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bioRxiv2018

Head-to-Head Comparison of Three Methods of Quantifying Competitive Fitness in C. elegans

Organismal fitness is relevant in many contexts in biology. The most meaningful experimental measure of fitness is competitive fitness, when two or more entities (e.g., genotypes) are allowed to compete directly. In theory, competitive fitness is simple to measure: an experimental population is initiated with the different types in known proportions and allowed to evolve under experimental conditions to a predefined endpoint. In practice, there are several obstacles to obtaining robust estimates of competitive fitness in multicellular organisms, the most pervasive of which is simply the time it takes to count many individuals of different types from many replicate populations. Methods by which counting can be automated in high throughput are desirable, but for automated methods to be useful, the bias and technical variance associated with the method must be (a) known, and (b) sufficiently small relative to other sources of bias and variance to make the effort worthwhile.\n\nThe nematode Caenorhabditis elegans is an important model organism, and the fitness effects of genotype and environmental conditions are often of interest. We report a comparison of three experimental methods of quantifying competitive fitness, in which wild-type strains are competed against GFP-marked competitors under standard laboratory conditions. Population samples were split into three replicates and counted (1) \"by eye\" from a saved image, (2) from the same image using CellProfiler image analysis software, and (3) with a large particle flow cytometer (a \"worm sorter\"). From 720 replicate samples, neither the frequency of wild-type worms nor the among-sample variance differed significantly between the three methods. CellProfiler and the worm sorter provide at least a tenfold increase in sample handling speed with little (if any) bias or increase in variance.

evolutionary biology↗

bioRxiv2018

Full Bayesian comparative phylogeography from genomic data

A challenge to understanding biological diversification is accounting for community-scale processes that cause multiple, co-distributed lineages to co-speciate. Such processes predict non-independent, temporally clustered divergences across taxa. Approximate-likelihood Bayesian computation (ABC) approaches to inferring such patterns from comparative genetic data are very sensitive to prior assumptions and often biased toward estimating shared divergences. We introduce a full-likelihood Bayesian approach, ecoevolity, which takes full advantage of information in genomic data. By analytically integrating over gene trees, we are able to directly calculate the likelihood of the population history from genomic data, and efficiently sample the model-averaged posterior via Markov chain Monte Carlo algorithms. Using simulations, we find that the new method is much more accurate and precise at estimating the number and timing of divergence events across pairs of populations than existing approximate-likelihood methods. Our full Bayesian approach also requires several orders of magnitude less computational time than existing ABC approaches. We find that despite assuming unlinked characters (e.g., unlinked single-nucleotide polymorphisms), the new method performs better if this assumption is violated in order to retain the constant characters of whole linked loci. In fact, retaining constant characters allows the new method to robustly estimate the correct number of divergence events with high posterior probability in the face of character-acquisition biases, which commonly plague loci assembled from reduced-representation genomic libraries. We apply our method to genomic data from four pairs of insular populations of Gekko lizards from the Philippines that are not expected to have co-diverged. Despite all four pairs diverging very recently, our method strongly supports that they diverged independently, and these results are robust to very disparate prior assumptions.

evolutionary biology↗

bioRxiv2018

Peculiar features of the plastids of the colourless alga Euglena longa and photosynthetic euglenophytes unveiled by transcriptome analyses

Background: Euglenophytes are an interesting algal group that emerged within the ancestrally plastid-lacking Euglenozoa phylum by acquiring a plastid from a green algal donor. However, the knowledge of euglenophyte plastid biology and evolution is highly incomplete, partly because euglenophytes have so far been little studied on a genome- and transcriptome-wide scale. Transcriptome data from only a single species, Euglena gracilis, have been exploited to functional insights, but aspects of the plastid biology have been largely neglected.\n\nResults: To expand the resources for studying euglenophyte biology and to improve our knowledge of the euglenophyte plastid function and evolution, we sequenced and analysed the transcriptome of the non-photosynthetic species Euglena longa. The transcriptomic data confirmed the absence of genes for the photosynthetic machinery in this species, but provided a number of candidate plastid-localized proteins bearing the same type of N-terminal bipartite topogenic signals (BTSs) as known from the photosynthetic species E. gracilis. Further comparative analyses using transcriptome assemblies available for E. gracilis and two additional photosynthetic euglenophytes of the genus Eutreptiella enabled us to unveil several salient aspects of the basic plastid infrastructure in euglenophytes. First, a number of plastidial proteins seem to reach the organelle as C-terminal translational fusions with other BTS-bearing proteins. Second, the conventional eubacteria-derived plastidial ribosomal protein L24 is missing and seems to have been replaced by very different homologs of the archaeo-eukaryotic origin. Third, no homologs of any key component of the TOC/TIC system (translocon of the outer/inner chloroplast membrane) and the plastid division apparatus are discernible in euglenophytes, and the machinery for intraplastidial protein targeting has been simplified by the loss of the cpSRP/cpFtsY system and the SEC2 translocon. Lastly, euglenophytes proved to encode a plastid-targeted homolog of the termination factor Rho horizontally acquired from a Lambdaproteobacteria-related donor, suggesting an unprecedented modification of the transcription mechanism in their plastid.\n\nConclusions: Our study suggests that the euglenophyte plastid has been substantially remodelled comparted to its green algal progenitor by both loss of original and acquisition of novel molecular components, making it a particularly interesting subject for further studies.

evolutionary biology↗

bioRxiv2018

Annotation of phenotypes using ontologies: a Gold Standard for the training and evaluation of natural language processing systems

Natural language descriptions of organismal phenotypes - a principal object of study in biology, are abundant in biological literature. Expressing these phenotypes as logical statements using formal ontologies would enable large-scale analysis on phenotypic information from diverse systems. However, considerable human effort is required to make the semantics of phenotype descriptions amenable to machine reasoning by (a) recognizing appropriate on-tological terms for entities in text and (b) stringing these terms into logical statements. Most existing Natural Language Processing tools stop at entity recognition, leaving a need for tools that can assist with both aspects of the task. The recently described Semantic CharaParser aims to meet this need. We describe the first expert-curated Gold Standard corpus for ontology-based annotation of phenotypes from the systematics literature. We use it to evaluate Semantic CharaParsers annotations and explore differences in performance between humans and machine. We use four annotation accuracy metrics that can account for both semantically identical and similar matches. We found that machine-human consistency was significantly lower than inter-curator (human-human) consistency. Surprisingly, allowing curators access to external information that was not available to Semantic CharaParser did not significantly increase the similarity of their annotations to the Gold Standard nor have a significant effect on inter-curator consistency. We found that the similarity of machine annotations to the Gold Standard increased after new ontology terms relevant to the input text had been added. Evaluation by the original authors of the character descriptions indicated that the Gold Standard annotations came closer to representing their intended meaning than did either the curator or machine annotations. These findings point toward ways to better design of software to augment human curators, and the Gold Standard corpus will allow training and assessment of new tools to improve phenotype annotation accuracy at scale.

evolutionary biology↗

bioRxiv2016

A catalogue of Bilaterian-specific genes - their function and expression profiles in early development

Bilateria constitute a monophyletic group of organisms comprising about 99% of all living animals. Since their initial radiation about 540Mya they have evolved a plethora of traits and body forms allowing them to conquer almost any habitat on earth. There are only few truly uniting and shared morphological features retained across the phylum. Unsurprisingly, also the genetic toolkit of bilateria is highly diverged.\n\nIn the light of this divergence we investigated if a set of Bilaterian-specific genes exists and, beyond this, if such genes are related with respect to function and expression patterns among organisms as distant as fly, worm and fish. Using a conservative pyramidal approach of orthology inference we first employed BLAST to extract a set of protein-coding genes which has orthologs in all major branches of Bilateria, but no homologs in non-Bilaterian species. To characterize the proteins with respect to function, we developed a new method for multi-species GO analysis and augmented it by a human-curated annotation based on an extensive literature search. Finally, we extracted characteristic developmental expression profiles for Bilateria from the detailed data available for three model organisms and we explored the relation between expression and function.\n\nWe find 85 clusters of pan-bilaterian proteins. Although some of these proteins belong to common developmental processes, they cover a wide range of biological components, from transcription factors to metabolic enzymes. The 85 groups include myoD, an important regulator of mesodermal cell fate and muscle development, and prospero and several other factors involved in nervous system development. They reveal a so far unknown connection between bilaterian key innovations (mesoderm, complex nervous system) and the emergence of new genes in the ancestor of bilaterians. In addition, the majority of these genes tends to be highly expressed when the adult body plan is constructed. These observations are compatible with the idea that bilaterians are characterized by the unfolding of an additional developmental phase, namely the transition of the larva to morphologically distinct adults.\n\nAuthor SummaryBilateria represent by far the largest and morphologically most diverse clade of all extant animals. The bilaterian radiation dates back to the so-called Cambrian explosion of species. Although bilateria show a large variety of very distinct body plans, they are also characterized by several common developmental and morphological properties, upon which their monophyly is based. Here, we wanted to know whether these common phenotypic features may also have a common genetic basis, manifested by a set of bilaterian lineage-specific genes. To address this question we compared the proteomes of bilaterian and non-bilaterian species and extracted an initial set of a few hundred candidate proteins. Their underlying genes were further post-processed by means of orthology clustering, multi-species GO enrichment, expression analysis and extensive literature mining. This resulted in a set of 85 clusters of orthologous genes with roles in body morphology-, neuronal system-and muscle development, as well as in cell-cell signalling processes. These genes can be regarded as very promising candidates for further investigation of the genetic basis of a pan-bilaterian pheno-or morphotype and they should be highly interesting targets for functional studies in non-model organisms.

Evolutionary Biology↗

bioRxiv2016

A Model for Brain Life History Evolution

Mathematical modeling of brain evolution is scarce, possibly due in part to the difficulty of describing how brain relates to fitness. Yet such modeling is needed to formalize verbal arguments and deepen our understanding of brain evolution. To address this issue, we combine elements of life history and metabolic theories to formulate a metabolically explicit mathematical model for brain life history evolution. We assume that some of the brains energetic expense is due to production (learning) and maintenance (memory) of skills (or cognitive abilities, knowledge, information, etc.). We also assume that individuals use skills to extract energy from the environment, and can allocate this energy to grow and maintain the body, including brain and reproductive tissues. Our model can be used to ask what fraction of growth energy should be allocated to the growth of brain and other tissues at each age under various biological settings as a result of natural selection. We apply the model to find uninvadable allocation strategies under a \"me-against-nature\" setting, namely when overcoming environmentally determined energy-extraction challenges does not involve any interactions with other individuals (possibly except caregivers), and using parameter values for modern humans. The uninvadable strategies yield predictions for brain and body mass throughout ontogeny, as well as for the ages at maturity, adulthood, and brain growth arrest. We find that (1) a me-against-nature setting is enough to generate adult brain and body mass of ancient human scale, (2) large brains are favored by intermediately challenging environments, moderately effective skills, and metabolically expensive memory, and (3) adult skill number is proportional to brain mass when metabolic costs of memory saturate the brain metabolic rate allocated to skills. Overall, our model is a step towards a quantitative theory of brain life history evolution yielding testable quantitative predictions as ecological, demographic, and social factors vary.\n\nAuthor SummaryUnderstanding what promotes the evolution of a given feature is often helped by mathematical modeling. However, mathematical modeling of brain evolution has remained scarce, possibly because of difficulties describing mathematically how the brain relates to reproductive success, which is the currency of evolution. Here we combine elements of two research fields that have previously been successful at detailing how a feature impacts reproductive success (life history theory) and at predicting the individuals body mass throughout its life without the need to describe in detail the inner workings of the body (metabolic theory). We apply the model to a setting where individuals must extract energy from the environment without interacting with other individuals except caregivers (\"me-against-nature\") and parameterize the model with data from humans. In this setting, the model can correctly predict a variety of human features, including large brain sizes. Our model can be used to obtain testable quantitative predictions in terms of brain mass throughout an individuals life from assumed hypotheses promoting brain evolution, such as harsh environments or plentiful social interactions.

Evolutionary Biology↗

bioRxiv2018

Golden Orbweavers Ignore Biological Rules: Phylogenomic and Comparative Analyses Unravel a Complex Evolution of Sexual Size Dimorphism

Instances of sexual size dimorphism (SSD) provide the context for rigorous tests of biological rules of size evolution, such as Copes Rule (phyletic size increase), Renschs Rule (allometric patterns of male and female size), as well as male and female body size optima. In certain spider groups, such as the golden orbweavers (Nephilidae), extreme female-biased SSD (eSSD, female:male body length [≥] 2) is the norm. Nephilid genera construct webs of exaggerated proportions which can be aerial, arboricolous, or intermediate (hybrid). First, we established the backbone phylogeny of Nephilidae using 367 Anchored Hybrid Enrichment (AHE) markers, then combined these data with classical markers for a reference species-level phylogeny. Second, we used the phylogeny to test Cope and Renschs Rules, sex specific size optima, and the coevolution of web size, type, and features with female and male body size and their ratio, SSD. Male, but not female, size increases significantly over time, and refutes Copes Rule. Allometric analyses reject the converse, Renschs Rule. Male and female body sizes are uncorrelated. Female size evolution is random, but males evolve towards an optimum size (3.2-4.9 mm). Overall, female body size correlates positively with absolute web size. However, intermediate sized females build the largest webs (of the hybrid type), giant female Nephila and Trichonephila build smaller webs (of the aerial type), and the smallest females build the smallest webs (of the arboricolous type). We propose taxonomic changes based on the criteria of clade age, monophyly and exclusivity, classification information content, diagnosability, and arachnological community practice. We resurrect the family Nephilidae Simon 1894 that contains Clitaetra Simon 1889, the Cretaceous Geratonephila Poinar & Buckley 2012, Herennia Thorell 1877, Indoetra Kuntner 2006, new rank, Nephila Leach 1815, Nephilengys L. Koch 1872, Nephilingis Kuntner 2013, and Trichonephila Dahl 1911, new rank. We propose the new clade Orbipurae to contain Araneidae Clerck 1757, Phonognathidae Simon 1894, new rank, and Nephilidae. Nephilid female gigantism is a phylogenetically-ancient phenotype (over 100 ma), as is eSSD, though their magnitudes vary by lineage and, to some extent, biogeographically.

evolutionary biology↗

bioRxiv2016

Contribution of mobile elements to the uniqueness of human genome with more than 15,000 human-specific insertions

Mobile elements (MEs) collectively constituted to at least 51% of the human genome. Due to their past incremental accumulation and ongoing DNA transposition of members from certain subfamilies, MEs serve as a significant source for both inter- and intra-species genetic diversity during primate and human evolution. Since MEs can exert direct impact on gene function via a plethora of mechanism, it is believed that the ME-derived genetic diversity has contributed to the phenotypic differences between human and non-human primates, as well as among human populations and individuals. To define the specific contribution of MEs in making Human sapiens as a biologically unique species, we aim to compile a complete list of MEs that are only uniquely present in the human genome, i.e., human-specific MEs (HS-MEs).\n\nBy making use of the most recent reference genome sequences for human and many other primates and a unbiased more robust and integrative multi-way comparative genomic approach, we identified a total of 15,463 HS-MEs. This list of HS-MEs represents a 120% increase from prior studies with over 8,000 being newly identified as HS-MEs. Collectively, these ~15,000 HS-MEs have contributed to a total of 15 million base pair (Mbp) sequence increase through insertion, generation of target site duplications, and transductions, as well as a 0.5 Mbp sequence loss via insertion- mediated deletions, leading to a net total of 14.5 Mbp genome size increase. Other new observations made with these HS-MEs include: 1) identification of several additional ME subfamilies with significant transposition activities not visible with prior smaller datasets (e.g. L1HS, L1PA2, and HERV-K); 2) A clear similarity of the retrotransposition mechanism among L1, Alus, and SVAs that is distinct from HERVs based on the pre- integration site sequence motifs; 3) Y-chromosome as a strikingly hot target for HS-MEs, particularly for LTRs, which showed an insertion rate 15 times higher than the genome average; 4) among the ME types, SVAs seem to show a very strong bias in inserting into existing SVAs. Among the HS-MEs, more than 8,000 elements were integrated into the vicinity of ~4900 unique genes, in regions including CDS, untranslated exon regions, promoters, and introns of protein coding genes, as well as promoters and exons of non- coding RNAs. In seven cases, MEs participate in protein coding. Furthermore, 1,213 HS-MEs contributed to a total of 3,124 experimentally identified binding sites for 146 of the 161 transcriptional factors in association with 622 genes. All these data suggest that these HS-MEs, despite being very young, already showed sufficient sign for their participation in gene function via regulation of transcription, splicing, and protein coding, with more potential for future participation.\n\nIn conclusion, our results demonstrate that the amount of MEs uniquely occurred in the human genome is much higher than previously known, and we predict that the same is true regarding their impact on human genome evolution and function. The comprehensive list of HS-MEs provides an important reference resource for studying the impact of DNA transposition in human genome evolution and gene function.

evolutionary biology↗

bioRxiv2013

A Scalable Formulation for Engineering Combination Therapies for Evolutionary Dynamics of Disease

It has been shown that optimal controller synthesis for positive systems can be formulated as a linear program. Leveraging these results, we propose a scalable iterative algorithm for the systematic design of sparse, small gain feedback strategies that stabilize the evolutionary dynamics of a generic disease model. We achieve the desired feedback structure by augmenting the optimization problems with {ell}1 and {ell}2 regularization terms, and illustrate our method on an example inspired by an experimental study aimed at finding appropriate HIV neutralizing antibody therapy combinations in the presence of escape mutants.

Evolutionary Biology↗

bioRxiv2013

Population genomics of parallel hybrid zones in the mimetic butterflies, H. melpomene and H. erato

Hybrid zones can be valuable tools for studying evolution and identifying genomic regions responsible for adaptive divergence and underlying phenotypic variation. Hybrid zones between subspecies of Heliconius butterflies can be very narrow and are maintained by strong selection acting on colour pattern. The co-mimetic species H. erato and H. melpomene have parallel hybrid zones where both species undergo a change from one colour pattern form to another. We use restriction associated DNA sequencing to obtain several thousand genome wide sequence markers and use these to analyse patterns of population divergence across two pairs of parallel hybrid zones in Peru and Ecuador. We compare two approaches for analysis of this type of data; alignment to a reference genome and de novo assembly, and find that alignment gives the best results for species both closely (H. melpomene) and distantly (H. erato, ~15% divergent) related to the reference sequence. Our results confirm that the colour pattern controlling loci account for the majority of divergent regions across the genome, but we also detect other divergent regions apparently unlinked to colour pattern differences. We also use association mapping to identify previously unmapped colour pattern loci, in particular the Ro locus. Finally, we identify within our sample a new cryptic population of H. timareta in Ecuador, which occurs at relatively low altitude and is mimetic with H. melpomene malleti.

Evolutionary Biology↗

bioRxiv2013

Genome-wide targets of selection: female response to experimental removal of sexual selection in Drosophila melanogaster

Despite the common assumption that promiscuity should in general be favored in males, but not in females, to date there is no consensus on the general impact of multiple mating on female fitness. Notably, very little is known about the genetic and physiological features underlying the female response to sexual selection pressures. By combining an experimental evolution approach with genomic techniques, we investigated the effects of single and multiple matings on female fecundity and gene expression. We experimentally manipulated the mating system in replicate populations of Drosophila melanogaster by removing sexual selection, with the aim of testing differences in short term post-mating effects of females evolved under different mating strategies. We show that monogamous females suffer decreased fecundity, a decrease that was partially recovered by experimentally reversing the selection pressure back to the ancestral promiscuous state. The post-mating gene expression profiles of monogamous females differ significantly from promiscuous females, involving 9% of the genes tested. These transcripts are active in several tissues, mainly ovaries, neural tissues and midgut, and are involved in metabolic processes, reproduction and signaling pathways. Our results demonstrate how the female post-mating response can evolve under different mating systems, and provide novel insights into the genes targeted by sexual selection in females, by identifying a list of candidate genes responsible for the decrease in female fecundity in the absence of promiscuity.

Evolutionary Biology↗

bioRxiv2013

The Origin of Human-infecting Avian Influenza A H6N1 Virus

In this study, we retraced the origin of the reported avian influenza A H6N1 virus infecting a 20-year-old woman in Taiwan. As we know, this is the first reported case of human infection by the H6N1 virus, because this subtype virus usually circulates in birds and poultry. Therefore it is crucial to know how this virus attained the ability to infect humans. Using phylogenetic analysis, we found that this virus was derived from reassortments of multiple lineages of H6N1 viruses and H5N2 viruses. The results deepen our understanding of how the new human-infecting virus originated and based on these we discussed possible explanations for the H6N1 infection of humans. Our results, together with recent studies of H7N9 viruses which result in severe disorders, suggest that reassortments among avian-type viruses are quite often, which may sometimes result in fatal infections in humans. Thus a close watch on the circulation of avian influenza viruses is pretty necessary.

Evolutionary Biology↗

bioRxiv2013

Natural Allelic Variations of Xenobiotic Enzymes Pleiotropically Affect Sexual Dimorphism in Oryzias latipes

Summary Summary Highlights Results and Discussion Accession Numbers Reference Sexual dimorphisms, which are phenotypic differences between males and females, are driven by sexual selection [1, 2]. Interestingly, sexually selected traits show geographic variations within species despite strong directional selective pressures [3, 4]. However, genetic factors that regulate varied sexual differences remain unknown. In this study, we show that polymorphisms in cytochrome P450 (CYP) 1B1, which encodes a xenobiotic-metabolising enzyme, are associated with local differences of sexual dimorphisms in the anal fin morphology of medaka fish (Oryzias latipes). High and low activity CYP1B1 alleles increased and decreased differences in anal fin sizes ...

Evolutionary Biology↗

bioRxiv2013

Predictability of adaptive evolution under the successive fixation assumption

Predicting the course of evolution is critical for solving current biomedical challenges such as cancer and the evolution of drug resistant pathogens. One approach to studying evolutionary predictability is to observe repeated, independent evolutionary trajectories of similar organisms under similar selection pressures in order to empirically characterize this adaptive fitness landscape. As this approach is infeasible for many natural systems, a number of recent studies have attempted to gain insight into the adaptive fitness landscape by testing the plausibility of different orders of appearance for a specific set of adaptive mutations in a single adaptive trajectory. While this approach is technically feasible for systems with very few available adaptive mutations, the usefulness of this approach for predicting evolution in situations with highly polygenic adaptation is unknown. It is also unclear whether the presence of stable adaptive polymorphisms can influence the predictability of evolution as measured by these methods. In this work, we simulate adaptive evolution under Fishers geometric model to study evolutionary predictability. Remarkably, we find that the predictability estimated by these methods are anti-correlated, and that the presence of stable adaptive polymorphisms can both qualitatively and quantitatively change the predictability of evolution.

Evolutionary Biology↗

bioRxiv2013

Species Delimitation using Genome-Wide SNP Data

The multi-species coalescent has provided important progress for evolutionary inferences, including increasing the statistical rigor and objectivity of comparisons among competing species delimitation models. However, Bayesian species delimitation methods typically require brute force integration over gene trees via Markov chain Monte Carlo (MCMC), which introduces a large computation burden and precludes their application to genomic-scale data. Here we combine a recently introduced dynamic programming algorithm for estimating species trees that bypasses MCMC integration over gene trees with sophisticated methods for estimating marginal likelihoods, needed for Bayesian model selection, to provide a rigorous and computationally tractable technique for genome-wide species delimitation. We provide a critical yet simple correction that brings the likelihoods of different species trees, and more importantly their corresponding marginal likelihoods, to the same common denominator, which enables direct and accurate comparisons of competing species delimitation models using Bayes factors. We test this approach, which we call Bayes factor delimitation (*with genomic data; BFD*), using common species delimitation scenarios with computer simulations. Varying the numbers of loci and the number of samples suggest that the approach can distinguish the true model even with few loci and limited samples per species. Misspecification of the prior for population size{theta} has little impact on support for the true model. We apply the approach to West African forest geckos (Hemidactylus fasciatus complex) using genome-wide SNP data data. This new Bayesian method for species delimitation builds on a growing trend for objective species delimitation methods with explicit model assumptions that are easily tested.

Evolutionary Biology↗

bioRxiv2013

An Adaptive Threshold in Mammalian Neocortical Evolution

Expansion of the neocortex is a hallmark of human evolution. However, it remains an open question what adaptive mechanisms facilitated its expansion. Here we show, using gyrencephaly index (GI) and other physiological and life-history data for 102 mammalian species, that gyrencephaly is an ancestral mammalian trait. We provide evidence that the evolution of a highly folded neocortex, as observed in humans, requires the traversal of a threshold of [~]109 neurons, and that species above and below the threshold exhibit a bimodal distribution of physiological and life-history traits, establishing two phenotypic groups. We identify, using discrete mathematical models, proliferative divisions of pro-genitors in the basal compartment of the developing neocortex as evolutionarily necessary and sufficient for generating a fourteen-fold increase in daily prenatal neuron production and thus traversal of the neuronal threshold. Finally, using RNA-seq data from fetal human neocortical germinal zones, we show a genomic correlate to the neuron threshold in the differential conservation of long intergenic non-coding RNA. (see arXiv:1304.5412)

Evolutionary Biology↗

bioRxiv2013

Evaluating the use of ABBA-BABA statistics to locate introgressed loci

Several methods have been proposed to test for introgression across genomes. One method tests for a genome-wide excess of shared derived alleles between taxa using Pattersons D statistic, but does not establish which loci show such an excess or whether the excess is due to introgression or ancestral population structure. Several recent studies have extended the use of D by applying the statistic to small genomic regions, rather than genome-wide. Here, we use simulations and whole genome data from Heliconius butterflies to investigate the behavior of D in small genomic regions. We find that D is unreliable in this situation as it gives inflated values when effective population size is low, causing D outliers to cluster in genomic regions of reduced diversity. As an alternative, we propose a related statistic [Formula] a modified version of a statistic originally developed to estimate the genome-wide fraction of admixture. [Formula] is not subject to the same biases as D, and is better at identifying introgressed loci. Finally, we show that both D and [Formula] outliers tend to cluster in regions of low absolute divergence (dXY), which can confound a recently proposed test for differentiating introgression from shared ancestral variation at individual loci.

Evolutionary Biology↗

bioRxiv2013

The importance of population growth and regulation in human life history evolution

Explaining the evolution of human life history characteristics remains an outstanding problem to evolutionary anthropologists. Progress is hindered by common misunderstandings of how selection works in age-structured populations. I review two important results of life history theory related to demography. First, different life history strategies evolve under density-independent and density-dependent population growth. Second, and more poorly appreciated, different kinds of density-dependence also select for different life history strategies; assuming zero population growth alone is insufficient to determine the optimal strategy. I show that these facts are more than methodological niceties by reanalyzing the model by Kaplan et al. (2000) and showing that the results depend strongly on the form of population regulation assumed. This analysis suggests that progress in human life history theory requires better understanding of the demography of our ancestors. I close with a discussion of empirical implications.

Evolutionary Biology↗