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

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

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

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

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

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.

Independent molecular basis of convergent highland adaptation in maize

Shohei Takuno, Peter Ralph, Kelly Swarts, Rob J Elshire, Jeffrey C Glaubitz, Edward S. Buckler, Matthew B Hufford, Jeff Ross-Ibarra
doi: http://dx.doi.org/10.1101/013607

Convergent evolution occurs when multiple species/subpopulations adapt to similar environments via similar phenotypes. We investigate here the molecular basis of convergent adaptation in maize to highland climates in Mexico and South America using genome-wide SNP data. Taking advantage of archaeological data on the arrival of maize to the highlands, we infer demographic models for both populations, identifying evidence of a strong bottleneck and rapid expansion in South America. We use these models to then identify loci showing an excess of differentiation as a means of identifying putative targets of natural selection, and compare our results to expectations from recently developed theory on convergent adaptation. Consistent with predictions across a wide array of parameter space, we see limited evidence for convergent evolution at the nucleotide level in spite of strong similarities in overall phenotypes. Instead, we show that selection appears to have predominantly acted on standing genetic variation, and that introgression from wild teosinte populations appears to have played a role in highland adaptation in Mexican maize.

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.

Bias in Estimators of Archaic Admixture

Alan R. Rogers, Ryan J. Bohlender
(Submitted on 20 Dec 2014)

This article evaluates bias in one class of methods used to estimate archaic admixture in modern humans. These methods study the pattern of allele sharing among modern and archaic genomes. They are sensitive to “ghost” admixture, which occurs when a population receives archaic DNA from sources not acknowledged by the statistical model. The effect of ghost admixture depends on two factors: branch-length bias and population-size bias. Branch-length bias occurs because a given amount of admixture has a larger effect if the two populations have been separated for a long time. Population-size bias occurs because differences in population size distort branch lengths in the gene genealogy. In the absence of ghost admixture, these effects are small. They become important, however, in the presence of ghost admixture. Estimators differ in the pattern of response. Increasing a given parameter may inflate one estimator but deflate another. For this reason, comparisons among estimators are informative. Using such comparisons, this article supports previous findings that the archaic population was small and that Europeans received little gene flow from archaic populations other than Neanderthals. It also identifies an inconsistency in estimates of archaic admixture into Melanesia.

Genetic Analysis of Substrain Divergence in NOD Mice

Petr Simecek, Gary A Churchill, Hyuna Yang, Lucy B Rowe, Lieselotte Herberg, David V Serreze, Edward H Leiter
doi: http://dx.doi.org/10.1101/013037

The NOD mouse is a polygenic model for type 1 diabetes that is characterized by insulitis, a leukocytic infiltration of the pancreatic islets. During ~35 years since the original inbred strain was developed in Japan, NOD substrains have been established at different laboratories around the world. Although environmental differences among NOD colonies capable of impacting diabetes incidence have been recognized, differences arising from genetic divergence have not previously been analyzed. We illustrate the importance of intersubstrain genetic differences by showing a difference in diabetes incidence between two substrains (NOD/ShiLtJ and NOD/Bom) maintained in a common environment. We use both Mouse Diversity Array and Whole Exome Capture Sequencing platforms to identify genetic differences distinguishing 5 NOD substrains. We describe 64 SNPs, and 2 short indels that differ in coding regions of the 5 NOD substrains. A 100 kb deletion on Chromosome 3 distinguishes NOD/ShiLtJ and NOD/ShiLtDvs from 3 other substrains, while a 111 kb deletion in the Icam2 gene on Chromosome 11 is unique to the NOD/ShiLtDvs genome. The extent of genetic divergence for NOD substrains is compared to similar studies for C57BL6 and BALB/c substrains. As mutations are fixed to homozygosity by continued inbreeding, significant differences in substrain phenotypes are to be expected. These results emphasize the importance of using embryo freezing methods to minimize genetic drift within substrains.