Detecting Signatures Of Selection In Regulatory Variation

A substantial amount of phenotypic diversity results from changes in gene regulation. Understanding how regulatory diversity evolves is therefore a key priority in identifying mechanisms of adaptive change. However, in contrast to powerful models of sequence evolution, we lack a consensus model of regulatory evolution. Furthermore, recent work has shown that many of the comparative approaches used to study gene regulation are subject to biases that can lead to false signatures of selection. In this review, we first outline the main approaches for describing regulatory evolution and their inherent biases. Next, we bridge the gap between the fields of comparative phylogenetic methods and transcriptomics to reinforce the main pitfalls of inferring regulatory selection and use simulation studies to show that shifts in tissue composition can heavily bias inferences of selection. We close by highlighting the multi-dimensional nature of regulatory variation and identifying major, unanswered questions in disentangling how selection acts on the transcriptome.

HIV Protease and Integrase Empirical Substitution Models of Evolution: Protein-Specific Models Outperform Generalist Models

Diverse phylogenetic methods require a substitution model of evolution that should mimic, as accurately as possible, the real substitution process. At the protein level, empirical substitution models have traditionally been based on a large number of different proteins from particular taxonomic levels. However, these models assume that all of the proteins of a taxonomic level evolve under the same substitution patterns. We believe that this assumption is highly unrealistic and should be relaxed by considering protein-specific substitution models that account for protein-specific selection processes. In order to test this hypothesis, we inferred and evaluated four new empirical substitution models for the protease and integrase of HIV and other viruses. We found that these models more accurately fit, compared with any of the currently available empirical substitution models, the evolutionary process of these proteins. We conclude that evolutionary inferences from protein sequences are more accurate if they are based on protein-specific substitution models rather than taxonomic-specific (generalist) substitution models. We also present four new empirical substitution models of protein evolution that could be useful for phylogenetic inferences of viral protease and integrase.

Real-time and remote MCMC trace inspection with Beastiary

Bayesian phylogenetic methods have gained substantial popularity in the last decade, due to their ability to incorporate independent information and fit complex models. Most Bayesian implementations rely on Markov chain Monte Carlo (MCMC), which in turn requires careful interpretation of the output to assess the statistical validity of any resulting inferences. Here we describe Beastiary, a package for real-time and remote inspection of log flies generated by MCMC analysis commonly utilised in Bayesian phylogenetic analysis. Beastiary is an easily deployed web-sever that can be used to summarise and visualise the output of many popular software packages including BEAST, BEAST2, RevBayes, and MrBayes. We describe the overall design and implementation of Beastiary and some typical use cases, with a particular focus on the capability of monitoring analyses from remote servers.

Returning to the roots: resolution, reproducibility, and robusticity in the phylogenetic inference of Dissorophidae (Amphibia: Temnospondyli)

The phylogenetic relationships of most Paleozoic tetrapod clades remain poorly resolved, which is variably attributed to a lack of study, the limitations of inference from phenotypic data, and constant revision of best practices. While refinement of phylogenetic methods continues to be important, any phylogenetic analysis is inherently constrained by the underlying dataset that it analyzes. Therefore, it becomes equally important to assess the accuracy of these datasets, especially when a select few are repeatedly propagated. While repeat analyses of these datasets may appear to constitute a working consensus, they are not in fact independent, and it becomes especially important to evaluate the accuracy of these datasets in order to assess whether a seeming consensus is robust. Here I address the phylogeny of the Dissorophidae, a speciose clade of Paleozoic temnospondyls. This group is an ideal case study among temnospondyls for exploring phylogenetic methods and datasets because it has been extensively studied (eight phylogenetic studies to date) but with most (six studies) using a single matrix that has been propagated with very little modification. In spite of the conserved nature of the matrix, dissorophid studies have produced anything but a conserved topology. Therefore, I analyzed an independently designed matrix, which recovered less resolution and some disparate nodes compared to previous studies. In order to reconcile these differences, I carefully examined previous matrices and analyses. While some differences are a matter of personal preference (e.g., analytical software), others relate to discrepancies with respect to what are currently considered as best practices. The most concerning discovery was the identification of pervasive dubious scorings that extend back to the origins of the widely propagated matrix. These include scores for skeletal features that are entirely unknown in a given taxon (e.g., postcrania in Cacops woehri) and characters for which there appear to be unstated working assumptions to scoring that are incompatible with the character definitions (e.g., scoring of taxa with incomplete skulls for characters based on skull length). Correction of these scores and other pervasive errors recovered a distinctly less resolved topology than previous studies, more in agreement with my own matrix. This suggests that previous analyses may have been compromised, and that the only real consensus of dissorophid phylogeny is the lack of one.

Revticulate: An R framework for interaction with RevBayes

1: Phylogenetic methods are increasingly complex. Researchers need to make many choices about how to model different aspects of the data appropriately. It is increasingly common to deploy hierarchical Bayesian models in which different data types may be described by different processes. This necessitates tools to help users understand model assumptions more clearly.2: We describe the package \code{Revticulate}, which provides an R-based interface to the software RevBayes. RevBayes is a Bayesian phylogenetics program that implements an R-like computing language, but does not interface with R itself. Revticulate was designed to allow communication between an R session, and all of its associated capabilities, such as plotting and simulation, and a RevBayes session.3: Revticulate can be used to copy objects from RevBayes into R. We provide several usage examples demonstrating how objects, such as such as random variables drawn from probability distributions and phylogenetic trees, can be generated in RevBayes. We then show how these objects can be used with R's phylogenetic ecosystem to plot a phylogenetic tree, or with base R functions to simulate the behavior of a particular probability. 4: Revticulate is a broadly useful software. Revticulate can be used alongside popular document preparation packages, such as Knitr and pkgdown to generate attractive reports, tutorials, and websites. This means that researchers who are looking to communicate their work in RevBayes can do that very easily using Revticulate, enabling rapid generation of reproducible research outputs.

Bayesian phylogenetic analysis of linguistic data using BEAST

Bayesian phylogenetic methods provide a set of tools to efficiently evaluate large linguistic datasets by reconstructing phylogenies—family trees—that represent the history of language families. These methods provide a powerful way to test hypotheses about prehistory, regarding the subgrouping, origins, expansion, and timing of the languages and their speakers. Through phylogenetics, we gain insights into the process of language evolution in general and into how fast individual features change in particular. This article introduces Bayesian phylogenetics as applied to languages. We describe substitution models for cognate evolution, molecular clock models for the evolutionary rate along the branches of a tree, and tree generating processes suitable for linguistic data. We explain how to find the best-suited model using path sampling or nested sampling. The theoretical background of these models is supplemented by a practical tutorial describing how to set up a Bayesian phylogenetic analysis using the software tool BEAST2.

Latrocimicinae completes the phylogeny of Cimicidae: meeting old morphologic data rather than modern host phylogeny

The family Cimicidae includes obligate hematophagous ectoparasites (bed bugs and their relatives) with high veterinary/medical importance. The evolutionary relationships of Cimicidae and their hosts have recently been reported in a phylogenetic context, but in the relevant study, one of the six subfamilies, the bat-specific Latrocimicinae, was not represented. In this study the only known species of Latrocimicinae, i.e., Latrocimex spectans, was analyzed with molecular and phylogenetic methods based on four (two nuclear and two mitochondrial) genetic markers. The completed subfamily-level phylogeny of Cimicidae showed that Latrocimicinae is most closely related to Haematosiphoninae (ectoparasites of birds and humans), with which it shares systematically important morphologic characters, but not hosts. Moreover, in the phylogenetic analyses, cimicid bugs that are known to infest phylogenetically distant bat hosts clustered together (e.g., Leptocimex and Stricticimex within Cacodminae), while cimicid subfamilies (Latrocimicinae, Primicimicinae) that are known to infest bat hosts from closely related superfamilies clustered distantly. In conclusion, adding Latrocimicinae significantly contributed to the resolution of the phylogeny of Cimicidae. The close phylogenetic relationship between Latrocimicinae and Haematosiphoninae is consistent with long-known morphologic data. At the same time, phylogenetic relationships of genera within subfamilies are inconsistent with the phylogeny of relevant hosts. Graphical abstract

Macroevolutionary Trade-Offs and Trends in Life History Traits of Cephalopods Through a Comparative Phylogenetic Approach

One of the major mechanisms responsible for the animals’ fitness dynamics is fecundity. Fecundity as a trait does not evolve independently, and rather interacts with other traits such as body and egg size. Here, our aim was to correctly infer the macroevolutionary trade-offs between body length, egg length, and potential fecundity, using cephalopods as study model. The correlated evolution among those traits was inferred by comparative phylogenetic methods. Literature data on biological and reproductive traits (body length, egg length, and potential fecundity) was obtained for 90 cephalopod species, and comparative phylogenetic methods based on a previous molecular phylogeny were used to test the correlated evolution hypothesis. Additionally, we estimated the phylogenetic signal and fitted five different evolutionary models to each trait. All traits showed high phylogenetic signal, and the selected model suggested an evolutionary trend toward increasing body length, egg length, and fecundity in relation to the ancestral state. Evidence of correlated evolution between body length and fecundity was observed, although this relationship was not detected between body length and egg length. The robust inverse relationship between fecundity and egg length indicates that cephalopods evolved a directional selection that favored an increase of fecundity and a reduction of egg length in larger species, or an increase in egg length with the concomitant reduction of fecundity and body length in order to benefit offspring survival. The use of phylogenetic comparative methods allowed us to properly detect macroevolutionary trade-offs.

Phylogenetic reconciliation reveals extensive ancestral recombination in Sarbecoviruses and the SARS-CoV-2 lineage

An accurate understanding of the evolutionary history of rapidly-evolving viruses like SARS-CoV-2, responsible for the COVID-19 pandemic, is crucial to tracking and preventing the spread of emerging pathogens. However, viruses undergo frequent recombination, which makes it difficult to trace their evolutionary history using traditional phylogenetic methods. Here, we present a phylogenetic workflow, virDTL, for analyzing viral evolution in the presence of recombination. Our approach leverages reconciliation methods developed for inferring horizontal gene transfer in prokaryotes, and, compared to existing tools, is uniquely able to identify ancestral recombinations while accounting for several sources of inference uncertainty, including in the construction of a strain tree, estimation and rooting of gene family trees, and reconciliation itself. We apply this workflow to the Sarbecovirus subgenus and demonstrate how a principled analysis of predicted recombination gives insight into the evolution of SARS-CoV-2. In addition to providing confirming evidence for the horseshoe bat as its zoonotic origin, we identify several ancestral recombination events that merit further study.

Pathogens detected in the tick Haemaphysalis concinna in Western Poland: known and unknown threats

In recent years, a new focus of the relict tick Haemaphysalis concinna was discovered in Western Poland, near Wolsztyn, Greater Poland voivodeship. This species may play an important role in the circulation of pathogens of medical and veterinary importance. In the present study we tested 880 juvenile ticks collected from rodents, including 427 H. concinna, 443 Ixodes ricinus and 10 Dermacentor reticulatus for three of the most common pathogens vectored by ticks in Poland: Rickettsia and Babesia spp. and Borrelia burgdorferi s.l. Additionally, molecular techniques were applied for accurate identification of tick host species (the voles Microtus and Alexandromys). Our study found differences in the range and prevalence of vectored pathogens between the three tick species. DNA of all three pathogens was found in I. ricinus. In juvenile H. concinna, DNA of Babesia microti, Borrelia afzelii and Rickettsia sp. was identified. Moreover, DNA of a new unnamed Babesia species related to B. crassa, was found in two H. concinna nymphs. This genotype of Babesia was previously identified in H. concinna in the Far East and then in Central Europe. DNA of Rickettsia raoulti and B. afzelii was detected in D. reticulatus nymphs. Among rodent hosts, Alexandromys oeconomus seems to be host of the highest significance for juvenile tick stages and was the only host species with B. afzelii detected in blood samples. Using phylogenetic methods, we confirmed a clear division between rodents from the genera Microtus and Alexandromys. Moreover, we found that A. oeconomus trapped in Western Poland clustered with a Central European A. oeconomus allopatric phylogroup.