Bayesian Inference of Divergence Times and Feeding Evolution in Grey Mullets (Mugilidae)

Bayesian Inference of Divergence Times and Feeding Evolution in Grey Mullets (Mugilidae)

Francesco Santini , Michael R. May , Giorgio Carnevale , Brian R. Moore
doi: http://dx.doi.org/10.1101/019075

Grey mullets (Mugilidae, Ovalentariae) are coastal fishes found in near-shore environments of tropical, subtropical, and temperate regions within marine, brackish, and freshwater habitats throughout the world. This group is noteworthy both for the highly conserved morphology of its members—which complicates species identification and delimitation—and also for the uncommon herbivorous or detritivorous diet of most mullets. In this study, we first attempt to identify the number of mullet species, and then—for the resulting species—estimate a densely sampled time-calibrated phylogeny using three mitochondrial gene regions and three fossil calibrations. Our results identify two major subgroups of mullets that diverged in the Paleocene/Early Eocene, followed by an Eocene/Oligocene radiation across both tropical and subtropical habitats. We use this phylogeny to explore the evolution of feeding preference in mullets, which indicates multiple independent origins of both herbivorous and detritivorous diets within this group. We also explore correlations between feeding preference and other variables, including body size, habitat (marine, brackish, or freshwater), and geographic distribution (tropical, subtropical, or temperate). Our analyses reveal: (1) a positive correlation between trophic index and habitat (with herbivorous and/or detritivorous species predominantly occurring in marine habitats); (2) a negative correlation between trophic index and geographic distribution (with herbivorous species occurring predominantly in subtropical and temperate regions), and; (3) a negative correlation between body size and geographic distribution (with larger species occurring predominantly in subtropical and temperate regions).

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Standing genetic variation as a major contributor to adaptation in the Virginia chicken lines selection experiment

Standing genetic variation as a major contributor to adaptation in the Virginia chicken lines selection experiment

Zheya Sheng , Mats E Pettersson , Christa F Honaker , Paul B Siegel , Örjan Carlborg
doi: http://dx.doi.org/10.1101/018721

Artificial selection has, for decades, provided a powerful approach to study the genetics of adaptation. Using selective-sweep mapping, it is possible to identify genomic regions in populations where the allele-frequencies have diverged during selection. To avoid misleading signatures of selection, it is necessary to show that a sweep has an effect on the selected trait before it can be considered adaptive. Here, we confirm candidate selective-sweeps on a genome-wide scale in one of the longest, on-going bi-directional selection experiments in vertebrates, the Virginia high and low body-weight selected chicken lines. The candidate selective-sweeps represent standing genetic variants originating from the common base-population. Using a deep-intercross between the selected lines, 16 of 99 evaluated regions were confirmed to contain adaptive selective-sweeps based on their association with the selected trait, 56-day body-weight. Although individual additive effects were small, the fixation for alternative alleles in the high and low body-weight lines across these loci contributed at least 40% of the divergence between them and about half of the additive genetic variance present within and between the lines after 40 generations of selection. The genetic variance contributed by the sweeps corresponds to about 85% of the additive genetic variance of the base-population, illustrating that these loci were major contributors to the realised selection-response. Thus, the gradual, continued, long- term selection response in the Virginia lines was likely due to a considerable standing genetic variation in a highly polygenic genetic architecture in the base-population with contributions from a steady release of selectable genetic variation from new mutations and epistasis throughout the course of selection.

The complex admixture history and recent southern origins of Siberian populations

The complex admixture history and recent southern origins of Siberian populations

Irina Pugach , Rostislav Matveev , Viktor Spitsyn , Sergey Makarov , Innokentiy Novgorodov , Vladimir Osakovsky , Mark Stoneking , Brigitte Pakendorf
doi: http://dx.doi.org/10.1101/018770

Although Siberia was inhabited by modern humans at an early stage, there is still debate over whether this area remained habitable during the extremely cold period of the Last Glacial Maximum or whether it was subsequently repopulated by peoples with a recent shared ancestry. Previous studies of the genetic history of Siberian populations were hampered by the extensive admixture that appears to have taken place among these populations, since commonly used methods assume a tree-like population history and at most single admixture events. We therefore developed a new method based on the covariance of ancestry components, which we validated with simulated data, in order to investigate this potentially complex admixture history and to distinguish the effects of shared ancestry from prehistoric migrations and contact. We furthermore adapted a previously devised method of admixture dating for use with multiple events of gene flow, and applied these methods to whole-genome genotype data from over 500 individuals belonging to 20 different Siberian ethnolinguistic groups. The results of these analyses indicate that there have indeed been multiple layers of admixture detectable in most of the Siberian populations, with considerable differences in the admixture histories of individual populations, and with the earliest events dated to not more than 4500 years ago. Furthermore, most of the populations of Siberia included here, even those settled far to the north, can be shown to have a southern origin. These results provide support for a recent population replacement in this region, with the northward expansions of different populations possibly being driven partly by the advent of pastoralism, especially reindeer domestication. These newly developed methods to analyse multiple admixture events should aid in the investigation of similarly complex population histories elsewhere.

Exploring genetic variation in the tomato (Solanum section Lycopersicon) clade by whole-genome sequencing

Exploring genetic variation in the tomato (Solanum section Lycopersicon) clade by whole-genome sequencing

Saulo A. Aflitos, Elio Schijlen, Richard Finkers, Sandra Smit, Jun Wang, Gengyun Zhang, Ning Li, Likai Mao, Hans de Jong, Freek Bakker, Barbara Gravendeel, Timo Breit, Rob Dirks, Henk Huits, Darush Struss, Ruth Wagner, Hans van Leeuwen, Roeland van Ham, Laia Fito, Laëtitia Guigner, Myrna Sevilla, Philippe Ellul, Eric W. Ganko, Arvind Kapur, Emmanuel Reclus, Bernard de Geus, Henri van de Geest, Bas te Lintel Hekkert, Jan C. Van Haarst, Lars Smits, Andries Koops, Gabino Sanchez Perez, Dick de Ridder, Sjaak van Heusden, Richard Visser, Zhiwu Quan, Jiumeng Min, Li Liao, Xiaoli Wang, Guangbiao Wang, Zhen Yue, Xinhua Yang, Na Xu, Eric Schranz, Eric F. Smets, Rutger A. Vos, Han Rauwerda, Remco Ursem, Cees Schuit, Mike Kerns, Jan van den Berg, Wim H. Vriezen, Antoine Janssen, Torben Jahrman, Frederic Moquet, Julien Bonnet, Sander A. Peters
(Submitted on 21 Apr 2015)

Genetic variation in the tomato clade was explored by sequencing a selection of 84 tomato accessions and related wild species representative for the Lycopersicon, Arcanum, Eriopersicon, and Neolycopersicon groups. We present a reconstruction of three new reference genomes in support of our comparative genome analyses. Sequence diversity in commercial breeding lines appears extremely low, indicating the dramatic genetic erosion of crop tomatoes. This is reflected by the SNP count in wild species which can exceed 10 million i.e. 20 fold higher than in crop accessions. Comparative sequence alignment reveals group, species, and accession specific polymorphisms, which explain characteristic fruit traits and growth habits in tomato accessions. Using gene models from the annotated Heinz reference genome, we observe a bias in dN/dS ratio in fruit and growth diversification genes compared to a random set of genes, which probably is the result of a positive selection. We detected highly divergent segments in wild S. lycopersicum species, and footprints of introgressions in crop accessions originating from a common donor accession. Phylogenetic relationships of fruit diversification and growth specific genes from crop accessions show incomplete resolution and are dependent on the introgression donor. In contrast, whole genome SNP information has sufficient power to resolve the phylogenetic placement of each accession in the four main groups in the Lycopersicon clade using Maximum Likelihood analyses. Phylogenetic relationships appear correlated with habitat and mating type and point to the occurrence of geographical races within these groups and thus are of practical importance for introgressive hybridization breeding. Our study illustrates the need for multiple reference genomes in support of tomato comparative genomics and Solanum genome evolution studies.

Low levels of transposable element activity in Drosophila mauritiana: causes and consequences

Low levels of transposable element activity in Drosophila mauritiana: causes and consequences

Robert Kofler , Christian Schlötterer
doi: http://dx.doi.org/10.1101/018218

Transposable elements (TEs) are major drivers of genomic and phenotypic evolution, yet many questions about their biology remain poorly understood. Here, we compare TE abundance between populations of the two sister species D. mauritiana und D. simulans and relate it to the more distantly related D. melanogaster. The low population frequency of most TE insertions in D. melanogaster and D. simulans has been a key feature of several models of TE evolution. In D. mauritiana, however, the majority of TE insertions are fixed (66%). We attribute this to a lower transposition activity of up to 47 TE families in D. mauritiana, rather than stronger purifying selection. Only three families, including the extensively studied Mariner, may have a higher activity in D. mauritiana. This remarkable difference in TE activity between two recently diverged Drosophila species (≈ 250,000 years), also supports the hypothesis that TE copy numbers in Drosophila may not reflect a stable equilibrium where the rate of TE gains equals the rate of TE losses by negative selection. We propose that the transposition rate heterogeneity results from the contrasting ecology of the two species: the extent of vertical extinction of TE families and horizontal acquisition of active TE copies may be very different between the colonizing D. simulans and the island endemic D. mauritiana. Our findings provide novel insights in the evolution of TEs in Drosophila and suggest that the ecology of the host species could be a major, yet underappreciated, factor governing the evolutionary dynamics of TEs.

Fast principal components analysis reveals independent evolution of ADH1B gene in Europe and East Asia

Fast principal components analysis reveals independent evolution of ADH1B gene in Europe and East Asia

Kevin J Galinsky , Gaurav Bhatia , Po-Ru Loh , Stoyan Georgiev , Sayan Mukherjee , Nick J Patterson , Alkes L Price
doi: http://dx.doi.org/10.1101/018143

Principal components analysis (PCA) is a widely used tool for inferring population structure and correcting confounding in genetic data. We introduce a new algorithm, FastPCA, that leverages recent advances in random matrix theory to accurately approximate top PCs while reducing time and memory cost from quadratic to linear in the number of individuals, a computational improvement of many orders of magnitude. We apply FastPCA to a cohort of 54,734 European Americans, identifying 5 distinct subpopulations spanning the top 4 PCs. Using a new test for natural selection based on population differentiation along these PCs, we replicate previously known selected loci and identify three new signals of selection, including selection in Europeans at the ADH1B gene. The coding variant rs1229984 has previously been associated to alcoholism and shown to be under selection in East Asians; we show that it is a rare example of independent evolution on two continents.

The African wolf is a missing link in the wolf-like canid phylogeny

The African wolf is a missing link in the wolf-like canid phylogeny

Eli K. Rueness , Pål Trosvik , Anagaw Atickem , Claudio Sillero-Zubiri , Emiliano Trucchi
doi: http://dx.doi.org/10.1101/017996

Here we present the first genomic data for the African wolf (Canis aureus lupaster) and conclusively demonstrate that it is a unique taxon and not a hybrid between other canids. These animals are commonly misclassified as golden jackals (Canis aureus) and have never been included in any large-scale studies of canid diversity and biogeography, or in investigations of the early stages of dog domestication. Applying massive Restriction Site Associated DNA (RAD) sequencing, 110481 polymorphic sites across the genome of 7 individuals of African wolf were aligned and compared with other wolf-like canids (golden jackal, Holarctic grey wolf, Ethiopian wolf, side-striped jackal and domestic dog). Analyses of this extensive sequence dataset (ca. 8.5Mb) show conclusively that the African wolves represent a distinct taxon more closely related to the Holarctic grey wolf than to the golden jackal. Our results strongly indicate that the distribution of the golden jackal needs to be re-evaluated and point towards alternative hypotheses for the evolution of the rare and endemic Ethiopian wolf (Canis simensis). Furthermore, the extension of the grey wolf phylogeny and distribution opens new possible scenarios for the timing and location of dog domestication.