Molecular approaches to species delimitation are increasingly used to ascertain the number of species in a sample prior to taxonomic, ecological or physiological studies. Although multilocus ...approaches are gaining fast in popularity, single‐gene methods still predominate in the literature. However, available simulation benchmarks of these methods focus exclusively on species‐poor samples and/or tree‐based approaches: as a result, travellers in the land of single‐locus species delimitation lack a comprehensive “hitchhiker's guide” highlighting the sweet spots and dangers on their road. To fill this gap, we compared the performances of distance‐based (ABGD, “automatic barcode gap discovery”), allele sharing‐based (haplowebs) and tree‐based approaches (GMYC, “generalized mixed Yule‐coalescent” and PTP, “Poisson tree processes”) to detect interspecific boundaries in samples of 6, 60 and 120 simulated species with various speciation rates, effective population sizes, mutation rates and sampling patterns. We found that all approaches performed poorly when population sizes and speciation rates were large, with haplowebs yielding best results followed by ABGD then tree‐based approaches. The latter's error type was mostly oversplitting, whereas ABGD chiefly overlumped and haplowebs leaned either way depending on simulation parameters: such widely divergent error patterns suggest that, if all three types of methods agree, then the resulting delimitation is probably correct. Perfect congruence being quite rare, travellers in search of a one‐size‐fit‐all approach to single‐locus species delimitation should forget it; however, our hitchhiker's guide raises hope that such species delimitation's Holy Grail may be found in the relatively uncharted nearby land of multilocus species delimitation.
Most single-locus molecular approaches to species delimitation available to date have been designed and tested on data sets comprising at least tens of species, whereas the opposite case ...(species-poor data sets for which the hypothesis that all individuals are conspecific cannot by rejected beforehand) has rarely been the focus of such attempts. Here we compare the performance of barcode gap detection, haplowebs and generalized mixed Yule-coalescent (GMYC) models to delineate chimpanzees and bonobos using nuclear sequence markers, then apply these single-locus species delimitation methods to data sets of one, three, or six species simulated under a wide range of population sizes, speciation rates, mutation rates and sampling efforts. Our results show that barcode gap detection and GMYC models are unable to delineate species properly in data sets composed of one or two species, two situations in which haplowebs outperform them. For data sets composed of three or six species, bGMYC and haplowebs outperform the single-threshold and multiple-threshold versions of GMYC, whereas a clear barcode gap is only observed when population sizes and speciation rates are both small. The latter conditions represent a "sweet spot" for molecular taxonomy where all the single-locus approaches tested work well; however, the performance of these methods decreases strongly when population sizes and speciation rates are high, suggesting that multilocus approaches may be necessary to tackle such cases.
Since the latter part of 2020, SARS-CoV-2 evolution has been characterised by the emergence of viral variants associated with distinct biological characteristics. While the main research focus has ...centred on the ability of new variants to increase in frequency and impact the effective reproductive number of the virus, less attention has been placed on their relative ability to establish transmission chains and to spread through a geographic area. Here, we describe a phylogeographic approach to estimate and compare the introduction and dispersal dynamics of the main SARS-CoV-2 variants - Alpha, Iota, Delta, and Omicron - that circulated in the New York City area between 2020 and 2022. Notably, our results indicate that Delta had a lower ability to establish sustained transmission chains in the NYC area and that Omicron (BA.1) was the variant fastest to disseminate across the study area. The analytical approach presented here complements non-spatially-explicit analytical approaches that seek a better understanding of the epidemiological differences that exist among successive SARS-CoV-2 variants of concern.
In eusocial insects, worker polymorphism is shaped by several factors, including colony size, queen mating frequency, and the timing of queen-worker differentiation during larval development. In a ...comparative study of 18 species of
Cataglyphis
desert ants representing a wide range of worker sizes, we used phylogenetically controlled analyses to examine correlations between worker head width variation (i.e., worker polymorphism) and multiple social traits, namely, mature colony size, mean worker head width, queen head width, queen-worker head width dimorphism, and within-colony genetic relatedness, resulting from multiple mating by queens. We found that worker polymorphism was positively correlated with mature colony size, mean worker head width, and queen head width. In contrast, worker polymorphism was not correlated with queen-worker dimorphism and within-colony genetic relatedness. These results underscore that evolution of worker polymorphism and social traits are correlated. They also illustrate that additional research using multivariate approaches is needed to further clarify the evolution of insect societies.
Significance statement
In eusocial insects, worker morphological variation (i.e., worker polymorphism) is tightly linked to division of labor. Multiple factors are supposed to shape the evolution of worker polymorphism. Using phylogenetically controlled analyses of worker head width variation from 18 species of
Cataglyphis
desert ants, we show that worker polymorphism positively correlates with mature colony size, mean worker head width, and queen size. These results highlight that the evolution of worker polymorphism and social traits are correlated. Identifying the mechanisms underlying these relationships could provide major insights into the development and evolution of insect societies.
Understanding the causes and consequences of the emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants of concern is crucial to pandemic control yet difficult to achieve ...because they arise in the context of variable human behavior and immunity. We investigated the spatial invasion dynamics of lineage B.1.1.7 by jointly analyzing UK human mobility, virus genomes, and community-based polymerase chain reaction data. We identified a multistage spatial invasion process in which early B.1.1.7 growth rates were associated with mobility and asymmetric lineage export from a dominant source location, enhancing the effects of B.1.1.7's increased intrinsic transmissibility. We further explored how B.1.1.7 spread was shaped by nonpharmaceutical interventions and spatial variation in previous attack rates. Our findings show that careful accounting of the behavioral and epidemiological context within which variants of concern emerge is necessary to interpret correctly their observed relative growth rates.
SERAPHIM ("Studying Environmental Rasters and PHylogenetically Informed Movements") is a suite of computational methods developed to study phylogenetic reconstructions of spatial movement in an ...environmental context. SERAPHIM extracts the spatio-temporal information contained in estimated phylogenetic trees and uses this information to calculate summary statistics of spatial spread and to visualize dispersal history. Most importantly, SERAPHIM enables users to study the impact of customized environmental variables on the spread of the study organism. Specifically, given an environmental raster, SERAPHIM computes environmental "weights" for each phylogeny branch, which represent the degree to which the environmental variable impedes (or facilitates) lineage movement. Correlations between movement duration and these environmental weights are then assessed, and the statistical significances of these correlations are evaluated using null distributions generated by a randomization procedure. SERAPHIM can be applied to any phylogeny whose nodes are annotated with spatial and temporal information. At present, such phylogenies are most often found in the field of emerging infectious diseases, but will become increasingly common in other biological disciplines as population genomic data grows.
SERAPHIM 1.0 is freely available from http://evolve.zoo.ox.ac.uk/ R package, source code, example files, tutorials and a manual are also available from this website.
simon.dellicour@kuleuven.be or oliver.pybus@zoo.ox.ac.ukSupplementary information: Supplementary data are available at Bioinformatics online.
After the first wave of SARS-CoV-2 infections in spring 2020, Europe experienced a resurgence of the virus starting in late summer 2020 that was deadlier and more difficult to contain
. Relaxed ...intervention measures and summer travel have been implicated as drivers of the second wave
. Here we build a phylogeographical model to evaluate how newly introduced lineages, as opposed to the rekindling of persistent lineages, contributed to the resurgence of COVID-19 in Europe. We inform this model using genomic, mobility and epidemiological data from 10 European countries and estimate that in many countries more than half of the lineages circulating in late summer resulted from new introductions since 15 June 2020. The success in onward transmission of newly introduced lineages was negatively associated with the local incidence of COVID-19 during this period. The pervasive spread of variants in summer 2020 highlights the threat of viral dissemination when restrictions are lifted, and this needs to be carefully considered in strategies to control the current spread of variants that are more transmissible and/or evade immunity. Our findings indicate that more effective and coordinated measures are required to contain the spread through cross-border travel even as vaccination is reducing disease burden.
Computational analyses of pathogen genomes are increasingly used to unravel the dispersal history and transmission dynamics of epidemics. Here, we show how to go beyond historical reconstructions and ...use spatially-explicit phylogeographic and phylodynamic approaches to formally test epidemiological hypotheses. We illustrate our approach by focusing on the West Nile virus (WNV) spread in North America that has substantially impacted public, veterinary, and wildlife health. We apply an analytical workflow to a comprehensive WNV genome collection to test the impact of environmental factors on the dispersal of viral lineages and on viral population genetic diversity through time. We find that WNV lineages tend to disperse faster in areas with higher temperatures and we identify temporal variation in temperature as a main predictor of viral genetic diversity through time. By contrasting inference with simulation, we find no evidence for viral lineages to preferentially circulate within the same migratory bird flyway, suggesting a substantial role for non-migratory birds or mosquito dispersal along the longitudinal gradient.
Viral rebound upon stopping combined antiretroviral therapy poses a major barrier toward an HIV cure. Cellular and anatomical sources responsible for reinitiating viral replication remain a subject ...of ardent debate, despite extensive research efforts. To unravel the source of rebounding viruses, we conducted a large-scale HIV-STAR (HIV-1 sequencing before analytical treatment interruption to identify the anatomically relevant HIV reservoir) clinical trial. We collected samples from 11 participants and compared the genetic composition of (pro)viruses collected under treatment from different cellular and anatomical compartments with that of plasma viruses sampled during analytical treatment interruption. We found a remarkably heterogeneous source of viral rebound. In addition, irrespective of the compartment or cell subset, genetically identical viral expansions played a significant role in viral rebound. Our study suggests that although there does not seem to be a primary source for rebound HIV, cellular proliferation is an important driver of HIV persistence and should therefore be considered in future curative strategies.
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•HIV-1 sequences sampled from different reservoirs were compared to rebound viruses in 11 individuals•Rebound viruses can originate from various cellular and anatomical compartments•Cellular proliferation is an important driver of HIV persistence•Cure strategies should take into account the lack of a prominent HIV rebound origin
De Scheerder et al. conduct an in-depth investigation into the origins of HIV rebound. They show that viral rebound originates from multiple compartments and cell proliferation is a driver of viral persistence. Future HIV cure strategies will need to overcome the challenges associated with heterogeneous viral rebound.
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