keyword
MENU ▼
Read by QxMD icon Read
search

Diversification rate

keyword
https://www.readbyqxmd.com/read/29342307/using-phylogenomic-data-to-explore-the-effects-of-relaxed-clocks-and-calibration-strategies-on-divergence-time-estimation-primates-as-a-test-case
#1
Mario Dos Reis, Gregg F Gunnell, José Barba-Montoya, Alex Wilkins, Ziheng Yang, Anne D Yoder
Primates have long been a test case for the development of phylogenetic methods for divergence time estimation. Despite a large number of studies, however, the timing of origination of crown Primates relative to the K-Pg boundary and the timing of diversification of the main crown groups remain controversial. Here we analysed a dataset of 372 taxa (367 Primates and 5 outgroups, 3.4 million aligned base pairs) that includes nine primate genomes. We systematically explore the effect of different interpretations of fossil calibrations and molecular clock models on primate divergence time estimates...
January 12, 2018: Systematic Biology
https://www.readbyqxmd.com/read/29335414/evolutionary-history-of-coleoptera-revealed-by-extensive-sampling-of-genes-and-species
#2
Shao-Qian Zhang, Li-Heng Che, Yun Li, Dan Liang, Hong Pang, Adam Ślipiński, Peng Zhang
Beetles (Coleoptera) are the most diverse and species-rich group of insects, and a robust, time-calibrated phylogeny is fundamental to understanding macroevolutionary processes that underlie their diversity. Here we infer the phylogeny and divergence times of all major lineages of Coleoptera by analyzing 95 protein-coding genes in 373 beetle species, including ~67% of the currently recognized families. The subordinal relationships are strongly supported as Polyphaga (Adephaga (Archostemata, Myxophaga)). The series and superfamilies of Polyphaga are mostly monophyletic...
January 15, 2018: Nature Communications
https://www.readbyqxmd.com/read/29334415/early-burst-in-body-size-evolution-is-uncoupled-from-species-diversification-in-diving-beetles-dytiscidae
#3
Aurélie Désamoré, Benjamin Laenen, Kelly B Miller, Johannes Bergsten
Changes in morphology are often thought to be linked to changes in species diversification, which is expected to leave a signal of Early Burst (EB) in phenotypic traits. However, such signal is rarely recovered in empirical phylogenies, even for groups with well-known adaptive radiation. Using a comprehensive phylogenetic approach in Dytiscidae, which harbors ~4,300 species with as much as 50-fold variation in body size among them, we ask whether pattern of species diversification correlates with morphological evolution...
January 15, 2018: Molecular Ecology
https://www.readbyqxmd.com/read/29333059/innate-food-aversions-and-culturally-transmitted-food-taboos-in-pregnant-women-in-rural-southwest-india-separate-systems-to-protect-the-fetus
#4
Caitlyn D Placek, Purnima Madhivanan, Edward H Hagen
Pregnancy increases women's nutritional requirements, yet causes aversions to nutritious foods. Most societies further restrict pregnant women's diet with food taboos. Pregnancy food aversions are theorized to protect mothers and fetuses from teratogens and pathogens or increase dietary diversity in response to resource scarcity. Tests of these hypotheses have had mixed results, perhaps because many studies are in Westernized populations with reliable access to food and low exposure to pathogens. If pregnancy food aversions are adaptations, however, then they likely evolved in environments with uncertain access to food and high exposure to pathogens...
November 2017: Evolution and Human Behavior: Official Journal of the Human Behavior and Evolution Society
https://www.readbyqxmd.com/read/29330955/intrinsic-constraints-on-the-diversification-of-neotropical-cichlid-adductor-mandibulae-size
#5
Jessica Arbour, Hernán López-Fernández
The diversification of functional traits may be constrained by intrinsic factors, such as structural, mechanical, developmental, or physiological limitations. We explored the biomechanical and constructional constraints on the size of the major jaw closing muscles, the adductor mandibulae complex (AM), in a diverse clade of freshwater fish - the Neotropical cichlids. Using phylogenetic comparative methods, we contrasted patterns of size variation and diversification rates of three AM divisions with variables describing head size and biomechanical coefficients describing force and velocity transmission...
February 2018: Anatomical Record: Advances in Integrative Anatomy and Evolutionary Biology
https://www.readbyqxmd.com/read/29324757/genome-downsizing-physiological-novelty-and-the-global-dominance-of-flowering-plants
#6
Kevin A Simonin, Adam B Roddy
The abrupt origin and rapid diversification of the flowering plants during the Cretaceous has long been considered an "abominable mystery." While the cause of their high diversity has been attributed largely to coevolution with pollinators and herbivores, their ability to outcompete the previously dominant ferns and gymnosperms has been the subject of many hypotheses. Common among these is that the angiosperms alone developed leaves with smaller, more numerous stomata and more highly branching venation networks that enable higher rates of transpiration, photosynthesis, and growth...
January 2018: PLoS Biology
https://www.readbyqxmd.com/read/29299533/cooperating-h3n2-influenza-virus-variants-are-not-detectable-in-primary-clinical-samples
#7
Katherine S Xue, Alexander L Greninger, Ailyn Pérez-Osorio, Jesse D Bloom
The high mutation rates of RNA viruses lead to rapid genetic diversification, which can enable cooperative interactions between variants in a viral population. We previously described two distinct variants of H3N2 influenza virus that cooperate in cell culture. These variants differ by a single mutation, D151G, in the neuraminidase protein. The D151G mutation reaches a stable frequency of about 50% when virus is passaged in cell culture. However, it is unclear whether selection for the cooperative benefits of D151G is a cell culture phenomenon or whether the mutation is also sometimes present at appreciable frequency in virus populations sampled directly from infected humans...
January 2018: MSphere
https://www.readbyqxmd.com/read/29299121/klf15-promotes-the-proliferation-and-metastasis-of-lung-adenocarcinoma-cells-and-has-potential-as-a-cancer-prognostic-marker
#8
Lihua Gao, Hongmei Qiu, Jian Liu, Yuzhen Ma, Jia Feng, Li Qian, Jianguo Zhang, Yifei Liu, Tingting Bian
Lung adenocarcinoma (LADC)is a general form of non-small cell lung cancer that represents a significant threat to public health worldwide. The 5-year-survival rate for LADC is currently below 15%. The transcription factor KLF15, also called kidney-enriched KLF (KKLF), has been proven to play a role in inhibiting proliferation and diversification of carcinoma cells, including those of the endometrium, pancreas and breast, but the involvement of KLF15 in LADC has not previously been studied. In this study, we compared the in vitro expression of KLF15 in human LADC tissues and adjacent normal lung tissues...
December 15, 2017: Oncotarget
https://www.readbyqxmd.com/read/29290090/rates-of-gut-microbiome-divergence-in-mammals
#9
Alex H Nishida, Howard Ochman
The variation and taxonomic diversity among mammalian gut microbiomes raises several questions about the factors that contribute to the rates and patterns of change in these microbial communities. By comparing the microbiome compositions of 112 species representing 14 mammalian orders, we assessed how host and ecological factors contribute to microbiome diversification. Except in rare cases, the same bacterial phyla predominate in mammalian gut microbiomes, and there has been some convergence of microbiome compositions according to dietary category across all mammalians lineages except Chiropterans (bats), which possess high proportions of Proteobacteria and tend to be most similar to one another regardless of diet...
December 31, 2017: Molecular Ecology
https://www.readbyqxmd.com/read/29281664/diversification-rates-host-plant-shifts-and-an-updated-molecular-phylogeny-of-andean-eois-moths-lepidoptera-geometridae
#10
Patrick Strutzenberger, Gunnar Brehm, Brigitte Gottsberger, Florian Bodner, Carlo Lutz Seifert, Konrad Fiedler
Eois is one of the best-investigated genera of tropical moths. Its close association with Piper plants has inspired numerous studies on life histories, phylogeny and evolutionary biology. This study provides an updated view on phylogeny, host plant use and temporal patterns of speciation in Eois. Using sequence data (2776 bp) from one mitochondrial (COI) and one nuclear gene (Ef1-alpha) for 221 Eois species, we confirm and reinforce previous findings regarding temporal patterns of diversification. Deep diversification within Andean Eois took place in the Miocene followed by a sustained high rate of diversification until the Pleistocene when a pronounced slowdown of speciation is evident...
2017: PloS One
https://www.readbyqxmd.com/read/29274113/robustness-of-the-approximate-likelihood-of-the-protracted-speciation-model
#11
Camille Anna Simonet, Raphaël Scherrer, Artur Rego-Costa, Rampal S Etienne
The protracted speciation model presents a realistic and parsimonious explanation for the observed slowdown in lineage accumulation through time, by accounting for the fact that speciation takes time. A method to compute the likelihood for this model given a phylogeny is available and allows estimation of its parameters (rate of initiation of speciation, rate of completion of speciation, and extinction rate) and statistical comparison of this model to other proposed models of diversification. However this likelihood computation method makes an approximation of the protracted speciation model to be mathematically tractable: it sometimes counts fewer species than one would do from a biological perspective...
December 22, 2017: Journal of Evolutionary Biology
https://www.readbyqxmd.com/read/29273445/selective-pressure-on-the-protein-coding-genes-of-the-pufferfish-is-correlated-with-phenotypic-traits
#12
Hyeonju Ahn, Chul Lee, Bo-Hye Nam, Eun Bae Kim, Kelsey Caetano-Anolles, Heebal Kim
The pufferfish accumulates neurotoxic tetrodotoxin in its body and inflates by filling its stomach with water. These traits are unique to this species, and may be a result of adaptation post-divergence of Tetraodontidae. However, evolution of the protein-coding genes in the pufferfish has not yet been well elucidated. Detection of positive selection on these genes can help us understand the mechanisms associated with functional evolution. We downloaded well-annotated gene information of two pufferfish species, Takifugu rubripes and Tetraodon nigroviridis, from the public ENSEMBL database...
December 19, 2017: Marine Genomics
https://www.readbyqxmd.com/read/29247848/refining-the-biogeographical-scenario-of-the-land-snail-cornu-aspersum-aspersum-natural-spatial-expansion-and-human-mediated-dispersal-in-the-mediterranean-basin
#13
Stéphanie Sherpa, Armelle Ansart, Luc Madec, Marie-Claire Martin, Stéphane Dréano, Annie Guiller
The land snail Cornu aspersum aspersum, native to the Mediterranean region, has been the subject of several anatomical and molecular studies leading to recognize two divergent lineages, named "East" and "West" according to their geographical distribution in North Africa. The first biogeographical scenario proposed the role of Oligocene paleogeographic events and Quaternary glacial refugia to explain spatial patterns of genetic variation. The aim of this study was to refine this scenario using molecular and morphometric data from 169 populations sampled across Mediterranean islands and continents...
December 13, 2017: Molecular Phylogenetics and Evolution
https://www.readbyqxmd.com/read/29242826/a-triassic-plesiosaurian-skeleton-and-bone-histology-inform-on-evolution-of-a-unique-body-plan
#14
Tanja Wintrich, Shoji Hayashi, Alexandra Houssaye, Yasuhisa Nakajima, P Martin Sander
Secondary marine adaptation is a major pattern in amniote evolution, accompanied by specific bone histological adaptations. In the aftermath of the end-Permian extinction, diverse marine reptiles evolved early in the Triassic. Plesiosauria is the most diverse and one of the longest-lived clades of marine reptiles, but its bone histology is least known among the major marine amniote clades. Plesiosaurians had a unique and puzzling body plan, sporting four evenly shaped pointed flippers and (in most clades) a small head on a long, stiffened neck...
December 2017: Science Advances
https://www.readbyqxmd.com/read/29242165/molecular-phylogeny-and-divergence-of-the-map-turtles-emydidae-graptemys
#15
Robert C Thomson, Phillip Q Spinks, H Bradley Shaffer
The map turtles (genus Graptemys) comprise a morphologically diverse clade that forms a major component of the southeastern US hotspot of chelonian diversity. Map turtles have experienced both recent and rapid diversification resulting in long-standing uncertainty regarding species boundaries and phylogenetic relationships within the genus as well as timing of their divergence. We present a phylogeny for the group that includes geographically representative sampling for all described species and subspecies...
December 11, 2017: Molecular Phylogenetics and Evolution
https://www.readbyqxmd.com/read/29239487/evolution-of-skull-shape-in-the-family-salamandridae-amphibia-caudata
#16
Ana Ivanović, Jan W Arntzen
We carried out a comparative morphometric analysis of 56 species of salamandrid salamanders, representing 19 out of 21 extant genera, with the aim of uncovering the major patterns of skull shape diversification, and revealing possible trends and directions of evolutionary change. To do this we used micro-computed tomography scanning and three-dimensional geometric morphometrics, along with a well-resolved molecular phylogeny. We found that allometry explains a relatively small amount of shape variation across taxa...
December 14, 2017: Journal of Anatomy
https://www.readbyqxmd.com/read/29233706/molecular-systematics-and-biogeography-of-lowland-antpittas-aves-grallariidae-the-role-of-vicariance-and-dispersal-in-the-diversification-of-a-widespread-neotropical-lineage
#17
Lincoln Carneiro, Gustavo A Bravo, Natalia Aristizábal, Andrés M Cuervo, Alexandre Aleixo
We infer phylogenetic relationships, divergence times, and the diversification history of the avian Neotropical antpitta genera Hylopezus and Myrmothera (Grallariidae), based on sequence data (3139 base pairs) from two mitochondrial (ND2 and ND3) and three nuclear markers (TGFB2, MUSK and FGB-I5) from 142 individuals of the 12 currently recognized species in Hylopezus and Myrmothera and 5 outgroup species. Phylogenetic analyses recovered 19 lineages clustered into two major clades, both distributed in Central and South America...
December 9, 2017: Molecular Phylogenetics and Evolution
https://www.readbyqxmd.com/read/29226306/symbioses-with-nitrogen-fixing-bacteria-nodulation-and-phylogenetic-data-across-legume-genera
#18
Michelle E Afkhami, D Luke Mahler, Jean H Burns, Marjorie G Weber, Martin F Wojciechowski, Janet Sprent, Sharon Y Strauss
How species interactions shape global biodiversity and influence diversification is a central - but also data-hungry - question in evolutionary ecology. Microbially-based mutualisms are widespread and could cause diversification by ameliorating stress and thus allowing organisms to colonize and adapt to otherwise unsuitable habitats. Yet the role of these interactions in generating species diversity has received limited attention, especially across large taxonomic groups. In the massive angiosperm family Leguminosae, plants often associate with root-nodulating bacteria that ameliorate nutrient stress by fixing atmospheric nitrogen...
December 11, 2017: Ecology
https://www.readbyqxmd.com/read/29211107/trypanosoma-janseni-n-sp-trypanosomatida-trypanosomatidae-isolated-from-didelphis-aurita-mammalia-didelphidae-in-the-atlantic-rainforest-of-rio-de-janeiro-brazil-integrative-taxonomy-and-phylogeography-within-the-trypanosoma-cruzi-clade
#19
Camila Madeira Tavares Lopes, Rubem Figueiredo Sadok Menna-Barreto, Márcio Galvão Pavan, Mirian Cláudia De Souza Pereira, André Luiz R Roque
BACKGROUND: Didelphis spp. are a South American marsupial species that are among the most ancient hosts for the Trypanosoma spp. OBJECTIVES: We characterise a new species (Trypanosoma janseni n. sp.) isolated from the spleen and liver tissues of Didelphis aurita in the Atlantic Rainforest of Rio de Janeiro, Brazil. METHODS: The parasites were isolated and a growth curve was performed in NNN and Schneider's media containing 10% foetal bovine serum...
January 2018: Memórias do Instituto Oswaldo Cruz
https://www.readbyqxmd.com/read/29206203/de-novo-rna-sequencing-and-expression-analysis-of-aconitum-carmichaelii-to-analyze-key-genes-involved-in-the-biosynthesis-of-diterpene-alkaloids
#20
Megha Rai, Amit Rai, Noriaki Kawano, Kayo Yoshimatsu, Hiroki Takahashi, Hideyuki Suzuki, Nobuo Kawahara, Kazuki Saito, Mami Yamazaki
Aconitum carmichaelii is an important medicinal herb used widely in China, Japan, India, Korea, and other Asian countries. While extensive research on the characterization of metabolic extracts of A. carmichaelii has shown accumulation of numerous bioactive metabolites including aconitine and aconitine-type diterpene alkaloids, its biosynthetic pathway remains largely unknown. Biosynthesis of these secondary metabolites is tightly controlled and mostly occurs in a tissue-specific manner; therefore, transcriptome analysis across multiple tissues is an attractive method to identify the molecular components involved for further functional characterization...
December 5, 2017: Molecules: a Journal of Synthetic Chemistry and Natural Product Chemistry
keyword
keyword
8592
1
2
Fetch more papers »
Fetching more papers... Fetching...
Read by QxMD. Sign in or create an account to discover new knowledge that matter to you.
Remove bar
Read by QxMD icon Read
×

Search Tips

Use Boolean operators: AND/OR

diabetic AND foot
diabetes OR diabetic

Exclude a word using the 'minus' sign

Virchow -triad

Use Parentheses

water AND (cup OR glass)

Add an asterisk (*) at end of a word to include word stems

Neuro* will search for Neurology, Neuroscientist, Neurological, and so on

Use quotes to search for an exact phrase

"primary prevention of cancer"
(heart or cardiac or cardio*) AND arrest -"American Heart Association"