SEARCH · Search bioRxiv

Results for “Evolutionary Biology”

Search indexed bioRxiv preprints in genomics, neuroscience, cell biology and bioinformatics. Read source abstracts and check manuscript versions; preprints are not peer reviewed.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 1,369 records · Page 76Linked to original sources

bioRxiv2016

Exploring evolutionary relationships across the genome using topology weighting

We introduce the concept of topology weighting, a method for quantifying relationships between taxa that are not necessarily monophyletic, and visualising how these relationships change across the genome. A given set of taxa can be related in a limited number of ways, but if each taxon is represented by multiple sequences, the number of possible topologies becomes very large. Topology weighting reduces this complexity by quantifying the contribution of each 'taxon topology' to the full tree. We describe our method for topology weighting by iterative sampling of sub-trees (Twisst), and test it on both simulated and real genomic data. Overall, we show that this is an informative and versatile approach, suitable for exploring relationships in almost any genomic dataset.\n\nScripts to implement the method described are available at github.com/simonhmartin/twisst.

Evolutionary Biology↗

bioRxiv2016

Gene-culture co-inheritance of a behavioral trait.

Human behavioral traits are complex phenotypes that result from both genetic and cultural transmission. But different inheritance systems need not favor the same phenotypic outcome. What happens when there are conflicting selection forces in the two domains? To address this question, we derive a Price equation that incorporates both cultural and genetic inheritance of a phenotype where the effects of genes and culture are additive. We then use this equation to investigate whether a genetically maladaptive phenotype can evolve under dual transmission. We examine the special case of altruism using an illustrative model, and show that cultural selection can overcome genetic selection when the variance in culture is sufficiently high with respect to genes. Finally, we show how our basic result can be extended to non-additive effects models. We discuss the implications of our results for understanding the evolution of maladaptive behaviors.

Evolutionary Biology↗

bioRxiv2016

A functional analysis of the contribution of climatic niche divergence to adaptive radiation

Elucidating how ecological and evolutionary mechanisms interact to produce and maintain biodiversity is a fundamental problem in evolutionary ecology. We investigate this issue by focusing on how physiological evolution affects performance and species coexistence along the thermal niche axis in replicated radiations of Anolis lizards, groups best known for resource partitioning based on morphological divergence. We find repeated divergence in thermal physiology within these radiations, and that this divergence significantly affects performance within natural thermal environments. Morphologically similar species that co-occur invariably differ in their thermal physiology, providing evidence that physiological divergence facilitates species co-existence within anole communities. Despite repeated divergence in traits of demonstrable ecological importance, phylogenetic comparative analyses indicate that physiological traits have evolved more slowly than key morphological traits related to the structural niche. Phylogenetic analyses also reveal that physiological divergence is correlated with divergence in broad-scale habitat climatic features commonly used to estimate thermal niche evolution, but that the latter incompletely predicts variation in the former. We provide comprehensive evidence for repeated adaptive evolution of physiological divergence within Anolis adaptive radiations, including the complementary roles of physiological and morphological divergence in promoting community-level diversity. We recommend greater integration of performance-based traits into analyses of climatic niche evolution, as they facilitate a more complete understanding of the phenotypic and ecological consequences of climatic divergence.

Evolutionary Biology↗

bioRxiv2016

Genome-scale rates of evolutionary change in bacteria

Estimating the rates at which bacterial genomes evolve is critical to understanding major evolutionary and ecological processes such as disease emergence, long-term host-pathogen associations, and short-term transmission patterns. The surge in bacterial genomic data sets provides a new opportunity to estimate these rates and reveal the factors that shape bacterial evolutionary dynamics. For many organisms estimates of evolutionary rate display an inverse association with the time-scale over which the data are sampled. However, this relationship remains unexplored in bacteria due to the difficulty in estimating genome-wide evolutionary rates, which are impacted by the extent of temporal structure in the data and the prevalence of recombination. We collected 36 whole genome sequence data sets from 16 species of bacterial pathogens to systematically estimate and compare their evolutionary rates and assess the extent of temporal structure in the absence of recombination. The majority (28/36) of data sets possessed sufficient clock-like structure to robustly estimate evolutionary rates. However, in some species reliable estimates were not possible even with \"ancient DNA\" data sampled over many centuries, suggesting that they evolve very slowly or that they display extensive rate variation among lineages. The robustly estimated evolutionary rates spanned several orders of magnitude, from 10-6 to 10-8 nucleotide substitutions site-1 year-1. This variation was largely attributable to sampling time, which was strongly negatively associated with estimated evolutionary rates, with this relationship best described by an exponential decay curve. To avoid potential estimation biases such time-dependency should be considered when inferring evolutionary time-scales in bacteria.

Evolutionary Biology↗

bioRxiv2016

A unifying comparative phylogenetic framework including traits coevolving across interacting lineages

Models of phenotypic evolution fit to phylogenetic comparative data are widely used to make inferences regarding the tempo and mode of trait evolution. A wide range of models is already available for this type of analysis, and the field is still under active development. One of the most needed developments concerns models that better account for the effect of within- and between-clade interspecific interactions on trait evolution, that can result from processes as diverse as competition, predation, parasitism, or mutualism. Here, we begin by developing a very general comparative phylogenetic framework for (multi)-trait evolution that can be applied to both ultrametric and non-ultrametric trees. This framework not only encapsulates all previous classical models of univariate and multivariate phenotypic evolution, but also paves the way for the consideration of a much broader series of models in which lineages co-evolve, meaning that trait changes in one lineage are influenced by the value of traits in other, interacting lineages. Next, we provide a standard way for deriving the probabilistic distribution of traits at tip branches under our framework. We show that a multivariate normal distribution remains the expected distribution for a broad class of models accounting for interspecific interactions. Our derivations allow us to fit various models efficiently, and in particular greatly reduce the computation time needed to fit the recently proposed phenotype matching model. Finally, we illustrate the utility of our framework by developing a toy model for mutualistic coevolution. Our framework should foster a new era in the study of coevolution from comparative data.

Evolutionary Biology↗

bioRxiv2016

XRN1 is a Species-Specific Virus Restriction Factor in Yeasts

In eukaryotes, the degradation of cellular mRNAs is accomplished by Xrn1p and the cytoplasmic exosome. Because viral RNAs often lack canonical caps or poly-A tails, they can also be vulnerable to degradation by these host exonucleases. Yeast lack sophisticated mechanisms of innate and adaptive immunity, but do use RNA degradation as an antiviral defense mechanism. One model is that the RNA of yeast viruses is subject to degradation simply as a side effect of the intrinsic exonuclease activity of proteins involved in RNA metabolism. Contrary to this model, we find a highly refined, species-specific relationship between Xrn1p and the \"L-A\" totiviruses of different Saccharomyces yeast species. We show that the gene XRN1 has evolved rapidly under positive natural selection in Saccharomyces yeast, resulting in high levels of Xrn1p protein sequence divergence from one yeast species to the next. We also show that these sequence differences translate to differential interactions with the L-A virus, where Xrn1p from S. cerevisiae is most efficient at controlling the L-A virus that chronically infects S. cerevisiae, and Xrn1p from S. kudriavzevii is most efficient at controlling the L-A-like virus that we have discovered within S. kudriavzevii. All Xrn1p orthologs are equivalent in their interaction with another virus-like parasite, the Ty1 retrotransposon. Thus, the activity of Xrn1p against totiviruses is not simply an incidental consequence of the enzymatic activity of Xrn1p, but rather Xrn1p co-evolves with totiviruses to maintain its potent antiviral activity and limit viral propagation in Saccharomyces yeasts. Consistent with this, we demonstrated that Xrn1p physically interacts with the Gag protein encoded by the L-A virus, suggesting a host-virus interaction that is more complicated than just Xrn1p-mediated nucleolytic digestion of viral RNAs.

Evolutionary Biology↗

bioRxiv2016

A non-zero variance of Tajima’s estimator for two sequences even for infinitely many unlinked loci

The population-scaled mutation rate,{theta} , is informative on the effective population size and is thus widely used in population genetics. We show that for two sequences and n unlinked loci, Tajimas estimator ([Formula]), which is the average number of pairwise differences, is not consistent and therefore its variance does not vanish even as n [->] {infty}. The non-zero variance of [Formula] results from a (weak) correlation between coalescence times even at unlinked loci, which, in turn, is due to the underlying fixed pedigree shared by all genealogies. We derive the correlation coefficient under a diploid, discrete-time, Wright-Fisher model, and we also derive a simple, closed-form lower bound. We also obtain empirical estimates of the correlation of coalescence times under demographic models inspired by large-scale human genealogies. While the effect we de scribe is small [Formula], it is important to recognize this feature of statistical population genetics, which runs counter to commonly held notions about unlinked loci.

Evolutionary Biology↗

bioRxiv2016

High GC Content Causes De Novo Created Proteins to be Intrinsically Disordered

De novo creation of protein coding genes involves formation of short ORFs from noncoding regions; some of these ORFs might then become fixed in the population. De novo created proteins need to, at the bare minimum, not cause serious harm to the organism, meaning that they should for instance not cause aggregation. Therefore, although the creation of the short ORFs could be truly random, but the fixation should be of subject to some selective pressure. The selective forces acting on de novo created proteins have been elusive and contradictory results have been reported. In Drosophila they are more disordered, i.e. are enriched in polar residues, than ancient proteins, while the opposite trend is present in yeast. To the best of our knowledge no valid explanation for this difference has been proposed.\n\nTo solve this riddle we studied structural properties and age of all proteins in 187 eukaryotic species. We find that, on average, there are small differences between proteins of different ages, with the exception that younger proteins are shorter. However, when we take the GC content into account we find that this can explain the opposite trends observed in yeast (low GC) and drosophila (high GC). GC content is correlated with codons coding for disorder-promoting amino acids, and inversely correlated with transmembrane, helix and sheet promoting residues. We find that for the youngest proteins, i.e. the ones that are most likely to be de novo created, there exists a strong correlation with GC and structural properties. In contrast, this strong relationship is not seen for ancient proteins. This leads us to propose that structural features are not a strong determining factor for fixation of de novo created genes. Instead these proteins resemble random proteins given a particular GC level. The dependency on GC content is then gradually weakened during evolution.\n\nAuthor SummaryWe show that the GC content of a genomic area is of great importance for the properties of a protein-coding de novo created gene. The GC content affects the frequency of the codons and this affects the probability for each amino acid to be included in a de novo created protein. The codons encoding for Ala, Pro and Glu contain 80% GC, while codons for Lys, Phe, Asn, Tyr and Ile contain 20% or less. Pro and Gly are disorder-promoting, while Phe, Tyr and Ile are order-promoting. Therefore random protein sequences at a high GC will be more disordered than the ones created at a low GC. The structural properties of the youngest (orphan) proteins match to a large degree the properties of random proteins when the GC content is taken into account. In contrast structural properties of ancient proteins only show a weak correlation with GC content. This suggests that even after fixation of de novo created proteins largely resemble random proteins given a certain GC content. Thereafter, during evolution the correlation between structural properties and GC weakens.

Evolutionary Biology↗

bioRxiv2016

Pherotype polymorphism in Streptococcus pneumoniae and its effects on population structure and recombination

Natural transformation in the Gram-positive pathogen Streptococcus pneumoniae occurs when cells become \"competent\", a state that is induced in response to high extracellular concentrations of a secreted peptide signal called CSP (Competence Stimulating Peptide) encoded by the comC locus. Two main CSP signal types (pherotypes) are known to dominate the pherotype diversity across strains. Using thousands of fully sequenced pneumococcal genomes, we confirm that pneumococcal populations are highly genetically structured and that there is significant variation among diverged populations in pherotype frequencies; most carry only a single pherotype. Moreover, we find that the relative frequencies of the two dominant pherotypes significantly vary within a small range across geographical sites. It has been variously proposed that pherotypes either promote genetic exchange among cells expressing the same pherotype, or conversely that they promote recombination between strains bearing different pherotypes. We distinguish these hypotheses using a bioinformatics approach by estimating recombination frequencies within and between pherotypes across 4,089 full genomes. Despite underlying population structure, we observe extensive recombination between populations; additionally, we found significantly higher rates of genetic exchange between strains expressing different pherotypes than among isolates carrying the same pherotype. Our results indicate that pherotypes do not restrict, and marginally facilitate, recombination between strains. Furthermore, our results suggest that the CSP balanced polymorphism does not causally underlie population differentiation. Therefore, when strains carrying different pherotypes encounter one another during co-colonization, genetic exchange can freely occur.

Evolutionary Biology↗

bioRxiv2016

Viral outbreaks involve destabilised viruses: evidence from Ebola, Influenza and Zika

Recent history has provided us with one pandemic (Influenza A/H1N1) and two severe viral outbreaks (Ebola and Zika). In all three cases, post-hoc analyses have given us deep insights into what triggered these outbreaks, their timing, evolutionary dynamics, and phylogeography, but the genomic characteristics of outbreak viruses are still unclear. To address this outstanding question, we searched for a common denominator between these recent outbreaks, positing that the genome of outbreak viruses is in an unstable evolutionary state, while that of non-outbreak viruses is stabilized by a network of correlated substitutions. Here, we show that during regular epidemics, viral genomes are indeed stabilized by a dense network of weakly correlated sites, and that these networks disappear during pandemics and outbreaks when rates of evolution increase transiently. Post-pandemic, these evolutionary networks are progressively re-established. We finally show that destabilization is not caused by substitutions targeting epitopes, but more likely by changes in the environment sensu lato. Our results prompt for a new interpretation of pandemics as being associated with evolutionary destabilized viruses.

Evolutionary Biology↗

bioRxiv2016

Natural and laboratory mutations in kuzbanian are associated with heavy metal stress phenotypes in Drosophila melanogaster

Organisms must cope with altered environmental conditions such as high concentrations of heavy metals. Stress response to heavy metals is mediated by the metal-responsive transcription factor 1 (MTF-1), which is conserved from Drosophila to humans. MTF-1 binds to metal response elements (MREs) and changes the expression of target genes. kuzbanian (kuz), a metalloendopeptidase that activates the evolutionary conserved Notch signaling pathway, has been identified as an MTF-1 target gene. We have previously identified a putatively adaptive transposable element in the Drosophila melanogaster genome, named FBti0019170, inserted in a kuz intron. In this work, we investigated whether laboratory-induced mutations in kuz are associated with zinc stress phenotypes. We found that both embryos and adult flies overexpressing kuz are more tolerant to zinc compared with wild-type flies. On the other hand, we found that the effect of FBti0019170 on zinc stress tolerance depends on developmental stage and genetic background. Moreover, in the majority of the genetic backgrounds analyzed, FBti0019170 has a deleterious effect in unpolluted environments in pre-adult stages. These results highlight the complexity of natural mutations and suggest that besides laboratory-induced mutations natural mutations need to be studied in order to accurately characterize gene function and evolution.

Evolutionary Biology↗

bioRxiv2016

Escherichia coli populations adapt to complex, unpredictable fluctuations by minimizing trade-offs across environments

In nature, organisms are simultaneously exposed to multiple stresses (i.e. complex environments) that often fluctuate unpredictably. While both these factors have been studied in isolation, the interaction of the two remains poorly explored. To address this issue, we selected laboratory populations of Escherichia coli under complex (i.e. stressful combinations of pH, H2O2 and NaCl) unpredictably fluctuating environments for ~900 generations. We compared the growth rates and the corresponding trade-off patterns of these populations to those that were selected under constant values of the component stresses (i.e. pH, H2O2 and NaCl) for the same duration. The fluctuation-selected populations had greater mean growth rate and lower variation for growth rate over all the selection environments experienced. However, while the populations selected under constant stresses experienced trade-offs in the environments other than those in which they were selected, the fluctuation-selected populations could by-pass the across-environment trade-offs almost entirely. Interestingly, trade-offs were found between growth rates and carrying capacities. The results suggest that complexity and fluctuations can strongly affect the underlying trade-off structure in evolving populations.

Evolutionary Biology↗

bioRxiv2016

Evolution of copper resistance in the kiwifruit pathogen Pseudomonas syringae pv. actinidiae through acquisition of integrative conjugative elements and plasmids

SUMMARYLateral gene transfer can precipitate rapid evolutionary change. In 2010 the global pandemic of kiwifruit canker disease caused by Pseudomonas syringae pv. actinidiae (Psa) reached New Zealand. At the time of introduction, the single clone responsible for the outbreak was sensitive to copper, however, analysis of a sample of isolates taken in 2015 and 2016 showed that a quarter were copper resistant. Genome sequences of seven strains showed that copper resistance - comprising czc/cusABC and copABCD systems - along with resistance to arsenic and cadmium, was acquired via uptake of integrative conjugative elements (ICEs), but also plasmids. Comparative analysis showed ICEs to have a mosaic structure, with one being a tripartite arrangement of two different ICEs and a plasmid that were isolated in 1921 (USA), 1968 (NZ) and 1988 (Japan), from P. syringae pathogens of millet, wheat and kiwifruit, respectively. Two of the Psa ICEs were nearly identical to two ICEs isolated from kiwifruit leaf colonists prior to the introduction of Psa into NZ. Additionally, we show ICE transfer in vitro and in planta, analyze fitness consequences of ICE carriage, capture the de novo formation of novel recombinant ICEs, and explore ICE host-range.\n\nORIGINALITY-SIGNIFICANT STATEMENTLateral gene transfer is a major evolutionary force, but its immediacy is often overlooked. Between 2008 and 2010 a single virulent clone of the kiwifruit pathogen Pseudomonas syringae pv. actinidiae spread to kiwifruit growing regions of the world. After arrival in New Zealand it acquired genetic determinants of copper resistance in the form of integrative conjugative elements and plasmids. Components of these elements are evident in distantly related bacteria from millet (USA, 1921), kiwifruit (Japan, 1988) and wheat (New Zealand, 1968). Additional laboratory experiments capture evidence of the dynamism underpinning the evolution of these elements in real time and further emphasize the potent role that lateral gene transfer plays in microbial evolution.

Evolutionary Biology↗

bioRxiv2016

Further confirmation for unknown archaic ancestry in Andaman and South Asia.

In a recent paper1, we have derived three main conclusions: i) that all Asian and Pacific populations share a single origin and expansion out of Africa, contradicting an earlier proposal of two independent waves; ii) that populations from South and Southeast Asia harbor a small proportion of ancestry from an unknown extinct hominin - different from the Neanderthal and the Denisovan - which is absent in Europeans; and, iii) that the characteristic distinctive phenotypes (including very short stature) of Andamanese do not reflect an ancient African origin, but have resulted from strong natural selection on genes related to human body size. Although the single wave out of Africa2 and single origin for Asian and Pacific populations have been confirmed3, the existence of admixture with an extinct hominin has been challenged by Skoglund et al.4, as they were unable to replicate our results in their data sets. While we had used a wide variety of statistical methods and data sets from diverse populations to draw our inference, Skoglund et al.4 have used only one method (D-stats5, for the whole genome, not specifically for the relevant genomic regions) and compared only with the Asians, not even with the Europeans. Skoglund et al.4 have alleged that our statistical treatment of the data was faulty and have pointed out some possible sources of error. We have reexamined our data focusing on possible sources of error flagged by Skoglund et al4. We have also performed new analyses. The reexamination and new analyses have bolstered our confidence that our earlier inferences were correct and have resulted in an improved model of introgression of modern humans with a hitherto unknown archaic ancestry. We also propose a possible reason for the inability of Skoglund et al.4 to validate our inference.

Evolutionary Biology↗

bioRxiv2016

Estimating time to the common ancestor for a beneficial allele

The haplotypes of a beneficial allele carry information about its history that can shed light on its age and putative cause for its increase in frequency. Specifically, the signature of an alleles age is contained in the pattern of local ancestry that mutation and recombination impose on its haplotypic background. We provide a method to exploit this pattern and infer the time to the common ancestor of a positively selected allele following a rapid increase in frequency. We do so using a hidden Markov model which leverages the length distribution of the shared ancestral haplotype, the accumulation of derived mutations on the ancestral background, and the surrounding background haplotype diversity. Using simulations, we demonstrate how the inclusion of information from both mutation and recombination events increases accuracy relative to approaches that only consider a single type of event. We also show the behavior of the estimator in cases where data do not conform to model assumptions, and provide some diagnostics for assessing and improving inference. Using the method, we analyze population-specific patterns in the 1000 Genomes Project data to provide a global perspective on the timing of adaptation for several variants which show evidence of recent selection and functional relevance to diet, skin pigmentation, and morphology in humans.

Evolutionary Biology↗

bioRxiv2016

Metazoan ribotoxin genes acquired by Horizontal Gene Transfer

Ribosome inactivating proteins (RIPs) are RNA N-glycosidases that depurinate a specific adenine residue in the conserved sarcin/ricin loop of 28S rRNA. These enzymes are widely distributed among plants and their presence has also been confirmed in several bacterial species. Recently, we reported for the first time in silico evidence of RIP encoding genes in metazoans, in two closely related species of insects: Aedes aegypti and Culex quinquefasciatus. Here, we have experimentally confirmed the presence of these genes in mosquitoes and attempted to unveil their evolutionary history. A detailed study was conducted, including evaluation of taxonomic distribution, phylogenetic inferences and microsynteny analyses, indicating that the culicine RIP genes derived from a single Horizontal Gene Transfer (HGT) event, probably from a Cyanobacterial donor species. Moreover, evolutionary analyses show that, after transference, these genes evolved under purifying selection, strongly suggesting that they play functional roles in these organisms. In this work we confirm the presence of RIP genes in Culicinae species, and show solid evidence supporting the hypothesis that these genes are derived from a single prokaryotic transferred gene through HGT. In addition, clear evidence of purifying selection pressure has been recorded, supporting the hypothesis that these genes are functional within this subfamily.

Evolutionary Biology↗

bioRxiv2016

Inference of the distribution of selection coefficients for new nonsynonymous mutations using large samples

The distribution of fitness effects (DFE) has considerable importance in population genetics. To date, estimates of the DFE come from studies using a small number of individuals. Thus, estimates of the proportion of moderately to strongly deleterious new mutations may be unreliable because such variants are unlikely to be segregating in the data. Additionally, the true functional form of the DFE is unknown, and estimates of the DFE differ significantly between studies. Here we present a flexible and computationally tractable method, called Fit{partial}a{partial}i, to estimate the DFE using the site frequency spectrum from a large number of individuals. We apply our approach to the frequency spectrum of 1300 Europeans from the Exome Sequencing Project ESP6400 dataset, 1298 Danes from the LuCamp dataset, and 432 Europeans from the 1000 Genomes Project to estimate the DFE of deleterious nonsynonymous mutations. We infer significantly fewer (0.38-0.84x) strongly deleterious mutations with selection coefficient |s| > 0.01 and more (1.24-1.43x) weakly deleterious mutations with selection coefficient |s| < 0.001 compared to previous estimates. Furthermore, a DFE that is a mixture distribution of a point mass at neutrality plus a gamma distribution fits best to two of the three datasets. Our results suggest that nearly neutral forces play a larger role in human evolution than previously thought.

Evolutionary Biology↗

bioRxiv2016

Reinforcement of conspecific sperm precedence weakens sexual selection in sympatric populations of Drosophila

Sexual selection is well recognized as a driver of reproductive isolation between lineages. However, selection for increased reproductive isolation could reciprocally change the outcomes of sexual selection, when these processes share a genetic basis. Direct selection for reproductive isolation occurs in the context of reinforcement, where selection acts to increase prezygotic barriers to reduce the cost of heterospecific matings. Many studies of reinforcement focus on premating reproductive barriers, however postmating traits-such as conspecific sperm precedence (CSP)-can also respond to reinforcing selection. We tested whether i) CSP responded to reinforcing selection, and ii) this response in sympatric populations altered intraspecific sperm competition (ISC) and the strength of sexual selection, with the sister species Drosophila pseudoobscura and D. persimilis. We used sperm competition experiments to evaluate differences in CSP and ISC between two sympatric and two allopatric populations of D. pseudoobscura. Using multiple genotypes for each population allowed us to estimate not only patterns of phenotype divergence, but also the opportunity for sexual selection within each population. Consistent with a pattern of reinforcement, the sympatric populations had higher mean CSP. Moreover, ISC was altered in sympatric populations, where we observed decreased average offensive sperm competitive ability against conspecific males, allowing less opportunity for sexual selection to operate within these populations. These data demonstrate that strong reinforcing selection for reproductive isolation can have consequences for sexual selection and sexual interactions within species, in these important postmating sperm competition traits.

Evolutionary Biology↗