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Molecular Biology and Evolution

Jaqueline Hess, Inger Skrede, Maryam Chaib De Mares, Matthieu Hainaut, Bernard Henrissat, Anne Pringle
Fungi are evolutionary shape shifters and adapt quickly to new environments. Ectomycorrhizal (EM) symbioses are mutualistic associations between fungi and plants and have evolved repeatedly and independently across the fungal tree of life, suggesting lineages frequently reconfigure genome content to take advantage of open ecological niches. To date analyses of genomic mechanisms facilitating EM symbioses have involved comparisons of distantly related species, but here, we use the genomes of three EM and two asymbiotic (AS) fungi from the genus Amanita as well as an AS outgroup to study genome evolution following a single origin of symbiosis...
September 18, 2018: Molecular Biology and Evolution
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September 11, 2018: Molecular Biology and Evolution
Grant L Filowitz, Rajendhran Rajakumar, Katherine L O'Shaughnessy, Martin J Cohn
Vertebrate estrogen receptors (ERs) perform numerous cell signaling and transcriptional regulatory functions. ERɑ (Esr1) and ERβ (Esr2) likely evolved from an ancestral receptor that duplicated and diverged at the protein and cis-regulatory levels, but the evolutionary history of ERs, including the timing of proposed duplications, remains unresolved. Here we report on identification of two distinct ERs in cartilaginous fishes and demonstrate their orthology to ERα and ERβ. Phylogenetic analyses place the ERα/ERβ duplication near the base of crown gnathostomes (jawed vertebrates)...
September 10, 2018: Molecular Biology and Evolution
João Raimundo, Rómulo Sobral, Sara Laranjeira, M Manuela R Costa
The establishment of new interactions between transcriptional regulators increases the regulatory diversity that drives phenotypic novelty. To understand how such interactions evolve, we have studied a regulatory module (DDR) composed by three MYB-like proteins: DIVARICATA (DIV), RADIALIS (RAD) and DIV-and-RAD-Interacting Factor (DRIF). The DIV and DRIF proteins form a transcriptional complex that is disrupted in the presence of RAD, a small interfering peptide, due to the formation of RAD-DRIF dimers. This dynamic interaction result is a molecular switch mechanism responsible for the control of distinct developmental processes in plants...
September 7, 2018: Molecular Biology and Evolution
Simon Laurin-Lemay, Nicolas Rodrigue, Nicolas Lartillot, Hervé Philippe
A key question in molecular evolutionary biology concerns the relative roles of mutation and selection in shaping genomic data. Moreover, features of mutation and selection are heterogeneous along the genome and over time. Mechanistic codon substitution models based on the mutation-selection framework are promising approaches to separating these effects. In practice, however, several complications arise, since accounting for such heterogeneities often implies handling models of high dimensionality (e.g., amino acid preferences), or leads to across-site dependence (e...
September 7, 2018: Molecular Biology and Evolution
Avital Sharir-Ivry, Yu Xia
Enzymes are known to fine-tune their sequences to optimize catalytic function, yet quantitative evolutionary design principles of enzymes remain elusive on the proteomic scale. Recently, it was found that the catalytic site in enzymes induces long-range evolutionary constraint, where even sites distant to the catalytic site are more conserved than expected. Given that protein-fold usage is generally different between enzymes and non-enzymes, it remains an open question to what extent this long-range evolutionary constraint in enzymes is dictated, either directly or indirectly, by the special three-dimensional structure of the enzyme...
September 7, 2018: Molecular Biology and Evolution
Logan W Cole, Wenhu Guo, Jeffrey P Mower, Jeffrey D Palmer
For 30 years, it has been clear that angiosperm mitochondrial genomes evolve rapidly in sequence arrangement (i.e., synteny), yet absolute rates of rearrangement have not been measured in any plant group, nor is it known how much these rates vary. To investigate these issues, we sequenced and reconstructed the rearrangement history of seven mitochondrial genomes in Monsonia (Geraniaceae). We show that rearrangements (occurring mostly as inversions) take place at generally high rates in these genomes, but also uncover significant variation in rearrangement rates...
September 7, 2018: Molecular Biology and Evolution
Sanzhen Liu, James C Schnable, Alina Ott, Cheng-Ting Eddy Yeh, Nathan M Springer, Jianming Yu, Gary Muehlbauer, Marja C P Timmermans, Michael J Scanlon, Patrick S Schnable
Meiotic recombination is an evolutionary force that generates new genetic diversity upon which selection can act. While multiple studies have assessed genome-wide patterns of recombination and specific cases of intragenic recombination, few studies have assessed intragenic recombination genome-wide in higher eukaryotes. We identified recombination events within or near genes in a population of maize recombinant inbred lines (RILs) using RNA-sequencing data. Our results are consistent with case studies that have shown that intragenic crossovers cluster at the 5' ends of some genes...
September 4, 2018: Molecular Biology and Evolution
Quinn K Langdon, David Peris, Brian Kyle, Chris Todd Hittinger
The genomics era has expanded our knowledge about the diversity of the living world, yet harnessing high-throughput sequencing data to investigate alternative evolutionary trajectories, such as hybridization, is still challenging. Here we present sppIDer, a pipeline for the characterization of interspecies hybrids and pure species, that illuminates the complete composition of genomes. sppIDer maps short-read sequencing data to a combination genome built from reference genomes of several species of interest and assesses the genomic contribution and relative ploidy of each parental species, producing a series of colorful graphical outputs ready for publication...
September 1, 2018: Molecular Biology and Evolution
Vojtech Vacek, Lukáš V F Novák, Sebastian C Treitli, Petr Táborský, Ivan Cepicka, Martin Kolísko, Patrick J Keeling, Vladimír Hampl
The oxymonad Monocercomonoides exilis was recently reported to be the first eukaryote that has completely lost the mitochondrial compartment. It was proposed that an important prerequisite for such a radical evolutionary step was the acquisition of the SUF Fe-S cluster assembly pathway from prokaryotes, making the mitochondrial ISC pathway dispensable. We have investigated genomic and transcriptomic data from six oxymonad species and their relatives, composing the group Preaxostyla (Metamonada, Excavata), for the presence and absence of enzymes involved in Fe-S cluster biosynthesis...
September 1, 2018: Molecular Biology and Evolution
Fatima Foflonker, Devin Mollegard, Meichin Ong, Hwan Su Yoon, Debashish Bhattacharya
Understanding how microalgae adapt to rapidly changing environments is not only important to science but can help clarify the potential impact of climate change on the biology of primary producers. We sequenced and analyzed the nuclear genome of multiple Picochlorum isolates (Chlorophyta) to elucidate strategies of environmental adaptation. It was previously found that coordinated gene regulation is involved in adaptation to salinity stress, and here we show that gene gain and loss also play key roles in adaptation...
September 1, 2018: Molecular Biology and Evolution
Jialin Liu, Marc Robinson-Rechavi
A driving hypothesis of Evo-Devo is that animal morphological diversity is shaped both by adaptation and by developmental constraints. Here we have tested Darwin's "selection opportunity" hypothesis, according to which high evolutionary divergence in late development is due to strong positive selection. We contrasted it to a "developmental constraint" hypothesis, according to which late development is under relaxed negative selection. Indeed, the highest divergence between species, both at the morphological and molecular levels, is observed late in embryogenesis and post-embryonically...
September 1, 2018: Molecular Biology and Evolution
Ran Zhao, Takeshi Takeuchi, Yi-Jyun Luo, Akito Ishikawa, Tatsushi Kobayashi, Ryo Koyanagi, Alejandro Villar-Briones, Lixy Yamada, Hitoshi Sawada, Shunsuke Iwanaga, Kiyohito Nagai, Noriyuki Satoh, Kazuyoshi Endo
Molluscan shells, mainly composed of calcium carbonate, also contain organic components such as proteins and polysaccharides. Shell organic matrices construct frameworks of shell structures and regulate crystallization processes during shell formation. To date, a number of shell matrix proteins (SMPs) have been identified, and their functions in shell formation have been studied. However, previous studies focused only on SMPs extracted from adult shells, secreted after metamorphosis.Using proteomic analyses combined with genomic and transcriptomic analyses, we have identified 31 SMPs from larval shells of the pearl oyster, Pinctada fucata, and 111 from the Pacific oyster, Crassostrea gigas...
August 31, 2018: Molecular Biology and Evolution
Charleston W K Chiang, Serghei Mangul, Christopher R Robles, Sriram Sankararam
As are most non-European populations, the Han Chinese are relatively understudied in population and medical genetics studies. From low-coverage whole-genome sequencing of 11,670 Han Chinese women we present a catalog of 25,057,223 variants, including 548,401 novel variants that are seen at least 10 times in our dataset. Individuals from this dataset came from 24 out of 33 administrative divisions across China (including 19 provinces, 4 municipalities, and 1 autonomous region), thus allowing us to study population structure, genetic ancestry, and local adaptation in Han Chinese...
August 30, 2018: Molecular Biology and Evolution
Leslie S Babonis, Melissa B DeBiasse, Warren R Francis, Lynne M Christianson, Anthony G Moss, Steven H D Haddock, Mark Q Martindale, Joseph F Ryan
The origin of novel traits can promote expansion into new niches and drive speciation. Ctenophores (comb jellies) are unified by their possession of a novel cell type: the colloblast, an adhesive cell found only in the tentacles. Although colloblast-laden tentacles are fundamental for prey capture among ctenophores, some species have tentacles lacking colloblasts and others have lost their tentacles completely. We used transcriptomes from 36 ctenophore species to identify gene losses that occurred specifically in lineages lacking colloblasts and tentacles...
August 30, 2018: Molecular Biology and Evolution
Leonardo Arias, Roland Schröder, Alexander Hübner, Guillermo Barreto, Mark Stoneking, Brigitte Pakendorf
Human populations often exhibit contrasting patterns of genetic diversity in the mtDNA and the non-recombining portion of the Y-chromosome (NRY), which reflect sex-specific cultural behaviors and population histories. Here, we sequenced 2.3 Mb of the NRY from 284 individuals representing more than 30 Native-American groups from Northwestern Amazonia (NWA) and compared these data to previously generated mtDNA genomes from the same groups, to investigate the impact of cultural practices on genetic diversity and gain new insights about NWA population history...
August 29, 2018: Molecular Biology and Evolution
Jade Southworth, Paul Armitage, Brandon Fallon, Holly Dawson, Jaroslaw Bryk, Martin Carr
Choanoflagellates and filastereans are the closest known single celled relatives of Metazoa within Holozoa and provide insight into how animals evolved from their unicellular ancestors. Codon usage bias has been extensively studied in metazoans, with both natural selection and mutation pressure playing important roles in different species. The disparate nature of metazoan codon usage patterns prevents the reconstruction of ancestral traits. However, traits conserved across holozoan protists highlight characteristics in the unicellular ancestors of Metazoa...
August 29, 2018: Molecular Biology and Evolution
Adam C Palmer, Remy Chait, Roy Kishony
Bacteria regulate genes to survive antibiotic stress, but regulation can be far from perfect. When regulation is not optimal, mutations that change gene expression can contribute to antibiotic resistance. It is not systematically understood to what extent natural gene regulation is or is not optimal for distinct antibiotics, and how changes in expression of specific genes quantitatively affect antibiotic resistance. Here we discover a simple quantitative relation between fitness, gene expression and antibiotic potency, which rationalizes our observation that a multitude of genes and even innate antibiotic defence mechanisms have expression that is critically non-optimal under antibiotic treatment...
August 28, 2018: Molecular Biology and Evolution
Vincent Ranwez, Emmanuel J P Douzery, Cédric Cambon, Nathalie Chantret, Frédéric Delsuc
Multiple sequence alignment is a prerequisite for many evolutionary analyses. MACSE is a multiple sequence alignment program that explicitly accounts for the underlying codon structure of protein-coding nucleotide sequences. Its unique characteristic allows building reliable codon alignments even in the presence of frameshifts. This facilitates downstream analyses such as selection pressure estimation based on the ratio of non-synonymous to synonymous substitutions. Here, we present MACSE v2, a major update with an improved version of the initial algorithm enriched with a complete toolkit to handle multiple alignments of protein-coding sequences...
August 25, 2018: Molecular Biology and Evolution
Jody Hey, Yujin Chung, Arun Sethuraman, Joseph Lachance, Sarah Tishkoff, Vitor C Sousa, Yong Wang
Phylogeny estimation is difficult for closely related populations and species, especially if they have been exchanging genes. We present a hierarchical Bayesian, Markov-chain Monte Carlo method with a state space that includes all possible phylogenies in a full Isolation-with-Migration model framework. The method is based on a new type of genealogy augmentation called a 'hidden genealogy' that enables efficient updating of the phylogeny. This is the first likelihood-based method to fully incorporate directional gene flow and genetic drift for estimation of a species or population phylogeny...
August 20, 2018: Molecular Biology and Evolution
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