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Ancestral character reconstruction

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https://www.readbyqxmd.com/read/28228094/sfreemap-a-simulation-free-tool-for-stochastic-mapping
#1
Diego Pasqualin, Marcos Barbeitos, Fabiano Silva
BACKGROUND: Stochastic mapping is frequently used in comparative biology to simulate character evolution, enabling the probabilistic computation of statistics such as number of state transitions along a tree and distribution of states in its internal nodes. Common implementations rely on Continuous-time Markov Chain simulations whose parameters are difficult to adjust and subjected to inherent inaccuracy. Thus, researchers must run a large number of simulations in order to obtain adequate estimates...
February 22, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28219758/resolving-relationships-at-the-animal-fungal-divergence-a-molecular-phylogenetic-study-of-the-protist-trichomycetes-ichthyosporea-eccrinida
#2
Nicole K Reynolds, Matthew E Smith, Eric D Tretter, Justin Gause, Dustin Heeney, Matías J Cafaro, James F Smith, Stephen J Novak, William A Bourland, Merlin M White
Trichomycetes is a group of microorganisms that was considered a class of fungi comprising four orders of commensal, gut-dwelling endosymbionts obligately associated with arthropods. Since molecular phylogenies revealed two of those orders (Amoebidiales and Eccrinales = "protist trichos") to be closely related to members of the protist class Ichthyosporea (= Mesomycetozoea), trichomycetes have been considered an ecological association of both early-diverging fungi and protists. Understanding of the taxonomy, evolution, and diversity of the protist trichos is lacking largely due to the difficulties inherent in species collection that have contributed to undersampling and understudy...
February 17, 2017: Molecular Phylogenetics and Evolution
https://www.readbyqxmd.com/read/28185578/fast-ancestral-gene-order-reconstruction-of-genomes-with-unequal-gene-content
#3
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/28065919/force-of-habit-shrubs-trees-and-contingent-evolution-of-wood-anatomical-diversity-using-croton-euphorbiaceae-as-a-model-system
#4
Rafael Arévalo, Benjamin W van Ee, Ricarda Riina, Paul E Berry, Alex C Wiedenhoeft
BACKGROUND AND AIMS: Wood is a major innovation of land plants, and is usually a central component of the body plan for two major plant habits: shrubs and trees. Wood anatomical syndromes vary between shrubs and trees, but no prior work has explicitly evaluated the contingent evolution of wood anatomical diversity in the context of these plant habits. METHODS: Phylogenetic comparative methods were used to test for contingent evolution of habit, habitat and wood anatomy in the mega-diverse genus Croton (Euphorbiaceae), across the largest and most complete molecular phylogeny of the genus to date...
January 8, 2017: Annals of Botany
https://www.readbyqxmd.com/read/28024450/age-estimation-for-the-genus-cymbidium-orchidaceae-epidendroideae-with-implementation-of-fossil-data-calibration-using-molecular-markers-its2-matk-and-phylogeographic-inference-from-ancestral-area-reconstruction
#5
Ruchishree Konhar, Manish Debnath, Jean Valrie Marbaniang, Devendra Kumar Biswal, Pramod Tandon
Intercontinental dislocations between tropical regions harboring two-thirds of the flowering plants have always drawn attention from taxonomists and biogeographers. One such family belonging to angiosperms is Orchidaceae with an herbaceous habit and high species diversity in the tropics. Here, we investigate the evolutionary and biogeographical history of the genus Cymbidium, which represents a monophyletic subfamily (Epidendroideae) of the orchids and comprises 50 odd species that are distinctly distributed in tropical to temperate regions...
November 9, 2016: Journal of Bioinformatics and Computational Biology
https://www.readbyqxmd.com/read/27998816/out-of-southern-africa-origin-biogeography-and-age-of-the-aizooideae-aizoaceae
#6
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/27989673/phylogenomics-and-morphology-of-extinct-paleognaths-reveal-the-origin-and-evolution-of-the-ratites
#7
Takahiro Yonezawa, Takahiro Segawa, Hiroshi Mori, Paula F Campos, Yuichi Hongoh, Hideki Endo, Ayumi Akiyoshi, Naoki Kohno, Shin Nishida, Jiaqi Wu, Haofei Jin, Jun Adachi, Hirohisa Kishino, Ken Kurokawa, Yoshifumi Nogi, Hideyuki Tanabe, Harutaka Mukoyama, Kunio Yoshida, Armand Rasoamiaramanana, Satoshi Yamagishi, Yoshihiro Hayashi, Akira Yoshida, Hiroko Koike, Fumihito Akishinonomiya, Eske Willerslev, Masami Hasegawa
The Palaeognathae comprise the flightless ratites and the volant tinamous, and together with the Neognathae constitute the extant members of class Aves. It is commonly believed that Palaeognathae originated in Gondwana since most of the living species are found in the Southern Hemisphere [1-3]. However, this hypothesis has been questioned because the fossil paleognaths are mostly from the Northern Hemisphere in their earliest time (Paleocene) and possessed many putative ancestral characters [4]. Uncertainties regarding the origin and evolution of Palaeognathae stem from the difficulty in estimating their divergence times [1, 2] and their remarkable morphological convergence...
January 9, 2017: Current Biology: CB
https://www.readbyqxmd.com/read/27989631/molecular-phylogeny-character-evolution-and-historical-biogeography-of-cryptanthus-otto-a-dietr-bromeliaceae
#8
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/27974324/the-evolutionary-history-of-eugenia-sect-phyllocalyx-myrtaceae-corroborates-historically-stable-areas-in-the-southern-atlantic-forests
#9
Mariana de Oliveira Bünger, Fiorella Fernanda Mazine, Félix Forest, Marcelo Leandro Bueno, João Renato Stehmann, Eve J Lucas
BACKGROUND AND AIMS: Eugenia sect. Phyllocalyx Nied. includes 14 species endemic to the Neotropics, mostly distributed in the Atlantic coastal forests of Brazil. Here the first comprehensive phylogenetic study of this group is presented, and this phylogeny is used as the basis to evaluate the recent infrageneric classification in Eugenia sensu lato (s.l.) to test the history of the evolution of traits in the group and test hypotheses associated with the history of this clade. METHODS: A total of 42 taxa were sampled, of which 14 were Eugenia sect...
December 2016: Annals of Botany
https://www.readbyqxmd.com/read/27943584/cytogenetic-features-of-rrna-genes-across-land-plants-analysis-of-the-plant-rdna-database
#10
Sònia Garcia, Ales Kovařík, Andrew R Leitch, Teresa Garnatje
The online resource http://www.plantrdnadatabase.com/ stores information on the 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 2949 karyotypes, from 1791 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
#11
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/27878942/morphological-evolution-of-the-mammalian-jaw-adductor-complex
#12
Stephan Lautenschlager, Pamela Gill, Zhe-Xi Luo, Michael J Fagan, Emily J Rayfield
The evolution of the mammalian jaw during the transition from non-mammalian synapsids to crown mammals is a key event in vertebrate history and characterised by the gradual reduction of its individual bones into a single element and the concomitant transformation of the jaw joint and its incorporation into the middle ear complex. This osteological transformation is accompanied by a rearrangement and modification of the jaw adductor musculature, which is thought to have allowed the evolution of a more-efficient masticatory system in comparison to the plesiomorphic synapsid condition...
November 23, 2016: Biological Reviews of the Cambridge Philosophical Society
https://www.readbyqxmd.com/read/27856652/evolution-of-rosaceae-fruit-types-based-on-nuclear-phylogeny-in-the-context-of-geological-times-and-genome-duplication
#13
Yezi Xiang, Chien-Hsun Huang, Yi Hu, Jun Wen, Shisheng Li, Tingshuang Yi, Hongyi Chen, Jun Xiang, Hong Ma
Fruits are the defining feature of angiosperms, likely have contributed to angiosperm successes by protecting and dispersing seeds, and provide foods to humans and other animals, with many morphological types and important ecological and agricultural implications. Rosaceae is a family with ∼3000 species and an extraordinary spectrum of distinct fruits, including fleshy peach, apple, and strawberry prized by their consumers, as well as dry achenetum and follicetum with features facilitating seed dispersal, excellent for studying fruit evolution...
November 17, 2016: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/27736882/phylogenetic-systematics-biogeography-and-ecology-of-the-electric-fish-genus-brachyhypopomus-ostariophysi-gymnotiformes
#14
William G R Crampton, Carlos David de Santana, Joseph C Waddell, Nathan R Lovejoy
A species-level phylogenetic reconstruction of the Neotropical bluntnose knifefish genus Brachyhypopomus (Gymnotiformes, Hypopomidae) is presented, based on 60 morphological characters, approximately 1100 base pairs of the mitochondrial cytb gene, and approximately 1000 base pairs of the nuclear rag2 gene. The phylogeny includes 28 species of Brachyhypopomus and nine outgroup species from nine other gymnotiform genera, including seven in the superfamily Rhamphichthyoidea (Hypopomidae and Rhamphichthyidae). Parsimony and Bayesian total evidence phylogenetic analyses confirm the monophyly of the genus, and identify nine robust species groups...
2016: PloS One
https://www.readbyqxmd.com/read/27677839/the-complex-evolutionary-history-of-the-tympanic-middle-ear-in-frogs-and-toads-anura
#15
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
#16
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/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/27520931/historical-biogeography-of-the-fern-genus-deparia-athyriaceae-and-its-relation-with-polyploidy
#18
Li-Yaung Kuo, Atsushi Ebihara, Wataru Shinohara, Germinal Rouhan, Kenneth R Wood, Chun-Neng Wang, Wen-Liang Chiou
The wide geographical distribution of many fern species is related to their high dispersal ability. However, very limited studies surveyed biological traits that could contribute to colonization success after dispersal. In this study, we applied phylogenetic approaches to infer historical biogeography of the fern genus Deparia (Athyriaceae, Eupolypods II). Because polyploids are suggested to have better colonization abilities and are abundant in Deparia, we also examined whether polyploidy could be correlated to long-distance dispersal events and whether polyploidy could play a role in these dispersals/establishment and range expansion...
November 2016: Molecular Phylogenetics and Evolution
https://www.readbyqxmd.com/read/27484647/partially-incorrect-fossil-data-augment-analyses-of-discrete-trait-evolution-in-living-species
#19
Mark N Puttick
Ancestral state reconstruction of discrete character traits is often vital when attempting to understand the origins and homology of traits in living species. The addition of fossils has been shown to alter our understanding of trait evolution in extant taxa, but researchers may avoid using fossils alongside extant species if only few are known, or if the designation of the trait of interest is uncertain. Here, I investigate the impacts of fossils and incorrectly coded fossils in the ancestral state reconstruction of discrete morphological characters under a likelihood model...
August 2016: Biology Letters
https://www.readbyqxmd.com/read/27473344/the-function-and-evolution-of-male-and-female-genitalia-in-phyllophaga-harris-scarab-beetles-coleoptera-scarabaeidae
#20
Maxi Polihronakis Richmond, Jane Park, Charles S Henry
Genitalia diversity in insects continues to fuel investigation of the function and evolution of these dynamic structures. While most studies have focused on variation in male genitalia, an increasing number of studies on female genitalia have uncovered comparable diversity among females, but often at a much finer morphological scale. In this study, we analyze the function and evolution of male and female genitalia in Phyllophaga scarab beetles, a group in which both sexes exhibit genitalic diversity. To document the interaction of male and female structures during mating, we dissected flash-frozen mating pairs from three Phyllophaga species and investigated fine scale morphology using SEM...
July 30, 2016: Journal of Evolutionary Biology
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