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bioRxiv2015

Ebola virus is evolving but not changing: no evidence for functional change in EBOV from 1976 to the 2014 outbreak

The Ebola epidemic is having a devastating impact in West Africa. Sequencing of Ebola viruses from infected individuals has revealed extensive genetic variation, leading to speculation that the virus may be adapting to the human host and accounting for the scale of the 2014 outbreak. We show that so far there is no evidence for adaptation of EBOV to humans. We analyze the putatively functional changes associated with the current and previous Ebola outbreaks, and find no significant molecular changes. Observed amino acid replacements have minimal effect on protein structure, being neither stabilizing nor destabilizing. Replacements are not found in regions of the proteins associated with known functions and tend to occur in disordered regions. This observation indicates that the difference between the current and previous outbreaks is not due to the observed evolutionary change of the virus. Instead, epidemiological factors must be responsible for the unprecedented spread of EBOV.

Evolutionary Biology↗

bioRxiv2015

An exon-capture system for the entire class Ophiuroidea

AO_SCPCAPBSTRACTC_SCPCAPWe present an exon-capture system for an entire class of marine invertebrates, the Ophiuroidea, built upon a phylogenetically diverse transcriptome foundation. The system captures ~90 percent of the 1552 exon target, across all major lineages of the quarter-billion year old extant crown group. Key features of our system are: 1) basing the target on an alignment of orthologous genes determined from 52 transcriptomes spanning the phylogenetic diversity and trimmed to remove anything difficult to capture, map or align, 2) use of multiple artificial representatives based on ancestral states rather than exemplars to improve capture and mapping of the target, 3) mapping reads to a multi-reference alignment, and 4) using patterns of site polymorphism to distinguish among paralogy, polyploidy, allelic differences and sample contamination. The resulting data gives a well-resolved tree (currently standing at 417 samples, 275,352 bp, 91% data-complete) that will transform our understanding of ophiuroid evolution and biogeography.

Evolutionary Biology↗

bioRxiv2015

Harsh environments and "fast" human life histories: What does the theory say?

AO_SCPLOWBSTRACTC_SCPLOWA common belief among human life history researchers is that \"harsher\" environments - i.e., those with higher mortality rates and resource stress - select for \"fast\" life histories, i.e. earlier reproduction and faster senescence. I show that these \"harsh environments, fast life histories\" - or HEFLH - hypotheses are poorly supported by evolutionary theory. First, I use a simple model to show that effects of environmental harshness on life history evolution are incredibly diverse. In particular, small changes in basic but poorly understood variables - e.g., whether and how population density affects vital rates - can cause selection to favor very different life histories. Furthermore, I show that almost all life history theory used to justify HEFLH hypotheses is misapplied in the first place. The reason is that HEFLH hypotheses usually treat plastic responses to heterogeneous environmental conditions within a population, whereas the theory used to justify such hypotheses treat genetic responses to environmental changes across an entire population. Counter-intuitively, the predictions of the former do not generally apply to the latter: the optimal response to a harsh environment within a large heterogeneous environment is not necessarily the optimal strategy of a population uniformly inhabiting the same harsh environment. I discuss these theoretical results in light of the current state of empirical research.

Evolutionary Biology↗

bioRxiv2015

Molecular evolutionary consequences of island colonisation

Island endemics are likely to experience population bottlenecks; they also have restricted ranges. Therefore we expect island species to have small effective population sizes (Ne) and reduced genetic diversity compared to their mainland counterparts. As a consequence, island species may have inefficient selection and reduced adaptive potential. We used both polymorphisms and substitutions to address these predictions, improving on the approach of recent studies that only used substitution data. This allowed us to directly test the assumption that island species have small values of Ne. We found that island species had significantly less genetic diversity than mainland species; however, this pattern could be attributed to a subset of island species that had undergone a recent population bottleneck. When these species were excluded from the analysis, island and mainland species had similar levels of genetic diversity, despite island species occupying considerably smaller areas than their mainland counterparts. We also found no overall difference between island and mainland species in terms of effectiveness of selection or mutation rate. Our evidence suggests that island colonisation has no lasting impact on molecular evolution. This surprising result highlights gaps in our knowledge of the relationship between census and effective population size.

Evolutionary Biology↗

bioRxiv2015

Epistasis and Entropy

Epistasis is a key concept in the theory of adaptation. Indicators of epistasis are of interest for large system where systematic fitness measurements may not be possible. Some recent approaches depend on information theory. We show that considering shared entropy for pairs of loci can be misleading. The reason is that shared entropy does not imply epistasis for the pair. This observation holds true also in the absence of higher order epistasis. We discuss a refined approach for identifying pairwise interactions using entropy.

Evolutionary Biology↗

bioRxiv2015

Natural Selection Shapes the Mosaic Ancestry of the Drosophila Genetic Reference Panel and the D. melanogaster Reference Genome

North American populations of Drosophila melanogaster are thought to derive from both European and African source populations, but despite their importance for genetic research, patterns of admixture along their genomes are essentially undocumented. Here, I infer geographic ancestry along genomes of the Drosophila Genetic Reference Panel (DGRP) and the D. melanogaster reference genome. Overall, the proportion of African ancestry was estimated to be 20% for the DGRP and 9% for the reference genome. Based on the size of admixture tracts and the approximate timing of admixture, I estimate that the DGRP population underwent roughly 13.9 generations per year. Notably, ancestry levels varied strikingly among genomic regions, with significantly less African introgression on the X chromosome, in regions of high recombination, and at genes involved in specific processes such as circadian rhythm. An important role for natural selection during the admixture process was further supported by a genome-wide signal of ancestry disequilibrium, in that many between-chromosome pairs of loci showed a deficiency of Africa-Europe allele combinations. These results support the hypothesis that admixture between partially genetically isolated Drosophila populations led to natural selection against incompatible genetic variants, and that this process is ongoing. The ancestry blocks inferred here may be relevant for the performance of reference alignment in this species, and may bolster the design and interpretation of many population genetic and association mapping studies.

Evolutionary Biology↗

bioRxiv2015

Coevolutionary analyses require phylogenetically deep alignments and better null models to accurately detect inter-protein contacts within and between species

When biomolecules physically interact, natural selection operates on them jointly. Contacting positions in protein and RNA structures exhibit correlated patterns of sequence evolution due to constraints imposed by the interaction, and molecular arms races can develop between interacting proteins in pathogens and their hosts. To evaluate how well methods developed to detect coevolving residues within proteins can be adapted for cross-species, inter-protein analysis, we used statistical criteria to quantify the performance of these methods in detecting inter-protein residues within 8 angstroms of each other in the co-crystal structures of 33 bacterial protein interactions. We also evaluated their performance for detecting known residues at the interface of a host-virus protein complex with a partially solved structure. Our quantitative benchmarking showed that all coevolutionary methods clearly benefit from alignments with many sequences. Methods that aim to detect direct correlations generally outperform other approaches. However, faster mutual information based methods are occasionally competitive in small alignments and with relaxed false positive rates. All commonly used null distributions are anti-conservative and have high false positive rates in some scenarios, although the empirical distribution of scores performs reasonably well with deep alignments. We conclude that coevolutionary analysis of cross-species protein interactions holds great promise but requires sequencing many more species pairs.

Evolutionary Biology↗

bioRxiv2015

Key role of amino acid repeat expansions in the functional diversification of duplicated transcription factors

The high regulatory complexity of vertebrates has been related to two closely spaced whole genome duplications (2R-WGD) that occurred before the divergence of the major vertebrate groups. Following these events, many developmental transcription factors (TFs) were retained in multiple copies and subsequently specialized in diverse functions, whereas others reverted to their singleton state. TFs are known to be generally rich in amino acid repeats or low-complexity regions (LCRs), such as polyalanine or polyglutamine runs, which can evolve rapidly and potentially influence the transcriptional activity of the protein. Here we test the hypothesis that LCRs have played a major role in the diversification of TF gene duplicates. We find that nearly half of the TF gene families (107 out of 237) originated during the 2R-WGD contain LCRs, compared to only a small percentage of the non-duplicated TF genes used as a control (15 out of 115). At the individual gene level, we observe that twice as many duplicated TFs have gained LCRs as non-duplicated TFs. In addition, duplicated TFs preferentially accumulate certain LCR types, the most prominent of which are alanine repeats. We experimentally test the role of alanine-rich LCRs in two different TF gene families, PHOX2A/PHOX2B and LHX2/LHX9. In both cases, the presence of the alanine-rich LCR in one of the copies (PHOX2B and LHX2) significantly increases the capacity of the TF to activate transcription. Taken together, the results provide strong evidence that LCRs are important driving forces of evolutionary change in duplicated genes.

Evolutionary Biology↗

bioRxiv2015

Mitochondrial Genomes of Giant Deers Suggest their Late Survival in Central Europe

The giant deer Megaloceros giganteus is among the most fascinating Late Pleistocene Eurasian megafauna that became extinct at the end of the last ice age. Important questions persist regarding its phylogenetic relationship to contemporary taxa and the reasons for its extinction. We analyzed two large ancient cervid bone fragments recovered from cave sites in the Swabian Jura (Baden-Wurttemberg, Germany) dated to 12,000 years ago. Using hybridization capture in combination with next generation sequencing, we were able to reconstruct nearly complete mitochondrial genomes from both specimens. Both mtDNAs cluster phylogenetically with fallow deer and show high similarity to previously studied partial Megaloceros giganteus DNA from Kamyshlov in western Siberia and Killavullen in Ireland. The unexpected presence of Megaloceros giganteus in Southern Germany after the Ice Age suggests a later survival in Central Europe than previously proposed. The complete mtDNAs provide strong phylogenetic support for a Dama-Megaloceros clade. Furthermore, isotope analyses support an increasing competition between giant deer, red deer, and reindeer after the Last Glacial Maximum, which might have contributed to the extinction of Megaloceros in Central Europe.

Evolutionary Biology↗

bioRxiv2015

Selection constrains phenotypic evolution in a functionally important plant trait

A long-standing idea is that the macroevolutionary adaptive landscape - a map of phenotype to fitness - constrains evolution because certain phenotypes are fit, while others are universally unfit. Such constraints should be evident in traits that, across many species, cluster around particular modal values, with few intermediates between modes. Here, I compile a new global database of 599 species from 94 plant families showing that stomatal ratio, an important functional trait affecting photosynthesis, is multimodal, hinting at distinct peaks in the adaptive landscape. The dataset confirms that most plants have all their stomata on the lower leaf surface (hypostomy), but shows for the first time that species with roughly half their stomata on each leaf surface (amphistomy) form a distinct mode in the trait distribution. Based on a new evolutionary process model, this multimodal pattern is unlikely without constraint. Further, multimodality has evolved repeatedly across disparate families, evincing long-term constraint on the adaptive landscape. A simple cost-benefit model of stomatal ratio demonstrates that selection alone is sufficient to generate an adaptive landscape with multiple peaks. Finally, phylogenetic comparative methods indicate that life history evolution drives shifts between peaks. This implies that the adaptive benefit conferred by amphistomy - increased photosynthesis - is most important in plants with fast life histories, challenging existing ideas that amphistomy is an adaptation to thick leaves and open habitats. I conclude that peaks in the adaptive landscape have been constrained by selection over much of land plant evolution, leading to predictable, repeatable patterns of evolution.

Evolutionary Biology↗

bioRxiv2015

Non-adaptive evolution of the m. palmaris longus in the Homininae.

The palmaris longus muscle is widely recognized for its notable variability in living humans. These variations include not only muscle belly reversal, distinct double muscle bellies, duplication and triplication, but also total uni-or bilateral agenesis (absence). A review of the literature and data novel to this study illustrate that different populations of humans exhibit remarkable variation in the frequency of palmaris longus agenesis, from less than 5% of Chinese to nearly 65% of Indians. Comparative dissection-derived data reveal substantial variation in palmaris longus agenesis (PLA) in populations of extant humans (H. sapiens), chimpanzees (Pan spp.), and gorillas (Gorilla spp.) - but not orangutans (Pongo spp.), which apparently always develop this muscle. From this pattern, we infer that palmaris longus is undergoing non-adaptive, stochastic evolution in the extant African Homininae, while it continues to have adaptive purpose in Pongo, likely due to the orangutans greater degree of arboreality than the African apes and humans. Clinical evidence supports this conclusion, at least as it applies to humans. This study highlights the utility of comparative soft tissue data collection and interpretation in elucidating the evolution of anatomical structures that do not fossilize.

Evolutionary Biology↗

bioRxiv2015

Fecundity selection theory: concepts and evidence

Fitness results from the optimal balance between survival, mating success and fecundity. The interactions between these three components of fitness vary importantly depending on the selective context, from positive covariation between them, to antagonistic pleiotropic relationships when fitness increases in one reduce fitness of others. Therefore, elucidating the routes through which selection shapes life history and phenotypic adaptations via these fitness components is of primary significance to understand ecological and evolutionary dynamics. However, while the fitness components mediated by natural (survival) and sexual (mating success) selection have extensively been debated from most possible perspectives, fecundity selection remains considerably less studied. Here, we review the theory, evidence and implications of fecundity selection as a driver of sex-specific adaptive evolution. Based on accumulating literature on the life-history, phenotypic and ecological aspects of fecundity, we (i) suggest that fecundity is restricted to refer to brood size per reproductive episode, while annual and lifetime fecundity should not be used interchangeably with fecundity as they represent different life history parameters; (ii) provide a generalized redefinition of fecundity selection that encompasses any traits that influence fecundity in any direction (from high to low) and in either sex; (iii) review the (macro)ecological basis of fecundity selection (e.g., ecological pressures that influence predictable spatial variation in fecundity); (iv) suggest that most ecological theories of fecundity selection should be tested in organisms other than birds; (v) argue that the longstanding fecundity selection hypothesis of female-biased sexual size dimorphism (SSD) has gained inconsistent support, that strong fecundity selection does not necessarily drive female-biased SSD, and that this form of SSD can be driven by other selective pressures; and (vi) discuss cases in which fecundity selection operates on males.

Evolutionary Biology↗

bioRxiv2015

Risks inherent to mitochondrial replacement

The UK Government has recently been debating whether or not to legislate to allow mitochondrial replacement (MR) to be used in the clinic. However, we are concerned that some of the science of MR has been misunderstood, or otherwise given only fleeting consideration. We set out our arguments below and offer a way forward to ensure that MR can safely deliver the health benefits it promises for those suffering from mitochondrial-related diseases\n\nRecent innovations that enable mitochondrial DNA (mtDNA) mutations to be eliminated from the germline, by replacing mutated mitochondria within an oocyte with mitochondria from a healthy donor female1-3, offer hope for the eradication of several debilitating and lethal mitochondrial diseases. The potential for clinical application of MR has received widespread support4,5, but has also provoked safety and ethical concerns from the public ...

Evolutionary Biology↗

bioRxiv2015

Catch me if you can: Adaptation from standing genetic variation to a moving phenotypic optimum

Adaptation lies at the heart of Darwinian evolution. Accordingly, numerous studies have tried to provide a formal framework for the description of the adaptive process. Out of these, two complementary modelling approaches have emerged: While so-called adaptive-walk models consider adaptation from the successive fixation of de-novo mutations only, quantitative genetic models assume that adaptation proceeds exclusively from pre-existing standing genetic variation. The latter approach, however, has focused on short-term evolution of population means and variances rather than on the statistical properties of adaptive substitutions. Our aim is to combine these two approaches by describing the ecological and genetic factors that determine the genetic basis of adaptation from standing genetic variation in terms of the effect-size distribution of individual alleles. Specifically, we consider the evolution of a quantitative trait to a gradually changing environment. By means of analytical approximations, we derive the distribution of adaptive substitutions from standing genetic variation, that is, the distribution of the phenotypic effects of those alleles from the standing variation that become fixed during adaptation. Our results are checked against individual-based simulations. We find that, compared to adaptation from de-novo mutations, (i) adaptation from standing variation proceeds by the fixation of more alleles of small effect; (ii) populations that adapt from standing genetic variation can traverse larger distances in phenotype space and, thus, have a higher potential for adaptation if the rate of environmental change is fast rather than slow.

Evolutionary Biology↗

bioRxiv2015

Association mapping reveals the role of mutation-selection balance in the maintenance of genomic variation for gene expression.

The evolutionary forces that maintain genetic variation for quantitative traits within populations remain poorly understood. One hypothesis suggests that variation is maintained by a balance between new mutations and their removal by selection and drift. Theory predicts that this mutation-selection balance will result in an excess of low-frequency variants and a negative correlation between minor allele frequency and selection coefficients. Here, we test these predictions using the genetic loci associated with total expression variation (eQTLs) and allele-specific expression variation (aseQTLs) mapped within a single population of the plant Capsella grandiflora. In addition to finding eQTLs and aseQTLs for a large fraction of genes, we show that alleles at these loci are rarer than expected and exhibit a negative correlation between phenotypic effect size and frequency. Overall, our results show that the distribution of frequencies and effect sizes of the loci responsible for local expression variation within a single, outcrossing population are consistent with mutation-selection balance.\n\nSignificanceBiologists have long sought to explain why we see genetic variation for traits in populations despite the expectation that selection will remove most variation. We address this question by using gene expression as a model trait and identifying the genetic loci that affect gene expression in a single, large population of the plant Capsella grandiflora. Alleles at loci that affect expression were rarer than expected by chance and there was a negative correlation between phenotypic effect size and frequency of these alleles. These observations are consistent with mutation-selection balance, the hypothesis that variation is maintained by a balance between new mutations and their removal by selection and drift.

Evolutionary Biology↗

bioRxiv2015

Tandem repeat variation in human and great ape populations and its impact on gene expression divergence

Tandem repeats (TR) are stretches of DNA that are highly variable in length and mutate rapidly, and thus an important source of genetic variation. This variation is highly informative for population and conservation genetics, and has also been associated with several pathological conditions and with gene expression regulation. However, genome-wide surveys of TR variation have been scarce due to the technical difficulties derived from short-read technology.\n\nHere, we explored the genome-wide diversity of TRs in a panel of 83 human and nonhuman great ape genomes, and their impact on gene expression evolution. We found that populations and species diversity patterns can be efficiently captured with short TRs (repeat unit length 1-5 base pairs) with potential applications in conservation genetics. We also examined the potential evolutionary role of TRs in gene expression differences between humans and primates by using 30,275 larger TRs (repeat unit length 2-50 base pairs). About one third of the 13,035 one-to-one orthologous genes contained TRs within 5 kilobase pairs of their transcription start site, and had higher expression divergence than genes without such TRs. The same observation held for genes with repeats in their 3 untranslated region, in introns, and in exons. Using our polymorphism data for the shortest TRs, we found that genes with polymorphic repeats in their promoters showed higher expression divergence in humans and chimpanzees compared to genes with fixed or no TRs in the promoters. Our findings highlight the potential contribution of TRs to recent human evolution through gene regulation.

Evolutionary Biology↗

bioRxiv2015

Speciation in Heliconius Butterflies: Minimal Contact Followed by Millions of Generations of Hybridisation

Documenting the full extent of gene flow during speciation poses a challenge, as species ranges change over time and current rates of hybridisation might not reflect historical trends. Theoretical work has emphasized the potential for speciation in the face of ongoing hybridisation, and the genetic mechanisms that might facilitate this process. However, elucidating how the rate of gene flow between species may have changed over time has proved difficult. Here we use Approximate Bayesian Computation (ABC) to fit a model of speciation between the Neotropical butterflies Heliconius melpomene and Heliconius cydno. These species are ecologically divergent, rarely hybridize and display female hybrid sterility. Nevertheless, previous genomic studies suggests pervasive gene flow between them, extending deep into their past, and potentially throughout the speciation process. By modelling the rates of gene flow during early and later stages of speciation, we find that these species have been hybridising for hundreds of thousands of years, but have not done so continuously since their initial divergence. Instead, it appears that gene flow was rare or absent for as long as a million years in the early stages of speciation. Therefore, by dissecting the timing of gene flow between these species, we are able to reject a scenario of purely sympatric speciation in the face of continuous gene flow. We suggest that the period of minimal contact early in speciation may have allowed for the accumulation of genomic changes that later enabled these species to remain distinct despite a dramatic increase in the rate of hybridisation.

Evolutionary Biology↗

bioRxiv2015

Recent evolution in Rattus norvegicus is shaped by declining effective population size

The brown rat, Rattus norvegicus, is both a notorious pest and a frequently used model in biomedical research. By analysing genome sequences of 12 wild-caught brown rats from their ancestral range in NE China, along with the sequence of a black rat, R. rattus, we investigate the selective and demographic forces shaping variation in the genome. We estimate that the recent effective population size (Ne) of this species = 1.24 x 105, based on silent site diversity. We compare patterns of diversity in these genomes with patterns in multiple genome sequences of the house mouse (Mus musculus castaneus), which has a much larger Ne. This reveals an important role for variation in the strength of genetic drift in mammalian genome evolution. By a Pairwise Sequentially Markovian Coalescent (PSMC) analysis of demographic history, we infer that there has been a recent population size bottleneck in wild rats, which we date to approximately 20,000 years ago. Consistent with this, wild rat populations have experienced an increased flux of mildly deleterious mutations, which segregate at higher frequencies in protein-coding genes and conserved noncoding elements (CNEs). This leads to negative estimates of the rate of adaptive evolution () in proteins and CNEs, a result which we discuss in relation to the strongly positive estimates observed in wild house mice. As a consequence of the population bottleneck, wild rats also show a markedly slower decay of linkage disequilibrium with physical distance than wild house mice.

Evolutionary Biology↗