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Ancestral state reconstruction

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https://www.readbyqxmd.com/read/29242780/an-expanded-phylogeny-for-the-genus-phytophthora
#1
Xiao Yang, Brett M Tyler, Chuanxue Hong
A comprehensive phylogeny representing 142 described and 43 provisionally named Phytophthora species is reported here for this rapidly expanding genus. This phylogeny features signature sequences of 114 ex-types and numerous authentic isolates that were designated as representative isolates by the originators of the respective species. Multiple new subclades were assigned in clades 2, 6, 7, and 9. A single species P. lilii was placed basal to clades 1 to 5, and 7. Phytophthora stricta was placed basal to other clade 8 species, P...
December 2017: IMA Fungus
https://www.readbyqxmd.com/read/29230900/expression-of-a-carotenoid-modifying-gene-and-evolution-of-red-colouration-in-weaverbirds-ploceidae
#2
Hanlu Twyman, Maria Prager, Nicholas I Mundy, Staffan Andersson
Red carotenoid colours in birds are widely assumed to be sexually selected quality indicators, but this rests on a very incomplete understanding of genetic mechanisms and honesty-mediating costs. Recent progress was made by the implication of the gene CYP2J19 as an avian carotenoid ketolase, catalysing the synthesis of red C4-ketocarotenoids from yellow dietary precursors, and potentially a major mechanism behind red coloration in birds. Here we investigate the role of CYP2J19 in the spectacular colour diversification of African weaverbirds (Ploceidae), represented by five genera and 16 species; eight red, seven yellow, and one without carotenoid coloration...
December 12, 2017: Molecular Ecology
https://www.readbyqxmd.com/read/29222065/testing-the-monophyly-of-simaba-simaroubaceae-evidence-from-five-molecular-regions-and-morphology
#3
Marcelo Fernando Devecchi, William Wayt Thomas, Gregory M Plunkett, José Rubens Pirani
Generic circumscriptions in the mostly pantropical family Simaroubaceae are somewhat controversial. Simaba is the largest genus, currently defined as exclusively neotropical, with around 25 species of trees and shrubs, but both its limits and infrageneric classification have been a matter of discussion and divergence. Traditionally, species of the genus have been treated in three sections: Simaba sect. Tenuiflorae, S. sect. Floribundae and S. sect. Grandiflorae, but a phylogenetic analysis suggested that the latter two may not be monophyletic...
December 5, 2017: Molecular Phylogenetics and Evolution
https://www.readbyqxmd.com/read/29207942/a-reconstruction-of-sexual-modes-throughout-animal-evolution
#4
Daniel A Sasson, Joseph F Ryan
BACKGROUND: Although most extant animals have separate sexes, simultaneous hermaphrodites can be found in lineages throughout the animal kingdom. However, the sexual modes of key ancestral nodes including the last common ancestor (LCA) of all animals remain unclear. Without these data, it is difficult to infer the reproductive-state transitions that occurred early in animal evolution, and thus a broad understanding of the evolution of animal reproduction remains elusive. In this study, we use a composite phylogeny from four previously published studies, two alternative topologies (ctenophores or sponges as sister to the rest of animals), and multiple phylogenetic approaches to conduct the most extensive analysis to date of the evolution of animal sexual modes...
December 6, 2017: BMC Evolutionary Biology
https://www.readbyqxmd.com/read/29196678/resolving-kangaroo-phylogeny-and-overcoming-retrotransposon-ascertainment-bias
#5
William G Dodt, Susanne Gallus, Matthew J Phillips, Maria A Nilsson
Reconstructing phylogeny from retrotransposon insertions is often limited by access to only a single reference genome, whereby support for clades that do not include the reference taxon cannot be directly observed. Here we have developed a new statistical framework that accounts for this ascertainment bias, allowing us to employ phylogenetically powerful retrotransposon markers to explore the radiation of the largest living marsupials, the kangaroos and wallabies of the genera Macropus and Wallabia. An exhaustive in silico screening of the tammar wallaby (Macropus eugenii) reference genome followed by experimental screening revealed 29 phylogenetically informative retrotransposon markers belonging to a family of endogenous retroviruses...
December 1, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29164751/style-polymorphism-in-linum-linaceae-a-case-of-mediterranean-parallel-evolution
#6
J Ruiz-Martín, R Santos-Gally, M Escudero, J J Midgley, R Pérez-Barrales, J Arroyo
Heterostyly is a sex polymorphism which has challenged evolutionary biologists ever since Darwin. One of the lineages where heterostyly, and related stylar conditions, appears more frequently is the family Linaceae and its most diverse and widespread genus, Linum. Thus, this group is particularly suitable for testing competing hypotheses about ancestral and transitional stages on the evolutionary building up of heterostyly. We generated a well-resolved phylogeny of Linum based on extensive sampling and plastid and nuclear DNA sequences, and used it to trace the evolution of character states of style polymorphism and its association with traits related to pollination and breeding systems, obtained from our samples and the literature...
November 22, 2017: Plant Biology
https://www.readbyqxmd.com/read/29162549/diversification-dynamics-and-transoceanic-eurasian-australian-disjunction-in-the-genus-picris-compositae-induced-by-the-interplay-of-shifts-in-intrinsic-extrinsic-traits-and-paleoclimatic-oscillations
#7
Marek Slovák, Jaromír Kučera, Hans Walter Lack, Jotham Ziffer-Berger, Andrea Melicharková, Eliška Záveská, Peter Vďačný
Understanding transcontinental biogeographic patterns has been one of the main foci of the field of biogeography. While multiple explanations for transcontinental disjunctions have been proposed, little is still known about the relative importance of intrinsic and extrinsic traits for the diversification dynamics of disjunct taxa. Here, we study the evolutionary history of the genus Picris L. (Compositae), a great model for investigating the diversification dynamics of transoceanic bipolar disjunct organisms...
November 18, 2017: Molecular Phylogenetics and Evolution
https://www.readbyqxmd.com/read/29138301/genomic-variation-and-evolution-of-vibrio-parahaemolyticus-st36-over-the-course-of-a-transcontinental-epidemic-expansion
#8
Jaime Martinez-Urtaza, Ronny van Aerle, Michel Abanto, Julie Haendiges, Robert A Myers, Joaquin Trinanes, Craig Baker-Austin, Narjol Gonzalez-Escalona
Vibrio parahaemolyticus is the leading cause of seafood-related infections with illnesses undergoing a geographic expansion. In this process of expansion, the most fundamental change has been the transition from infections caused by local strains to the surge of pandemic clonal types. Pandemic clone sequence type 3 (ST3) was the only example of transcontinental spreading until 2012, when ST36 was detected outside the region where it is endemic in the U.S. Pacific Northwest causing infections along the U.S. northeast coast and Spain...
November 14, 2017: MBio
https://www.readbyqxmd.com/read/29134623/repeated-evolution-and-reversibility-of-self-fertilization-in-the-volvocine-green-algae
#9
Erik R Hanschen, Matthew D Herron, John J Wiens, Hisayoshi Nozaki, Richard E Michod
Outcrossing and self-fertilization are fundamental strategies of sexual reproduction, each with different evolutionary costs and benefits. Self-fertilization is thought to be an evolutionary "dead-end" strategy, beneficial in the short term but costly in the long term, resulting in self-fertilizing species that occupy only the tips of phylogenetic trees. Here, we use volvocine green algae to investigate the evolution of self-fertilization. We use ancestral-state reconstructions to show that self-fertilization has repeatedly evolved from outcrossing ancestors and that multiple reversals from selfing to outcrossing have occurred...
November 14, 2017: Evolution; International Journal of Organic Evolution
https://www.readbyqxmd.com/read/29127737/genomic-data-from-arthropods-reveal-high-conservation-but-divergent-evolutionary-pattern-of-polycomb-trithorax-group-genes-in-arthropods
#10
Feng Jiang, Qing Liu, Xiang Liu, Xian-Hui Wang, Le Kang
Epigenetic gene control is maintained by chromatin-associated Polycomb group (PcG) and Trithorax group (TrxG) genes, which act antagonistically via the interplay between PcG and TrxG regulation to generate silenced or permissive transcriptional states. In this study, we searched for PcG/TrxG genes in 180 arthropod genomes, covering all the sequenced arthropod genomes at the time of conducting this study, to perform a global investigation of PcG/TrxG genes in a phylogenetic frame. Results of ancestral state reconstruction analysis revealed that the ancestor of arthropod species has an almost complete repertoire of PcG/TrxG genes, and most of these genes were seldom lost above order level...
November 11, 2017: Insect Science
https://www.readbyqxmd.com/read/29113924/why-are-there-so-many-sedges-sumatroscirpeae-a-missing-piece-in-the-evolutionary-puzzle-of-the-giant-genus-carex-cyperaceae
#11
Étienne Léveillé-Bourret, Julian R Starr, Bruce A Ford
For over a century, the origins and mechanisms underlying the diversification of the enormous temperate genus Carex (>2100 species; Cariceae, Cyperaceae) have remained largely speculative. Characteristics such as its diverse ecology, varied biogeography, and intriguing cytology have made Carex a powerful model for studying plant evolution, but its uncertain sister-group relationships hinder its use in studies that depend on accurate ancestral state estimates and biogeographic inferences. To identify the sister to Carex, we estimated the phylogeny of all genera in the Cariceae-Dulichieae-Scirpeae clade (CDS) using three plastid and two nuclear ribosomal markers...
November 4, 2017: Molecular Phylogenetics and Evolution
https://www.readbyqxmd.com/read/29111476/phylogenomics-and-evolution-of-floral-traits-in-the-neotropical-tribe-malmeeae-annonaceae
#12
J C Lopes, L W Chatrou, R Mello-Silva, P J Rudall, M G Sajo
Androdioecy is the rarest sexual system among plants. The majority of androdioecious species are herbaceous plants that have evolved from dioecious ancestors. Nevertheless, some woody and androdioecious plants have hermaphrodite ancestors, as in the Annonaceae, where androdioecious genera have arisen several times in different lineages. The majority of androdioecious species of Annonaceae belong to the Neotropical tribe Malmeeae. In addition to these species, Pseudoxandra spiritus-sancti was recently confirmed to be androdioecious...
October 27, 2017: Molecular Phylogenetics and Evolution
https://www.readbyqxmd.com/read/29079624/deciphering-the-origin-evolution-and-physiological-function-of-the-subtelomeric-aryl-alcohol-dehydrogenase-gene-family-in-the-yeast-saccharomyces-cerevisiae
#13
Dong-Dong Yang, Gustavo M de Billerbeck, Jin-Jing Zhang, Frank Rosenzweig, Jean-Marie Francois
Homology searches indicate that Saccharomyces cerevisiae strain BY4741 contains seven redundant genes that encode putative aryl-alcohol dehydrogenases (AAD). Yeast AADs are located in subtelomeric regions of different chromosomes, and their functional role(s) remain enigmatic. Here, we show that two of these genes, AAD4 and AAD14, encode functional enzymes that reduce aliphatic and aryl-aldehydes concomitant with oxidation of cofactor NADPH, and that Aad4p and Aad14p exhibit different substrate preference patterns...
October 27, 2017: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/29079378/mitochondrial-phylogenomics-and-genome-rearrangements-in-the-barklice-insecta-psocodea
#14
Kazunori Yoshizawa, Kevin P Johnson, Andrew D Sweet, Izumi Yao, Rodrigo L Ferreira, Stephen L Cameron
The mitochondrial genome arrangement in the insect order Psocodea (booklice, barklice, and parasitic lice) is extremely variable. Genome organization ranges from the rearrangement of a few tRNAs and protein coding genes, through extensive tRNA and protein coding gene rearrangements, to subdivision into multiple mini-chromosomes. Evolution of the extremely modified mitochondrial genome in parasitic lice (Phthiraptera) has been the subject of several studies, but limited information is available regarding the mitochondrial genome organization of the more plesiomorphic, free-living Psocodea (formerly known as the "Psocoptera")...
October 24, 2017: Molecular Phylogenetics and Evolution
https://www.readbyqxmd.com/read/29073890/prey-preference-follows-phylogeny-evolutionary-dietary-patterns-within-the-marine-gastropod-group-cladobranchia-gastropoda-heterobranchia-nudibranchia
#15
Jessica A Goodheart, Adam L Bazinet, Ángel Valdés, Allen G Collins, Michael P Cummings
BACKGROUND: The impact of predator-prey interactions on the evolution of many marine invertebrates is poorly understood. Since barriers to genetic exchange are less obvious in the marine realm than in terrestrial or freshwater systems, non-allopatric divergence may play a fundamental role in the generation of biodiversity. In this context, shifts between major prey types could constitute important factors explaining the biodiversity of marine taxa, particularly in groups with highly specialized diets...
October 26, 2017: BMC Evolutionary Biology
https://www.readbyqxmd.com/read/29046381/trunk-dental-tissue-evolved-independently-from-underlying-dermal-bony-plates-but-is-associated-with-surface-bones-in-living-odontode-bearing-catfish
#16
Carlos J Rivera-Rivera, Juan I Montoya-Burgos
Although oral dental tissue is a vertebrate attribute, trunk dental tissue evolved in several extinct vertebrate lineages but is rare among living species. The question of which processes trigger dental-tissue formation in the trunk remains open, and would shed light on odontogenesis evolution. Extra-oral dental structures (odontodes) in the trunk are associated with underlying dermal bony plates, leading us to ask whether the formation of trunk bony plates is necessary for trunk odontodes to emerge. To address this question, we focus on Loricarioidei: an extant, highly diverse group of catfish whose species all have odontodes...
October 25, 2017: Proceedings. Biological Sciences
https://www.readbyqxmd.com/read/29043053/ecological-niche-comparison-and-molecular-phylogeny-segregate-the-invasive-moss-species-campylopus-introflexus-leucobryaceae-bryophyta-from-its-closest-relatives
#17
Renato Gama, Jesús Aguirre-Gutiérrez, Michael Stech
The delimitation of the invasive moss species Campylopus introflexus from its closest relative, Campylopus pilifer, has been long debated based on morphology. Previous molecular phylogenetic reconstructions based on the nuclear ribosomal internal transcribed spacers (ITS) 1 and 2 showed that C. pilifer is split into an Old World and a New World lineage, but remained partly inconclusive concerning the relationships between these two clades and C. introflexus. Analyses of an extended ITS dataset displayed statistically supported incongruence between ITS1 and ITS2...
October 2017: Ecology and Evolution
https://www.readbyqxmd.com/read/29024751/phylogenomics-reveals-habitat-associated-body-shape-divergence-in-oryzias-woworae-species-group-teleostei-adrianichthyidae
#18
Daniel F Mokodongan, Javier Montenegro, Koji Mochida, Shingo Fujimoto, Asano Ishikawa, Ryo Kakioka, Lengxob Yong, Mulis, Renny K Hadiaty, Ixchel F Mandagi, Kawilarang W A Masengi, Nakatada Wachi, Yasuyuki Hashiguchi, Jun Kitano, Kazunori Yamahira
The Oryzias woworae species group, composed of O. asinua, O. wolasi, and O. woworae, is widely distributed in southeastern Sulawesi, an island in the Indo-Australian Archipelago. Deep-elongated body shape divergence is evident among these three species to the extent that it is used as a species-diagnostic character. These fishes inhabit a variety of habitats, ranging from upper streams to ponds, suggesting that the body shape divergence among the three species may reflect adaptation to local environments. First, our geometric morphometrics among eight local populations of this species group revealed that the three species cannot be separated by body shape and that riverine populations had more elongated bodies and longer caudal parts than lacustrine populations...
October 9, 2017: Molecular Phylogenetics and Evolution
https://www.readbyqxmd.com/read/29020180/molecular-tracing-of-the-geographical-origin-of-human-immunodeficiency-virus-type-1-infection-and-patterns-of-epidemic-spread-among-migrants-who-inject-drugs-in-athens
#19
Dimitrios Paraskevis, Evangelia Kostaki, Georgios K Nikolopoulos, Vana Sypsa, Mina Psichogiou, Julia Del Amo, Ioannis Hodges-Mameletzis, Dimitra Paraskeva, Athanasios Skoutelis, Meni Malliori, Leslie Williams, Samuel R Friedman, Georgios L Daikos, Angelos Hatzakis
Background: High numbers of human immunodeficiency virus type 1 (HIV-1) infections among people who inject drugs (PWID) have been diagnosed in Athens, Greece, since 2011. We aimed to trace the geographic origin of HIV-1 infection for migrants who inject drugs and to investigate whether transmissions occur more frequently among migrants than among Greek nationals. Methods: Multiple cross-sectional studies were pooled to assemble all persons diagnosed with HIV-1 in Greece between 1 January 2011 and 31 October 2014...
November 29, 2017: Clinical Infectious Diseases: An Official Publication of the Infectious Diseases Society of America
https://www.readbyqxmd.com/read/28993971/ancestral-sequence-reconstruction-with-maximum-parsimony
#20
Lina Herbst, Mareike Fischer
One of the main aims in phylogenetics is the estimation of ancestral sequences based on present-day data like, for instance, DNA alignments. One way to estimate the data of the last common ancestor of a given set of species is to first reconstruct a phylogenetic tree with some tree inference method and then to use some method of ancestral state inference based on that tree. One of the best-known methods both for tree inference and for ancestral sequence inference is Maximum Parsimony (MP). In this manuscript, we focus on this method and on ancestral state inference for fully bifurcating trees...
October 5, 2017: Bulletin of Mathematical Biology
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