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Ancestral character reconstruction

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https://www.readbyqxmd.com/read/28491066/robust-phylogeny-of-tetrastigma-vitaceae-based-on-ten-plastid-dna-regions-implications-for-infrageneric-classification-and-seed-character-evolution
#1
Sadaf Habib, Viet-Cuong Dang, Stefanie M Ickert-Bond, Jin-Long Zhang, Li-Min Lu, Jun Wen, Zhi-Duan Chen
Tetrastigma (Miq.) Planch. is one of the most species-rich genera of the economically and agronomically important grape family Vitaceae. It includes ca. 95 species widely distributed in the tropics and subtropics of Asia and Australia. Species of Tetrastigma exhibit great diversity in both vegetative and reproductive characters. Here we inferred a well-supported phylogeny of Tetrastigma based on ten chloroplast DNA regions with an expanded taxon sampling of 72 species and two varieties. Our molecular results support six major clades within Tetrastigma and the relationships among these clades were well-resolved...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28480566/cranial-suture-complexity-in-caviomorph-rodents-rodentia-ctenohystrica
#2
Guido Buezas, Federico Becerra, Aldo Vassallo
Due to their flexibility, sutures are regions that experience greater strains than the surrounding rigid cranial bones. Cranial sutures differ in their degree of interdigitation or complexity. There is evidence indicating that a more convoluted suture better enables the absorption of high stresses coming from dynamic masticatory forces, and other functions. The Order Rodentia is an interesting clade to study this because of its taxa with diverse chewing modes. Due to repeated loading resulting from gnawing and grinding, energy absorption by the sutures might be a crucial factor in these mammals...
May 7, 2017: Journal of Morphology
https://www.readbyqxmd.com/read/28470778/multiple-innovations-underpinned-branching-form-diversification-in-mosses
#3
Yoan Coudert, Neil E Bell, Claude Edelin, C Jill Harrison
Broad-scale evolutionary comparisons have shown that branching forms arose by convergence in vascular plants and bryophytes, but the trajectory of branching form diversification in bryophytes is unclear. Mosses are the most species-rich bryophyte lineage and two sub-groups are circumscribed by alternative reproductive organ placements. In one, reproductive organs form apically, terminating growth of the primary shoot (gametophore) axis. In the other, reproductive organs develop on very short lateral branches...
May 4, 2017: New Phytologist
https://www.readbyqxmd.com/read/28462054/evolution-of-developmental-sequences-in-lepidosaurs
#4
Tomasz Skawiński, Bartosz Borczyk
BACKGROUND: Lepidosaurs, a group including rhynchocephalians and squamates, are one of the major clades of extant vertebrates. Although there has been extensive phylogenetic work on this clade, its interrelationships are a matter of debate. Morphological and molecular data suggest very different relationships within squamates. Despite this, relatively few studies have assessed the utility of other types of data for inferring squamate phylogeny. METHODS: We used developmental sequences of 20 events in 29 species of lepidosaurs...
2017: PeerJ
https://www.readbyqxmd.com/read/28428869/rapid-maximum-likelihood-ancestral-state-reconstruction-of-continuous-characters-a-rerooting-free-algorithm
#5
Eric W Goolsby
Ancestral state reconstruction is a method used to study the evolutionary trajectories of quantitative characters on phylogenies. Although efficient methods for univariate ancestral state reconstruction under a Brownian motion model have been described for at least 25 years, to date no generalization has been described to allow more complex evolutionary models, such as multivariate trait evolution, non-Brownian models, missing data, and within-species variation. Furthermore, even for simple univariate Brownian motion models, most phylogenetic comparative R packages compute ancestral states via inefficient tree rerooting and full tree traversals at each tree node, making ancestral state reconstruction extremely time-consuming for large phylogenies...
April 2017: Ecology and Evolution
https://www.readbyqxmd.com/read/28403902/phylodynamics-of-foot-and-mouth-disease-virus-o-panasia-in-vietnam-2010-2014
#6
Barbara Brito, Steven J Pauszek, Michael Eschbaumer, Carolina Stenfeldt, Helena C de Carvalho Ferreira, Le T Vu, Nguyen T Phuong, Bui H Hoang, Nguyen D Tho, Pham V Dong, Phan Q Minh, Ngo T Long, Donald P King, Nick J Knowles, Do H Dung, Luis L Rodriguez, Jonathan Arzt
Foot-and-mouth disease virus (FMDV) is endemic in Vietnam, a country that plays an important role in livestock trade within Southeast Asia. The large populations of FMDV-susceptible species in Vietnam are important components of food production and of the national livelihood. In this study, we investigated the phylogeny of FMDV O/PanAsia in Vietnam, reconstructing the virus' ancestral host species (pig, cattle or buffalo), clinical stage (subclinical carrier or clinically affected) and geographical location...
April 13, 2017: Veterinary Research
https://www.readbyqxmd.com/read/28389155/integrative-taxonomy-of-ciliates-assessment-of-molecular-phylogenetic-content-and-morphological-homology-testing
#7
REVIEW
Peter Vďačný
The very diverse and comparatively complex morphology of ciliates has given rise to numerous taxonomic concepts. However, the information content of the utilized molecular markers has seldom been explored prior to phylogenetic analyses and taxonomic decisions. Likewise, robust testing of morphological homology statements and the apomorphic nature of diagnostic characters of ciliate taxa is rarely carried out. Four phylogenetic techniques that may help address these issues are reviewed. (1) Split spectrum analysis serves to determine the exact number and quality of nucleotide positions supporting individual nodes in phylogenetic trees and to discern long-branch artifacts that cause spurious phylogenies...
February 24, 2017: European Journal of Protistology
https://www.readbyqxmd.com/read/28387789/evolution-of-wood-anatomical-characters-in-nepenthes-and-close-relatives-of-caryophyllales
#8
Rachel Schwallier, Barbara Gravendeel, Hugo de Boer, Stephan Nylinder, Bertie Joan van Heuven, Anton Sieder, Sukaibin Sumail, Rogier van Vugt, Frederic Lens
Background and Aims: Nepenthes attracts wide attention with its spectacularly shaped carnivorous pitchers, cultural value and horticultural curiosity. Despite the plant's iconic fascination, surprisingly little anatomical detail is known about the genus beyond its modified leaf tip traps. Here, the wood anatomical diversity of Nepenthes is explored. This diversity is further assessed with a phylogenetic framework to investigate whether the wood characters within the genus are relevant from an evolutionary or ecological perspective, or rather depend on differences in developmental stages, growth habits, substrates or precipitation...
April 6, 2017: Annals of Botany
https://www.readbyqxmd.com/read/28331531/an-integrative-systematic-framework-helps-to-reconstruct-skeletal-evolution-of-glass-sponges-porifera-hexactinellida
#9
Martin Dohrmann, Christopher Kelley, Michelle Kelly, Andrzej Pisera, John N A Hooper, Henry M Reiswig
BACKGROUND: Glass sponges (Class Hexactinellida) are important components of deep-sea ecosystems and are of interest from geological and materials science perspectives. The reconstruction of their phylogeny with molecular data has only recently begun and shows a better agreement with morphology-based systematics than is typical for other sponge groups, likely because of a greater number of informative morphological characters. However, inconsistencies remain that have far-reaching implications for hypotheses about the evolution of their major skeletal construction types (body plans)...
2017: Frontiers in Zoology
https://www.readbyqxmd.com/read/28325970/making-the-most-of-your-host-the-metrosideros-feeding-psyllids-hemiptera-psylloidea-of-the-hawaiian-islands
#10
Diana M Percy
The Hawaiian psyllids (Psylloidea, Triozidae) feeding on Metrosideros (Myrtaceae) constitute a remarkable radiation of more than 35 species. This monophyletic group has diversified on a single, highly polymorphic host plant species, Metrosideros polymorpha. Eleven Metrosideros-feeding species included in the Insects of Hawaii by Zimmerman are redescribed, and an additional 25 new species are described. Contrary to previous classifications that placed the Metrosideros-feeders in two genera, Trioza Foerster, 1848 and Kuwayama Crawford, 1911, all 36 named species are placed in Pariaconus Enderlein, 1926; and the relationship of this genus to other Pacific taxa within the family Triozidae, and other Austro-Pacific taxa feeding on host plants in Myrtaceae is clarified...
2017: ZooKeys
https://www.readbyqxmd.com/read/28323053/species-delimitation-and-phylogenetic-reconstruction-of-the-sinipercids-perciformes-sinipercidae-based-on-target-enrichment-of-thousands-of-nuclear-coding-sequences
#11
Shuli Song, Jinliang Zhao, Chenhong Li
The sinipercids are freshwater fishes endemic to East Asia, mainly in China. Phylogenetic studies on the sinipercids have made great progress in the last decades, but interspecific relationships and evolutionary history of the sinipercids remain unresolved. Lack of distinctive morphological characters leads to problems in validating of some species, such as Siniperca loona. Moreover, genetic data are needed to delimitate species pairs with explicit hypothesis testing, such as in S. chuatsi vs. S. kneri and Coreoperca whiteheadi vs...
March 18, 2017: Molecular Phylogenetics and Evolution
https://www.readbyqxmd.com/read/28288945/species-level-phylogeny-fruit-evolution-and-diversification-history-of-geranium-geraniaceae
#12
Thomas Marcussen, Andrea S Meseguer
The cosmopolitan genus Geranium L. (Geraniaceae) consists of c. 350 species distributed in temperate habitats worldwide, with most of its diversity concentrated in the Mediterranean region. Unlike other genera in Geraniaceae, the species of Geranium present contrasting seed discharge syndromes, i.e. the 'Erodium-type' (ET), the 'carpel-projection type' (CP), the 'seed-ejection type' (SE), and the 'inoperative type' (IT), which have been used to delimit major groups within the genus. However, phylogenetic relationships within Geranium are unknown and so is the evolution of the different seed discharge mechanisms...
May 2017: Molecular Phylogenetics and Evolution
https://www.readbyqxmd.com/read/28288942/endemic-palm-species-shed-light-on-habitat-shifts-and-the-assembly-of-the-cerrado-and-restinga-floras
#13
Christine D Bacon, Monica Moraes R, Carlos Jaramillo, Alexandre Antonelli
Species expansions into new habitats are often associated with physiological adaptations, for instance when rain forest lineages colonize dry habitats. Although such shifts have been documented for the Brazilian savanna (Cerrado), little is known about the biogeographic origin of species occupying an extreme South American habitat type, the coastal dunes (Restinga). We examined the formation of this poorly known, endangered habitat by reconstructing the evolutionary history of two endemic species. Due to the proposed recency and uniqueness of this habitat, we hypothesized that Restinga species of the palm genus Allagoptera to be recently evolved and to present derived morphological characters...
March 10, 2017: Molecular Phylogenetics and Evolution
https://www.readbyqxmd.com/read/28245223/phylogeny-and-chromosomal-diversification-in-the-dichroplus-elongatus-species-group-orthoptera-melanoplinae
#14
Elio R D Castillo, Alberto Taffarel, Maximiliano M Maronna, María Marta Cigliano, Octavio M Palacios-Gimenez, Diogo C Cabral-de-Mello, Dardo A Martí
In an attempt to track the chromosomal differentiation in the Dichroplus elongatus species group, we analyzed the karyotypes of four species with classical cytogenetic and mapping several multigene families through fluorescent in situ hybridization (FISH). We improved the taxon sampling of the D. elongatus species group adding new molecular data to infer the phylogeny of the genus and reconstruct the karyotype evolution. Our molecular analyses recovered a fully resolved tree with no evidence for the monophyly of Dichroplus...
2017: PloS One
https://www.readbyqxmd.com/read/28228094/sfreemap-a-simulation-free-tool-for-stochastic-mapping
#15
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
#16
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...
April 2017: Molecular Phylogenetics and Evolution
https://www.readbyqxmd.com/read/28185578/fast-ancestral-gene-order-reconstruction-of-genomes-with-unequal-gene-content
#17
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
#18
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...
March 1, 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
#19
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
#20
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
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