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bioRxiv2015

Replaying Evolution to Test the Cause of Extinction of One Ecotype in an Experimentally Evolved Population

In a long-term evolution experiment with Escherichia coli, bacteria in one of twelve populations evolved the ability to consume citrate, a previously unexploited resource in a glucose-limited medium. This innovation led to the frequency-dependent coexistence of citrate-consuming (Cit+) and non-consuming (Cit-) ecotypes, with Cit- bacteria persisting on the exogenously supplied glucose as well as other carbon molecules released by the Cit+ bacteria. After more than 10,000 generations of coexistence, however, the Cit- lineage went extinct; cells with the Cit- phenotype dropped to levels below detection, and the Cit- clade could not be detected by molecular assays based on its unique genotype. We hypothesized that this extinction event was a deterministic outcome of evolutionary change within the population, specifically the appearance of a more-fit Cit+ ecotype that competitively excluded the Cit- ecotype. We tested this hypothesis by re-evolving the population from one frozen sample taken just prior to the extinction and from another sample taken several thousand generations earlier, in each case for 500 generations and with 20-fold replication. To our surprise, the Cit- type did not go extinct in any of these replays, and Cit- cells also persisted in a single replicate that was propagated for 3,000 generations. Even more unexpectedly, we showed that the Cit- ecotype could reinvade the Cit+ population after its extinction. Taken together, these results indicate that the extinction of the Cit- ecotype was not a deterministic outcome driven by competitive exclusion by the Cit+ ecotype. The extinction also cannot be explained by demographic stochasticity, as the population size of the Cit- ecotype should have been many thousands of cells even during the daily transfer events. Instead, we infer that the extinction must have been caused by a rare chance event in which some aspect of the experimental conditions was inadvertently perturbed.

Evolutionary Biology↗

bioRxiv2015

Genetic loci with parent of origin effects cause hybrid seed lethality between Mimulus species

The classic finding in both flowering plants and mammals that hybrid lethality often depends on parent of origin effects suggests that divergence in the underlying loci might be an important source of hybrid incompatibilities between species. In flowering plants, there is now good evidence from diverse taxa that seed lethality arising from interploidy crosses is often caused by endosperm defects associated with deregulated imprinted genes. A similar seed lethality phenotype occurs in many crosses between closely related diploid species, but the genetic basis of this form of early-acting F1 postzygotic reproductive isolation is largely unknown. Here, we show that F1 hybrid seed lethality is an exceptionally strong isolating barrier between two closely related Mimulus species, M. guttatus and M. tilingii, with reciprocal crosses producing less than 1% viable seeds. Using a powerful crossing design and high-resolution genetic mapping, we identify both maternally- and paternally-derived loci that contribute to hybrid seed incompatibility. Strikingly, these two sets of loci are largely non-overlapping, providing strong evidence that genes with parent of origin effects are the primary driver of F1 hybrid seed lethality between M. guttatus and M. tilingii. We find a highly polygenic basis for both parental components of hybrid seed lethality suggesting that multiple incompatibility loci have accumulated to cause strong postzygotic isolation between these closely related species. Our genetic mapping experiment also reveals hybrid transmission ratio distortion and chromosomal differentiation, two additional correlates of functional and genomic divergence between species.

Evolutionary Biology↗

bioRxiv2015

Early modern human dispersal from Africa: genomic evidence for multiple waves of migration

BackgroundAnthropological and genetic data agree in indicating the African continent as the main place of origin for modern human. However, it is unclear whether early modern humans left Africa through a single, major process, dispersing simultaneously over Asia and Europe, or in two main waves, first through the Arab peninsula into Southern Asia and Oceania, and later through a Northern route crossing the Levant.\n\nResultsHere we show that accurate genomic estimates of the divergence times between European and African populations are more recent than those between Australo-Melanesia and Africa, and incompatible with the effects of a single dispersal. This difference cannot possibly be accounted for by the effects of hybridization with archaic human forms in Australo-Melanesia. Furthermore, in several populations of Asia we found evidence for relatively recent genetic admixture events, which could have obscured the signatures of the earliest processes.\n\nConclusionsWe conclude that the hypothesis of a single major human dispersal from Africa appears hardly compatible with the observed historical and geographical patterns of genome diversity, and that Australo-Melanesian populations seem still to retain a genomic signature of a more ancient divergence from Africa

Evolutionary Biology↗

bioRxiv2015

First-step Mutations during Adaptation to Thermal Stress Shift the Expression of Thousands of Genes Back toward the Pre-stressed State

The temporal change of phenotypes during the adaptive process remain largely unexplored, as do the genetic changes that affect these phenotypic changes. Here we focused on three mutations that rose to high frequency in the early stages of adaptation within 12 Escherichia coli populations subjected to thermal stress (42{degrees}C). All of the mutations were in the rpoB gene, which encodes the RNA polymerase beta subunit. For each mutation, we measured the growth curves and gene expression (mRNAseq) of clones at 42{degrees}C. We also compared growth and gene expression to their ancestor under unstressed (37{degrees}C) and stressed conditions (42{degrees}C). Each of the three mutations changed the expression of hundreds of genes and conferred large fitness advantages, apparently through the restoration of global gene expression from the stressed towards the pre-stressed state. Finally, we compared the phenotypic characteristics of one mutant, I572L, to two high-temperature adapted clones that have this mutation plus additional background mutations. The background mutations increased fitness, but they did not substantially change gene expression. We conclude that early mutations in a global transcriptional regulator cause extensive changes in gene expression, many of which are likely under positive selection for their effect in restoring the pre-stress physiology.

Evolutionary Biology↗

bioRxiv2015

Transcriptomes of plant gametophytes have a higher proportion of rapidly evolving and young genes than sporophytes

Reproductive traits in plants tend to evolve rapidly due to various causes that include plant-pollinator coevolution and pollen competition, but the genomic basis of reproductive trait evolution is still largely unknown. To characterise evolutionary patterns of genome wide gene expression in reproductive tissues and to compare them to developmental stages of the sporophyte, we analysed evolutionary conservation and genetic diversity of protein-coding genes using microarray-based transcriptome data from three plant species, Arabidopsis thaliana, rice (Oryza sativa) and soybean (Glycine max). In all three species a significant shift in gene expression occurs during gametogenesis in which genes of younger evolutionary age and higher genetic diversity contribute significantly more to the transcriptome than in other stages. We refer to this phenomenon as \"evolutionary bulge\" during plant reproductive development because it differentiates the gametophyte from the sporophyte. The extent of the bulge pattern is much stronger than the transcriptomic hourglass, which postulates that during early embryo development an increased proportion of ancient and conserved genes contribute to the total transcriptome. In the three plant species, we observed an hourglass pattern only in A. thaliana but not in rice or soybean, which suggests that unlike the evolutionary bulge of reproductive genes the transcriptomic hourglass is not a general pattern of plant embryogenesis, which is consistent with the absence of a morphologically defined phylotypic stage in plant development.

Evolutionary Biology↗

bioRxiv2015

Purging of deleterious variants due to drift and founder effect in Italian populations with extended autozygosity

Purging through inbreeding occurs when consanguineous marriages increases the rate at which deleterious alleles are present in a homozygous state. In this study we carried out low-read depth (4-10x) whole-genome sequencing in 568 individuals from three Italian founder populations, and compared it to data from other Italian and European populations from the 1000 Genomes Project. We show extended consanguinity and depletion of homozygous genotypes at potentially detrimental sites in the founder populations compared to outbred populations. However these patterns are not compatible with the hypothesis of consanguinity driving the purging of highly deleterious mutations according to simulations. Therefore we conclude that genetic drift and the founder effect should be responsible for the observed purging of deleterious variants.

Evolutionary Biology↗

bioRxiv2015

Assessment of cladistic data availability for living mammals

Analyses of living and fossil taxa are crucial for understanding changes in biodiversity through time. The Total Evidence method allows living and fossil taxa to be combined in phylogenies, by using molecular data for living taxa and morphological data for both living and fossil taxa. With this method, substantial overlap of morphological data among living and fossil taxa is crucial for accurately inferring topology. However, although molecular data for living species is widely available, scientists using and generating morphological data mainly focus on fossils. Therefore, there is a gap in our knowledge of neontological morphological data even in well-studied groups such as mammals.\n\nWe investigated the amount of morphological (cladistic) data available for living mammals and how this data was phylogenetically distributed across orders. 22 of 28 mammalian orders have <25% species with available morphological data; this has implications for the accurate placement of fossil taxa, although the issue is less pronounced at higher taxonomic levels. In most orders, species with available data are randomly distributed across the phylogeny, which may reduce the impact of the problem. We suggest that increased morphological data collection efforts for living taxa are needed to produce accurate Total Evidence phylogenies.

Evolutionary Biology↗

bioRxiv2015

Estimating K in Genetic Mixture Models

A key quantity in the analysis of structured populations is the parameter K, which describes the number of subpopulations that make up the total population. Inference of K ideally proceeds via the model evidence, which is equivalent to the likelihood of the model. However, the evidence in favour of a particular value of K cannot usually be computed exactly, and instead programs such as SO_SCPLOWTRUCTUREC_SCPLOW make use of simple heuristic estimators to approximate this quantity. We show - using simulated data sets small enough that the true evidence can be computed exactly - that these simple heuristics often fail to estimate the true evidence, and that this can lead to incorrect conclusions about K. Our proposed solution is to use thermodynamic integration (TI) to estimate the model evidence. After outlining the TI methodology we demonstrate the effectiveness of this approach using a range of simulated data sets. We find that TI can be used to obtain estimates of the model evidence that are orders of magnitude more accurate and precise than those based on simple heuristics. Furthermore, estimates of K based on these values are found to be more reliable than those based on a suite of model comparison statistics. Our solution is implemented for models both with and without admixture in the software TO_SCPLOWRUEC_SCPLOWK.

Evolutionary Biology↗

bioRxiv2015

Coalescence with background and balancing selection in systems with bi- and uniparental reproduction: contrasting partial asexuality and selfing

Uniparental reproduction in diploids, via asexual reproduction or selfing, reduces the independence with which separate loci are transmitted across generations. This is expected to increase the extent to which a neutral marker is affected by selection elsewhere in the genome. Such effects have previously been quantified in coalescent models involving selfing. Here we examine the effects of background selection and balancing selection in diploids capable of both sexual and asexual reproduction (i.e., partial asexuality). We find that the effect of background selection on reducing coalescent time (and effective population size) can be orders of magnitude greater when rates of sex are low than when sex is common. This is because asexuality enhances the effects of background selection through both a recombination effect and a segregation effect. We show that there are several reasons that the strength of background selection differs between systems with partial asexuality and those with comparable levels of uniparental reproduction via selfing. Expectations for reductions in Ne via background selection have been verified using stochastic simulations. In contrast to background selection, balancing selection increases the coalescent time for a linked neutral site. With partial asexuality, the effect of balancing selection is somewhat dependent upon the mode of selection (e.g., heterozygote advantage vs. negative frequency dependent selection) in a manner that does not apply to selfing. This is because the frequency of heterozygotes, which are required for recombination onto alternative genetic backgrounds, is more dependent on the pattern of selection with partial asexuality than with selfing.

Evolutionary Biology↗

bioRxiv2015

Adaptation to temporally fluctuating environments by the evolution of maternal effects

Most organisms live in ever-challenging temporally fluctuating environments. Theory suggests that the evolution of anticipatory (or deterministic) maternal effects underlies adaptation to environments that regularly fluctuate every other generation because of selection for increased offspring performance. Evolution of maternal bet-hedging reproductive strategies that randomize offspring phenotypes is in turn expected to underlie adaptation to irregularly fluctuating environments. Although maternal effects are ubiquitous their adaptive significance is unknown since they can easily evolve as a correlated response to selection for increased maternal performance. Using the nematode Caenorhabditis elegans, we show the experimental evolution of maternal provisioning of offspring with glycogen, in populations facing a novel anoxia hatching environment every other generation. As expected with the evolution of deterministic maternal effects, improved embryo hatching survival under anoxia evolved at the expense of fecundity and glycogen provisioning when mothers experienced anoxia early in life. Unexpectedly, populations facing an irregularly fluctuating anoxia hatching environment failed to evolve maternal bet-hedging reproductive strategies. Instead, adaptation in these populations should have occurred through the evolution of balancing trade-offs over multiple generations, since they evolved reduced fitness over successive generations in anoxia but did not go extinct during experimental evolution. Mathematical modelling confirms our conclusion that adaptation to a wide range of patterns of environmental fluctuations hinges on the existence of deterministic maternal effects, and that they are generally much more likely to contribute to adaptation than maternal bet-hedging reproductive strategies.

Evolutionary Biology↗

bioRxiv2015

Self-organized patterning and morphogenesis in embryonic epithelia from antagonistic signals and fiber networks. (Topic: Establishment of Spatial and Temporal Patterns)

A number of universals can be observed in the developing embryos of all phyla. An attempt is made here to describe some of these with a simple model, one consisting of two mutually repelling regions of gene patterning produced by signaling pathways, two acting at each growth phase. The diffusion of ligands is short range, nearest or near neighbors, but the transcription patterns extend over many cellular diameters. The universals discussed are: gastrulation, formation of a blastopore, patterning of stem cells as surrounding compartments (propagating anew with each growth phase, to the adult), the origin of bilaterality, the prevalence of segmentation, and the general ability to regenerate and duplicate. The origin of organ sizes are determined by the parameters of the signaling pathways involved, independent of cell sizes or numbers. The important fiber mesh, or fiber network that can also extend over many cell diameters is also briefly discussed, and is seen as a partner with the signaling pathways in the overall patterning.

Evolutionary Biology↗

bioRxiv2015

Conflict and cooperation in eukaryogenesis: implications for the timing of endosymbiosis and the evolution of sex

The complex eukaryotic cell is a result of an ancient endosymbiosis and one of the major evolutionary transitions. The timing of key eukaryotic innovations relative to the acquisition of mitochondria remains subject to considerable debate, yet the evolutionary process itself might constrain the order of these events. Endosymbiosis entailed levels-of-selection conflicts, and mechanisms of conflict mediation had to evolve for eukaryogenesis to proceed. The initial mechanisms of conflict mediation were based on the pathways inherited from prokaryotic symbionts and led to metabolic homeostasis in the eukaryotic cell, while later mechanisms (e.g., mitochondrial gene transfer) contributed to the expansion of the eukaryotic genome. Perhaps the greatest opportunity for conflict arose with the emergence of sex involving whole-cell fusion. While early evolution of cell fusion may have affected symbiont acquisition, sex together with the competitive symbiont behaviour would have destabilized the emerging higher-level unit. Cytoplasmic mixing, on the other hand, would have been beneficial for selfish endosymbionts, capable of using their own metabolism to manipulate the life history of the host. Given the results of our mathematical modelling, we argue that sex represents a rather late proto-eukaryotic innovation, allowing for the growth of the chimeric nucleus and contributing to the successful completion of the evolutionary transition.

Evolutionary Biology↗

bioRxiv2015

Stable recombination hotspots in birds

Although the DNA-binding protein PRDM9 plays a critical role in the specification of meiotic recombination hotspots in mice and apes, it appears to be absent from many vertebrate species, including birds. To learn about the determinants of fine-scale recombination rates and their evolution in natural populations lacking PRDM9, we inferred fine-scale recombination maps from population resequencing data for two bird species, the zebra finch Taeniopygia guttata, and the long-tailed finch, Poephila acuticauda, whose divergence is on par with that between human and chimpanzee. We find that both bird species have hotspots, and these are enriched near CpG islands and transcription start sites. In sharp contrast to what is seen in mice and apes, the hotspots are largely shared between the two species, with indirect evidence of conservation extending across bird species tens of millions of years diverged. These observations link the evolution of hotspots to their genetic architecture, suggesting that in the absence of PRDM9 binding specificity, accessibility of the genome to the cellular recombination machinery, particularly around functional genomic elements, both enables increased recombination and constrains its evolution.

Evolutionary Biology↗

bioRxiv2015

Temporal patterns of damage and decay kinetics of DNA retrieved from plant herbarium specimens

Herbaria archive a record of changes of worldwide plant biodiversity harboring millions of specimens that contain DNA suitable for genome sequencing. To profit from this resource, it is fundamental to understand in detail the process of DNA degradation in herbarium specimens. We investigated patterns of DNA fragmentation -length and base composition at breaking points-, and nucleotide misincorporation by analyzing 86 herbarium samples spanning the last 300 years using Illumina shot-gun sequencing. We found an exponential decay relationship between DNA fragmentation and time, and estimated a per nucleotide fragmentation rate of 1.66 x 10-4 per year, which is ten times faster than the rate estimated for fossilized bones. Additionally, we found that strand breaks occur specially before purines, and that depurination-driven DNA breakage occurs constantly through time and can to a great extent explain decreasing fragment length over time. Similar of what has been found analyzing ancient DNA from bones, we found a strong correlation between the deamination-driven accumulation of cytosine (C) to thymine (T) substitutions and time, which reinforces the importance of substitution patterns to authenticate the ancient/historical nature of DNA fragments. Accurate estimations of DNA degradation through time will allow informed decisions about laboratory and computational procedures to take advantage of the vast collection of worldwide herbarium specimens.

Evolutionary Biology↗

bioRxiv2015

Non-paradoxical evolutionary stability of the recombination initiation landscape in Saccharomycetes

The nonrandom distribution of meiotic recombination shapes heredity and genetic diversification. A widely held view is that individual hotspots -- favored sites of recombination initiation -- are always ephemeral because they evolve rapidly toward extinction. An alternative view, often ignored or dismissed as implausible, predicts conservation of the positions of hotspots if they are chromosomal features under selective constraint, such as gene promoters. Here we empirically test opposite predictions of these theories by comparing genome-wide maps of meiotic recombination initiation from widely divergent species in the Saccharomyces clade. We find that the frequent overlap of hotspots with promoters is true of the species tested and, consequently, hotspot positions are well conserved. Remarkably, however, the relative strength of individual hotspots is also highly conserved, as are larger-scale features of the distribution of recombination initiation. This stability, not predicted by prior models, suggests that the particular shape of the yeast recombination landscape is adaptive, and helps in understanding evolutionary dynamics of recombination in other species.

Evolutionary Biology↗

bioRxiv2015

Long-term natural selection affects patterns of neutral divergence on the X chromosome more than the autosomes.

Natural selection reduces neutral population genetic diversity near coding regions of the genome because recombination has not had time to unlink selected alleles from nearby neutral regions. For ten sub-species of great apes, including human, we show that long-term selection affects estimates of divergence on the X differently from the autosomes. Divergence increases with increasing distance from genes on both the X chromosome and autosomes, but increases faster on the X chromosome than autosomes, resulting in increasing ratios of X/A divergence in putatively neutral regions. Similarly, divergence is reduced more on the X chromosome in neutral regions near conserved regulatory elements than on the autosomes. Consequently estimates of male mutation bias, which rely on comparing neutral divergence between the X and autosomes, are twice as high in neutral regions near genes versus far from genes. Our results suggest filters for putatively neutral genomic regions differ between the X and autosomes.

Evolutionary Biology↗

bioRxiv2015

Phylogenetic effective sample size

In this paper I address the question -- how large is a phylogenetic sample? I propose a definition of a phylogenetic effective sample size for Brownian motion and Ornstein-Uhlenbeck processes -- the regression effective sample size. I discuss how mutual information can be used to define an effective sample size in the non-normal process case and compare these two definitions to an already present concept of effective sample size (the mean effective sample size). Through a simulation study I find that the AICc is robust if one corrects for the number of species or effective number of species. Lastly I discuss how the concept of the phylogenetic effective sample size can be useful for biodiversity quantification, identification of interesting clades and deciding on the importance of phylogenetic correlations.

Evolutionary Biology↗

bioRxiv2015

Dis-integrating the fly: A mutational perspective on phenotypic integration and covariation

The structure of environmentally induced phenotypic covariation can influence the effective strength and magnitude of natural selection. Yet our understanding of the factors that contribute to and influence the evolutionary lability of such covariation is poor. Most studies have either examined environmental variation without accounting for covariation, or examined phenotypic and genetic covariation without distinguishing the environmental component. In this study we examined the effect of mutational perturbations on different properties of environmental covariation, as well as mean shape. We use strains of Drosophila melanogaster bearing well-characterized mutations known to influence wing shape, as well as naturally-derived strains, all reared under carefully-controlled conditions and with the same genetic background. We find that mean shape changes more freely than the covariance structure, and that different properties of the covariance matrix change independently from each other. The perturbations affect matrix orientation more than they affect matrix eccentricity or total variance. Yet, mutational effects on matrix orientation do not cluster according to the developmental pathway that they target. These results suggest that it might be useful to consider a more general concept of decanalization, involving all aspects of variation and covariation.

Evolutionary Biology↗