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Diversification

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https://www.readbyqxmd.com/read/29451915/synchronic-historical-patterns-of-species-diversification-in-seasonal-aplocheiloid-killifishes-of-the-semi-arid-brazilian-caatinga
#1
Wilson J E M Costa, Pedro F Amorim, José Leonardo O Mattos
The Caatinga is the largest nucleus of seasonally dry tropical forests in South America, but little is known about the evolutionary history and biogeography of endemic organisms. Evolutionary diversification and distribution of terrestrial vertebrates endemic to the Caatinga have been explained by palaeogeographical Neogene episodes, mostly related to changes in the course of the São Francisco River, the largest river in the region. Our objective is to estimate the timing of divergence of two endemic groups of short-lived seasonal killifishes inhabiting all ecoregions of the Caatinga, testing the occurrence of synchronic events of spatial diversification in light of available data on regional palaeogeography...
2018: PloS One
https://www.readbyqxmd.com/read/29451903/stability-lies-in-flowers-plant-diversification-mediating-shifts-in-arthropod-food-webs
#2
Marcelo Mendes Haro, Luís Cláudio Paterno Silveira, Andrew Wilby
Arthropod community composition in agricultural landscapes is dependent on habitat characteristics, such as plant composition, landscape homogeneity and the presence of key resources, which are usually absent in monocultures. Manipulating agroecosystems through the insertion of in-field floral resources is a useful technique to reduce the deleterious effects of habitat simplification. Food web analysis can clarify how the community reacts to the presence of floral resources which favour ecosystem services such as biological control of pest species...
2018: PloS One
https://www.readbyqxmd.com/read/29449488/natural-noncanonical-protein-splicing-yields-products-with-diverse-%C3%AE-amino-acid-residues
#3
Brandon I Morinaka, Edgars Lakis, Marjan Verest, Maximilian J Helf, Thibault Scalvenzi, Anna L Vagstad, James Sims, Shinichi Sunagawa, Muriel Gugger, Jörn Piel
Current textbook knowledge holds that the structural scope of ribosomal biosynthesis is based exclusively on α-amino acid backbone topology. Here we report the genome-guided discovery of bacterial pathways that posttranslationally create β-amino acid-containing products. The transformation is widespread in bacteria and is catalyzed by an enzyme belonging to a previously uncharacterized radical S -adenosylmethionine family. We show that the β-amino acids result from an unusual protein splicing process involving backbone carbon-carbon bond cleavage and net excision of tyramine...
February 16, 2018: Science
https://www.readbyqxmd.com/read/29448063/an-ant-genus-group-prenolepis-illuminates-the-biogeography-and-drivers-of-insect-diversification-in-the-indo-pacific
#4
Pável Matos-Maraví, Ronald M Clouse, Eli M Sarnat, Evan P Economo, John S LaPolla, Michaela Borovanska, Christian Rabeling, Jesse Czekanski-Moir, Fransina Latumahina, Edward O Wilson, Milan Janda
The Malay Archipelago and the tropical South Pacific (hereafter the Indo-Pacific region) are considered biodiversity hotspots, yet a general understanding of the origins and diversification of species-rich groups in the region remains elusive. We aimed to test hypotheses for the evolutionary processes driving insect species diversity in the Indo-Pacific using a higher-level and comprehensive phylogenetic hypothesis for an ant clade consisting of seven genera. We estimated divergence times and reconstructed the biogeographical history of ant species in the Prenolepis genus-group (Formicidae: Formicinae: Lasiini)...
February 12, 2018: Molecular Phylogenetics and Evolution
https://www.readbyqxmd.com/read/29447391/comparative-analysis-of-epidermal-differentiation-genes-of-crocodilians-suggests-new-models-for-the-evolutionary-origin-of-avian-feather-proteins
#5
Karin Brigit Holthaus, Bettina Strasser, Julia Lachner, Supawadee Sukseree, Wolfgang Sipos, Anton Weissenbacher, Erwin Tschachler, Lorenzo Alibardi, Leopold Eckhart
The epidermis of amniotes forms a protective barrier against the environment and the differentiation program of keratinocytes, the main cell type in the epidermis, has undergone specific alterations in the course of adaptation of amniotes to a broad variety of environments and lifestyles. The epidermal differentiation complex (EDC) is a cluster of genes expressed at late stages of keratinocyte differentiation in both sauropsids and mammals. In the present study we identified and analyzed the crocodilian equivalent of the EDC...
February 12, 2018: Genome Biology and Evolution
https://www.readbyqxmd.com/read/29447228/chromosomal-distribution-of-pta-535-pta-86-pta-713-35s-rdna-repetitive-sequences-in-interspecific-hexaploid-hybrids-of-common-wheat-triticum-aestivum-l-and-spelt-triticum-spelta-l
#6
Klaudia Goriewa-Duba, Adrian Duba, Michał Kwiatek, Halina Wiśniewska, Urszula Wachowska, Marian Wiwart
Fluorescent in situ hybridization (FISH) relies on fluorescent-labeled probes to detect specific DNA sequences in the genome, and it is widely used in cytogenetic analyses. The aim of this study was to determine the karyotype of T. aestivum and T. spelta hybrids and their parental components (three common wheat cultivars and five spelt breeding lines), to identify chromosomal aberrations in the evaluated wheat lines, and to analyze the distribution of polymorphisms of repetitive sequences in the examined hybrids...
2018: PloS One
https://www.readbyqxmd.com/read/29447216/genome-mining-of-streptomyces-scabrisporus-nf3-reveals-symbiotic-features-including-genes-related-to-plant-interactions
#7
Corina Diana Ceapă, Melissa Vázquez-Hernández, Stefany Daniela Rodríguez-Luna, Angélica Patricia Cruz Vázquez, Verónica Jiménez Suárez, Romina Rodríguez-Sanoja, Elena R Alvarez-Buylla, Sergio Sánchez
Endophytic bacteria are wide-spread and associated with plant physiological benefits, yet their genomes and secondary metabolites remain largely unidentified. In this study, we explored the genome of the endophyte Streptomyces scabrisporus NF3 for discovery of potential novel molecules as well as genes and metabolites involved in host interactions. The complete genomes of seven Streptomyces and three other more distantly related bacteria were used to define the functional landscape of this unique microbe. The S...
2018: PloS One
https://www.readbyqxmd.com/read/29446804/t6ss-intraspecific-competition-orchestrates-vibrio-cholerae-genotypic-diversity
#8
REVIEW
Benjamin Kostiuk, Daniel Unterweger, Daniele Provenzano, Stefan Pukatzki
Vibrio cholerae is a diverse species that inhabits a wide range of environments from copepods in brackish water to the intestines of humans. In order to remain competitive, V. cholerae uses the versatile type-VI secretion system (T6SS) to secrete anti-prokaryotic and anti-eukaryotic effectors. In addition to competing with other bacterial species, V. cholerae strains also compete with one another. Some strains are able to coexist, and are referred to as belonging to the same compatibility group. Challenged by diverse competitors in various environments, different V...
September 2017: International Microbiology: the Official Journal of the Spanish Society for Microbiology
https://www.readbyqxmd.com/read/29446800/biology-of-vibrio-cholera-editorial-overview
#9
EDITORIAL
Felipe Cava
In this monographic issue, we have the pleasure to present contributions from six of the leading laboratories at the forefront of Vibrio cholerae genetics, ecology and evolution, together with a brief tribute by Diego Romero to Doctor Jaime Ferrán y Clua, a pioneering Spanish bacteriologist who developed the first vaccine against this pathogen. V. cholerae is a free-living aquatic bacterium that interacts with and infects a variety of organisms. In humans it causes cholera, the deadly diarrhoea that was responsible for millions of deaths during seven pandemics since 1817, and still thousands every year...
September 2017: International Microbiology: the Official Journal of the Spanish Society for Microbiology
https://www.readbyqxmd.com/read/29446460/a-multivariate-ecogeographic-analysis-of-macaque-craniodental-variation
#10
Nicole D S Grunstra, Philipp Mitteroecker, Robert A Foley
OBJECTIVES: To infer the ecogeographic conditions that underlie the evolutionary diversification of macaques, we investigated the within- and between-species relationships of craniodental dimensions, geography, and environment in extant macaque species. We studied evolutionary processes by contrasting macroevolutionary patterns, phylogeny, and within-species associations. MATERIALS AND METHODS: Sixty-three linear measurements of the permanent dentition and skull along with data about climate, ecology (environment), and spatial geography were collected for 711 specimens of 12 macaque species and analyzed by a multivariate approach...
February 15, 2018: American Journal of Physical Anthropology
https://www.readbyqxmd.com/read/29445148/temporal-requirements-for-isl1-in-sympathetic-neuron-proliferation-differentiation-and-diversification
#11
Qingquan Zhang, Ru Huang, Youqiong Ye, Xiaoxia Guo, Jun Lu, Fugui Zhu, Xiaohui Gong, Qitong Zhang, Jie Yan, Lina Luo, Shaowei Zhuang, Yihan Chen, Xiaodong Zhao, Sylvia M Evans, Cizhong Jiang, Xingqun Liang, Yunfu Sun
Malformations of the sympathetic nervous system have been associated with cardiovascular instability, gastrointestinal dysfunction, and neuroblastoma. A better understanding of the factors regulating sympathetic nervous system development is critical to the development of potential therapies. Here, we have uncovered a temporal requirement for the LIM homeodomain transcription factor ISL1 during sympathetic nervous system development by the analysis of two mutant mouse lines: an Isl1 hypomorphic line and mice with Isl1 ablated in neural crest lineages...
February 14, 2018: Cell Death & Disease
https://www.readbyqxmd.com/read/29445119/conservation-of-a-ph-sensitive-structure-in-the-c-terminal-region-of-spider-silk-extends-across-the-entire-silk-gene-family
#12
Michelle Strickland, Victor Tudorica, Milan Řezáč, Neil R Thomas, Sara L Goodacre
Spiders produce multiple silks with different physical properties that allow them to occupy a diverse range of ecological niches, including the underwater environment. Despite this functional diversity, past molecular analyses show a high degree of amino acid sequence similarity between C-terminal regions of silk genes that appear to be independent of the physical properties of the resulting silks; instead, this domain is crucial to the formation of silk fibers. Here, we present an analysis of the C-terminal domain of all known types of spider silk and include silk sequences from the spider Argyroneta aquatica, which spins the majority of its silk underwater...
February 15, 2018: Heredity
https://www.readbyqxmd.com/read/29444377/a-biomechanical-analysis-of-prognathous-and-orthognathous-insect-head-capsules-evidence-for-a-many-to-one-mapping-of-ridge-strain-to-head-strain
#13
Alexander Blanke, Manuel Pinheiro, Peter J Watson, Michael J Fagan
Insect head shapes are remarkably variable but the influences of these changes on biomechanical performance are unclear. Among "basal" winged insects, such as dragonflies, mayflies, earwigs, and stoneflies, some of the most prominent anatomical changes are the general mouthpart orientation, eye size and the connection of the endoskeleton to the head. Here, we assess these variations as well as differing ridge and sclerite configurations using modern engineering methods including multibody dynamics modelling and finite element analysis in order to quantify and compare the influence of anatomical changes on strain in particular head regions and the whole head...
February 14, 2018: Journal of Evolutionary Biology
https://www.readbyqxmd.com/read/29444302/rab-gtpases-in-the-basal-land-plant-marchantia-polymorpha
#14
Naoki Minamino, Takehiko Kanazawa, Atsuko Era, Kazuo Ebine, Akihiko Nakano, Takashi Ueda
The RAB GTPase is an evolutionarily conserved machinery component of membrane trafficking, which is the fundamental system for cell viability and higher-order biological functions. The composition of RAB GTPases in each organism is closely related to the complexity and organization of the membrane-trafficking pathway, which has been developed uniquely to realize the organism-specific membrane trafficking system. Comparative genomics has suggested that terrestrialization and/or multicellularization were associated with the expansion of membrane trafficking pathways in green plants, which has yet to be validated in basal land plant lineages...
February 10, 2018: Plant & Cell Physiology
https://www.readbyqxmd.com/read/29443947/vertebrate-genome-evolution-in-the-light-of-fish-cytogenomics-and-rdnaomics
#15
REVIEW
Radka Symonová, W Mike Howell
To understand the cytogenomic evolution of vertebrates, we must first unravel the complex genomes of fishes, which were the first vertebrates to evolve and were ancestors to all other vertebrates. We must not forget the immense time span during which the fish genomes had to evolve. Fish cytogenomics is endowed with unique features which offer irreplaceable insights into the evolution of the vertebrate genome. Due to the general DNA base compositional homogeneity of fish genomes, fish cytogenomics is largely based on mapping DNA repeats that still represent serious obstacles in genome sequencing and assembling, even in model species...
February 14, 2018: Genes
https://www.readbyqxmd.com/read/29440180/resistance-promoting-effects-of-ependymoma-treatment-revealed-through-genomic-analysis-of-multiple-recurrences-in-a-single-patient
#16
Christopher A Miller, Sonika Dahiya, Tiandao Li, Robert Fulton, Matthew D Smyth, Gavin P Dunn, Joshua B Rubin, Elaine R Mardis
BACKGROUND: As in other brain tumors, multiple recurrences after complete resection and irradiation of supratentorial ependymoma are common and frequently result in patient death. This standard-of-care treatment was established in the pre-genomic era without the ability to evaluate the effect that mutagenic therapies may exert on tumor evolution and in promoting resistance, recurrence, and death. We seized a rare opportunity to characterize treatment effects and the evolution of a single patient's ependymoma across four recurrences after different therapies...
February 13, 2018: Cold Spring Harbor Molecular Case Studies
https://www.readbyqxmd.com/read/29438538/testing-the-role-of-the-red-queen-and-court-jester-as-drivers-of-the-macroevolution-of-apollo-butterflies
#17
Fabien L Condamine, Jonathan Rolland, Sebastian Höhna, Felix A H Sperling, Isabel Sanmartín
In macroevolution, the Red Queen (RQ) model posits that biodiversity dynamics depend mainly on species-intrinsic biotic factors such as interactions among species or life-history traits, while the Court Jester (CJ) model states that extrinsic environmental abiotic factors have a stronger role. Until recently, a lack of relevant methodological approaches has prevented the unraveling of contributions from these two types of factors to the evolutionary history of a lineage. Here we take advantage of the rapid development of new macroevolution models that tie diversification rates to changes in paleoenvironmental (extrinsic) and/or biotic (intrinsic) factors...
February 9, 2018: Systematic Biology
https://www.readbyqxmd.com/read/29438308/diversification-of-secondary-metabolite-biosynthetic-gene-clusters-coincides-with-lineage-divergence-in-streptomyces
#18
Mallory J Choudoir, Charles Pepe-Ranney, Daniel H Buckley
We have identified Streptomyces sister-taxa which share a recent common ancestor and nearly identical small subunit (SSU) rRNA gene sequences, but inhabit distinct geographic ranges demarcated by latitude and have sufficient genomic divergence to represent distinct species. Here, we explore the evolutionary dynamics of secondary metabolite biosynthetic gene clusters (SMGCs) following lineage divergence of these sister-taxa. These sister-taxa strains contained 310 distinct SMGCs belonging to 22 different gene cluster classes...
February 13, 2018: Antibiotics
https://www.readbyqxmd.com/read/29436503/diversity-change-during-the-rise-of-tetrapods-and-the-impact-of-the-carboniferous-rainforest-collapse
#19
Emma M Dunne, Roger A Close, David J Button, Neil Brocklehurst, Daniel D Cashmore, Graeme T Lloyd, Richard J Butler
The Carboniferous and early Permian were critical intervals in the diversification of early four-limbed vertebrates (tetrapods), yet the major patterns of diversity and biogeography during this time remain unresolved. Previous estimates suggest that global tetrapod diversity rose continuously across this interval and that habitat fragmentation following the 'Carboniferous rainforest collapse' (CRC) drove increased endemism among communities. However, previous work failed to adequately account for spatial and temporal biases in sampling...
February 14, 2018: Proceedings. Biological Sciences
https://www.readbyqxmd.com/read/29435262/ecological-drivers-of-song-evolution-in-birds-disentangling-the-effects-of-habitat-and-morphology
#20
Elizabeth Perrault Derryberry, Nathalie Seddon, Graham Earnest Derryberry, Santiago Claramunt, Glenn Fairbanks Seeholzer, Robb Thomas Brumfield, Joseph Andrew Tobias
Environmental differences influence the evolutionary divergence of mating signals through selection acting either directly on signal transmission ("sensory drive") or because morphological adaptation to different foraging niches causes divergence in "magic traits" associated with signal production, thus indirectly driving signal evolution. Sensory drive and magic traits both contribute to variation in signal structure, yet we have limited understanding of the relative role of these direct and indirect processes during signal evolution...
February 2018: Ecology and Evolution
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