A Spatial Framework for Understanding Population Structure and Admixture.

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A Spatial Framework for Understanding Population Structure and Admixture.
Gideon Bradburd, Peter L. Ralph, Graham Coop
doi: http://dx.doi.org/10.1101/013474

Geographic patterns of genetic variation within modern populations, produced by complex histories of migration, can be difficult to infer and visually summarize. A general consequence of geographically limited dispersal is that samples from nearby locations tend to be more closely related than samples from distant locations, and so genetic covariance often recapitulates geographic proximity. We use genome-wide polymorphism data to build “geogenetic maps”, which, when applied to stationary populations, produces a map of the geographic positions of the populations, but with distances distorted to reflect historical rates of gene flow. In the underlying model, allele frequency covariance is a decreasing function of geogenetic distance, and nonlocal gene flow such as admixture can be identified as anomalously strong covariance over long distances. This admixture is explicitly co-estimated and depicted as arrows, from the source of admixture to the recipient, on the geogenetic map. We demonstrate the utility of this method on a circum-Tibetan sampling of the greenish warbler (Phylloscopus trochiloides), in which we find evidence for gene flow between the adjacent, terminal populations of the ring species. We also analyze a global sampling of human populations, for which we largely recover the geography of the sampling, with support for significant histories of admixture in many samples. This new tool for understanding and visualizing patterns of population structure is implemented in a Bayesian framework in the program SpaceMix.

The effect of the dispersal kernel on isolation-by-distance in a continuous population

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The effect of the dispersal kernel on isolation-by-distance in a continuous population
Tara N. Furstenau, Reed A. Cartwright
Comments: 18 pages (main); 4 pages (supp)
Subjects: Populations and Evolution (q-bio.PE)

Under models of isolation-by-distance, population structure is determined by the probability of identity-by-descent between pairs of genes according to the geographic distance between them. Well established analytical results indicate that the relationship between geographical and genetic distance depends mostly on the neighborhood size of the population, $N_b = 4{\pi}{\sigma}^2 D_e$, which represents a standardized measure of dispersal. To test this prediction, we model local dispersal of haploid individuals on a two-dimensional torus using four dispersal kernels: Rayleigh, exponential, half-normal and triangular. When neighborhood size is held constant, the distributions produce similar patterns of isolation-by-distance, confirming predictions. Considering this, we propose that the triangular distribution is the appropriate null distribution for isolation-by-distance studies. Under the triangular distribution, dispersal is uniform within an area of $4{\pi}{\sigma}^2$ (i.e. the neighborhood area), which suggests that the common description of neighborhood size as a measure of a local panmictic population is valid for popular families of dispersal distributions. We further show how to draw from the triangular distribution efficiently and argue that it should be utilized in other studies in which computational efficiency is important

Geographic range size is predicted by plant mating system

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Geographic range size is predicted by plant mating system
Dena Grossenbacher, Ryan Briscoe Runquist, Emma Goldberg, Yaniv Brandvain
doi: http://dx.doi.org/10.1101/013417

Species ranges vary enormously, and even closest relatives may differ in range size by several orders of magnitude. With data from hundreds of species spanning 20 genera and generic sections, we show that plant species that autonomously reproduce via self-pollination consistently have larger geographic ranges than their close relatives that generally require two parents for reproduction. Further analyses strongly implicate autonomous fertilization in causing this relationship, as it is not driven by traits such as polyploidy or annual life history whose evolution is sometimes correlated with the transition to autonomous self-fertilization. Furthermore, we find that selfers occur at higher maximum latitudes and that disparity in range size between selfers and outcrossers increases with time since their separation. Together, these results show that autonomous reproduction – a critical biological trait that eliminates mate limitation and thus potentially increases the probability of establishment – increases range size.

Sifting through 2014 on Haldane’s Sieve

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2014 was the second full year of Haldane’s Sieve, which we started in 2012 to bring attention to preprints in population and evolutionary genetics. This year we had over 100,000 visitors from across the globe; the most viewed posts were:

Too packed to change: site-specific substitution rates and side-chain packing in protein evolution

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Too packed to change: site-specific substitution rates and side-chain packing in protein evolution
María Laura Marcos, Julian Echave
doi: http://dx.doi.org/10.1101/013359

In protein evolution, due to functional and biophysical constraints, the rates of amino acid substitution differ from site to site. Among the best predictors of site-specific rates is packing density. The packing density measure that best correlates with rates is the weighted contact number (WCN), the sum of inverse square distances between the site’s Cα and the other Cαs . According to a mechanistic stress model proposed recently, rates are determined by packing because mutating packed sites stresses and destabilizes the protein’s active conformation. While WCN is a measure of Cα packing, mutations replace side chains, which prompted us to consider whether a site’s evolutionary divergence is constrained by main-chain packing or side-chain packing. To address this issue, we extended the stress theory to model side chains explicitly. The theory predicts that rates should depend solely on side-chain packing. We tested these predictions on a data set of structurally and functionally diverse monomeric enzymes. We found that, on average, side-chain contact density (WCNρ ) explains 39.1% of among-sites rate variation, larger than main-chain contact density (WCNα ) which explains 32.1%. More importantly, the independent contribution of WCNα is only 0.7%. Thus, as predicted by the stress theory, site-specific evolutionary rates are determined by side-chain packing.

High-resolution genomic surveillance of 2014 ebolavirus using shared subclonal variants

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High-resolution genomic surveillance of 2014 ebolavirus using shared subclonal variants

Kevin J Emmett, Albert K Lee, Hossein Khiabanian, Raul Rabadan
doi: http://dx.doi.org/10.1101/013318

Viral outbreaks, such as the 2014 ebolavirus, can spread rapidly and have complex evolutionary dynamics, including coinfection and bulk transmission of multiple viral populations. Genomic surveillance can be hindered when the spread of the outbreak exceeds the evolutionary rate, in which case consensus approaches will have limited resolution. Deep sequencing of infected patients can identify genomic variants present in intrahost populations at subclonal frequencies (i.e. <50%). Shared subclonal variants (SSVs) can provide additional phylogenetic resolution and inform about disease transmission patterns. Here, we use metrics from population genetics to analyze data from the 2014 ebolavirus outbreak in Sierra Leone and identify phylogenetic signal arising from SSVs. We use methods derived from information theory to measure a lower bound on transmission bottleneck size that is larger than one founder population, yet significantly smaller than the intrahost effective population. Our results demonstrate the important role of shared subclonal variants in genomic surveillance.

Reconstructing gene content in the last common ancestor of cellular life: is it possible, should it be done, and are we making any progress?

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Reconstructing gene content in the last common ancestor of cellular life: is it possible, should it be done, and are we making any progress?

Arcady Mushegian
doi: http://dx.doi.org/10.1101/013326

I review recent literature on the reconstruction of gene repertoire of the Last Universal Common Ancestor of cellular life (LUCA). The form of the phylogenetic record of cellular life on Earth is important to know in order to reconstruct any ancestral state; therefore I also discuss the emerging understanding that this record does not take the form of a tree. I argue that despite this, “tree-thinking” remains an essential component in evolutionary thinking and that “pattern pluralism” in evolutionary biology can be only epistemological, but not ontological.

The evolutionarily stable distribution of fitness effects

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The evolutionarily stable distribution of fitness effects

Daniel P. Rice, Benjamin H. Good, Michael M. Desai
doi: http://dx.doi.org/10.1101/013052

The distribution of fitness effects of new mutations (the DFE) is a key parameter in determining the course of evolution. This fact has motivated extensive efforts to measure the DFE or to predict it from first principles. However, just as the DFE determines the course of evolution, the evolutionary process itself constrains the DFE. Here, we analyze a simple model of genome evolution in a constant environment in which natural selection drives the population toward a dynamic steady state where beneficial and deleterious substitutions balance. The distribution of fitness effects at this steady state is stable under further evolution, and provides a natural null expectation for the DFE in a population that has evolved in a constant environment for a long time. We calculate how the shape of the evolutionarily stable DFE depends on the underlying population genetic parameters. We show that, in the absence of epistasis, the ratio of beneficial to deleterious mutations of a given fitness effect obeys a simple relationship independent of population genetic details. Finally, we analyze how the stable DFE changes in the presence of a simple form of diminishing returns epistasis.

DNA-guided establishment of canonical nucleosome patterns in a eukaryotic genome

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DNA-guided establishment of canonical nucleosome patterns in a eukaryotic genome

Leslie Y Beh, Noam Kaplan, Manuel M Muller, Tom W Muir, Laura F Landweber
doi: http://dx.doi.org/10.1101/013250

A conserved hallmark of eukaryotic chromatin architecture is the distinctive array of well-positioned nucleosomes downstream of transcription start sites (TSS). Recent studies indicate that trans-acting factors establish this stereotypical array. Here, we present the first genome-wide in vitro and in vivo nucleosome maps for the ciliate Tetrahymena thermophila. In contrast with previous studies in yeast, we find that the stereotypical nucleosome array is preserved in the in vitro reconstituted map, which is governed only by the DNA sequence preferences of nucleosomes. Remarkably, this average in vitro pattern arises from the presence of subsets of nucleosomes, rather than the whole array, in individual Tetrahymena genes. Variation in GC content contributes to the positioning of these sequence-directed nucleosomes, and affects codon usage and amino acid composition in genes. We propose that these ‘seed’ nucleosomes may aid the AT-rich Tetrahymena genome – which is intrinsically unfavorable for nucleosome formation – in establishing nucleosome arrays in vivo in concert with trans-acting factors, while minimizing changes to the coding sequences they are embedded within.

Model Inadequacy and Mistaken Inferences of Trait-Dependent Speciation

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Model Inadequacy and Mistaken Inferences of Trait-Dependent Speciation

Daniel L. Rabosky, Emma E. Goldberg
(Submitted on 22 Dec 2014)

Species richness varies widely across the tree of life, and there is great interest in identifying ecological, geographic, and other factors that affect rates of species proliferation. Recent methods for explicitly modeling the relationships among character states, speciation rates, and extinction rates on phylogenetic trees- BiSSE, QuaSSE, GeoSSE, and related models – have been widely used to test hypotheses about character state-dependent diversification rates. Here, we document the disconcerting ease with which neutral traits are inferred to have statistically significant associations with speciation rate. We first demonstrate this unfortunate effect for a known model assumption violation: shifts in speciation rate associated with a character not included in the model. We further show that for many empirical phylogenies, characters simulated in the absence of state-dependent diversification exhibit an even higher Type I error rate, indicating that the method is susceptible to additional, unknown model inadequacies. For traits that evolve slowly, the root cause appears to be a statistical framework that does not require replicated shifts in character state and diversification. However, spurious associations between character state and speciation rate arise even for traits that lack phylogenetic signal, suggesting that phylogenetic pseudoreplication alone cannot fully explain the problem. The surprising severity of this phenomenon suggests that many trait-diversification relationships reported in the literature may not be real. More generally, we highlight the need for diagnosing and understanding the consequences of model inadequacy in phylogenetic comparative methods.