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Ancestral state reconstruction

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https://www.readbyqxmd.com/read/29924339/phylogenomic-evidence-overturns-current-conceptions-of-social-evolution-in-wasps-vespidae
#1
P K Piekarski, J M Carpenter, A R Lemmon, E Moriarty Lemmon, B J Sharanowski
The hypothesis that eusociality originated once in Vespidae has shaped interpretation of social evolution for decades and has driven the supposition that preimaginal morphophysiological differences between castes were absent at the outset of eusociality. Many researchers also consider casteless nest-sharing an antecedent to eusociality. Together, these ideas endorse a stepwise progression of social evolution in wasps (solitary → casteless nest-sharing → eusociality with rudimentary behavioral castes → eusociality with preimaginal caste-biasing → morphologically differentiated castes)...
June 19, 2018: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/29922257/evolution-and-diversity-of-biosynthetic-gene-clusters-in-fusarium
#2
Koen Hoogendoorn, Lena Barra, Cees Waalwijk, Jeroen S Dickschat, Theo A J van der Lee, Marnix H Medema
Plant pathogenic fungi in the Fusarium genus cause severe damage to crops, resulting in great financial losses and health hazards. Specialized metabolites synthesized by these fungi are known to play key roles in the infection process, and to provide survival advantages inside and outside the host. However, systematic studies of the evolution of specialized metabolite-coding potential across Fusarium have been scarce. Here, we apply a combination of bioinformatic approaches to identify biosynthetic gene clusters (BGCs) across publicly available genomes from Fusarium , to group them into annotated families and to study gain/loss events of BGC families throughout the history of the genus...
2018: Frontiers in Microbiology
https://www.readbyqxmd.com/read/29899358/glutamine-89-is-a-key-residue-in-the-allosteric-modulation-of-human-serine-racemase-activity-by-atp
#3
Andrea V Canosa, Serena Faggiano, Marialaura Marchetti, Stefano Armao, Stefano Bettati, Stefano Bruno, Riccardo Percudani, Barbara Campanini, Andrea Mozzarelli
Serine racemase (SR) catalyses two reactions: the reversible racemisation of L-serine and the irreversible dehydration of L- and D-serine to pyruvate and ammonia. SRs are evolutionarily related to serine dehydratases (SDH) and degradative threonine deaminases (TdcB). Most SRs and TdcBs - but not SDHs - are regulated by nucleotides. SR binds ATP cooperatively and the nucleotide allosterically stimulates the serine dehydratase activity of the enzyme. A H-bond network comprising five residues (T52, N86, Q89, E283 and N316) and water molecules connects the active site with the ATP-binding site...
June 13, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29898985/the-unique-phylogenetic-position-of-a-novel-tick-borne-phlebovirus-ensures-an-ixodid-origin-of-the-genus-phlebovirus
#4
Keita Matsuno, Masahiro Kajihara, Ryo Nakao, Naganori Nao, Akina Mori-Kajihara, Mieko Muramatsu, Yongjin Qiu, Shiho Torii, Manabu Igarashi, Nodoka Kasajima, Keita Mizuma, Kentaro Yoshii, Hirofumi Sawa, Chihiro Sugimoto, Ayato Takada, Hideki Ebihara
The recent emergence of novel tick-borne RNA viruses has complicated the epidemiological landscape of tick-borne infectious diseases, posing a significant challenge to public health systems that seek to counteract tick-borne diseases. The identification of two novel tick-borne phleboviruses (TBPVs), severe fever with thrombocytopenia syndrome virus (SFTSV) and Heartland virus (HRTV), as causative agents of severe illness in humans has accelerated the investigation and discoveries of novel TBPVs. In the present study, we isolated a novel TBPV designated Mukawa virus (MKWV) from host-questing Ixodes persulcatus females captured in Japan...
June 27, 2018: MSphere
https://www.readbyqxmd.com/read/29872008/insights-into-the-evolution-of-bacterial-flagellar-motors-from-high-throughput-in-situ-electron-cryotomography-and-subtomogram-averaging
#5
Florian M Rossmann, Morgan Beeby
In situ structural information on molecular machines can be invaluable in understanding their assembly, mechanism and evolution. Here, the use of electron cryotomography (ECT) to obtain significant insights into how an archetypal molecular machine, the bacterial flagellar motor, functions and how it has evolved is described. Over the last decade, studies using a high-throughput, medium-resolution ECT approach combined with genetics, phylogenetic reconstruction and phenotypic analysis have revealed surprising structural diversity in flagellar motors...
June 1, 2018: Acta Crystallographica. Section D, Structural Biology
https://www.readbyqxmd.com/read/29869401/disentangling-historical-signal-and-pollinator-selection-on-the-micromorphology-of-flowers-an-example-from-the-floral-epidermis-of-the-nymphaeaceae
#6
Mario Coiro, Maria Rosaria Barone Lumaga
The family Nymphaeaceae includes most of the diversity among the ANA-grade angiosperms. Among the species of this family, floral structures and pollination strategies are quite varied. The genus Victoria, as well as subgenera Lotos and Hydrocallis in Nymphaea, presents night-blooming, scented flowers pollinated by scarab beetles. Such similar pollination strategies have led to macromorphological similarities among the flowers of these species, which could be interpreted as homologies or convergences based on different phylogenetic hypotheses about the relationships of these groups...
June 5, 2018: Plant Biology
https://www.readbyqxmd.com/read/29863984/harnessing-the-power-of-phylogenomics-to-disentangle-the-directionality-and-signatures-of-interkingdom-host-jumping-in-the-parasitic-fungal-genus-tolypocladium
#7
C Alisha Quandt, Will Patterson, Joseph W Spatafora
Host specialization is common among parasitic fungi; however, there are examples when transitions in host specificity between disparately related hosts have occurred. Here, we examine the interkingdom host jump from insect pathogenicity and mycoparasitism in Tolypocladium. Previous phylogenetic inferences made using only a few genes and with poor support reconstructed an ancestral character state of insect pathogenesis, a transition to mycoparasitism, and reversions to insect pathogenesis. To further explore the directionality and genes underlying the transitions in host, we sequenced two additional species of Tolypocladium (T...
January 2018: Mycologia
https://www.readbyqxmd.com/read/29860531/comparative-genomics-reveals-a-burst-of-homoplasy-free-numt-insertions
#8
Bin Liang, Ning Wang, Nan Li, Rebecca T Kimball, Edward L Braun
Mitochondrial DNA sequences are frequently transferred into the nuclear genome, giving rise to numts (nuclear mitochondrial DNA segments). In the absence of whole genomes, avian numts have been suggested to be rare and relatively short. We examined 64 bird genomes to test hypotheses regarding numt frequency, distribution among taxa, and likelihood of homoplasy. We discovered 100-fold variation in numt number across species. Two songbirds, Geospiza fortis (Darwin's finch) and Zonotrichia albicollis (white-throated sparrow) had the largest number of numts...
May 31, 2018: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/29808578/evidence-for-convergent-evolution-of-host-parasitic-manipulation-in-response-to-environmental-conditions
#9
Raquel G Loreto, João P M Araújo, Ryan M Kepler, Kimberly R Fleming, Corrie S Moreau, David P Hughes
Environmental conditions exert strong selection on animal behavior. We tested the hypothesis that the altered behavior of hosts due to parasitic manipulation is also subject to selection imposed by changes in environmental conditions over time. Our model system is ants manipulated by parasitic fungi to bite onto vegetation. We analyzed the correlation between forest type (tropical vs. temperate) and the substrate where the host bites (biting substrate: leaf vs. twigs), the time required for the fungi to reach reproductive maturity, and the phylogenetic relationship among specimens from tropical and temperate forests from different parts of the globe...
May 28, 2018: Evolution; International Journal of Organic Evolution
https://www.readbyqxmd.com/read/29807154/molecular-phylogeny-of-the-genus-fissidens-fissidentaceae-bryophyta-and-a-refinement-of-the-infrageneric-classification
#10
Tadashi Suzuki, Yuya Inoue, Hiromi Tsubota
The genus Fissidens (ca. 440 spp.) is one of the phylogenetically poorly studied groups of mosses (Bryophyta). While various classifications of this genus have been proposed, no attempt at a classification of the genus based on combined molecular and morphological evidence has been made. Here, we present for the first time a comprehensive phylogenetic tree consisting of 50 representatives of Fissidens, reconstructed using sequence data from chloroplast rbcL and rps4 genes. Ancestral state reconstructions provide three clear apomorphies within Fissidens: peristome teeth, limbidium and chromosome number...
May 25, 2018: Molecular Phylogenetics and Evolution
https://www.readbyqxmd.com/read/29804807/early-evolution-of-modern-birds-structured-by-global-forest-collapse-at-the-end-cretaceous-mass-extinction
#11
Daniel J Field, Antoine Bercovici, Jacob S Berv, Regan Dunn, David E Fastovsky, Tyler R Lyson, Vivi Vajda, Jacques A Gauthier
The fossil record and recent molecular phylogenies support an extraordinary early-Cenozoic radiation of crown birds (Neornithes) after the Cretaceous-Paleogene (K-Pg) mass extinction [1-3]. However, questions remain regarding the mechanisms underlying the survival of the deepest lineages within crown birds across the K-Pg boundary, particularly since this global catastrophe eliminated even the closest stem-group relatives of Neornithes [4]. Here, ancestral state reconstructions of neornithine ecology reveal a strong bias toward taxa exhibiting predominantly non-arboreal lifestyles across the K-Pg, with multiple convergent transitions toward predominantly arboreal ecologies later in the Paleocene and Eocene...
May 12, 2018: Current Biology: CB
https://www.readbyqxmd.com/read/29795540/methods-for-phylogenetic-analysis-of-microbiome-data
#12
REVIEW
Alex D Washburne, James T Morton, Jon Sanders, Daniel McDonald, Qiyun Zhu, Angela M Oliverio, Rob Knight
How does knowing the evolutionary history of microorganisms affect our analysis of microbiological datasets? Depending on the research question, the common ancestry of microorganisms can be a source of confounding variation, or a scaffolding used for inference. For example, when performing regression on traits, common ancestry is a source of dependence among observations, whereas when searching for clades with correlated abundances, common ancestry is the scaffolding for inference. The common ancestry of microorganisms and their genes are organized in trees-phylogenies-which can and should be incorporated into analyses of microbial datasets...
June 2018: Nature Microbiology
https://www.readbyqxmd.com/read/29778724/a-tangle-of-forms-and-phylogeny-extensive-morphological-homoplasy-and-molecular-clock-heterogeneity-in-bonnetina-and-related-tarantulas
#13
David Ortiz, Oscar F Francke, Jason E Bond
Tarantula spider systematics has long been considered problematic. Species diagnosis and phylogenetic hypotheses have historically relied on morphological features, which are known to be relatively conserved and/or highly homoplastic across the family. Morphology-based attempts to clarify the phylogeny of the highly diverse New World Theraphosinae, have only been moderately successful, and the time-frame of tarantulas' evolution is nearly terra incognita. Here we present a molecular phylogenetic analysis of the Theraphosinae genus Bonnetina and related lineages, employing one mitochondrial (COI) and five nuclear (ITS1, EF1G, MID1IP1, MRPL44, and I3568) loci...
May 17, 2018: Molecular Phylogenetics and Evolution
https://www.readbyqxmd.com/read/29774232/multiple-origins-of-green-blood-in-new-guinea-lizards
#14
Zachary B Rodriguez, Susan L Perkins, Christopher C Austin
Several species of lizards from the megadiverse island of New Guinea have evolved green blood. An unusually high concentration of the green bile pigment biliverdin in the circulatory system of these lizards makes the blood, muscles, bones, tongue, and mucosal tissues bright green in color, eclipsing the crimson color from their red blood cells. This is a remarkable physiological feature because bile pigments are toxic physiological waste products of red blood cell catabolism and, when chronically elevated, cause jaundice in humans and all other vertebrates...
May 2018: Science Advances
https://www.readbyqxmd.com/read/29771364/broad-genomic-sampling-reveals-a-smut-pathogenic-ancestry-of-the-fungal-clade-ustilaginomycotina
#15
Teeratas Kijpornyongpan, Stephen J Mondo, Kerrie Barry, Laura Sandor, Juna Lee, Anna Lipzen, Jasmyn Pangilinan, Kurt LaButti, Matthieu Hainaut, Bernard Henrissat, Igor V Grigoriev, Joseph W Spatafora, M Catherine Aime
Ustilaginomycotina is home to a broad array of fungi including important plant pathogens collectively called smut fungi. Smuts are biotrophs that produce characteristic perennating propagules called teliospores, one of which, Ustilago maydis, is a model genetic organism. Broad exploration of smut biology has been hampered by limited phylogenetic resolution of Ustilaginiomycotina as well as an overall lack of genomic data for members of this subphylum. In this study, we sequenced eight Ustilaginomycotina genomes from previously unrepresented lineages, deciphered ordinal-level phylogenetic relationships for the subphylum, and performed comparative analyses...
May 15, 2018: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/29765681/-salishicetus-meadi-a-new-aetiocetid-from-the-late-oligocene-of-washington-state-and-implications-for-feeding-transitions-in-early-mysticete-evolution
#16
Carlos Mauricio Peredo, Nicholas D Pyenson
Living baleen whales, or Mysticeti, lack teeth and instead feed using keratinous baleen plates to sieve prey-laden water. This feeding strategy is profoundly different from that of their toothed ancestors, which processed prey using the differentiated dentition characteristic of mammals. The fossil record of mysticetes reveals stem members that include extinct taxa with dentition, illuminating the morphological states that preceded the loss of teeth and the subsequent origin of baleen. The relationships among stem mysticetes, including putative clades such as Mammalodontidae and Aetiocetidae, remain debatable...
April 2018: Royal Society Open Science
https://www.readbyqxmd.com/read/29746704/the-evolutionary-history-of-colour-polymorphism-in-ischnura-damselflies
#17
Rosa A Sánchez-Guillén, Adolfo Cordero-Rivera, Anais Rivas-Torres, Maren Wellenreuther, Seth Bybee, Bengt Hansson, María I Velasquez-Vélez, Emilio Realpe, Jesús R Chávez-Ríos, Fabricio Villalobos, Henri Dumont
A major challenge in evolutionary biology consists of understanding how genetic and phenotypic variation is created and maintained. In the present study, we investigated the origin(s) and evolutionary patterns of the female-limited colour polymorphism in ischnuran damselflies. These consist of the presence of one to three colour morphs: one androchrome morph with a colouration that is similar to the male, and two gynochrome morphs (infuscans and aurantiaca) with female-specific colouration. We (i) documented the colour and mating system of 44 of the 75 taxa within the genus Ischnura, (ii) reconstructed the evolutionary history of colour and mating system to identify the ancestral state, (iii) evaluated the stability of the colour morph status over time, and (iv) tested for a correlation between colour and mating system...
May 10, 2018: Journal of Evolutionary Biology
https://www.readbyqxmd.com/read/29742313/phylogenetic-comparative-analysis-supports-aposematic-colouration-body-size-association-in-millipede-assassins-hemiptera-reduviidae-ectrichodiinae
#18
Michael Forthman, Christiane Weirauch
The diversity of colour patterns and its importance in interactions with the environment make colouration in animals an intriguing research focus. Aposematic colouration is positively correlated with body size in certain groups of animals, suggesting that warning colours are more effective or that crypsis is harder to achieve in larger animals. Surprisingly, this relationship has not been recovered in studies investigating insects, which may have been confounded by a focus on aposematic taxa that are also gregarious...
May 9, 2018: Journal of Evolutionary Biology
https://www.readbyqxmd.com/read/29733978/molecular-phylogeny-of-maldanidae-annelida-multiple-losses-of-tube-capping-plates-and-evolutionary-shifts-in-habitat-depth
#19
Genki Kobayashi, Ryutaro Goto, Tsuyoshi Takano, Shigeaki Kojima
Inter-familial relationships of the phylum Annelida have been widely studied using molecular phylogenetic/genomic approaches; however, intra-familial relationships remain scarcely investigated in most annelid families. The Maldanidae (bamboo worms) comprise more than 280 species of 40 genera and six subfamilies that occur in various environments from intertidal to hadal zones. Within this family, the taxon Maldanoplaca, which consists of four subfamilies (Maldaninae, Notoproctinae, Nicomachinae, and Euclymeninae), was proposed based on the presence of cephalic and anal plates...
May 4, 2018: Molecular Phylogenetics and Evolution
https://www.readbyqxmd.com/read/29733432/evolution-on-the-backbone-apocynaceae-phylogenomics-and-new-perspectives-on-growth-forms-flowers-and-fruits
#20
Mark Fishbein, Tatyana Livshultz, Shannon C K Straub, André O Simões, Julien Boutte, Angela McDonnell, Abbey Foote
PREMISE OF THE STUDY: We provide the largest phylogenetic analyses to date of Apocynaceae in terms of taxa and molecular data as a framework for analyzing the evolution of vegetative and reproductive traits. METHODS: We produced maximum-likelihood phylogenies of Apocynaceae using 21 plastid loci sampled from 1045 species (nearly 25% of the family) and complete plastomes from 73 species. We reconstructed ancestral states and used model comparisons in a likelihood framework to analyze character evolution across Apocynaceae...
March 2018: American Journal of Botany
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