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Ancestral state reconstruction

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https://www.readbyqxmd.com/read/29046381/trunk-dental-tissue-evolved-independently-from-underlying-dermal-bony-plates-but-is-associated-with-surface-bones-in-living-odontode-bearing-catfish
#1
Carlos J Rivera-Rivera, Juan I Montoya-Burgos
Although oral dental tissue is a vertebrate attribute, trunk dental tissue evolved in several extinct vertebrate lineages but is rare among living species. The question of which processes trigger dental-tissue formation in the trunk remains open, and would shed light on odontogenesis evolution. Extra-oral dental structures (odontodes) in the trunk are associated with underlying dermal bony plates, leading us to ask whether the formation of trunk bony plates is necessary for trunk odontodes to emerge. To address this question, we focus on Loricarioidei: an extant, highly diverse group of catfish whose species all have odontodes...
October 25, 2017: Proceedings. Biological Sciences
https://www.readbyqxmd.com/read/29043053/ecological-niche-comparison-and-molecular-phylogeny-segregate-the-invasive-moss-species-campylopus-introflexus-leucobryaceae-bryophyta-from-its-closest-relatives
#2
Renato Gama, Jesús Aguirre-Gutiérrez, Michael Stech
The delimitation of the invasive moss species Campylopus introflexus from its closest relative, Campylopus pilifer, has been long debated based on morphology. Previous molecular phylogenetic reconstructions based on the nuclear ribosomal internal transcribed spacers (ITS) 1 and 2 showed that C. pilifer is split into an Old World and a New World lineage, but remained partly inconclusive concerning the relationships between these two clades and C. introflexus. Analyses of an extended ITS dataset displayed statistically supported incongruence between ITS1 and ITS2...
October 2017: Ecology and Evolution
https://www.readbyqxmd.com/read/29024751/phylogenomics-reveals-habitat-associated-body-shape-divergence-in-oryzias-woworae-species-group-teleostei-adrianichthyidae
#3
Daniel F Mokodongan, Javier Montenegro, Koji Mochida, Shingo Fujimoto, Asano Ishikawa, Ryo Kakioka, Lengxob Yong, Mulis, Renny K Hadiaty, Ixchel F Mandagi, Kawilarang W A Masengi, Nakatada Wachi, Yasuyuki Hashiguchi, Jun Kitano, Kazunori Yamahira
The Oryzias woworae species group, composed of O. asinua, O. wolasi, and O. woworae, is widely distributed in southeastern Sulawesi, an island in the Indo-Australian Archipelago. Deep-elongated body shape divergence is evident among these three species to the extent that it is used as a species-diagnostic character. These fishes inhabit a variety of habitats, ranging from upper streams to ponds, suggesting that the body shape divergence among the three species may reflect adaptation to local environments. First, our geometric morphometrics among eight local populations of this species group revealed that the three species cannot be separated by body shape and that riverine populations had more elongated bodies and longer caudal parts than lacustrine populations...
October 9, 2017: Molecular Phylogenetics and Evolution
https://www.readbyqxmd.com/read/29020180/molecular-tracing-of-the-geographical-origin-of-hiv-1-infection-and-patterns-of-epidemic-spread-among-migrants-who-inject-drugs-in-athens
#4
D Paraskevis, E Kostaki, G K Nikolopoulos, V Sypsa, M Psichogiou, J Del Amo, I Hodges-Mameletzis, D Paraskeva, A Skoutelis, M Malliori, L Williams, S R Friedman, G L Daikos, A Hatzakis
Background: High numbers of HIV-1 infections among people who inject drugs (PWID) have been diagnosed in Athens, Greece since 2011. We aimed to trace the geographic origin of HIV-1 infection for migrant who inject drugs and to investigate whether transmissions occur more frequently among migrants than among Greek nationals. Methods: Multiple cross-sectional studies were pooled to assemble all persons diagnosed with HIV-1 in Greece between 1/1/2011-31/10/2014. Phylogenetic analyses used maximum likelihood estimation...
August 16, 2017: Clinical Infectious Diseases: An Official Publication of the Infectious Diseases Society of America
https://www.readbyqxmd.com/read/28993971/ancestral-sequence-reconstruction-with-maximum-parsimony
#5
Lina Herbst, Mareike Fischer
One of the main aims in phylogenetics is the estimation of ancestral sequences based on present-day data like, for instance, DNA alignments. One way to estimate the data of the last common ancestor of a given set of species is to first reconstruct a phylogenetic tree with some tree inference method and then to use some method of ancestral state inference based on that tree. One of the best-known methods both for tree inference and for ancestral sequence inference is Maximum Parsimony (MP). In this manuscript, we focus on this method and on ancestral state inference for fully bifurcating trees...
October 5, 2017: Bulletin of Mathematical Biology
https://www.readbyqxmd.com/read/28993654/ctenophore-relationships-and-their-placement-as-the-sister-group-to-all-other-animals
#6
Nathan V Whelan, Kevin M Kocot, Tatiana P Moroz, Krishanu Mukherjee, Peter Williams, Gustav Paulay, Leonid L Moroz, Kenneth M Halanych
Ctenophora, comprising approximately 200 described species, is an important lineage for understanding metazoan evolution and is of great ecological and economic importance. Ctenophore diversity includes species with unique colloblasts used for prey capture, smooth and striated muscles, benthic and pelagic lifestyles, and locomotion with ciliated paddles or muscular propulsion. However, the ancestral states of traits are debated and relationships among many lineages are unresolved. Here, using 27 newly sequenced ctenophore transcriptomes, publicly available data and methods to control systematic error, we establish the placement of Ctenophora as the sister group to all other animals and refine the phylogenetic relationships within ctenophores...
October 9, 2017: Nature ecology & evolution
https://www.readbyqxmd.com/read/28948216/glaciation-as-a-migratory-switch
#7
Robert M Zink, Aubrey S Gardner
Migratory behavior in birds is evolutionarily plastic, but it is unclear how this behavior responded during glacial cycles. One view is that at glacial maxima, species simply shifted their breeding ranges south of glacial ice and remained migratory. To test this hypothesis, we constructed ecological niche models for breeding and wintering ranges of 56 species, finding that 70% of currently long-distance North American migrant species likely lacked suitable breeding habitat in North America at the Last Glacial Maximum (LGM), and we hypothesized that they reverted to the ancestral state of being tropical sedentary residents...
September 2017: Science Advances
https://www.readbyqxmd.com/read/28948111/the-evolutionary-history-of-stomatopoda-crustacea-malacostraca-inferred-from-molecular-data
#8
Cara Van Der Wal, Shane T Ahyong, Simon Y W Ho, Nathan Lo
The crustacean order Stomatopoda comprises seven superfamilies of mantis shrimps, found in coastal waters of the tropics and subtropics. These marine carnivores bear notable raptorial appendages for smashing or spearing prey. We investigated the evolutionary relationships among stomatopods using phylogenetic analyses of three mitochondrial and two nuclear markers. Our analyses recovered the superfamily Gonodactyloidea as polyphyletic, with Hemisquilla as the sister group to all other extant stomatopods. A relaxed molecular clock, calibrated by seven fossil-based age constraints, was used to date the origin and major diversification events of stomatopods...
2017: PeerJ
https://www.readbyqxmd.com/read/28912340/donor-recipient-identification-in-para-and-poly-phyletic-trees-under-alternative-hiv-1-transmission-hypotheses-using-approximate-bayesian-computation
#9
Ethan O Romero-Severson, Ingo Bulla, Nick Hengartner, Inês Bártolo, Ana Abecasis, José M Azevedo-Pereira, Nuno Taveira, Thomas Leitner
Diversity of the founding population of Human Immunodeficiency Virus Type 1 (HIV-1) transmissions raises many important biological, clinical, and epidemiological issues. In up to 40% of sexual infections there is clear evidence for multiple founding variants, which can influence the efficacy of putative prevention methods and the reconstruction of epidemiologic histories. To infer who-infected-whom and to compute the probability of alternative transmission scenarios, while explicitly taking phylogenetic uncertainty into account, we created an Approximate Bayesian Computation (ABC) method based on a set of statistics measuring phylogenetic topology, branch lengths, and genetic diversity...
September 14, 2017: Genetics
https://www.readbyqxmd.com/read/28902834/alternative-evolutionary-histories-in-the-sequence-space-of-an-ancient-protein
#10
Tyler N Starr, Lora K Picton, Joseph W Thornton
To understand why molecular evolution turned out as it did, we must characterize not only the path that evolution followed across the space of possible molecular sequences but also the many alternative trajectories that could have been taken but were not. A large-scale comparison of real and possible histories would establish whether the outcome of evolution represents an optimal state driven by natural selection or the contingent product of historical chance events; it would also reveal how the underlying distribution of functions across sequence space shaped historical evolution...
September 21, 2017: Nature
https://www.readbyqxmd.com/read/28878063/mitochondrial-phylogenomics-of-hemiptera-reveals-adaptive-innovations-driving-the-diversification-of-true-bugs
#11
Hu Li, John M Leavengood, Eric G Chapman, Daniel Burkhardt, Fan Song, Pei Jiang, Jinpeng Liu, Xuguo Zhou, Wanzhi Cai
Hemiptera, the largest non-holometabolous order of insects, represents approximately 7% of metazoan diversity. With extraordinary life histories and highly specialized morphological adaptations, hemipterans have exploited diverse habitats and food sources through approximately 300 Myr of evolution. To elucidate the phylogeny and evolutionary history of Hemiptera, we carried out the most comprehensive mitogenomics analysis on the richest taxon sampling to date covering all the suborders and infraorders, including 34 newly sequenced and 94 published mitogenomes...
September 13, 2017: Proceedings. Biological Sciences
https://www.readbyqxmd.com/read/28870171/evolution-of-mobile-genetic-element-composition-in-an-epidemic-methicillin-resistant-staphylococcus-aureus-temporal-changes-correlated-with-frequent-loss-and-gain-events
#12
Dorota Jamrozy, Francesc Coll, Alison E Mather, Simon R Harris, Ewan M Harrison, Alasdair MacGowan, Andreas Karas, Tony Elston, M Estée Török, Julian Parkhill, Sharon J Peacock
BACKGROUND: Horizontal transfer of mobile genetic elements (MGEs) that carry virulence and antimicrobial resistance genes mediates the evolution of methicillin-resistant Staphylococcus aureus, and the emergence of new MRSA clones. Most MRSA lineages show an association with specific MGEs and the evolution of MGE composition following clonal expansion has not been widely studied. RESULTS: We investigated the genomes of 1193 S. aureus bloodstream isolates, 1169 of which were MRSA, collected in the UK and the Republic of Ireland between 2001 and 2010...
September 4, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28835561/rapid-functional-and-evolutionary-changes-follow-gene-duplication-in-yeast
#13
Samina Naseeb, Ryan M Ames, Daniela Delneri, Simon C Lovell
Duplication of genes or genomes provides the raw material for evolutionary innovation. After duplication a gene may be lost, recombine with another gene, have its function modified or be retained in an unaltered state. The fate of duplication is usually studied by comparing extant genomes and reconstructing the most likely ancestral states. Valuable as this approach is, it may miss the most rapid evolutionary events. Here, we engineered strains of Saccharomyces cerevisiae carrying tandem and non-tandem duplications of the singleton gene IFA38 to monitor (i) the fate of the duplicates in different conditions, including time scale and asymmetry of gene loss, and (ii) the changes in fitness and transcriptome of the strains immediately after duplication and after experimental evolution...
August 30, 2017: Proceedings. Biological Sciences
https://www.readbyqxmd.com/read/28819749/time-dependent-asymmetric-linear-parsimonious-ancestral-state-reconstruction
#14
Gilles Didier
The time-dependent-asymmetric-linear parsimony is an ancestral state reconstruction method which extends the standard linear parsimony (a.k.a. Wagner parsimony) approach by taking into account both branch lengths and asymmetric evolutionary costs for reconstructing quantitative characters (asymmetric costs amount to assuming an evolutionary trend toward the direction with the lowest cost). A formal study of the influence of the asymmetry parameter shows that the time-dependent-asymmetric-linear parsimony infers states which are all taken among the known states, except for some degenerate cases corresponding to special values of the asymmetry parameter...
August 17, 2017: Bulletin of Mathematical Biology
https://www.readbyqxmd.com/read/28812736/the-evolution-and-population-diversity-of-human-specific-segmental-duplications
#15
Megan Y Dennis, Lana Harshman, Bradley J Nelson, Osnat Penn, Stuart Cantsilieris, John Huddleston, Francesca Antonacci, Kelsi Penewit, Laura Denman, Archana Raja, Carl Baker, Kenneth Mark, Maika Malig, Nicolette Janke, Claudia Espinoza, Holly A F Stessman, Xander Nuttle, Kendra Hoekzema, Tina A Lindsay-Graves, Richard K Wilson, Evan E Eichler
Segmental duplications contribute to human evolution, adaptation and genomic instability but are often poorly characterized. We investigate the evolution, genetic variation and coding potential of human-specific segmental duplications (HSDs). We identify 218 HSDs based on analysis of 322 deeply sequenced archaic and contemporary hominid genomes. We sequence 550 human and nonhuman primate genomic clones to reconstruct the evolution of the largest, most complex regions with protein-coding potential (N = 80 genes from 33 gene families)...
February 17, 2017: Nature ecology & evolution
https://www.readbyqxmd.com/read/28776667/relating-appendicular-skeletal-variation-of-sigmodontine-rodents-to-locomotion-modes-in-a-phylogenetic-context
#16
Ludmilla Carvalho Coutinho, João Alves de Oliveira
Sigmodontinae rodents constitute the second-largest subfamily among mammals. Alongside the taxonomic diversity, they are also ecologically diverse, exhibiting a wide array of locomotion modes, with semifossorial, terrestrial, semiaquatic, scansorial, arboreal, and saltatorial forms. To understand the ecomorphologic aspects that allow these rodents to display such locomotion diversity, we analyzed 35 qualitative characters of the appendicular skeleton (humerus, ulna, radius, scapula, femur, tibia, ilium, ischium and pubis) in 795 specimens belonging to 64 species, 34 genera and 10 tribes, representing all locomotion modes assigned to this subfamily...
August 4, 2017: Journal of Anatomy
https://www.readbyqxmd.com/read/28768477/hostplant-change-and-paleoclimatic-events-explain-diversification-shifts-in-skipper-butterflies-family-hesperiidae
#17
Ranjit Kumar Sahoo, Andrew D Warren, Steve C Collins, Ullasa Kodandaramaiah
BACKGROUND: Skippers (Family: Hesperiidae) are a large group of butterflies with ca. 4000 species under 567 genera. The lack of a time-calibrated higher-level phylogeny of the group has precluded understanding of its evolutionary past. We here use a 10-gene dataset to reconstruct the most comprehensive time-calibrated phylogeny of the group, and explore factors that affected the diversification of these butterflies. RESULTS: Ancestral state reconstructions show that the early hesperiid lineages utilized dicots as larval hostplants...
August 2, 2017: BMC Evolutionary Biology
https://www.readbyqxmd.com/read/28745397/tempo-and-mode-of-performance-evolution-across-multiple-independent-origins-of-adhesive-toe-pads-in-lizards
#18
Travis J Hagey, Josef C Uyeda, Kristen E Crandell, Jorn A Cheney, Kellar Autumn, Luke J Harmon
Understanding macroevolutionary dynamics of trait evolution is an important endeavor in evolutionary biology. Ecological opportunity can liberate a trait as it diversifies through trait space, while genetic and selective constraints can limit diversification. While many studies have examined the dynamics of morphological traits, diverse morphological traits may yield the same or similar performance and as performance is often more proximately the target of selection, examining only morphology may give an incomplete understanding of evolutionary dynamics...
October 2017: Evolution; International Journal of Organic Evolution
https://www.readbyqxmd.com/read/28726643/reconstructed-ancestral-enzymes-reveal-that-negative-selection-drove-the-evolution-of-substrate-specificity-in-adp-dependent-kinases
#19
Víctor Castro-Fernandez, Alejandra Herrera-Morande, Ricardo Zamora, Felipe Merino, Felipe Gonzalez-Ordenes, Felipe Padilla-Salinas, Humberto M Pereira, Jose Brandão-Neto, Richard C Garratt, Victoria Guixe
One central goal in molecular evolution is to pinpoint the mechanisms and evolutionary forces that cause an enzyme to change its substrate specificity; however, these processes remain largely unexplored. Using the glycolytic ADP-dependent kinases of archaea, including the orders Thermococcales, Methanosarcinales, and Methanococcales, as a model and employing an approach involving paleoenzymology, evolutionary statistics, and protein structural analysis, we could track changes in substrate specificity during ADP-dependent kinase evolution along with the structural determinants of these changes...
September 22, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/28719578/de-novo-active-sites-for-resurrected-precambrian-enzymes
#20
Valeria A Risso, Sergio Martinez-Rodriguez, Adela M Candel, Dennis M Krüger, David Pantoja-Uceda, Mariano Ortega-Muñoz, Francisco Santoyo-Gonzalez, Eric A Gaucher, Shina C L Kamerlin, Marta Bruix, Jose A Gavira, Jose M Sanchez-Ruiz
Protein engineering studies often suggest the emergence of completely new enzyme functionalities to be highly improbable. However, enzymes likely catalysed many different reactions already in the last universal common ancestor. Mechanisms for the emergence of completely new active sites must therefore either plausibly exist or at least have existed at the primordial protein stage. Here, we use resurrected Precambrian proteins as scaffolds for protein engineering and demonstrate that a new active site can be generated through a single hydrophobic-to-ionizable amino acid replacement that generates a partially buried group with perturbed physico-chemical properties...
July 18, 2017: Nature Communications
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