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Diversification rate

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
Wei Zhou, Yu Yu, Mei Yang, Lizhang Chen, Shuiyuan Xiao
BACKGROUND: Mental health policy can be an essential and powerful tool to improve a population's mental health. However, around one third of countries do not possess a mental health policy, and there are large disparities in population coverage rates between high- and low-income countries. The goal of this study is to identify the transition and implementation challenges of mental health policies in both high-income countries (HICs) as well as middle- and low-income countries (MLICs)...
May 18, 2018: BMC Psychiatry
Andrea Sánchez-Vallet, Simone Fouché, Isabelle Fudal, Fanny E Hartmann, Jessica L Soyer, Aurélien Tellier, Daniel Croll
Filamentous pathogens, including fungi and oomycetes, pose major threats to global food security. Crop pathogens cause damage by secreting effectors that manipulate the host to the pathogen's advantage. Genes encoding such effectors are among the most rapidly evolving genes in pathogen genomes. Here, we review how the major characteristics of the emergence, function, and regulation of effector genes are tightly linked to the genomic compartments where these genes are located in pathogen genomes. The presence of repetitive elements in these compartments is associated with elevated rates of point mutations and sequence rearrangements with a major impact on effector diversification...
May 16, 2018: Annual Review of Phytopathology
Thomas W Hearing, Thomas H P Harvey, Mark Williams, Melanie J Leng, Angela L Lamb, Philip R Wilby, Sarah E Gabbott, Alexandre Pohl, Yannick Donnadieu
The oceans of the early Cambrian (~541 to 509 million years ago) were the setting for a marked diversification of animal life. However, sea temperatures-a key component of the early Cambrian marine environment-remain unconstrained, in part because of a substantial time gap in the stable oxygen isotope (δ18 O) record before the evolution of euconodonts. We show that previously overlooked sources of fossil biogenic phosphate have the potential to fill this gap. Pristine phosphatic microfossils from the Comley Limestones, UK, yield a robust δ18 O signature, suggesting sea surface temperatures of 20° to 25°C at high southern paleolatitudes (~65°S to 70°S) between ~514 and 509 million years ago...
May 2018: Science Advances
Emmanuel F A Toussaint, Andrew Short
Beetles have colonized freshwater habitats multiple times throughout their evolutionary history. Some of these aquatic lineages are associated exclusively with waterfall-like habitats, often with modified morphologies to cope with their unusual way of life. The historical biogeography of such cascade beetle lineages has been shown to strongly reflect ancient tectonic events. We focus on the pantropical genus Oocyclus of which species dwell in waterfalls and associated habitats. We infer the first molecular phylogeny of Oocyclus using a dataset of seven gene fragments...
May 7, 2018: Molecular Phylogenetics and Evolution
Stephen A Smith, Joseph W Brown
PREMISE OF THE STUDY: Large phylogenies can help shed light on macroevolutionary patterns that inform our understanding of fundamental processes that shape the tree of life. These phylogenies also serve as tools that facilitate other systematic, evolutionary, and ecological analyses. Here we combine genetic data from public repositories (GenBank) with phylogenetic data (Open Tree of Life project) to construct a dated phylogeny for seed plants. METHODS: We conducted a hierarchical clustering analysis of publicly available molecular data for major clades within the Spermatophyta...
March 2018: American Journal of Botany
Paul Treacy, Pamela Jagger, Conghe Song, Qi Zhang, Richard E Bilsborrow
In the late 1990s, China's Yangtze and Yellow River Basins suffered devastating natural disasters widely attributed to the degradation of soil and water resources. The Government of China responded with a number of major environmental programs, the most expensive and influential of which, the Grain for Green (GfG) Program, was implemented widely from 1999. Under the GfG Program-also known as the Sloping Land Conversion or Conversion of Cropland to Forest Program-the central government compensates farmers to convert cropland on steep slopes or otherwise ecologically sensitive areas to forest or grassland...
May 8, 2018: Environmental Management
Emanuela Di Martino, Jeremy B C Jackson, Paul D Taylor, Kenneth G Johnson
Marine biodiversity in the Coral Triangle is several times higher than anywhere else, but why this is true is unknown because of poor historical data. To address this, we compared the first available record of fossil cheilostome bryozoans from Indonesia with the previously sampled excellent record from the Caribbean. These two regions differ several-fold in species richness today, but cheilostome diversity was strikingly similar until the end of the Miocene 5.3 million years ago so that the modern disparity must have developed more recently...
April 2018: Science Advances
Andrew G Simpson, Peter J Wagner, Scott L Wing, Charles B Fenster
BACKGROUND: Phylogenetic comparative methods allow us to test evolutionary hypotheses without the benefit of an extensive fossil record. These methods, however, make simplifying assumptions, among them that clades are always increasing or stable in diversity, an assumption we know to be false. This study simulates hypothetical clades to test whether the Binary State Speciation and Extinction (BiSSE) method can be used to correctly detect relative differences in diversification rate between ancestral and derived character states even as net diversification rates are declining overall...
May 8, 2018: BMC Evolutionary Biology
Simon J Brandl, Christopher H R Goatley, David R Bellwood, Luke Tornabene
Teleost fishes are the most diverse group of vertebrates on Earth. On tropical coral reefs, their species richness exceeds 6000 species; one tenth of total vertebrate biodiversity. A large proportion of this diversity is composed of cryptobenthic reef fishes (CRFs): bottom-dwelling, morphologically or behaviourally cryptic species typically less than 50 mm in length. Yet, despite their diversity and abundance, these fishes are both poorly defined and understood. Herein we provide a new quantitative definition and synthesise current knowledge on the diversity, distribution and life history of CRFs...
May 7, 2018: Biological Reviews of the Cambridge Philosophical Society
Anjani Kumar, Anshu Priya, Tanzeel Ahmed, Christine Grundström, Neema Negi, Thomas Grundström
B lymphocytes optimize Ab responses by somatic hypermutation (SH), which introduces point mutations in the variable regions of the Ab genes and by class-switch recombination (CSR), which changes the expressed C region exon of the IgH. These Ab diversification processes are initiated by the deaminating enzyme activation-induced cytidine deaminase followed by many DNA repair enzymes, ultimately leading to deletions and a high mutation rate in the Ab genes, whereas DNA lesions made by activation-induced cytidine deaminase are repaired with low error rate on most other genes...
May 4, 2018: Journal of Immunology: Official Journal of the American Association of Immunologists
Ron Geller, Sebastian Pechmann, Ashley Acevedo, Raul Andino, Judith Frydman
Acquisition of mutations is central to evolution; however, the detrimental effects of most mutations on protein folding and stability limit protein evolvability. Molecular chaperones, which suppress aggregation and facilitate polypeptide folding, may alleviate the effects of destabilizing mutations thus promoting sequence diversification. To illuminate how chaperones can influence protein evolution, we examined the effect of reduced activity of the chaperone Hsp90 on poliovirus evolution. We find that Hsp90 offsets evolutionary trade-offs between protein stability and aggregation...
May 3, 2018: Nature Communications
Evan P Economo, Nitish Narula, Nicholas R Friedman, Michael D Weiser, Benoit Guénard
The latitudinal diversity gradient-the tendency for more species to occur toward the equator-is the dominant pattern of life on Earth, yet the mechanisms responsible for it remain largely unexplained. Recently, the analysis of global data has led to advances in understanding, but these advances have been mostly limited to vertebrates and trees and have not provided consensus answers. Here we synthesize large-scale geographic, phylogenetic, and fossil data for an exemplar invertebrate group-ants-and investigate whether the latitudinal diversity gradient arose due to higher rates of net diversification in the tropics, or due to a longer time period to accumulate diversity due to Earth's climatic history...
May 3, 2018: Nature Communications
Jie Meng, Ting Wang, Li Li, Guofan Zhang
Pacific oyster (Crassostrea gigas) distribute a steep gradient of environmental stress between intertidal and subtidal habits and provide insight into population-scale patterns and underlying processes of variation in physiological tolerance. In this study, 1-year-old-F1 oysters, collected from subtidal and intertidal habitats, were obtained after common garden experiment. Genetic differentiation and physiological responses under air exposure were examined to determine whether they had evolved into local adapted subpopulations...
April 26, 2018: Marine Environmental Research
Nicolas Chazot, Donna Lisa De-Silva, Keith R Willmott, André V L Freitas, Gerardo Lamas, James Mallet, Carlos E Giraldo, Sandra Uribe, Marianne Elias
The Neotropical region is the most biodiverse on Earth, in a large part due to the highly diverse tropical Andean biota. The Andes are a potentially important driver of diversification within the mountains and for neighboring regions. We compared the role of the Andes in diversification among three subtribes of Ithomiini butterflies endemic to the Neotropics, Dircennina, Oleriina, and Godyridina. The diversification patterns of Godyridina have been studied previously. Here, we generate the first time-calibrated phylogeny for the largest ithomiine subtribe, Dircennina, and we reanalyze a published phylogeny of Oleriina to test different biogeographic scenarios involving the Andes within an identical framework...
April 2018: Ecology and Evolution
Jacob B Landis, Douglas E Soltis, Zheng Li, Hannah E Marx, Michael S Barker, David C Tank, Pamela S Soltis
PREMISE OF THE STUDY: Polyploidy or whole-genome duplication (WGD) pervades the evolutionary history of angiosperms. Despite extensive progress in our understanding of WGD, the role of these events in promoting diversification is still not well understood. We seek to clarify the possible association between WGD and diversification rates in flowering plants. METHODS: Using a previously published phylogeny spanning all land plants (31,749 tips) and WGD events inferred from analyses of the 1000 Plants (1KP) transcriptome data, we analyzed the association of WGDs and diversification rates following numerous WGD events across the angiosperms...
March 2018: American Journal of Botany
Rosa Fernández, Robert J Kallal, Dimitar Dimitrov, Jesús A Ballesteros, Miquel A Arnedo, Gonzalo Giribet, Gustavo Hormiga
Dating back to almost 400 mya, spiders are among the most diverse terrestrial predators [1]. However, despite considerable effort [1-9], their phylogenetic relationships and diversification dynamics remain poorly understood. Here, we use a synergistic approach to study spider evolution through phylogenomics, comparative transcriptomics, and lineage diversification analyses. Our analyses, based on ca. 2,500 genes from 159 spider species, reject a single origin of the orb web (the "ancient orb-web hypothesis") and suggest that orb webs evolved multiple times since the late Triassic-Jurassic...
April 21, 2018: Current Biology: CB
Daniel Spalink, Kevin Stoffel, Genevieve K Walden, Amanda M Hulse-Kemp, Theresa A Hill, Allen Van Deynze, Lynn Bohs
The integration of genomics and phylogenetics allows new insight into the structure of gene tree discordance, the relationships among gene position, gene history, and rate of evolution, as well as the correspondence of gene function, positive selection, and gene ontology enrichment across lineages. We explore these issues using the tribe Capsiceae (Solanaceae), which is comprised of the genera Lycianthes and Capsicum (peppers). In combining the annotated genomes of Capsicum with newly sequenced transcriptomes of four species of Lycianthes and Capsicum, we develop phylogenies for 6,747 genes, and construct a backbone species tree using both concordance and explicit phylogenetic network approaches...
April 24, 2018: Molecular Phylogenetics and Evolution
Rowan J Schley, Manuel de la Estrella, Oscar Alejandro Pérez-Escobar, Anne Bruneau, Timothy Barraclough, Félix Forest, Bente Klitgård
The flora of the Neotropics is unmatched in its diversity, however the mechanisms by which diversity has accumulated are debated and largely unclear. The Brownea clade (Leguminosae) is a characteristic component of the Neotropical flora, and the species within it are diverse in their floral morphology, attracting a wide variety of pollinators. This investigation aimed to estimate species divergence times and infer relationships within the group, in order to test whether the Brownea clade followed the 'cradle' or 'museum' model of diversification, i...
April 24, 2018: Molecular Phylogenetics and Evolution
Swati Singh, Sandip Das, R Geeta
Novel morphological structures allowed adaptation to dry conditions in early land plants. The cuticle, one such novelty, plays diverse roles in tolerance to abiotic and biotic stresses and plant development. Cuticular waxes represent a major constituent of the cuticle and are comprised of an assortment of chemicals that include, among others, very long chain fatty acids (VLCFAs). Members of the β-ketoacyl coenzyme A synthases (KCS) gene family code for enzymes that are essential for fatty acid biosynthesis...
April 23, 2018: Molecular Phylogenetics and Evolution
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