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Ancestral state reconstruction

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https://www.readbyqxmd.com/read/28819749/time-dependent-asymmetric-linear-parsimonious-ancestral-state-reconstruction
#1
Gilles Didier
The time-dependent-asymmetric-linear parsimony is an ancestral state reconstruction method which extends the standard linear parsimony (a.k.a. Wagner parsimony) approach by taking into account both branch lengths and asymmetric evolutionary costs for reconstructing quantitative characters (asymmetric costs amount to assuming an evolutionary trend toward the direction with the lowest cost). A formal study of the influence of the asymmetry parameter shows that the time-dependent-asymmetric-linear parsimony infers states which are all taken among the known states, except for some degenerate cases corresponding to special values of the asymmetry parameter...
August 17, 2017: Bulletin of Mathematical Biology
https://www.readbyqxmd.com/read/28812736/the-evolution-and-population-diversity-of-human-specific-segmental-duplications
#2
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 from 33 gene families)...
February 17, 2017: Nature ecology & evolution
https://www.readbyqxmd.com/read/28776667/relating-appendicular-skeletal-variation-of-sigmodontine-rodents-to-locomotion-modes-in-a-phylogenetic-context
#3
Ludmilla Carvalho Coutinho, João Alves de Oliveira
Sigmodontinae rodents constitute the second-largest subfamily among mammals. Alongside the taxonomic diversity, they are also ecologically diverse, exhibiting a wide array of locomotion modes, with semifossorial, terrestrial, semiaquatic, scansorial, arboreal, and saltatorial forms. To understand the ecomorphologic aspects that allow these rodents to display such locomotion diversity, we analyzed 35 qualitative characters of the appendicular skeleton (humerus, ulna, radius, scapula, femur, tibia, ilium, ischium and pubis) in 795 specimens belonging to 64 species, 34 genera and 10 tribes, representing all locomotion modes assigned to this subfamily...
August 4, 2017: Journal of Anatomy
https://www.readbyqxmd.com/read/28768477/hostplant-change-and-paleoclimatic-events-explain-diversification-shifts-in-skipper-butterflies-family-hesperiidae
#4
Ranjit Kumar Sahoo, Andrew D Warren, Steve C Collins, Ullasa Kodandaramaiah
BACKGROUND: Skippers (Family: Hesperiidae) are a large group of butterflies with ca. 4000 species under 567 genera. The lack of a time-calibrated higher-level phylogeny of the group has precluded understanding of its evolutionary past. We here use a 10-gene dataset to reconstruct the most comprehensive time-calibrated phylogeny of the group, and explore factors that affected the diversification of these butterflies. RESULTS: Ancestral state reconstructions show that the early hesperiid lineages utilized dicots as larval hostplants...
August 2, 2017: BMC Evolutionary Biology
https://www.readbyqxmd.com/read/28745397/tempo-and-mode-of-performance-evolution-across-multiple-independent-origins-of-adhesive-toe-pads-in-lizards
#5
Travis J Hagey, Josef C Uyeda, Kristen E Crandell, Jorn A Cheney, Kellar Autumn, Luke J Harmon
Understanding macroevolutionary dynamics of trait evolution is an important endeavor in evolutionary biology. Ecological opportunity can liberate a trait as it diversifies through trait space, while genetic and selective constraints can limit diversification. While many studies have examined the dynamics of morphological traits, diverse morphological traits may yield the same or similar performance and as performance is often more proximately the target of selection, examining only morphology may give an incomplete understanding of evolutionary dynamics...
July 26, 2017: Evolution; International Journal of Organic Evolution
https://www.readbyqxmd.com/read/28726643/reconstructed-ancestral-enzymes-reveal-that-negative-selection-drove-the-evolution-of-substrate-specificity-in-adp-dependent-kinases
#6
Víctor Castro-Fernandez, Alejandra Herrera-Morande, Ricardo Zamora, Felipe Merino, Felipe Gonzalez-Ordenes, Felipe Padilla-Salinas, Humberto M Pereira, Jose Brandão-Neto, Richard C Garratt, Victoria Guixe
One central goal in molecular evolution is to pinpoint the mechanisms and evolutionary forces that cause an enzyme to change its substrate specificity; however, these processes remain largely unexplored. Using the glycolytic ADP-dependent kinases of archaea, including the orders Thermococcales, Methanosarcinales, and Methanococcales, as a model and employing an approach involving paleoenzymology, evolutionary statistics, and protein structural analysis, we could track changes in substrate specificity during ADP-dependent kinase evolution along with the structural determinants of these changes...
July 18, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/28719578/de-novo-active-sites-for-resurrected-precambrian-enzymes
#7
Valeria A Risso, Sergio Martinez-Rodriguez, Adela M Candel, Dennis M Krüger, David Pantoja-Uceda, Mariano Ortega-Muñoz, Francisco Santoyo-Gonzalez, Eric A Gaucher, Shina C L Kamerlin, Marta Bruix, Jose A Gavira, Jose M Sanchez-Ruiz
Protein engineering studies often suggest the emergence of completely new enzyme functionalities to be highly improbable. However, enzymes likely catalysed many different reactions already in the last universal common ancestor. Mechanisms for the emergence of completely new active sites must therefore either plausibly exist or at least have existed at the primordial protein stage. Here, we use resurrected Precambrian proteins as scaffolds for protein engineering and demonstrate that a new active site can be generated through a single hydrophobic-to-ionizable amino acid replacement that generates a partially buried group with perturbed physico-chemical properties...
July 18, 2017: Nature Communications
https://www.readbyqxmd.com/read/28709985/molecular-phylogeny-of-miltogramminae-diptera-sarcophagidae-implications-for-classification-systematics-and-evolution-of-larval-feeding-strategies
#8
Marcin Piwczyński, Thomas Pape, Edyta Deja-Sikora, Marcin Sikora, Kamran Akbarzadeh, Krzysztof Szpila
Miltogramminae is one of the phylogenetically most poorly studied taxa of the species-rich family Sarcophagidae (Diptera). Most species are kleptoparasites in nests of solitary aculeate wasps and bees, although parasitoids and saprophagous species are also known, and the ancestral miltogrammine life habit remains unsettled. Here, we present for the first time a comprehensive phylogenetic tree consisting of 58 representatives of Miltogramminae, reconstructed using sequence data from three mitochondrial (COI, cytB, ND4) and one nuclear (Ef-1α) genes...
July 11, 2017: Molecular Phylogenetics and Evolution
https://www.readbyqxmd.com/read/28696285/early-paleocene-landbird-supports-rapid-phylogenetic-and-morphological-diversification-of-crown-birds-after-the-k-pg-mass-extinction
#9
Daniel T Ksepka, Thomas A Stidham, Thomas E Williamson
Evidence is accumulating for a rapid diversification of birds following the K-Pg extinction. Recent molecular divergence dating studies suggest that birds radiated explosively during the first few million years of the Paleocene; however, fossils from this interval remain poorly represented, hindering our understanding of morphological and ecological specialization in early neoavian birds. Here we report a small fossil bird from the Nacimiento Formation of New Mexico, constrained to 62.221-62.517 Ma. This partial skeleton represents the oldest arboreal crown group bird known...
July 25, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28679721/the-importance-of-offshore-origination-revealed-through-ophiuroid-phylogenomics
#10
Guadalupe Bribiesca-Contreras, Heroen Verbruggen, Andrew F Hugall, Timothy D O'Hara
Our knowledge of macro-evolutionary processes in the deep sea is poor, leading to much speculation about whether the deep sea is a source or sink of evolutionary adaptation. Here, we use a phylogenetic approach, on large molecular (688 species, 275 kbp) and distributional datasets (104 513 records) across an entire class of marine invertebrates (Ophiuroidea), to infer rates of bathymetric range shift over time between shallow and deep water biomes. Biome conservation is evident through the phylogeny, with the majority of species in most clades distributed within the same bathome...
July 12, 2017: Proceedings. Biological Sciences
https://www.readbyqxmd.com/read/28674236/molecular-systematics-of-indian-alysicarpus-fabaceae-based-on-analyses-of-nuclear-ribosomal-dna-sequences
#11
Akram Gholami, Shweta Subramaniam, R Geeta, Arun K Pandey
Alysicarpus Necker ex Desvaux (Fabaceae, Desmodieae) consists of ~30 species that are distributed in tropical and subtropical regions of theworld. In India, the genus is represented by ca. 18 species, ofwhich seven are endemic. Sequences of the nuclear Internal transcribed spacer from38 accessions representing 16 Indian specieswere subjected to phylogenetic analyses. The ITS sequence data strongly support the monophyly of the genus Alysicarpus. Analyses revealed four major well-supported clades within Alysicarpus...
June 2017: Journal of Genetics
https://www.readbyqxmd.com/read/28667673/on-the-presence-of-the-patella-in-frogs
#12
Virginia Abdala, Miriam C Vera, María Laura Ponssa
The patella is one of the most studied sesamoids. Historically, the patella is described as a big sesamoid embedded in the tendon of the quadriceps femoris muscle. This sesamoid is studied from developmental, functional, clinical and anatomical perspectives. The presence of a patella is reported in squamatans, birds and mammals. Lissamphibians are identified as the major lineage that fail to develop a patella. However, this sesamoid is reported at least once in anurans, but without detailed anatomical discussions...
July 1, 2017: Anatomical Record: Advances in Integrative Anatomy and Evolutionary Biology
https://www.readbyqxmd.com/read/28651535/molecular-phylogeny-reveals-food-plasticity-in-the-evolution-of-true-ladybird-beetles-coleoptera-coccinellidae-coccinellini
#13
Hermes E Escalona, Andreas Zwick, Hao-Sen Li, Jiahui Li, Xingmin Wang, Hong Pang, Diana Hartley, Lars S Jermiin, Oldřich Nedvěd, Bernhard Misof, Oliver Niehuis, Adam Ślipiński, Wioletta Tomaszewska
BACKGROUND: The tribe Coccinellini is a group of relatively large ladybird beetles that exhibits remarkable morphological and biological diversity. Many species are aphidophagous, feeding as larvae and adults on aphids, but some species also feed on other hemipterous insects (i.e., heteropterans, psyllids, whiteflies), beetle and moth larvae, pollen, fungal spores, and even plant tissue. Several species are biological control agents or widespread invasive species (e.g., Harmonia axyridis (Pallas))...
June 26, 2017: BMC Evolutionary Biology
https://www.readbyqxmd.com/read/28637223/millions-of-years-behind-slow-adaptation-of-ruminants-to-grasslands
#14
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
#15
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
#16
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
#17
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
#18
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
#19
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
#20
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
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