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Todd J Widhelm, Francesca R Bertoletti, Matt J Asztalos, Joel A Mercado-Díaz, Jen-Pan Huang, Bibiana Moncada, Robert Lücking, Nicolas Magain, Emmanuël Sérusiaux, Bernard Goffinet, Nicholas Crouch, Roberta Mason-Gamer, H Thorsten Lumbsch
A major challenge to evolutionary biologists is to understand how biodiversity is distributed through space and time and across the tree of life. Diversification of organisms is influenced by many factors that act at different times and geographic locations but it is still not clear which have a significant impact and how drivers interact. To study diversification, we chose the lichen genus Sticta, by sampling through most of the global range and producing a time tree. We estimate that Sticta originated about 30 million years ago, but biogoegraphic analysis was unclear in estimating the origin of the genus...
April 12, 2018: Molecular Phylogenetics and Evolution
Thomas E White
Iridescence, a change in hue with viewing or illumination geometry, is a common feature of colour patterns in nature, though its significance remains elusive. Recent studies of floral iridescence reveal its functional versatility in enhancing the detection and discrimination of resources by insect viewers, as well as augmenting higher-level processes of memory and perception. Coupled with a known evolutionary lability, these results suggest intriguing possibilities for how this optical curiosity may act as a key to diversification...
April 11, 2018: Trends in Ecology & Evolution
João P Morais-Silva, Alessandra V de Oliveira, Thomaz M C Fabrin, Nathália Alves Diamante, Sônia M A P Prioli, Augusto Frota, Weferson J da Graça, Alberto J Prioli
The current analysis investigates whether the uplift of the Serra da Esperança and the Ponta Grossa Arch in the Serra Geral resulted in ichthyofaunistic changes in adjacent basins. For this, we describe the phylogeographic structure among populations of Trichomycterus collected in hydrographic basins in southern Brazil by using partial nucleotide sequences of the mitochondrial gene Cytochrome C Oxidase subunit I. Analyses revealed that the nomenclature Trichomycterus davisi fails to contain the whole genetic diversity range found in the collected specimens and indicates at least six genetic lineages in Trichomycterus...
March 13, 2018: Zebrafish
Ping-Li Liu, Yuan Huang, Peng-Hao Shi, Meng Yu, Jian-Bo Xie, LuLu Xie
Lectin receptor-like kinases (LecRLKs) play important roles in plant development and stress responses. Although genome-wide studies of LecRLKs have been performed in several species, a comprehensive analysis including evolutionary, structural and functional analysis has not been carried out in soybean (Glycine max). In this study, we identified 185 putative LecRLK genes in the soybean genome, including 123 G-type, 60 L-type and 2 C-type LecRLK genes. Tandem duplication and segmental duplication appear to be the main mechanisms of gene expansion in the soybean LecRLK (GmLecRLK) gene family...
April 12, 2018: Scientific Reports
Robert H Proctor, Susan P McCormick, Hye-Seon Kim, Rosa E Cardoza, April M Stanley, Laura Lindo, Amy Kelly, Daren W Brown, Theresa Lee, Martha M Vaughan, Nancy J Alexander, Mark Busman, Santiago Gutiérrez
Trichothecenes are a family of terpenoid toxins produced by multiple genera of fungi, including plant and insect pathogens. Some trichothecenes produced by the fungus Fusarium are among the mycotoxins of greatest concern to food and feed safety because of their toxicity and frequent occurrence in cereal crops, and trichothecene production contributes to pathogenesis of some Fusarium species on plants. Collectively, fungi produce over 150 trichothecene analogs: i.e., molecules that share the same core structure but differ in patterns of substituents attached to the core structure...
April 2018: PLoS Pathogens
Patricia J Simner, Annukka A R Antar, Stephanie Hao, James Gurtowski, Pranita D Tamma, Clare Rock, Belita N A Opene, Tsigereda Tekle, Karen C Carroll, Michael C Schatz, Winston Timp
Objectives: In this study, we characterize a concurrent disseminated infection with a virulent hypermucoviscous (HMV) Klebsiella pneumoniae and an OXA-181-producing XDR K. pneumoniae from a patient with recent hospitalization in India. During exposure to meropenem therapy, the highly susceptible HMV K. pneumoniae became resistant to carbapenems, consistent with the acquisition of blaOXA-181. Methods: Twelve K. pneumoniae isolates were recovered from the patient and the hospital room environment over a 3 month hospitalization...
April 10, 2018: Journal of Antimicrobial Chemotherapy
Kurt B Petersen, Martin Burd
Heterospory was a pivotal evolutionary innovation for land plants, but it has never been clear why it evolved. We used the geographic distributions of 114 species of the heterosporous lycophyte Selaginella to explore the functional ecology of microspore and megaspore size, traits that would be correlated with many aspects of a species' regeneration niche. We characterized habitats at a global scale using leaf area index (LAI), a measure of foliage density and thus shading, and net primary productivity (NPP), a measure of growth potential...
April 12, 2018: Evolution; International Journal of Organic Evolution
José Lorente-Sorolla, Marta Truchado-Garcia, Kimberly J Perry, Jonathan Q Henry, Cristina Grande
Background: Sall (Spalt-like) proteins are zinc-finger transcription factors involved in a number of biological processes. They have only been studied in a few model organisms, such as Drosophila melanogaster , Caenorhabditis elegans , Schmidtea mediterranea and some vertebrates. Further taxon sampling is critical to understand the evolution and diversification of this protein and its functional roles in animals. Results: Using genome and transcriptome mining, we confirmed the presence of sall genes in a range of additional animal taxa, for which their presence had not yet been described...
2018: EvoDevo
Sophie F Roerink, Nobuo Sasaki, Henry Lee-Six, Matthew D Young, Ludmil B Alexandrov, Sam Behjati, Thomas J Mitchell, Sebastian Grossmann, Howard Lightfoot, David A Egan, Apollo Pronk, Niels Smakman, Joost van Gorp, Elizabeth Anderson, Stephen J Gamble, Chris Alder, Marc van de Wetering, Peter J Campbell, Michael R Stratton, Hans Clevers
Every cancer originates from a single cell. During expansion of the neoplastic cell population, individual cells acquire genetic and phenotypic differences from each other. Here, to investigate the nature and extent of intra-tumour diversification, we characterized organoids derived from multiple single cells from three colorectal cancers as well as from adjacent normal intestinal crypts. Colorectal cancer cells showed extensive mutational diversification and carried several times more somatic mutations than normal colorectal cells...
April 11, 2018: Nature
Laurent A F Frantz, Anna Rudzinski, Abang Mansyursyah Surya Nugraha, Allowen Evin, James Burton, Ardern Hulme-Beaman, Anna Linderholm, Ross Barnett, Rodrigo Vega, Evan K Irving-Pease, James Haile, Richard Allen, Kristin Leus, Jill Shephard, Mia Hillyer, Sarah Gillemot, Jeroen van den Hurk, Sharron Ogle, Cristina Atofanei, Mark G Thomas, Friederike Johansson, Abdul Haris Mustari, John Williams, Kusdiantoro Mohamad, Chandramaya Siska Damayanti, Ita Djuwita Wiryadi, Dagmar Obbles, Stephano Mona, Hally Day, Muhammad Yasin, Stefan Meker, Jimmy A McGuire, Ben J Evans, Thomas von Rintelen, Simon Y W Ho, Jeremy B Searle, Andrew C Kitchener, Alastair A Macdonald, Darren J Shaw, Robert Hall, Peter Galbusera, Greger Larson
The high degree of endemism on Sulawesi has previously been suggested to have vicariant origins, dating back to 40 Ma. Recent studies, however, suggest that much of Sulawesi's fauna assembled over the last 15 Myr. Here, we test the hypothesis that more recent uplift of previously submerged portions of land on Sulawesi promoted diversification and that much of its faunal assemblage is much younger than the island itself. To do so, we combined palaeogeographical reconstructions with genetic and morphometric datasets derived from Sulawesi's three largest mammals: the babirusa, anoa and Sulawesi warty pig...
April 11, 2018: Proceedings. Biological Sciences
Paul Leo Greenwood, Drewe M Ferguson
Beef production extends over almost half of Australia, with about 47,000 cattle producers that contribute about 20% ($A12.7 billion GVP) of the total value of farm production in Australia. Australia is one of the world's most efficient producers of cattle and was the world's third largest beef exporter in 2016. The Australian beef industry had 25 million head of cattle in 2016-17, with a national beef breeding herd of 11.5 million head. Australian beef production includes pasture based cow-calf systems, a backgrounding or grow-out period on pasture, and feedlot or pasture finishing...
April 12, 2018: Asian-Australasian Journal of Animal Sciences
Christine A Arbour, Thilini D Kondasinghe, Hasina Y Saraha, Teanna L Vorlicek, Jennifer L Stockdill
C-Terminal cysteine peptide acids are difficult to access without epimerization of the cysteine α-stereocenter. Diversification of the C-terminus after solid-phase peptide synthesis poses an even greater challenge because of the proclivity of the cysteine α-stereocenter to undergo deprotonation upon activation of the C-terminal carboxylic acid. We present herein two general strategies to access C-terminal cysteine peptide derivatives without detectable epimerization, diketopiperazine formation, or piperidinylalanine side products...
January 14, 2018: Chemical Science
Alexandra K Brooks, Thomas Gaj
CRISPR-Cas9 is a versatile tool for genome engineering that has revolutionized biotechnology and is poised to impact medicine. Recent advances in the identification of unique CRISPR systems, as well as the re-engineering of the Cas9 protein for expanded function, has enabled the diversification of the CRISPR genome engineering toolbox. In this review, we highlight these innovations and discuss how advances in CRISPR technology can lead to breakthroughs in the field of gene therapy.
April 4, 2018: Current Opinion in Biotechnology
Kenisha Russell Jonsson, Neli Demireva
Concerns about the diversification of Britain, and its impact on social capital and health are widely debated. The literature has however produced a fuzzy discourse, full of assumptions and claims that are rarely tested. We attempt to disentangle some of these assumptions by providing empirical evidence on the mediating and moderating influence of inter-ethnic conflict and contact, and examine whether they underlie the erosion of health among minorities and white British respondents residing in diverse local areas...
March 7, 2018: Social Science & Medicine
Radim Šumbera, Jarmila Krásová, Leonid A Lavrenchenko, Sewnet Mengistu, Afework Bekele, Ondřej Mikula, Josef Bryja
Root-rats of the genus Tachyoryctes (Spalacidae) are subterranean herbivores occupying open humid habitats in the highlands of Eastern Africa. There is strong disagreement about species diversity of the genus, because some authors accept two species, while others more than ten. Species with relatively high surface activity, the giant root-rat Tachyoryctes macrocephalus, which is by far largest member of the genus, and the more fossorial African root-rat Tachyoryctes splendens, which eventually has been divided up to 12-13 species, represent two major morphological forms within the genus...
April 4, 2018: Molecular Phylogenetics and Evolution
Liang Xu, Rampal S Etienne
Whether there are ecological limits to species diversification is a hotly debated topic. Molecular phylogenies show slowdowns in lineage accumulation, suggesting that speciation rates decline with increasing diversity. A maximum likelihood method to detect diversity-dependent diversification from phylogenetic branching times exists, but it assumes that diversity-dependence is a global phenomenon and therefore ignores that the underlying species interactions are mostly local, and not all species in the phylogeny co-occur locally...
April 6, 2018: Evolution; International Journal of Organic Evolution
Aamena Alshamsi, Flávio L Pinheiro, Cesar A Hidalgo
Countries and cities are likely to enter economic activities that are related to those that are already present in them. Yet, while these path dependencies are universally acknowledged, we lack an understanding of the diversification strategies that can optimally balance the development of related and unrelated activities. Here, we develop algorithms to identify the activities that are optimal to target at each time step. We find that the strategies that minimize the total time needed to diversify an economy target highly connected activities during a narrow and specific time window...
April 6, 2018: Nature Communications
B Taboada, P Isa, A L Gutiérrez-Escolano, R M Del Ángel, J E Ludert, N Vázquez, M A Tapia-Palacios, P Chávez, E Garrido, A C Espinosa, L E Eguiarte, S López, V Souza, C F Arias
The Cuatro Ciénegas Basin (CCB) is located in the Chihuahuan desert, in the Mexican state of Coahuila; it has been characterized as a site with a biological high diversity despite its extreme oligotrophic conditions. It has the greatest number of endemic species in North America, containing abundant living microbialites (including stromatolites and microbial mats), and diverse microbial communities. With the hypothesis that this large biodiversity and the geographic structure should be reflected in the virome, the viral communities in 11 different locations of three drainage systems: Churince, La Becerra, and Pozas Rojas and in the intestinal content of 3 different fish species were analyzed, looking for both eukaryotic and prokaryotic RNA and DNA viruses, using NGS methods...
April 6, 2018: Applied and Environmental Microbiology
Teofil Nakov, Jeremy M Beaulieu, Andrew J Alverson
Patterns of species richness are commonly linked to life history strategies. In diatoms, an exceptionally diverse lineage of photosynthetic heterokonts important for global photosynthesis and burial of atmospheric carbon, lineages with different locomotory and reproductive traits differ dramatically in species richness, but any potential association between life history strategy and diversification has not been tested in a phylogenetic framework. We constructed a time-calibrated, 11-gene, 1151-taxon phylogeny of diatoms - the most inclusive diatom species tree to date...
April 6, 2018: New Phytologist
Oscar Inostroza-Michael, Cristian E Hernandez, Enrique Rodriguez-Serrano, Jorge Avaria-Llautureo, Marcelo M Rivadeneira
Among the earliest macroecological patterns documented, is the range and body size relationship, characterized by a minimum geographic range size imposed by the species' body size. This boundary for the geographic range size increases linearly with body size and has been proposed to have implications in lineages evolution and conservation. Nevertheless, the macroevolutionary processes involved in the origin of this boundary and its consequences on lineage diversification has been poorly explored. We evaluate the macroevolutionary consequences of the difference (hereafter the distance) between the observed and the minimum range sizes required by the species' body size, to untangle its role on the diversification of a Neotropical species-rich bird clade using trait-dependent diversification models...
April 6, 2018: Evolution; International Journal of Organic Evolution
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