journal
MENU ▼
Read by QxMD icon Read
search

BMC Evolutionary Biology

journal
https://www.readbyqxmd.com/read/27905886/multi-locus-phylogeny-using-topotype-specimens-sheds-light-on-the-systematics-of-niviventer-rodentia-muridae-in-china
#1
Bin Zhang, Kai He, Tao Wan, Peng Chen, Guozheng Sun, Shaoying Liu, Truong Son Nguyen, Liangkong Lin, Xuelong Jiang
BACKGROUND: Niviventer is a genus of white-bellied rats that are among the most common rodents in the Indo-Sundaic region. The taxonomy of the genus has undergone extensive revisions and remains controversial. The current phylogeny is unresolved and was developed primarily on the basis of mitochondrial genes. Identification is extremely difficult, and a large number of GenBank sequences seem to be problematic. We extensively sampled specimens of Niviventer in China and neighboring northern Vietnam, including topotypes of the most reported species (n = 6), subspecies (n = 8), and synonyms (n = 4)...
December 1, 2016: BMC Evolutionary Biology
https://www.readbyqxmd.com/read/27905882/plasticity-in-growth-of-farmed-and-wild-atlantic-salmon-is-the-increased-growth-rate-of-farmed-salmon-caused-by-evolutionary-adaptations-to-the-commercial-diet
#2
Alison Catherine Harvey, Monica Favnebøe Solberg, Eva Troianou, Gary Robert Carvalho, Martin Ian Taylor, Simon Creer, Lise Dyrhovden, Ivar Helge Matre, Kevin Alan Glover
BACKGROUND: Domestication of Atlantic salmon for commercial aquaculture has resulted in farmed salmon displaying substantially higher growth rates than wild salmon under farming conditions. In contrast, growth differences between farmed and wild salmon are much smaller when compared in the wild. The mechanisms underlying this contrast between environments remain largely unknown. It is possible that farmed salmon have adapted to the high-energy pellets developed specifically for aquaculture, contributing to inflated growth differences when fed on this diet...
December 1, 2016: BMC Evolutionary Biology
https://www.readbyqxmd.com/read/27905874/are-sexually-selected-traits-affected-by-a-poor-environment-early-in-life
#3
Regina Vega-Trejo, Michael D Jennions, Megan L Head
BACKGROUND: Challenging conditions experienced early in life, such as a restricted diet, can detrimentally affect key life-history traits. Individuals can reduce these costs by delaying their sexual maturation, albeit at the price of the later onset of breeding, to eventually reach the same adult size as individuals that grow up in a benevolent environment. Delayed maturation can, however, still lead to other detrimental morphological and physiological changes that become apparent later in adulthood (e...
December 1, 2016: BMC Evolutionary Biology
https://www.readbyqxmd.com/read/27905871/phyinformr-phylogenetic-experimental-design-and-phylogenomic-data-exploration-in-r
#4
Alex Dornburg, J Nick Fisk, Jules Tamagnan, Jeffrey P Townsend
BACKGROUND: Analyses of phylogenetic informativeness represent an important step in screening potential or existing datasets for their proclivity toward convergent or parallel evolution of molecular sites. However, while new theory has been developed from which to predict the utility of sequence data, adoption of these advances have been stymied by a lack of software enabling application of advances in theory, especially for large next-generation sequence data sets. Moreover, there are no theoretical barriers to application of the phylogenetic informativeness or the calculation of quartet internode resolution probabilities in a Bayesian setting that more robustly accounts for uncertainty, yet there is no software with which a computationally intensive Bayesian approach to experimental design could be implemented...
December 1, 2016: BMC Evolutionary Biology
https://www.readbyqxmd.com/read/27903261/discrete-phenotypes-are-not-underpinned-by-genome-wide-genetic-differentiation-in-the-squat-lobster-munida-gregaria-crustacea-decapoda-munididae-a-multi-marker-study-covering-the-patagonian-shelf
#5
Chen Wang, Shobhit Agrawal, Jürgen Laudien, Vreni Häussermann, Christoph Held
BACKGROUND: DNA barcoding has demonstrated that many discrete phenotypes are in fact genetically distinct (pseudo)cryptic species. Genetically identical, isogenic individuals, however, can also express similarly different phenotypes in response to a trigger condition, e.g. in the environment. This alternative explanation to cryptic speciation often remains untested because it requires considerable effort to reject the hypothesis that the observed underlying genetic homogeneity of the different phenotypes may be trivially caused by too slowly evolving molecular markers...
December 1, 2016: BMC Evolutionary Biology
https://www.readbyqxmd.com/read/27903259/differential-variation-patterns-between-hubs-and-bottlenecks-in-human-protein-protein-interaction-networks
#6
Erli Pang, Yu Hao, Ying Sun, Kui Lin
BACKGROUND: The identification, description and understanding of protein-protein networks are important in cell biology and medicine, especially for the study of system biology where the focus concerns the interaction of biomolecules. Hubs and bottlenecks refer to the important proteins of a protein interaction network. Until now, very little attention has been paid to differentiate these two protein groups. RESULTS: By integrating human protein-protein interaction networks and human genome-wide variations across populations, we described the differences between hubs and bottlenecks in this study...
December 1, 2016: BMC Evolutionary Biology
https://www.readbyqxmd.com/read/27903256/revealing-hidden-species-diversity-in-closely-related-species-using-nuclear-snps-ssrs-and-dna-sequences-a-case-study-in-the-tree-genus-milicia
#7
Kasso Daïnou, Céline Blanc-Jolivet, Bernd Degen, Priscilla Kimani, Dyana Ndiade-Bourobou, Armel S L Donkpegan, Félicien Tosso, Esra Kaymak, Nils Bourland, Jean-Louis Doucet, Olivier J Hardy
BACKGROUND: Species delimitation in closely related plant taxa can be challenging because (i) reproductive barriers are not always congruent with morphological differentiation, (ii) use of plastid sequences might lead to misinterpretation, (iii) rare species might not be sampled. We revisited molecular-based species delimitation in the African genus Milicia, currently divided into M. regia (West Africa) and M. excelsa (from West to East Africa). We used 435 samples collected in West, Central and East Africa...
December 1, 2016: BMC Evolutionary Biology
https://www.readbyqxmd.com/read/27899070/multigene-phylogenetic-analysis-redefines-dung-beetles-relationships-and-classification-coleoptera-scarabaeidae-scarabaeinae
#8
Sergei Tarasov, Dimitar Dimitrov
BACKGROUND: Dung beetles (subfamily Scarabaeinae) are popular model organisms in ecology and developmental biology, and for the last two decades they have experienced a systematics renaissance with the adoption of modern phylogenetic approaches. Within this period 16 key phylogenies and numerous additional studies with limited scope have been published, but higher-level relationships of this pivotal group of beetles remain contentious and current classifications contain many unnatural groupings...
November 29, 2016: BMC Evolutionary Biology
https://www.readbyqxmd.com/read/27894257/evidence-of-functional-divergence-in-msp7-paralogous-proteins-a-molecular-evolutionary-and-phylogenetic-analysis
#9
Diego Garzón-Ospina, Johanna Forero-Rodríguez, Manuel A Patarroyo
BACKGROUND: The merozoite surface protein 7 (MSP7) is a Plasmodium protein which is involved in parasite invasion; the gene encoding it belongs to a multigene family. It has been proposed that MSP7 paralogues seem to be functionally redundant; however, recent experiments have suggested that they could have different roles. RESULTS: The msp7 multigene family has been described in newly available Plasmodium genomes; phylogenetic relationships were established in 12 species by using different molecular evolutionary approaches for assessing functional divergence amongst MSP7 members...
November 28, 2016: BMC Evolutionary Biology
https://www.readbyqxmd.com/read/27887566/the-common-redstart-as-a-suitable-model-to-study-cuckoo-host-coevolution-in-a-unique-ecological-context
#10
Peter Samaš, Jarkko Rutila, Tomáš Grim
BACKGROUND: Co-evolutionary arms-races result in spatio-temporally dynamic relationships between interacting species, e.g., brood parasites and their avian hosts. However, majority of avian co-evolutionary studies are limited to "snap-shots" of a single breeding season in an open-nesting host. In a long-term study (11 breeding seasons), we explored a unique system between the brood parasitic common cuckoo (Cuculus canorus) and its host, the common redstart (Phoenicurus phoenicurus) which is exceptional among all cuckoo hosts due to being a cavity nester...
November 25, 2016: BMC Evolutionary Biology
https://www.readbyqxmd.com/read/27887563/the-trans-generational-impact-of-population-density-signals-on-host-parasite-interactions
#11
Jessica Michel, Dieter Ebert, Matthew D Hall
BACKGROUND: The density of a host population is a key parameter underlying disease transmission, but it also has implications for the expression of disease through its effect on host physiology. In response to higher densities, individuals are predicted to either increase their immune investment in response to the elevated risk of parasitism, or conversely to decrease their immune capacity as a consequence of the stress of a crowded environment. However, an individual's health is shaped by many different factors, including their genetic background, current environmental conditions, and maternal effects...
November 25, 2016: BMC Evolutionary Biology
https://www.readbyqxmd.com/read/27881071/genome-wide-analyses-of-chitin-synthases-identify-horizontal-gene-transfers-towards-bacteria-and-allow-a-robust-and-unifying-classification-into-fungi
#12
Isabelle R Gonçalves, Sophie Brouillet, Marie-Christine Soulié, Simonetta Gribaldo, Catherine Sirven, Noémie Charron, Martine Boccara, Mathias Choquer
BACKGROUND: Chitin, the second most abundant biopolymer on earth after cellulose, is found in probably all fungi, many animals (mainly invertebrates), several protists and a few algae, playing an essential role in the development of many of them. This polysaccharide is produced by type 2 glycosyltransferases, called chitin synthases (CHS). There are several contradictory classifications of CHS isoenzymes and, as regards their evolutionary history, their origin and diversity is still a matter of debate...
November 24, 2016: BMC Evolutionary Biology
https://www.readbyqxmd.com/read/27884104/phylogeography-reveals-an-ancient-cryptic-radiation-in-east-asian-tree-frogs-hyla-japonica-group-and-complex-relationships-between-continental-and-island-lineages
#13
Christophe Dufresnes, Spartak N Litvinchuk, Amaël Borzée, Yikweon Jang, Jia-Tang Li, Ikuo Miura, Nicolas Perrin, Matthias Stöck
BACKGROUND: In contrast to the Western Palearctic and Nearctic biogeographic regions, the phylogeography of Eastern-Palearctic terrestrial vertebrates has received relatively little attention. In East Asia, tectonic events, along with Pleistocene climatic conditions, likely affected species distribution and diversity, especially through their impact on sea levels and the consequent opening and closing of land-bridges between Eurasia and the Japanese Archipelago. To better understand these effects, we sequenced mitochondrial and nuclear markers to determine phylogeographic patterns in East-Asian tree frogs, with a particular focus on the widespread H...
November 23, 2016: BMC Evolutionary Biology
https://www.readbyqxmd.com/read/27855631/a-core-phylogeny-of-dictyostelia-inferred-from-genomes-representative-of-the-eight-major-and-minor-taxonomic-divisions-of-the-group
#14
Reema Singh, Christina Schilde, Pauline Schaap
BACKGROUND: Dictyostelia are a well-studied group of organisms with colonial multicellularity, which are members of the mostly unicellular Amoebozoa. A phylogeny based on SSU rDNA data subdivided all Dictyostelia into four major groups, but left the position of the root and of six group-intermediate taxa unresolved. Recent phylogenies inferred from 30 or 213 proteins from sequenced genomes, positioned the root between two branches, each containing two major groups, but lacked data to position the group-intermediate taxa...
November 17, 2016: BMC Evolutionary Biology
https://www.readbyqxmd.com/read/27855630/structural-differences-and-differential-expression-among-rhabdomeric-opsins-reveal-functional-change-after-gene-duplication-in-the-bay-scallop-argopecten-irradians-pectinidae
#15
Anita J Porath-Krause, Autum N Pairett, Davide Faggionato, Bhagyashree S Birla, Kannan Sankar, Jeanne M Serb
BACKGROUND: Opsins are the only class of proteins used for light perception in image-forming eyes. Gene duplication and subsequent functional divergence of opsins have played an important role in expanding photoreceptive capabilities of organisms by altering what wavelengths of light are absorbed by photoreceptors (spectral tuning). However, new opsin copies may also acquire novel function or subdivide ancestral functions through changes to temporal, spatial or the level of gene expression...
November 17, 2016: BMC Evolutionary Biology
https://www.readbyqxmd.com/read/27852219/computer-vision-applied-to-herbarium-specimens-of-german-trees-testing-the-future-utility-of-the-millions-of-herbarium-specimen-images-for-automated-identification
#16
Jakob Unger, Dorit Merhof, Susanne Renner
BACKGROUND: Global Plants, a collaborative between JSTOR and some 300 herbaria, now contains about 2.48 million high-resolution images of plant specimens, a number that continues to grow, and collections that are digitizing their specimens at high resolution are allocating considerable recourses to the maintenance of computer hardware (e.g., servers) and to acquiring digital storage space. We here apply machine learning, specifically the training of a Support-Vector-Machine, to classify specimen images into categories, ideally at the species level, using the 26 most common tree species in Germany as a test case...
November 16, 2016: BMC Evolutionary Biology
https://www.readbyqxmd.com/read/27852214/time-scale-of-minor-hiv-1-complex-circulating-recombinant-forms-from-central-and-west-africa
#17
Edson Delatorre, Gonzalo Bello
BACKGROUND: Several HIV-1 circulating recombinant forms with a complex mosaic structure (CRFs_cpx) circulate in central and western African regions. Here we reconstruct the evolutionary history of some of these complex CRFs (09_cpx, 11_cpx, 13_cpx and 45_cpx) and further investigate the dissemination dynamic of the CRF11_cpx clade by using a Bayesian coalescent-based method. RESULTS: The analysis of two HIV-1 datasets comprising 181 pol (36 CRF09_cpx, 116 CRF11_cpx, 20 CRF13_cpx and 9 CRF45_cpx) and 125 env (12 CRF09_cpx, 67 CRF11_cpx, 17 CRF13_cpx and 29 CRF45_cpx) sequences pointed to quite consistent onset dates for CRF09_cpx (~1966: 1958-1979), CRF11_cpx (~1957: 1950-1966) and CRF13_cpx (~1965: 1958-1973) clades; while some divergence was found for the estimated date of origin of CRF45_cpx clade [pol = 1970 (1964-1976); env = 1960 (1952-1969)]...
November 16, 2016: BMC Evolutionary Biology
https://www.readbyqxmd.com/read/27835948/development-of-a-toolbox-to-dissect-host-endosymbiont-interactions-and-protein-trafficking-in-the-trypanosomatid-angomonas-deanei
#18
Jorge Morales, Sofia Kokkori, Diana Weidauer, Jarrod Chapman, Eugene Goltsman, Daniel Rokhsar, Arthur R Grossman, Eva C M Nowack
BACKGROUND: Bacterial endosymbionts are found across the eukaryotic kingdom and profoundly impacted eukaryote evolution. In many endosymbiotic associations with vertically inherited symbionts, highly complementary metabolic functions encoded by host and endosymbiont genomes indicate integration of metabolic processes between the partner organisms. While endosymbionts were initially expected to exchange only metabolites with their hosts, recent evidence has demonstrated that also host-encoded proteins can be targeted to the bacterial symbionts in various endosymbiotic systems...
November 11, 2016: BMC Evolutionary Biology
https://www.readbyqxmd.com/read/27832758/carriers-of-human-mitochondrial-dna-macrohaplogroup-m-colonized-india-from-southeastern-asia
#19
Patricia Marrero, Khaled K Abu-Amero, Jose M Larruga, Vicente M Cabrera
BACKGROUND: From a mtDNA dominant perspective, the exit from Africa of modern humans to colonize Eurasia occurred once, around 60 kya, following a southern coastal route across Arabia and India to reach Australia short after. These pioneers carried with them the currently dominant Eurasian lineages M and N. Based also on mtDNA phylogenetic and phylogeographic grounds, some authors have proposed the coeval existence of a northern route across the Levant that brought mtDNA macrohaplogroup N to Australia...
November 10, 2016: BMC Evolutionary Biology
https://www.readbyqxmd.com/read/27829374/the-role-of-prezygotic-isolation-mechanisms-in-the-divergence-of-two-parasite-species
#20
Tina Henrich, Martin Kalbe
BACKGROUND: The formation of reproductive barriers in diverging lineages is a prerequisite to complete speciation according to the biological species concept. In parasites with complex life cycles, speciation may be driven by adaptation to different intermediate hosts, yet diverging lineages can still share the same definitive host where reproduction takes place. In these cases, prezygotic isolation mechanisms should evolve very early and be particularly strong, preventing costly unfavourable matings...
November 9, 2016: BMC Evolutionary Biology
journal
journal
35553
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"