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

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

Abayomi S Olabode, Xiaowei Jiang, David L Robertson, Simon C Lovell
doi: http://dx.doi.org/10.1101/014480

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.

Origins of cattle on Chirikof Island, Alaska

Origins of cattle on Chirikof Island, Alaska

Jared E. Decker, Jeremy F. Taylor, Matthew A. Cronin, Leeson J. Alexander, Juha Kantanen, Ann Millbrooke, Robert D. Schnabel, Michael D. MacNeil
doi: http://dx.doi.org/10.1101/014415

Feral livestock may harbor genetic variation of commercial, scientific, historical or esthetic value. Origins and uniqueness of feral cattle on Chirikof Island, Alaska are uncertain. The island is now part of the Alaska Maritime Wildlife Refuge and Federal wildlife managers want grazing to cease, presumably leading to demise of the cattle. Here we characterize the Chirikof Island cattle relative to extant breeds and discern their origins. Our analyses support the inference that Russian cattle arrived first on Chirikof Island, then approximately 95 years ago the first European taurine cattle were introduced to the island, and finally Hereford cattle were introduced about 40 years ago. While clearly Bos taurus taurus, the Chirikof Island cattle appear at least as distinct as other recognized breeds. Further, this mixture of European and East-Asian cattle is unique compared to other North American breeds and we find evidence that natural selection in the relatively harsh environment of Chirikof Island has further impacted their genetic architecture. These results provide an objective basis for decisions regarding conservation of the Chirikof Island cattle.

The Time-Scale of Recombination Rate Evolution in Great Apes

The Time-Scale of Recombination Rate Evolution in Great Apes

Laurie S Stevison, August E Woerner, Jeffrey M Kidd, Joanna L Kelley, Krishna R Veeramah, Kimberly F McManus, Carlos D Bustamante, Michael F Hammer, Jeffrey D Wall
doi: http://dx.doi.org/10.1101/013755

We present three linkage-disequilibrium (LD)-based recombination maps generated using whole-genome sequencing data of 10 Nigerian chimpanzees, 13 bonobos, and 15 western gorillas, collected as part of the Great Ape Genome Project (Prado-Martinez et al. 2013). Using species-specific PRDM9 sequences to predict potential binding sites, we identified an important role for PRDM9 in predicting recombination rate variation broadly across great apes. Our results are contrary to previous research that PRDM9 is not associated with recombination in western chimpanzees (Auton et al. 2012). Additionally, we show that fewer hotspots are shared among chimpanzee subspecies than within human populations, further narrowing the time-scale of complete hotspot turnover. We quantified the variation in the biased distribution of recombination rates towards recombination hotspots across great apes. We found that correlations between broad-scale recombination rates decline more rapidly than nucleotide divergence between species. We also compared the skew of recombination rates at centromeres and telomeres between species and show a skew from chromosome means extending as far as 10‐15 Mb from chromosome ends. Further, we examined broad-scale recombination rate changes near a translocation in gorillas and found minimal differences as compared to other great ape species perhaps because the coordinates relative to the chromosome ends were unaffected. Finally, based on multiple linear regression analysis, we found that various correlates of recombination rate persist throughout primates including repeats, diversity, divergence and local effective population size (Ne). Our study is the first to analyze within- and between-species genome-wide recombination rate variation in several close relatives.

The P-element strikes again: the recent invasion of natural Drosophila simulans populations

The P-element strikes again: the recent invasion of natural Drosophila simulans populations

Robert Kofler, Tom Hill, Viola Nolte, Andrea Betancourt, Christian Schlötterer
doi: http://dx.doi.org/10.1101/013722

The P-element is one of the best understood eukaryotic transposable elements. It invaded Drosophila melanogaster populations within a few decades, but was thought to be absent from close relatives, including D. simulans. Five decades after the spread in D. melanogaster, we provide evidence that the P-element has also invaded D. simulans. P-elements in D. simulans appear to have been acquired recently from D. melanogaster probably via a single horizontal transfer event. Expression data indicate that the P-element is processed in the germline of D. simulans, and genomic data show an enrichment of P-element insertions in putative origins of replication, similar to that seen in D. melanogaster. This ongoing spread of the P-element in natural populations provides an unique opportunity to understand the dynamics of transposable element spreads and the associated piRNA defense mechanisms.

Distributions of topological tree metrics between a species tree and a gene tree

Distributions of topological tree metrics between a species tree and a gene tree

Jing Xi, Jin Xie, Ruriko Yoshida
(Submitted on 10 Jan 2015)

In order to conduct a statistical analysis on a given set of phylogenetic gene trees, we often use a distance measure between two trees. In a statistical distance-based method to analyze discordance between gene trees, it is a key to decide “biological meaningful” and “statistically well-distributed” distance between trees. Thus, in this paper, we study the distributions of the three tree distance metrics: the edge difference, the path difference, and the precise K interval cospeciation distance, between two trees: first, we focus on distributions of the three tree distances between two random unrooted trees with n leaves (n≥4); and then we focus on the distributions the three tree distances between a fixed rooted species tree with n leaves and a random gene tree with n leaves generated under the coalescent process with given the species tree. We show some theoretical results as well as simulation study on these distributions.

The origin and evolution of maize in the American Southwest

The origin and evolution of maize in the American Southwest

Rute R da Fonseca, Bruce D Smith, Nathan Wales, Enrico Cappellini, Pontus Skoglund, Matteo Fumagalli, José Alfredo Samaniego, Christian Carøe, María C Ávila-Arcos, David E Hufnagel, Thorfinn Sand Korneliussen, Filipe Garrett Vieira, Mattias Jakobsson, Bernardo Arriaza, Eske Willerslev, Rasmus Nielsen, Matthew B Hufford, Anders Albrechtsen, Jeffrey Ross-Ibarra, M Thomas P Gilbert
doi: http://dx.doi.org/10.1101/013540

Maize offers an ideal system through which to demonstrate the potential of ancient population genomic techniques for reconstructing the evolution and spread of domesticates. The diffusion of maize from Mexico into the North American Southwest (SW) remains contentious with the available evidence being restricted to morphological studies of ancient maize plant material. We captured 1 Mb of nuclear DNA from 32 archaeological maize samples spanning 6000 years and compared them with modern landraces including those from the Mexican West coast and highlands. We found that the initial diffusion of domesticated maize into the SW is likely to have occurred through a highland route. However, by 2000 years ago a Pacific coastal corridor was also being used. Furthermore, we could distinguish between genes that were selected for early during domestication (such as zagl1 involved in shattering) from genes that changed in the SW context (e.g. related to sugar content and adaptation to drought) likely as a response to the local arid environment and new cultural uses of maize.

SWS2 visual pigment evolution as a test of historically contingent patterns of plumage color evolution in Warblers

SWS2 visual pigment evolution as a test of historically contingent patterns of plumage color evolution in Warblers

Natasha Bloch, James M Morrow, Belinda SW Chang, Trevor D Price
doi: http://dx.doi.org/10.1101/013573

Distantly related clades that occupy similar environments may differ due to the lasting imprint of their ancestors – historical contingency. The New World warblers (Parulidae) and Old World warblers (Phylloscopidae) are ecologically similar clades that differ strikingly in plumage coloration. We studied genetic and functional evolution of the short-wavelength sensitive visual pigments (SWS2 and SWS1) to ask if altered color perception could contribute to the plumage color differences between clades. We show SWS2 is short-wavelength shifted in birds that occupy open environments, such as finches, compared to those in closed environments, including warblers. Sequencing of opsin genes and phylogenetic reconstructions indicate New World warblers were derived from a finch-like form that colonized from the Old World 15-20Ma. During this process the SWS2 gene accumulated 6 substitutions in branches leading to New World warblers, inviting the hypothesis that passage through a finch-like ancestor resulted in SWS2 evolution. In fact, we show spectral tuning remained similar across warblers as well as the finch ancestor. Results reject the hypothesis of historical contingency based on opsin spectral tuning, but point to evolution of other aspects of visual pigment function. Using the approach outlined here, historical contingency becomes a generally testable theory in systems where genotype and phenotype can be connected.