Morphological data is lacking for living mammals
Thomas Guillerme, Natalie Cooper
doi: http://dx.doi.org/10.1101/022970

Combining living and fossil in the same analysis data is crucial for studying changes in global biodiversity through time. One method allowing to combine this data is the Total Evidence method that uses both molecular data for living species and morphological data for both living and fossil species. With this method, a good overlap of morphological data between living and fossil taxa is crucial for accurately inferring the phylogenies’ topology. Since the advent of DNA, molecular data has become easily and widely available. However, despite two centuries of morphological studies, scientists using and generating such data mainly focus on palaeontological data. Therefore, there is a gap in our knowledge of neontological morphological data even in well studied groups such as mammals. In this study, we quantify the morphological data available for living mammal taxa. We then analyse the structure of the available data by testing if it is clustered or evenly spread across the phylogeny. We found that 78% of mammalian orders have less than 25% data available at the species level. However, we found that the available is often randomly distributed among these orders apart from six of them where the data is clustered

Non-paradoxical evolutionary stability of the recombination initiation landscape in SaccharomycetesIsabel Lam, Scott Keeney
doi: http://dx.doi.org/10.1101/023176

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.

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

Aneil Agrawal, Matthew Hartfield
doi: http://dx.doi.org/10.1101/022996

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.

ASTRID: Accurate Species TRees from Internode Distances

Pranjal Vachaspati, Tandy Warnow
doi: http://dx.doi.org/10.1101/023036

Background: Incomplete lineage sorting (ILS), modelled by the multi-species coalescent (MSC), is known to create discordance between gene trees and species trees, and lead to inaccurate species tree estimations unless appropriate methods are used to estimate the species tree. While many statistically consistent methods have been developed to estimate the species tree in the presence of ILS, only ASTRAL-2 and NJst have been shown to have good accuracy on large datasets. Yet, NJst is generally slower and less accurate than ASTRAL-2, and cannot run on some datasets. Results: We have redesigned NJst to enable it to run on all datasets, and we have expanded its design space so that it can be used with different distance-based tree estimation methods. The resultant method, ASTRID, is statistically consistent under the MSC model, and has accuracy that is competitive with ASTRAL-2. Furthermore, ASTRID is much faster than ASTRAL-2, completing in minutes on some datasets for which ASTRAL-2 used hours. Conclusions: ASTRID is a new coalescent-based method for species tree estimation that is competitive with the best current method in terms of accuracy, while being much faster. ASTRID is available in open source form on github.

Estimating K in Genetic Mixture Models

Robert Verity, Richard Nichols
doi: http://dx.doi.org/10.1101/022988

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 STRUCTURE 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 TrueK.

Adaptation to temporally fluctuating environments by the evolution of maternal effects

Snigdhadip Dey, Steve Proulx, Henrique Teotonio
doi: http://dx.doi.org/10.1101/023044

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.

Plant reproductive development is characterised by a transcriptomic evolutionary bulge

Toni I Gossmann, Dounia Saleh, Marc W Schmid, Michael A Spence, Karl Schmid
doi: http://dx.doi.org/10.1101/022939

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

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

Alejandra Rodriguez-Verdugo, Olivier Tenaillon, Brandon Gaut
doi: http://dx.doi.org/10.1101/022905

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°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°C. We also compared growth and gene expression to their ancestor under unstressed (37°C) and stressed conditions (42°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.

Purging of deleterious variants in Italian founder populations with extended autozygosity

Massimiliano Cocca, Marc Pybus, Pier Francesco Palamara, Erik Garrison, Michela Traglia, Cinzia F Sala, Sheila Ulivi, Yasin Memari, Anja Kolb-Kokocinski, Richard Durbin, Paolo Gasparini, Daniela Toniolo, Nicole Soranzo, Vincenza Colonna
doi: http://dx.doi.org/10.1101/022947

Purging through inbreeding defines the process through which deleterious alleles can be removed from populations by natural selection when exposed in homozygosis through the occurrence of consanguineous marriage. 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 depletion of homozygous genotypes at potentially detrimental sites in the founder populations compared to outbred populations and observe patterns consistent with consanguinity driving the accelerated purging of highly deleterious mutations.

Genetic loci with parent of origin effects cause hybrid seed lethality between Mimulus species
Austin G Garner, Amanda M Kenney, Lila Fishman, Andrea L Sweigart
doi: http://dx.doi.org/10.1101/022863

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.