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Evolutionary dynamics

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https://www.readbyqxmd.com/read/28821744/exploring-the-sequence-based-prediction-of-folding-initiation-sites-in-proteins
#1
Daniele Raimondi, Gabriele Orlando, Rita Pancsa, Taushif Khan, Wim F Vranken
Protein folding is a complex process that can lead to disease when it fails. Especially poorly understood are the very early stages of protein folding, which are likely defined by intrinsic local interactions between amino acids close to each other in the protein sequence. We here present EFoldMine, a method that predicts, from the primary amino acid sequence of a protein, which amino acids are likely involved in early folding events. The method is based on early folding data from hydrogen deuterium exchange (HDX) data from NMR pulsed labelling experiments, and uses backbone and sidechain dynamics as well as secondary structure propensities as features...
August 18, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28821587/drift-induced-selection-between-male-and-female-heterogamety
#2
Carl Veller, Pavitra Muralidhar, George W A Constable, Martin A Nowak
Evolutionary transitions between male and female heterogamety are common in both vertebrates and invertebrates. Theoretical studies of these transitions have found that, when all genotypes are equally fit, continuous paths of intermediate equilibria link the two sex chromosome systems. This observation has led to a belief that neutral evolution along these paths can drive transitions, and that arbitrarily small fitness differences among sex chromosome genotypes can determine the system to which evolution leads...
August 16, 2017: Genetics
https://www.readbyqxmd.com/read/28821552/differences-in-temperature-and-water-chemistry-shape-distinct-diversity-patterns-in-thermophilic-microbial-communities
#3
Cecilia M Chiriac, Edina Szekeres, Knut Rudi, Andreea Baricz, Adriana Hegedus, Nicolae Dragoş, Cristian Coman
This study presents the biodiversity and ecology of microbial mats developed in thermal gradients (20-65 °C) in the surroundings of three drillings (CH, CI, MB) tapping a hyperthermal aquifer from Romania. Using a metabarcoding approach, 16S rRNA genes were sequenced from both DNA and RNA transcripts (cDNA) and compared. The relationships between the microbial diversity and the physico-chemical factors were explored. Additionally, the cDNA data was used for in silico functionality predictions, bringing new insights into the functional potential and dynamics of these communities...
August 18, 2017: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/28817588/phylogeography-of-the-reticulated-python-malayopython-reticulatus-ssp-conservation-implications-for-the-worlds-most-traded-snake-species
#4
Gillian Murray-Dickson, Muhammad Ghazali, Rob Ogden, Rafe Brown, Mark Auliya
As an important economic natural resource in Southeast Asia, reticulated pythons (Malayopython reticulatus ssp.) are primarily harvested from the wild for their skins-which are prized in the luxury leather goods industry. Trade dynamics of this CITES Appendix II listed species are complex and management approaches on the country or regional level appear obscure. Little is known about the actual geographic point-of-harvest of snakes, how genetic diversity is partitioned across the species range, how current harvest levels may affect the genetic viability of populations, and whether genetic structure could (or should) be accounted for when managing harvest quotas...
2017: PloS One
https://www.readbyqxmd.com/read/28814792/genetic-regulatory-effects-modified-by-immune-activation-contribute-to-autoimmune-disease-associations
#5
Sarah Kim-Hellmuth, Matthias Bechheim, Benno Pütz, Pejman Mohammadi, Yohann Nédélec, Nicholas Giangreco, Jessica Becker, Vera Kaiser, Nadine Fricker, Esther Beier, Peter Boor, Stephane E Castel, Markus M Nöthen, Luis B Barreiro, Joseph K Pickrell, Bertram Müller-Myhsok, Tuuli Lappalainen, Johannes Schumacher, Veit Hornung
The immune system plays a major role in human health and disease, and understanding genetic causes of interindividual variability of immune responses is vital. Here, we isolate monocytes from 134 genotyped individuals, stimulate these cells with three defined microbe-associated molecular patterns (LPS, MDP, and 5'-ppp-dsRNA), and profile the transcriptomes at three time points. Mapping expression quantitative trait loci (eQTL), we identify 417 response eQTLs (reQTLs) with varying effects between conditions...
August 16, 2017: Nature Communications
https://www.readbyqxmd.com/read/28814525/structure-guided-functional-annotation-of-the-influenza-a-virus-ns1-protein-reveals-dynamic-evolution-of-the-p85%C3%AE-binding-site-during-circulation-in-humans
#6
Antonio M Lopes, Patricia Domingues, Roland Zell, Benjamin G Hale
Rational characterization of virulence and host-adaptive markers in the multifunctional influenza A virus NS1 protein is hindered by a lack of comprehensive knowledge about NS1-host protein-protein interfaces. Here, we surveyed the impact of amino-acid variation in NS1 at its structurally-defined binding site for host p85β, a regulator of phosphoinositide-3 kinase (PI3K) signaling. Structure-guided alanine-scanning of all viral residues at this interface defined 10 positions contributing to the interaction, with residues 89, 95, 98, 133, 145 and 162 being most important...
August 16, 2017: Journal of Virology
https://www.readbyqxmd.com/read/28814516/baculovirus-molecular-evolution-via-gene-turnover-and-recurrent-positive-selection-of-key-genes
#7
Tom Hill, Robert L Unckless
Hosts and viruses are locked in an evolutionary arms race. Hosts are constantly evolving to suppress virulence and replication, while viruses, reliant on host machinery for survival and reproduction, develop counter-strategies to escape this immune defense. Viruses must also adapt to novel conditions when establishing themselves in a host species. Both processes provide strong selection for viral adaptation. Understanding adaptive evolution in insect viruses can help us better understand adaptive evolution in general, and is important due to their use as biocontrol agents, and for protecting ecologically or economically important species from outbreaks...
August 16, 2017: Journal of Virology
https://www.readbyqxmd.com/read/28814266/lack-of-satellite-dna-species-specific-homogenization-and-relationship-to-chromosomal-rearrangements-in-monitor-lizards-varanidae-squamata
#8
Ornjira Prakhongcheep, Watcharaporn Thapana, Aorarat Suntronpong, Worapong Singchat, Khampee Pattanatanang, Rattanin Phatcharakullawarawat, Narongrit Muangmai, Surin Peyachoknagul, Kazumi Matsubara, Tariq Ezaz, Kornsorn Srikulnath
BACKGROUND: Satellite DNAs (stDNAs) are highly repeated sequences that constitute large portions of any genome. The evolutionary dynamics of stDNA (e.g. copy number, nucleotide sequence, location) can, therefore, provide an insight into genome organization and evolution. We investigated the evolutionary origin of VSAREP stDNA in 17 monitor lizards (seven Asian, five Australian, and five African) at molecular and cytogenetic level. RESULTS: Results revealed that VSAREP is conserved in the genome of Asian and Australian varanids, but not in African varanids, suggesting that these sequences are either differentiated or lost in the African varanids...
August 16, 2017: BMC Evolutionary Biology
https://www.readbyqxmd.com/read/28812932/celebrating-wobble-decoding-half-a-century-and-still-much-is-new
#9
Paul F Agris, Emily R Eruysal, Amithi Narendran, Ville Y P Väre, Sweta Vangaveti, Srivathsan V Ranganathan
A simple post-transcriptional modification of tRNA, deamination of adenosine to inosine at the first, or wobble, position of the anticodon, inspired Francis Crick's Wobble Hypothesis 50 years ago. Many more naturally-occurring modifications have been elucidated and continue to be discovered. The post-transcriptional modifications of tRNA's anticodon domain are the most diverse and chemically complex of any RNA modifications. Their contribution with regards to chemistry, structure and dynamics reveal individual and combined effects on tRNA function in recognition of cognate and wobble codons...
August 16, 2017: RNA Biology
https://www.readbyqxmd.com/read/28812721/predicting-evolution
#10
Michael Lässig, Ville Mustonen, Aleksandra M Walczak
The face of evolutionary biology is changing: from reconstructing and analysing the past to predicting future evolutionary processes. Recent developments include prediction of reproducible patterns in parallel evolution experiments, forecasting the future of individual populations using data from their past, and controlled manipulation of evolutionary dynamics. Here we undertake a synthesis of central concepts for evolutionary predictions, based on examples of microbial and viral systems, cancer cell populations, and immune receptor repertoires...
February 21, 2017: Nature ecology & evolution
https://www.readbyqxmd.com/read/28812640/five-palaeobiological-laws-needed-to-understand-the-evolution-of-the-living-biota
#11
Charles R Marshall
The foundations of several disciplines can be expressed as simple quantitative laws, for example, Newton's laws or the laws of thermodynamics. Here I present five laws derived from fossil data that describe the relationships among species extinction and longevity, species richness, origination rates, extinction rates and diversification. These statements of our palaeobiological knowledge constitute a dimension largely hidden from view when studying the living biota, which are nonetheless crucial to the study of evolution and ecology even for groups with poor or non-existent fossil records...
May 23, 2017: Nature ecology & evolution
https://www.readbyqxmd.com/read/28812622/species-rich-networks-and-eco-evolutionary-synthesis-at-the-metacommunity-level
#12
Hirokazu Toju, Masato Yamamichi, Paulo R Guimarães, Jens M Olesen, Akihiko Mougi, Takehito Yoshida, John N Thompson
Understanding how ecological and evolutionary processes interdependently structure biosphere dynamics is a major challenge in the era of worldwide ecosystem degradation. However, our knowledge of 'eco-evolutionary feedbacks' depends largely on findings from simple systems representing limited spatial scales and involving few species. Here we review recent conceptual developments for the understanding of multispecies coevolutionary processes and then discuss how new lines of concepts and methods will accelerate the integration of ecology and evolutionary biology...
January 24, 2017: Nature ecology & evolution
https://www.readbyqxmd.com/read/28812620/tipping-points-in-the-dynamics-of-speciation
#13
Patrik Nosil, Jeffrey L Feder, Samuel M Flaxman, Zachariah Gompert
Speciation can be gradual or sudden and involve few or many genetic changes. Inferring the processes generating such patterns is difficult, and may require consideration of emergent and non-linear properties of speciation, such as when small changes at tipping points have large effects on differentiation. Tipping points involve positive feedback and indirect selection stemming from associations between genomic regions, bi-stability due to effects of initial conditions and evolutionary history, and dependence on modularity of system components...
January 24, 2017: Nature ecology & evolution
https://www.readbyqxmd.com/read/28812603/climate-change-upends-selection-on-ornamentation-in-a-wild-bird
#14
Simon R Evans, Lars Gustafsson
Secondary sexual traits have high heritabilities and are exposed to strong, environmentally sensitive selection, and so are expected to evolve rapidly in response to sustained environmental change. We examine the eco-evolutionary dynamics of ornament expression in a long-term study population of collared flycatchers, Ficedula albicollis, in which forehead patch size, which positively influences male reproductive success, declined markedly over 34 years. Annual fitness selection on forehead patch size switched from positive to negative during the study, a reversal that is accounted for by rising spring temperatures at the breeding site: highly ornamented males were selectively favoured following cold breeding seasons but selected against following warm breeding seasons...
January 23, 2017: Nature ecology & evolution
https://www.readbyqxmd.com/read/28812601/recent-extinctions-disturb-path-to-equilibrium-diversity-in-caribbean-bats
#15
Luis Valente, Rampal S Etienne, Liliana M Dávalos
Islands are ideal systems to model temporal changes in biodiversity and reveal the influence of humans on natural communities. Although theory predicts biodiversity on islands tends towards an equilibrium value, the recent extinction of large proportions of island biotas complicates testing this model. The well-preserved subfossil record of Caribbean bats-involving multiple insular radiations-provides a rare opportunity to model diversity dynamics in an insular community. Here, we reconstruct the diversity trajectory in noctilionoid bats of the Greater Antilles by applying a dynamic model of colonization, extinction and speciation to phylogenetic and palaeontological data including all known extinct and extant species...
January 9, 2017: Nature ecology & evolution
https://www.readbyqxmd.com/read/28812559/evolution-alters-the-consequences-of-invasions-in-experimental-communities
#16
Cara A Faillace, Peter J Morin
Evolution has the capacity to alter the course of biological invasions, although such changes remain mostly unexplored by experiments. Integrating evolution into studies of invasions is important, because species traits can potentially evolve in ways that either moderate or exacerbate the impacts of invasions. We have assessed whether species evolved during experimental invasions by comparing the performance of founder populations and their potentially evolved descendants in communities of ciliates and rotifers...
November 21, 2016: Nature ecology & evolution
https://www.readbyqxmd.com/read/28812259/evolutionary-dynamics-in-the-fungal-polarization-network-a-mechanistic-perspective
#17
REVIEW
Eveline T Diepeveen, Leila Iñigo de la Cruz, Liedewij Laan
Polarity establishment underlies proper cell cycle completion across virtually all organisms. Much progress has been made in generating an understanding of the structural and functional components of this process, especially in model species. Here we focus on the evolutionary dynamics of the fungal polarization protein network in order to determine general components and mechanistic principles, species- or lineage-specific adaptations and the evolvability of the network. The currently available genomic and proteomic screens in a variety of fungal species have shown three main characteristics: (1) certain proteins, processes and functions are conserved throughout the fungal clade; (2) orthologous functions can never be assumed, as various cases have been observed of homologous loci with dissimilar functions; (3) species have, typically, various species- or lineage-specific proteins incorporated in their polarization network...
August 15, 2017: Biophysical Reviews
https://www.readbyqxmd.com/read/28811877/alternative-reproductive-strategies-and-the-maintenance-of-female-color-polymorphism-in-damselflies
#18
Rosa A Sánchez-Guillén, Maren Wellenreuther, Jesús R Chávez-Ríos, Christopher D Beatty, Anais Rivas-Torres, María Velasquez-Velez, Adolfo Cordero-Rivera
Genetic polymorphisms are powerful model systems to study the maintenance of diversity in nature. In some systems, polymorphisms are limited to female coloration; these are thought to have arisen as a consequence of reducing male mating harassment, commonly resulting in negative frequency-dependent selection on female color morphs. One example is the damselfly Ischnura elegans, which shows three female color morphs and strong sexual conflict over mating rates. Here, we present research integrating male tactics, and female evolutionary strategies (female mating behavior and morph-specific female fecundity) in populations with different morph-specific mating frequencies, to obtain an understanding of mating rates in nature that goes beyond the mere measure of color frequencies...
August 2017: Ecology and Evolution
https://www.readbyqxmd.com/read/28811876/individual-quality-and-age-but-not-environmental-or-social-conditions-modulate-costs-of-reproduction-in-a-capital-breeder
#19
Lucie Debeffe, Jocelyn Poissant, Philip D McLoughlin
Costs associated with reproduction are widely known to play a role in the evolution of reproductive tactics with consequences to population and eco-evolutionary dynamics. Evaluating these costs as they pertain to species in the wild remains an important goal of evolutionary ecology. Individual heterogeneity, including differences in individual quality (i.e., among-individual differences in traits associated with survival and reproduction) or state, and variation in environmental and social conditions can modulate the costs of reproduction; however, few studies have considered effects of these factors simultaneously...
August 2017: Ecology and Evolution
https://www.readbyqxmd.com/read/28811387/selection-constrains-high-rates-of-tandem-repetitive-dna-mutation-in-daphnia-pulex
#20
Jullien M Flynn, Ian Caldas, Melania E Cristescu, Andrew G Clark
A long-standing evolutionary puzzle is that all eukaryotic genomes contain large amounts of tandemly-repeated DNA whose sequence motifs and abundance vary greatly among even closely related species. To elucidate the evolutionary forces governing tandem repeat dynamics, quantification of the rates and patterns of mutations in repeat copy number and tests of its selective neutrality are necessary. Here we used whole-genome sequences of 28 mutation accumulation (MA) lines of Daphnia pulex in addition to six isolates from a non-MA population originating from the same progenitor to both estimate mutation rates of abundances of repeat sequences and evaluate the selective regime acting upon them...
August 15, 2017: Genetics
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