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Molecular Biology and Evolution

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https://www.readbyqxmd.com/read/30428072/the-many-nuanced-evolutionary-consequences-of-duplicated-genes
#1
Ashley I Teufel, Mackenzie M Johnson, Jon M Laurent, Aashiq H Kachroo, Edward M Marcotte, Claus O Wilke
Gene duplication is seen as a major source of structural and functional divergence in genome evolution. Under the conventional models of sub- or neofunctionalizaton, functional changes arise in one of the duplicates after duplication. However, we suggest here that the presence of a duplicated gene can result in functional changes to its interacting partners. We explore this hypothesis by in-silico evolution of a heterodimer when one member of the interacting pair is duplicated. We examine how a range of selection pressures and protein structures leads to differential patterns of evolutionary divergence...
November 14, 2018: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/30428071/genomic-evidence-of-local-adaptation-to-climate-and-diet-in-indigenous-siberians
#2
Brian Hallmark, Tatiana M Karafet, PingHsun Hsieh, Ludmila P Osipova, Joseph C Watkins, Michael F Hammer
The indigenous inhabitants of Siberia live in some of the harshest environments on earth, experiencing extended periods of severe cold temperatures, dramatic variation in photoperiod, and limited and highly variable food resources. While the successful long-term settlement of this area by humans required multiple behavioral and cultural innovations, the nature of the underlying genetic changes has generally remained elusive. In this study, we used a three-part approach to identify putative targets of positive natural selection in Siberians...
November 14, 2018: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/30428070/methods-for-estimating-demography-and-detecting-between-locus-differences-in-the-effective-population-size-and-mutation-rate
#3
Kai Zeng, Benjamin C Jackson
It is known that the effective population size (Ne) and the mutation rate (u) vary across the genome. Here we show that ignoring this heterogeneity may lead to biased estimates of past demography. To solve the problem, we develop new methods for jointly inferring past changes in population size and detecting variation in Ne and u between loci. These methods rely on either polymorphism data alone or both polymorphism and divergence data. In addition to inferring demography, we can use the methods to study a variety of questions: (1) comparing sex chromosomes to autosomes (for finding evidence for male-driven evolution, an unequal sex ratio, or sex-biased demographic changes); (2) analysing multi-locus data from within autosomes or sex chromosomes (for studying determinants of variability in Ne and u)...
November 14, 2018: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/30403808/recombination-and-large-structural-variations-shape-interspecific-edible-bananas-genomes
#4
Franc-Christophe Baurens, Guillaume Martin, Catherine Hervouet, Frédéric Salmon, David Yohomé, Sébastien Ricci, Mathieu Rouard, Remy Habas, Arnaud Lemainque, Nabila Yahiaoui, Angélique D'Hont
Admixture and polyploidization are major recognized eukaryotic genome evolutionary processes. Their impacts on genome dynamics vary among systems and are still partially deciphered. Many banana cultivars are triploid (sometimes diploid) interspecific hybrids between Musa acuminata (A genome) and M. balbisiana (B genome). They have no or very low fertility, are vegetatively propagated and have been classified as 'AB', 'AAB' or 'ABB' based on morphological characters. We used NGS sequence data to characterize the A vs...
November 6, 2018: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/30398664/loss-of-gene-body-methylation-in-eutrema-salsugineum-is-associated-with-reduced-gene-expression
#5
Aline Muyle, Brandon S Gaut
Gene body methylation (gbM) is typically characterized by DNA methylation in the CG context within coding regions, and is associated with constitutive genes that have moderate to high expression levels. A recent study discovered the loss of gbM in two plant species (Eutrema salsugineum and Conringia planisiliqua), illustrating that gbM is not necessary for survival and reproduction. The same paper stated there was no detectable effect of gbM loss on gene expression (GE). Here, we reanalyzed the GE data and accounted for experimental variability in expression level estimates...
November 6, 2018: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/30398642/localizing-and-classifying-adaptive-targets-with-trend-filtered-regression
#6
Mehreen R Mughal, Michael DeGiorgio
Identifying genomic locations of natural selection from sequence data is an ongoing challenge in population genetics. Current methods utilizing information combined from several summary statistics typically assume no correlation of summary statistics regardless of the genomic location from which they are calculated. However, due to linkage disequilibrium, summary statistics calculated at nearby genomic positions are highly correlated. We introduce an approach termed Trendsetter that accounts for the similarity of statistics calculated from adjacent genomic regions through trend filtering, while reducing the effects of multicollinearity through regularization...
November 6, 2018: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/30395322/on-the-regulatory-evolution-of-new-genes-throughout-their-life-history
#7
Jia-Yu Zhang, Qi Zhou
Every gene has a birthplace and an age, i.e., a cis-regulatory environment and an evolution lifespan since its origination, yet how the two shape the evolution trajectories of genes remains unclear. Here we address this basic question by comparing phylogenetically dated new genes in the context of both their ages and origination mechanisms. In both Drosophila and vertebrates, we confirm a clear 'out of the testis' transition from the specifically expressed young genes to the broadly expressed old housekeeping genes, observed only in testis but not in other tissues...
November 3, 2018: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/30395254/tipping-the-scales-the-migration-selection-balance-leans-toward-selection-in-snake-venoms
#8
Mark J Margres, Austin Patton, Kenneth P Wray, Alyssa T B Hassinger, Micaiah J Ward, Emily Moriarty Lemmon, Alan R Lemmon, Darin R Rokyta
The migration-selection interaction is the strongest determinant of whether a beneficial allele increases in frequency within a population. Results of empirical studies examining the role of gene adaptive context, however, have largely been equivocal, with examples of opposing outcomes being repeatedly documented (e.g., local adaptation with high levels of gene flow versus gene swamping). We compared neutral genomic and venom expression divergence for three sympatric pit vipers with differing ecologies to determine if and how migration-selection disequilibria result in local adaptation...
November 3, 2018: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/30388255/a-polygenic-genetic-architecture-of-flowering-time-in-the-worldwide-arabidopsis-thaliana-population
#9
Yanjun Zan, Örjan Carlborg
Here, we report an empirical study of the polygenic basis underlying the evolution of complex traits. Flowering time variation measured at 10 and 16 °C in the 1,001-genomes Arabidopsis thaliana collection of natural accessions were used as a model. The polygenic architecture of flowering time was defined as the 48 loci that were significantly associated with flowering time - at 10 and/or 16 °C and/or their difference - in this population. Contributions from alleles at flowering time associated loci to global and local adaptation were explored by evaluating their distribution across genetically and geographically defined subpopulations across the native range of the species...
November 2, 2018: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/30380122/detection-of-shared-balancing-selection-in-the-absence-of-trans-species-polymorphism
#10
Xiaoheng Cheng, Michael DeGiorgio
Trans-species polymorphism has been widely used as a key sign of long-term balancing selection across multiple species. However, such sites are often rare in the genome, and could result from mutational processes or technical artifacts. Few methods are yet available to specifically detect footprints of transspecies balancing selection without using trans-species polymorphic sites. In this study, we develop summary- and model-based approaches that are each specifically tailored to uncover regions of long-term balancing selection shared by a set of species by using genomic patterns of intra-specific polymorphism and inter-specific fixed differences...
October 31, 2018: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/30376122/changes-in-biological-pathways-during-6-000-years-of-civilization-in-europe
#11
Evgeny Chekalin, Alexandr Rubanovich, Tatiana V Tatarinova, Artem Kasianov, Nicole Bender, Marina Chekalina, Kaspar Staub, Nikola Koepke, Frank Rühli, Sergey Bruskin, Irina Morozova
The beginning of civilization was a turning point in human evolution. With increasing separation from the natural environment, mankind stimulated new adaptive reactions in response to new environmental factors. In this paper, we describe direct signs of these reactions in the European population during the past 6,000 years. By comparing whole-genome data between Late Neolithic/Bronze Age individuals and modern Europeans, we revealed biological pathways that are significantly differently enriched in non-synonymous SNPs in these two groups and which therefore could be shaped by cultural practices during the past six millennia...
October 30, 2018: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/30371871/evolution-of-portulacineae-marked-by-gene-tree-conflict-and-gene-family-expansion-associated-with-adaptation-to-harsh-environments
#12
Ning Wang, Ya Yang, Michael J Moore, Samuel F Brockington, Joseph F Walker, Joseph W Brown, Bin Liang, Tao Feng, Caroline Edwards, Jessica Mikenas, Julia Olivieri, Vera Hutchison, Alfonso Timoneda, Tommy Stoughton, Raúl Puente, Lucas C Majure, Urs Eggli, Stephen A Smith
Several plant lineages have evolved adaptations that allow survival in extreme and harsh environments including many families within the plant clade Portulacineae (Caryophyllales) such as the Cactaceae, Didiereaceae, and Montiaceae. Here, using newly generated transcriptomic data, we reconstructed the phylogeny of Portulacineae and examined potential correlates between molecular evolution and adaptation to harsh environments. Our phylogenetic results were largely congruent with previous analyses, but we identified several early diverging nodes characterized by extensive gene tree conflict...
October 29, 2018: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/30364966/phylotranscriptomic-insights-into-the-diversification-of-endothermic-thunnus-tunas
#13
Adam Ciezarek, Owen Osborne, Oliver N Shipley, Edward J Brooks, Sean Tracey, Jaime McAllister, Luke Gardner, Michael J E Sternberg, Barbara Block, Vincent Savolainen
Birds, mammals, and certain fishes, including tunas, opahs and lamnid sharks, are endothermic, conserving internally generated, metabolic heat to maintain body or tissue temperatures above that of the environment. Bluefin tunas are commercially important fishes worldwide and some populations are threatened. They are renowned for their endothermy, maintaining elevated temperatures of the oxidative locomotor muscle, viscera, brain and eyes, and occupying cold, productive high-latitude waters. Less cold-tolerant tunas, such as yellowfin tuna, by contrast, remain in warm-temperate to tropical waters year-round, reproducing more rapidly than most temperate bluefin tuna populations, providing resiliency in the face of large scale industrial fisheries...
October 26, 2018: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/30351418/extreme-lewontin-s-paradox-in-ubiquitous-marine-phytoplankton-species
#14
Dmitry A Filatov
Larger populations are expected to have larger genetic diversity. However, as pointed out by Lewontin in 1974, the range of population sizes exceeds the range of genetic diversity by many orders of magnitude (aka "Lewontin's paradox", LP). The reasons for LP remain obscure. Here I report an extreme case of LP in astronomically large populations of the ubiquitous unicellular marine phytoplankton species Emiliania huxleyi (Haptophyta) - the species that accounts for 10 to 20% of primary productivity in the oceans and its blooms are so extensive that they are visible from space...
October 23, 2018: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/30351416/tanglegrams-are-misleading-for-visual-evaluation-of-tree-congruence
#15
Damien M de Vienne
Evolutionary Biologists are often faced with the need to compare phylogenetic trees. One popular method consists in visualizing the trees face to face with links connecting matching taxa. These tanglegrams are optimized beforehand so that the number of lines crossing (the entanglement) is minimal. This representation is implicitly justified by the expectation that the level of entanglement is correlated with the level of similarity (or congruence) between the trees compared. Using simulations, I show that this correlation is actually very weak, which should preclude the use of such technique for getting insight into the level of congruence between trees...
October 23, 2018: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/30351396/two-methods-for-mapping-and-visualizing-associated-data-on-phylogeny-using-ggtree
#16
Guangchuang Yu, Tommy Tsan-Yuk Lam, Huachen Zhu, Yi Guan
Ggtree is a comprehensive R package for visualizing and annotating phylogenetic trees with associated data. It can also map and visualize associated external data on phylogenies with two general methods. Method 1 allows external data to be mapped on the tree structure and used as visual characteristic in tree and data visualization. Method 2 plots the data with the tree side by side using different geometric functions after re-ordering the data based on the tree structure. These two methods integrate data with phylogeny for further exploration and comparison in the evolutionary biology context...
October 23, 2018: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/30351378/functional-consequences-of-the-evolution-of-matrimony-a-meiosis-specific-inhibitor-of-polo-kinase
#17
Amanda M Bonner, R Scott Hawley
Meiosis is a defining characteristic of eukaryotes, believed to have evolved only once, over one billion years ago. While the general progression of meiotic events is conserved across multiple diverse organisms, the specific pathways and proteins involved can be highly divergent, even within species from the same genus. Here we investigate the rapid evolution of Matrimony (Mtrm), a female meiosis-specific regulator of Polo kinase (Polo) in Drosophila. Mtrm physically interacts with Polo and is required to restrict the activity of Polo during meiosis...
October 23, 2018: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/30325443/secreted-bacterial-adenosine-deaminase-is-an-evolutionary-precursor-of-adenosine-deaminase-growth-factor
#18
Maksym Skaldin, Minna Tuittila, Andrey V Zavialov, Anton V Zavialov
Adenosine deaminases (ADAs) play a pivotal role in regulating the level of adenosine, an important signaling molecule that controls a variety of cellular responses. Two distinct ADAs, ADA1 and adenosine deaminase growth factor (ADGF aka ADA2), are known. Cytoplasmic ADA1 plays a key role in purine metabolism and is widely distributed from prokaryotes to mammals. On the other hand, secreted ADGF/ADA2 is a cell-signaling protein that was thought to be present only in multicellular organisms. Here, we discovered a bacterial homologue of ADGF/ADA2...
October 16, 2018: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/30304531/new-insight-into-parrots-mitogenomes-indicates-that-their-ancestor-contained-a-duplicated-region
#19
Adam Dawid Urantowka, Aleksandra Kroczak, Tony Silva, Rafael Zamora Padrón, Nuhacet Fernández Gallardo, Julie Blanch, Barry Blanch, Pawel Mackiewicz
Mitochondrial genomes of vertebrates are generally thought to evolve under strong selection for size reduction and gene order conservation. Therefore, a growing number of mitogenomes with duplicated regions changes our view on the genome evolution. Among Aves, order Psittaciformes (parrots) is especially noteworthy because of its large morphological, ecological and taxonomical diversity, which offers an opportunity to study genome evolution in various aspects. Former analyses showed that tandem duplications comprising the control region with adjacent genes are restricted to several lineages in which the duplication occurred independently...
October 10, 2018: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/30295892/functional-conservation-of-a-developmental-switch-in-mammals-since-the-jurassic-age
#20
Jayati Mookerjee-Basu, Xiang Hua, Lu Ge, Emmanuelle Nicolas, Qin Li, Philip Czyzewicz, Dai Zhongping, Suraj Peri, Juan I FuxmanBass, Albertha J M Walhout, Dietmar J Kappes
ThPOK is a "master regulator" of T lymphocyte lineage choice, whose presence or absence is sufficient to dictate development to the CD4 or CD8 lineages, respectively. Induction of ThPOK is critically regulated at the transcriptional level, via a lineage-specific silencer element, SilThPOK. Here, we take advantage of the available genome sequence data as well as site-specific gene targeting technology, to evaluate the functional conservation of ThPOK regulation across mammalian evolution, and assess the importance of motif grammar (order and orientation of TF binding sites) on SilThPOK function in vivo...
October 8, 2018: Molecular Biology and Evolution
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