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Ancestral state reconstruction

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https://www.readbyqxmd.com/read/27882577/sesamoid-bones-in-tuatara-sphenodon-punctatus-investigated-with-x-ray-microtomography-and-implications-for-sesamoid-evolution-in-lepidosauria
#1
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...
November 24, 2016: Journal of Morphology
https://www.readbyqxmd.com/read/27808231/evolution-of-sex-biased-gene-expression-in-a-dioecious-plant
#2
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
#3
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
#4
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
#5
Sean Harrington, Tod 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 favors 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
#6
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
#7
Marisol Sánchez-García, P 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...
October 21, 2016: 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
#8
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
https://www.readbyqxmd.com/read/27742475/colonization-and-diversification-of-aquatic-insects-on-three-macaronesian-archipelagos-using-59-nuclear-loci-derived-from-a-draft-genome
#9
Sereina Rutschmann, Harald Detering, Sabrina Simon, David H Funk, Jean-Luc Gattolliat, Samantha J Hughes, Pedro M Raposeiro, Rob DeSalle, Michel Sartori, Michael T Monaghan
The study of processes driving diversification requires a fully sampled and well resolved phylogeny, although a lack of phylogenetic markers remains a limitation for many non-model groups. Multilocus approaches to the study of recent diversification provide a powerful means to study the evolutionary process, but their application remains restricted because multiple unlinked loci with suitable variation for phylogenetic or coalescent analysis are not available for most non-model taxa. Here we identify novel, putative single-copy nuclear DNA (nDNA) phylogenetic markers to study the colonization and diversification of an aquatic insect species complex, Cloeon dipterum L...
October 11, 2016: Molecular Phylogenetics and Evolution
https://www.readbyqxmd.com/read/27732575/fossil-evidence-of-the-avian-vocal-organ-from-the-mesozoic
#10
Julia A Clarke, Sankar Chatterjee, Zhiheng Li, Tobias Riede, Federico Agnolin, Franz Goller, Marcelo P Isasi, Daniel R Martinioni, Francisco J Mussel, Fernando E Novas
From complex songs to simple honks, birds produce sounds using a unique vocal organ called the syrinx. Located close to the heart at the tracheobronchial junction, vocal folds or membranes attached to modified mineralized rings vibrate to produce sound. Syringeal components were not thought to commonly enter the fossil record, and the few reported fossilized parts of the syrinx are geologically young (from the Pleistocene and Holocene (approximately 2.5 million years ago to the present)). The only known older syrinx is an Eocene specimen that was not described or illustrated...
October 12, 2016: Nature
https://www.readbyqxmd.com/read/27718282/into-the-andes-multiple-independent-colonizations-drive-montane-diversity-in-the-neotropical-clearwing-butterflies-godyridina
#11
Nicolas Chazot, Keith R Willmott, Fabien L Condamine, Donna Lisa De-Silva, André V L Freitas, Gerardo Lamas, Hélène Morlon, Carlos E Giraldo, Chris D Jiggins, Mathieu Joron, James Mallet, Sandra Uribe, Marianne Elias
Understanding why species richness peaks along the Andes is a fundamental question in the study of Neotropical biodiversity. Several biogeographic and diversification scenarios have been proposed in the literature, but there is confusion about the processes underlying each scenario, and assessing their relative contribution is not straightforward. Here, we propose to refine these scenarios into a framework which evaluates four evolutionary mechanisms: higher speciation rate in the Andes, lower extinction rates in the Andes, older colonization times and higher colonization rates of the Andes from adjacent areas...
November 2016: Molecular Ecology
https://www.readbyqxmd.com/read/27717969/multiple-origins-of-gigantism-in-stem-baleen-whales
#12
Cheng-Hsiu Tsai, Naoki Kohno
Living baleen whales (Mysticeti) include the world's largest animals to have ever lived-blue whales (Balaenoptera musculus) can reach more than 30 m. However, the gigantism in baleen whales remains little explored. Here, we compiled all published stem mysticetes from the Eocene and Oligocene and then mapped the estimated body size onto different phylogenies that suggest distinct evolutionary histories of baleen whales. By assembling all known stem baleen whales, we present three novel findings in early mysticete evolution...
December 2016: Die Naturwissenschaften
https://www.readbyqxmd.com/read/27685856/characterization-of-botrytis-cinerea-negative-stranded-rna-virus-1-a-new-mycovirus-related-to-plant-viruses-and-a-reconstruction-of-host-pattern-evolution-in-negative-sense-ssrna-viruses
#13
Livia Donaire, Israel Pagán, María A Ayllón
The molecular characterization of a novel negative single-stranded RNA virus infecting the plant pathogenic fungus Botrytis cinerea is reported here. Comparison of the sequence of Botrytis cinerea negative-stranded RNA virus 1 (BcNSRV-1) showed a strong identity with RNA dependent RNA polymerases (RdRps) of plant pathogenic emaraviruses and tospoviruses. We have also found all the molecular signatures present in the RdRp of the genus Emaravirus and in other genera of family Bunyaviridae: the conserved TPD triplet and RY dinucleotide, the three basic residues in premotif A and the conserved motifs A, B, C, D, and E...
September 26, 2016: Virology
https://www.readbyqxmd.com/read/27677839/the-complex-evolutionary-history-of-the-tympanic-middle-ear-in-frogs-and-toads-anura
#14
Martín O Pereyra, Molly C Womack, J Sebastián Barrionuevo, Boris L Blotto, Diego Baldo, Mariane Targino, Jhon Jairo Ospina-Sarria, Juan M Guayasamin, Luis A Coloma, Kim L Hoke, Taran Grant, Julián Faivovich
Most anurans possess a tympanic middle ear (TME) that transmits sound waves to the inner ear; however, numerous species lack some or all TME components. To understand the evolution of these structures, we undertook a comprehensive assessment of their occurrence across anurans and performed ancestral character state reconstructions. Our analysis indicates that the TME was completely lost at least 38 independent times in Anura. The inferred evolutionary history of the TME is exceptionally complex in true toads (Bufonidae), where it was lost in the most recent common ancestor, preceding a radiation of >150 earless species...
September 28, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27649395/a-comprehensive-study-of-cyanobacterial-morphological-and-ecological-evolutionary-dynamics-through-deep-geologic-time
#15
Josef C Uyeda, Luke J Harmon, Carrine E Blank
Cyanobacteria have exerted a profound influence on the progressive oxygenation of Earth. As a complementary approach to examining the geologic record-phylogenomic and trait evolutionary analyses of extant species can lead to new insights. We constructed new phylogenomic trees and analyzed phenotypic trait data using novel phylogenetic comparative methods. We elucidated the dynamics of trait evolution in Cyanobacteria over billion-year timescales, and provide evidence that major geologic events in early Earth's history have shaped-and been shaped by-evolution in Cyanobacteria...
2016: PloS One
https://www.readbyqxmd.com/read/27646682/cyprininae-phylogeny-revealed-independent-origins-of-the-tibetan-plateau-endemic-polyploid-cyprinids-and-their-diversifications-related-to-the-neogene-uplift-of-the-plateau
#16
Xuzhen Wang, Xiaoni Gan, Junbing Li, Yiyu Chen, Shunping He
Origin and diversification of the Tibetan polyploid cyprinids (schizothoracins) may help us to explore relationships between diversification of the cyprinids and the Tibetan Plateau uplift. Cyprininae phylogeny was analyzed using mitochondrial and nuclear DNA sequences to trace origins of polyploidy and diversifications of schizothoracins. Ancestral states reconstruction for ploidy levels indicated that the Cyprininae was diploid origin and the schizothoracin clades tetraploid origins. There were two diversification rate shifts along with diversification of the cyprinine fishes in response to the Tibetan uplift...
September 20, 2016: Science China. Life Sciences
https://www.readbyqxmd.com/read/27640952/phylogeny-of-helieae-gentianaceae-resolving-taxonomic-chaos-in-a-neotropical-clade
#17
Maria Fernanda Calió, Katherine B Lepis, José Rubens Pirani, Lena Struwe
The monophyletic and Neotropical tribe Helieae of the worldwide family Gentianaceae (Gentianales, Asterids, Angiospermae) is well known for its problematic generic classifications. An initial phylogenetic analysis of Helieae shed light onto the relationships between genera, and indicated that traditional generic limits did not correspond to monophyletic groups. In order to obtain a more thorough understanding of generic relationships within the group, we enhanced sampling within the so-called Symbolanthus clade and performed phylogenetic analyses from DNA sequences from one plastid region (matK) and two nuclear regions (ITS and 5S-NTS), plus 112 morphological characters, which were analyzed separately and in combination, using parsimony and Bayesian approaches...
September 15, 2016: Molecular Phylogenetics and Evolution
https://www.readbyqxmd.com/read/27638319/novel-insights-into-the-origin-and-diversification-of-photosynthesis-based-on-analyses-of-conserved-indels-in-the-core-reaction-center-proteins
#18
Bijendra Khadka, Mobolaji Adeolu, Robert E Blankenship, Radhey S Gupta
The evolution and diversification of different types of photosynthetic reaction centers (RCs) remains an important unresolved problem. We report here novel sequence features of the core proteins from Type I RCs (RC-I) and Type II RCs (RC-II) whose analyses provide important insights into the evolution of the RCs. The sequence alignments of the RC-I core proteins contain two conserved inserts or deletions (indels), a 3 amino acid (aa) indel that is uniquely found in all RC-I homologs from Cyanobacteria (both PsaA and PsaB) and a 1 aa indel that is specifically shared by the Chlorobi and Acidobacteria homologs...
September 16, 2016: Photosynthesis Research
https://www.readbyqxmd.com/read/27622880/behavioral-plasticity-and-the-origins-of-novelty-the-evolution-of-the-rattlesnake-rattle
#19
Bradley C Allf, Paul A P Durst, David W Pfennig
Environmentally induced behavior (behavioral plasticity) has long been hypothesized to promote the origins of novel morphological traits, but this idea remains controversial. One context in which this hypothesis can be evaluated is animal communication, where behavior and morphology are often linked. Here, we examined the evolution of one of nature's most spectacular communication signals: the rattlesnake rattle. We specifically evaluated whether rattlesnake rattling behavior-and, hence, the rattle-originated from a simple behavior: vibrating the tail when threatened...
October 2016: American Naturalist
https://www.readbyqxmd.com/read/27611687/the-impact-of-reconstruction-methods-phylogenetic-uncertainty-and-branch-lengths-on-inference-of-chromosome-number-evolution-in-american-daisies-melampodium-asteraceae
#20
Jamie McCann, Gerald M Schneeweiss, Tod F Stuessy, Jose L Villaseñor, Hanna Weiss-Schneeweiss
Chromosome number change (polyploidy and dysploidy) plays an important role in plant diversification and speciation. Investigating chromosome number evolution commonly entails ancestral state reconstruction performed within a phylogenetic framework, which is, however, prone to uncertainty, whose effects on evolutionary inferences are insufficiently understood. Using the chromosomally diverse plant genus Melampodium (Asteraceae) as model group, we assess the impact of reconstruction method (maximum parsimony, maximum likelihood, Bayesian methods), branch length model (phylograms versus chronograms) and phylogenetic uncertainty (topological and branch length uncertainty) on the inference of chromosome number evolution...
2016: PloS One
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