Author Archives: Joe Pickrell

Multilocus Species Trees Show the Recent Adaptive Radiation of the Mimetic Heliconius Butterflies

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Multilocus Species Trees Show the Recent Adaptive Radiation of the Mimetic Heliconius Butterflies

Krzysztof M Kozak, Niklas Wahlberg, Andrew Neild, Kanchon K Dasmahapatra, James Mallet, Chris D Jiggins

Müllerian mimicry among Neotropical Heliconiini butterflies is an excellent example of natural selection, and is associated with the diversification of a large continental-scale radiation. Some of the processes driving the evolution of mimicry rings are likely to generate incongruent phylogenetic signals across the assemblage, and thus pose a challenge for systematics. We use a dataset of 22 mitochondrial and nuclear markers from 92% of species in the tribe to re-examine the phylogeny of Heliconiini with both supermatrix and multi-species coalescent approaches, characterise the patterns of conflicting signal and compare the performance of various methodological approaches to reflect the heterogeneity across the data. Despite the large extent of reticulate signal and strong conflict between markers, nearly identical topologies are consistently recovered by most of the analyses, although the supermatrix approach fails to reflect the underlying variation in the history of individual loci. The first comprehensive, time-calibrated phylogeny of this group is used to test the hypotheses of a diversification rate increase driven by the dramatic environmental changes in the Amazonia over the past 23 million years, or changes caused by diversity-dependent effects on the rate of diversification. We find that the tribe Heliconiini had doubled its rate of speciation around 11 Ma and that the presently most speciose genus Heliconius started diversifying rapidly at 10 Ma, likely in response to the recent drastic changes in topography of the region. Our study provides comprehensive evidence for a rapid adaptive radiation among an important insect radiation in the most biodiverse region of the planet.

New whole genome de novo assemblies of three divergent strains of rice (O. sativa) documents novel gene space of aus and indica

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New whole genome de novo assemblies of three divergent strains of rice (O. sativa) documents novel gene space of aus and indica

Michael C Schatz, Lyza G Maron, Joshua C Stein, Alejandro Hernandez Wences, James Gurtowski, Eric Biggers, Hayan Lee, Melissa Kramer, Eric Antonio, Elena Ghiban, Mark H Wright, Jer-ming Chia, Doreen Ware, Susan R McCouch, William Richard McCombie

The use of high throughput genome-sequencing technologies has uncovered a large extent of structural variation in eukaryotic genomes that makes important contributions to genomic diversity and phenotypic variation. Currently, when the genomes of different strains of a given organism are compared, whole genome resequencing data are aligned to an established reference sequence. However when the reference differs in significant structural ways from the individuals under study, the analysis is often incomplete or inaccurate. Here, we use rice as a model to explore the extent of structural variation among strains adapted to different ecologies and geographies, and show that this variation can be significant, often matching or exceeding the variation present in closely related human populations or other mammals. We demonstrate how improvements in sequencing and assembly technology allow rapid and inexpensive de novo assembly of next generation sequence data into high-quality assemblies that can be directly compared to provide an unbiased assessment. Using this approach, we are able to accurately assess the ?pan-genome? of three divergent rice varieties and document several megabases of each genome absent in the other two. Many of the genome-specific loci are annotated to contain genes, reflecting the potential for new biological properties that would be missed by standard resequencing approaches. We further provide a detailed analysis of several loci associated with agriculturally important traits, illustrating the utility of our approach for biological discovery. All of the data and software are openly available to support further breeding and functional studies of rice and other species.

Group A Rotavirus NSP4 is Under Negative Selective Pressure

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Group A Rotavirus NSP4 is Under Negative Selective Pressure

Jackson Cordeiro Lima, Paulo Bandiera-Paiva
(Submitted on 2 Apr 2014)

Rotavirus (RV) is the major etiologic agent of severe infantile gastroenteritis; its genome has 11 segments of double stranded RNA, encoding 12 proteins. The non-structural protein 4 (NSP4) encoded by segment 10 is multifunctional. The aim of this study is to analyze the selective pressure driving the NSP4 of RV, through the ratio of non-synonymous substitutions per synonymous substitutions (dN/dS). Our results show that NSP4 is under negative evolutionary pressure (84.57% of the amino acid sequence) and no site was found under positive selection. This may support other evolutionary studies of different RV proteins or viral agents.

Most viewed on Haldane’s Sieve: March 2014

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The most viewed preprints on Haldane’s Sieve in March 2014 were (note that there are six rather than the usual five because two posts had the exact same number of views at the time of this writing):

Flexible isoform-level differential expression analysis with Ballgown

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Flexible isoform-level differential expression analysis with Ballgown

Alyssa C Frazee, Geo Pertea, Andrew E Jaffe, Ben Langmead, Steven L Salzberg, Jeffrey T Leek

We have built a statistical package called Ballgown for estimating differential expression of genes, transcripts, or exons from RNA sequencing experiments. Ballgown is designed to work with the popular Cufflinks transcript assembly software and uses well-motivated statistical methods to provide estimates of changes in expression. It permits statistical analysis at the transcript level for a wide variety of experimental designs, allows adjustment for confounders, and handles studies with continuous covariates. Ballgown provides improved statistical significance estimates as compared to the Cuffdiff differential expression tool included with Cufflinks. We demonstrate the flexibility of the Ballgown package by re-analyzing 667 samples from the GEUVADIS study to identify transcript-level eQTLs and identify non-linear artifacts in transcript data. Our package is freely available from: https://github.com/alyssafrazee/ballgown

The distribution of the quasispecies for the Wright-Fisher model on the sharp peak landscape

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The distribution of the quasispecies for the Wright-Fisher model on the sharp peak landscape

Joseba Dalmau
(Submitted on 27 Mar 2014)

We consider the classical Wright-Fisher model with mutation and selection. Mutations occur independently in each locus, and selection is performed according to the sharp peak landscape. In the asymptotic regime studied in [3], a quasispecies is formed. We find explicitly the distribution of this quasispecies, which turns out to be the same distribution as for the Moran model.

Selscan: an efficient multi-threaded program to perform EHH-based scans for positive selection

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Selscan: an efficient multi-threaded program to perform EHH-based scans for positive selection

Zachary A Szpiech, Ryan D Hernandez
(Submitted on 26 Mar 2014)

Haplotype-based scans to detect natural selection are useful to identify recent or ongoing positive selection in genomes. As both real and simulated genomic datasets grow larger, spanning thousands of samples and millions of markers, there is a need for a fast and efficient implementation of these scans for general use. Here we present selscan, an efficient multi-threaded application that implements Extended Haplotype Homozygosity (EHH), Integrated Haplotype Score (iHS), and Cross-population Extended Haplotype Homozygosity (XPEHH). selscan performs extremely well on both simulated and real data and over an order of magnitude faster than existing available implementations. It calculates iHS on chromosome 22 (22,147 loci) across 204 CEU haplotypes in 502s on one thread (77s on 16 threads) and calculates XPEHH for the same data relative to 210 YRI haplotypes in 907s on one thread (107s on 16 threads). Source code and binaries (Windows, OSX and Linux) are available at this https URL.

Weedy Adaptation in Setaria spp.: VI. S. faberi Seed hull shape as soil germination signal antenna

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Weedy Adaptation in Setaria spp.: VI. S. faberi Seed hull shape as soil germination signal antenna

J.L. Donnelly, D.C. Adams, J. Dekker
(Submitted on 27 Mar 2014)

Ecological selection forces for weedy and domesticated traits have influenced the evolution of seed shape in Setaria resulting in similarity in seed shape that reflects similarity in ecological function rather than reflecting phylogenetic relatedness. Seeds from two diploid subspecies of Setaria viridis, consisting of one weedy subspecies and two races of the domesticated subspecies, and four other polyploidy weedy species of Setaria. We quantified seed shape from the silhouettes of the seeds in two separate views. Differences in shape were compared to ecological role (weed vs. crop) and the evolutionary trajectory of shape change by phylogenetic grouping from a single reference species was calculated. Idealized three-dimensional models were created to examine the differences in shape relative to surface area and volume. All populations were significantly different in shape, with crops easily distinguished from weeds, regardless of relatedness between the taxa. Trajectory of shape change varied by view, but separated crops from weeds and phylogenetic groupings. Three-dimensional models gave further evidence of differences in shape reflecting adaptation for environmental exploitation. The selective forces for weedy and domesticated traits have exceeded phylogenetic constraints, resulting in seed shape similarity due to ecological role rather than phylogenetic relatedness. Seed shape and surface-to-volume ratio likely reflect the importance of the water film that accumulates on the seed surface when in contact with soil particles. Seed shape may also be a mechanism of niche separation between taxa.

Multidimensional epistasis and the transitory advantage of sex

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Multidimensional epistasis and the transitory advantage of sex

Stefan Nowak, Johannes Neidhart, Ivan G. Szendro, Joachim Krug
(Submitted on 25 Mar 2014)

Identifying and quantifying the benefits of sex and recombination is a long standing problem in evolutionary theory. In particular, contradictory claims have been made about the existence of a benefit of recombination on high dimensional fitness landscapes in the presence of sign epistasis. Here we present a comparative numerical study of sexual and asexual evolutionary dynamics on tunably rugged model landscapes, paying special attention to the temporal development of the evolutionary advantage of recombination and the link between population diversity and the rate of adaptation. We show that the adaptive advantage of recombination on static rugged landscapes is strictly transitory. At early times an advantage of recombination through the Fisher-Muller effect is generally observed, but this effect is reversed at longer times by the much more efficient trapping of recombining populations at local fitness peaks. These findings are explained by means of well established results for a setup with only two loci. In accordance with the Red Queen hypothesis the transitory advantage can be prolonged indefinitely in fluctuating environments, and it is maximal when the environment fluctuates on the same time scale on which trapping at local optima typically occurs.

Range Expansion of Heterogeneous Populations

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Range Expansion of Heterogeneous Populations

Matthias Reiter (1), Steffen Rulands (1), Erwin Frey (1 contributed equally)
(Submitted on 25 Mar 2014)

Risk spreading in bacterial populations is generally regarded as a strategy to maximize survival. Here, we study its role during range expansion of a genetically diverse population where growth and motility are two alternative traits. We find that during the initial expansion phase fast growing cells do have a selective advantage. By contrast, asymptotically, generalists balancing motility and reproduction are evolutionarily most successful. These findings are rationalized by a set of coupled Fisher equations complemented by stochastic simulations.