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BMC Evolutionary Biology

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https://www.readbyqxmd.com/read/29914372/inferring-demographic-parameters-in-bacterial-genomic-data-using-bayesian-and-hybrid-phylogenetic-methods
#1
Sebastian Duchene, David A Duchene, Jemma L Geoghegan, Zoe A Dyson, Jane Hawkey, Kathryn E Holt
BACKGROUND: Recent developments in sequencing technologies make it possible to obtain genome sequences from a large number of isolates in a very short time. Bayesian phylogenetic approaches can take advantage of these data by simultaneously inferring the phylogenetic tree, evolutionary timescale, and demographic parameters (such as population growth rates), while naturally integrating uncertainty in all parameters. Despite their desirable properties, Bayesian approaches can be computationally intensive, hindering their use for outbreak investigations involving genome data for a large numbers of pathogen isolates...
June 19, 2018: BMC Evolutionary Biology
https://www.readbyqxmd.com/read/29914368/phylogenetic-and-genomic-analyses-of-the-ribosomal-oxygenases-riox1-no66-and-riox2-mina53-provide-new-insights-into-their-evolution
#2
Katharina E Bräuer, Kevin Brockers, Jasmin Moneer, Annette Feuchtinger, Evi Wollscheid-Lengeling, Andreas Lengeling, Alexander Wolf
BACKGROUND: Translation of specific mRNAs can be highly regulated in different cells, tissues or under pathological conditions. Ribosome heterogeneity can originate from variable expression or post-translational modifications of ribosomal proteins. The ribosomal oxygenases RIOX1 (NO66) and RIOX2 (MINA53) modify ribosomal proteins by histidine hydroxylation. A similar mechanism is present in prokaryotes. Thus, ribosome hydroxylation may be a well-conserved regulatory mechanism with implications in disease and development...
June 19, 2018: BMC Evolutionary Biology
https://www.readbyqxmd.com/read/29909776/the-evolution-of-a-series-of-behavioral-traits-is-associated-with-autism-risk-genes-in-cavefish
#3
Masato Yoshizawa, Alexander Settle, Meredith C Hermosura, Lillian J Tuttle, Nicolas Cetraro, Courtney N Passow, Suzanne E McGaugh
BACKGROUND: An essential question in evolutionary biology is whether shifts in a set of polygenic behaviors share a genetic basis across species. Such a behavioral shift is seen in the cave-dwelling Mexican tetra, Astyanax mexicanus. Relative to surface-dwelling conspecifics, cavefish do not school (asocial), are hyperactive and sleepless, adhere to a particular vibration stimulus (imbalanced attention), behave repetitively, and show elevated stress hormone levels. Interestingly, these traits largely overlap with the core symptoms of human autism spectrum disorder (ASD), raising the possibility that these behavioral traits are underpinned by a similar set of genes (i...
June 18, 2018: BMC Evolutionary Biology
https://www.readbyqxmd.com/read/29907080/decadal-stability-in-genetic-variation-and-structure-in-the-intertidal-seaweed-fucus-serratus-heterokontophyta-fucaceae
#4
Alexander Jueterbock, James A Coyer, Jeanine L Olsen, Galice Hoarau
BACKGROUND: The spatial distribution of genetic diversity and structure has important implications for conservation as it reveals a species' strong and weak points with regard to stability and evolutionary capacity. Temporal genetic stability is rarely tested in marine species other than commercially important fishes, but is crucial for the utility of temporal snapshots in conservation management. High and stable diversity can help to mitigate the predicted northward range shift of seaweeds under the impact of climate change...
June 15, 2018: BMC Evolutionary Biology
https://www.readbyqxmd.com/read/29898669/morphology-of-the-bryozoan-cinctipora-elegans-cyclostomata-cinctiporidae-with-first-data-on-its-sexual-reproduction-and-the-cyclostome-neuro-muscular-system
#5
Thomas F Schwaha, Stephan Handschuh, Andrew N Ostrovsky, Andreas Wanninger
BACKGROUND: Cyclostome bryozoans are an ancient group of marine colonial suspension-feeders comprising approximately 700 extant species. Previous morphological studies are mainly restricted to skeletal characters whereas data on soft tissues obtained by state-of-the-art methods are still lacking. In order to contribute to issues related to cyclostome ground pattern reconstruction, we analyzed the morphology of the neuromuscular system Cinctipora elegans by means of immunocytochemical staining, confocal laser scanning microscopy, histological sections and microCT imaging...
June 14, 2018: BMC Evolutionary Biology
https://www.readbyqxmd.com/read/29898656/natural-variation-in-genes-potentially-involved-in-plant-architecture-and-adaptation-in-switchgrass-panicum-virgatum-l
#6
Bochra A Bahri, Guillaume Daverdin, Xiangyang Xu, Jan-Fang Cheng, Kerrie W Barry, E Charles Brummer, Katrien M Devos
BACKGROUND: Advances in genomic technologies have expanded our ability to accurately and exhaustively detect natural genomic variants that can be applied in crop improvement and to increase our knowledge of plant evolution and adaptation. Switchgrass (Panicum virgatum L.), an allotetraploid (2n = 4× = 36) perennial C4 grass (Poaceae family) native to North America and a feedstock crop for cellulosic biofuel production, has a large potential for genetic improvement due to its high genotypic and phenotypic variation...
June 14, 2018: BMC Evolutionary Biology
https://www.readbyqxmd.com/read/29898661/chinstrap-penguin-population-genetic-structure-one-or-more-populations-along-the-southern-ocean
#7
Isidora Mura-Jornet, Carolina Pimentel, Gisele P M Dantas, Maria Virginia Petry, Daniel González-Acuña, Andrés Barbosa, Andrew D Lowther, Kit M Kovacs, Elie Poulin, Juliana A Vianna
BACKGROUND: Historical factors, demography, reproduction and dispersal are crucial in determining the genetic structure of seabirds. In the Antarctic marine environment, penguins are a major component of the avian biomass, dominant predators and important bioindicators of ecological change. Populations of chinstrap penguins have decreased in nearly all their breeding sites, and their range is expanding throughout the Antarctic Peninsula. Population genetic structure of this species has been studied in some colonies, but not between breeding colonies in the Antarctic Peninsula or at the species' easternmost breeding colony (Bouvetøya)...
June 13, 2018: BMC Evolutionary Biology
https://www.readbyqxmd.com/read/29884143/embryonic-expression-patterns-and-phylogenetic-analysis-of-panarthropod-sox-genes-insight-into-nervous-system-development-segmentation-and-gonadogenesis
#8
Ralf Janssen, Emil Andersson, Ellinor Betnér, Sifra Bijl, Will Fowler, Lars Höök, Jake Leyhr, Alexander Mannelqvist, Virginia Panara, Kate Smith, Sydney Tiemann
BACKGROUND: Sox (Sry-related high-mobility-group box) genes represent important factors in animal development. Relatively little, however, is known about the embryonic expression patterns and thus possible function(s) of Sox genes during ontogenesis in panarthropods (Arthropoda+Tardigrada+Onychophora). To date, studies have been restricted exclusively to higher insects, including the model system Drosophila melanogaster, with no comprehensive data available for any other arthropod group, or any tardigrade or onychophoran...
June 8, 2018: BMC Evolutionary Biology
https://www.readbyqxmd.com/read/29879905/correction-to-a-new-species-of-xenoturbella-from-the-western-pacific-ocean-and-the-evolution-of-xenoturbella
#9
Hiroaki Nakano, Hideyuki Miyazawa, Akiteru Maeno, Toshihiko Shiroishi, Keiichi Kakui, Ryo Koyanagi, Miyuki Kanda, Noriyuki Satoh, Akihito Omori, Hisanori Kohtsuka
After publication of Nakano et al. (2017) [1], the authors became aware of the fact that the new species-group name erected for the two specimens of a Japanese xenoturbellid species in the article is not available because Nakano et al. (2017) [1] does not meet the requirement of the amendment of Article 8.5.3 of the International Code of Zoological Nomenclature (the Code) [2]. The authors therefore describe the two xenoturbellids as a new species again in this correction article. Methods for morphological observation, DNA extraction and sequencing were as described in Nakano et al...
June 7, 2018: BMC Evolutionary Biology
https://www.readbyqxmd.com/read/29879898/unraveling-historical-introgression-and-resolving-phylogenetic-discord-within-catostomus-osteichthys-catostomidae
#10
Max R Bangs, Marlis R Douglas, Steven M Mussmann, Michael E Douglas
BACKGROUND: Porous species boundaries can be a source of conflicting hypotheses, particularly when coupled with variable data and/or methodological approaches. Their impacts can often be magnified when non-model organisms with complex histories of reticulation are investigated. One such example is the genus Catostomus (Osteichthys, Catostomidae), a freshwater fish clade with conflicting morphological and mitochondrial phylogenies. The former is hypothesized as reflecting the presence of admixed genotypes within morphologically distinct lineages, whereas the latter is interpreted as the presence of distinct morphologies that emerged multiple times through convergent evolution...
June 7, 2018: BMC Evolutionary Biology
https://www.readbyqxmd.com/read/29879897/expected-and-unexpected-evolution-of-plant-rna-editing-factors-clb19-crr28-and-rare1-retention-of-clb19-despite-a-phylogenetically-deep-loss-of-its-two-known-editing-targets-in-poaceae
#11
Anke Hein, Volker Knoop
BACKGROUND: C-to-U RNA editing in mitochondria and chloroplasts and the nuclear-encoded, RNA-binding PPR proteins acting as editing factors present a wide field of co-evolution between the different genetic systems in a plant cell. Recent studies on chloroplast editing factors RARE1 and CRR28 addressing one or two chloroplast editing sites, respectively, found them strictly conserved among 65 flowering plants as long as one of their RNA editing targets remained present. RESULTS: Extending the earlier sampling to 117 angiosperms with high-quality genome or transcriptome data, we find more evidence confirming previous conclusions but now also identify cases for expected evolutionary transition states such as retention of RARE1 despite loss of its editing target or the degeneration of CRR28 truncating its carboxyterminal DYW domain...
June 7, 2018: BMC Evolutionary Biology
https://www.readbyqxmd.com/read/29879896/homeotic-transformations-reflect-departure-from-the-mammalian-rule-of-seven-cervical-vertebrae-in-sloths-inferences-on-the-hox-code-and-morphological-modularity-of-the-mammalian-neck
#12
Christine Böhmer, Eli Amson, Patrick Arnold, Anneke H van Heteren, John A Nyakatura
BACKGROUND: Sloths are one of only two exceptions to the mammalian 'rule of seven' vertebrae in the neck. As a striking case of breaking the evolutionary constraint, the explanation for the exceptional number of cervical vertebrae in sloths is still under debate. Two diverging hypotheses, both ultimately linked to the low metabolic rate of sloths, have been proposed: hypothesis 1 involves morphological transformation of vertebrae due to changes in the Hox gene expression pattern and hypothesis 2 assumes that the Hox gene expression pattern is not altered and the identity of the vertebrae is not changed...
June 7, 2018: BMC Evolutionary Biology
https://www.readbyqxmd.com/read/29879895/the-inference-of-gray-whale-eschrichtius-robustus-historical-population-attributes-from-whole-genome-sequences
#13
Anna Brüniche-Olsen, Rick Westerman, Zuzanna Kazmierczyk, Vladimir V Vertyankin, Celine Godard-Codding, John W Bickham, J Andrew DeWoody
BACKGROUND: Commercial whaling caused extensive demographic declines in many great whale species, including gray whales that were extirpated from the Atlantic Ocean and dramatically reduced in the Pacific Ocean. The Eastern Pacific gray whale has recovered since the 1982 ban on commercial whaling, but the Western Pacific gray whale-once considered possibly extinct-consists of only about 200 individuals and is considered critically endangered by some international authorities. Herein, we use whole-genome sequencing to investigate the demographic history of gray whales from the Pacific and use environmental niche modelling to make predictions about future gene flow...
June 7, 2018: BMC Evolutionary Biology
https://www.readbyqxmd.com/read/29855267/influence-of-genome-and-bio-ecology-on-the-prevalence-of-genome-exchange-in-unisexuals-of-the-ambystoma-complex
#14
France Beauregard, Bernard Angers
BACKGROUND: Unisexuals of the blue-spotted salamander complex are thought to reproduce by kleptogenesis. Genome exchanges associated with this sperm-dependent mode of reproduction are expected to result in a higher genetic variation and multiple ploidy levels compared to clonality. However, the existence of some populations exclusively formed of genetically identical individuals suggests that factors could prevent genome exchanges. This study aimed at assessing the prevalence of genome exchange among unisexuals of the Ambystoma laterale-jeffersonianum complex from 10 sites in the northern part of their distribution...
May 31, 2018: BMC Evolutionary Biology
https://www.readbyqxmd.com/read/29848319/mind-the-gap-the-mitochondrial-control-region-and-its-power-as-a-phylogenetic-marker-in-echinoids
#15
Omri Bronstein, Andreas Kroh, Elisabeth Haring
BACKGROUND: In Metazoa, mitochondrial markers are the most commonly used targets for inferring species-level molecular phylogenies due to their extremely low rate of recombination, maternal inheritance, ease of use and fast substitution rate in comparison to nuclear DNA. The mitochondrial control region (CR) is the main non-coding area of the mitochondrial genome and contains the mitochondrial origin of replication and transcription. While sequences of the cytochrome oxidase subunit 1 (COI) and 16S rRNA genes are the prime mitochondrial markers in phylogenetic studies, the highly variable CR is typically ignored and not targeted in such analyses...
May 30, 2018: BMC Evolutionary Biology
https://www.readbyqxmd.com/read/29848310/origin-evolution-and-divergence-of-plant-class-c-gh9-endoglucanases
#16
Siddhartha Kundu, Rita Sharma
BACKGROUND: Glycoside hydrolases of the GH9 family encode cellulases that predominantly function as endoglucanases and have wide applications in the food, paper, pharmaceutical, and biofuel industries. The partitioning of plant GH9 endoglucanases, into classes A, B, and C, is based on the differential presence of transmembrane, signal peptide, and the carbohydrate binding module (CBM49). There is considerable debate on the distribution and the functions of these enzymes which may vary in different organisms...
May 30, 2018: BMC Evolutionary Biology
https://www.readbyqxmd.com/read/29848299/a-targeted-in-situ-hybridization-screen-identifies-putative-seminal-fluid-proteins-in-a-simultaneously-hermaphroditic-flatworm
#17
Michael Weber, Julia Wunderer, Birgit Lengerer, Robert Pjeta, Marcelo Rodrigues, Lukas Schärer, Peter Ladurner, Steven A Ramm
BACKGROUND: Along with sperm, in many taxa ejaculates also contain large numbers of seminal fluid proteins (SFPs). SFPs and sperm are transferred to the mating partner, where they are thought to play key roles in mediating post-mating sexual selection. They modulate the partner's behavior and physiology in ways that influence the reproductive success of both partners, thus potentially leading to sexual conflict. Despite the presumed general functional and evolutionary significance of SFPs, their identification and characterization has to date focused on just a few animal groups, predominantly insects and mammals...
May 30, 2018: BMC Evolutionary Biology
https://www.readbyqxmd.com/read/29843598/cryptic-plutella-species-show-deep-divergence-despite-the-capacity-to-hybridize
#18
Kym D Perry, Gregory J Baker, Kevin J Powis, Joanne K Kent, Christopher M Ward, Simon W Baxter
BACKGROUND: Understanding genomic and phenotypic diversity among cryptic pest taxa has important implications for the management of pests and diseases. The diamondback moth, Plutella xylostella L., has been intensively studied due to its ability to evolve insecticide resistance and status as the world's most destructive pest of brassicaceous crops. The surprise discovery of a cryptic species endemic to Australia, Plutella australiana Landry & Hebert, raised questions regarding the distribution, ecological traits and pest status of the two species, the capacity for gene flow and whether specific management was required...
May 29, 2018: BMC Evolutionary Biology
https://www.readbyqxmd.com/read/29843594/the-effects-of-repeated-whole-genome-duplication-events-on-the-evolution-of-cytokinin-signaling-pathway
#19
Elisabeth Kaltenegger, Svetlana Leng, Alexander Heyl
BACKGROUND: It is thought that after whole-genome duplications (WGDs), a large fraction of the duplicated gene copies is lost over time while few duplicates are retained. Which factors promote survival or death of a duplicate remains unclear and the underlying mechanisms are poorly understood. According to the model of gene dosage balance, genes encoding interacting proteins are predicted to be preferentially co-retained after WGDs. Among these are genes encoding proteins involved in complexes or in signal transduction...
May 29, 2018: BMC Evolutionary Biology
https://www.readbyqxmd.com/read/29843591/correction-to-mandibulate-convergence-in-an-armoured-cambrian-stem-chelicerate
#20
Cédric Aria, Jean-Bernard Caron
The original article [1] had 4 paragraphs which contained erroneous information. In this correction article the correct and incorrect information is shown.
May 29, 2018: BMC Evolutionary Biology
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