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Results for “Evolutionary Biology”

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bioRxiv2015

Dating ancient human samples using the recombination clock

The study of human evolution has been revolutionized by inferences from ancient DNA analyses. Key to these is the reliable estimation of the age of ancient specimens. The current best practice is radiocarbon dating, which relies on characterizing the decay of radioactive carbon isotope (14C), and is applicable for dating up to 50,000-year-old samples. Here, we introduce a new genetic method that uses recombination clock for dating. The key idea is that an ancient genome has evolved less than the genomes of extant individuals. Thus, given a molecular clock provided by the steady accumulation of recombination events, one can infer the age of the ancient genome based on the number of missing years of evolution. To implement this idea, we take advantage of the shared history of Neanderthal gene flow into non-Africans that occurred around 50,000 years ago. Using the Neanderthal ancestry decay patterns, we estimate the Neanderthal admixture time for both ancient and extant samples. The difference in these admixture dates then provides an estimate of the age of the ancient genome. We show that our method provides reliable results in simulations. We apply our method to date five ancient Eurasian genomes with radiocarbon dates ranging between 12,000 to 45,000 years and recover consistent age estimates. Our method provides a complementary approach for dating ancient human samples and is applicable to ancient non-African genomes with Neanderthal ancestry. Extensions of this methodology that use older shared events may be able to date ancient genomes that fall beyond the radiocarbon frontier.\n\nSignificanceWe introduce a new genetic method for dating ancient human samples that uses the recombination clock. The main idea relies on the insight that an ancient genome lacks several thousand years of evolution compared to genomes of living individuals. To infer the age of ancient genomes, we take advantage of the shared history of Neanderthal gene flow into non-Africans that occurred around 50,000 years ago. By characterizing the dates of Neanderthal gene flow in ancient and extant genomes and quantifying the difference in these dates, we estimate the age of the ancient specimen. Our method is applicable for dating ancient samples more recent than the Neanderthal mixture event, so on par with radiocarbon dating, providing a complementary approach for dating.

Evolutionary Biology↗

bioRxiv2015

Crowdsourced geometric morphometrics enable rapid large-scale collection and analysis of phenotypic data

1. Advances in genomics and informatics have enabled the production of large phylogenetic trees. However, the ability to collect large phenotypic datasets has not kept pace. 2. Here, we present a method to quickly and accurately gather morphometric data using crowdsourced image-based landmarking. 3. We find that crowdsourced workers perform similarly to experienced morphologists on the same digitization tasks. We also demonstrate the speed and accuracy of our method on seven families of ray-finned fishes (Actinopterygii). 4. Crowdsourcing will enable the collection of morphological data across vast radiations of organisms, and can facilitate richer inference on the macroevolutionary processes that shape phenotypic diversity across the tree of life.

Evolutionary Biology↗

bioRxiv2015

Hybrid-Lambda: simulation of multiple merger and Kingman gene genealogies in species networks and species trees

BackgroundThere has been increasing interest in coalescent models which admit multiple mergers of ancestral lineages; and to model hybridization and coalescence simultaneously.\n\nResultsHybrid-Lambda is a software package that simulates gene genealogies under multiple merger and Kingmans coalescent processes within species networks or species trees. Hybrid-Lambda allows different coalescent processes to be specified for different populations, and allows for time to be converted between generations and coalescent units, by specifying a population size for each population. In addition, Hybrid-Lambda can generate simulated datasets, assuming the infinitely many sites mutation model, and compute the FST statistic. As an illustration, we apply Hybrid-Lambda to infer the time of subdivision of certain marine invertebrates under different coalescent processes.\n\nConclusionsHybrid-Lambda makes it possible to investigate biogeographic concordance among high fecundity species exhibiting skewed offspring distribution.

Evolutionary Biology↗

bioRxiv2015

Estimating the effect of competition on trait evolution using maximum likelihood inference

Many classical ecological and evolutionary theoretical frameworks posit that competition between species is an important selective force. For example, in adaptive radiations, resource competition between evolving lineages plays a role in driving phenotypic diversification and exploration of novel ecological space. Nevertheless, current models of trait evolution fit to phylogenies and comparative datasets are not designed to incorporate the effect of competition. The most advanced models in this direction are diversity-dependent models where evolutionary rates depend on lineage diversity. However, these models still treat changes in traits in one branch as independent of the value of traits on other branches, thus ignoring the effect of species similarity on trait evolution. Here, we consider a model where the evolutionary dynamics of traits involved in interspecific interactions are influenced by species similarity in trait values and where we can specify which lineages are in sympatry. We develop a maximum-likelihood based approach to fit this model to combined phylogenetic and phenotypic data. Using simulations, we demonstrate that the approach accurately estimates the simulated parameter values across a broad range of parameter space. Additionally, we develop tools for specifying the biogeographic context in which trait evolution occurs. In order to compare models, we also apply these biogeographic methods to specify which lineages interact sympatrically for two diversity-dependent models. Finally, we fit these various models to morphological data from a classical adaptive radiation (Greater Antillean Anolis lizards). We show that models that account for competition and geography perform better than other models. The matching competition model is an important new tool for studying the influence of interspecific interactions, in particular competition, on phenotypic evolution. More generally, it constitutes a step toward a better integration of interspecific interactions in many ecological and evolutionary processes.

Evolutionary Biology↗

bioRxiv2015

Evolution of color phenotypes in two distantly related species of stick insect: different ecological regimes acting on similar genetic architectures

Recurrent (e.g. parallel or convergent) evolution is widely cited as evidence for natural selections central role in evolution but can also highlight constraints affecting evolution. Here we describe the evolution of green and melanistic color phenotypes in two species of stick insect: Timema podura and T. cristinae. We show that similar color phenotypes of these species (1) cluster in phenotypic space and (2) confer crypsis on different plant microhabitats. We then use genome-wide association mapping to determine the genetic architecture of color in T. podura, and compare this to previous results in T. cristinae. In both species, color is under simple genetic control, dominance relationships of melanistic and green alleles are the same, and SNPs associated with color phenotypes colocalize to the same genomic region. These results differ from those of typical parallel phenotypes because the form of selection acting on color differs between species: a balance of multiple sources of selection acting within host species maintains the color polymorphism in T. cristinae whereas T. podura color phenotypes are under divergent selection between hosts. Our results highlight how different adaptive landscapes can result in the evolution of similar phenotypic variation, and suggest the same genomic region is involved.

Evolutionary Biology↗

bioRxiv2015

Perturbative formulation of general continuous-time Markov model of sequence evolution via insertions/deletions, Part IV: Incorporation of substitutions and other mutations

BackgroundInsertions and deletions (indels) account for more nucleotide differences between two related DNA sequences than substitutions do, and thus it is imperative to develop a stochastic evolutionary model that enables us to reliably calculate the probability of the sequence evolution through indel processes. In a separate paper (Ezawa, Graur and Landan 2015a), we established the theoretical basis of our ab initio perturbative formulation of a continuous-time Markov model of the evolution of an entire sequence via insertions and deletions along time axis. In other separate papers (Ezawa, Graur and Landan 2015b,c), we also developed various analytical and computational methods to concretely calculate alignment probabilities via our formulation. In terms of frequencies, however, substitutions are usually more common than indels. Moreover, many experiments suggest that other mutations, such as genomic rearrangements and recombination, also play some important roles in sequence evolution.\n\nResultsHere, we extend our ab initio perturbative formulation of a genuine evolutionary model so that it can incorporate other mutations. We give a sufficient set of conditions that the probability of evolution via both indels and substitutions is factorable into the product of an overall factor and local contributions. We also show that, under a set of conditions, the probability can be factorized into two sub-probabilities, one via indels alone and the other via substitutions alone. Moreover, we show that our formulation can be extended so that it can also incorporate genomic rearrangements, such as inversions and duplications. We also discuss how to accommodate some other types of mutations within our formulation.\n\nConclusionsOur ab initio perturbative formulation thus extended could in principle describe the stochastic evolution of an entire sequence along time axis via major types of mutations.\n\n[This paper and three other papers (Ezawa, Graur and Landan 2015a,b,c) describe a series of our efforts to develop, apply, and extend the ab initio perturbative formulation of a general continuous-time Markov model of indels.]

Evolutionary Biology↗

bioRxiv2015

The constant philopater hypothesis: a new life history invariant for dispersal evolution

Life history invariants play a pivotal role in the study of social adaptation: they provide theoretical hypotheses that can be empirically tested, and benchmark frameworks against which new theoretical developments can be understood. Here we derive a novel invariant for dispersal evolution: the \"constant philopater hypothesis\" (CPH). Specifically, we find that, irrespective of variation in maternal fecundity, all mothers are favoured to produce exactly the same number of philopatric offspring, with high-fecundity mothers investing proportionally more, and low-fecundity mothers investing proportionally less, into dispersing offspring. This result holds for female and male dispersal, under haploid, diploid and haplodiploid modes of inheritance, irrespective of the sex ratio, local resource availability, and whether mother or offspring controls the latters dispersal propensity. We explore the implications of this result for evolutionary conflicts of interest - and the exchange and withholding of contextual information - both within and between families, and we show that the CPH is the fundamental invariant that underpins and explains a wider family of invariance relationships that emerge from the study of social evolution.

Evolutionary Biology↗

bioRxiv2015

Detection of adaptive shifts on phylogenies using shifted stochastic processes on a tree

Comparative and evolutive ecologists are interested in the distribution of quantitative traits among related species. The classical framework for these distributions consists of a random process running along the branches of a phylogenetic tree relating the species. We consider shifts in the process parameters, which reveal fast adaptation to changes of ecological niches. We show that models with shifts are not identifiable in general. Constraining the models to be parsimonious in the number of shifts partially alleviates the problem but several evolutionary scenarios can still provide the same joint distribution for the extant species. We provide a recursive algorithm to enumerate all the equivalent scenarios and to count the effectively different scenarios. We introduce an incomplete-data framework and develop a maximum likelihood estimation procedure based on the EM algorithm. Finally, we propose a model selection procedure, based on the cardinal of effective scenarios, to estimate the number of shifts and prove an oracle inequality.

Evolutionary Biology↗

bioRxiv2015

Mammalian development does not recapitulate suspected key transformations in the evolution of the mammalian middle ear

The tympanic ring, malleus and incus of the mammalian middle ear derive from the ancestral primary jaw joint of land vertebrates. In Mesozoic mammals, evolutionary detachment of the mammalian middle ear from the lower jaw occurred when Meckels cartilage - the last connection between the middle ear bones and the dentary - disappeared. This disappearance is famously recapitulated in early mammalian development. By extension, it was suggested that other developmental processes also recapitulate specific evolutionary processes that led to mammalian middle ear detachment in Mesozoic mammals. Specifically, developmental posterior/medial displacement and negative allometry of the growing ear ossicles relative to the lower jaw are thought to reflect evolutionary triggers of mammalian middle ear detachment. However, these hypotheses rest on scant developmental data, and have not been tested in a quantitative framework. Here we show, based on CT scans of developmental series of several marsupials and monotremes, that negative allometry of mammalian middle ear bones relative to the skull occurs only after mammalian middle ear detachment, ruling it out as a developmental detachment trigger. There is also no positional change of ectotympanic or malleus relative to the dentary. The mammalian middle ear bones are differently positioned in two monotreme species, a recent change which is not developmentally recapitulated. Together, our results challenge the developmental prerequisites of previously proposed evolutionary detachment processes, arguing specifically against causal links between mammalian middle ear detachment and brain expansion. Our data are more consistent with a biomechanical detachment trigger relating to the onset of dentary function, but more biomechanical work and palaeontological data are required to test this notion.

Evolutionary Biology↗

bioRxiv2015

Infinitely Long Branches and an Informal Test of Common Ancestry

The evidence for universal common ancestry (UCA) is vast and persuasive, and a phylogenetic test was proposed for quantifying its odds against independently originated sequences based on the comparison between one and several trees [1]. This test was successfully applied to a well-supported homologous sequence alignment, being however criticized once simulations showed that even alignments without any phylogenetic structure could mislead its conclusions [2]. Despite claims to the contrary [3], we believe that the counterexample successfully showed a drawback of the test, of relying on good alignments.\n\nHere we present a simplified version of this counterexample, which can be interpreted as a tree with arbitrarily long branches, and where the test again fails. We also present another simulation showing circumstances whereby any sufficiently similar alignment will favor UCA irrespective of the true independent origins for the sequences. We therefore conclude that the test should not be trusted unless convergence has already been ruled out a priori. Finally, we present a class of frequentist tests that perform better than the purportedly formal UCA test.

Evolutionary Biology↗

bioRxiv2015

Distribution of gene tree histories under the coalescent model with gene flow

We propose a coalescent model for three species that allows gene flow between both pairs of sister populations. The model is designed to analyze multilocus genomic sequence alignments, with one sequence sampled from each of the three species. The model is formulated using a Markov chain representation, which allows use of matrix exponentiation to compute analytical expressions for the probability density of gene tree genealogies. The gene tree history distribution as well as the gene tree topology distribution under this coalescent model with gene flow are then calculated via numerical integration. We analyze the model to compare the distributions of gene tree topologies and gene tree histories for species trees with differing effective population sizes and gene flow rates. Our results suggest conditions under which the species tree and associated parameters are not identifiable from the gene tree topology distribution when gene flow is present, but indicate that the gene tree history distribution may identify the species tree and associated parameters. Thus, the gene tree history distribution can be used to infer parameters such as the ancestral effective population sizes and the rates of gene flow in a maximum likelihood (ML) framework. We conduct computer simulations to evaluate the performance of our method in estimating these parameters, and we apply our method to an Afrotropical mosquito data set (Fontaine et al., 2015) to demonstrate the usefulness of our method for the analysis of empirical data.

Evolutionary Biology↗

bioRxiv2015

Trait Evolution on Phylogenetic Networks

Species may evolve on a reticulate network due to hybridization or other gene flow rather than on a strictly bifurcating tree, but comparative methods to deal with trait evolution on a network are lacking. We create such a method, which uses a Brownian motion model. Our method seeks to separately or jointly detect a bias in trait value coming from hybridization ({beta}) and a burst of variation at the time of hybridization (vH) associated with the hybridization event, as well as traditional Brownian motion parameters of ancestral state () and rate of evolution ({sigma}2) of Brownian motion, as well as measurement error of the tips (SE). We test the method with extensive simulations. We also apply the model to two empirical examples, cichlid body size and Nicotiana drought tolerance, and find substantial measurement error and a hint that hybrids have greater drought tolerance in the latter case. The new methods are available in CRAN R package BMhyd.

Evolutionary Biology↗

bioRxiv2015

Decreased transcription factor binding levels nearby primate pseudogenes suggests regulatory degeneration

Characteristics of pseudogene degeneration at the coding level are well-known, such as a shift towards neutral rates of nonsynonymous substitutions and gain of frameshift mutations. In contrast, degeneration of pseudogene transcriptional regulation is not well understood. Here, we test two predictions of regulatory degeneration along the pseudogenized lineage: (1) decreased transcription factor binding and (2) accelerated evolution in putative cis-regulatory regions.\n\nWe find evidence for decreased TF binding levels nearby two primate pseudogenes compared to functional liver genes. We also find evidence for pseudogene-lineage-specific relaxation of sequence constraint on a fragment of the promoter of the primate pseudogene urate oxidase (Uox) and a nearby cis-regulatory module (CRM). However, the majority of TF-bound sequences nearby pseudogenes do not show evidence for lineage-specific accelerated rates of evolution. We conclude that decreases in TF binding level could be a marker for regulatory degeneration, while sequence degeneration in most CRMs may be obscured by background rates of TF binding site turnover.

Evolutionary Biology↗

bioRxiv2015

More efficacious drugs lead to harder selective sweeps in the evolution of drug resistance in HIV-1

In the early days of HIV treatment, drug resistance occurred rapidly and predictably in all patients, but under modern treatments, resistance arises slowly, if at all. The probability of resistance should be controlled by the rate of generation of resistant mutations. If many adaptive mutations arise simultaneously, then adaptation proceeds by soft selective sweeps in which multiple adaptive mutations spread concomitantly, but if adaptive mutations occur rarely in the population, then a single adaptive mutation should spread alone in a hard selective sweep. Here we use 6,717 HIV-1 consensus sequences from patients treated with first-line therapies between 1989 and 2013 to confirm that the transition from fast to slow evolution of drug resistance was indeed accompanied with the expected transition from soft to hard selective sweeps. This suggests more generally that evolution proceeds via hard sweeps if resistance is unlikely and via soft sweeps if it is likely.

Evolutionary Biology↗

bioRxiv2015

Core variability in substitution rates and the basal sequence characteristics of the human genome

Accurate knowledge on the core components of substitution rates is of vital importance to understand genome evolution and dynamics. By performing a single-genome and direct analysis of 39894 retrotransposon remnants, we reveal germline sequence-dependent nucleotide substitution rates that can be assigned to each position in the human genome. Benefiting from the data made available in such detail, we show that a simulated genome, generated by equilibrating a random DNA sequence solely using our rate constants, exhibits nucleotide organisation close to that in the human genome. We next generate the germline basal substitution propensity (BSP) profile of the human genome and show a decreased tendency of moieties with low BSP to undergo somatic mutations in many cancer types.

Evolutionary Biology↗

bioRxiv2015

Life history effects on the molecular clock of autosomes and sex chromosomes

One of the foundational results of molecular evolution is that the rate at which neutral substitutions accumulate on a lineage equals the rate at which mutations arise. Traits that affect rates of mutation therefore also affect the phylogenetic \"molecular clock\". We consider the effects of sex-specific generation times and mutation rates in species with two sexes. In particular, we focus on the effects that the age of onset of male puberty and rates of spermatogenesis have likely had in extant hominines (i.e., human, chimpanzee and gorilla), considering a model that approximates features of the mutational process in most mammals and birds and some other vertebrates. As we show, this model helps explain and reconcile a number of seemingly puzzling observations. In hominines, it can explain the puzzlingly low X-to-autosome ratios of substitution rates and how the ratios and rates of autosomal substitutions differ among lineages. Importantly, it suggests how to translate pedigree-based estimates of human mutation rates into split times among apes, given sex-specific life histories. In so doing, it helps bridge the gap between estimates of split times of apes based on fossil and molecular evidence. Finally, considering these effects can help to reconcile recent evidence that changes in generation times should have small effects on mutation rates in humans with classic studies suggesting that they have had major effects on rates of evolution in the mammalian phylogeny.

Evolutionary Biology↗

bioRxiv2015

Gap gene regulatory dynamics evolve along a genotype network

Developmental gene networks implement the dynamic regulatory mechanisms that pattern and shape the organism. Over evolutionary time, the wiring of these networks changes, yet the patterning outcome is often preserved, a phenomenon known as \"system drift\". System drift is illustrated by the gap gene network--involved in segmental patterning--in dipteran insects. In the classic model organism Drosophila melanogaster and the non-model scuttle fly Megaselia abdita, early activation and placement of gap gene expression domains show significant quantitative differences, yet the final patterning output of the system is essentially identical in both species. In this detailed modeling analysis of system drift, we use gene circuits which are fit to quantitative gap gene expression data in M. abdita and compare them to an equivalent set of models from D. melanogaster. The results of this comparative analysis show precisely how compensatory regulatory mechanisms achieve equivalent final patterns in both species. We discuss the larger implications of the work in terms of \"genotype networks\" and the ways in which the structure of regulatory networks can influence patterns of evolutionary change (evolvability).

Evolutionary Biology↗

bioRxiv2015

S/HIC: Robust identification of soft and hard sweeps using machine learning

Detecting the targets of adaptive natural selection from whole genome sequencing data is a central problem for population genetics. However, to date most methods have shown sub-optimal performance under realistic demographic scenarios. Moreover, over the past decade there has been a renewed interest in determining the importance of selection from standing variation in adaptation of natural populations, yet very few methods for inferring this model of adaptation at the genome scale have been introduced. Here we introduce a new method, S/HIC, which uses supervised machine learning to precisely infer the location of both hard and soft selective sweeps. We show that S/HIC has unrivaled accuracy for detecting sweeps under demographic histories that are relevant to human populations, and distinguishing sweeps from linked as well as neutrally evolving regions. Moreover we show that S/HIC is uniquely robust among its competitors to model misspecification. Thus even if the true demographic model of a population differs catastrophically from that specified by the user, S/HIC still retains impressive discriminatory power. Finally we apply S/HIC to the case of resequencing data from human chromosome 18 in a European population sample and demonstrate that we can reliably recover selective sweeps that have been identified earlier using less specific and sensitive methods.

Evolutionary Biology↗