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Diversification rate

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https://www.readbyqxmd.com/read/28444897/aging-asexual-lineages-and-the-evolutionary-maintenance-of-sex
#1
E K H Ho, A F Agrawal
Finite populations of asexual and highly selfing species suffer from a reduced efficacy of selection. Such populations are thought to decline in fitness over time due to accumulating slightly deleterious mutations or failing to adapt to changing conditions. These within-population processes that lead non-recombining species to extinction may help maintain sex and outcrossing through species level selection. Although inefficient selection is proposed to elevate extinction rates over time, previous models of species selection for sex assumed constant diversification rates...
April 26, 2017: Evolution; International Journal of Organic Evolution
https://www.readbyqxmd.com/read/28439466/arrival-and-diversification-of-mabuyine-skinks-squamata-scincidae-in-the-neotropics-based-on-a-fossil-calibrated-timetree
#2
Anieli Guirro Pereira, Carlos G Schrago
BACKGROUND: The evolution of South American Mabuyinae skinks holds significant biogeographic interest because its sister lineage is distributed across the African continent and adjacent islands. Moreover, at least one insular species, Trachylepis atlantica, has independently reached the New World through transoceanic dispersal. To clarify the evolutionary history of both Neotropical lineages, this study aimed to infer an updated timescale using the largest species and gene sampling dataset ever assembled for this group...
2017: PeerJ
https://www.readbyqxmd.com/read/28437487/crop-and-varietal-diversification-of-rainfed-rice-based-cropping-systems-for-higher-productivity-and-profitability-in-eastern-india
#3
B Lal, Priyanka Gautam, B B Panda, R Raja, Teekam Singh, R Tripathi, M Shahid, A K Nayak
Rice-rice system and rice fallows are no longer productive in Southeast Asia. Crop and varietal diversification of the rice based cropping systems may improve the productivity and profitability of the systems. Diversification is also a viable option to mitigate the risk of climate change. In Eastern India, farmers cultivate rice during rainy season (June-September) and land leftovers fallow after rice harvest in the post-rainy season (November-May) due to lack of sufficient rainfall or irrigation amenities...
2017: PloS One
https://www.readbyqxmd.com/read/28431159/likelihood-of-tree-topologies-with-fossils-and-diversification-rate-estimation
#4
Gilles Didier, Marine Fau, Michel Laurin
Since the diversification process cannot be directly observed at the human scale, it has to be studied from the information available, namely the extant taxa and the fossil record. In this sense, phylogenetic trees including both extant taxa and fossils are the most complete representations of the diversification process that one can get. Such phylogenetic trees can be reconstructed from molecular and morphological data, to some extent. Among the temporal information of such phylogenetic trees, fossil ages are by far the most precisely known (divergence times are inferences calibrated mostly with fossils)...
April 18, 2017: Systematic Biology
https://www.readbyqxmd.com/read/28430886/intrinsic-protein-disorder-reduces-small-scale-gene-duplicability
#5
Sanghita Banerjee, Felix Feyertag, David Alvarez-Ponce
Whereas the rate of gene duplication is relatively high, only certain duplications survive the filter of natural selection and can contribute to genome evolution. However, the reasons why certain genes can be retained after duplication whereas others cannot remain largely unknown. Many proteins contain intrinsically disordered regions (IDRs), whose structures fluctuate between alternative conformational states. Due to their high flexibility, IDRs often enable protein-protein interactions and are the target of post-translational modifications...
April 19, 2017: DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes
https://www.readbyqxmd.com/read/28414099/molecular-evolution-of-the-plastid-genome-during-diversification-of-the-cotton-genus
#6
Zhiwen Chen, Corrinne E Grover, Pengbo Li, Yumei Wang, Hushuai Nie, Yanpeng Zhao, Meiyan Wang, Fang Liu, Zhongli Zhou, Xingxing Wang, Xiaoyan Cai, Kunbo Wang, Jonathan F Wendel, Jinping Hua
Cotton (Gossypium spp.) is commonly grouped into eight diploid genomic groups, designated A-G and K, and one tetraploid genomic group, namely AD. To gain insight into the phylogeny of Gossypium and molecular evolution of the chloroplast genome duringdiversification, chloroplast genomes (cpDNA) from 6 D-genome and 2 G-genome species of Gossypium (G. armourianum D2-1, G. harknessii D2-2, G. davidsonii D3-d, G. klotzschianum D3-k, G. aridum D4, G. trilobum D8, and G. australe G2, G. nelsonii G3) were newly reported here...
April 13, 2017: Molecular Phylogenetics and Evolution
https://www.readbyqxmd.com/read/28408947/diversification-rates-in-ctenodactylidae-rodentia-mammalia-from-mongolia
#7
Adriana Oliver, Oscar Sanisidro, Bayarmaa Baatarjav, Ichinnorov Niiden, Gudrun Daxner-Höck
Gundis, or comb rats, are rodents of the family Ctenodactylidae. Extant gundis are restricted to Africa and represent a vestige of the diversity that the ctenodactylids attained at both palaeoecological and palaeobiogeographical levels. Here, we present an updated review of the Ctenodactylidae from the Valley of Lakes, Mongolia, based on the study of large collections now available. We have recognised 13 valid species of ctenodactylids grouped into five genera: Karakoromys, Huangomys, Tataromys, Yindirtemys, and Prodistylomys...
2017: Paleobiodivers Paleoenviron
https://www.readbyqxmd.com/read/28407248/evolutionary-priority-effects-persist-in-anthropogenically-created-habitats-but-not-through-nonnative-plant-invasion
#8
Angela J Brandt, William G Lee, Andrew J Tanentzap, Ella Hayman, Tadashi Fukami, Barbara J Anderson
Evolutionary priority effects, where early-arriving lineages occupy niche space via diversification and preclude dominance of later arrivals, have been observed in alpine and forest communities. However, the potential for evolutionary priority effects to persist in an era of rapid global change remains unclear. Here, we use a natural experiment of historical disturbance in New Zealand to test whether anthropogenic changes in available habitat and nonnative invasion eliminate the role of evolutionary priority effects in community assembly...
April 13, 2017: New Phytologist
https://www.readbyqxmd.com/read/28400153/spatiotemporal-diversification-of-intrapatient-genomic-clones-and-early-drug-development-concepts-realize-the-roadmap-of-precision-cancer-medicine
#9
REVIEW
Dimitrios H Roukos
The unmet clinical needs of high relapse and cancer-related death rates are reflected by the poor understanding of the genome-wide mutational landscape and molecular mechanisms orchestrating therapeutic resistance. Emerging potential solutions to this challenge include the exploration of cancer genome dynamic evolution in time and space. Breakthrough next-generation sequencing (NGS) applications including multiregional NGS for intratumor heterogeneity identification, repeated cell-free DNA/circulating tumor DNA-NGS for detecting circulating genomic subclones and their comparison to reveal intrapatient heterogeneity (IPH) could identify the dynamic emergence of resistant subclones in the neoadjuvant, adjuvant and metastatic setting...
April 8, 2017: Drug Discovery Today
https://www.readbyqxmd.com/read/28399690/peer-assessment-in-the-objective-structured-clinical-examination-a-scoping-review
#10
Rishad Khan, Michael W C Payne, Saad Chahine
BACKGROUND: The objective structured clinical examination (OSCE), originally designed with experts assessing trainees' competence, is more frequently employed with an element of peer assessment and feedback. Although peer assessment in higher education has been studied, its role in OSCEs has not reviewed. AIMS: The aim of this study is to conduct a scoping review and explore the role of peer assessment and feedback in the OSCE. METHODS: Electronic database and hand searching yielded 507 articles...
April 11, 2017: Medical Teacher
https://www.readbyqxmd.com/read/28394942/evidence-for-the-evolutionary-steps-leading-to-meca-mediated-%C3%AE-lactam-resistance-in-staphylococci
#11
Joana Rolo, Peder Worning, Jesper Boye Nielsen, Rita Sobral, Rory Bowden, Ons Bouchami, Peter Damborg, Luca Guardabassi, Vincent Perreten, Henrik Westh, Alexander Tomasz, Hermínia de Lencastre, Maria Miragaia
The epidemiologically most important mechanism of antibiotic resistance in Staphylococcus aureus is associated with mecA-an acquired gene encoding an extra penicillin-binding protein (PBP2a) with low affinity to virtually all β-lactams. The introduction of mecA into the S. aureus chromosome has led to the emergence of methicillin-resistant S. aureus (MRSA) pandemics, responsible for high rates of mortality worldwide. Nonetheless, little is known regarding the origin and evolution of mecA. Different mecA homologues have been identified in species belonging to the Staphylococcus sciuri group representing the most primitive staphylococci...
April 2017: PLoS Genetics
https://www.readbyqxmd.com/read/28387233/north-andean-origin-and-diversification-of-the-largest-ithomiine-butterfly-genus
#12
Donna Lisa De-Silva, Luísa L Mota, Nicolas Chazot, Ricardo Mallarino, Karina L Silva-Brandão, Luz Miryam Gómez Piñerez, André V L Freitas, Gerardo Lamas, Mathieu Joron, James Mallet, Carlos E Giraldo, Sandra Uribe, Tiina Särkinen, Sandra Knapp, Chris D Jiggins, Keith R Willmott, Marianne Elias
The Neotropics harbour the most diverse flora and fauna on Earth. The Andes are a major centre of diversification and source of diversity for adjacent areas in plants and vertebrates, but studies on insects remain scarce, even though they constitute the largest fraction of terrestrial biodiversity. Here, we combine molecular and morphological characters to generate a dated phylogeny of the butterfly genus Pteronymia (Nymphalidae: Danainae), which we use to infer spatial, elevational and temporal diversification patterns...
April 7, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28381621/hummingbird-pollination-and-the-diversification-of-angiosperms-an-old-and-successful-association-in-gesneriaceae
#13
Martha Liliana Serrano-Serrano, Jonathan Rolland, John L Clark, Nicolas Salamin, Mathieu Perret
The effects of specific functional groups of pollinators in the diversification of angiosperms are still to be elucidated. We investigated whether the pollination shifts or the specific association with hummingbirds affected the diversification of a highly diverse angiosperm lineage in the Neotropics. We reconstructed a phylogeny of 583 species from the Gesneriaceae family and detected diversification shifts through time, inferred the timing and amount of transitions among pollinator functional groups, and tested the association between hummingbird pollination and speciation and extinction rates...
April 12, 2017: Proceedings. Biological Sciences
https://www.readbyqxmd.com/read/28377533/nonselective-bottlenecks-control-the-divergence-and-diversification-of-phase-variable-bacterial-populations
#14
Jack Aidley, Shweta Rajopadhye, Nwanekka M Akinyemi, Lea Lango-Scholey, Christopher D Bayliss
Phase variation occurs in many pathogenic and commensal bacteria and is a major generator of genetic variability. A putative advantage of phase variation is to counter reductions in variability imposed by nonselective bottlenecks during transmission. Genomes of Campylobacter jejuni, a widespread food-borne pathogen, contain multiple phase-variable loci whose rapid, stochastic variation is generated by hypermutable simple sequence repeat tracts. These loci can occupy a vast number of combinatorial expression states (phasotypes) enabling populations to rapidly access phenotypic diversity...
April 4, 2017: MBio
https://www.readbyqxmd.com/read/28373546/uplift-driven-diversification-in-the-hengduan-mountains-a-temperate-biodiversity-hotspot
#15
Yaowu Xing, Richard H Ree
A common hypothesis for the rich biodiversity found in mountains is uplift-driven diversification-that orogeny creates conditions favoring rapid in situ speciation of resident lineages. We tested this hypothesis in the context of the Qinghai-Tibetan Plateau (QTP) and adjoining mountain ranges, using the phylogenetic and geographic histories of multiple groups of plants to infer the tempo (rate) and mode (colonization versus in situ diversification) of biotic assembly through time and across regions. We focused on the Hengduan Mountains region, which in comparison with the QTP and Himalayas was uplifted more recently (since the late Miocene) and is smaller in area and richer in species...
April 3, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28363794/adaptive-evolution-of-insect-selective-excitatory-%C3%AE-type-sodium-channel-neurotoxins-from-scorpion-venom
#16
Wenlan Wu, Zhongjie Li, Yibao Ma
Insect selective excitatory β-type sodium channel neurotoxins from scorpion venom (β-NaScTxs) are composed of about 70-76 amino acid residues and share a common scaffold stabilized by four unique disulfide bonds. The phylogenetic analysis of these toxins was hindered by limited sequence data. In our recent study, two new insect selective excitatory β-NaScTxs, LmIT and ImIT, were isolated from Lychas mucronatus and Isometrus maculatus, respectively. With the sequences previously reported, we examined the adaptive molecular evolution of insect selective excitatory β-NaScTxs by estimating the nonsynonymous-to-synonymous rate ratio (ω=dN/dS)...
March 28, 2017: Peptides
https://www.readbyqxmd.com/read/28347887/using-phylogenomics-to-understand-the-link-between-biogeographic-origins-and-regional-diversification-in-ratsnakes
#17
Xin Chen, Alan R Lemmon, Emily Moriarty Lemmon, R Alexander Pyron, Frank T Burbrink
Globally distributed groups may show regionally distinct rates of diversification, where speciation is elevated given timing and sources of ecological opportunity. However, for most organisms, nearly complete sampling at genomic-data scales to reduce topological error in all regions is unattainable, thus hampering conclusions related to biogeographic origins and rates of diversification. We explore processes leading to the diversity of global ratsnakes and test several important hypotheses related to areas of origin and enhanced diversification upon colonizing new continents...
March 24, 2017: Molecular Phylogenetics and Evolution
https://www.readbyqxmd.com/read/28346661/a-major-shift-in-diversification-rate-helps-explain-macroevolutionary-patterns-in-primate-species-diversity
#18
Jessica H Arbour, Sharlene E Santana
Primates represent one of the most species rich, wide ranging, and ecologically diverse clades of mammals. What major macroevolutionary factors have driven their diversification and contributed to the modern distribution of primate species remains widely debated. We employed phylogenetic comparative methods to examine the role of clade age and evolutionary rate heterogeneity in the modern distribution of species diversity of Primates. Primate diversification has accelerated since its origin, with decreased extinction leading to a shift to even higher evolutionary rates in the most species rich family (Cercopithecidae)...
March 27, 2017: Evolution; International Journal of Organic Evolution
https://www.readbyqxmd.com/read/28345864/triple-stage-mass-spectrometry-unravels-the-heterogeneity-of-an-endogenous-protein-complex
#19
Gili Ben-Nissan, Mikhail E Belov, David Morgenstern, Yishai Levin, Orly Dym, Galina Arkind, Carni Lipson, Alexander A Makarov, Michal Sharon
Protein complexes often represent an ensemble of different assemblies with distinct functions and regulation. This increased complexity is enabled by the variety of protein diversification mechanisms that exist at every step of the protein biosynthesis pathway, such as alternative splicing and post transcriptional and translational modifications. The resulting variation in subunits can generate compositionally distinct protein assemblies. These different forms of a single protein complex may comprise functional variances that enable response and adaptation to varying cellular conditions...
April 6, 2017: Analytical Chemistry
https://www.readbyqxmd.com/read/28338049/breeding-system-and-spatial-isolation-from-congeners-strongly-constrain-seed-set-in-an-insect-pollinated-apomictic-tree-sorbus-subcuneata-rosaceae
#20
Tracey J Hamston, Robert J Wilson, Natasha de Vere, Tim C G Rich, Jamie R Stevens, James E Cresswell
In plants, apomixis results in the production of clonal offspring via seed and can provide reproductive assurance for isolated individuals. However, many apomicts require pollination to develop functional endosperm for successful seed set (pseudogamy) and therefore risk pollination-limitation, particularly in self-incompatible species that require heterospecific pollen. We used microsatellite paternity analysis and hand pollinations to investigate pollen-limitation in Sorbus subcuneata, a threatened endemic tree that co-occurs with its congener, S...
March 24, 2017: Scientific Reports
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