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Ancestral state 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/28467456/mosasauroid-phylogeny-under-multiple-phylogenetic-methods-provides-new-insights-on-the-evolution-of-aquatic-adaptations-in-the-group
#4
Tiago R Simões, Oksana Vernygora, Ilaria Paparella, Paulina Jimenez-Huidobro, Michael W Caldwell
Mosasauroids were a successful lineage of squamate reptiles (lizards and snakes) that radiated during the Late Cretaceous (95-66 million years ago). They can be considered one of the few lineages in the evolutionary history of tetrapods to have acquired a fully aquatic lifestyle, similarly to whales, ichthyosaurs and plesiosaurs. Despite a long history of research on this group, their phylogenetic relationships have only been tested so far using traditional (unweighted) maximum parsimony. However, hypotheses of mosasauroid relationships and the recently proposed multiple origins of aquatically adapted pelvic and pedal features in this group can be more thoroughly tested by methods that take into account variation in branch lengths and evolutionary rates...
2017: PloS One
https://www.readbyqxmd.com/read/28462054/evolution-of-developmental-sequences-in-lepidosaurs
#5
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/28447337/reconstructing-the-ancestral-vertebrate-brain
#6
REVIEW
Fumiaki Sugahara, Yasunori Murakami, Juan Pascual-Anaya, Shigeru Kuratani
Highly complicated morphologies and sophisticated functions of vertebrate brains have been established through evolution. However, the origin and early evolutionary history of the brain remain elusive, owing to lack of information regarding the brain architecture of extant and fossil species of jawless vertebrates (agnathans). Comparative analyses of the brain of less studied cyclostomes (only extant agnathan group, consisting of lampreys and hagfish) with the well-known sister group of jawed vertebrates (gnathostomes) are the only tools we have available to illustrate the ancestral architecture of the vertebrate brain...
April 26, 2017: Development, Growth & Differentiation
https://www.readbyqxmd.com/read/28444351/comparative-genomic-analysis-of-set-domain-family-reveals-the-origin-expansion-and-putative-function-of-the-arthropod-specific-smyda-genes-as-histone-modifiers-in-insects
#7
Feng Jiang, Qing Liu, Yanli Wang, Jie Zhang, Huimin Wang, Tianqi Song, Meiling Yang, Xianhui Wang, Le Kang
The SET domain is an evolutionarily conserved motif present in histone lysine methyltransferases, which are important in the regulation of chromatin and gene expression in animals. In this study, we searched for SET domain-containing genes (SET genes) in all of the 147 arthropod genomes sequenced at the time of carrying out this experiment to understand the evolutionary history by which SET domain have evolved in insects. Phylogenetic and ancestral state reconstruction analysis revealed an arthropod-specific SET gene family, named SmydA, which is ancestral to arthropod animals and specifically diversified during insect evolution...
April 22, 2017: GigaScience
https://www.readbyqxmd.com/read/28439466/arrival-and-diversification-of-mabuyine-skinks-squamata-scincidae-in-the-neotropics-based-on-a-fossil-calibrated-timetree
#8
Anieli Guirro Pereira, Carlos G Schrago
BACKGROUND: The evolution of South American Mabuyinae skinks holds significant biogeographic interest because its sister lineage is distributed across the African continent and adjacent islands. Moreover, at least one insular species, Trachylepis atlantica, has independently reached the New World through transoceanic dispersal. To clarify the evolutionary history of both Neotropical lineages, this study aimed to infer an updated timescale using the largest species and gene sampling dataset ever assembled for this group...
2017: PeerJ
https://www.readbyqxmd.com/read/28434199/repeated-evolution-of-digital-adhesion-in-geckos-a-reply-to-harrington-and-reeder
#9
Tony Gamble, Eli Greenbaum, Todd R Jackman, Anthony P Russell, Aaron M Bauer
We published a phylogenetic comparative analysis that found geckos had gained and lost adhesive toepads multiple times over their long evolutionary history (Gamble et al. 2012). This was consistent with decades of morphological studies showing geckos had evolved adhesive toepads on multiple occasions and that the morphology of geckos with ancestrally padless digits can be distinguished from secondarily padless forms. Recently, Harrington and Reeder (2017) reanalyzed data from Gamble et al. (2012) and found little support for the multiple origins hypothesis...
April 23, 2017: Journal of Evolutionary Biology
https://www.readbyqxmd.com/read/28428869/rapid-maximum-likelihood-ancestral-state-reconstruction-of-continuous-characters-a-rerooting-free-algorithm
#10
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/28406561/lower-ilium-evolution-in-apes-and-hominins
#11
Ashley S Hammond, Sergio Almécija
Elucidating the pelvic morphology of the Pan-Homo last common ancestor (LCA) is crucial for understanding ape and human evolution. The pelvis of Ardipithecus ramidus has been the basis of controversial interpretations of the LCA pelvis. In particular, it was proposed that the lower ilium became elongate independently in the orangutan and chimpanzee clades, making these taxa poor analogues for the pelvis of the LCA. This study examines the variation in relative lower ilium height between and within living and fossil hominoid species (and other anthropoids), and models its evolution using available fossil hominoids as calibration points...
May 2017: Anatomical Record: Advances in Integrative Anatomy and Evolutionary Biology
https://www.readbyqxmd.com/read/28403902/phylodynamics-of-foot-and-mouth-disease-virus-o-panasia-in-vietnam-2010-2014
#12
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/28389535/experimental-evaluation-of-host-adaptation-of-lactobacillus-reuteri-to-different-vertebrate-species
#13
Rebbeca M Duar, Steven A Frese, Xiaoxi B Lin, Samodha C Fernando, Thomas E Burkey, Guergana Tasseva, Daniel A Peterson, Jochen Blom, Cory Q Wenzel, Christine M Szymanski, Jens Walter
The species Lactobacillus reuteri has diversified into host-specific lineages implying a long term association with different vertebrates. Strains from rodent lineages show specific adaptations to mice, but the processes underlying the evolution of L. reuteri in other hosts remain unknown. We administered three standardized inocula composed of strains from different host-confined lineages to mice, pigs, chickens and humans. The ecological performance of each strain in the gastrointestinal tract of each host was determined by typing random colonies recovered from fecal samples collected over five consecutive days post-administration...
April 7, 2017: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/28387789/evolution-of-wood-anatomical-characters-in-nepenthes-and-close-relatives-of-caryophyllales
#14
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/28382230/mountain-colonisation-miniaturisation-and-ecological-evolution-in-a-radiation-of-direct-developing-new-guinea-frogs-choerophryne-microhylidae
#15
Paul M Oliver, Amy Iannella, Stephen J Richards, Michael S Y Lee
AIMS: Mountain ranges in the tropics are characterised by high levels of localised endemism, often-aberrant evolutionary trajectories, and some of the world's most diverse regional biotas. Here we investigate the evolution of montane endemism, ecology and body size in a clade of direct-developing frogs (Choerophryne, Microhylidae) from New Guinea. METHODS: Phylogenetic relationships were estimated from a mitochondrial molecular dataset using Bayesian and maximum likelihood approaches...
2017: PeerJ
https://www.readbyqxmd.com/read/28356450/terrestrial-reproduction-as-an-adaptation-to-steep-terrain-in-african-toads
#16
H Christoph Liedtke, Hendrik Müller, Julian Hafner, Johannes Penner, David J Gower, Tomáš Mazuch, Mark-Oliver Rödel, Simon P Loader
How evolutionary novelties evolve is a major question in evolutionary biology. It is widely accepted that changes in environmental conditions shift the position of selective optima, and advancements in phylogenetic comparative approaches allow the rigorous testing of such correlated transitions. A longstanding question in vertebrate biology has been the evolution of terrestrial life histories in amphibians and here, by investigating African bufonids, we test whether terrestrial modes of reproduction have evolved as adaptations to particular abiotic habitat parameters...
March 29, 2017: Proceedings. Biological Sciences
https://www.readbyqxmd.com/read/28345775/quantification-of-the-position-and-depth-of-the-flexor-hallucis-longus-groove-in-euarchontans-with-implications-for-the-evolution-of-primate-positional-behavior
#17
Gabriel S Yapuncich, Erik R Seiffert, Doug M Boyer
OBJECTIVE: On the talus, the position and depth of the groove for the flexor hallucis longus tendon have been used to infer phylogenetic affinities and positional behaviors of fossil primates. This study quantifies aspects of the flexor hallucis longus groove (FHLG) to test if: (1) a lateral FHLG is a derived strepsirrhine feature, (2) a lateral FHLG reflects inverted and abducted foot postures, and (3) a deeper FHLG indicates a larger muscle. METHODS: We used linear measurements of microCT-generated models from a sample of euarchontans (n = 378 specimens, 125 species) to quantify FHLG position and depth...
March 27, 2017: American Journal of Physical Anthropology
https://www.readbyqxmd.com/read/28345239/the-anatomy-of-the-blood-vascular-system-of-the-giant-vestimentiferan-tubeworm-riftia-pachyptila-siboglinidae-annelida
#18
Nadezhda N Rimskaya-Korsakova, Sergey V Galkin, Vladimir V Malakhov
The giant dimensions of vestimentiferan Riftia pachyptila (Jones, ) are achieved thanks to the well-developed vascular system. In the vestimentum, there is a complicated net of lacunae, including the brain blood supply and the ventral lacuna underlying the ciliary field. The trunk region has an extensive network of blood vessels feeding the gonads («rete mirabile»). The thick muscular lining of the mesenterial vessels in the trunk and the dorsal vessel in the opisthosome serves as an additional pump, pushing blood into numerous vessels in the segments...
June 2017: Journal of Morphology
https://www.readbyqxmd.com/read/28331531/an-integrative-systematic-framework-helps-to-reconstruct-skeletal-evolution-of-glass-sponges-porifera-hexactinellida
#19
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
#20
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
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