Ultraconserved Elements Reveal the Relationship Between Facultative Keratinophagy and Synanthropic Evolution in Clothes Moths

Synanthropic species live in close association with, or benefit from, humans. Despite their potential impacts to human health, little is known about the mechanisms driving synanthropic life-history evolution, evolutionary forces shaping diet among synanthropes, or how these combined factors affect population dynamics and/or speciation. The Tineidae moth family contains several synanthropic species, including the globally distributed pest species Tineola bissellellia, that contribute to the ~$1 billion worth of damage caused annually by keratinophagous synanthropes. Synanthropy among Tineidae is associated with a wide range of dietary strategies. While most tineids display obligate detritivory, synanthropic species are typically either facultatively or obligately keratinophagous. However, little is known about evolutionary relationships within Tineidae, hampering efforts to investigate the relationship between synanthropy and diet evolution. Here, to address this challenge, we extracted DNA from 39 tineid samples and two outgroups, including the closely related Tineola and Tinea genera, and generated genome-wide sequence data for thousands of ultraconserved elements (UCEs). Our phylogenetic analyses, using a concatenated maximum-likelihood-based approach, resulted in a well-supported, fully resolved phylogeny that demonstrates synanthropy has evolved multiple times and is consistently associated with facultative and obligate keratinophagy. Bayesian divergence time estimation indicates Cretaceous divergence among deep-branching tineid lineages, an ancestral origin of facultative keratinophagy, and a recent origin of the most economically important synanthropic pest, Tineola bissellellia, from within genus Tinea. Taken together, our results suggest that a shift to facultative keratinophagy was a key evolutionary innovation that has fuelled the repeated evolution of synanthropic life histories among this deep-diverging moth family.

Plate tectonics, cold adaptation and long-distance range expansion to remote archipelagos and the high Andes as drivers of a circumantarctic freshwater arthropod radiation

Disjunct distributions, characterised by spatially separated populations of related species, offer insights into historical biogeographic patterns and evolutionary processes. This study investigates the evolutionary history of the diving beetle subfamily Lancetinae through a phylogenomic approach incorporating ultraconserved elements (UCEs) and heritage genetic markers. Our findings support an early Miocene origin for Lancetinae, with subsequent diversification influenced by historical vicariance events and long-distance dispersal. The divergence from the closely related subfamily Coptotominae in the late Cretaceous is not consistent with a Gondwanan origin, although highlights a likely Pangean origin for these taxa. This research underscores the significant impact of Gondwanan fragmentation on biogeographic patterns and highlights the remarkable dispersal capabilities of Lancetinae beetles.

Aridification and major geotectonic landscape change shaped an extraordinary species radiation across a world's extreme elevational gradient

Understanding the profound influence of climatic and tectonic histories on adaptation and speciation is a crucial focus in biology research. While voyages like Humboldt's expedition shaped our understanding of adaptation, the origin of current biodiversity remains unclear - whether it arose in situ or through dispersal from analogous habitats. Situated in the geologically complex Australopacific region, our study focuses on Limbodessus diving beetles (Dytiscidae), a diverse genus distributed from underground aquifers in Western Australia to alpine meadows in New Guinea. Using low-coverage whole-genome sequencing, we established a time-calibrated phylogenetic tree, elucidating Limbodessus' origin in the mid-late Miocene, most likely in the Sahul continent (i.e., Australia and New Guinea) and western Pacific archipelagos. Our results provide evidence for parallel colonization and speciation at extreme altitudinal ends, driven by aridification in Australia, influencing subterranean colonization, and in situ diversification of alpine taxa by passive-uplifting of local biota in New Guinea. Furthermore, our findings highlight instances of subterranean speciation in isolated underground aquifers, marked by recurrent independent colonizations of this habitat.

South Asian maternal and paternal lineages in southern Thailand and the role of sex-biased admixture

Previous genome-wide studies have reported South Asian (SA) ancestry in several Mainland Southeast Asian (MSEA) populations; however, additional details concerning population history, in particular the role of sex-specific aspects of the SA admixture in MSEA populations can be addressed with uniparental markers. Here, we generated ∼2.3 mB sequences of the male-specific portions of the Y chromosome (MSY) of a Tai-Kadai (TK)-speaking Southern Thai group (SouthernThai_TK), and complete mitochondrial (mtDNA) genomes of the SouthernThai_TK and an Austronesian (AN)-speaking Southern Thai (SouthernThai_AN) group. We identified new mtDNA haplogroups, e.g. Q3, E1a1a1, B4a1a and M7c1c3 that have not previously reported in Thai populations, but are frequent in Island Southeast Asia and Oceania, suggesting interactions between MSEA and these regions. SA prevalent mtDNA haplogroups were observed at frequencies of ~35-45% in the Southern Thai groups; both of them showed more genetic relatedness to Austroasiatic (AA) speaking Mon than to any other group. For MSY, SouthernThai_TK had ~35% SA prevalent haplogroups and exhibited closer genetic affinity to Central Thais. We also analyzed published data from other MSEA populations and observed SA ancestry in some additional MSEA populations that also reflects sex-biased admixture; in general, most AA- and AN-speaking groups in MSEA were closer to SA than to TK groups based on mtDNA, but the opposite pattern was observed for the MSY. Overall, our results of new genetic lineages and sex-biased admixture from SA to MSEA groups attest to the additional value that uniparental markers can add to studies of genome-wide variation.

Identifying the Best Approximating Model in Bayesian Phylogenetics: Bayes Factors, Cross-Validation or wAIC?

There is still no consensus as to how to select models in Bayesian phylogenetics, and more generally in applied Bayesian statistics. Bayes factors are often presented as the method of choice, yet other approaches have been proposed, such as cross-validation or information criteria. Each of these paradigms raises specific computational challenges, but they also differ in their statistical meaning, being motivated by different objectives: either testing hypotheses or finding the best-approximating model. These alternative goals entail different compromises, and as a result, Bayes factors, cross-validation, and information criteria may be valid for addressing different questions. Here, the question of Bayesian model selection is revisited, with a focus on the problem of finding the best-approximating model. Several model selection approaches were re-implemented, numerically assessed and compared: Bayes factors, cross-validation (CV), in its different forms (k-fold or leave-one-out), and the widely applicable information criterion (wAIC), which is asymptotically equivalent to leave-one-out cross-validation (LOO-CV). Using a combination of analytical results and empirical and simulation analyses, it is shown that Bayes factors are unduly conservative. In contrast, CV represents a more adequate formalism for selecting the model returning the best approximation of the data-generating process and the most accurate estimates of the parameters of interest. Among alternative CV schemes, LOO-CV and its asymptotic equivalent represented by the wAIC, stand out as the best choices, conceptually and computationally, given that both can be simultaneously computed based on standard Markov chain Monte Carlo runs under the posterior distribution. [Bayes factor; cross-validation; marginal likelihood; model comparison; wAIC.].

Scalable Bayesian phylogenetics

Recent advances in Bayesian phylogenetics offer substantial computational savings to accommodate increased genomic sampling that challenges traditional inference methods. In this review, we begin with a brief summary of the Bayesian phylogenetic framework, and then conceptualize a variety of methods to improve posterior approximations via Markov chain Monte Carlo (MCMC) sampling. Specifically, we discuss methods to improve the speed of likelihood calculations, reduce MCMC burn-in, and generate better MCMC proposals. We apply several of these techniques to study the evolution of HIV virulence along a 1536-tip phylogeny and estimate the internal node heights of a 1000-tip SARS-CoV-2 phylogenetic tree in order to illustrate the speed-up of such analyses using current state-of-the-art approaches. We conclude our review with a discussion of promising alternatives to MCMC that approximate the phylogenetic posterior. This article is part of a discussion meeting issue 'Genomic population structures of microbial pathogens'.

Transmission history of SARS-CoV-2 in humans and white-tailed deer

The emergence of a novel pathogen in a susceptible population can cause rapid spread of infection. High prevalence of SARS-CoV-2 infection in white-tailed deer (Odocoileus virginianus) has been reported in multiple locations, likely resulting from several human-to-deer spillover events followed by deer-to-deer transmission. Knowledge of the risk and direction of SARS-CoV-2 transmission between humans and potential reservoir hosts is essential for effective disease control and prioritisation of interventions. Using genomic data, we reconstruct the transmission history of SARS-CoV-2 in humans and deer, estimate the case finding rate and attempt to infer relative rates of transmission between species. We found no evidence of direct or indirect transmission from deer to human. However, with an estimated case finding rate of only 4.2%, spillback to humans cannot be ruled out. The extensive transmission of SARS-CoV-2 within deer populations and the large number of unsampled cases highlights the need for active surveillance at the human–animal interface.

Himalayan orogeny and monsoon intensification explain species diversification in an endemic ginger (Hedychium: Zingiberaceae) from the Indo-Malayan Realm

The Indo-Malayan Realm is a biogeographic realm that extends from the Indian Subcontinent to the islands of Southeast Asia (Malay Archipelago). Despite being megadiverse, evolutionary hypotheses explaining taxonomic diversity in this region have been rare. Here, we investigate the role of geoclimatic events such as Himalayan orogeny and monsoon intensification in the diversification of the ginger-lilies (Hedychium J.Koenig: Zingiberaceae). We first built a comprehensive, time-calibrated phylogeny of Hedychium with 75% taxonomic and geographic sampling. We found that Hedychium is a very young lineage that originated in Northern Indo-Burma, in the Late Miocene (c. 10.6 Ma). This was followed by a late Neogene and early Quaternary diversification, with multiple dispersal events to Southern Indo-Burma, Himalayas, Peninsular India, and the Malay Archipelago. The most speciose clade IV i.e., the predominantly Indo-Burmese clade also showed a higher diversification rate, suggesting its recent rapid radiation. Our divergence dating and GeoHiSSE results demonstrate that the diversification of Hedychium was shaped by both the intensifications in the Himalayan uplift as well as the Asian monsoon. Ancestral character-state reconstructions identified the occurrence of vegetative dormancy in both clades I and II, whereas the strictly epiphytic growth behavior, island dwarfism, lack of dormancy, and a distinct environmental niche were observed only in the predominantly island clade i.e., clade III. Finally, we show that the occurrence of epiphytism in clade III corresponds with submergence due to sea-level changes, suggesting it to be an adaptive trait. Our study highlights the role of recent geoclimatic events and environmental factors in the diversification of plants within the Indo-Malayan Realm and the need for collaborative work to understand biogeographic patterns within this understudied region. This study opens new perspectives for future biogeographic studies in this region and provides a framework to explain the taxonomic hyperdiversity of the Indo-Malayan Realm.

Parallel power posterior analyses for fast computation of marginal likelihoods in phylogenetics

In Bayesian phylogenetic inference, marginal likelihoods can be estimated using several different methods, including the path-sampling or stepping-stone-sampling algorithms. Both algorithms are computationally demanding because they require a series of power posterior Markov chain Monte Carlo (MCMC) simulations. Here we introduce a general parallelization strategy that distributes the power posterior MCMC simulations and the likelihood computations over available CPUs. Our parallelization strategy can easily be applied to any statistical model despite our primary focus on molecular substitution models in this study. Using two phylogenetic example datasets, we demonstrate that the runtime of the marginal likelihood estimation can be reduced significantly even if only two CPUs are available (an average performance increase of 1.96x). The performance increase is nearly linear with the number of available CPUs. We record a performance increase of 13.3x for cluster nodes with 16 CPUs, representing a substantial reduction to the runtime of marginal likelihood estimations. Hence, our parallelization strategy enables the estimation of marginal likelihoods to complete in a feasible amount of time which previously needed days, weeks or even months. The methods described here are implemented in our open-source software RevBayes which is available from http://www.RevBayes.com.

St. Louis Encephalitis Virus in the Southwestern United States: A Phylogeographic Case for a Multi-Variant Introduction Event

Since the reemergence of St. Louis Encephalitis (SLE) Virus (SLEV) in the Southwest United States, identified during the 2015 outbreak in Arizona, SLEV has been seasonally detected within Culex spp. populations throughout the Southwest United States. Previous work revealed the 2015 outbreak was caused by an importation of SLEV genotype III, which had only been detected previously in Argentina. However, little is known about when the importation occurred or the transmission and genetic dynamics since its arrival into the Southwest. In this study, we sought to determine whether the annual detection of SLEV in the Southwest is due to enzootic cycling or new importations. To address this question, we analyzed 174 SLEV genomes (142 sequenced as part of this study) using Bayesian phylogenetic analyses to estimate the date of arrival into the American Southwest and characterize the underlying population structure of SLEV. Phylogenetic clustering showed that SLEV variants circulating in Maricopa and Riverside counties form two distinct populations with little evidence of inter-county transmission since the onset of the outbreak. Alternatively, it appears that in 2019, Yuma and Clark counties experienced annual importations of SLEV that originated in Riverside and Maricopa counties. Finally, the earliest representatives of SLEV genotype III in the Southwest form a polytomy that includes both California and Arizona samples. We propose that the initial outbreak most likely resulted from the importation of a population of SLEV genotype III variants, perhaps in multiple birds, possibly multiple species, migrating north in 2013, rather than a single variant introduced by one bird.

A transmissible cancer shifts from emergence to endemism in Tasmanian devils

Emerging infectious diseases pose one of the greatest threats to human health and biodiversity. Phylodynamics is often used to infer epidemiological parameters essential for guiding intervention strategies for human viruses such as severe acute respiratory syndrome coronavirus 2 (SARS-Cov-2). Here, we applied phylodynamics to elucidate the epidemiological dynamics of Tasmanian devil facial tumor disease (DFTD), a fatal, transmissible cancer with a genome thousands of times larger than that of any virus. Despite prior predictions of devil extinction, transmission rates have declined precipitously from ~3.5 secondary infections per infected individual to ~1 at present. Thus, DFTD appears to be transitioning from emergence to endemism, lending hope for the continued survival of the endangered Tasmanian devil. More generally, our study demonstrates a new phylodynamic analytical framework that can be applied to virtually any pathogen.

Phylogenetic inference enables reconstruction of a long-overlooked outbreak of almond leaf scorch disease (Xylella fastidiosa) in Europe

The recent introductions of the bacterium Xylella fastidiosa (Xf) into Europe are linked to the international plant trade. However, both how and when these entries occurred remains poorly understood. Here, we show how almond scorch leaf disease, which affects ~79% of almond trees in Majorca (Spain) and was previously attributed to fungal pathogens, was in fact triggered by the introduction of Xf around 1993 and subsequently spread to grapevines (Pierceʼs disease). We reconstructed the progression of almond leaf scorch disease by using broad phylogenetic evidence supported by epidemiological data. Bayesian phylogenetic inference predicted that both Xf subspecies found in Majorca, fastidiosa ST1 (95% highest posterior density, HPD: 1990–1997) and multiplex ST81 (95% HPD: 1991–1998), shared their most recent common ancestors with Californian Xf populations associated with almonds and grapevines. Consistent with this chronology, Xf-DNA infections were identified in tree rings dating to 1998. Our findings uncover a previously unknown scenario in Europe and reveal how Pierce’s disease reached the continent.

Eduardo Moralejo et al. report a phylogenetic reconstruction tracing the origin and progression of a European outbreak of the almond scorch disease pathogen Xylella fastidiosa (Xf). Their data suggest Xf was introduced into Europe via grafting from infected Californian buds and was subsequently spread by the meadow spittlebug to multiple plant hosts.

Detection and Genetic Characterization of Puumala Orthohantavirus S-Segment in Areas of France Non-Endemic for Nephropathia Epidemica

Puumala virus (PUUV) in Europe causes nephropathia epidemica (NE), a mild form of hemorrhagic fever with renal syndrome (HFRS). The incidence of NE is highly heterogeneous spatially, whereas the geographic distribution of the wild reservoir of PUUV, the bank vole, is essentially homogeneous. Our understanding of the processes driving this heterogeneity remains incomplete due to gaps in knowledge. Little is known about the current distribution and genetic variation of PUUV in the areas outside the well-identified zones of NE endemicity. We trapped bank voles in four forests in French regions in which NE is considered non-endemic, but sporadic NE cases have been reported recently. We tested bank voles for anti-PUUV IgG and characterized the S segment sequences of PUUV from seropositive animals. Phylogenetic analyses revealed specific amino-acid signatures and genetic differences between PUUV circulating in non-endemic and nearby NE-endemic areas. We also showed, in temporal surveys, that the amino-acid sequences of PUUV had undergone fewer recent changes in areas non-endemic for NE than in endemic areas. The evolutionary history of the current French PUUV clusters was investigated by phylogeographic approaches, and the results were considered in the context of the history of French forests. Our findings highlight the need to monitor the circulation and genetics of PUUV in a larger array of bank vole populations, to improve our understanding of the risk of NE.

Genetic diversity and evolution of Hantaan virus in China and its neighbors

BACKGROUND

Hantaan virus (HTNV; family Hantaviridae, order Bunyavirales) causes hemorrhagic fever with renal syndrome (HFRS), which has raised serious concerns in Eurasia, especially in China, Russia, and South Korea. Previous studies reported genetic diversity and phylogenetic features of HTNV in different parts of China, but the analyses from the holistic perspective are rare.

METHODOLOGY AND PRINCIPAL FINDINGS

To better understand HTNV genetic diversity and gene evolution, we analyzed all available complete sequences derived from the small (S) and medium (M) segments with bioinformatic tools. Eleven phylogenetic groups were defined and showed geographic clustering; 42 significant amino acid variant sites were found, and 19 of them were located in immune epitopes; nine recombinant events and eight reassortments with highly divergent sequences were found and analyzed. We found that sequences from Guizhou showed high genetic divergence, contributing to multiple lineages of the phylogenetic tree and also to the recombination and reassortment events. Bayesian stochastic search variable selection analysis revealed that Heilongjiang, Shaanxi, and Guizhou played important roles in HTNV evolution and migration; the virus may originate from Zhejiang Province in the eastern part of China; and the virus population size expanded from the 1980s to 1990s.

CONCLUSIONS/SIGNIFICANCE

These findings revealed the original and evolutionary features of HTNV, which will help to illustrate hantavirus epidemic trends, thus aiding in disease control and prevention.

Unraveling the Global Phylodynamic and Phylogeographic Expansion of Mycoplasma gallisepticum: Understanding the Origin and Expansion of This Pathogen in Ecuador

Mycoplasma gallisepticum (MG) is among the most significant problems in the poultry industry worldwide, representing a serious threat to international trade. Despite the fact that the mgc2 gene has been widely used for diagnostic and molecular characterization purposes, there is a lack of evidence supporting the reliability of this gene as a marker for molecular epidemiology approaches. Therefore, the current study aimed to assess the accuracy of the mgc2 gene for phylogenetic, phylodynamic, and phylogeographic evaluations. Furthermore, the global phylodynamic expansion of MG is described, and the origin and extension of the outbreak caused by MG in Ecuador were tracked and characterized. The results obtained strongly supported the use of the mgc2 gene as a reliable phylogenetic marker and accurate estimator for the temporal and phylogeographic structure reconstruction of MG. The phylodynamic analysis denoted the failures in the current policies to control MG and highlighted the imperative need to implement more sensitive methodologies of diagnosis and more efficient vaccines. Framed in Ecuador, the present study provides the first piece of evidence of the circulation of virulent field MG strains in Ecuadorian commercial poultry. The findings derived from the current study provide novel and significant insights into the origin, diversification, and evolutionary process of MG globally.

Whole genome sequencing of carbapenem-resistant Klebsiella pneumoniae: evolutionary analysis for outbreak investigation

Aim: Carbapenemase-resistant Enterobacteriaceae represents a major concern in hospital setting. Materials & methods: The evolutionary history of carbapenem-resistant Klebsiella pneumonia strains was analyzed by core genome multilocus sequence typing and Bayesian phylogenesis by whole genomes sequencing. Results: A great increase carbapenem-resistant K. pneumoniae causing blood stream infection was observed in the years 2015-2016. At multilocus sequence typing (MLST), they were prevalently ST512 and ST101. ST512 were core genome (cg)MLST 53, while ST101 mainly cgMLST453. The minimum-spanning tree, based on cgMLST, showed strains clustering based on the different STs. By Bayesian phylogenetic analysis, maximum clade credibility tree showed that strains were introduced in the year 2005 with the most probable location in the ICU ward. Two outbreaks by ST101 and ST512 strains with Tower T8 as the probable location were evidenced. Conclusion: Molecular epidemiology is a powerful tool to track the way of transmission of resistant bacteria within the hospital setting.

Islands as a crossroad of evolutionary lineages: A case study of Centaurea sect. Centaurea (Compositae) from Sardinia (Mediterranean Basin)

The Mediterranean Basin is a biodiversity hotspot, where islands play a key role because of their high biological diversity, degree of endemicity and human pressure. One of these islands, Sardinia, is a good evolutionary laboratory, especially for the study of complex genera, such as Centaurea. In particular, endemic species of Centaurea sect. Centaurea from Sardinia provides an interesting case study of plant evolution on continental islands. We attempted to clarify the processes leading to the diversification of Centaurea species on Sardinia using bi-parentally inherited nuclear markers and maternally inherited plastid markers. Our plastid results revealed the presence of five lineages of sect. Centaurea on the island. Three of them were defined as three species: C. ferulacea, C. filiformis and C. horrida. The other two lineages highlighted the complex evolutionary history of the two polyploids C. corensis and C. magistrorum. Multiple colonization events from the mainland involving the C. deusta and C. paniculata lineages among others, have led to the diversity of sect. Centaurea on Sardinia. One colonization event likely followed a southern path via the land connection between the mainland, the Calabrian Plate and Sardinia. A second pathway likely followed a northern connection, probably through the Tuscan Archipelago. Implications of these findings on conservation efforts for Centaurea endemics on Sardinia are also discussed.

Molecular epidemiology of HIV-1 infection in immigrant population in northern Italy

Human immunodeficiency virus-1 (HIV-1) is characterised by a vast genetic diversity classified into distinct phylogenetic strains and recombinant forms. We describe the HIV-1 molecular epidemiology and evolution of 129 consecutive HIV-1 positive migrants living in Milan (northern Italy). Polymerase gene sequences of 116 HIV-1 subtype-B positive patients were aligned with HIV-1 reference sequences (https://www.ncbi.nlm.nih.gov/) by using MAFFT alignment and edited by using Bioedit software. A maximum likelihood (ML) phylogenetic tree was performed by MEGA7 and was visualised by using FigTree v1.4.3. Of 129 migrants, 35 were born in Europe (28 in Eastern Europe), 70 in the Americas (67 in South America), 15 in Africa and nine in Asia; 76.4% were men who have sex with men (MSM). The serotype HIV-1-B prevailed (89.9%), followed by -C, -F1, -D and -A. Compared with 116 HIV-B patients, the 13 with HIV-non-B showed lower Nadir of CD4+ cell/mmc (P = 0.043), more frequently had sub Saharan origin (38.5 vs. 1.72%, P = 0.0001) and less frequently were MSM (40 vs. 74.5%, P = 0.02). The ML phylogenetic tree of the 116 HIV-1 subtype-B positive patients showed 13 statistically supported nodes (bootstrap > 70%). Most of the sequences included in these nodes have been isolated from male patients from the Americas and the most common risk factor was MSM. The low number of HIV-1 non-B subtype patients did not allow to perform this analysis. These results suggest a shift of HIV-1 prevention projects' focus and a continuous monitoring of HIV-1 molecular epidemiology among entry populations. Prevention efforts based on HIV molecular epidemiology may improve public health surveillance setting.

Marginal Likelihoods in Phylogenetics: A Review of Methods and Applications

By providing a framework of accounting for the shared ancestry inherent to all life, phylogenetics is becoming the statistical foundation of biology. The importance of model choice continues to grow as phylogenetic models continue to increase in complexity to better capture micro- and macroevolutionary processes. In a Bayesian framework, the marginal likelihood is how data update our prior beliefs about models, which gives us an intuitive measure of comparing model fit that is grounded in probability theory. Given the rapid increase in the number and complexity of phylogenetic models, methods for approximating marginal likelihoods are increasingly important. Here, we try to provide an intuitive description of marginal likelihoods and why they are important in Bayesian model testing. We also categorize and review methods for estimating marginal likelihoods of phylogenetic models, highlighting several recent methods that provide well-behaved estimates. Furthermore, we review some empirical studies that demonstrate how marginal likelihoods can be used to learn about models of evolution from biological data. We discuss promising alternatives that can complement marginal likelihoods for Bayesian model choice, including posterior-predictive methods. Using simulations, we find one alternative method based on approximate-Bayesian computation to be biased. We conclude by discussing the challenges of Bayesian model choice and future directions that promise to improve the approximation of marginal likelihoods and Bayesian phylogenetics as a whole.

Phylogenetic Analysis of Multi-Drug Resistant Klebsiella pneumoniae Strains From Duodenoscope Biofilm: Microbiological Surveillance and Reprocessing Improvements for Infection Prevention

Duodenoscopes have been described as potential vehicles of patient-to-patient transmission of multi-drug resistant organisms. Carbapenem-resistant Enterobacteriaceae duodenoscope related infections have been described by the Center for Disease Control and the US Food and Drug Administration consequently to outbreaks occurring in the United States. These evidences suggested that improved microbiological surveillance and endoscope design optimization could represent valid tools to improve infection control. At this aim, in this study an example of duodenoscope microbiological surveillance and reprocessing improvement analyzing strains component of bacterial biofilm by phylogenetic analysis has been proposed. From September 2016 to December 2017, duodenoscope instruments were subjected to microbial surveillance by post-reprocessing cultures of liquid collected by internal channels of instruments after injection and aspiration cycles and membrane filtration. During surveillance seventeen Klebsiella pneumoniae, of which 10/17 (58.8%) MDR and KPC strains were collected from duodenoscope instruments plus one MDR Klebsiella pneumoniae strain from the rectal swab performed before ERCP procedure in an inpatient. The surveillance allowed evidencing potential failure of reprocessing procedure and performing consequent reprocessing improvements including the contaminated instruments quarantine until their negativity. Phylogenetic analysis of whole genome sequence of duodenoscope strains plus inpatients MDR strains, showed intermixing between duodenoscopes and inpatients, as evidenced by minimum spanning tree and time-scale Maximum Clade Credibility tree. In minimum spanning tree, three groups have been evidenced. Group I including Klebsiella pneumoniae strains, isolated from inpatients before microbiological surveillance adoption; group II including intermixed Klebsiella pneumoniae strains isolated from inpatients and Klebsiella pneumoniae strains isolated from duedonoscopes and group III including Klebsiella pneumoniae strains exclusively from duedonoscope instruments. In the Maximum Credibility Tree, a statistically supported cluster including two Klebsiella pneumoniae strains from duedonoscope instruments and one strains isolated from an inpatient was showed. From the first microbiologic surveillance performed on September 2016 and after the reprocessing improvement adoption, none MDR or susceptible Klebsiella pneumoniae strain was isolated in the following surveillance periods. In conclusion, these results should encourage hospital board to perform microbiological surveillance of duodenoscopes as well as of patients, by rectal swabs culture, and rapid molecular testing for antimicrobial resistance before any endoscopic invasive procedure.

Genomic epidemiology of syphilis reveals independent emergence of macrolide resistance across multiple circulating lineages

Syphilis is a sexually transmitted infection caused by Treponema pallidum subspecies pallidum and may lead to severe complications. Recent years have seen striking increases in syphilis in many countries. Previous analyses have suggested one lineage of syphilis, SS14, may have expanded recently, indicating emergence of a single pandemic azithromycin-resistant cluster. Here we use direct sequencing of T. pallidum combined with phylogenomic analyses to show that both SS14- and Nichols-lineages are simultaneously circulating in clinically relevant populations in multiple countries. We correlate the appearance of genotypic macrolide resistance with multiple independently evolved SS14 sub-lineages and show that genotypically resistant and sensitive sub-lineages are spreading contemporaneously. These findings inform our understanding of the current syphilis epidemic by demonstrating how macrolide resistance evolves in Treponema subspecies and provide a warning on broader issues of antimicrobial resistance.

Large-Scale Comparative Analysis of Codon Models Accounting for Protein and Nucleotide Selection

There are numerous sources of variation in the rate of synonymous substitutions inside genes, such as direct selection on the nucleotide sequence, or mutation rate variation. Yet scans for positive selection rely on codon models which incorporate an assumption of effectively neutral synonymous substitution rate, constant between sites of each gene. Here we perform a large-scale comparison of approaches which incorporate codon substitution rate variation and propose our own simple yet effective modification of existing models. We find strong effects of substitution rate variation on positive selection inference. More than 70% of the genes detected by the classical branch-site model are presumably false positives caused by the incorrect assumption of uniform synonymous substitution rate. We propose a new model which is strongly favored by the data while remaining computationally tractable. With the new model we can capture signatures of nucleotide level selection acting on translation initiation and on splicing sites within the coding region. Finally, we show that rate variation is highest in the highly recombining regions, and we propose that recombination and mutation rate variation, such as high CpG mutation rate, are the two main sources of nucleotide rate variation. Although we detect fewer genes under positive selection in Drosophila than without rate variation, the genes which we detect contain a stronger signal of adaptation of dynein, which could be associated with Wolbachia infection. We provide software to perform positive selection analysis using the new model.

High-Performance Computing in Bayesian Phylogenetics and Phylodynamics Using BEAGLE

In this chapter, we focus on the computational challenges associated with statistical phylogenomics and how use of the broad-platform evolutionary analysis general likelihood evaluator (BEAGLE), a high-performance library for likelihood computation, can help to substantially reduce computation time in phylogenomic and phylodynamic analyses. We discuss computational improvements brought about by the BEAGLE library on a variety of state-of-the-art multicore hardware, and for a range of commonly used evolutionary models. For data sets of varying dimensions, we specifically focus on comparing performance in the Bayesian evolutionary analysis by sampling trees (BEAST) software between multicore central processing units (CPUs) and a wide range of graphics processing cards (GPUs). We put special emphasis on computational benchmarks from the field of phylodynamics, which combines the challenges of phylogenomics with those of modelling trait data associated with the observed sequence data. In conclusion, we show that for increasingly large molecular sequence data sets, GPUs can offer tremendous computational advancements through the use of the BEAGLE library, which is available for software packages for both Bayesian inference and maximum-likelihood frameworks.

Human hepatitis E virus circulation in Bulgaria: Deep Bayesian phylogenetic analysis for viral spread control in the country

Hepatitis E virus (HEV) infection in Bulgaria is endemic, as demonstrated by the seroprevalence of antibody against the virus in the general population and by the high prevalence of clinical cases registered. In this study, a deep Bayesian phylogenetic analysis has been performed to provide information on the genetic diversity and the spread of HEV genotypes in Bulgaria. Three different data sets of HEV virus was built for genotyping by the maximum likelihood method, for evolutionary rate estimated by Bayesian Markov Chain Monte Carlo approach, for demographic history investigation and for selective pressure analysis. The evolutionary rate for genotype 3e, was 351 × 10-3 substitution/site/year (95% highest posterior density [95% HPD]: 145 × 10 -3 -575 × 10 -3 ). The root of the time to the most recent common ancestor of the Bayesian maximum clade credibility tree of HEV 3e genotype corresponded to 1965 (HPD 95% 1949-1994). The Bulgarian sequences mainly clustered in the main clade (clade A). The monophyletic clade included all Bulgarian genotype 3e sequences. The demographic history showed a slight growth from 1995 to 2000, followed by a sort of bottleneck in 2010s, a peak in 2011 and a new growth to 2015. Selection pressure analysis did not show sites under positive pressure but 64 statistically significant sites under negative selection. Molecular epidemiological surveillance by Bayesian phylogeny of HEV virus can contribute to trace the way of human infection after contact with swine source directly or heating meat improving public health control.

HIV-2 Infection in a Migrant from Gambia: The History of the Disease Combined with Phylogenetic Analysis Revealed the Real Source of Infection

Human immunodeficiency virus type 2 (HIV-2) infection prevalence is increasing in some European countries. The increasing migratory flow from countries where HIV-2 is endemic has facilitated the spread of the virus into Europe and other regions. We describe a case of HIV-2 infection in a migrant individual in the Asylum Seekers Centre (ASC) in Italy. The patient's virus was sequenced and found to be a typical HIV-2 genotype A virus. Bayesian evolutionary analysis revealed that the HIV-2 sequence from migrant dated back to 1986 in a subcluster, including sequences from Guinea Bissau. This was coherent with the history of the migrant who lived in Guinea Bissau from his birth until 1998 when he was 13 years old. Monitoring for HIV-2 infection in migrants from western Africa is necessary using adequate molecular tools to improve the diagnosis and understand the real origin of infection.

Phylogeography of H5N1 avian influenza virus in Indonesia

Highly pathogenic avian influenza (HPAI) viruses of the H5N1 subtype are a major concern to human and animal health in Indonesia. This study aimed to characterize transmission dynamics of H5N1 over time using novel Bayesian phylogeography methods to identify factors which have influenced the spread of H5N1 in Indonesia. We used publicly available hemagglutinin sequence data sampled between 2003 and 2016 to model ancestral state reconstruction of HPAI H5N1 evolution. We found strong support for H5N1 transmission routes between provinces in Java Island and inter-island transmissions, such as between Nusa Tenggara and Kalimantan Islands, not previously described. The spread is consistent with wild bird flyways and poultry trading routes. H5N1 migration was associated with the regions of high chicken densities and low human development indices. These results can be used to inform more targeted planning of H5N1 control and prevention activities in Indonesia.

Genotype I hepatitis A virus introduction in Italy: Bayesian phylogenetic analysis to date different epidemics

Despite a significant decrease in acute hepatitis A in the last 2 decades in Italy, outbreaks were observed occurring mostly in southern Italy. In this study, Bayesian phylogenetic analysis was used to analyze the origin of these epidemics. With this aim, 5 different data sets of hepatitis A virus sequences were built to perform genotyping by the neighbor-joining method to estimate the evolutionary rates by using a Bayesian Markov chain Monte Carlo approach and to investigate the demographic history by independent Markov chain Monte Carlo runs enforcing both a strict and relaxed clock. The estimated mean value of the evolutionary rate, representing Ia and Ib strains, was 1.21 × 10-3 and 2.0 × 10-3 substitutions/site/year, respectively. The Bayesian maximum clade credibility tree of hepatitis A virus (HAV) Ia and Ib strains showed that Italian sequences mostly formed separate clusters. The root of the time for the most recent common ancestor (tMRCA) for HAV Ia and Ib strains dated back to 1981 and to 1988, respectively, showing in both cases different epidemic entrances. Phylodynamic analysis showed that genotype Ia increased in 1997, when the Apulia epidemic started, then suffered a bottleneck, probably consequent to vaccination and to the herd immunity, followed by a new increase in virus population in the years 2013-2014 consequent to the epidemic caused by the ingestion of mixed frozen berries. A similar trend without an evident bottleneck was observed also in the case of genotype Ib. In conclusion, the Bayesian phylogenetic analysis represents a good tool to measure the effectiveness of the public health plans used for HAV control.

Phylogeny of the Genus Dichotrachelus (Coleoptera: Curculionidae: Cyclominae)

A phylogenetic analysis of the genus Dichotrachelus (Curculionidae: Cyclominae) was carried out, based on a morphological matrix and, for some species, on mitochondrial cytochrome oxidase I sequences. Bayesian Inference, Maximum Likelihood and Maximum Parsimony were implemented and the results were compared. The genus is found to be isolated in the subfamily, not related to the only other Palaearctic tribe (Hipporhinini) and possibly nearer to the south-American genera of Cyclominae of the tribe Listroderini. Among these, Macrostyphlus is also equally associated to mosses as the host plant. In Dichotrachelus, two main clades were recognized, one distributed in the western part of the Mediterranean region (Iberian Peninsula, northern Africa and southern France) and the second distributed in the Alps and Apennines. Within each clade, some differentiated monophyletic subgroups could be identified. An evaluation of the most important characters that led to the phylogenetic reconstruction indicated the male genital sclerite as the most useful structure to characterize the different clades.

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

PREMISE OF THE STUDY

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.

METHODS

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.

KEY RESULTS

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.

CONCLUSIONS

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.

Pleistocene North African genomes link Near Eastern and sub-Saharan African human populations

North Africa is a key region for understanding human history, but the genetic history of its people is largely unknown. We present genomic data from seven 15,000-year-old modern humans, attributed to the Iberomaurusian culture, from Morocco. We find a genetic affinity with early Holocene Near Easterners, best represented by Levantine Natufians, suggesting a pre-agricultural connection between Africa and the Near East. We do not find evidence for gene flow from Paleolithic Europeans to Late Pleistocene North Africans. The Taforalt individuals derive one-third of their ancestry from sub-Saharan Africans, best approximated by a mixture of genetic components preserved in present-day West and East Africans. Thus, we provide direct evidence for genetic interactions between modern humans across Africa and Eurasia in the Pleistocene.

In-depth phylodynamics, evolutionary analysis and in silico predictions of universal epitopes of Influenza A subtypes and Influenza B viruses

This study applied High-Performance Computing to explore the high-resolution phylodynamics and the evolutionary dynamics of Influenza viruses (IVs) A and B and their subtypes in-depth to identify peptide-based candidates for broad-spectrum vaccine targets. For this purpose, we collected all the available Hemagglutinin (HA) and Neuraminidase (NA) nucleotide and amino acid sequences (more than 100,000) of IVs isolated from all the reservoirs and intermediate hosts species, from all geographic ranges and from different isolation sources, covering a period of almost one century of sampling years. We highlight that despite the constant changes in Influenza evolutionary dynamics over time, which are responsible for the generation of novel strains, our study identified the presence of highly conserved peptides distributed in all the HA and NA found in H1-H18 and N1-N11 IAV subtypes and IBVs. Additionally, predictions through computational methods showed that these peptides could have a strong affinity to bind to HLA-A∗02:01/HLA-DRB1∗01:01 major histocompatibility complex (MHC) class I and II molecules, therefore acting as a double ligand. Moreover, epitope prediction in antigens from pathogens responsible for secondary bacterial infection was also studied. These findings show that the regions mapped here may potentially be explored as universal epitope-based candidates to develop therapies leading to a broader response against the infection induced by all circulating IAVs, IBVs and Influenza-associated bacterial infections.

More on the Best Evolutionary Rate for Phylogenetic Analysis

The accumulation of genome-scale molecular data sets for nonmodel taxa brings us ever closer to resolving the tree of life of all living organisms. However, despite the depth of data available, a number of studies that each used thousands of genes have reported conflicting results. The focus of phylogenomic projects must thus shift to more careful experimental design. Even though we still have a limited understanding of what are the best predictors of the phylogenetic informativeness of a gene, there is wide agreement that one key factor is its evolutionary rate; but there is no consensus as to whether the rates derived as optimal in various analytical, empirical, and simulation approaches have any general applicability. We here use simulations to infer optimal rates in a set of realistic phylogenetic scenarios with varying tree sizes, numbers of terminals, and tree shapes. Furthermore, we study the relationship between the optimal rate and rate variation among sites and among lineages. Finally, we examine how well the predictions made by a range of experimental design methods correlate with the observed performance in our simulations.We find that the optimal level of divergence is surprisingly robust to differences in taxon sampling and even to among-site and among-lineage rate variation as often encountered in empirical data sets. This finding encourages the use of methods that rely on a single optimal rate to predict a gene's utility. Focusing on correct recovery either of the most basal node in the phylogeny or of the entire topology, the optimal rate is about 0.45 substitutions from root to tip in average Yule trees and about 0.2 in difficult trees with short basal and long-apical branches, but all rates leading to divergence levels between about 0.1 and 0.5 perform reasonably well.Testing the performance of six methods that can be used to predict a gene's utility against our simulation results, we find that the probability of resolution, signal-noise analysis, and Fisher information are good predictors of phylogenetic informativeness, but they require specification of at least part of a model tree. Likelihood quartet mapping also shows very good performance but only requires sequence alignments and is thus applicable without making assumptions about the phylogeny. Despite them being the most commonly used methods for experimental design, geometric quartet mapping and the integration of phylogenetic informativeness curves perform rather poorly in our comparison. Instead of derived predictors of phylogenetic informativeness, we suggest that the number of sites in a gene that evolve at near-optimal rates (as inferred here) could be used directly to prioritize genes for phylogenetic inference. In combination with measures of model fit, especially with respect to compositional biases and among-site and among-lineage rate variation, such an approach has the potential to greatly improve marker choice and should be tested on empirical data.

The genetic diversity of hepatitis A genotype I in Bulgaria

The purpose of this study was to analyze sequences of hepatitis A virus (HAV) Ia and Ib genotypes from Bulgarian patients to investigate the molecular epidemiology of HAV genotype I during the years 2012 to 2014. Around 105 serum samples were collected by the Department of Virology of the National Center of Infectious and Parasitic Diseases in Bulgaria. The sequenced region encompassed the VP1/2A region of HAV genome. The sequences obtained from the samples were 103. For the phylogenetic analyses, 5 datasets were built to investigate the viral gene in/out flow among distinct HAV subpopulations in different geographic areas and to build a Bayesian dated tree, Bayesian phylogenetic and migration pattern analyses were performed. HAV Ib Bulgarian sequences mostly grouped into a single clade. This indicates that the Bulgarian epidemic is partially compartmentalized. It originated from a limited number of viruses and then spread through fecal-oral local transmission. HAV Ia Bulgarian sequences were intermixed with European sequences, suggesting that an Ia epidemic is not restricted to Bulgaria but can affect other European countries. The time-scaled phylogeny reconstruction showed the root of the tree dating in 2008 for genotype Ib and in 1999 for genotype Ia with a second epidemic entrance in 2003. The Bayesian skyline plot for genotype Ib showed a slow but continuous growth, sustained by fecal-oral route transmission. For genotype Ia, there was an exponential growth followed by a plateau, which suggests better infection control. Bidirectional viral flow for Ib genotype, involving different Bulgarian areas, was observed, whereas a unidirectional flow from Sofia to Ihtiman for genotype Ia was highlighted, suggesting the fecal-oral transmission route for Ia.

Ancient symbiosis confers desiccation resistance to stored grain pest beetles

Microbial symbionts of insects provide a range of ecological traits to their hosts that are beneficial in the context of biotic interactions. However, little is known about insect symbiont-mediated adaptation to the abiotic environment, for example, temperature and humidity. Here, we report on an ancient clade of intracellular, bacteriome-located Bacteroidetes symbionts that are associated with grain and wood pest beetles of the phylogenetically distant families Silvanidae and Bostrichidae. In the saw-toothed grain beetle Oryzaephilus surinamensis, we demonstrate that the symbionts affect cuticle thickness, melanization and hydrocarbon profile, enhancing desiccation resistance and thereby strongly improving fitness under dry conditions. Together with earlier observations on symbiont contributions to cuticle biosynthesis in weevils, our findings indicate that convergent acquisitions of bacterial mutualists represented key adaptations enabling diverse pest beetle groups to survive and proliferate under the low ambient humidity that characterizes dry grain storage facilities.

Population dynamics of hepatitis C virus subtypes in injecting drug users on methadone maintenance treatment in China associated with economic and health reform

The extensive genetic heterogeneity of hepatitis C virus (HCV) requires in-depth understanding of the population dynamics of different viral subtypes for more effective control of epidemic outbreaks. We analysed HCV sequences data from 125 participants in Wuhan, China. These participants were newly infected by subtype 1b (n=13), 3a (n=15), 3b (n=50) and 6a (n=39) while on methadone maintenance treatment (MMT). Bayesian phylogenies and demographic histories were inferred for these subtypes. Participants infected with HCV-1b and 3a were clustered in well-supported monophyletic clades, indicating local subepidemics. Subtypes 3b and 6a strains were intermixed with other Chinese isolates, as well as isolates from other Asian countries, reflecting ongoing across geographic boundary transmissions. Subtypes 1b and 3a declined continuously during the past ten years, consistent with the health and economic reform in China, while subtype 3b showed ongoing exponential growth and 6a was characterized by several epidemic waves, possibly related to the recently growing number of travellers between China and other Asian countries. In conclusion, results of this study suggest that HCV subtype 3b and 6a subepidemics in China are currently not under control, and new epidemic waves may emerge given the rapid increase in international travelling following substantial economic growth.

Adaptive MCMC in Bayesian phylogenetics: an application to analyzing partitioned data in BEAST

MOTIVATION

Advances in sequencing technology continue to deliver increasingly large molecular sequence datasets that are often heavily partitioned in order to accurately model the underlying evolutionary processes. In phylogenetic analyses, partitioning strategies involve estimating conditionally independent models of molecular evolution for different genes and different positions within those genes, requiring a large number of evolutionary parameters that have to be estimated, leading to an increased computational burden for such analyses. The past two decades have also seen the rise of multi-core processors, both in the central processing unit (CPU) and Graphics processing unit processor markets, enabling massively parallel computations that are not yet fully exploited by many software packages for multipartite analyses.

RESULTS

We here propose a Markov chain Monte Carlo (MCMC) approach using an adaptive multivariate transition kernel to estimate in parallel a large number of parameters, split across partitioned data, by exploiting multi-core processing. Across several real-world examples, we demonstrate that our approach enables the estimation of these multipartite parameters more efficiently than standard approaches that typically use a mixture of univariate transition kernels. In one case, when estimating the relative rate parameter of the non-coding partition in a heterochronous dataset, MCMC integration efficiency improves by > 14-fold.

AVAILABILITY AND IMPLEMENTATION

Our implementation is part of the BEAST code base, a widely used open source software package to perform Bayesian phylogenetic inference.

CONTACT

guy.baele@kuleuven.be.

SUPPLEMENTARY INFORMATION

Supplementary data are available at Bioinformatics online.

Multi-drug resistant Klebsiella pneumoniae strains circulating in hospital setting: whole-genome sequencing and Bayesian phylogenetic analysis for outbreak investigations

Carbapenems resistant Enterobacteriaceae infections are increasing worldwide representing an emerging public health problem. The application of phylogenetic and phylodynamic analyses to bacterial whole genome sequencing (WGS) data have become essential in the epidemiological surveillance of multi-drug resistant nosocomial pathogens. Between January 2012 and February 2013, twenty-one multi-drug resistant K. pneumoniae strains, were collected from patients hospitalized among different wards of the University Hospital Campus Bio-Medico. Epidemiological contact tracing of patients and Bayesian phylogenetic analysis of bacterial WGS data were used to investigate the evolution and spatial dispersion of K. pneumoniae in support of hospital infection control. The epidemic curve of incident K. pneumoniae cases showed a bimodal distribution of cases with two peaks separated by 46 days between November 2012 and January 2013. The time-scaled phylogeny suggested that K. pneumoniae strains isolated during the study period may have been introduced into the hospital setting as early as 2007. Moreover, the phylogeny showed two different epidemic introductions in 2008 and 2009. Bayesian genomic epidemiology is a powerful tool that promises to improve the surveillance and control of multi-drug resistant pathogens in an effort to develop effective infection prevention in healthcare settings or constant strains reintroduction.

Phylodynamic applications in 21st century global infectious disease research

BACKGROUND

Phylodynamics, the study of the interaction between epidemiological and pathogen evolutionary processes within and among populations, was originally defined in the context of rapidly evolving viruses and used to characterize transmission dynamics. The concept of phylodynamics has evolved since the early 21st century, extending its reach to slower-evolving pathogens, including bacteria and fungi, and to the identification of influential factors in disease spread and pathogen population dynamics.

RESULTS

The phylodynamic approach has now become a fundamental building block for the development of comparative phylogenetic tools capable of incorporating epidemiological surveillance data with molecular sequences into a single statistical framework. These innovative tools have greatly enhanced scientific investigations of the temporal and geographical origins, evolutionary history, and ecological risk factors associated with the growth and spread of viruses such as human immunodeficiency virus (HIV), Zika, and dengue and bacteria such as Methicillin-resistant Staphylococcus aureus.

CONCLUSIONS

Capitalizing on an extensive review of the literature, we discuss the evolution of the field of infectious disease epidemiology and recent accomplishments, highlighting the advancements in phylodynamics, as well as the challenges and limitations currently facing researchers studying emerging pathogen epidemics across the globe.

Species delimitation and phylogeography of the Pectenia species-complex: A misunderstood case of species-pairs in lichenized fungi, where reproduction mode does not delimit lineages

The main goal of this work was to study species boundaries in the genus Pectenia and elucidate the biogeographic history of the four currently accepted species. To accomplish this, we included 92 specimens across the range of Pectenia in Europe and northern Africa. We used three nuclear loci and assessed species circumscription using two Bayesian coalescent-based methods and the Bayes Factor approach. We reviewed the value of reproductive mode and other morphological features as predictors of monophyletic groups. Our results suggest that the production of asexual propagules and sexual structures are not characterizing monophyletic groups. The genus includes two morphologically well-characterized main lineages, where one lineage is composed by two sub-lineages that are with a case of cryptic speciation explained by a biogeographic pattern. We suggest treating the two lineages as two species, which are characterized by lobe structure: Pectenia plumbea and P. atlantica. Both of these species include samples with asexual propagules and apothecia, and thus do not correspond to any of the earlier morphologically defined species. The results of the biogeographic analysis indicate that the Mediterranean basin is the most likely ancestral distribution area of P. plumbea, whereas P. atlantica probably originated in Macaronesia.

Origin and evolutionary dynamics of Hepatitis B virus (HBV) genotype E in Madagascar

Africa is one of the endemic regions of HBV infection. In particular, genotype E is highly endemic in most of sub-Saharan Africa such as West African countries where it represents more than 90% of total infections. Madagascar, which is classified as a high endemic area for HBV and where the most prevalent genotype is E, might play a relevant role in the dispersion of this genotype due to its crucial position in the Indian Ocean. The aim of this study was to investigate the origin, population dynamics, and circulation of HBV-E genotype in Madagascar through high-resolution phylogenetic and phylodynamic approaches. The phylogenetic tree indicated that Malagasy isolates were intermixed and closely related with sequences mostly from West African countries. The Bayesian tree highlighted three statistically supported clusters of Malagasy strains which dated back to the years 1981 (95% HPD: 1971-1992), 1986 (95% HPD: 1974-1996), and 1989 (95% HPD: 1974-2001). Population dynamics analysis showed an exponential increase in the number of HBV-E infections approximately from the year 1975 until 2000s. The migration analysis was also performed and a dynamic pattern of gene flow was identified. In conclusion, this study confirms previous observation of HBV-E circulation in Africa and expands these findings at Madagascar demonstrating its recent introduction, and highlighting the role of the African countries in the spread of HBV-E genotype. Further studies on molecular epidemiology of HBV genotype E are needed to clarify the evolutionary history of this genotype.

Emerging Concepts of Data Integration in Pathogen Phylodynamics

Phylodynamics has become an increasingly popular statistical framework to extract evolutionary and epidemiological information from pathogen genomes. By harnessing such information, epidemiologists aim to shed light on the spatio-temporal patterns of spread and to test hypotheses about the underlying interaction of evolutionary and ecological dynamics in pathogen populations. Although the field has witnessed a rich development of statistical inference tools with increasing levels of sophistication, these tools initially focused on sequences as their sole primary data source. Integrating various sources of information, however, promises to deliver more precise insights in infectious diseases and to increase opportunities for statistical hypothesis testing. Here, we review how the emerging concept of data integration is stimulating new advances in Bayesian evolutionary inference methodology which formalize a marriage of statistical thinking and evolutionary biology. These approaches include connecting sequence to trait evolution, such as for host, phenotypic and geographic sampling information, but also the incorporation of covariates of evolutionary and epidemic processes in the reconstruction procedures. We highlight how a full Bayesian approach to covariate modeling and testing can generate further insights into sequence evolution, trait evolution, and population dynamics in pathogen populations. Specific examples demonstrate how such approaches can be used to test the impact of host on rabies and HIV evolutionary rates, to identify the drivers of influenza dispersal as well as the determinants of rabies cross-species transmissions, and to quantify the evolutionary dynamics of influenza antigenicity. Finally, we briefly discuss how data integration is now also permeating through the inference of transmission dynamics, leading to novel insights into tree-generative processes and detailed reconstructions of transmission trees. [Bayesian inference; birth–death models; coalescent models; continuous trait evolution; covariates; data integration; discrete trait evolution; pathogen phylodynamics.

Domestication and Divergence of Saccharomyces cerevisiae Beer Yeasts

Whereas domestication of livestock, pets, and crops is well documented, it is still unclear to what extent microbes associated with the production of food have also undergone human selection and where the plethora of industrial strains originates from. Here, we present the genomes and phenomes of 157 industrial Saccharomyces cerevisiae yeasts. Our analyses reveal that today’s industrial yeasts can be divided into five sublineages that are genetically and phenotypically separated from wild strains and originate from only a few ancestors through complex patterns of domestication and local divergence. Large-scale phenotyping and genome analysis further show strong industry-specific selection for stress tolerance, sugar utilization, and flavor production, while the sexual cycle and other phenotypes related to survival in nature show decay, particularly in beer yeasts. Together, these results shed light on the origins, evolutionary history, and phenotypic diversity of industrial yeasts and provide a resource for further selection of superior strains.

PaperClip

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We sequenced and phenotyped 157 S. cerevisiae yeasts

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Present-day industrial yeasts originate from only a few domesticated ancestors

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Beer yeasts show strong genetic and phenotypic hallmarks of domestication

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Domestication of industrial yeasts predates microbe discovery

Klebsiella pneumoniae blaKPC-3 nosocomial epidemic: Bayesian and evolutionary analysis

K. pneumoniae isolates carrying blaKPC-3 gene were collected to perform Bayesian phylogenetic and selective pressure analysis and to apply homology modeling to the KPC-3 protein. A dataset of 44 bla_kpc-3 gene sequences from clinical isolates of K. pneumoniae was used for Bayesian phylogenetic, selective pressure analysis and homology modeling. The mean evolutionary rate for bla_kpc-3 gene was 2.67×10^-3 substitution/site/year (95% HPD: 3.4×10^-4-5.59×10^-3). The root of the Bayesian tree dated back to the year 2011 (95% HPD: 2007-2012). Two main clades (I and II) were identified. The population dynamics analysis showed an exponential growth from 2011 to 2013 and the reaching of a plateau. The phylogeographic reconstruction showed that the root of the tree had a probable common ancestor in the general surgery ward. Selective pressure analysis revealed twelve positively selected sites. Structural analysis of KPC-3 protein predicted that the amino acid mutations are destabilizing for the protein and could alter the substrate specificity. Phylogenetic analysis and homology modeling of blaKPC-3 gene could represent a useful tool to follow KPC spread in nosocomial setting and to evidence amino acid substitutions altering the substrate specificity.

Revisiting Recombination Signal in the Tick-Borne Encephalitis Virus: A Simulation Approach

The hypothesis of wide spread reticulate evolution in Tick-Borne Encephalitis virus (TBEV) has recently gained momentum with several publications describing past recombination events involving various TBEV clades. Despite a large body of work, no consensus has yet emerged on TBEV evolutionary dynamics. Understanding the occurrence and frequency of recombination in TBEV bears significant impact on epidemiology, evolution, and vaccination with live vaccines. In this study, we investigated the possibility of detecting recombination events in TBEV by simulating recombinations at several locations on the virus' phylogenetic tree and for different lengths of recombining fragments. We derived estimations of rates of true and false positive for the detection of past recombination events for seven recombination detection algorithms. Our analytical framework can be applied to any investigation dealing with the difficult task of distinguishing genuine recombination signal from background noise. Our results suggest that the problem of false positives associated with low detection P-values in TBEV, is more insidious than generally acknowledged. We reappraised the recombination signals present in the empirical data, and showed that reliable signals could only be obtained in a few cases when highly genetically divergent strains were involved, whereas false positives were common among genetically similar strains. We thus conclude that recombination among wild-type TBEV strains may occur, which has potential implications for vaccination with live vaccines, but that these events are surprisingly rare.

Genomic Epidemiology of Methicillin-Resistant Staphylococcus aureus in a Neonatal Intensive Care Unit

Despite infection prevention efforts, neonatal intensive care unit (NICU) patients remain at risk of Methicillin-resistant Staphylococcus aureus (MRSA) infection. Modes of transmission for healthcare-associated (HA) and community-associated (CA) MRSA remain poorly understood and may vary by genotype, hindering the development of effective prevention and control strategies. From 2008–2010, all patients admitted to a level III NICU were screened for MRSA colonization, and all available isolates were spa-typed. Spa-type t008, the most prevalent CA- genotype in the United States, spa-type t045, a HA- related genotype, and a convenience sample of strains isolated from 2003–2011, underwent whole-genome sequencing and phylodynamic analysis. Patient risk factors were compared between colonized and noncolonized infants, and virulence and resistance genes compared between spa-type t008 and non-t008 strains. Epidemiological and genomic data were used to estimate MRSA importations and acquisitions through transmission reconstruction. MRSA colonization was identified in 9.1% (177/1940) of hospitalized infants and associated with low gestational age and birth weight. Among colonized infants, low gestational age was more common among those colonized with t008 strains. Our data suggest that approximately 70% of colonizations were the result of transmission events within the NICU, with the remainder likely to reflect importations of “outside” strains. While risk of transmission within the NICU was not affected by spa-type, patterns of acquisition and importation differed between t008 and t045 strains. Phylodynamic analysis showed the effective population size of spa-type t008 has been exponentially increasing in both community and hospital, with spa-type t008 strains possessed virulence genes not found among t045 strains; t045 strains, in contrast, appeared to be of more recent origin, with a possible hospital source. Our data highlight the importance of both intra-NICU transmission and recurrent introductions in maintenance of MRSA colonization within the NICU environment, as well as spa-type-specific differences in epidemiology.

The global spread of Middle East respiratory syndrome: an analysis fusing traditional epidemiological tracing and molecular phylodynamics

BACKGROUND

Since its discovery in 2012, over 1700 confirmed cases of Middle East Respiratory Syndrome (MERS) have been documented worldwide and more than a third of those cases have died. While the greatest number of cases has occurred in Saudi Arabia, the recent export of MERS-coronavirus (MERS-CoV) to Republic of Korea showed that a pandemic is a possibility that cannot be ignored. Due to the deficit of knowledge in transmission methodology, targeted treatment and possible vaccines, understanding this virus should be a priority. Our aim was to combine epidemiological data from literature with genetic information from viruses sequenced around the world to present a phylodynamic picture of MERS spread molecular level to global scale.

METHODS

We performed a qualitative meta-analysis of all laboratory confirmed cases worldwide to date based on literature, with emphasis on international transmission and healthcare associated infections. In parallel, we used publicly available MERS-CoV genomes from GenBank to create a phylogeographic tree, detailing geospatial timeline of viral evolution.

RESULTS

Several healthcare associated outbreaks starting with the retrospectively identified hospital outbreak in Jordan to the most recent outbreak in Riyadh, Saudi Arabia have occurred. MERS has also crossed many oceans, entering multiple nations in eight waves between 2012 and 2015. In this paper, the spatiotemporal history of MERS cases, as documented epidemiologically, was examined by Bayesian phylogenetic analysis. Distribution of sequences into geographic clusters and interleaving of MERS-CoV sequences from camels among those isolated from humans indicated that multiple zoonotic introductions occurred in endemic nations. We also report a summary of basic reproduction numbers for MERS-CoV in humans and camels.

CONCLUSION

Together, these analyses can help us identify factors associated with viral evolution and spread as well as establish efficacy of infection control measures. The results are especially pertinent to countries without current MERS-CoV endemic, since their unfamiliarity makes them particularly susceptible to uncontrollable spread of a virus that may be imported by travelers.

The phylogenetic and evolutionary history of Kokobera virus

OBJECTIVE

To estimate the genetic diversity of Kokobera virus, the date of origin and the spread among different viruses in the endemic regions of Australia.

METHODS

Two datasets were built. The first consisting of 29 sequences of the NS5/3' UTR region of Kokobera group downloaded from GenBank, the second including only 24 sequences of Kokobera viruses, focus is on this group.

RESULTS

Bayesian time analysis revealed two different entries in Australia of Kokobera virus in the 50s years with the dated ancestor in 1861 year. Clades A and B showed a clear separation of the Kokobera sequences according to the geographic region.

CONCLUSIONS

Data from the study showed as Kokobera virus, despite of its ancient origin and its circulation before the European colonization, remained limited to the Australian country and nowadays limited mostly to the regions were Australian marsupials are mostly found.