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Ancestral state reconstruction

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https://www.readbyqxmd.com/read/28637223/millions-of-years-behind-slow-adaptation-of-ruminants-to-grasslands
#1
Olja Toljagic, Kjetil L Voje, Michael Matschiner, Lee Hsiang Liow, Thomas F Hansen
The Late-Cretaceous appearance of grasses, followed by the Cenozoic advancement of grasslands as dominant biomes, has contributed to the evolution of a range of specialized herbivores adapted to new diets, as well as to increasingly open and arid habitats. Many mammals including ruminants, the most diversified ungulate suborder, evolved high-crowned (hypsodont) teeth as an adaptation to tooth-wearing diets and habitats. The impact of different causes of tooth wear is still a matter of debate, and the temporal pattern of hypsodonty evolution in relation to the evolution of grasslands remains unclear...
June 20, 2017: Systematic Biology
https://www.readbyqxmd.com/read/28620997/morphology-and-evolution-of-the-oral-shield-in-marsupial-neonates-including-the-newborn-monito-del-monte-dromiciops-gliroides-marsupialia-microbiotheria-pouch-young
#2
Nanette Y Schneider, Yamila Gurovich
Newborn marsupials can be arranged into three grades of developmental complexity based on their external form, as well as based on their organ systems and their cytology. The dasyurids are considered the least developed marsupials at birth, while didelphids and peramelids are intermediate, and macropods are the most developed. Currently there is still little information on caenolestid and microbiotherid development at birth. Developmental stages can be graded as G1, G2 and G3, with G1 being the least developed at birth, and G3 the most developed...
July 2017: Journal of Anatomy
https://www.readbyqxmd.com/read/28584090/paleogenomics-of-echinoids-reveals-an-ancient-origin-for-the-double-negative-specification-of-micromeres-in-sea-urchins
#3
Jeffrey R Thompson, Eric M Erkenbrack, Veronica F Hinman, Brenna S McCauley, Elizabeth Petsios, David J Bottjer
Establishing a timeline for the evolution of novelties is a common, unifying goal at the intersection of evolutionary and developmental biology. Analyses of gene regulatory networks (GRNs) provide the ability to understand the underlying genetic and developmental mechanisms responsible for the origin of morphological structures both in the development of an individual and across entire evolutionary lineages. Accurately dating GRN novelties, thereby establishing a timeline for GRN evolution, is necessary to answer questions about the rate at which GRNs and their subcircuits evolve, and to tie their evolution to paleoenvironmental and paleoecological changes...
June 6, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28583078/the-conquering-of-north-america-dated-phylogenetic-and-biogeographic-inference-of-migratory-behavior-in-bee-hummingbirds
#4
Yuyini Licona-Vera, Juan Francisco Ornelas
BACKGROUND: Geographical and temporal patterns of diversification in bee hummingbirds (Mellisugini) were assessed with respect to the evolution of migration, critical for colonization of North America. We generated a dated multilocus phylogeny of the Mellisugini based on a dense sampling using Bayesian inference, maximum-likelihood and maximum parsimony methods, and reconstructed the ancestral states of distributional areas in a Bayesian framework and migratory behavior using maximum parsimony, maximum-likelihood and re-rooting methods...
June 5, 2017: BMC Evolutionary Biology
https://www.readbyqxmd.com/read/28580430/the-evolution-and-population-diversity-of-human-specific-segmental-duplications
#5
Megan Y Dennis, Lana Harshman, Bradley J Nelson, Osnat Penn, Stuart Cantsilieris, John Huddleston, Francesca Antonacci, Kelsi Penewit, Laura Denman, Archana Raja, Carl Baker, Kenneth Mark, Maika Malig, Nicolette Janke, Claudia Espinoza, Holly A F Stessman, Xander Nuttle, Kendra Hoekzema, Tina A Lindsay-Graves, Richard K Wilson, Evan E Eichler
Segmental duplications contribute to human evolution, adaptation and genomic instability but are often poorly characterized. We investigate the evolution, genetic variation and coding potential of human-specific segmental duplications (HSDs). We identify 218 HSDs based on analysis of 322 deeply sequenced archaic and contemporary hominid genomes. We sequence 550 human and nonhuman primate genomic clones to reconstruct the evolution of the largest, most complex regions with protein-coding potential (n=80 genes/33 gene families)...
2017: Nature ecology & evolution
https://www.readbyqxmd.com/read/28555871/microanatomical-diversification-of-the-zona-pellucida-in%C3%A2-aplochelioid-killifishes
#6
A W Thompson, A I Furness, C Stone, C M Rade, G Ortí
This study investigates zona pellucida (ZP) ultrastructure in fertilized eggs of annual killifishes (suborder Aplocheiloidei), a group of highly specialized fishes that are able to survive desiccation for several weeks to months before they hatch. Little is known about ZP or chorionic ultrastructure sustaining these life-history modes, so scanning electron microscopy (SEM) was used to describe this trait in a large number of aplocheiloids with a focus on the family Rivulidae and the genus Hypsolebias. New images of ZP ultrastructure for 52 aplocheiloid species are provided, more than doubling the number characterized thus far...
May 28, 2017: Journal of Fish Biology
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
#7
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
#8
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
#9
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
#10
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
#11
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
#12
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
#13
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 domains have evolved in insects. Phylogenetic and ancestral state reconstruction analysis revealed an arthropod-specific SET gene family, named SmydA, that is ancestral to arthropod animals and specifically diversified during insect evolution...
June 1, 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
#14
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
#15
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
#16
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
#17
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
#18
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
#19
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
#20
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...
May 1, 2017: Annals of Botany
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