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Molecular Ecology

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https://www.readbyqxmd.com/read/29165929/spatial-population-genomics-of-the-brown-rat-rattus-norvegicus-in-new-york-city
#1
Matthew Combs, Emily E Puckett, Jonathan Richardson, Destiny Mims, Jason Munshi-South
Human commensal species such as rodent pests are often widely distributed across cities and threaten both infrastructure and public health. Spatially-explicit population genomic methods provide insights into movements for cryptic pests that drive evolutionary connectivity across multiple spatial scales. We examined spatial patterns of neutral genome-wide variation in brown rats (Rattus norvegicus) across Manhattan, New York City (NYC) using 262 samples and 61,401 SNPs to understand: 1) relatedness among nearby individuals and the extent of spatial genetic structure in a discrete urban landscape; 2) the geographic origin of NYC rats, using a large, previously-published dataset of global rat genotypes; and 3) heterogeneity in gene flow across the city, particularly deviations from isolation-by-distance...
November 22, 2017: Molecular Ecology
https://www.readbyqxmd.com/read/29165848/ecological-disturbance-influences-adaptive-divergence-despite-high-gene-flow-in-golden-perch-macquaria-ambigua-implications-for-management-and-resilience-to-climate-change
#2
Catherine R M Attard, Chris J Brauer, Jonathan Sandoval-Castillo, Leanne K Faulks, Peter Unmack, Dean M Gilligan, Luciano B Beheregaray
Populations that are adaptively divergent but maintain high gene flow may have greater resilience to environmental change as gene flow allows the spread of alleles that have already been tested elsewhere. In addition, populations naturally subjected to ecological disturbance may already hold resilience to future environmental change. Confirming this necessitates ecological genomic studies of high dispersal, generalist species. Here we perform one such study on golden perch (Macquaria ambigua) in the Murray-Darling Basin (MDB), Australia using a genome-wide SNP dataset...
November 22, 2017: Molecular Ecology
https://www.readbyqxmd.com/read/29165845/wolbachia-infection-alters-the-relative-abundance-of-resident-bacteria-in-adult-aedes-aegypti-mosquitoes-but-not-larvae
#3
Michelle D Audsley, Andrei Seleznev, D Albert Joubert, Megan Woolfit, Scott L O'Neill, Elizabeth A McGraw
Insect-symbiont interactions are known to play key roles in host functions and fitness. The common insect endosymbiont Wolbachia can reduce the ability of several human pathogens, including arboviruses and the malaria parasite, to replicate in insect hosts. Wolbachia does not naturally infect Aedes aegypti, the primary vector of dengue virus, but transinfected Ae. aegypti have anti-dengue virus properties and are currently being trialled as a dengue biocontrol strategy. Here, we assess the impact of Wolbachia infection of Ae...
November 22, 2017: Molecular Ecology
https://www.readbyqxmd.com/read/29165844/oral-microbiomes-from-hunter-gatherers-and-traditional-farmers-reveal-shifts-in-commensal-balance-and-pathogen-load-linked-to-diet
#4
Florent Lassalle, Matteo Spagnoletti, Matteo Fumagalli, Liam Shaw, Mark Dyble, Catherine Walker, Mark G Thomas, Andrea Bamberg Migliano, Francois Balloux
Maladaptation to modern diets has been implicated in several chronic disorders. Given the higher prevalence of disease such as dental caries and chronic gum diseases in industrialized societies, we sought to investigate the impact of different subsistence strategies on oral health and physiology, as documented by the oral microbiome. To control for confounding variables such as environment and host genetics, we sampled saliva from three pairs of populations of hunter-gatherers and traditional farmers living in close proximity in the Philippines...
November 22, 2017: Molecular Ecology
https://www.readbyqxmd.com/read/29164717/antibiotics-reduce-genetic-diversity-of-core-species-in-the-honeybee-gut-microbiome
#5
Kasie Raymann, Louis-Marie Bobay, Nancy A Moran
The gut microbiome plays a key role in animal health, and perturbing it can have detrimental effects. One major source of perturbation to microbiomes, in humans and human-associated animals, is exposure to antibiotics. Most studies of how antibiotics affect the microbiome have used amplicon sequencing of highly conserved 16S rRNA sequences, as in a recent study showing that antibiotic treatment severely alters the species-level composition of the honeybee gut microbiome. But because the standard 16S rRNA-based methods cannot resolve closely related strains, strain-level changes could not be evaluated...
November 22, 2017: Molecular Ecology
https://www.readbyqxmd.com/read/29154412/the-impact-of-mating-systems-and-dispersal-on-fine-scale-genetic-structure-at-maternally-paternally-and-biparentally-inherited-markers
#6
Robyn E Shaw, Sam C Banks, Rod Peakall
For decades, studies have focused on how dispersal and mating systems influence genetic structure across populations or social-groups. However, we still lack a thorough understanding of how these processes and their interaction, shape spatial genetic patterns over a finer-scale (tens - hundreds of metres). Using uniparentally inherited markers may help answer these questions, yet their potential has not been fully explored. Here, we use individual-level simulations to investigate the effects of dispersal and mating system on fine-scale genetic structure at autosomal, mitochondrial and Y chromosome markers...
November 20, 2017: Molecular Ecology
https://www.readbyqxmd.com/read/29148600/new-evidence-for-the-recent-divergence-of-devil-s-hole-pupfish-and-the-plausibility-of-elevated-mutation-rates-in-endangered-taxa
#7
Christopher H Martin, Sebastian Höhna
Saglam et al. (2016) recently argued that the Devil's Hole Pupfish (Cyprinodon diabolis), a conservation icon with the smallest known species range, was isolated 60 kya based on a new genomic dataset. If true, this would be a radically long timescale for any species to persist at population sizes less than 500 individuals, in contrast to conservation genetics theory. However, here we argue that their analyses and interpretation are inappropriate. They placed highly restrictive prior distributions on divergence times, which do not appropriately model the large uncertainty and result in removing nearly all uncertainty from their analyses, and chose among models by assuming that pupfishes exhibit human mutation rates...
November 17, 2017: Molecular Ecology
https://www.readbyqxmd.com/read/29134741/contemporary-evolution-of-a-lepidopteran-species-heliothis-virescens-in-response-to-modern-agricultural-practices
#8
Megan L Fritz, Alexandra M DeYonke, Alexie Papanicolaou, Stephen Micinski, John Westbrook, Fred Gould
Adaptation to human-induced environmental change has the potential to profoundly influence the genomic architecture of affected species. This is particularly true in agricultural ecosystems, where anthropogenic selection pressure is strong. Heliothis virescens primarily feeds on cotton in its larval stages and US populations have been declining since the widespread planting of transgenic cotton, which endogenously expresses proteins derived from Bacillus thuringiensis (Bt). No physiological adaptation to Bt toxin has been found in the field, so adaptation in this altered environment could involve: 1) shifts in host plant selection mechanisms to avoid cotton, 2) changes in detoxification mechanisms required for cotton-feeding versus feeding on other hosts, or 3) loss of resistance to previously used management practices including insecticides...
November 13, 2017: Molecular Ecology
https://www.readbyqxmd.com/read/29134738/fungal-community-reveals-less-dispersal-limitation-and-potentially-more-connected-network-than-that-of-bacteria-in-bamboo-forest-soils
#9
Xian Xiao, Yuting Liang, Sai Zhou, Shunyao Zhuang, Bo Sun
A central aim of current microbial ecology research is to investigate the mechanisms shaping the assembly of soil microbial communities. Despite the importance of bacterial and fungal mediation of carbon cycling in forest ecosystems, knowledge concerning their distribution patterns and underlying mechanisms remains insufficient. Here, soils were sampled from six bamboo forests across the main planting area of Moso bamboo in southern China. The bacterial and fungal diversities were assessed by sequencing 16S rRNA and ITS gene amplicons, respectively, with an Illumina MiSeq...
November 13, 2017: Molecular Ecology
https://www.readbyqxmd.com/read/29134729/maintaining-their-genetic-distance-little-evidence-for-introgression-between-widely-hybridising-species-of-geum-with-contrasting-mating-systems
#10
Crispin Y Jordan, Konrad Lohse, Frances Turner, Marian Thomson, Karim Gharbi, Richard A Ennos
Within the plant kingdom many genera contain sister lineages with contrasting outcrossing and inbreeding mating systems that are known to hybridise. The evolutionary fate of these sister lineages is likely to be influenced by the extent to which they exchange genes. We measured gene flow between outcrossing Geum rivale and selfing G. urbanum, sister species that hybridise in contemporary populations. We generated and used a draft genome of G. urbanum to develop dd-RAD data scorable in both species. Coalescent analysis of RAD data from allopatric populations indicated that the species diverged 2-3 Mya, and that historical gene flow between them was extremely low (1 migrant every 25 generations)...
November 13, 2017: Molecular Ecology
https://www.readbyqxmd.com/read/29134727/a-srna-in-a-reduced-mutualistic-symbiont-genome-regulates-its-own-gene-expression
#11
Margaret W Thairu, Siyuan Cheng, Allison K Hansen
Similar to other nutritional endosymbionts that are obligate for host survival, the mutualistic aphid endosymbiont, Buchnera, has a highly reduced genome with few regulatory elements. Until recently, it was thought that aphid hosts were primarily responsible for regulating their symbiotic relationship. However, we recently revealed that Buchnera displays differential protein regulation, but not mRNA expression. We also identified a number of conserved small RNAs (sRNAs) that are expressed among Buchnera taxa...
November 13, 2017: Molecular Ecology
https://www.readbyqxmd.com/read/29134724/biogeography-of-mutualistic-fungi-cultivated-by-leafcutter-ants
#12
Ulrich G Mueller, Heather D Ishak, Sofia M Bruschi, Chad C Smith, Jacob J Herman, Scott E Solomon, Alexander S Mikheyev, Christian Rabeling, Jarrod J Scott, Michael Cooper, Andre Rodrigues, Adriana Ortiz, Carlos Roberto F Brandão, John E Lattke, Fernando C Pagnocca, Stephen A Rehner, Ted R Schultz, Heraldo L Vasconcelos, Rachelle M M Adams, Martin Bollazzi, Rebecca M Clark, Anna G Himler, John S LaPolla, Inara R Leal, Robert A Johnson, Flavio Roces, Jeffrey Sosa-Calvo, Rainer Wirth, Maurício Bacci
Leafcutter ants propagate co-evolving fungi for food. The nearly 50 species of leafcutter ants (Atta, Acromyrmex) range from Argentina to the USA, with the greatest species diversity in southern South America. We elucidate the biogeography of fungi cultivated by leafcutter ants using DNA-sequence and microsatellite-marker analyses of 474 cultivars collected across the leafcutter range. Fungal cultivars belong to two clades (Clade-A, Clade-B). The dominant and widespread Clade-A cultivars form three genotype-clusters, with their relative prevalence corresponding to southern South America, northern South America, and Central & North America...
November 13, 2017: Molecular Ecology
https://www.readbyqxmd.com/read/29134719/temporal-genetic-patterns-of-diversity-and-structure-evidence-chaotic-genetic-patchiness-in-a-spiny-lobster
#13
Cecilia Villacorta-Rath, Carla A Souza, Nicholas P Murphy, Bridget S Green, Caleb Gardner, Jan M Strugnell
Population structure of many marine organisms is spatially patchy and varies within and between years, a phenomenon defined as chaotic genetic patchiness. This results from the combination of planktonic larval dispersal and environmental stochasticity. Additionally, in species with bi-partite life, post-settlement selection can magnify these genetic differences. The high fecundity (up to 500,000 eggs annually) and protracted larval duration (12-24 months) and dispersal of the southern rock lobster, Jasus edwardsii, make it a good test species for chaotic genetic patchiness and selection during early benthic life...
November 13, 2017: Molecular Ecology
https://www.readbyqxmd.com/read/29134713/comparative-ecological-transcriptomics-and-the-contribution-of-gene-expression-to-the-evolutionary-potential-of-a-threatened-fish
#14
Chris J Brauer, Peter J Unmack, Luciano B Beheregaray
Understanding whether small populations with low genetic diversity can respond to rapid environmental change via phenotypic plasticity is an outstanding research question in biology. RNA sequencing (RNA-seq) has recently provided the opportunity to examine variation in gene expression, a surrogate for phenotypic variation, in non-model species. We used a comparative RNA-seq approach to assess expression variation within and among adaptively divergent populations of a threatened freshwater fish, Nannoperca australis, found across a steep hydroclimatic gradient in the Murray-Darling Basin, Australia...
November 13, 2017: Molecular Ecology
https://www.readbyqxmd.com/read/29134711/x-exceptionalism-in-caenorhabditis-speciation
#15
Asher D Cutter
Speciation genetics research in diverse organisms shows the X-chromosome to be exceptional in how it contributes to 'rules' of speciation. Until recently, however, the nematode phylum has been nearly silent on this issue, despite the model organism Caenorhabditis elegans having touched most other topics in biology. Studies of speciation with Caenorhabditis accelerated with the recent discovery of species pairs showing partial inter-fertility. The resulting genetic analyses of reproductive isolation in nematodes demonstrate key roles for the X-chromosome in hybrid male sterility and inviability, opening up new understanding of the genetic causes of Haldane's rule, Darwin's corollary to Haldane's rule, and enabling tests of the large-X effect hypothesis...
November 13, 2017: Molecular Ecology
https://www.readbyqxmd.com/read/29134710/isolation-by-distance-not-incipient-ecological-speciation-explains-genetic-differentiation-in-an-andean-songbird-aves-furnariidae-cranioleuca-antisiensis-line-cheeked-spinetail-despite-near-three-fold-body-size-change-across-an-environmental-gradient
#16
Glenn F Seeholzer, Robb T Brumfield
During the process of ecological speciation, reproductive isolation results from divergent natural selection and leads to a positive correlation between genetic divergence and adaptive phenotypic divergence, i.e. isolation-by-adaptation (IBA). In natural populations, phenotypic differentiation is often autocorrelated with geographic distance, making IBA difficult to distinguish from the neutral expectation of isolation-by-distance (IBD). We examined these two alternatives in a dramatic case of clinal phenotypic variation in an Andean songbird, the Line-cheeked Spinetail (Cranioleuca antisiensis)...
November 13, 2017: Molecular Ecology
https://www.readbyqxmd.com/read/29134709/light-sensing-by-opsins-and-fungal-ecology-nop-1-modulates-entry-into-sexual-reproduction-in-response-to-environmental-cues
#17
Zheng Wang, Junrui Wang, Ning Li, Jigang Li, Frances Trail, Jay C Dunlap, Jeffrey P Townsend
Understanding the genetic basis of the switch from asexual to sexual lifestyles in response to sometimes rapid environmental changes is one of the major challenges in fungal ecology. Light appears to play a critical role in the switch-but fungal genomes harbor diverse light sensors. Fungal opsins are homologous to bacterial green-light sensory rhodopsins, and their organismal functions in fungi have not been well understood. Three of these opsin-like proteins were widely distributed across fungal genomes, but homologs of the Fusarium opsin-like protein CarO were present only in plant-associated fungi...
November 13, 2017: Molecular Ecology
https://www.readbyqxmd.com/read/29117634/spatial-variability-of-marine-bacterial-and-archaeal-communities-along-the-particulate-matter-continuum
#18
Mireia Mestre, Isabel Ferrera, Encarna Borrull, Eva Ortega-Retuerta, Susan Mbedi, Hans-Peter Grossart, M Montserrat Sala
Biotic and abiotic particles shape the microspatial architecture that defines the microbial aquatic habitat, being particles highly variable in size and quality along oceanic horizontal and vertical gradients. We analyzed the prokaryotic (bacterial and archaeal) diversity and community composition present in 6 distinct particle size classes ranging from the pico- to the microscale (0.2 to 200 μm). Further, we studied their variations along oceanographic horizontal (from the coast to open oceanic waters) and vertical (from the ocean surface into the meso- and bathypelagic ocean) gradients...
November 8, 2017: Molecular Ecology
https://www.readbyqxmd.com/read/29117633/ancient-symbiosis-confers-desiccation-resistance-to-stored-grain-pest-beetles
#19
Tobias Engl, Nadia Eberl, Carla Gorse, Theresa Krüger, Thorsten H P Schmidt, Rudy Plarre, Cornel Adler, Martin Kaltenpoth
Microbial symbionts of insects provide a range of ecological traits to their hosts that are beneficial in the context of biotic interactions. However, little is known about insect symbiont-mediated adaptation to the abiotic environment, e.g. temperature and humidity. Here we report on an ancient clade of intracellular, bacteriome-located Bacteroidetes symbionts that are associated with grain and wood pest beetles of the phylogenetically distant families Silvanidae and Bostrichidae. In the saw-toothed grain beetle Oryzaephilus surinamensis, we demonstrate that the symbionts affect cuticle thickness, melanization and hydrocarbon profile, enhancing desiccation resistance and thereby strongly improving fitness under dry conditions...
November 8, 2017: Molecular Ecology
https://www.readbyqxmd.com/read/29117632/living-quarters-of-a-living-fossil-uncovering-the-current-distribution-pattern-of-the-rediscovered-hula-painted-frog-latonia-nigriventer-using-environmental-dna
#20
Sharon Renan, Sarig Gafny, R G Bina Perl, Uri Roll, Yoram Malka, Miguel Vences, Eli Geffen
One of the greatest challenges of effective conservation measures is the correct identification of sites where rare and elusive organisms reside. The recently rediscovered Hula painted frog (Latonia nigriventer) has not been seen for many decades, and was therefore categorized extinct. Since its rediscovery in 2011, individuals from the critically endangered species have been found, with great effort, only in four restricted sites. We applied the environmental DNA (eDNA) approach to search for new populations of the Hula painted frog in suitable aquatic habitats...
November 8, 2017: Molecular Ecology
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