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"Evolutionary history"

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https://www.readbyqxmd.com/read/28531958/unique-postglacial-evolution-of-the-hornbeam-carpinus-betulus-l-in-the-carpathians-and-the-balkan-peninsula-revealed-by-chloroplast-dna
#1
Dragoş Postolache, Flaviu Popescu, Ladislav Paule, Dalibor Ballian, Peter Zhelev, Sorina Fărcaş, Juraj Paule, Ovidiu Badea
The Balkan Peninsula is one of the largest and most important European glacial refugia. However, the evolutionary history and phylogeographic pattern of temperate tree species that survived in the Balkans glacial refugia and their contribution to the genetic structure of the current population in the Carpathian Mountains remains poorly understood. Using polymerase chain reaction - restriction fragment length polymorphism (PCR-RFLP), and extensive population sampling, we explored the phylogeographic pattern of Carpinus betulus in both the Balkan Peninsula and the Carpathian region...
May 17, 2017: Science of the Total Environment
https://www.readbyqxmd.com/read/28531202/the-role-of-density-dependent-and-independent-processes-in-spawning-habitat-selection-by-salmon-in-an-arctic-riverscape
#2
Brock M Huntsman, Jeffrey A Falke, James W Savereide, Katrina E Bennett
Density-dependent (DD) and density-independent (DI) habitat selection is strongly linked to a species' evolutionary history. Determining the relative importance of each is necessary because declining populations are not always the result of altered DI mechanisms but can often be the result of DD via a reduced carrying capacity. We developed spatially and temporally explicit models throughout the Chena River, Alaska to predict important DI mechanisms that influence Chinook salmon spawning success. We used resource-selection functions to predict suitable spawning habitat based on geomorphic characteristics, a semi-distributed water-and-energy balance hydrologic model to generate stream flow metrics, and modeled stream temperature as a function of climatic variables...
2017: PloS One
https://www.readbyqxmd.com/read/28524717/first-molecular-evidence-of-mus-musculus-bactrianus-in-nepal-inferred-from-the-mitochondrial-dna-cytochrome-b-gene-sequences
#3
Pradeep Adhikari, Sang-Hyun Han, Yoo-Kyung Kim, Tae-Wook Kim, Tej Bahadur Thapa, Naresh Subedi, Prabhat Adhikari, Hong-Shik Oh
To identify the house mice collected in Pokhara and Lumbini of Nepal at the subspecies level, morphological and molecular analyses were carried out. Morphologically, two populations collected in Pokhara and Lumbini were distinguished by fur colour, but there was no significant difference in external measurements (p > .05). The phylogenetic analysis results revealed that the haplotypes sequences of mitochondrial DNA (mtDNA) Cytochrome B (CytB) gene distinguished into two distinct clades on a phylogenetic tree representing two subspecies, Mus musculus bactrianus and M...
May 19, 2017: Mitochondrial DNA. Part A. DNA Mapping, Sequencing, and Analysis
https://www.readbyqxmd.com/read/28523015/transcription-factors-in-fungi-tfome-dynamics-three-major-families-and-dual-specificity-tfs
#4
Ekaterina Shelest
Transcription factors (TFs) are essential regulators of gene expression in a cell; the entire repertoire of TFs (TFome) of a species reflects its regulatory potential and the evolutionary history of the regulatory mechanisms. In this work, I give an overview of fungal TFs, analyze TFome dynamics, and discuss TF families and types of particular interest. Whole-genome annotation of TFs in more than 200 fungal species revealed ~80 families of TFs that are typically found in fungi. Almost half of the considered genomes belonged to basidiomycetes and zygomycetes, which have been underrepresented in earlier annotations due to dearth of sequenced genomes...
2017: Frontiers in Genetics
https://www.readbyqxmd.com/read/28522998/genetic-polymorphism-in-wine-yeasts-mechanisms-and-methods-for-its-detection
#5
REVIEW
José M Guillamón, Eladio Barrio
The processes of yeast selection for using as wine fermentation starters have revealed a great phenotypic diversity both at interspecific and intraspecific level, which is explained by a corresponding genetic variation among different yeast isolates. Thus, the mechanisms involved in promoting these genetic changes are the main engine generating yeast biodiversity. Currently, an important task to understand biodiversity, population structure and evolutionary history of wine yeasts is the study of the molecular mechanisms involved in yeast adaptation to wine fermentation, and on remodeling the genomic features of wine yeast, unconsciously selected since the advent of winemaking...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28516231/molecular-evolution-of-type-ii-mage-genes-from-ancestral-maged2-gene-and-their-phylogenetic-resolution-of-basal-mammalian-clades
#6
Marcos De Donato, Sunday O Peters, Tanveer Hussain, Hectorina Rodulfo, Bolaji N Thomas, Masroor E Babar, Ikhide G Imumorin
Type II melanoma-associated antigens (MAGE) are a subgroup of about a dozen proteins found in various locations in the genome and expressed in normal tissues, thus are not related to cancer as the type I MAGE genes. This gene family exists as a single copy in non-mammals and monotremata, but found as two copies in metatherians and occur as a diverse group in all eutherians. Our studies suggest MAGED2 as the ancestor of this subfamily and the most likely evolutionary history of eutherian type II MAGE genes is hereby proposed based on synteny conservation, phylogenetic relations, genome location, homology conservation, and the protein and gene structures...
May 17, 2017: Mammalian Genome: Official Journal of the International Mammalian Genome Society
https://www.readbyqxmd.com/read/28515896/a-worldwide-phylogeography-of-the-whiteworm-lichens-thamnolia-reveals-three-lineages-with-distinct-habitats-and-evolutionary-histories
#7
Ioana Onuţ-Brännström, Leif Tibell, Hanna Johannesson
Thamnolia is a lichenized fungus with an extremely wide distribution, being encountered in arctic and alpine environments in most continents. In this study, we used molecular markers to investigate the population structure of the fungal symbiont and the associated photosynthetic partner of Thamnolia. By analyzing molecular, morphological, and chemical variation among 253 specimens covering the species distribution range, we revealed the existence of three mycobiont lineages. One lineage (Lineage A) is confined to the tundra region of Siberia and the Aleutian Islands, a second (Lineage B) is found in the high alpine region of the Alps and the Carpathians Mountains, and a third (Lineage C) has a worldwide distribution and covers both the aforementioned ecosystems...
May 2017: Ecology and Evolution
https://www.readbyqxmd.com/read/28515739/patterns-of-inter-chromosomal-gene-conversion-on-the-male-specific-region-of-the-human-y-chromosome
#8
REVIEW
Beniamino Trombetta, Eugenia D'Atanasio, Fulvio Cruciani
The male-specific region of the human Y chromosome (MSY) is characterized by the lack of meiotic recombination and it has long been considered an evolutionary independent region of the human genome. In recent years, however, the idea that human MSY did not have an independent evolutionary history begun to emerge with the discovery that inter-chromosomal gene conversion (ICGC) can modulate the genetic diversity of some portions of this genomic region. Despite the study of the dynamics of this molecular mechanism in humans is still in its infancy, some peculiar features and consequences of it can be summarized...
2017: Frontiers in Genetics
https://www.readbyqxmd.com/read/28514638/the-evolution-of-cooperation-interacting-phenotypes-among-social-partners
#9
Mat Edenbrow, Bronwyn H Bleakley, Safi K Darden, Charles R Tyler, Indar W Ramnarine, Darren P Croft
Models of cooperation among nonkin suggest that social assortment is important for the evolution of cooperation. Theory predicts that interacting phenotypes, whereby an individual's behavior depends on the behavior of its social partners, can drive such social assortment. We measured repeated indirect genetic effects (IGEs) during cooperative predator inspection in eight populations of Trinidadian guppies (Poecilia reticulata) that vary in their evolutionary history of predation. Four broad patterns emerged that were dependent on river, predation history, and sex: (i) current partner behavior had the largest effect on focal behavior, with fish from low-predation habitats responding more to their social partners than fish from high-predation habitats; (ii) different focal/partner behavior combinations can generate cooperation; (iii) some high-predation fish exhibited carryover effects across social partners; and (iv) high-predation fish were more risk averse...
June 2017: American Naturalist
https://www.readbyqxmd.com/read/28512377/species-delimitation-and-description-of-mesocriconema-nebraskense-n-sp-nematoda-criconematidae-a-morphologically-cryptic-parthenogenetic-species-from-north-american-grasslands
#10
Magdalena Olson, Timothy Harris, Rebecca Higgins, Peter Mullin, Kirsten Powers, Sean Olson, Thomas O Powers
Nematode surveys of North American grasslands conducted from 2010 to 2015 frequently recovered a species of criconematid nematode morphologically resembling Mesocriconema curvatum. These specimens were recovered from remnant native prairies in the central tallgrass ecoregion of North America, and not from surrounding agroecosystems. Historical records indicate that M. curvatum is a cosmopolitan species feeding on a wide range of agronomic and native plants. DNA barcoding indicates North American grasslands contain at least 10 phylogenetically distinct lineages of Mesocriconema that resemble, but are not, M...
March 2017: Journal of Nematology
https://www.readbyqxmd.com/read/28512347/insight-into-the-global-evolution-of-rodentia-associated-morbilli-related-paramyxoviruses
#11
Wissem Ghawar, Hervé Pascalis, Jihéne Bettaieb, Julien Mélade, Adel Gharbi, Mohamed Ali Snoussi, Dhafer Laouini, Steven M Goodman, Afif Ben Salah, Koussay Dellagi
One portion of the family Paramyxoviridae is a group of Unclassified Morbilli-Related Viruses (UMRV) recently recognized in wild small mammals. At a global level, the evolutionary history of these viruses is not properly understood and the relationships between UMRV and their hosts still remain largely unstudied. The present study revealed, for the first time, that Rodentia associated UMRV emerged from a common ancestor in southern Africa more than 4000 years ago. Sequenced UMRV originating from different regions in the world, clustered into four well-supported viral lineages, which suggest that strain diversification occurred during host dispersal and associated exchanges, with purifying selection pressure as the principal evolutionary force...
May 16, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28510761/the-diversity-of-carbon-dioxide-concentrating-mechanisms-in-marine-diatoms-as-inferred-from-their-genetic-content
#12
Chen Shen, Christopher L Dupont, Brian M Hopkinson
Marine diatoms are one of the most ecologically significant primary producers in the ocean. Most diatoms use a CO2-concentrating mechanism (CCM) to overcome the scarcity of CO2 in the ocean and limitations of the carbon-fixing enzyme Rubisco. However, the CCMs in model diatoms differ substantially in their genetic make-up and structural organization. To assess the extent of CCM diversity in marine diatoms more generally, we analyzed genome and transcriptome data from 31 diatom strains to identify putative CCM genes, examine the overall CCM architecture, and study CCM development in the context of the evolutionary history of these diatoms...
May 16, 2017: Journal of Experimental Botany
https://www.readbyqxmd.com/read/28510607/recent-evolutionary-history-of-chrysoperla-externa-hagen-1861-neuroptera-chrysopidae-in-brazil
#13
Adriana C Morales-Corrêa E Castro, Nara Cristina Chiarini Pena Barbosa
This work aimed to elucidate the distribution of Chrysoperla externa haplotypes and investigate whether it exhibits structure based on genetic composition as opposed to geographic location. The genetic diversity of C. externa, analyzed by AMOVA using the COI and 16S rRNA genes as mitochondrial markers, showed significant haplotype structure arising from genetic differences that was not associated with sampling location. This was reflected in the network grouping. Bayesian inference showed that haplotype distribution may have its origins in C...
2017: PloS One
https://www.readbyqxmd.com/read/28510184/footprint-of-the-eastern-euroasian-past-in-italian-populations-of-cryptotaenia-thomasii-ten-dc
#14
Anna Maria Palermo, Liliana Bernardo, Domenico Gargano, Giuseppe Pellegrino
BACKGROUND: The knowledge of the genetic architecture of closely related species and/or populations of a single species can be very useful to shed light on the processes that led to their current distributions. The present study provides a preliminary evaluation of the conservation status of the populations of Cryptotaenia thomasii, a very narrow endemic species occurring in southern Italy. Previous studies showed that C. thomasii was phylogenetically closely related to C. flahaultii, endemic species of Caucasus, and to evaluate its conservation status and the genetic variability of plant species the internal transcribed spacers (ITSs) of nuclear ribosomal DNA were sequenced and the SNPs were analyzed...
December 2017: Botanical Studies (Taipei, Taiwan)
https://www.readbyqxmd.com/read/28505307/sexual-dimorphism-and-retinal-mosaic-diversification-following-the-evolution-of-a-violet-receptor-in-butterflies
#15
Kyle J McCulloch, Furong Yuan, Ying Zhen, Matthew L Aardema, Gilbert Smith, Jorge Llorente-Bousquets, Peter Andolfatto, Adriana D Briscoe
Numerous animal lineages have expanded and diversified the opsin-based photoreceptors in their eyes underlying color vision behavior. However, the selective pressures giving rise to new photoreceptors and their spectral tuning remain mostly obscure. Previously, we identified a violet receptor (UV2) that is the result of a UV opsin gene duplication specific to Heliconius butterflies. At the same time the violet receptor evolved, Heliconius evolved UV-yellow coloration on their wings, due to the pigment 3-hydroxykynurenine (3-OHK) and the nanostructure architecture of the scale cells...
May 15, 2017: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/28505209/genetic-identification-and-evolutionary-trends-of-the-seagrass-halophila-nipponica-in-temperate-coastal-waters-of-korea
#16
Young Kyun Kim, Seung Hyeon Kim, Joo Mi Yi, Chang-Keun Kang, Frederick Short, Kun-Seop Lee
Although seagrass species in the genus Halophila are generally distributed in tropical or subtropical regions, H. nipponica has been reported to occur in temperate coastal waters of the northwestern Pacific. Because H. nipponica occurs only in the warm temperate areas influenced by the Kuroshio Current and shows a tropical seasonal growth pattern, such as severely restricted growth in low water temperatures, it was hypothesized that this temperate Halophila species diverged from tropical species in the relatively recent evolutionary past...
2017: PloS One
https://www.readbyqxmd.com/read/28502769/tracing-the-enterococci-from-paleozoic-origins-to-the-hospital
#17
François Lebreton, Abigail L Manson, Jose T Saavedra, Timothy J Straub, Ashlee M Earl, Michael S Gilmore
We examined the evolutionary history of leading multidrug resistant hospital pathogens, the enterococci, to their origin hundreds of millions of years ago. Our goal was to understand why, among the vast diversity of gut flora, enterococci are so well adapted to the modern hospital environment. Molecular clock estimation, together with analysis of their environmental distribution, phenotypic diversity, and concordance with host fossil records, place the origins of the enterococci around the time of animal terrestrialization, 425-500 mya...
May 18, 2017: Cell
https://www.readbyqxmd.com/read/28501611/multilocus-phylogeny-and-statistical-biogeography-clarify-the-evolutionary-history-of-major-lineages-of-turtles
#18
Anieli G Pereira, Juliana Sterli, Filipe R R Moreira, Carlos G Schrago
Despite their complex evolutionary history and the rich fossil record, the higher level phylogeny and historical biogeography of living turtles have not been investigated in a comprehensive and statistical framework. To tackle these issues, we assembled a large molecular dataset, maximizing both taxonomic and gene sampling. As different models provide alternative biogeographical scenarios, we have explicitly tested such hypotheses in order to reconstruct a robust biogeographical history of Testudines. We scanned publicly available databases for nucleotide sequences and composed a dataset comprising 13 loci for 294 living species of Testudines, which accounts for all living genera and 85% of their extant species diversity...
May 10, 2017: Molecular Phylogenetics and Evolution
https://www.readbyqxmd.com/read/28500327/metazoan-ribosome-inactivating-protein-encoding-genes-acquired-by-horizontal-gene-transfer
#19
Walter J Lapadula, Paula L Marcet, María L Mascotti, M Virginia Sanchez-Puerta, Maximiliano Juri Ayub
Ribosome inactivating proteins (RIPs) are RNA N-glycosidases that depurinate a specific adenine residue in the conserved sarcin/ricin loop of 28S rRNA. These enzymes are widely distributed among plants and their presence has also been confirmed in several bacterial species. Recently, we reported for the first time in silico evidence of RIP encoding genes in metazoans, in two closely related species of insects: Aedes aegypti and Culex quinquefasciatus. Here, we have experimentally confirmed the presence of these genes in mosquitoes and attempted to unveil their evolutionary history...
May 12, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28499469/phylogenetically-diverse-groups-of-bradyrhizobium-isolated-from-nodules-of-tree-and-annual-legume-species-growing-in-ethiopia
#20
Tulu Degefu, Endalkachew Wolde-Meskel, Kedir Woliy, Åsa Frostegård
Bacteria belonging to the genus Bradyrhizobium nodulate various leguminous woody plants and herbs, including economically important crops such as soybean, peanut and cowpea. Here we analysed 39 Bradyrhizobium strains originating from root nodules of the leguminous trees and crops Acacia saligna, Faidherbia albida, Erythrina brucei, Albizia gummifera, Millettia ferruginea, Cajanus cajan, Vigna unguiculata and Phaseolus vulgaris, growing in southern Ethiopia. Multilocus sequence analyses (MLSA) of the 16S rRNA, glnII, recA, gyrB and dnaK genes and the ITS region grouped the test strains into seven well-supported genospecies (I-VII), six of which occupied distinct positions excluding all hitherto defined Bradyrhizobium species...
April 26, 2017: Systematic and Applied Microbiology
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