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Ancestral state reconstruction

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https://www.readbyqxmd.com/read/28185578/fast-ancestral-gene-order-reconstruction-of-genomes-with-unequal-gene-content
#1
Pedro Feijão, Eloi Araujo
BACKGROUND: During evolution, genomes are modified by large scale structural events, such as rearrangements, deletions or insertions of large blocks of DNA. Of particular interest, in order to better understand how this type of genomic evolution happens, is the reconstruction of ancestral genomes, given a phylogenetic tree with extant genomes at its leaves. One way of solving this problem is to assume a rearrangement model, such as Double Cut and Join (DCJ), and find a set of ancestral genomes that minimizes the number of events on the input tree...
November 11, 2016: BMC Bioinformatics
https://www.readbyqxmd.com/read/28170397/bayesian-phylogeography-of-influenza-a-h3n2-for-the-2014-15-season-in-the-united-states-using-three-frameworks-of-ancestral-state-reconstruction
#2
Daniel Magee, Marc A Suchard, Matthew Scotch
Ancestral state reconstruction in Bayesian phylogeography of virus pandemics have been improved by utilizing a Bayesian stochastic search variable selection (BSSVS) framework. Recently, this framework has been extended to model the transition rate matrix between discrete states as a generalized linear model (GLM) of genetic, geographic, demographic, and environmental predictors of interest to the virus and incorporating BSSVS to estimate the posterior inclusion probabilities of each predictor. Although the latter appears to enhance the biological validity of ancestral state reconstruction, there has yet to be a comparison of phylogenies created by the two methods...
February 7, 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/28167205/vascular-budding-in-symplegma-brakenhielmi-and-the-evolution-of-coloniality-in-styelid-ascidians
#3
Stefania Gutierrez, Federico D Brown
Individuals of colonial animals (e.g. zooids) are in continuous turnover. In ascidians colonial or solitary species have evolved by convergence multiple times. Colonial Botryllus and Botrylloides are well-studied genera that exhibit colony-wide developmental mechanisms that regulate synchronous and orchestrated cycles of budding and turnover of zooids. The origins of modular developmental mechanisms that facilitated the evolution of coloniality in this group remain unclear. To reconstruct ancestral states of coloniality we studied Symplegma brakenhielmi, a sister taxon of the botryllids...
February 3, 2017: Developmental Biology
https://www.readbyqxmd.com/read/28148749/open-cup-nests-evolved-from-roofed-nests-in-the-early-passerines
#4
J Jordan Price, Simon C Griffith
The architectural diversity of nests in the passerine birds (order Passeriformes) is thought to have played an important role in the adaptive radiation of this group, which now comprises more than half of avian species and occupies nearly all terrestrial ecosystems. Here, we present an extensive survey and ancestral state reconstruction of nest design across the passerines, focusing on early Australian lineages and including members of nearly all passerine families worldwide. Most passerines build open cup-shaped nests, whereas a minority build more elaborate domed structures with roofs...
February 8, 2017: Proceedings. Biological Sciences
https://www.readbyqxmd.com/read/28097663/the-evolution-of-male-nuptial-colour-in-a-sexually-dimorphic-group-of-fishes-percidae-etheostomatinae
#5
P J Ciccotto, T C Mendelson
To test hypotheses explaining variation in elaborate male colouration across closely related species groups, ancestral-state reconstructions and tests of phylogenetic signal and correlated evolution were used to examine the evolution of male body and fin colouration in a group of sexually dichromatic stream fishes known as darters (Percidae: Etheostomatinae). The presence or absence of red-orange and blue-green male colour traits were scored across six body regions in 99 darter species using a recently estimated amplified fragment length polymorphism (AFLP) phylogeny for comparative analyses...
January 18, 2017: Journal of Fish Biology
https://www.readbyqxmd.com/read/28025288/characterization-of-cycloidea-like-genes-in-proteaceae-a-basal-eudicot-family-with-multiple-shifts-in-floral-symmetry
#6
Hélène L Citerne, Elisabeth Reyes, Martine Le Guilloux, Etienne Delannoy, Franck Simonnet, Hervé Sauquet, Peter H Weston, Sophie Nadot, Catherine Damerval
BACKGROUND AND AIMS: The basal eudicot family Proteaceae (approx. 1700 species) shows considerable variation in floral symmetry but has received little attention in studies of evolutionary development at the genetic level. A framework for understanding the shifts in floral symmetry in Proteaceae is provided by reconstructing ancestral states on an upated phylogeny of the family, and homologues of CYCLOIDEA (CYC), a key gene for the control of floral symmetry in both monocots and eudicots, are characterized...
December 26, 2016: Annals of Botany
https://www.readbyqxmd.com/read/28008088/exploring-the-past-and-the-future-of-protein-evolution-with-ancestral-sequence-reconstruction-the-retro-approach-to-protein-engineering
#7
REVIEW
Yosephine Gumulya, Elizabeth M J Gillam
A central goal in molecular evolution is to understand the ways in which genes and proteins evolve in response to changing environments. In the absence of intact DNA from fossils, ancestral sequence reconstruction (ASR) can be used to infer the evolutionary precursors of extant proteins. To date, ancestral proteins belonging to eubacteria, archaea, yeast and vertebrates have been inferred that have been hypothesized to date from between several million to over 3 billion years ago. ASR has yielded insights into the early history of life on Earth and the evolution of proteins and macromolecular complexes...
January 1, 2017: Biochemical Journal
https://www.readbyqxmd.com/read/28008087/evolutionary-drivers-of-thermoadaptation-in-enzyme-catalysis
#8
Vy Nguyen, Christopher Wilson, Marc Hoemberger, John B Stiller, Roman V Agafonov, Steffen Kutter, Justin English, Douglas L Theobald, Dorothee Kern
With early life likely to have existed in a hot environment, enzymes had to cope with an inherent drop in catalytic speed caused by lowered temperature. Here we characterize the molecular mechanisms underlying thermoadaptation of enzyme catalysis in adenylate kinase using ancestral sequence reconstruction spanning 3 billion years of evolution. We show that evolution solved the enzyme's key kinetic obstacle-how to maintain catalytic speed on a cooler Earth-by exploiting transition-state heat capacity. Tracing the evolution of enzyme activity and stability from the hot-start toward modern hyperthermophilic, mesophilic, and psychrophilic organisms illustrates active pressure versus passive drift in evolution on a molecular level, refutes the debated activity/stability trade-off, and suggests that the catalytic speed of adenylate kinase is an evolutionary driver for organismal fitness...
January 20, 2017: Science
https://www.readbyqxmd.com/read/27998816/out-of-southern-africa-origin-biogeography-and-age-of-the-aizooideae-aizoaceae
#9
Cornelia Klak, Pavel Hanáček, Peter V Bruyns
The Aizooideae is an early-diverging lineage within the Aizoaceae. It is most diverse in southern Africa, but also has endemic species in Australasia, Eurasia and South America. We derived a phylogenetic hypothesis from Bayesian and Maximum Likelihood analyses of plastid DNA-sequences. We find that one of the seven genera, the fynbos-endemic Acrosanthes, does not belong to the Aizooideae, but is an ancient sister-lineage to the subfamilies Mesembryanthemoideae & Ruschioideae. Galenia and Plinthus are embedded inside Aizoon and Aizoanthemum is polyphyletic...
December 18, 2016: Molecular Phylogenetics and Evolution
https://www.readbyqxmd.com/read/27998815/total-evidence-phylogeny-and-the-evolution-of-adult-bioluminescence-in-fireflies-coleoptera-lampyridae
#10
Gavin J Martin, Marc A Branham, Michael F Whiting, Seth M Bybee
Fireflies are some of the most captivating organisms on the planet. They have a rich history as subjects of scientific study, especially in relation to their bioluminescent behavior. Yet, the phylogenetic relationships of fireflies are still poorly understood. Here, we present the first total evidence approach to reconstruct lampyrid phylogeny using both a molecular matrix from six loci and an extensive morphological matrix. Using this phylogeny we test the hypothesis that adult bioluminescence evolved after the origin of the firefly clade...
December 18, 2016: Molecular Phylogenetics and Evolution
https://www.readbyqxmd.com/read/27989631/molecular-phylogeny-character-evolution-and-historical-biogeography-of-cryptanthus-otto-a-dietr-bromeliaceae
#11
Geyner A S Cruz, Georg Zizka, Daniele Silvestro, Elton M C Leme, Katharina Schulte, Ana M Benko-Iseppon
Cryptanthus comprises 72 species endemic to eastern Brazil with a center of diversity in the Atlantic Forest. The majority of the species are threatened due to habitat loss. We reconstructed phylogenetic relationships in Cryptanthus based on amplified fragment length polymorphisms (AFLP) including 48 species and 109 accessions. The Bayesian phylogenetic analysis revealed four major lineages in Cryptanthus and provided further evidence for the paraphyly of subgen. Hoplocryptanthus, while subgenus Cryptanthus was resolved as monophyletic...
October 27, 2016: Molecular Phylogenetics and Evolution
https://www.readbyqxmd.com/read/27943584/cytogenetic-features-of-rrna-genes-across-land-plants-analysis-of-the-plant-rdna-database
#12
Sònia Garcia, Ales Kovařík, Andrew R Leitch, Teresa Garnatje
The online resource www.plantrdnadatabase.com stores information on number, chromosomal locations and structure of the 5S and 18S-5.8S-26S (35S) ribosomal DNAs (rDNA) in plants. This resource was exploited to study relationships between rDNA locus number, distribution, the occurrence of linked (L-type) and separated (S-type) 5S and 35S rDNA units, chromosome number, genome size and ploidy level. The analyses presented summarise current knowledge on rDNA locus numbers and distribution in plants. We analysed 2,949 karyotypes, from 1,791 species and 86 plant families and performed ancestral character state reconstructions...
December 10, 2016: Plant Journal: for Cell and Molecular Biology
https://www.readbyqxmd.com/read/27882577/sesamoid-bones-in-tuatara-sphenodon-punctatus-investigated-with-x-ray-microtomography-and-implications-for-sesamoid-evolution-in-lepidosauria
#13
Sophie Regnault, John R Hutchinson, Marc E H Jones
Sesamoids bones are small intra-tendinous (or ligamentous) ossifications found near joints and are often variable between individuals. Related bones, lunulae, are found within the menisci of certain joints. Several studies have described sesamoids and lunulae in lizards and their close relatives (Squamata) as potentially useful characters in phylogenetic analysis, but their status in the extant outgroup to Squamata, tuatara (Sphenodon), remains unclear. Sphenodon is the only living rhynchocephalian, but museum specimens are valuable and difficult to replace...
January 2017: Journal of Morphology
https://www.readbyqxmd.com/read/27808231/evolution-of-sex-biased-gene-expression-in-a-dioecious-plant
#14
Niklaus Zemp, Raquel Tavares, Aline Muyle, Deborah Charlesworth, Gabriel A B Marais, Alex Widmer
Separate sexes and sex-biased gene expression have repeatedly evolved in animals and plants, but the underlying changes in gene expression remain unknown. Here, we studied a pair of plant species, one in which separate sexes and sex chromosomes evolved recently and one which maintained hermaphrodite flowers resembling the ancestral state, to reconstruct expression changes associated with the evolution of dioecy. We found that sex-biased gene expression has evolved in autosomal and sex-linked genes in the dioecious species...
November 3, 2016: Nature Plants
https://www.readbyqxmd.com/read/27795231/robustness-of-reconstructed-ancestral-protein-functions-to-statistical-uncertainty
#15
Geeta N Eick, Jamie T Bridgham, Douglas P Anderson, Michael J Harms, Joseph W Thornton
Hypotheses about the functions of ancient proteins and the effects of historical mutations on them are often tested using ancestral protein reconstruction (APR)-phylogenetic inference of ancestral sequences followed by synthesis and experimental characterization. Usually, some sequence sites are ambiguously reconstructed, with two or more statistically plausible states. The extent to which the inferred functions and mutational effects are robust to uncertainty about the ancestral sequence has not been studied systematically...
October 30, 2016: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/27792743/the-evolutionary-basis-of-naturally-diverse-rice-leaves-anatomy
#16
Jolly Chatterjee, Jacqueline Dionora, Abigail Elmido-Mabilangan, Samart Wanchana, Vivek Thakur, Anindya Bandyopadhyay, Darshan S Brar, William Paul Quick
Rice contains genetically and ecologically diverse wild and cultivated species that show a wide variation in plant and leaf architecture. A systematic characterization of leaf anatomy is essential in understanding the dynamics behind such diversity. Therefore, leaf anatomies of 24 Oryza species spanning 11 genetically diverse rice genomes were studied in both lateral and longitudinal directions and possible evolutionary trends were examined. A significant inter-species variation in mesophyll cells, bundle sheath cells, and vein structure was observed, suggesting precise genetic control over these major rice leaf anatomical traits...
2016: PloS One
https://www.readbyqxmd.com/read/27792262/rate-heterogeneity-across-squamata-misleading-ancestral-state-reconstruction-and-the-importance-of-proper-null-model-specification
#17
S Harrington, T W Reeder
The binary-state speciation and extinction (BiSSE) model has been used in many instances to identify state-dependent diversification and reconstruct ancestral states. However, recent studies have shown that the standard procedure of comparing the fit of the BiSSE model to constant-rate birth-death models often inappropriately favours the BiSSE model when diversification rates vary in a state-independent fashion. The newly developed HiSSE model enables researchers to identify state-dependent diversification rates while accounting for state-independent diversification at the same time...
October 28, 2016: Journal of Evolutionary Biology
https://www.readbyqxmd.com/read/27769924/evolution-of-electric-communication-signals-in-the-south-american-ghost-knifefishes-gymnotiformes-apteronotidae-a-phylogenetic-comparative-study-using-a-sequence-based-phylogeny
#18
Adam R Smith, Melissa R Proffitt, Winnie W Ho, Claire B Mullaney, Javier A Maldonado-Ocampo, Nathan R Lovejoy, José A Alves-Gomes, G Troy Smith
The electric communication signals of weakly electric ghost knifefishes (Gymnotiformes: Apteronotidae) provide a valuable model system for understanding the evolution and physiology of behavior. Apteronotids produce continuous wave-type electric organ discharges (EODs) that are used for electrolocation and communication. The frequency and waveform of EODs, as well as the structure of transient EOD modulations (chirps), vary substantially across species. Understanding how these signals have evolved, however, has been hampered by the lack of a well-supported phylogeny for this family...
October 18, 2016: Journal of Physiology, Paris
https://www.readbyqxmd.com/read/27767208/is-the-switch-to-an-ectomycorrhizal-state-an-evolutionary-key-innovation-in-mushroom-forming-fungi-a-case-study-in-the-tricholomatineae-agaricales
#19
Marisol Sánchez-García, Patrick Brandon Matheny
Although fungi are one of the most diverse groups of organisms, little is known about the processes that shape their high taxonomic diversity. This study focuses on evolution of ectomycorrhizal (ECM) mushroom-forming fungi, symbiotic associates of many trees and shrubs, in the suborder Tricholomatineae of the Agaricales. We used the BiSSE model and BAMM to test the hypothesis that the ECM habit represents an evolutionary key innovation that allowed the colonization of new niches followed by an increase in diversification rate...
January 2017: Evolution; International Journal of Organic Evolution
https://www.readbyqxmd.com/read/27765146/stem-members-of-platyrrhini-are-distinct-from-catarrhines-in-at-least-one-derived-cranial-feature
#20
Ethan L Fulwood, Doug M Boyer, Richard F Kay
The pterion, on the lateral aspect of the cranium, is where the zygomatic, frontal, sphenoid, squamosal, and parietal bones approach and contact. The configuration of these bones distinguishes New and Old World anthropoids: most extant platyrrhines exhibit contact between the parietal and zygomatic bones, while all known catarrhines exhibit frontal-alisphenoid contact. However, it is thought that early stem-platyrrhines retained the apparently primitive catarrhine condition. Here we re-evaluate the condition of key fossil taxa using μCT (micro-computed tomography) imaging...
November 2016: Journal of Human Evolution
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