene content, as well as the core genome SNPs based phylogenetic reconstruction, were derived from the whole sequenced genomes. A Bayesian inference method was applied to identify the branches on which the phenotype distribution evolves within sub-lineages. Two different Genome Wide Association Studies (i.e. gene- and SNP-based GWAS) were independently performed in order to link genetic mutations to the phenotype of interest.The genomic analyses presented in this study were successfully applied on the selected dataset. The Bayesian phylogenetic approach emphasized an association with “slow” growth ability at 2 °C of the lineage I, as well as CC9 of the lineage II. Moreover, both gene- and SNP-GWAS approaches displayed significant statistical associations with the tested phenotype. A list of 114 significantly associated genes, including genes already known to be involved in the cold adaption mechanism of L. monocytogenes and genes associated to mobile genetic elements (MGE), resulted from the gene-GWAS. On the other hand, a group of 184 highly associated SNPs were highlighted by SNP-GWAS, including SNPs detected in genes which were already likely involved in cold adaption; hypothetical proteins; and intergenic regions where for example promotors and regulators can be located.The successful application of combined bioinformatics approaches associating WGS-genotypes and specific phenotypes, could contribute to improve prediction of microbial behaviors in food. The implementation of this information in hazard identification and exposure assessment processes will open new possibilities to feed QMRA-models.

Phylogeny and evolutionary history of diplobathrid crinoids (Echinodermata)

AbstractOrder Diplobathrida is a major clade of camerate crinoids spanning the Ordovician–Mississippian, yet phylogenetic relationships have only been inferred for Ordovician taxa. This has hampered efforts to construct a comprehensive tree of life for crinoids and develop a classification scheme that adequately reflects diplobathrid evolutionary history. Here, I apply maximum parsimony and Bayesian phylogenetic approaches to the fossil record of diplobathrids to infer the largest tree of fossil crinoids to date, with over 100 genera included. Recovered trees provide a framework for evaluating the current classification of diplobathrids. Notably, previous suborder divisions are not supported, and superfamily divisions will require significant modification. Although numerous revisions are required for families, most can be retained through reassignment of genera. In addition, recovered trees were used to produce phylogeny‐based estimates of diplobathrid lineage diversity. By accounting for ghost lineages, phylogeny‐based richness estimates offer greater insight into diversification and extinction dynamics than traditional taxonomy‐based approaches alone and provide a detailed summary of the ~150 million‐year evolutionary history of Diplobathrida. This study constitutes a major step toward producing a phylogeny of the Crinoidea and documenting crinoid diversity dynamics. In addition, it will serve as a framework for subsequent phylogeny‐based investigations of macroevolutionary questions.

Inferring demographic parameters in bacterial genomic data using Bayesian and hybrid phylogenetic methods

BackgroundRecent developments in sequencing technologies make it possible to obtain genome sequences from a large number of isolates in a very short time. Bayesian phylogenetic approaches can take advantage of these data by simultaneously inferring the phylogenetic tree, evolutionary timescale, and demographic parameters (such as population growth rates), while naturally integrating uncertainty in all parameters. Despite their desirable properties, Bayesian approaches can be computationally intensive, hindering their use for outbreak investigations involving genome data for a large numbers of pathogen isolates. An alternative to using full Bayesian inference is to use a hybrid approach, where the phylogenetic tree and evolutionary timescale are estimated first using maximum likelihood. Under this hybrid approach, demographic parameters are inferred from estimated trees instead of the sequence data, using maximum likelihood, Bayesian inference, or approximate Bayesian computation. This can vastly reduce the computational burden, but has the disadvantage of ignoring the uncertainty in the phylogenetic tree and evolutionary timescale.ResultsWe compared the performance of a fully Bayesian and a hybrid method by analysing six whole-genome SNP data sets from a range of bacteria and simulations. The estimates from the two methods were very similar, suggesting that the hybrid method is a valid alternative for very large datasets. However, we also found that congruence between these methods is contingent on the presence of strong temporal structure in the data (i.e. clocklike behaviour), which is typically verified using a date-randomisation test in a Bayesian framework. To reduce the computational burden of this Bayesian test we implemented a date-randomisation test using a rapid maximum likelihood method, which has similar performance to its Bayesian counterpart.ConclusionsHybrid approaches can produce reliable inferences of evolutionary timescales and phylodynamic parameters in a fraction of the time required for fully Bayesian analyses. As such, they are a valuable alternative in outbreak studies involving a large number of isolates.

Evolutionary analyses of Sindbis virus strains isolated from mosquitoes in Kenya.

Sindbis virus (SINV) is a mosquito borne virus maintained in nature in a mosquito-bird cycle, with human outbreaks known to occur in Northern Europe and parts of Africa. We analyzed five SINV strains isolated in Kenya from five different mosquito species and geographic locations between 2007 and 2013. Phylogenetic relationships and evolutionary inferences were performed using maximum likelihood and Bayesian phylogenetic inference approaches. Selection analyses were carried out based on the virus envelope glycoproteins (E1, E2) and non-structural protein (nsP4) genes. Phylogenetic analysis revealed that all the Kenyan SINV isolates belonged to genotype 1 with selection analyses suggesting that SINV E1, E2 and nsP4 protein encoding genes were predominantly evolving under negative selection.