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bioRxiv2015

Genome-wide and single-base resolution DNA methylomes of the Sea Lamprey (Petromyzon marinus) Reveal Gradual Transition of the Genomic Methylation Pattern in Early Vertebrates

In eukaryotes, cytosine methylation is a primary heritable epigenetic modification of the genome that regulates many cellular processes. While the whole-genome methylation pattern has been generally conserved in different eukaryotic groups, invertebrates and vertebrates exhibit two distinct patterns. Whereas almost all CpG sites are methylated in most vertebrates, with the exception of short unmethylated regions call CpG islands, the most frequent pattern in invertebrate animals is mosaic methylation, comprising domains of heavily methylated DNA interspersed with domains that are methylation free. The mechanism by which the genome methylation pattern transited from a mosaic to a global pattern and the role of the one or two-round whole-genome duplication in this transition remain largely elusive, partly owing to the lack of methylome data from early vertebrates. In this study, we used the whole-genome bisulfite-sequencing technology to investigate the genome-wide methylation in three tissues (heart, muscle, and sperm) from the sea lamprey, an extant Agarthan vertebrate. Analyses of methylation level and the extent of CpG dinucleotide depletion of geneencoding, intergenic and promoter regions revealed a gradual increase in the methylation level from invertebrates to vertebrates, with the sea lamprey exhibiting an intermediate position. In addition, the methylation level of the majority of CpGs was intermediate in each sea lamprey tissue, indicating a high level of heterogeneity of methylation status between individual cells. In this regard, we defined the genomic methylation pattern of sea lamprey as \"global genomic DNA intermediate methylation\". The methylation features in different genomic regions, such as the transcription start site (TSS) region of the gene body, exon-intron boundaries, transposons, as well as genes grouping with different expression levels, supported the gradual methylation transition hypothesis. We further discussed that the copy number difference in DNA methylation transferases and the loss of the PWWP domain and/or DNTase domain in DNMT3 sub-family enzymes may have contributed to the methylation pattern transition in early vertebrates. These findings demonstrate an intermediate genomic methylation pattern between invertebrates and jawed vertebrates, providing evidence that supports the hypothesis that methylation patterns underwent a gradual transition from invertebrates (mosaic) to vertebrates (global).

Evolutionary Biology↗

bioRxiv2015

Male sex pheromone components in the butterfly Heliconius melpomene

Sex specific pheromones are known to play an important role in butterfly courtship, and may influence both individual reproductive success and reproductive isolation between species. Extensive ecological, behavioural and genetic studies of Heliconius butterflies have made a substantial contribution to our understanding of speciation. Male pheromones, although long suspected to play an important role, have received relatively little attention in this genus. Here, we combine morphological, chemical, and behavioural analyses of male pheromones in the Neotropical butterfly Heliconius melpomene. First, we identify putative androconia that are specialized brush-like scales that lie within the shiny grey region of the male hindwing. We then describe putative male sex pheromone compounds, which are largely confined to the androconial region of the hindwing of mature males, but are absent in immature males and females. Finally, behavioural choice experiments reveal that females of H. melpomene, H. erato and H. timareta strongly discriminate against conspecific males which have their androconial region experimentally blocked. As well as demonstrating the importance of chemical signalling for female mate choice in Heliconius butterflies, the results describe structures involved in release of the pheromone and a list of potential male sex pheromone compounds.

Evolutionary Biology↗

bioRxiv2015

Empirical evidence for heterozygote advantage in adapting diploid populations of Saccharomyces cerevisiae

Adaptation in diploids is predicted to proceed via mutations that are at least partially dominant in fitness. Recently we argued that many adaptive mutations might also be commonly overdominant in fitness. Natural (directional) selection acting on overdominant mutations should drive them into the population but then, instead of bringing them to fixation, should maintain them as balanced polymorphisms via heterozygote advantage. If true, this would make adaptive evolution in sexual diploids differ drastically from that of haploids. Unfortunately, the validity of this prediction has not yet been tested experimentally. Here we performed 4 replicate evolutionary experiments with diploid yeast populations (Saccharomyces cerevisiae) growing in glucose-limited continuous cultures. We sequenced 24 evolved clones and identified initial adaptive mutations in all four chemostats. The first adaptive mutations in all four chemostats were three CNVs, all of which proved to be overdominant in fitness. The fact that fitness overdominant mutations were always the first step in independent adaptive walks strongly supports the prediction that heterozygote advantage can arise as a common outcome of directional selection in diploids and demonstrates that overdominance of de novo adaptive mutations in diploids is not rare.

Evolutionary Biology↗

bioRxiv2015

Accelerated DNA evolution in rats is driven by differential methylation in sperm

Lamarckian inheritance has been largely discredited until the recent discovery of transgenerational epigenetic inheritance. However, transgenerational epigenetic inheritance is still under debate for unable to rule out DNA sequence changes as the underlying cause for heritability. Here, through profiling of the sperm methylomes and genomes of two recently diverged rat subspecies, we analyzed the relationship between epigenetic variation and DNA variation, and their relative contribution to evolution of species. We found that only epigenetic markers located in differentially methylated regions (DMRs) between subspecies, but not within subspecies, can be stably and effectively passed through generations. DMRs in response to both random and stable environmental difference show increased nucleotide diversity, and we demonstrated that it is variance of methylation level but not deamination caused by methylation driving increasing of nucleotide diversity in DMRs, indicating strong relationship between environment-associated changes of chromatin accessibility and increased nucleotide diversity. Further, we detected that accelerated fixation of DNA variants occur only in inter-subspecies DMRs in response to stable environmental difference but not intra-subspecies DMRs in response to random environmental difference or non-DMRs, indicating that this process is possibly driven by environment-associated fixation of divergent methylation status. Our results thus establish a bridge between Lamarckian inheritance and Darwinian selection.

Evolutionary Biology↗

bioRxiv2015

Evolutionary dynamics of a quantitative trait in a finite asexual population.

In finite populations, mutation limitation and genetic drift can hinder evolutionary diversification. We consider the evolution of a quantitative trait in an asexual population whose size can vary and depends explicitly on the trait. Previous work showed that evolutionary branching is certain (\"deterministic branching\") above a threshold population size, but uncertain (\"stochastic branching\") below it. Using the stationary distribution of the populations trait variance, we identify three qualitatively different sub-domains of \"stochastic branching\" and illustrate our results using a model of social evolution. We find that in very small populations, branching will almost never be observed; in intermediate populations, branching is intermittent, arising and disappearing over time; in larger populations, finally, branching is expected to occur and persist for substantial periods of time. Our study provides a clearer picture of the ecological conditions that facilitate the appearance and persistence of novel evolutionary lineages in the face of genetic drift.

Evolutionary Biology↗

bioRxiv2015

Mutation is a sufficient and robust predictor of genetic variation for mitotic spindle traits in C. elegans

Different types of phenotypic traits consistently exhibit different levels of genetic variation in natural populations. There are two potential explanations: either mutation produces genetic variation at different rates, or natural selection removes or promotes genetic variation at different rates. Whether mutation or selection is of greater general importance is a longstanding unresolved question in evolutionary genetics. Where the input of genetic variation by mutation differs between traits, it is usually uncertain whether the difference is the result of different mutational effects (\"mutational robustness\") or different numbers of underlying loci (\"mutational target\"), although conventional wisdom favors the latter. We report mutational variances (VM) for 19 traits related to the first mitotic cell division in C. elegans, and compare them to the standing genetic variances (VG) for the same suite of traits in a worldwide collection C. elegans. Two robust conclusions emerge. First, the mutational process is highly repeatable: the correlation between VM in two independent sets of mutation accumulation lines is ~0.9. Second, VM for a trait is a very good predictor of VG for that trait: the correlation between VM and VG is ~0.9. This result is predicted for a population at mutation-selection balance; it is not predicted if balancing selection plays a primary role in maintaining genetic variation. Goodness- of-fit of the data to two simple models of mutation suggest that differences in mutational effects may be a more important cause of differences in VM between traits than differences in the size of the mutational target.

Evolutionary Biology↗

bioRxiv2015

Extreme positive allometry of animal adhesive pads and the size limits of adhesion-based climbing.

Organismal functions are size-dependent whenever body surfaces supply body volumes. Larger organisms can develop strongly folded internal surfaces for enhanced diffusion, but in many cases areas cannot be folded so that their enlargement is constrained by anatomy, presenting a problem for larger animals. Here, we study the allometry of adhesive pad area in 225 climbing animal species, covering more than seven orders of magnitude in weight. Across all taxa, adhesive pad area showed extreme positive allometry and scaled with weight, implying a 200-fold increase of relative pad area from mites to geckos. However, allometric scaling coefficients for pad area systematically decreased with taxonomic level, and were close to isometry when evolutionary history was accounted for, indicating that the substantial anatomical changes required to achieve increases in relative pad area are limited by phylogenetic constraints. Using a comparative phylogenetic approach, we found that the departure from isometry is almost exclusively caused by large differences in size-corrected pad area between arthropods and vertebrates. To mitigate the expected decrease of weight-specific adhesion within closely related taxa where pad area scaled close to isometry, data for several taxa suggest that the pads adhesive strength increased for larger animals. The combination of adjustments in relative pad area for distantly related taxa and changes in adhesive strength for closely related groups helps explain how climbing with adhesive pads has evolved in animals varying over seven orders of magnitude in body weight. Our results illustrate the size limits of adhesion-based climbing, with profound implications for large-scale bio-inspired adhesives.

Evolutionary Biology↗

bioRxiv2015

On the Apportionment of Population Structure

Measures of population differentiation, such as FST, are traditionally derived from the partition of diversity within and between populations. However, the emergence of population clusters from multilocus analysis is a function of genetic structure (departures from panmixia) rather than of diversity. If the populations are close to panmixia, slight differences between the mean pairwise distance within and between populations (low FST) can manifest as strong separation between the populations, thus population clusters are often evident even when the vast majority of diversity is partitioned within populations rather than between them. For any given FST value, clusters can be tighter (more panmictic) or looser (more stratified), and in this respect higher FST does not always imply stronger differentiation. In this study we propose a measure for the partition of structure, denoted EST, which is more consistent with results from clustering schemes. Crucially, our measure is based on a statistic of the data that is a good measure of internal structure, mimicking the information extracted by unsupervised clustering or dimensionality reduction schemes. To assess the utility of our metric, we ranked various human (HGDP) population pairs based on FST and EST and found substantial differences in ranking order. In some cases examined, most notably among isolated Amazonian tribes, EST ranking seems more consistent with demographic, phylogeographic and linguistic measures of classification compared to FST. Thus, EST may at times outperform FST in identifying evolutionary significant differentiation.

Evolutionary Biology↗

bioRxiv2015

Archaic adaptive introgression in TBX15/WARS2

A recent study conducted the first genome-wide scan for selection in Inuit from Greenland using SNP chip data. Here, we report that selection in the region with the second most extreme signal of positive selection in Greenlandic Inuit favored a deeply divergent haplotype that is closely related to the sequence in the Denisovan genome, and was likely introgressed from an archaic population. The region contains two genes, WARS2 and TBX15, and has previously been associated with adipose tissue differentiation and body-fat distribution in humans. We show that the adaptively introgressed allele has been under selection in a much larger geographic region than just Greenland. Furthermore, it is associated with changes in expression of WARS2 and TBX15 in multiple tissues including the adrenal gland and subcutaneous adipose tissue, and with regional DNA methylation changes in TBX15.

Evolutionary Biology↗

bioRxiv2015

Genetic diversity on the human X chromosome does not support a strict pseudoautosomal boundary

Unlike the autosomes, recombination between the X chromosome and Y chromosome often thought to be constrained to two small pseudoautosomal regions (PARs) at the tips of each sex chromosome. The PAR1 spans the first 2.7 Mb of the proximal arm of the human sex chromosomes, while the much smaller PAR2 encompasses the distal 320 kb of the long arm of each sex chromosome. In addition to the PAR1 and PAR2, there is a human-specific X-transposed region that was duplicated from the X to the Y. The X-transposed region is often not excluded from X-specific analyses, unlike the PARs, because it is not thought to routinely recombine. Genetic diversity is expected to be higher in recombining regions than in non-recombining regions because recombination reduces the effect of linked selection. In this study, we investigate patterns of genetic diversity in noncoding regions across the entire X chromosome of a global sample of 26 unrelated genetic females. We observe that genetic diversity in the PAR1 is significantly greater than the non-recombining regions (nonPARs). However, rather than an abrupt drop in diversity at the pseudoautosomal boundary, there is a gradual reduction in diversity from the recombining through the non-recombining region, suggesting that recombination between the human sex chromosomes spans across the currently defined pseudoautosomal boundary. In contrast, diversity in the PAR2 is not significantly elevated compared to the nonPAR, suggesting that recombination is not obligatory in the PAR2. Finally, diversity in the X-transposed region is higher than the surrounding nonPAR regions, providing evidence that recombination may occur with some frequency between the X and Y in the XTR.

Evolutionary Biology↗

bioRxiv2015

Modeling Continuous Admixture

Human migration and human isolation serve as the driving forces of modern human civilization. Recent migrations of long isolated populations have resulted in genetically admixed populations. The history of population admixture is generally complex; however, understanding the admixture process is critical to both evolutionary and medical studies. Here, we utilized admixture induced linkage disequilibrium (LD) to infer occurrence of continuous admixture events, which is common for most existing admixed populations. Unlike previous studies, we expanded the typical continuous admixture model to a more general admixture scenario with isolation after a certain duration of continuous gene flow. Based on the extended models, we developed a method based on weighted LD to infer the admixture history considering continuous and complex demographic process of gene flow between populations. We evaluated the performance of the method by computer simulation and applied our method to real data analysis of a few well-known admixed populations.

Evolutionary Biology↗

bioRxiv2015

Bat Accelerated Regions Identify a Bat Forelimb Specific Enhancer in the HoxD Locus

The molecular events leading to the development of the bat wing remain largely unknown, and are thought to be caused, in part, by changes in gene expression during limb development. These expression changes could be instigated by variations in gene regulatory enhancers. Here, we used a comparative genomics approach to identify regions that evolved rapidly in the bat ancestor but are highly conserved in other vertebrates. We discovered 166 bat accelerated regions (BARs) that overlap H3K27ac and p300 ChIP-seq peaks in developing mouse limbs. Using a mouse enhancer assay, we show that five Myotis lucifugus BARs drive gene expression in the developing mouse limb, with the majority showing differential enhancer activity compared to the mouse orthologous BAR sequences. These include BAR116, which is located telomeric to the HoxD cluster and had robust forelimb expression for the M. lucifugus sequence and no activity for the mouse sequence at embryonic day 12.5. Developing limb expression analysis of Hoxd10-Hoxd13 in Miniopterus natalensis bats showed a high-forelimb weak-hindlimb expression for Hoxd10-Hoxd11, similar to the expression trend observed for M. lucifugus BAR116 in mice, suggesting that it could be involved in the regulation of the bat HoxD complex. Combined, our results highlight novel regulatory regions that could be instrumental for the morphological differences leading to the development of the bat wing.\n\nAuthor SummaryThe limb is a classic example of vertebrate homology and is represented by a large range of morphological structures such as fins, legs and wings. The evolution of these structures could be driven by alterations in gene regulatory elements that have critical roles during development. To identify elements that may contribute to bat wing development, we characterized sequences that are conserved between vertebrates, but changed significantly in the bat lineage. We then overlapped these sequences with predicted developing limb enhancers as determined by ChIP-seq, finding 166 bat accelerated sequences (BARs). Five BARs that were tested for enhancer activity in mice all drove expression in the limb. Testing the mouse orthologous sequence showed that three had differences in their limb enhancer activity as compared to the bat sequence. Of these, BAR116 was of particular interest as it is located near the HoxD locus, an essential gene complex required for proper spatiotemporal patterning of the developing limb. The bat BAR116 sequence drove robust forelimb expression but the mouse BAR116 sequence did not show enhancer activity. These experiments correspond to analyses of HoxD gene expressions in developing bat limbs, which had strong forelimb versus weak hindlimb expression for Hoxd10-11. Combined, our studies highlight specific genomic regions that could be important in shaping the morphological differences that led to the development of the bat wing.

Evolutionary Biology↗

bioRxiv2015

Low virulence evolves as a bet-hedging strategy in fluctuating environment

The effect of fluctuating environmental conditions (i.e. environmental stochasticity) on the evolution of virulence has been broadly overlooked, presumably due to a lack of connection between the fields of evolutionary epidemiology and insect ecology. Practitioners of the latter have known for a long time that stochastic environmental variations can impact the population dynamics of many insects, some of which are vectors of infectious diseases. Here we investigate whether environmental stochasticity affecting a vectors life history can have an indirect impact on the evolutionarily expected virulence of the parasite, using Chagas disease as an example. We model the evolution of virulence using the adaptive dynamics framework, showing that parasite virulence should decrease when the vector's dynamics randomly change in time. The decrease is even more pronounced when environmental variations are frequent and ample. This decrease in virulence can be viewed as a bet-hedging strategy: when a parasite is at a risk of not being transmitted (e.g. because vectors are scarce), its best option is to stay in the host longer - that is, to be less virulent. Lowering virulence is thus very similar to increasing iteroparity, a well-known risk-spreading strategy, and should be expected to evolve whenever parasite transmission varies randomly in time.

Evolutionary Biology↗

bioRxiv2015

Evolutionary dynamics of cytoplasmic segregation and fusion: Mitochondrial mixing facilitated the evolution of sex at the origin of eukaryotes

Sexual reproduction is a trait shared by all complex life, but explaining its origin and evolution remains a major theoretical challenge. Virtually all theoretical work on the evolution of sex has focused on the benefits of reciprocal recombination among nuclear genes, paying little attention to the dynamics of mitochondrial genes. Here I develop a mathematical model to study the evolution of alleles inducing cell fusion in an ancestral population of clonal proto-eukaryotes. Mitochondrial mixing masks the detrimental effects of faulty organelles and drives the evolution of sexual cell fusion despite the declining long-term population fitness. Cell-fusion alleles fix under negative epistatic interactions between mitochondrial mutations and strong purifying selection, low mutation load and weak mitochondrial-nuclear associations. I argue that similar conditions could have been maintained throughout the eukaryogenesis, favoring the evolution of sexual cell fusion and meiotic recombination without compromising the stability of the emerging complex cell.

Evolutionary Biology↗

bioRxiv2015

When three traits make a line: Evolution of phenotypic plasticity and genetic assimilation through linear reaction norms in stochastic environments

Genetic assimilation results from selection on phenotypic plasticity, but quantitative genetics models of linear reaction norms considering intercept and slope as traits do not fully incorporate the process of genetic assimilation. We argue that intercept-slope reaction norm models are insufficient representations of genetic effects on linear reaction norms, and that considering reaction norm intercept as a trait is unfortunate because the definition of this trait relates to a specific environmental value (zero) and confounds genetic effects on reaction norm elevation with genetic effects on environmental perception. Instead we suggest a model with three traits representing genetic effects that respectively (i) are independent of the environment, (ii) alter the sensitivity of the phenotype to the environment, and (iii) determine how the organism perceives the environment. The model predicts that, given sufficient additive genetic variation in environmental perception, the environmental value at which reaction norms tend to cross will respond rapidly to selection after an abrupt environmental change, and eventually become equal to the new mean environment. This readjustment of the zone of canalization becomes completed without changes in genetic correlations, genetic drift or imposing any fitness costs on maintaining plasticity. The asymptotic evolutionary outcome of this three-trait linear reaction norm generally entails a lower degree of phenotypic plasticity than the two-trait model, and maximum expected fitness does not occur at the mean trait values in the population.

Evolutionary Biology↗

bioRxiv2015

Genetic recombination as DNA repair

Maintenance of sexual reproduction and genetic recombination imposes physiological costs when compared to parthenogenic reproduction, most prominently: for maintaining the corresponding (molecular) machinery, for finding a mating partner, and through the decreased fraction of females in a population, which decreases the reproductive capacity. Based on principles from information theory, we have previously developed a new population genetic model, and applying it in simulations, we have recently hypothesized that all species maintain the maximum genomic complexity that is required by their niche and allowed by their mutation rate and selection intensity. Applying this idea to the complexity overhead of recombination maintenance, its costs must be more than compensated by an additional capacity for complexity in recombining populations. Here, we show a simple mechanism, where recombination helps to maintain larger biases of alleles frequencies in a population, so the advantageous alleles can have increased frequency. This allows recombining populations to maintain higher fitness and phenotypic efficiency in comparison with asexual populations with the same parameters. Random mating alone already significantly increases the ability to maintain genomic and phenotypic complexity. Sexual selection provides additional capacity for this complexity. The model can be considered as a unifying synthesis of previous hypotheses about the roles of recombination in Muller's ratchet, mutation purging and Red Queen dynamics, because the introduction of recombination both increases population frequencies of beneficial alleles and decreases detrimental ones. In addition, we suggest simple explanations for niche-dependent prevalence of transient asexuality and the exceptional asexual lineage of Bdelloid rotifers.

Evolutionary Biology↗

bioRxiv2015

An Invariants-based Method for Efficient Identification of Hybrid Species From Large-scale Genomic Data

Coalescent-based species tree inference has become widely used in the analysis of genome-scale multilocus and SNP datasets when the goal is inference of a species-level phylogeny. However, numerous evolutionary processes are known to violate the assumptions of a coalescence-only model and complicate inference of the species tree. One such process is hybrid speciation, in which a species shares its ancestry with two distinct species. Although many methods have been proposed to detect hybrid speciation, only a few have considered both hybridization and coalescence in a unified framework, and these are generally limited to the setting in which putative hybrid species must be identified in advance. Here we propose a method that can examine genome-scale data for a large number of taxa and detect those taxa that may have arisen via hybridization, as well as their potential \"parental\" taxa. The method is based on a model that considers both coalescence and hybridization together, and uses phylogenetic invariants to construct a test that scales well in terms of computational time for both the number of taxa and the amount of sequence data. We test the method using simulated data for up 20 taxa and 100,000bp, and find that the method accurately identifies both recent and ancient hybrid species in less than 30 seconds. We apply the method to two empirical datasets, one composed of Sistrurus rattlesnakes for which hybrid speciation is not supported by previous work, and one consisting of several species of Heliconius butterflies for which some evidence of hybrid speciation has been previously found.

Evolutionary Biology↗

bioRxiv2015

Independent evolution of ab- and adaxial stomatal density enables adaptation

O_LIAre organisms free to reach their adaptive optima or constrained by hard-wired developmental programs? Recent evidence suggests that the arrangement of stomata on abaxial (lower) and adaxial (upper) leaf surfaces may be an important adaptation in plants, but stomatal traits on each surface likely share developmental pathways that could hamper evolution.\nC_LIO_LIWe reviewed the quantitative genetics of stomatal density to look for loci that (1) affected ab- or adaxial density independently or (2) pleiotropically affected stomatal density on both surfaces. We also used phylogenetic comparative methods to test for independent versus correlated evolution of stomatal traits (density, size, and pore index) on each surface from 14 amphistomatous wild tomato taxa (Solanum; Solanaceae).\nC_LIO_LINaturally occurring and laboratory-induced genetic variation alters stomatal density on one surface without affecting the other, indicating that development does not strongly constrain the spectrum of available mutations. Among wild tomato taxa, traits most closely related to function (stomatal pore index and density) evolved independently on each surface, whereas stomatal size was constrained by correlated evolution.\nC_LIO_LIGenetics and phylogenetics demonstrate mostly independent evolution of stomatal function on each leaf surface, facilitating largely unfettered access to fitness optima.\nC_LI

Evolutionary Biology↗