First by Land, Then by Sea: Origins of Dietary Adaptations for Whales and Dolphins during Land to Sea Transition
(Source: Molecular Biology and Evolution)
Source: Molecular Biology and Evolution - November 6, 2016 Category: Molecular Biology Authors: Caspermeyer, J. Tags: News Source Type: research
TreeScaper: Visualizing and Extracting Phylogenetic Signal from Sets of Trees
Modern phylogenomic analyses often result in large collections of phylogenetic trees representing uncertainty in individual gene trees, variation across genes, or both. Extracting phylogenetic signal from these tree sets can be challenging, as they are difficult to visualize, explore, and quantify. To overcome some of these challenges, we have developed TreeScaper, an application for tree set visualization as well as the identification of distinct phylogenetic signals. GUI and command-line versions of TreeScaper and a manual with tutorials can be downloaded from https://github.com/whuang08/TreeScaper/releases. TreeScaper i...
Source: Molecular Biology and Evolution - November 6, 2016 Category: Molecular Biology Authors: Huang, W., Zhou, G., Marchand, M., Ash, J. R., Morris, D., Van Dooren, P., Brown, J. M., Gallivan, K. A., Wilgenbusch, J. C. Tags: Resources Source Type: research
A Thousand Fly Genomes: An Expanded Drosophila Genome Nexus
The Drosophila Genome Nexus is a population genomic resource that provides D. melanogaster genomes from multiple sources. To facilitate comparisons across data sets, genomes are aligned using a common reference alignment pipeline which involves two rounds of mapping. Regions of residual heterozygosity, identity-by-descent, and recent population admixture are annotated to enable data filtering based on the user’s needs. Here, we present a significant expansion of the Drosophila Genome Nexus, which brings the current data object to a total of 1,121 wild-derived genomes. New additions include 305 previously unpublished ...
Source: Molecular Biology and Evolution - November 6, 2016 Category: Molecular Biology Authors: Lack, J. B., Lange, J. D., Tang, A. D., Corbett-Detig, R. B., Pool, J. E. Tags: Resources Source Type: research
Gene Tree Discordance Can Generate Patterns of Diminishing Convergence over Time
Phenotypic convergence is an exciting outcome of adaptive evolution, occurring when different species find similar solutions to the same problem. Unraveling the molecular basis of convergence provides a way to link genotype to adaptive phenotypes, but can also shed light on the extent to which molecular evolution is repeatable and predictable. Many recent genome-wide studies have uncovered a striking pattern of diminishing convergence over time, ascribing this pattern to the presence of intramolecular epistatic interactions. Here, we consider gene tree discordance as an alternative cause of changes in convergence levels ov...
Source: Molecular Biology and Evolution - November 6, 2016 Category: Molecular Biology Authors: Mendes, F. K., Hahn, Y., Hahn, M. W. Tags: Methods Source Type: research
Fast, Accurate and Automatic Ancient Nucleosome and Methylation Maps with epiPALEOMIX
The first epigenomes from archaic hominins (AH) and ancient anatomically modern humans (AMH) have recently been characterized, based, however, on a limited number of samples. The extent to which ancient genome-wide epigenetic landscapes can be reconstructed thus remains contentious. Here, we present epiPALEOMIX, an open-source and user-friendly pipeline that exploits post-mortem DNA degradation patterns to reconstruct ancient methylomes and nucleosome maps from shotgun and/or capture-enrichment data. Applying epiPALEOMIX to the sequence data underlying 35 ancient genomes including AMH, AH, equids and aurochs, we investigat...
Source: Molecular Biology and Evolution - November 6, 2016 Category: Molecular Biology Authors: Hanghoj, K., Seguin-Orlando, A., Schubert, M., Madsen, T., Pedersen, J. S., Willerslev, E., Orlando, L. Tags: Methods Source Type: research
Natural Selection in the Great Apes
Natural selection is crucial for the adaptation of populations to their environments. Here, we present the first global study of natural selection in the Hominidae (humans and great apes) based on genome-wide information from population samples representing all extant species (including most subspecies). Combining several neutrality tests we create a multi-species map of signatures of natural selection covering all major types of natural selection. We find that the estimated efficiency of both purifying and positive selection varies between species and is significantly correlated with their long-term effective population s...
Source: Molecular Biology and Evolution - November 6, 2016 Category: Molecular Biology Authors: Cagan, A., Theunert, C., Laayouni, H., Santpere, G., Pybus, M., Casals, F., Prüfer, K., Navarro, A., Marques-Bonet, T., Bertranpetit, J., Andres, A. M. Tags: Discoveries Source Type: research
Fine-Tuning Motile Cilia and Flagella: Evolution of the Dynein Motor Proteins from Plants to Humans at High Resolution
The flagellum is a key innovation linked to eukaryogenesis. It provides motility by regulated cycles of bending and bend propagation, which are thought to be controlled by a complex arrangement of seven distinct dyneins in repeated patterns of outer- (OAD) and inner-arm dynein (IAD) complexes. Electron tomography showed high similarity of this axonemal repeat pattern across ciliates, algae, and animals, but the diversity of dynein sequences across the eukaryotes has not yet comprehensively been resolved and correlated with structural data. To shed light on the evolution of the axoneme I performed an exhaustive analysis of ...
Source: Molecular Biology and Evolution - November 6, 2016 Category: Molecular Biology Authors: Kollmar, M. Tags: Discoveries Source Type: research
The Evolution of Silicon Transport in Eukaryotes
Biosilicification (the formation of biological structures from silica) occurs in diverse eukaryotic lineages, plays a major role in global biogeochemical cycles, and has significant biotechnological applications. Silicon (Si) uptake is crucial for biosilicification, yet the evolutionary history of the transporters involved remains poorly known. Recent evidence suggests that the SIT family of Si transporters, initially identified in diatoms, may be widely distributed, with an extended family of related transporters (SIT-Ls) present in some nonsilicified organisms. Here, we identify SITs and SIT-Ls in a range of eukaryotes, ...
Source: Molecular Biology and Evolution - November 6, 2016 Category: Molecular Biology Authors: Marron, A. O., Ratcliffe, S., Wheeler, G. L., Goldstein, R. E., King, N., Not, F., de Vargas, C., Richter, D. J. Tags: Discoveries Source Type: research
Epistasis and Pleiotropy Affect the Modularity of the Genotype-Phenotype Map of Cross-Resistance in HIV-1
The genotype–phenotype (GP) map is a central concept in evolutionary biology as it describes the mapping of molecular genetic variation onto phenotypic trait variation. Our understanding of that mapping remains partial, especially when trying to link functional clustering of pleiotropic gene effects with patterns of phenotypic trait co-variation. Only on rare occasions have studies been able to fully explore that link and tend to show poor correspondence between modular structures within the GP map and among phenotypes. By dissecting the structure of the GP map of the replicative capacity of HIV-1 in 15 drug environm...
Source: Molecular Biology and Evolution - November 6, 2016 Category: Molecular Biology Authors: Polster, R., Petropoulos, C. J., Bonhoeffer, S., Guillaume, F. Tags: Discoveries Source Type: research
Source of CpG Depletion in the HIV-1 Genome
The dinucleotide CpG is highly underrepresented in the genome of human immunodeficiency virus type 1 (HIV-1). To identify the source of CpG depletion in the HIV-1 genome, we investigated two biological mechanisms: (1) CpG methylation-induced transcriptional silencing and (2) CpG recognition by Toll-like receptors (TLRs). We hypothesized that HIV-1 has been under selective evolutionary pressure by these mechanisms leading to the reduction of CpG in its genome. A CpG depleted genome would enable HIV-1 to avoid methylation-induced transcriptional silencing and/or to avoid recognition by TLRs that identify foreign CpG sequence...
Source: Molecular Biology and Evolution - November 6, 2016 Category: Molecular Biology Authors: Alinejad-Rokny, H., Anwar, F., Waters, S. A., Davenport, M. P., Ebrahimi, D. Tags: Discoveries Source Type: research
A Photoreceptor Contributes to the Natural Variation of Diapause Induction in Daphnia magna
Diapause is an adaptation that allows organisms to survive harsh environmental conditions. In species occurring over broad habitat ranges, both the timing and the intensity of diapause induction can vary across populations, revealing patterns of local adaptation. Understanding the genetic architecture of this fitness-related trait would help clarify how populations adapt to their local environments. In the cyclical parthenogenetic crustacean Daphnia magna, diapause induction is a phenotypic plastic life history trait linked to sexual reproduction, as asexual females have the ability to switch to sexual reproduction and pro...
Source: Molecular Biology and Evolution - November 6, 2016 Category: Molecular Biology Authors: Roulin, A. C., Bourgeois, Y., Stiefel, U., Walser, J.-C., Ebert, D. Tags: Discoveries Source Type: research
Loss and Gain of Human Acidic Mammalian Chitinase Activity by Nonsynonymous SNPs
Acidic mammalian chitinase (AMCase) is implicated in asthma, allergic inflammation, and food processing. Little is known about genetic and evolutional regulation of chitinolytic activity of AMCase. Here, we relate human AMCase polymorphisms to the mouse AMCase, and show that the highly active variants encoded by nonsynonymous single-nucleotide polymorphisms (nsSNPs) are consistent with the mouse AMCase sequence. The chitinolytic activity of the recombinant human AMCase was significantly lower than that of the mouse counterpart. By creating mouse-human chimeric AMCase protein we found that the presence of the N-terminal reg...
Source: Molecular Biology and Evolution - November 6, 2016 Category: Molecular Biology Authors: Okawa, K., Ohno, M., Kashimura, A., Kimura, M., Kobayashi, Y., Sakaguchi, M., Sugahara, Y., Kamaya, M., Kino, Y., Bauer, P. O., Oyama, F. Tags: Discoveries Source Type: research
Evolution of Protein Domain Repeats in Metazoa
Repeats are ubiquitous elements of proteins and they play important roles for cellular function and during evolution. Repeats are, however, also notoriously difficult to capture computationally and large scale studies so far had difficulties in linking genetic causes, structural properties and evolutionary trajectories of protein repeats. Here we apply recently developed methods for repeat detection and analysis to a large dataset comprising over hundred metazoan genomes. We find that repeats in larger protein families experience generally very few insertions or deletions (indels) of repeat units but there is also a signif...
Source: Molecular Biology and Evolution - November 6, 2016 Category: Molecular Biology Authors: Schüler, A., Bornberg-Bauer, E. Tags: Discoveries Source Type: research
Cis-Regulatory Evolution of Forkhead Box O1 (FOXO1), a Terminal Selector Gene for Decidual Stromal Cell Identity
We present molecular evidence placing the origin of DSC in the stem lineage of eutherians (extant placental mammals). The transcription factor forkhead box O1 (FOXO1) is a part of the core regulatory transcription factor complex (CoRC) that establishes the cell type identity of DSC. Decidualization, the process through which DSC differentiate from endometrial stromal fibroblasts, requires transcriptional upregulation of FOXO1. Contrary to other examples in mammals where gene recruitment is caused by the origin of an alternative promoter, FOXO1 is transcribed from the same promoter in DSC as in endometrial stromal fibroblas...
Source: Molecular Biology and Evolution - November 6, 2016 Category: Molecular Biology Authors: Park, Y., Nnamani, M. C., Maziarz, J., Wagner, G. P. Tags: Discoveries Source Type: research
Paternal Mitochondrial Transmission in Intra-Species Caenorhabditis briggsae Hybrids
To study mitochondrial–nuclear genetic interactions in the nematode Caenorhabditis briggsae, our three laboratories independently created 38 intra-species cytoplasmic–nuclear hybrid (cybrid) lines. Although the cross design combines maternal mitotypes with paternal nuclear genotypes, eight lines (21%) unexpectedly contained paternal mitotypes. All eight share in common ancestry of one of two genetically related strains. This unexpected parallel observation of paternal mitochondrial transmission, undesirable given our intent of creating cybrids, provides a serendipitous experimental model and framework to study ...
Source: Molecular Biology and Evolution - November 6, 2016 Category: Molecular Biology Authors: Ross, J. A., Howe, D. K., Coleman-Hulbert, A., Denver, D. R., Estes, S. Tags: Discoveries Source Type: research
