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"Evolutionary history"

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https://www.readbyqxmd.com/read/28812633/diversity-begets-diversity-in-competition-for-space
#1
Daniel S Maynard, Mark A Bradford, Daniel L Lindner, Linda T A van Diepen, Serita D Frey, Jessie A Glaeser, Thomas W Crowther
Competition can profoundly affect biodiversity patterns by determining whether similar species are likely to coexist. When species compete directly for space, competitive ability differences should theoretically promote trait and phylogenetic clustering, provided that niche differences are otherwise minimal. Yet many sessile communities exhibit high biodiversity despite minimal reliance on niche differentiation. A potential explanation is that intransitive competition ('rock-paper-scissors' competition) not only promotes species richness but also fosters coexistence among highly dissimilar species with different competitive strategies...
May 15, 2017: Nature ecology & evolution
https://www.readbyqxmd.com/read/28812620/tipping-points-in-the-dynamics-of-speciation
#2
Patrik Nosil, Jeffrey L Feder, Samuel M Flaxman, Zachariah Gompert
Speciation can be gradual or sudden and involve few or many genetic changes. Inferring the processes generating such patterns is difficult, and may require consideration of emergent and non-linear properties of speciation, such as when small changes at tipping points have large effects on differentiation. Tipping points involve positive feedback and indirect selection stemming from associations between genomic regions, bi-stability due to effects of initial conditions and evolutionary history, and dependence on modularity of system components...
January 24, 2017: Nature ecology & evolution
https://www.readbyqxmd.com/read/28812610/genome-wide-interrogation-advances-resolution-of-recalcitrant-groups-in-the-tree-of-life
#3
Dahiana Arcila, Guillermo Ortí, Richard Vari, Jonathan W Armbruster, Melanie L J Stiassny, Kyung D Ko, Mark H Sabaj, John Lundberg, Liam J Revell, Ricardo Betancur-R
Much progress has been achieved in disentangling evolutionary relationships among species in the tree of life, but some taxonomic groups remain difficult to resolve despite increasing availability of genome-scale data sets. Here we present a practical approach to studying ancient divergences in the face of high levels of conflict, based on explicit gene genealogy interrogation (GGI). We show its efficacy in resolving the controversial relationships within the largest freshwater fish radiation (Otophysi) based on newly generated DNA sequences for 1,051 loci from 225 species...
January 13, 2017: Nature ecology & evolution
https://www.readbyqxmd.com/read/28812602/prenatal-development-supports-a-single-origin-of-laryngeal-echolocation-in-bats
#4
Zhe Wang, Tengteng Zhu, Huiling Xue, Na Fang, Junpeng Zhang, Libiao Zhang, Jian Pang, Emma C Teeling, Shuyi Zhang
Bat laryngeal echolocation is considered as one of the most complex and diverse modes of auditory sensory perception in animals and its evolutionary history has been the cause of many scientific controversies in the past two decades. To date, the majority of scientific evidence supports that bats (Chiroptera) are divided into two subordinal groups: Yinpterochiroptera, containing the laryngeal echolocating superfamily Rhinolophidae as sister taxa to the non-laryngeal echolocating family Pteropodidae; and Yangochiroptera, containing all other laryngeal echolocating lineages...
January 9, 2017: Nature ecology & evolution
https://www.readbyqxmd.com/read/28810429/individual-differences-in-pain-sensitivity-predict-the-experience-of-unfairness
#5
Haixia Wang, Kefeng Li, Xiaofei Xie
Pain has shaped our evolutionary history, and pain-free experiences are critical for our health. There are, however, enormous individual differences in pain sensitivity, and the psychological consequences of this heterogeneity are only poorly understood. Here, we investigated whether individual differences in pain sensitivity predicted the experience of unfairness. We found that the magnitude of pain sensitivity correlated with the extent to which participants experienced unfairness. This association was due to the shared human alarm system of unfairness and pain sensitivity...
January 1, 2017: Journal of Health Psychology
https://www.readbyqxmd.com/read/28809850/function-related-replacement-of-bacterial-siderophore-pathways
#6
Hilke Bruns, Max Crüsemann, Anne-Catrin Letzel, Mohammad Alanjary, James O McInerney, Paul R Jensen, Stefan Schulz, Bradley S Moore, Nadine Ziemert
Bacterial genomes are rife with orphan biosynthetic gene clusters (BGCs) associated with secondary metabolism of unrealized natural product molecules. Often up to a tenth of the genome is predicted to code for the biosynthesis of diverse metabolites with mostly unknown structures and functions. This phenomenal diversity of BGCs coupled with their high rates of horizontal transfer raise questions about whether they are really active and beneficial, whether they are neutral and confer no advantage, or whether they are carried in genomes because they are parasitic or addictive...
August 15, 2017: ISME Journal
https://www.readbyqxmd.com/read/28808007/early-photosynthetic-eukaryotes-inhabited-low-salinity-habitats
#7
Patricia Sánchez-Baracaldo, John A Raven, Davide Pisani, Andrew H Knoll
The early evolutionary history of the chloroplast lineage remains an open question. It is widely accepted that the endosymbiosis that established the chloroplast lineage in eukaryotes can be traced back to a single event, in which a cyanobacterium was incorporated into a protistan host. It is still unclear, however, which Cyanobacteria are most closely related to the chloroplast, when the plastid lineage first evolved, and in what habitats this endosymbiotic event occurred. We present phylogenomic and molecular clock analyses, including data from cyanobacterial and chloroplast genomes using a Bayesian approach, with the aim of estimating the age for the primary endosymbiotic event, the ages of crown groups for photosynthetic eukaryotes, and the independent incorporation of a cyanobacterial endosymbiont by Paulinella Our analyses include both broad taxon sampling (119 taxa) and 18 fossil calibrations across all Cyanobacteria and photosynthetic eukaryotes...
August 14, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28805631/bumble-bee-ecophysiology-integrating-the-changing-environment-and-the-organism
#8
REVIEW
S Hollis Woodard
Bumble bees are among the most ecologically and economically important pollinators worldwide, yet many of their populations are being threatened by a suite of interrelated, human-mediated environmental changes. Here, I discuss recent progress in our understanding of bumble bee ecophysiology, including advances related to thermal biology in light of global warming; nutritional biology in the context of declining food resources; and the capacity for bumble bees to exhibit physiological plasticity or adaptations to novel or extreme environments, with reference to their evolutionary history and current biogeography...
August 2017: Current Opinion in Insect Science
https://www.readbyqxmd.com/read/28804953/basic-helix-loop-helix-transcription-factors-in-evolution-roles-in-development-of-mesoderm-and-neural-tissues
#9
REVIEW
Fuki Gyoja
Basic helix-loop-helix (bHLH) transcription factors have attracted the attention of developmental and evolutionary biologists for decades because of their conserved functions in mesodermal and neural tissue formation in both vertebrates and fruit flies. Their evolutionary history is of special interest because it will likely provide insights into developmental processes and refinement of metazoan-specific traits. This review briefly considers advances in developmental biological studies on bHLHs/HLHs. I also discuss recent genome-wide surveys and molecular phylogenetic analyses of these factors in a wide range of metazoans...
August 14, 2017: Genesis: the Journal of Genetics and Development
https://www.readbyqxmd.com/read/28798378/perception-of-facial-expressions-reveals-selective-affect-biased-attention-in-humans-and-orangutans
#10
Carla Pritsch, Silke Telkemeyer, Cordelia Mühlenbeck, Katja Liebal
Rapid detection and recognition of another individual's emotional state plays a pivotal role for humans and, most likely, other social species. Proper reactions contribute to an individual's survival in potentially dangerous situations; this is ensured by a preferential attention towards salient cues. The predisposition to attend to certain categories of affectively salient stimuli- also referred to as affect-biased attention - is likely shared with other species, since fast detection of and appropriate reaction to threats is crucial to survival...
August 10, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28798375/recurrent-horizontal-transfer-of-arsenite-methyltransferase-genes-facilitated-adaptation-of-life-to-arsenic
#11
Song-Can Chen, Guo-Xin Sun, Barry P Rosen, Si-Yu Zhang, Ye Deng, Bo-Kai Zhu, Christopher Rensing, Yong-Guan Zhu
The toxic metalloid arsenic has been environmentally ubiquitous since life first arose nearly four billion years ago and presents a challenge for the survival of all living organisms. Its bioavailability has varied dramatically over the history of life on Earth. As life spread, biogeochemical and climate changes cyclically increased and decreased bioavailable arsenic. To elucidate the history of arsenic adaptation across the tree of life, we reconstructed the phylogeny of the arsM gene that encodes the As(III) S-adenosylmethionine (SAM) methyltransferase...
August 10, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28797594/rare-endoparasitic-asteriomyzostomum-annelida-asteriomyzostomidae-from-japan-including-three-new-species-descriptions-and-their-phylogenetic-position-within-myzostomida
#12
Naoto Jimi, Takeya Moritaki, Hiroshi Kajihara
The rare myzostomid genus Asteriomyzostomum Jägersten, 1940 consists of two species, both parasitizing sea stars. The phylogenetic position of this genus among Myzostomida has not been previously shown using molecular data. In this study, three species of Asteriomyzostomum were collected from the Kumano Sea, Japan, and are described as A. jinshou sp. nov., A. monroeae sp. nov., and A. hercules sp. nov. Additional specimens of the genus Asteromyzostomum were also collected from the Kumano Sea and briefly reported as Asteromyzostomum sp...
August 7, 2017: Parasitology International
https://www.readbyqxmd.com/read/28797098/comparative-genomics-of-two-super-shedder-isolates-of-escherichia-coli-o157-h7
#13
Robab Katani, Rebecca Cote, Indira T Kudva, Chitrita DebRoy, Terrance M Arthur, Vivek Kapur
Shiga toxin-producing Escherichia coli O157:H7 (O157) are zoonotic foodborne pathogens and of major public health concern that cause considerable intestinal and extra-intestinal illnesses in humans. O157 colonize the recto-anal junction (RAJ) of asymptomatic cattle who shed the bacterium into the environment through fecal matter. A small subset of cattle, termed super-shedders (SS), excrete O157 at a rate (≥ 104 CFU/g of feces) that is several orders of magnitude greater than other colonized cattle and play a major role in the prevalence and transmission of O157...
2017: PloS One
https://www.readbyqxmd.com/read/28796200/new-infant-cranium-from-the-african-miocene-sheds-light-on-ape-evolution
#14
Isaiah Nengo, Paul Tafforeau, Christopher C Gilbert, John G Fleagle, Ellen R Miller, Craig Feibel, David L Fox, Josh Feinberg, Kelsey D Pugh, Camille Berruyer, Sara Mana, Zachary Engle, Fred Spoor
The evolutionary history of extant hominoids (humans and apes) remains poorly understood. The African fossil record during the crucial time period, the Miocene epoch, largely comprises isolated jaws and teeth, and little is known about ape cranial evolution. Here we report on the, to our knowledge, most complete fossil ape cranium yet described, recovered from the 13 million-year-old Middle Miocene site of Napudet, Kenya. The infant specimen, KNM-NP 59050, is assigned to a new species of Nyanzapithecus on the basis of its unerupted permanent teeth, visualized by synchrotron imaging...
August 9, 2017: Nature
https://www.readbyqxmd.com/read/28795290/development-and-characterization-of-24-chloroplast-microsatellite-markers-for-two-species-of-eranthis-ranunculaceae
#15
Ami Oh, Byoung-Un Oh
Chloroplast microsatellites for two Korean endemic species, Eranthis byunsanensis and E. pungdoensis (Ranunculaceae), were isolated to address the questions of their distributional patterns and evolutionary relationships, using next-generation sequencing. Twenty-four polymorphic chloroplast microsatellite markers for these two species were developed, and then characterized in 65 individuals (55 individuals of E. byunsanensis and 10 individuals of E. pungdoensis). The number of alleles per locus ranged from 2 to 9; the average number of alleles across all the loci scored 4...
August 9, 2017: Molecular Biology Reports
https://www.readbyqxmd.com/read/28795237/the-adaptive-evolution-database-taed-a-new-release-of-a-database-of-phylogenetically-indexed-gene-families-from-chordates
#16
Russell A Hermansen, Benjamin P Oswald, Stormy Knight, Stephen D Shank, David Northover, Katharine L Korunes, Stephen N Michel, David A Liberles
With the large collections of gene and genome sequences, there is a need to generate curated comparative genomic databases that enable interpretation of results in an evolutionary context. Such resources can facilitate an understanding of the co-evolution of genes in the context of a genome mapped onto a phylogeny, of a protein structure, and of interactions within a pathway. A phylogenetically indexed gene family database, the adaptive evolution database (TAED), is presented that organizes gene families and their evolutionary histories in a species tree context...
August 9, 2017: Journal of Molecular Evolution
https://www.readbyqxmd.com/read/28794275/did-true-frogs-dispersify
#17
Kin Onn Chan, Rafe M Brown
The interplay between range expansion and concomitant diversification is of fundamental interest to evolutionary biologists, particularly when linked to intercontinental dispersal and/or large scale extinctions. The evolutionary history of true frogs has been characterized by circumglobal range expansion. As a lineage that survived the Eocene-Oligocene extinction event (EOEE), the group provides an ideal system to test the prediction that range expansion triggers increased net diversification. We constructed the most densely sampled, time-calibrated phylogeny to date in order to: (i) characterize tempo and patterns of diversification; (ii) assess the impact of the EOEE; and (iii) test the hypothesis that range expansion was followed by increased net diversification...
August 2017: Biology Letters
https://www.readbyqxmd.com/read/28794033/ancient-evolution-and-dispersion-of-human-papillomavirus-type-58-variants
#18
Zigui Chen, Wendy C S Ho, Siaw Shi Boon, Priscilla T Y Law, Martin C W Chan, Rob DeSalle, Robert D Burk, Paul K S Chan
Human papillomavirus type 58 is found in 10-18% of cervical cancers in East Asia but rather uncommon elsewhere. The distribution and oncogenic potential of HPV58 variants appear to be heterogeneous since the E7 T20I/G63S variant is more prevalent in East Asia and confers 7-9 fold higher risk for cervical precancer and cancer. However, the underlying genomic mechanisms that explain the geographic and carcinogenic diversity of HPV58 variants are still poorly understood. In this study, we used a combination of phylogenetic analyses and bioinformatics to investigate the deep evolutionary history of HPV58 complete genome variants...
August 9, 2017: Journal of Virology
https://www.readbyqxmd.com/read/28792414/evolution-human-microbe-interactions-and-life-history-plasticity
#19
REVIEW
Graham Rook, Fredrik Bäckhed, Bruce R Levin, Margaret J McFall-Ngai, Angela R McLean
A bacterium was once a component of the ancestor of all eukaryotic cells, and much of the human genome originated in microorganisms. Today, all vertebrates harbour large communities of microorganisms (microbiota), particularly in the gut, and at least 20% of the small molecules in human blood are products of the microbiota. Changing human lifestyles and medical practices are disturbing the content and diversity of the microbiota, while simultaneously reducing our exposures to the so-called old infections and to organisms from the natural environment with which human beings co-evolved...
July 29, 2017: Lancet
https://www.readbyqxmd.com/read/28790409/plant-organ-evolution-revealed-by-phylotranscriptomics-in-arabidopsis-thaliana
#20
Li Lei, Joshua G Steffen, Edward J Osborne, Christopher Toomajian
The evolution of phenotypes occurs through changes both in protein sequence and gene expression levels. Though much of plant morphological evolution can be explained by changes in gene expression, examining its evolution has challenges. To gain a new perspective on organ evolution in plants, we applied a phylotranscriptomics approach. We combined a phylostratigraphic approach with gene expression based on the strand-specific RNA-seq data from seedling, floral bud, and root of 19 Arabidopsis thaliana accessions to examine the age and sequence divergence of transcriptomes from these organs and how they adapted over time...
August 8, 2017: Scientific Reports
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