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Molecular Ecology

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https://www.readbyqxmd.com/read/28742942/regulation-of-transposable-elements-interplay-between-te-encoded-regulatory-sequences-and-host-specific-trans-acting-factors-in-drosophila-melanogaster
#1
Ana Marija Jakšić, Robert Kofler, Christian Schlötterer
Transposable elements (TEs) are mobile genetic elements that can move around the genome and their expression is one precondition for this mobility. Because the insertion of TEs in new genomic positions is largely deleterious, the molecular mechanisms for transcriptional suppression have been extensively studied. In contrast, very little is known about their primary transcriptional regulation. Here, we characterize the expression dynamics of TE families in Drosophila melanogaster across a broad temperature range (13-29°C)...
July 25, 2017: Molecular Ecology
https://www.readbyqxmd.com/read/28742933/gene-expression-is-more-strongly-influenced-by-age-than-caste-in-the-ant-lasius-niger
#2
Eric R Lucas, Jonathan Romiguier, Laurent Keller
Phenotypic plasticity, where a single genome can give rise to different phenotypes, underlies many remarkable features of the natural world and occurs in a wide range of organisms. Understanding the transcriptional differences that underlie plastic phenotypes remains a major unsolved problem in biology. In many ants, females can develop into either queens or workers, two phenotypes with different morphology, behaviour and longevity. In comparison to workers, queens are larger, more fecund and longer-lived. Here, we study gene expression differences between queens and workers in the ant Lasius niger...
July 25, 2017: Molecular Ecology
https://www.readbyqxmd.com/read/28742928/shotgun-mitogenomics-across-body-size-classes-in-a-local-assemblage-of-tropical-diptera-phylogeny-species-diversity-and-mitochondrial-abundance-spectrum
#3
Le Qin Choo, Alex Crampton-Platt, Alfried P Vogler
Mitochondrial genomes can be assembled readily from shotgun sequenced DNA mixtures of mass-trapped arthropods ('mitochondrial metagenomics'), speeding up the taxonomic characterization. Bulk sequencing was conducted on some 800 individuals of Diptera obtained by canopy-fogging of a single tree in Borneo dominated by small (<1.5 mm) individuals. Specimens were split into five body-size classes for DNA extraction, to equalize read numbers across specimens and to study how body size, a key ecological trait, interacts with species and phylogenetic diversity...
July 25, 2017: Molecular Ecology
https://www.readbyqxmd.com/read/28742284/aquatic-animals-promote-antibiotic-resistance-gene-dissemination-in-water-via-conjugation-role-of-different-regions-within-the-zebra-fish-intestinal-tract-and-impact-on-fish-intestinal-microbiota
#4
Jialun Fu, Dong Yang, Min Jin, Weili Liu, Xin Zhao, Chenyu Li, Tianyu Zhao, Jingfeng Wang, Zhixian Gao, Zhiqiang Shen, Zhigang Qiu, Jun-Wen Li
The aqueous environment is one of many reservoirs of antibiotic resistance genes (ARGs). Fish, as important aquatic animals which possess ideal intestinal niches for bacteria to grow and multiply, may ingest antibiotic resistance bacteria from aqueous environment. The fish gut would be a suitable environment for conjugal gene transfer including those encoding antibiotic resistance. However, little is known in relation to the impact of ingested ARGs or ARB on gut microbiota. Here, we applied the cultivation method, qPCR, nuclear molecular genetic marker and 16S rDNA amplicon sequencing technologies to develop a plasmid-mediated ARG transfer model of zebrafish...
July 25, 2017: Molecular Ecology
https://www.readbyqxmd.com/read/28742230/allopatric-speciation-despite-historical-gene-flow-divergence-and-hybridization-in-carex-furva-and-c-lucennoiberica-cyperaceae-inferred-from-plastid-and-nuclear-rad-seq-data
#5
E Maguilla, M Escudero, A L Hipp, M Luceño
Gene flow among incipient species can act as a creative or destructive force in the speciation process, generating variation on which natural selection can act while, potentially, undermining population divergence. The flowering plant genus Carex exhibits a rapid and relatively recent radiation with many species limits still unclear. This is the case with the Iberian Peninsula (Spain and Portugal) endemic C. lucennoiberica, which lay unrecognized within Carex furva until its recent description as a new species...
July 25, 2017: Molecular Ecology
https://www.readbyqxmd.com/read/28734110/when-can-refuges-mediate-the-genetic-effects-of-fire-regimes-a-simulation-study-of-the-effects-of-topography-and-weather-on-neutral-and-adaptive-genetic-diversity-in-fire-prone-landscapes
#6
Sam C Banks, Ian D Davies, Geoffrey J Cary
Understanding how landscape heterogeneity mediates the effects of fire on biodiversity is increasingly important under global changes in fire regimes. We used a simulation experiment to investigate how fire regimes interact with topography and weather to shape neutral and selection-driven genetic diversity under alternative dispersal scenarios, and to explore the conditions under which micro-refuges can maintain genetic diversity of populations exposed to recurrent fire. Spatial heterogeneity in simulated fire frequency occurred in topographically-complex landscapes, with fire refuges and fire-prone 'hotspots' apparent...
July 22, 2017: Molecular Ecology
https://www.readbyqxmd.com/read/28734075/high-occurrence-of-jellyfish-predation-by-black-browed-and-campbell-albatross-identified-by-dna-metabarcoding
#7
Julie C McInnes, Rachael Alderman, Mary-Anne Lea, Ben Raymond, Bruce E Deagle, Richard A Phillips, Andrew Stanworth, David R Thompson, Paulo Catry, Henri Weimerskirch, Cristián G Suazo, Michaël Gras, Simon N Jarman
Gelatinous zooplankton are a large component of the animal biomass in all marine environments, but are considered to be uncommon in the diet of most marine top predators. However, the diets of key predator groups like seabirds have conventionally been assessed from stomach content analyses, which cannot detect most gelatinous prey. As marine top predators are used to identify changes in the overall species composition of marine ecosystems, such biases in dietary assessment may impact our detection of important ecosystem regime shifts...
July 22, 2017: Molecular Ecology
https://www.readbyqxmd.com/read/28734072/plant-species-richness-and-productivity-determine-the-diversity-of-soil-fungal-guilds-in-temperate-coniferous-forest-and-bog-habitats
#8
Indrek Hiiesalu, Mohammad Bahram, Leho Tedersoo
Fungi have important roles as decomposers, mycorrhizal root symbionts and pathogens in forest ecosystems, but there is limited information about their diversity and composition at the landscape-scale. This work aims to disentangle the factors underlying fungal richness and composition along the landscape-scale moisture, organic matter and productivity gradients. Using high-throughput sequencing, we identified soil fungi from 54 low-productivity Pinus sylvestris-dominated plots across three study areas in Estonia and determined the main predictors of fungal richness based on edaphic, floristic and spatial variables...
July 22, 2017: Molecular Ecology
https://www.readbyqxmd.com/read/28734070/genome-scans-on-experimentally-evolved-populations-reveal-candidate-regions-for-adaptation-to-plant-resistance-in-the-potato-cyst-nematode-globodera-pallida
#9
D Eoche-Bosy, M Gautier, M Esquibet, F Legeai, A Bretaudeau, O Bouchez, S Fournet, E Grenier, J Montarry
Improving resistance durability involves to be able to predict the adaptation speed of pathogen populations. Identifying the genetic bases of pathogen adaptation to plant resistances is a useful step to better understand and anticipate this phenomenon. Globodera pallida is a major pest of potato crop for which a resistance QTL, GpaVvrn , has been identified in Solanum vernei. However, its durability is threatened as G. pallida populations are able to adapt to the resistance in few generations. The aim of the present study was to investigate the genomic regions involved in the resistance breakdown by coupling experimental evolution and high-density genome scan...
July 22, 2017: Molecular Ecology
https://www.readbyqxmd.com/read/28734069/pathogen-richness-and-abundance-predict-patterns-of-adaptive-mhc-variation-in-insular-amphibians
#10
Supen Wang, Conghui Liu, Anthony B Wilson, Na Zhao, Xianping Li, Wei Zhu, Xu Gao, Xuan Liu, Yiming Li
The identification of the factors responsible for genetic variation and differentiation at adaptive loci can provide important insights into the evolutionary process, and is crucial for the effective management of threatened species. We studied the impact of environmental viral richness and abundance on functional diversity and differentiation of the MHC class Ia locus in populations of the black-spotted pond frog (Pelophylax nigromaculatus), an IUCN-listed species, on 24 land-bridge islands of the Zhoushan Archipelago and 3 nearby mainland sites...
July 22, 2017: Molecular Ecology
https://www.readbyqxmd.com/read/28734067/range-instability-leads-to-cytonuclear-discordance-in-a-morphologically-cryptic-ground-squirrel-species-complex
#11
Mark A Phuong, Ke Bi, Craig Moritz
The processes responsible for cytonuclear discordance frequently remain unclear. Here, we employed an exon capture dataset and demographic methods to test hypotheses generated by species distribution models to examine how contrasting histories of range stability vs. fluctuation have caused cytonuclear concordance and discordance in ground squirrel lineages from the Otospermophilus beecheyi species complex. Previous studies in O. beecheyi revealed three morphologically cryptic and highly divergent mitochondrial DNA lineages (named the Northern, Central, and Southern lineages based on geography) with only the Northern lineage exhibiting concordant divergence for nuclear genes...
July 22, 2017: Molecular Ecology
https://www.readbyqxmd.com/read/28734064/extensive-seed-and-pollen-dispersal-and-assortative-mating-in-the-rain-forest-tree-entandrophragma-cylindricum-meliaceae-inferred-from-indirect-and-direct-analyses
#12
F K Monthe, O J Hardy, J L Doucet, J Loo, J Duminil
Pollen and seed dispersal are key processes affecting the demographic and evolutionary dynamics of plant species, and are also important considerations for the sustainable management of timber trees. Through direct and indirect genetic analyses we studied the mating system and the extent of pollen and seed dispersal in an economically-important timber species, Entandrophragma cylindricum (Meliaceae). We genotyped adult trees, seeds and saplings from a 400-ha study plot in a natural forest from East Cameroon using eight nuclear microsatellite markers...
July 22, 2017: Molecular Ecology
https://www.readbyqxmd.com/read/28734054/population-demography-and-heterozygosity-fitness-correlations-in-natural-guppy-populations-an-examination-using-sexually-selected-fitness-traits
#13
Catherine E Grueber, John L Fitzpatrick, Alessandro Devigili, Clelia Gasparini, Indar W Ramnarine, Jonathan P Evans
Heterozygosity-fitness correlations (HFCs) have been examined in a wide diversity of contexts, and the results are often used to infer the role of inbreeding in natural populations. Although population demography, reflected in population-level genetic parameters such as allelic diversity or identity disequilibrium, is expected to play a role in the emergence and detectability of HFCs, direct comparisons of variation in HFCs across many populations of the same species, with different genetic histories, are rare...
July 22, 2017: Molecular Ecology
https://www.readbyqxmd.com/read/28734050/estimating-synchronous-demographic-changes-across-populations-using-habc-and-its-application-for-a-herpetological-community-from-northeastern-brazil
#14
Marcelo Gehara, Adrian Antonio Garda, Fernanda P Werneck, Eliana F Oliveira, Emanuel Masiero da Fonseca, Felipe Camurugi, Felipe M de Magalhães, Flávia Mol Lanna, Jack W Sites, Ricardo Marques, Ricardo Silveira-Filho, Vinícius A São Pedro, Guarino R Colli, Gabriel C Costa, Frank T Burbrink
Many studies propose that Quaternary climatic cycles contracted and /or expanded the ranges of species and biomes. Strong expansion-contraction dynamics of biomes presume concerted demographic changes of associated fauna. The analysis of temporal concordance of demographic changes can be used to test the influence of Quaternary climate on diversification processes. Hierarchical approximate Bayesian computation (hABC) is a powerful and flexible approach that models genetic data from multiple species, and can be used to estimate the temporal concordance of demographic processes...
July 22, 2017: Molecular Ecology
https://www.readbyqxmd.com/read/28731545/genome-scale-data-reveals-that-endemic-poecilia-populations-from-small-sulfidic-springs-display-no-evidence-of-inbreeding
#15
Anthony P Brown, Ryan Greenway, Samuel Morgan, Corey R Quackenbush, Luca Giordani, Lenin Arias-Rodriguez, Michael Tobler, Joanna L Kelley
Populations with limited ranges can be highly vulnerable to changes in their environment and are, thus, of high conservation concern. Populations that experience human-induced range reductions are often highly inbred and lack genetic diversity, but it is unknown whether this is also the case for populations with naturally small ranges. The fishes Poecilia sulphuraria (listed as critically endangered) and Poecilia thermalis, which are endemic to small hydrogen sulfide rich springs in southern Mexico, are examples of such populations with inherently small habitats...
July 21, 2017: Molecular Ecology
https://www.readbyqxmd.com/read/28731541/demography-and-genome-divergence-of-lake-and-stream-populations-of-an-east-african-cichlid-fish
#16
Bernd Egger, Marius Rösti, Astrid Böhne, Olivia Roth, Walter Salzburger
Disentangling the processes and mechanisms underlying divergent selection in diversification is facilitated by the comparative study of replicate population pairs that have diverged along a similar environmental gradient. Such a setting is realized in a cichlid fish from southern Lake Tanganyika, Astatotilapia burtoni, which occurs both within the lake proper as well as in various affluent rivers. Previous studies demonstrated that independent lake and stream populations show respectively similar adaptations to the two habitat regimes...
July 21, 2017: Molecular Ecology
https://www.readbyqxmd.com/read/28727261/more-than-meets-the-eye-the-barrier-effect-of-the-yangtze-river-outflow
#17
Gang Ni, Elizabeth Kern, Yun-Wei Dong, Qi Li, Joong-Ki Park
The Yangtze (Changjiang) River enters the East China Sea with huge annual freshwater and sediment deposits. This outflow, known as the Changjiang Diluted Water (CDW), causes striking ecological gradients that potentially shape coastal species' distribution and differentiation. The CDW has long been rendered as a marine biogeographic boundary separating cold-temperature and warm-water faunas, but it remains unclear whether and to what extent it acts as an intraspecific barrier. Here we synthesize published phylogeographic studies related to the CDW to address these issues...
July 20, 2017: Molecular Ecology
https://www.readbyqxmd.com/read/28727201/gene-expression-stasis-and-plasticity-following-migration-into-a-foreign-environment
#18
Brian K Lohman, William E Stutz, Daniel I Bolnick
Selection against migrants is key to maintaining genetic differences between populations linked by dispersal. However, migrants may mitigate fitness costs by proactively choosing among available habitats, or by phenotypic plasticity. We previously reported that a reciprocal transplant of lake and stream stickleback (Gasterosteus aculeatus) found little support for divergent selection. Here, we revisit that experiment to test whether phenotypic plasticity in gene expression may have helped migrants adjust to unfamiliar habitats...
July 20, 2017: Molecular Ecology
https://www.readbyqxmd.com/read/28727200/landscape-genetic-analyses-reveal-fine-scale-effects-of-forest-fragmentation-in-an-insular-tropical-bird
#19
Aurélie Khimoun, William Peterman, Cyril Eraud, Bruno Faivre, Nicolas Navarro, Stéphane Garnier
Within the framework of landscape genetics, resistance surface modelling is particularly relevant to explicitly test competing hypotheses about landscape effects on gene flow. To investigate how fragmentation of tropical forest affects population connectivity in a forest-specialist bird species, we optimized resistance surfaces without a priori specification, using least-cost (LCP) or resistance (IBR) distances. We implemented a two-step procedure in order i) to objectively define the landscape thematic resolution (level of detail in classification scheme to describe landscape variables) and spatial extent (area within the landscape boundaries) and then ii) to test the relative role of several landscape features (elevation, roads, land cover) in genetic differentiation in the Plumbeous Warbler (Setophaga plumbea)...
July 20, 2017: Molecular Ecology
https://www.readbyqxmd.com/read/28727195/patterns-of-divergence-across-the-geographic-and-genomic-landscape-of-a-butterfly-hybrid-zone-associated-with-a-climatic-gradient
#20
Sean F Ryan, Michael C Fontaine, Mark J Scriber, Michael E Pfrender, Shawn T O'Neil, Jessica J Hellmann
Hybrid zones are a valuable tool for studying the process of speciation and for identifying the genomic regions undergoing divergence and the ecological (extrinsic) and non-ecological (intrinsic) factors involved. Here, we explored the genomic and geographic landscape of divergence in a hybrid zone between Papilio glaucus and Papilio canadensis. Using a genome scan of 28,417 ddRAD SNPs, we identified genomic regions under possible selection and examined their distribution in the context of previously identified candidate genes for ecological adaptations...
July 20, 2017: Molecular Ecology
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