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Diversification rate

Olga Besharova, Verena M Suchanek, Raimo Hartmann, Knut Drescher, Victor Sourjik
Many bacteria primarily exist in nature as structured multicellular communities, so called biofilms. Biofilm formation is a highly regulated process that includes the transition from the motile planktonic to sessile biofilm lifestyle. Cellular differentiation within a biofilm is a commonly accepted concept but it remains largely unclear when, where and how exactly such differentiation arises. Here we used fluorescent transcriptional reporters to quantitatively analyze spatio-temporal expression patterns of several groups of genes during the formation of submerged Escherichia coli biofilms in an open static system...
2016: Frontiers in Microbiology
Shauna M Baillie, Andrew M Muir, Michael J Hansen, Charles C Krueger, Paul Bentzen
BACKGROUND: Adaptive radiation involving a colonizing phenotype that rapidly evolves into at least one other ecological variant, or ecotype, has been observed in a variety of freshwater fishes in post-glacial environments. However, few studies consider how phenotypic traits vary with regard to neutral genetic partitioning along ecological gradients. Here, we present the first detailed investigation of lake trout Salvelinus namaycush that considers variation as a cline rather than discriminatory among ecotypes...
October 19, 2016: BMC Evolutionary Biology
Jingjing Sherry Wu, Eric D Young, Elisabeth Glowatzki
: Auditory nerve fibers (ANFs) exhibit a range of spontaneous firing rates (SRs) that are inversely correlated with threshold for sounds. To probe the underlying mechanisms and time course of SR differentiation during cochlear maturation, loose-patch extracellular recordings were made from ANF dendrites using acutely excised rat cochlear preparations of different ages after hearing onset. Diversification of SRs occurred mostly between the second and the third postnatal week. Statistical properties of ANF spike trains showed developmental changes that approach adult-like features in older preparations...
October 12, 2016: Journal of Neuroscience: the Official Journal of the Society for Neuroscience
Nicolas Chazot, Keith R Willmott, Fabien L Condamine, Donna Lisa de-Silva, André V L Freitas, Gerardo Lamas, Hélène Morlon, Carlos E Giraldo, Chris D Jiggins, Mathieu Joron, James Mallet, Sandra Uribe, Marianne Elias
Understanding why species richness peaks along the Andes is a fundamental question in the study of Neotropical biodiversity. Several biogeographic and diversification scenarios have been proposed in the literature, but there is confusion about the processes underlying each scenario, and assessing their relative contribution is not straightforward. Here, we propose to refine these scenarios into a framework which evaluates four evolutionary mechanisms: higher speciation rate in the Andes, lower extinction rates in the Andes, older colonization times and higher colonization rates of the Andes from adjacent areas...
October 8, 2016: Molecular Ecology
Jonathan D Kennedy, Michael K Borregaard, Knud A Jønsson, Ben Holt, Jon Fjeldså, Carsten Rahbek
Regional variation in clade richness can be vast, reflecting differences in the dynamics of historical dispersal and diversification among lineages. Although it has been proposed that dispersal into new biogeographic regions may facilitate diversification, to date there has been limited assessment of the importance of this process in the generation, and maintenance, of broad-scale biodiversity gradients. To address this issue, we analytically derive biogeographic regions for a global radiation of passerine birds (the Corvides, c...
October 6, 2016: Evolution; International Journal of Organic Evolution
Marie-Therese Nödl, Alexandra Kerbl, Manfred G Walzl, Gerd B Müller, Heinz Gert de Couet
BACKGROUND: Cephalopods are a highly derived class of molluscs that adapted their body plan to a more active and predatory lifestyle. One intriguing adaptation is the modification of the ventral foot to form a bilaterally symmetric arm crown, which constitutes a true morphological novelty in evolution. In addition, this structure shows many diversifications within the class of cephalopods and therefore offers an interesting opportunity to study the molecular underpinnings of the emergence of phenotypic novelties and their diversification...
2016: Frontiers in Zoology
Liam W Harris, T Jonathan Davies
Explaining the uneven distribution of species richness across the branches of the tree of life has been a major challenge for evolutionary biologists. Advances in phylogenetic reconstruction, allowing the generation of large, well-sampled, phylogenetic trees have provided an opportunity to contrast competing hypotheses. Here, we present a new time-calibrated phylogeny of seed plant families using Bayesian methods and 26 fossil calibrations. While there are various published phylogenetic trees for plants which have a greater density of species sampling, we are still a long way from generating a complete phylogeny for all ~300,000+ plants...
2016: PloS One
Tanja Stadler, Jana Smrckova
Macroevolutionary studies recently shifted from only reconstructing the past state, i.e. the species phylogeny, to also infer the past speciation and extinction dynamics that gave rise to the phylogeny. Methods for estimating diversification dynamics are sensitive towards incomplete species sampling. We introduce a method to estimate time-dependent diversification rates from phylogenies where clades of a particular age are represented by only one sampled species. A popular example of this type of data is phylogenies on the genus- or family-level, i...
October 2016: Biology Letters
Katie E Davis, Jon Hill, Tim I Astrop, Matthew A Wills
Climate is a strong driver of global diversity and will become increasingly important as human influences drive temperature changes at unprecedented rates. Here we investigate diversification and speciation trends within a diverse group of aquatic crustaceans, the Anomura. We use a phylogenetic framework to demonstrate that speciation rate is correlated with global cooling across the entire tree, in contrast to previous studies. Additionally, we find that marine clades continue to show evidence of increased speciation rates with cooler global temperatures, while the single freshwater clade shows the opposite trend with speciation rates positively correlated to global warming...
October 4, 2016: Nature Communications
Marcia F Marston, Jennifer B H Martiny
Understanding the structure and origin of natural bacteriophage genomic diversity is important in elucidating how bacteriophages influence the mortality rates and composition of their host communities. Here we examine the genetic structure and genomic diversification of naturally occurring bacteriophages by analyzing the full genomic sequences of over 100 isolates of Synechococcus-infecting cyanophages collected over 15 years from coastal waters of Southern New England, USA. Our analysis revealed well-supported cyanophage genomic clusters (genome-wide average nucleotide identity (ANI) >93%) and subclusters (genome-wide ANI >98%) that remained consistent for a decade or longer...
October 1, 2016: Environmental Microbiology
Angélique Vétillard, Wafa Bouzid
Animal venoms are complex mixtures containing simple organic molecules, proteins, peptides, and other bioactive elements with extraordinary biological properties associated with their ability to act on a number of molecular receptors in the process of incapacitating their target organisms. In such a context, arthropod venoms are invaluable sources of bioactive substances, with therapeutic interest but the limited availability of some venom such as those from ants, has restricted the potential that these biomolecules could represent...
2016: Biologie Aujourd'hui
Jian Zu, Jinliang Wang, Gang Huang
We investigate the influence of asymmetric interactions on coevolutionary dynamics of a predator-prey system by using the theory of adaptive dynamics. We assume that the defense ability of prey and the attack ability of predators all can adaptively evolve, either caused by phenotypic plasticity or by behavioral choice, but there are certain costs in terms of their growth rate or death rate. The coevolutionary model is constructed from a deterministic approximation of random mutation-selection process. To sum up, if prey's trade-off curve is globally weakly concave, then five outcomes of coevolution are demonstrated, which depend on the intensity and shape of asymmetric predator-prey interactions and predator's trade-off shape...
2016: PloS One
John T Clarke, Graeme T Lloyd, Matt Friedman
Since Darwin, biologists have been struck by the extraordinary diversity of teleost fishes, particularly in contrast to their closest "living fossil" holostean relatives. Hypothesized drivers of teleost success include innovations in jaw mechanics, reproductive biology and, particularly at present, genomic architecture, yet all scenarios presuppose enhanced phenotypic diversification in teleosts. We test this key assumption by quantifying evolutionary rate and capacity for innovation in size and shape for the first 160 million y (Permian-Early Cretaceous) of evolution in neopterygian fishes (the more extensive clade containing teleosts and holosteans)...
October 11, 2016: Proceedings of the National Academy of Sciences of the United States of America
Jun Sung Hong, Eun-Jeong Yoon, Hyukmin Lee, Seok Hoon Jeong, Kyungwon Lee
A total of 431 Pseudomonas aeruginosa (PA) clinical isolates were collected from 29 general hospitals in Korea in 2015. Antimicrobial susceptibility was tested by the disk diffusion method and MICs of carbapenems were determined by agar dilution method. Carbapenemase genes were amplified by PCR and sequenced and the structures of class 1 integrons surrounding the carbapenemase gene cassettes were analyzed by PCR mapping. Multi-locus sequence typing (MLST) and pulsed-field gel electrophoresis (PFGE) were performed for strain typing...
September 26, 2016: Antimicrobial Agents and Chemotherapy
Ernesto Gianoli, Cristian Torres-Díaz, Eduardo Ruiz, Cristian Salgado-Luarte, Marco A Molina-Montenegro, Alfredo Saldaña, Rodrigo S Ríos
The climbing habit is a key innovation in plants: climbing taxa have higher species richness than non-climbing sister groups. We evaluated the hypothesis that climbing plant species show greater among-population genetic differentiation than non-climber species. We compared the among-population genetic distance in woody climbers (8 species, 30 populations) and trees (7 species, 29 populations) coexisting in 9 communities in a temperate rainforest. We also compared within-population genetic diversity in co-occurring woody climbers and trees in two communities...
September 27, 2016: Evolution; International Journal of Organic Evolution
Herinandrianina N Andriananjamanantsoa, Shannon Engberg, Edward E Louis, Luc Brouillet
Angraecum is the largest genus of subtribe Angraecinae (Orchidaceae) with about 221 species. Madagascar is the center of the diversity for the genus with ca. 142 species, of which 90% are endemic. The great morphological diversity associated with species diversification in the genus on the island of Madagascar offers valuable insights for macroevolutionary studies. Phylogenies of the Angraecinae have been published but a lack of taxon and character sampling and their limited taxonomic resolution limit their uses for macroevolutionary studies...
2016: PloS One
Jairo Patiño, Jian Wang, Matt A M Renner, S Robbert Gradstein, Benjamin Laenen, Nicolas Devos, A Jonathan Shaw, Alain Vanderpoorten
Why some species exhibit larger geographical ranges than others, and to what extent does variation in range size affect diversification rates, remains a fundamental, but largely unanswered question in ecology and evolution. Here, we implement phylogenetic comparative analyses and ancestral area estimations in Radula, a liverwort genus of Cretaceous origin, to investigate the mechanisms that explain differences in geographical range size and diversification rates among lineages. Range size was phylogenetically constrained in the two sub-genera characterized by their almost complete Australasian and Neotropical endemicity, respectively...
September 21, 2016: Molecular Phylogenetics and Evolution
Mark S Springer, Christopher A Emerling, Robert W Meredith, Jan E Janečka, Eduardo Eizirik, William J Murphy
The explosive, long fuse, and short fuse models represent competing hypotheses for the timing of placental mammal diversification. Support for the explosive model, which posits both interordinal and intraordinal diversification after the KPg mass extinction, derives from morphological cladistic studies that place Cretaceous eutherians outside of crown Placentalia. By contrast, most molecular studies favor the long fuse model wherein interordinal cladogenesis occurred in the Cretaceous followed by intraordinal cladogenesis after the KPg boundary...
September 19, 2016: Molecular Phylogenetics and Evolution
Zhen Ye, Pingping Chen, Wenjun Bu
This study investigated the influences of geographic isolation and climate fluctuation on the genetic diversity, speciation, and biogeography of the genus Pseudovelia (Hemiptera: Veliidae) in subtropical China and tropic Indo-China Peninsula. Species nucleotide and haplotype diversities decreased with reduction in species distribution limits. The gene tree was congruent with the taxonomy of monophyly, except for four species, P. contorta, P. extensa, P. tibialis tibialis, and P. vittiformis. The conflicts between the genes and species tree could be due to long-term isolation and incomplete lineage sorting...
2016: Scientific Reports
Josef C Uyeda, Luke J Harmon, Carrine E Blank
Cyanobacteria have exerted a profound influence on the progressive oxygenation of Earth. As a complementary approach to examining the geologic record-phylogenomic and trait evolutionary analyses of extant species can lead to new insights. We constructed new phylogenomic trees and analyzed phenotypic trait data using novel phylogenetic comparative methods. We elucidated the dynamics of trait evolution in Cyanobacteria over billion-year timescales, and provide evidence that major geologic events in early Earth's history have shaped-and been shaped by-evolution in Cyanobacteria...
2016: PloS One
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