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Results for “Evolutionary Biology”

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bioRxiv2015

Refining the Y chromosome phylogeny with southern African sequences

The recent availability of large-scale sequence data for the human Y chromosome has revolutionized analyses of and insights gained from this non-recombining, paternally inherited chromosome. However, the studies to date focus on Eurasian variation, and hence the diversity of early-diverging branches found in Africa has not been adequately documented. Here we analyze over 900 kb of Y chromosome sequence obtained from 547 individuals from southern African Khoisan and Bantuspeaking populations, identifying 232 new sequences from basal haplogroups A and B. We find new branches within haplogroups A2 and A3b1 and suggest that the prehistory of haplogroup B2a is more complex than previously suspected; this haplogroup is likely to have existed in Khoisan groups before the arrival of Bantu-speakers, who brought additional B2a lineages to southern Africa. Furthermore, we estimate older dates than obtained previously for both the A2-T node within the human Y chromosome phylogeny and for some individual haplogroups. Finally, there is pronounced variation in branch length between major haplogroups; haplogroups associated with Bantu-speakers have significantly longer branches. This likely reflects a combination of biases in the SNP calling process and demographic factors, such as an older average paternal age (hence a higher mutation rate), a higher effective population size, and/or a stronger effect of population expansion for Bantu-speakers than for Khoisan groups.

Evolutionary Biology↗

bioRxiv2015

The Fisher-Wright model with deterministic seed bank and selection

Seed banks are a common characteristics to many plant species, which allow storage of genetic diversity in the soil as dormant seeds for various periods of time. We investigate an above-ground population following a Fisher-Wright model with selection coupled with a deterministic seed bank assuming the length of the seed bank is kept constant and the number of seeds is large. To assess the combined impact of seed banks and selection on genetic diversity, we derive a general diffusion model. We compute the equilibrium solution of the site-frequency spectrum and derive the times to fixation of an allele with and without selection. Finally, it is demonstrated that seed banks enhance the effect of selection onto the site-frequency spectrum while slowing down the time until the mutation-selection equilibrium is reached.

Evolutionary Biology↗

bioRxiv2015

A Critical Review on the Use of Support Values in Tree Viewers and Bioinformatics Toolkits

Phylogenetic trees are routinely visualized to present and interpret the evolutionary relationships of species. Virtually all empirical evolutionary data studies contain a visualization of the inferred tree with branch support values. Ambiguous semantics in tree file formats can lead to erroneous tree visualizations and therefore to incorrect interpretations of phylogenetic analyses.\n\nHere, we discuss problems that can and do arise when displaying branch values on trees after re-rooting. Branch values are typically stored as node labels in the widely-used Newick tree format. However, such values are attributes of branches. Storing them as node labels can therefore yield errors when re-rooting trees. This depends on the mostly implicit semantics that tools deploy to interpret node labels.\n\nWe reviewed 10 tree viewers and 10 bioinformatics toolkits that can display and re-root trees. We found that 14 out of 20 of these tools do not permit users to select the semantics of node labels. Thus, unaware users might obtain incorrect results when rooting trees inferred by common phylogenetic inference programs. We illustrate such incorrect mappings for several test cases and real examples taken from the literature. This review has already led to improvements and workarounds in 8 of the tested tools. We suggest tools should provide an option that explicitly forces users to define the semantics of node labels.

Evolutionary Biology↗

bioRxiv2016

The Maintenance of Sex and David Lack’s Principle

Combining George C. Williams idea that evolutionary constraints prevent asexual mutants from arising more frequently in low fecundity organisms, like mammals and birds, with an earlier one by David Lack that the brood size of these organisms has an optimum, and producing larger broods reduces their fitness, leads to a novel hypothesis about the maintenance of sex in them. All else equal, the eggs of an asexual mutant female should simply start developing without fertilisation, and there is no reason to assume that they would stop doing so after the optimal number of offspring has been produced. Without a way to control their reproductive output, asexual mutants should over-reproduce and suffer a cost of doing so. Experimental studies suggest that the cost of enlarged broods could limit the advantage of asexual mutants considerably. Moreover, research discovered that increased reproductive effort reduces immune functions of low fecundity organisms. This offers a surprising synthesis between Williams constraint and Hamiltons parasite hypothesis on maintaining sex in low fecundity organisms: Compromised immune functions of asexual hosts may render them susceptible rather than adaptation on the side of parasites to overcome host resistance.

Evolutionary Biology↗

bioRxiv2016

Variation in the molecular clock of primates

Events in primate evolution are often dated by assuming a \"molecular clock\", i.e., a constant rate of substitution per unit time, but the validity of this assumption remains unclear. Among mammals, it is well known that there exists substantial variation in yearly substitution rates. Such variation is to be expected from differences in life-history traits, suggesting that it should also be found among primates. Motivated by these considerations, we analyze whole genomes from ten primate species, including Old World Monkeys (OWMs), New World Monkeys (NWMs) and apes, focusing on putatively neutral autosomal sites and controlling for possible effects of biased gene conversion and methylation at CpG sites. We find that substitution rates are {small tilde}65% higher in lineages leading from the hominoid-NWM ancestor to NWMs than to apes. Within apes, rates are {small tilde}2% higher in chimpanzees and {small tilde}7% higher in the gorilla than in humans. Substitution types subject to biased gene conversion show no more variation among species than those not subject to it. Not all mutation types behave similarly, however: in particular, transitions at CpG sites exhibit a more clock-like behavior than do other types, presumably due to their non-replicative origin. Thus, not only the total rate, but also the mutational spectrum varies among primates. This finding suggests that events in primate evolution are most reliably dated using CpG transitions. Taking this approach, we estimate that the average time to the most recent common ancestor of human and chimpanzee is 12.1 million years and their split time 7.9 million years.\n\nSignificance statementMuch of our understanding of the chronology of human evolution relies on the \"molecular clock\", i.e., a constant rate of substitutions per unit time. To evaluate the validity of this assumption, we analyze whole genome sequences from ten primate species. We find that there is substantial variation in the molecular clock between apes and monkeys, and rates even differ within hominoids. Importantly, not all mutation types behave similarly: notably, transitions at CpG sites exhibit a more clock-like behavior than other substitutions, presumably due to their non-replicative origin. Thus, the mutation spectra, and not just the overall substitution rates, are changing across primates. This finding further suggests that events in primate evolution are most reliably dated using CpG transitions.

Evolutionary Biology↗

bioRxiv2016

Evolution of corticosteroid specificity for human, chicken, alligator and frog glucocorticoid receptors

We investigated the evolution of the response of human, chicken, alligator and frog glucocorticoid receptors (GRs) to dexamethasone, cortisol, corticosterone, 11-deoxycorticosterone, 11-deoxycortisol and aldosterone. We find significant differences among these vertebrates in the transcriptional activation of their full length GRs by these steroids, indicating that there were changes in the specificity of the GR for steroids during the evolution of terrestrial vertebrates. To begin to study the role of interactions between different domains on the GR in steroid sensitivity and specificity for terrestrial GRs, we investigated transcriptional activation of truncated GRs containing their hinge domain and ligand binding domain (LBD) fused to a GAL4 DNA binding domain (GAL4 DBD). Compared to corresponding full length GRs, transcriptional activation of GAL4 DBD-GR hinge/LBD constructs required higher steroid concentrations and displayed altered steroid specificity, indicating that interactions between the hinge/LBD and other domains are important in glucocorticoid activation of these terrestrial GRs.

Evolutionary Biology↗

bioRxiv2016

How clonal are bacteria over time?

Bacteria and archaea reproduce clonally (vertical descent), but exchange genes by recombination (horizontal transfer). Recombination allows adaptive mutations or genes to spread rapidly within (or even between) species, and reduces the burden of deleterious mutations. Clonality - defined here as the balance between vertical and horizontal inheritance - is therefore a key microbial trait, determining how quickly a population can adapt and the size of its gene pool. Here, I discuss whether clonality varies over time and if it can be considered a stable trait of a given population. I show that, in some cases, clonality is clearly not static. For example, non-clonal (highly recombining) populations can give rise to clonal expansions, often of pathogens. However, an analysis of time-course metagenomic data from a lake suggests that a bacterial populations past clonality (as measured by its genetic diversity) is a good predictor of its future clonality. Clonality therefore appears to be relatively - but not completely - stable over evolutionary time.

Evolutionary Biology↗

bioRxiv2016

Tempo and mode of genome evolution in a 50,000-generation experiment

Adaptation depends on the rates, effects, and interactions of many mutations. We analyzed 264 genomes from 12 Escherichia coli populations to characterize their dynamics over 50,0 generations. The trajectories for genome evolution in populations that retained the ancestral mutation rate fit a model where most fixed mutations are beneficial, the fraction of beneficial mutations declines as fitness rises, and neutral mutations accumulate at a constant rate. We also compared these populations to lines evolved under a mutation-accumulation regime that minimizes selection. Nonsynonymous mutations, intergenic mutations, insertions, and deletions are overrepresented in the long-term populations, supporting the inference that most fixed mutations are favored by selection. These results illuminate the shifting balance of forces that govern genome evolution in populations adapting to a new environment.

Evolutionary Biology↗

bioRxiv2016

Bayesian inference of natural selection from allele frequency time series

The advent of accessible ancient DNA technology now allows the direct ascertainment of allele frequencies in ancestral populations, thereby enabling the use of allele frequency time series to detect and estimate natural selection. Such direct observations of allele frequency dynamics are expected to be more powerful than inferences made using patterns of linked neutral variation obtained from modern individuals. We developed a Bayesian method to make use of allele frequency time series data and infer the parameters of general diploid selection, along with allele age, in non-equilibrium populations. We introduce a novel path augmentation approach, in which we use Markov chain Monte Carlo to integrate over the space of allele frequency trajectories consistent with the observed data. Using simulations, we show that this approach has good power to estimate selection coefficients and allele age. Moreover, when applying our approach to data on horse coat color, we find that ignoring a relevant demographic history can significantly bias the results of inference. Our approach is made available in a C++ software package.

Evolutionary Biology↗

bioRxiv2016

A novel nuclear genetic code alteration in yeasts and the evolution of codon reassignment in eukaryotes

The genetic code is the universal cellular translation table to convert nucleotide into amino acid sequences. Changes to sense codons are expected to be highly detrimental. However, reassignments of single or multiple codons in mitochondria and nuclear genomes demonstrated that the code can evolve. Still, alterations of nuclear genetic codes are extremely rare leaving hypotheses to explain these variations, such as the codon capture, the genome streamlining and the ambiguous intermediate theory, in strong debate. Here, we report on a novel sense codon reassignment in Pachysolen tannophilus, a yeast related to the Pichiaceae. By generating proteomics data and using tRNA sequence comparisons we show that in Pachysolen CUG codons are translated as alanine and not as the universal leucine. The polyphyly of the CUG-decoding tRNAs in yeasts is best explained by a tRNA loss driven codon reassignment mechanism. Loss of the CUG-tRNA in the ancient yeast is followed by gradual decrease of respective codons and subsequent codon capture by tRNAs whose anticodon is outside the aminoacyl-tRNA synthetase recognition region. Our hypothesis applies to all nuclear genetic code alterations and provides several testable predictions. We anticipate more codon reassignments to be uncovered in existing and upcoming genome projects.

Evolutionary Biology↗

bioRxiv2016

Genome-wide patterns of regulatory divergence revealed by introgression lines

Understanding the genetic basis for changes in transcriptional regulation is an important aspect of understanding phenotypic evolution. Using interspecific introgression lines, we infer the mechanisms of divergence in genome-wide patterns of gene expression between the nightshades Solanum pennellii and S. lycopersicum (domesticated tomato). We find that cis- and frans-regulatory changes have had qualitatively similar contributions to divergence in this clade, unlike results from other systems. Additionally, expression data from four tissues (shoot apex, ripe fruit, pollen, and seed) suggest that introgressed regions in these hybrid lines tend to be down-regulated, while background (non-introgressed) genes tend to be up-regulated. Finally, we find no evidence for an association between the magnitude of differential expression in NILs and previously determined sterility phenotypes. Our results contradict previous predictions of the predominant role of cis- over frans-regulatory divergence between species, and do not support a major role for gross genome-wide misregulation in reproductive isolation between these species.

Evolutionary Biology↗

bioRxiv2016

Stress affects the epigenetic marks added by Bari-Jheh: a natural insertion associated with two adaptive phenotypes in Drosophila

Transposable elements are emerging as an important source of cis-acting regulatory sequences and epigenetic marks that could influence gene expression. However, few studies have dissected the role of specific transposable element insertions on epigenetic gene regulation. Bari-Jheh is a natural transposon that mediates resistance to oxidative stress by adding cis-regulatory sequences that affect expression of nearby genes. In this work, we integrated publicly available data with chromatin immunoprecipitation experiments to get a more comprehensive picture of Bari-Jheh molecular effects. We showed that Bari-Jheh was enriched for H3K9me3 in nonstress conditions, and for H3K9me3, H3K4me3 and H3K27me3 in oxidative stress conditions, which is consistent with expression changes in adjacent genes. We further showed that under oxidative stress conditions, H3K4me3 and H3K9me3 spread to the promoter region of Jheh1 gene. Finally, another insertion of the Bari1 family was associated with increased H3K27me3 in oxidative stress conditions suggesting that Bari1 histone marks are copy-specific. We concluded that besides adding cis-regulatory sequences, Bari-Jheh influences gene expression by affecting the local chromatin state.

Evolutionary Biology↗

bioRxiv2016

Statistics of Cellular Evolution in Leukemia: Allelic Variations in Patient Trajectories Based on Immune Repertoire Sequencing

The evolution of a cancer system consisting of cancer clones and normal cells is a complex dynamic process with multiple interacting factors including clonal expansion, somatic mutation, and sequential selection. As a typical example, in patients with chronic lymphocytic leukemia (CLL), a monoclonal population of transformed B cells expands to dominate the B cell population in the peripheral blood and bone marrow. This expansion of transformed B cells suggests that they might evolve through processes distinct from those of normal B cells. Recent advances in next generation sequencing enable the high-throughput identification and tracking of individual B cell clones through sequencing of the V-D-J junction segments of the immunoglobulin heavy chain (IGH). Here we developed a statistical approach to modeling cellular evolution of the immune repertoire. Adapting the infinitely many alleles model from population genetics, we studied abnormalities occurring in the immune repertoire of patients as substantial deviations from the null model. The Ewens sampling test (EST) distinguished the immune repertoires of CLL patients with imminent relapse from healthy controls and patients in sustained remission. Extensive simulations based on sequencing data showed that EST is sensitive in detecting cancer-related derangements of the IGH repertoire. In addition, we suggest two potentially useful parameters: the rate at which donors B cell clones enter the circulation and the average time to regenerate a transplanted immune repertoire, both of which help to distinguish relapsing CLL patients from those in sustained remission and provide additional information about the dynamics of immune reconstitution in the latter patients. We anticipate that our models and statistics will be useful in diagnosis and prognosis of leukemia, and may be adapted for application to other diseases related to adaptive immunity.

Evolutionary Biology↗

bioRxiv2016

A comparison of ancestral state reconstruction methods for quantitative characters

Choosing an ancestral state reconstruction method among the alternatives available for quantitative characters may be puzzling. We present here a comparison of five of them, namely the maximum likelihood, restricted maximum likelihood, generalized least squares, phylogenetic independent contrasts and squared parsimony methods.\n\nA review of the relations between these methods shows that the first three ones infer the same ancestral states and can only be distinguished by the distributions accounting for the reconstruction uncertainty which they provide.\n\nThe respective accuracy of the methods is assessed over character evolution simulated under a Brownian motion with (and without) drift. We start by giving the general form of ancestral state distributions conditioned on leaf states under the simulation model.\n\nAncestral distributions are used first, to give a theoretical lower bound of the expected reconstruction error, and second, to develop an original evaluation scheme which is more efficient than comparing the reconstructed and the simulated states.\n\nOur simulations show that: (i) the methods do not perform well as the evolution drift increases; (ii) the maximum likelihood method is generally the most accurate and (iii) not all the distributions of the reconstruction uncertainty provided by the methods are equally relevant.

Evolutionary Biology↗

bioRxiv2016

Evolutionary stability of jointly evolving traits in subdivided populations

The evolutionary stability of quantitative traits depends on whether a population can resist invasion by any mutant. While uninvadability is well understood in well-mixed populations, it is much less so in subdivided populations when multiple traits evolve jointly. Here, we investigate whether a spatially subdivided population at a monomorphic equilibrium for multiple traits can withstand invasion by any mutant, or is subject to diversifying selection. Our model also explores the among traits correlations arising from diversifying selection and how they depend on relatedness due to limited dispersal. We find that selection favours a positive (negative) correlation between two traits, when the selective effects of one trait on relatedness is positively (negatively) correlated to the indirect fitness effects of the other trait. We study the evolution of traits for which this matters: dispersal that decreases relatedness, and helping that has positive indirect fitness effects. We find that when dispersal cost is low and the benefits of helping accelerate faster than its costs, selection leads to the coexistence of mobile defectors and sessile helpers. Otherwise, the population evolves to a monomorphic state with intermediate helping and dispersal. Overall, our results highlight the importance of population subdivision for evolutionary stability and correlations among traits.

Evolutionary Biology↗

bioRxiv2016

Genetic evidence for natural selection in humans in the contemporary United States

Recent findings from molecular genetics now make it possible to test directly for natural selection by analyzing whether genetic variants associated with various phenotypes have been under selection. I leverage these findings to construct polygenic scores that use individuals' genotypes to predict their body mass index, educational attainment (EA), glucose concentration, height, schizophrenia, total cholesterol, and (in females) age at menarche. I then examine associations between these scores and fitness to test whether natural selection has been occurring. My study sample includes individuals of European ancestry born between 1931 and 1953 in the Health and Retirement Study, a representative study of the US population. My results imply that natural selection has been slowly favoring lower EA in both females and males, and are suggestive that natural selection may have favored a higher age at menarche in females. For EA, my estimates imply a rate of selection of about -1.5 months of education per generation (which pales in comparison with the increases in EA observed in contemporary times). Though they cannot be projected over more than one generation, my results provide additional evidence that humans are still evolving--albeit slowly, especially when compared to the rapid secular changes that have occurred over the past few generations due to cultural and environmental factors.

Evolutionary Biology↗

bioRxiv2016

Evolutionary inference across eukaryotes identifies specific pressures favoring mitochondrial gene retention

Since their endosymbiotic origin, mitochondria have lost most of their genes. Despite the central cellular importance of mtDNA, selective mechanisms underlying the evolution of its content across eukaryotes remain contentious, with no data-driven exploration of different hypotheses. We developed HyperTraPS, a powerful methodology coupling stochastic modelling with Bayesian inference to identify the ordering and causes of evolutionary events. Using a large dataset from over 2000 complete mitochondrial genomes, we inferred evolutionary trajectories of mtDNA gene loss across the eukaryotic tree of life. We find that proteins fulfilling central energetic roles in the assembly of mitochondrial complexes are prefentially retained in mitochondria across eukary-otes, biophysically supporting colocalization for redox regulation. We also provide the first quantitative evidence that a combination of GC content and protein hydrophobicity is required to explain mtDNA gene retention, and predicts the success of artificial gene transfer experiments. Our results demonstrate that a combination of these three characteristics explains most mtDNA gene variability, addressing the long-debated question of why particular genes are retained in mitochondrial genomes.

Evolutionary Biology↗

bioRxiv2016

Signatures of positive selection and local adaptation to urbanization in white-footed mice (Peromyscus leucopus)

Urbanization significantly alters natural ecosystems and has accelerated globally as humans move into dense urban centers. Urban wildlife populations are often highly fragmented by an inhospitable matrix of human infrastructure. Isolated populations may adapt in response to novel urban pressures, but few studies have found evidence of selection in urban environments. We used multiple approaches to examine signatures of selection in transcriptomes from white-footed mice (Peromyscus leucopus) in New York City. We analyzed transcriptomes from 48 P. leucopus individuals from three urban and three rural populations for evidence of rapid local adaption in isolated urban habitats. We generated a dataset of 154,770 SNPs and analyzed patterns of genetic differentiation between urban and rural sites. We also used genome scans and genotype-by-environment (GEA) analyses to identify signatures of selection in a large subset of genes. Neutral demographic processes may create allele frequency patterns that are indistinguishable from positive selection. Thus, we accounted for demography by simulating a neutral SNP dataset under the inferred demographic history for the sampled P. leucopus populations to serve as a null model for outlier analysis. We then annotated outlier genes and further validated them by associating allele frequency differences with two urbanization variables: percent impervious surface and human population density. Many candidate genes were involved in metabolic functions, especially dietary specialization. A subset of these genes have well-established roles in metabolizing lipids and carbohydrates, including transport of cholesterol and desaturation of fatty acids. Our results reveal clear genetic differentiation between rural and urban sites that resulted from rapid local adaptation and drift in urbanizing habitats. The specific outlier loci that we identified suggest that populations of P. leucopus are using novel food resources in urban habitats and selection pressures are acting to change metabolic pathways. Our findings support the idea that cities represent novel ecosystems with a unique set of selective pressures.

Evolutionary Biology↗