Using time-reversible Markov models is a very common practice in phylogenetic analysis, because although we expect many of their assumptions to be violated by empirical data, they provide high computational efficiency. However, these models lack the ability to infer the root placement of the estimated phylogeny. In order to compensate for the inability of these models to root the tree, many researchers use external information such as using outgroup taxa or additional assumptions such as molecular-clocks....
Sun Aug 02, 2020 03:00
Convergent phenotypic evolution provides some of the strongest evidence for adaptation. However, the extent to which recurrent phenotypic adaptation has arisen via parallelism at the molecular level remains unresolved, as does the evolutionary origin of alleles underlying such adaptation. Here, we investigate genetic mechanisms of convergent highland adaptation in maize landrace populations and evaluate the genetic sources of recurrently selected alleles. Population branch excess statistics reveal...
Sun Aug 02, 2020 03:00
The ribosome's common core, comprised of ribosomal RNA (rRNA) and universal ribosomal proteins, connects all life back to a common ancestor and serves as a window to relationships among organisms. The rRNA of the common core is most similar to rRNA of extant bacteria. In eukaryotes, the rRNA of the common core is decorated by expansion segments (ESs) that vastly increase its size. Supersized ESs have not been observed previously in Archaea, and the origin of eukaryotic ESs remains enigmatic. We discovered...
Sun Aug 02, 2020 03:00
The anatomy of sharks, rays, and chimaeras (chondrichthyans) is crucial to understanding the evolution of the cranial system in vertebrates, due to their position as the sister group to bony fishes (osteichthyans). Strikingly different arrangements of the head in the two constituent chondrichthyan groups - holocephalans and elasmobranchs - have played a pivotal role in the formation of evolutionary hypotheses targeting major cranial structures such as the jaws and pharynx. However, despite the advent...
Sun Aug 02, 2020 03:00
Recent biological invasions offer 'natural' laboratories to understand the genetics and ecology of adaptation, hybridization, and range limits. One of the most impressive and well-documented biological invasions of the 20th century began in 1957 when Apis mellifera scutellata honey bees swarmed out of managed experimental colonies in Brazil. This newly-imported subspecies, native to southern and eastern Africa, both hybridized with and out-competed previously-introduced European honey bee subspecies....
Sat Aug 01, 2020 03:00
The Saccharum Complex represents an hypothetical collective of species that were supposedly responsible, through interbreeding, for the origins of sugarcane. Though recent phylogenetic studies have cast doubt on the veracity of this hypothesis, it has cast a long shadow over the taxonomics of the Andropogoneae and the Saccharinae subtribe. Though evidence suggests that Saccharum s.s. is comprised of only three true species, according to Kews GrassBase there are as many as 34 species in Saccharum...
Sat Aug 01, 2020 03:00
The metaphor of fitness landscapes is common in evolutionary biology, as a way to visualise the change in allele or phenotypic frequencies of a population under selection. Understanding how different factors in the evolutionary process affect the trajectory of the population across the landscape is of interest to both theoretical and empirical evolutionary biologists. However, fitness landscape studies often have to rely heavily on mathematical methods that are not easy to access by biologically...
Sat Aug 01, 2020 03:00
Balancing selection is an important adaptive mechanism underpinning a wide range of phenotypes. Despite its relevance, the detection of recent balancing selection from genomic data is challenging as its signatures are qualitatively similar to those left by ongoing positive selection. In this study we developed and implemented two deep neural networks and tested their performance to predict loci under recent selection, either due to balancing selection or incomplete sweep, from population genomic...
Sat Aug 01, 2020 03:00
The evolution of multidrug resistance (MDR) is a pressing public health concern. Yet many aspects, such as the role played by population structure, remain poorly understood. Here we argue that studying MDR evolution by focusing upon the dynamical equations for linkage disequilibrium (LD) can greatly simplify the calculations, generate more insight, and provide a unified framework for understanding the role of population structure. We demonstrate how a general epidemiological model of MDR evolution...
Fri Jul 31, 2020 03:00
Seasonal influenza viruses repeatedly infect humans in part because they rapidly change their antigenic properties and evade host immune responses, necessitating frequent updates of the vaccine composition. Accurate predictions of strains circulating in the future could therefore improve the vaccine match. Here, we studied the predictability of frequency dynamics and fixation of amino acid substitutions.Current frequency was the strongest predictor of eventual fixation, as expected in neutral evolution....
Fri Jul 31, 2020 03:00
It is a broadly observed pattern that the non-recombining regions of sex-limited chromosomes (Y and W) accumulate more repeats than the rest of the genome, even in species like birds with a low genome-wide repeat content. Here we show that in birds with highly heteromorphic sex chromosomes, the W chromosome has a transposable element (TE) density of >55% compared to the genome-wide density of <10%, and contains over half of all full-length (thus potentially active) endogenous retroviruses (ERVs)...
Fri Jul 31, 2020 03:00
There are multiple hypotheses for the spectacular plant diversity found in deserts. We explore how different factors, including the roles of ecological opportunity and selection, promote diversification and disparification in Encelia, a lineage of woody plants in the deserts of the Americas. Using a nearly complete species-level phylogeny along with a broad set of phenotypic traits, we estimate divergence times and diversification rates, identify instances of hybridization, quantify trait disparity,...
Fri Jul 31, 2020 03:00
Access to reproduction is determined by an individual dominances rank in many species and is achieved through aggression and/or dominance signalling. In eusocial insects one or several dominant females (queens) monopolize reproduction but to what extent queens rely on aggression and signalling remains obscure. Aggression is costly and its efficiency depends on the group size, whereas signalling may reduce the risks and costs of aggression. Both strategies are used to regulate reproduction in social...
Sun Aug 02, 2020 03:00
While facultative sex is common in sexually reproducing species, for reasons of tractability most mathematical models assume that such sex is asynchronous in the population. In this paper, we develop a model of switching environments to instead capture the effect of an entire population transitioning synchronously between sexual and asexual modes of reproduction. We use this model to investigate the evolution of the number of self-incompatible mating types in finite populations, which empirically...
Fri Jul 31, 2020 03:00
In plants, large numbers of R genes, which segregate as loci with alternative alleles conferring different resistance to pathogens, have been maintained over a long evolutionary time. In theory, there seem to be no reason for hosts to harbor these susceptible alleles in view of their null contribution to resistance. As such, why should populations support disease-susceptible individuals along with disease-resistant individuals? In rice, a single copy R gene Pi-ta segregates for two expressed clades...
Fri Jul 31, 2020 03:00
Extracting insight from population genetic data often demands computationally intensive modeling. dadi is a popular program for fitting models of demographic history and natural selection to such data. Here, I show that running dadi on a Graphics Processing Unit (GPU) can speed computation by orders of magnitude compared to the CPU implementation, with minimal user burden. This speed increase enables the analysis of more complex models, which motivated the extension of dadi to four- and five-population...
Sun Aug 02, 2020 03:00
The geographic distribution of phenotypic variation among closely related populations is a valuable source of information about the evolutionary processes that generate and maintain biodiversity. Leapfrog distributions, in which phenotypically similar populations are disjunctly distributed and separated by one or more phenotypically distinct populations, represent geographic replicates for the existence of a phenotype, and are therefore especially informative. These geographic patterns have mostly...
Sun Aug 02, 2020 03:00
Many plants and animals adaptively downsize the number of already-produced propagules if resources become insufficient to raise all of them. In birds, mothers often induce hatching asynchrony by incubating first eggs before last eggs are laid, creating an age/size hierarchy within broods which selectively eliminates the smallest chicks in poor food conditions. However, mothers also deposit more testosterone into late-laid eggs, which boosts competitive abilities of younger chicks, counteracts the...
Fri Jul 31, 2020 03:00
Hybridization and genome duplication may cause serious damages but may also open unique opportunities to invade new ecological niches or adapt to novel environments better than their parents. Following the initial merging or multiplications, the subgenomes of hybrids and polyploids undergo considerable changes, often eliminating segments of one parental genome, phenomena known as loss of heterozygosity (LOH) and genome fractionation. Mechanisms causing such changes are not well understood, and remain...
Sun Aug 02, 2020 03:00
Despite the importance of natural selection in species evolutionary history, phylogenetic methods that take into account population-level processes ignore selection. Assuming neutrality is often based on the idea that selection occurs at a minority of loci in the genome and is unlikely to significantly compromise phylogenetic inferences. However, selection might behave more pervasively, as it the case of nearly neutral evolving mutations. Genome-wide processes like GC-bias and some of the variation...
Sun Aug 02, 2020 03:00
Dispersal plays a main role in determining spatial dynamics, and both theory and empirical evidence indicate that evolutionary optima exist for constitutive or plastic dispersal behaviour. Plasticity in dispersal can be influenced by factors both internal (state-dependent) or external (context-dependent) to individuals. Parasitism is interesting in this context, as it can influence both types of host dispersal plasticity: individuals can disperse in response to internal infection status but might...
Fri Jul 31, 2020 03:00
The adaptive potential of pathogens in novel or heterogeneous environments underpins the risk of disease epidemics. Antagonistic pleiotropy or differential resource allocation among life-history traits can constrain pathogen adaptation. However, we lack understanding how the genetic architecture of individual traits can generate trade-offs. Here, we report a large-scale study based on 145 global strains of the fungal wheat pathogen Zymoseptoria tritici from four continents. We measured 50 life-history...
Sun Aug 02, 2020 03:00
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