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Molecular Biology and Evolution

Svetlana Cherlin, Sarah E Heaps, Tom M W Nye, Richard J Boys, Tom A Williams, T Martin Embley
Most phylogenetic models assume that the evolutionary process is stationary and reversible. In addition to being biologically improbable, these assumptions also impair inference by generating models under which the likelihood does not depend on the position of the root. Consequently, the root of the tree cannot be inferred as part of the analysis. Yet identifying the root position is a key component of phylogenetic inference because it provides a point of reference for polarising ancestor/descendant relationships and therefore interpreting the tree...
November 15, 2017: Molecular Biology and Evolution
Sebastian Höhna, Lyndon M Coghill, Genevieve G Mount, Robert C Thomson, Jeremy M Brown
Tests of absolute model fit are crucial in model-based inference because poorly structured models can lead to biased parameter estimates. In Bayesian inference, posterior predictive simulations can be used to test absolute model fit. However such tests have not been commonly practiced in phylogenetic inference due to a lack of convenient and flexible software. Here we describe our newly implemented tests of model fit using posterior predictive testing, based on both data- and inference-based test statistics, in the phylogenetics software RevBayes...
November 10, 2017: Molecular Biology and Evolution
Han Chen, Chung-I Wu, Xionglei He
Although any genotype-phenotype relationships are a result of evolution, little is known about how natural selection and neutral drift, two distinct driving forces of evolution, operate to shape the relationships. By analysing ∼500 yeast quantitative traits we reveal a basic "supervisor-worker" gene architecture underlying a trait. Supervisors are often identified by "perturbational" approaches (such as gene deletion), while workers, which usually show small and statistically insignificant deletion effects, are tracked primarily by "observational" approaches that examine the correlation between gene activity and trait value across a number of conditions...
November 9, 2017: Molecular Biology and Evolution
Erica V Todd, Hui Liu, Melissa S Lamm, Jodi T Thomas, Kim Rutherford, Kelly C Thompson, John R Godwin, Neil J Gemmell
Phenotypic plasticity represents an elegant adaptive response of individuals to a change in their environment. Bluehead wrasses (Thalassoma bifasciatum) exhibit astonishing sexual plasticity, including female-to-male sex change and discrete male morphs that differ strikingly in behaviour, morphology and gonadal investment. Using RNA-seq transcriptome profiling, we examined the genes and physiological pathways underlying flexible behavioural and gonadal differences among female, dominant (bourgeois) male, and female-mimic (sneaker) male blueheads...
November 8, 2017: Molecular Biology and Evolution
Eleanor F Banwell, Bernard M A G Piette, Anne Taormina, Jonathan G Heddle
Even the simplest organisms are too complex to have spontaneously arisen fully-formed, yet precursors to first life must have emerged ab initio from their environment. A watershed event was the appearance of the first entity capable of evolution: the Initial Darwinian Ancestor. Here we suggest that nucleopeptide reciprocal replicators could have carried out this important role and contend that this is the simplest way to explain extant replication systems in a mathematically consistent way. We propose short nucleic- acid templates on which amino-acylated adapters assembled...
November 8, 2017: Molecular Biology and Evolution
Áine N O'Toole, Laurence D Hurst, Aoife McLysaght
An attractive and long-standing hypothesis regarding the evolution of genes after duplication posits that the duplication event creates new evolutionary possibilities by releasing a copy of the gene from constraint. Apparent support was found in numerous analyses, particularly the observation of higher rates of evolution in duplicated as compared to singleton genes. Could it, instead, be that more duplicable genes (owing to mutation, fixation or retention biases) are intrinsically faster evolving? To uncouple the measurement of rates of evolution from the determination of duplicate or singleton status, we measure the rates of evolution in singleton genes in outgroup primate lineages but classify these genes as to whether they have duplicated or not in a crown group of great apes...
November 7, 2017: Molecular Biology and Evolution
Jae Young Choi, Michael D Purugganan
Plant genomes contain numerous transposable elements (TEs), and many hypotheses on the evolutionary drivers that restrict TE activity have been postulated. Few models, however, have focused on the evolutionary epigenomic interaction between the plant host and its TE. The host genome recruits epigenetic factors, such as methylation, to silence TEs but methylation can spread beyond the TE sequence and influence the expression of nearby host genes. In this study, we investigated this epigenetic trade-off between TE and proximal host gene silencing by studying the epigenomic regulation of repressing long terminal repeat (LTR) retrotransposons (RTs) in Oryza sativa...
November 6, 2017: Molecular Biology and Evolution
M Andreína Pacheco, Nubia E Matta, Gediminas Valkiunas, Patricia G Parker, Beatriz Mello, Craig E Stanley, Miguel Lentino, M Alexandra Garcia-Amado, Michael Cranfield, Sergei L Kosakovsky Pond, Ananias A Escalante
Haemosporidians are a diverse group of vector-borne parasitic protozoa that includes the agents of human malaria; however, most of the described species are found in birds and reptiles. Although our understanding of these parasites' diversity has expanded by analyses of their mitochondrial genes, there is limited information on these genes' evolutionary rates. Here, 114 mitochondrial genomes (mtDNA) were studied from species belonging to four genera: Leucocytozoon, Haemoproteus, Hepatocystis, and Plasmodium...
November 6, 2017: Molecular Biology and Evolution
Sergey V Venev, Konstantin B Zeldovich
Prokaryotes evolved to thrive in an extremely diverse set of habitats, and their proteomes bear signatures of environmental conditions. Although correlations between amino acid usage and environmental temperature are well documented, understanding of the mechanisms of thermal adaptation remains incomplete. Here, we couple the energetic costs of protein folding and protein homeostasis to build a microscopic model explaining both the overall amino acid composition and its temperature trends. Low biosynthesis costs lead to low diversity of physical interactions between amino acid residues, which in turn makes proteins less stable and drives up chaperone activity to maintain appropriate levels of folded, functional proteins...
November 2, 2017: Molecular Biology and Evolution
Stefania Brandini, Paola Bergamaschi, Marco Fernando Cerna, Francesca Gandini, Francesca Bastaroli, Emilie Bertolini, Cristina Cereda, Luca Ferretti, Alberto Gómez-Carballa, Vincenza Battaglia, Antonio Salas, Ornella Semino, Alessandro Achilli, Anna Olivieri, Antonio Torroni
Recent and compelling archaeological evidence attests to human presence ∼14.5 thousand years ago (Kya) at multiple sites in South America and a very early exploitation of extreme high-altitude Andean environments. Considering that, according to genetic evidence, human entry into North America from Beringia most likely occurred ∼16 Kya, these archeological findings would imply an extremely rapid spread along the double continent. To shed light on this issue from a genetic perspective, we first completely sequenced 217 novel modern mitogenomes of Native American ancestry from the northwestern area of South America (Ecuador and Peru); we then evaluated them phylogenetically together with other available mitogenomes (430 samples, both modern and ancient) from the same geographic area and, finally, with all closely related mitogenomes from the entire double continent...
October 31, 2017: Molecular Biology and Evolution
Jananan Sylvestre Pathmanathan, Philippe Lopez, François-Joseph Lapointe, Eric Bapteste
Genes evolve by point mutations, but also by shuffling, fusion and fission of genetic fragments. Therefore, similarity between two sequences can be due to common ancestry producing homology, and/or partial sharing of component fragments. Disentangling these processes is especially challenging in large molecular datasets, because of computational time. In this article, we present CompositeSearch, a memory-efficient, fast and scalable method to detect composite gene families in large datasets (typically in the range of several million sequences)...
October 30, 2017: Molecular Biology and Evolution
Lin Zeng, Chen Ming, Yan Li, Ling-Yan Su, Yan-Hua Su, Newton O Otecko, Ambroise Dalecky, Stephen Donnellan, Ken Aplin, Xiao-Hui Liu, Ying Song, Zhang Zhibin, Ali Esmailizadeh, Saeed S Sohrabi, Hojjat Asadollahpour Nanaei, He-Qun Liu, Ming-Shan Wang, Solimane Ag Atteynine, Gérard Rocamora, Fabrice Brescia, Serge Morand, David M Irwin, Ming-Sheng Peng, Yong-Gang Yao, Haipeng Li, Dong-Dong Wu, Ya-Ping Zhang
The geographic origin and migration of the brown rat (Rattus norvegicus) remain subjects of considerable debate. In this study, we sequenced whole genomes of 110 wild brown rats with a diverse world-wide representation. We reveal that brown rats migrated out of southern East Asia, rather than northern Asia as formerly suggested, into the Middle East and then to Europe and Africa, thousands of years ago. Comparison of genomes from different geographical populations reveals that many genes involved in the immune system experienced positive selection in the wild brown rat...
October 26, 2017: Molecular Biology and Evolution
Cheng-Min Shi, Ziheng Yang
The phylogenetic relationships among extant gibbon species remain unresolved despite numerous efforts using morphological, behavorial, and genetic data and the sequencing of whole genomes. A major challenge in reconstructing the gibbon phylogeny is the radiative speciation process, which resulted in extremely short internal branches in the species phylogeny and extensive incomplete lineage sorting with extensive gene-tree heterogeneity across the genome. Here we analyze two genomic-scale datasets, with ∼10,000 putative noncoding and exonic loci, respectively, to estimate the species tree for the major groups of gibbons...
October 25, 2017: Molecular Biology and Evolution
Diep Thi Hoang, Olga Chernomor, Arndt von Haeseler, Bui Quang Minh, Sy Vinh Le
The standard bootstrap (SBS), despite being computationally intensive, is widely used in maximum likelihood phylogenetic analyses. We recently proposed the ultrafast bootstrap approximation (UFBoot) to reduce computing time while achieving more unbiased branch supports than SBS under mild model violations. UFBoot has been steadily adopted as an efficient alternative to SBS and other bootstrap approaches.Here, we present UFBoot2, which substantially accelerates UFBoot and reduces the risk of overestimating branch supports due to polytomies or severe model violations...
October 25, 2017: Molecular Biology and Evolution
Charles W Carter, Peter R Wills
Genetic coding is generally thought to have required ribozymes whose functions were taken over by polypeptide aminoacyl-tRNA synthetases (aaRS). Two discoveries about aaRS and their interactions with tRNA substrates now furnish a unifying rationale for the opposite conclusion: that the key processes of the Central Dogma of molecular biology emerged simultaneously and naturally from simple origins in a peptide•RNA partnership, eliminating the epistemological utility of a prior RNA world. First, the two aaRS classes likely arose from opposite strands of the same ancestral gene, implying a simple genetic alphabet...
October 24, 2017: Molecular Biology and Evolution
Katya Kosheleva, Michael M Desai
The rates and selective effects of beneficial mutations, together with population genetic factors such as population size and recombination rate, determine the outcomes of adaptation and the signatures this process leaves in patterns of genetic diversity. Previous experimental studies of microbial evolution have focused primarily on initially clonal populations, finding that adaptation is characterized by new strongly selected beneficial mutations that sweep rapidly to fixation. Here, we study evolution in diverse outcrossed yeast populations, tracking the rate and genetic basis of adaptation over time...
October 24, 2017: Molecular Biology and Evolution
Dongying Gao, Ye Chu, Han Xia, Chunming Xu, Karolina Heyduk, Brian Abernathy, Peggy Ozias-Akins, James H Leebens-Mack, Scott A Jackson
Even though lateral movements of transposons across families and even phyla within multicellular eukaryotic kingdoms have been found, little is known about transposon transfer between the kingdoms Animalia and Plantae. We discovered a novel non-LTR retrotransposon, AdLINE3, in a wild peanut species. Sequence comparisons and phylogenetic analyses indicated that AdLINE3 is a member of the RTE clade, originally identified in a nematode and rarely reported in plants. We identified RTE elements in 82 plants, spanning angiosperms to algae, including recently active elements in some flowering plants...
October 23, 2017: Molecular Biology and Evolution
Fen Peng, Scott Widmann, Andrea Wünsche, Kristina Duan, Katherine A Donovan, Renwick C J Dobson, Richard E Lenski, Tim F Cooper
The fitness effects of mutations can depend on the genetic backgrounds in which they occur and thereby influence future opportunities for evolving populations. In particular, mutations that fix in a population might change the selective benefit of subsequent mutations, giving rise to historical contingency. We examine these effects by focusing on mutations in a key metabolic gene, pykF , that arose independently early in the history of 12 Escherichia coli populations during a long-term evolution experiment...
October 23, 2017: Molecular Biology and Evolution
Andrea Ariani, Jorge Berny Mier Y Teran, Paul Gepts
The wild progenitor of common-bean has an exceptionally large distribution from northern Mexico to northwestern Argentina, unusual among crop wild progenitors. This research sought to document major events of range expansion that led to this distribution and associated environmental changes. Through the use of genotyping-by-sequencing (~20,000 SNPs) and geographic information systems applied to a sample of 246 accessions of wild P. vulgaris , including 157 genotypes of the Mesoamerican, 77 of the southern Andean and 12 of the Northern Peru-Ecuador gene pools, we identified five geographically distinct subpopulations...
October 23, 2017: Molecular Biology and Evolution
David A Turissini, Joseph A McGirr, Sonali S Patel, Jean R David, Daniel R Matute
Reproductive isolation is an intrinsic aspect of species formation. For that reason, the identification of the precise isolating traits, and the rates at which they evolve, is crucial to understanding how species originate and persist. Previous work has measured the rates of evolution of prezygotic and postzygotic barriers to gene flow, yet no systematic analysis has studied the rates of evolution of postmating-prezygotic (PMPZ) barriers. We measured the magnitude of two barriers to gene flow that act after mating occurs but before fertilization...
October 18, 2017: Molecular Biology and Evolution
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