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Molecular ecology

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https://www.readbyqxmd.com/read/28316119/animal-tracking-meets-migration-genomics-transcriptomic-analysis-of-a-partially-migratory-bird-species
#1
Paolo Franchini, Iker Irisarri, Adam Fudickar, Andreas Schmidt, Axel Meyer, Martin Wikelski, Jesko Partecke
Seasonal migration is a widespread phenomenon, which is found in many different lineages of animals. This spectacular behaviour allows animals to avoid seasonally adverse environmental conditions to exploit more favourable habitats. Migration has been intensively studied in birds, which display astonishing variation in migration strategies, thus providing a powerful system for studying the ecological and evolutionary processes that shape migratory behaviour. Despite intensive research, the genetic basis of migration remains largely unknown...
March 17, 2017: Molecular Ecology
https://www.readbyqxmd.com/read/28316112/molecular-ecology-studies-of-species-radiations-current-research-gaps-opportunities-and-challenges
#2
Marylaure de la Harpe, Margot Paris, Dirk N Karger, Jonathan Rolland, Michael Kessler, Nicolas Salamin, Christian Lexer
Understanding the drivers and limits of species radiations is a crucial goal of evolutionary genetics and molecular ecology, yet research on this topic has been hampered by the notorious difficulty of connecting micro- and macro-evolutionary approaches to studying the drivers of diversification. To chart the current research gaps, opportunities, and challenges of molecular ecology approaches to studying radiations, we examine the literature in the journal Molecular Ecology and re-visit recent high-profile examples of evolutionary genomic research on radiations...
March 18, 2017: Molecular Ecology
https://www.readbyqxmd.com/read/28301470/pleistocene-refugia-and-genetic-diversity-patterns-in-west-africa-insights-from-the-liana-chasmanthera-dependens-menispermaceae
#3
Andrew Chibuzor Iloh, Marco Schmidt, Alexandra Nora Muellner-Riehl, Oluwatoyin Temitayo Ogundipe, Juraj Paule
Processes shaping the African Guineo-Congolian rain forest, especially in the West African part, are not well understood. Recent molecular studies, based mainly on forest tree species, confirmed the previously proposed division of the western African Guineo-Congolian rain forest into Upper Guinea (UG) and Lower Guinea (LG) separated by the Dahomey Gap (DG). Here we studied nine populations in the area of the DG and the borders of LG and UG of the widespread liana species, Chasmanthera dependens (Menispermaceae) by amplified fragment length polymorphism (AFLP), a chloroplast DNA sequence marker, and modelled the distribution based on current as well as paleoclimatic data (Holocene Climate Optimum, ca...
2017: PloS One
https://www.readbyqxmd.com/read/28301237/aspergillosis-a-natural-infection-in-poultry-mycological-and-molecular-characterization-and-determination-of-gliotoxin-in-aspergillus-fumigatus-isolates
#4
Verónica Montes de Oca, Sara Esther Valdés, Carolina Segundo, Gabriela Guadalupe Gómez, José Ramírez, Roberto Arnulfo Cervantes
Aspergillosis affects all types of birds; it causes the loss of specimens with high ecologic value and also leads to significant economic losses within the poultry industry. The main etiologic agent is Aspergillus fumigatus , a filamentary fungus with multiple virulence factors, such as gliotoxin (GT), which is an immunosuppressive epipolythiodioxopiperazine molecule. Necropsy was performed on 73 poultry from different provenances, all of which presented with a respiratory semiology compatible with aspergillosis...
March 2017: Avian Diseases
https://www.readbyqxmd.com/read/28300110/the-plant-perceptron-connects-environment-to-development
#5
Ben Scheres, Wim H van der Putten
Plants cope with the environment in a variety of ways, and ecological analyses attempt to capture this through life-history strategies or trait-based categorization. These approaches are limited because they treat the trade-off mechanisms that underlie plant responses as a black box. Approaches that involve the molecular or physiological analysis of plant responses to the environment have elucidated intricate connections between developmental and environmental signals, but in only a few well-studied model species...
March 15, 2017: Nature
https://www.readbyqxmd.com/read/28299864/robust-inference-of-genetic-architecture-in-mapping-studies
#6
Jon Slate
The genetic architecture of a trait usually refers to the number and magnitude of loci that explain phenotypic variation. A description of genetic architecture can help us to understand how genetic variation is maintained, how traits have evolved and how phenotypes might respond to selection. However, linkage mapping and association studies can suffer from problems of bias, especially when conducted in natural populations where the opportunity to perform studies with very large sample sizes can be limited. In this issue of Molecular Ecology, Li and colleagues perform an association study of brain traits in ninespine sticklebacks Pungitius pungitius...
March 2017: Molecular Ecology
https://www.readbyqxmd.com/read/28298352/the-interactions-of-ants-with-their-biotic-environment
#7
EDITORIAL
Guillaume Chomicki, Susanne S Renner
This special feature results from the symposium 'Ants 2016: ant interactions with their biotic environments' held in Munich in May 2016 and deals with the interactions between ants and other insects, plants, microbes and fungi, studied at micro- and macroevolutionary levels with a wide range of approaches, from field ecology to next-generation sequencing, chemical ecology and molecular genetics. In this paper, we review key aspects of these biotic interactions to provide background information for the papers of this special feature After listing the major types of biotic interactions that ants engage in, we present a brief overview of ant/ant communication, ant/plant interactions, ant/fungus symbioses, and recent insights about ants and their endosymbionts...
March 15, 2017: Proceedings. Biological Sciences
https://www.readbyqxmd.com/read/28298348/a-phylogenetic-perspective-on-the-association-between-ants-hymenoptera-formicidae-and-black-yeasts-ascomycota-chaetothyriales
#8
Marie Vasse, Hermann Voglmayr, Veronika Mayer, Cécile Gueidan, Maximilian Nepel, Leandro Moreno, Sybren de Hoog, Marc-André Selosse, Doyle McKey, Rumsaïs Blatrix
The frequency and the geographical extent of symbiotic associations between ants and fungi of the order Chaetothyriales have been highlighted only recently. Using a phylogenetic approach based on seven molecular markers, we showed that ant-associated Chaetothyriales are scattered through the phylogeny of this order. There was no clustering according to geographical origin or to the taxonomy of the ant host. However, strains tended to be clustered according to the type of association with ants: strains from ant-made carton and strains from plant cavities occupied by ants ('domatia') rarely clustered together...
March 15, 2017: Proceedings. Biological Sciences
https://www.readbyqxmd.com/read/28296259/taxonomy-free-molecular-diatom-index-for-high-throughput-edna-biomonitoring
#9
Laure Apothéloz-Perret-Gentil, Arielle Cordonier, François Straub, Jennifer Iseli, Philippe Esling, Jan Pawlowski
Current biodiversity assessment and biomonitoring are largely based on the morphological identification of selected bioindicator taxa. Recently, several attempts have been made to use eDNA metabarcoding as an alternative tool. However, until now, most applied metabarcoding studies have been based on the taxonomic assignment of sequences that provides reference to morphospecies ecology. Usually, only a small portion of metabarcoding data can be used due to a limited reference database and a lack of phylogenetic resolution...
March 14, 2017: Molecular Ecology Resources
https://www.readbyqxmd.com/read/28296168/plant-xylem-hydraulics-what-we-understand-current-research-and-future-challenges
#10
Martin D Venturas, John S Sperry, Uwe G Hacke
Herein we review the current state-of-the-art of plant hydraulics in the context of plant physiology, ecology, and evolution, focusing on current and future research opportunities. We explain the physics of water transport in plants and the limits of this transport system, highlighting the relationships between xylem structure and function. We describe the great variety of techniques existing for evaluating xylem resistance to cavitation. We address several methodological issues and their connection with current debates on conduit refilling and exponential shape vulnerability curves...
March 14, 2017: Journal of Integrative Plant Biology
https://www.readbyqxmd.com/read/28295830/interspecific-hybridization-causes-long-term-phylogenetic-discordance-between-nuclear-and-mitochondrial-genomes-in-freshwater-fishes
#11
Graham P Wallis, Sophia Cameron-Christie, Hannah L Kennedy, Gemma Palmer, Tessa R Sanders, David J Winter
Classification, phylogeography and the testing of evolutionary hypotheses rely on correct estimation of species phylogeny. Early molecular phylogenies often relied on mtDNA alone, which acts as a single linkage group with one history. Over the last decade, the use of multiple nuclear sequences has often revealed conflict among gene trees. This observation can be attributed to hybridization, lineage sorting, paralogy or selection. Here we use 54 groups of fishes from 48 studies to estimate the degree of concordance between mitochondrial and nuclear gene trees in two ecological grades of fishes: marine and freshwater...
March 12, 2017: Molecular Ecology
https://www.readbyqxmd.com/read/28295044/novel-transcriptome-assembly-and-comparative-toxicity-pathway-analysis-in-mahi-mahi-coryphaena-hippurus-embryos-and-larvae-exposed-to-deepwater-horizon-oil
#12
Elvis Genbo Xu, Edward M Mager, Martin Grosell, E Starr Hazard, Gary Hardiman, Daniel Schlenk
The impacts of Deepwater Horizon (DWH) oil on morphology and function during embryonic development have been documented for a number of fish species, including the economically and ecologically important pelagic species, mahi-mahi (Coryphaena hippurus). However, further investigations on molecular events and pathways responsible for developmental toxicity have been largely restricted due to the limited molecular data available for this species. We sought to establish the de novo transcriptomic database from the embryos and larvae of mahi-mahi exposed to water accommodated fractions (HEWAFs) of two DWH oil types (weathered and source oil), in an effort to advance our understanding of the molecular aspects involved during specific toxicity responses...
March 15, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28291233/lysogeny-in-nature-mechanisms-impact-and-ecology-of-temperate-phages
#13
Cristina Howard-Varona, Katherine R Hargreaves, Stephen T Abedon, Matthew B Sullivan
Viruses that infect bacteria (phages) can influence bacterial community dynamics, bacterial genome evolution and ecosystem biogeochemistry. These influences differ depending on whether phages establish lytic, chronic or lysogenic infections. Although the first two produce virion progeny, with lytic infections resulting in cell destruction, phages undergoing lysogenic infections replicate with cells without producing virions. The impacts of lysogeny are numerous and well-studied at the cellular level, but ecosystem-level consequences remain underexplored compared to those of lytic infections...
March 14, 2017: ISME Journal
https://www.readbyqxmd.com/read/28290496/transcriptome-analysis-of-a-wild-bird-reveals-physiological-responses-to-the-urban-environment
#14
Hannah Watson, Elin Videvall, Martin N Andersson, Caroline Isaksson
Identifying the molecular basis of environmentally induced phenotypic variation presents exciting opportunities for furthering our understanding of how ecological processes and the environment can shape the phenotype. Urban and rural environments present free-living organisms with different challenges and opportunities, which have marked consequences for the phenotype, yet little is known about responses at the molecular level. We characterised transcriptomes from an urban and a rural population of great tits Parus major, demonstrating striking differences in gene expression profiles in both blood and liver tissues...
March 14, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28290270/host-associations-and-turnover-of-haemosporidian-parasites-in-manakins-aves-pipridae
#15
Alan Fecchio, Maria Svensson-Coelho, Jeffrey Bell, Vincenzo A Ellis, Matthew C Medeiros, Christopher H Trisos, John G Blake, Bette A Loiselle, Joseph A Tobias, Rebeka Fanti, Elyse D Coffey, Iubatã P DE Faria, João B Pinho, Gabriel Felix, Erika M Braga, Marina Anciães, Vasyl Tkach, John Bates, Christopher Witt, Jason D Weckstein, Robert E Ricklefs, Izeni P Farias
Parasites of the genera Plasmodium and Haemoproteus (Apicomplexa: Haemosporida) are a diverse group of pathogens that infect birds nearly worldwide. Despite their ubiquity, the ecological and evolutionary factors that shape the diversity and distribution of these protozoan parasites among avian communities and geographic regions are poorly understood. Based on a survey throughout the Neotropics of the haemosporidian parasites infecting manakins (Pipridae), a family of Passerine birds endemic to this region, we asked whether host relatedness, ecological similarity and geographic proximity structure parasite turnover between manakin species and local manakin assemblages...
March 14, 2017: Parasitology
https://www.readbyqxmd.com/read/28289905/expression-profile-of-desiccation-tolerance-factors-in-intertidal-seaweed-species-during-the-tidal-cycle
#16
Camila Fierro, Camilo López-Cristoffanini, Andrés Meynard, Carlos Lovazzano, Francisco Castañeda, Eduardo Guajardo, Loretto Contreras-Porcia
The transcriptional modulation of desiccation tolerance factors in P. orbicularis explains its successful recuperation after water deficit. Differential responses to air exposure clarify seaweed distribution along intertidal rocky zones. Desiccation-tolerant seaweed species, such as Pyropia orbicularis, can tolerate near 96% water loss during air exposure. To understand the phenotypic plasticity of P. orbicularis to desiccation, several tolerance factors were assessed by RT-qPCR, Western-blot analysis, and enzymatic assays during the natural desiccation-rehydration cycle...
March 13, 2017: Planta
https://www.readbyqxmd.com/read/28289787/changes-in-bacterial-diversity-associated-with-bioremediation-of-used-lubricating-oil-in-tropical-soils
#17
Naruemon Meeboon, Mary-Cathrine Leewis, Sireewan Kaewsuwan, Suppasil Maneerat, Mary Beth Leigh
Used lubricating oil (ULO) is a widespread contaminant, particularly throughout tropical regions, and may be a candidate for bioremediation. However, little is known about the biodegradation potential or basic microbial ecology of ULO-contaminated soils. This study aims to determine the effects of used ULO on bacterial community structure and diversity. Using a combination of culture-based (agar plate counts) and molecular techniques (16S rRNA gene sequencing and DGGE), we investigated changes in soil bacterial communities from three different ULO-contaminated soils collected from motorcycle mechanical workshops (soil A, B, and C)...
March 13, 2017: Archives of Microbiology
https://www.readbyqxmd.com/read/28288926/development-of-new-microsatellites-for-the-hookworm-ancylostoma-caninum-and-analysis-of-genetic-diversity-in-brazilian-populations
#18
Élida Mara Leite Rabelo, Rodrigo Rodrigues Cambraia de Miranda, Luis Fernando Viana Furtado, Rodrigo Aparecido Fernandes Redondo, Jacob Adam Tennessen, Michael Scott Blouin
Considering the great efforts towards formulating a vaccine against hookworms, and the concerns about the spread of drug resistance through hookworm populations, it is justified to study the molecular diversity and population genetic structure of these nematodes. This work had the aim to develop microsatellite markers to investigate the genetic structure and the molecular diversity of Brazilian populations of Ancylostoma caninum. Seven microsatellites markers were successfully used to characterize five Brazilian populations...
March 10, 2017: Infection, Genetics and Evolution
https://www.readbyqxmd.com/read/28286707/molecular-phylogenies-confirm-the-presence-of-two-cryptic-hemimycale-species-in-the-mediterranean-and-reveal-the-polyphyly-of-the-genera-crella-and-hemimycale-demospongiae-poecilosclerida
#19
Maria J Uriz, Leire Garate, Gemma Agell
BACKGROUND: Sponges are particularly prone to hiding cryptic species as their paradigmatic plasticity often favors species phenotypic convergence as a result of adaptation to similar habitat conditions. Hemimycale is a sponge genus (Family Hymedesmiidae, Order Poecilosclerida) with four formally described species, from which only Hemimycale columella has been recorded in the Atlanto-Mediterranean basin, on shallow to 80 m deep bottoms. Contrasting biological features between shallow and deep individuals of Hemimycale columella suggested larger genetic differences than those expected between sponge populations...
2017: PeerJ
https://www.readbyqxmd.com/read/28286510/genetic-structure-and-selection-of-a-core-collection-for-long-term-conservation-of-avocado-in-mexico
#20
Luis F Guzmán, Ryoko Machida-Hirano, Ernesto Borrayo, Moisés Cortés-Cruz, María Del Carmen Espíndola-Barquera, Elena Heredia García
Mexico, as the center of origin of avocado (Persea americama Mill.), harbors a wide genetic diversity of this species, whose identification may provide the grounds to not only understand its unique population structure and domestication history, but also inform the efforts aimed at its conservation. Although molecular characterization of cultivated avocado germplasm has been studied by several research groups, this had not been the case in Mexico. In order to elucidate the genetic structure of avocado in Mexico and the sustainable use of its genetic resources, 318 avocado accessions conserved in the germplasm collection in the National Avocado Genebank were analyzed using 28 markers [9 expressed sequence tag-Simple Sequence Repeats (SSRs) and 19 genomic SSRs]...
2017: Frontiers in Plant Science
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