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Ancestral character reconstruction

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https://www.readbyqxmd.com/read/28331531/an-integrative-systematic-framework-helps-to-reconstruct-skeletal-evolution-of-glass-sponges-porifera-hexactinellida
#1
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
#2
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
#3
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 17, 2017: Molecular Phylogenetics and Evolution
https://www.readbyqxmd.com/read/28288945/species-level-phylogeny-fruit-evolution-and-diversification-history-of-geranium-geraniaceae
#4
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...
March 10, 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
#5
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
#6
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
#7
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
#8
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 20, 2017: Molecular Phylogenetics and Evolution
https://www.readbyqxmd.com/read/28185578/fast-ancestral-gene-order-reconstruction-of-genomes-with-unequal-gene-content
#9
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
#10
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
#11
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
#12
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
#13
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
#14
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
#15
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
#16
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...
March 2017: 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
#17
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
#18
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
#19
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
#20
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
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