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Molecular Ecology

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https://www.readbyqxmd.com/read/29772096/signatures-of-diversifying-selection-and-convergence-acting-on-passerine-toll-like-receptor-4-in-an-evolutionary-context
#1
Tereza Králová, Tomáš Albrecht, Josef Bryja, David Hořák, Arild Johnsen, Jan T Lifjeld, Marian Novotný, Ondřej Sedláček, Hana Velová, Michal Vinkler
Positive selection acting on Toll-like receptors (TLRs) has been recently investigated to reveal evolutionary mechanisms of host-pathogen molecular co-adaptation. Much of this research, however, has focused mainly on the identification of sites predicted to be under positive selection, bringing little insight into the functional differences and similarities among species and a limited understanding of convergent evolution in the innate immune molecules. In this study we provide evidence of phenotypic variability in the avian TLR4 ligand-binding region (LBR), the direct interface between host and pathogen molecular structures...
May 17, 2018: Molecular Ecology
https://www.readbyqxmd.com/read/29772089/microevolutionary-selection-dynamics-acting-on-immune-genes-of-the-green-veined-white-butterfly-pieris-napi
#2
Naomi L P Keehnen, Jason Hill, Sören Nylin, Christopher W Wheat
Insects rely on their innate immune system to successfully mediate complex interactions with their microbiota, as well as the microbes present in the environment. Previous work has shown that components of the canonical immune gene repertoire evolve rapidly and have evolutionary characteristics originating from interactions with fast-evolving microorganisms. Although these interactions are likely to vary among populations, there is a poor understanding of the microevolutionary dynamics of immune genes, especially in non-Dipteran insects...
May 17, 2018: Molecular Ecology
https://www.readbyqxmd.com/read/29772088/predicting-genotypes-environmental-range-from-genome-environment-associations
#3
Stéphanie Manel, Marco Andrello, Karine Henry, Daphné Verdelet, Aude Darracq, Pierre-Edouard Guerin, Bruno Desprez, Pierre Devaux
Genome-environment association methods aim to detect genetic markers associated with environmental variables. The detected associations are usually analysed separately to identify the genomic regions involved in local adaptation. However, a recent study suggests that single-locus associations can be combined and used in a predictive way to estimate environmental variables for new individuals on the basis of their genotypes. Here, we introduce an original approach to predict the environmental range (values and upper and lower limits) of species genotypes from the genetic markers significantly associated with those environmental variables in an independent set of individuals...
May 17, 2018: Molecular Ecology
https://www.readbyqxmd.com/read/29761593/uncovering-the-drivers-of-host-associated-microbiota-with-joint-species-distribution-modeling
#4
Johannes R Björk, Francis K C Hui, Robert B O'Hara, Jose M Montoya
In addition to the processes structuring free-living communities, host-associated microbiota are directly or indirectly shaped by the host. Therefore, microbiota data have a hierarchical structure where samples are nested under one or several variables representing host-specific factors, often spanning multiple levels of biological organization. Current statistical methods do not accommodate this hierarchical data structure, and therefore cannot explicitly account for the effect of the host in structuring the microbiota...
May 14, 2018: Molecular Ecology
https://www.readbyqxmd.com/read/29752760/expression-plasticity-and-evolutionary-changes-extensively-shape-the-sugar-mimic-alkaloid-adaptation-of-non-digestive-glucosidase-in-lepidopteran-mulberry-specialist-insects
#5
Xiaotong Li, Liangen Shi, Xiangping Dai, Yajie Chen, Hongqing Xie, Min Feng, Yuyin Chen, Huabing Wang
During the co-evolutionary arms race between plants and herbivores, insects evolved systematic adaptive plasticity to minimise the chemical defence effects of their host plants. Previous studies mainly focused on the expressional plasticity of enzymes in detoxification and digestion. However, the expressional response and adaptive evolution of other fundamental regulators against host phytochemicals are largely unknown. Glucosidase II (GII), which is composed of a catalytic GIIα subunit and a regulatory GIIβ subunit, is an evolutionarily conserved enzyme that regulates glycoprotein folding...
May 12, 2018: Molecular Ecology
https://www.readbyqxmd.com/read/29752753/phoretic-dispersal-influences-parasite-population-genetic-structure
#6
Emily DiBlasi, Kevin P Johnson, Sydney A Stringham, Angela N Hansen, Andrew B Beach, Dale H Clayton, Sarah E Bush
Dispersal is a fundamental component of the life history of most species. Dispersal influences fitness, population dynamics, gene flow, genetic drift, and population genetic structure. Even small differences in dispersal can alter ecological interactions and trigger an evolutionary cascade. Linking such ecological processes with evolutionary patterns is difficult, but can be done in the proper comparative context. Here we investigate how differences in phoretic dispersal influence the population genetic structure of two different parasites of the same host species...
May 12, 2018: Molecular Ecology
https://www.readbyqxmd.com/read/29742304/plasticity-and-evolutionary-divergence-in-gene-expression-associated-with-alternative-habitat-use-in-larvae-of-the-european-fire-salamander
#7
Till Czypionka, Daniel J Goedbloed, Sebastian Steinfartz, Arne W Nolte
Transcriptomes of organisms reveal differentiation associated with the use of different habitats. However, this leaves open how much of the observed differentiation can be attributed to genetic differences or to transcriptional plasticity. In this study, we disentangle causes of differential gene expression in larvae of the European fire salamander from the Kottenforst forest in Germany. Larvae inhabit permanent streams and ephemeral ponds and represent an example of a young evolutionary split associated with contrasting ecological conditions...
May 9, 2018: Molecular Ecology
https://www.readbyqxmd.com/read/29742302/transcriptomic-analysis-of-skin-pigmentation-variation-in-the-virginia-opossum-didelphis-virginiana
#8
Sergio F Nigenda-Morales, Yibo Hu, James Beasley, Hugo A Ruiz-Piña, David Valenzuela-Galván, Robert K Wayne
Skin and coat pigmentation are two of the best-studied examples of traits under natural selection given their quantifiable fitness interactions with the environment (e.g. camouflage) and signaling with other organisms (e.g. warning coloration). Previous morphological studies have found that skin pigmentation variation in the Virginia opossum (Didelphis virginiana) is associated with variation in precipitation and temperatures across its distribution range following Gloger's rule (lighter pigmentation in temperate environments)...
May 9, 2018: Molecular Ecology
https://www.readbyqxmd.com/read/29742301/a-genomic-evaluation-of-taxonomic-trends-through-time-in-coast-horned-lizards-genus-phrynosoma
#9
Adam D Leaché, Matthew T McElroy, Anna Trinh
Determining the boundaries between species and deciding when to describe new species are challenging practices that are particularly difficult in groups with high levels of geographic variation. The coast horned lizards (Phrynosoma blainvillii, P. cerroense, and P. coronatum) have an extensive geographic distribution spanning many distinctive ecological regions ranging from northern California to the Cape Region of Baja California, Mexico, and populations differ substantially with respect to external morphology across much of this range...
May 9, 2018: Molecular Ecology
https://www.readbyqxmd.com/read/29740906/phylogenetic-patterns-of-ant-fungus-associations-indicate-that-farming-strategies-not-only-a-superior-fungal-cultivar-explain-the-ecological-success-of-leafcutter-ants
#10
Ulrich G Mueller, Melissa R Kardish, Heather D Ishak, April M Wright, Scott E Solomon, Sofia M Bruschi, Alexis L Carlson, Maurício Bacci
To elucidate fungicultural specializations contributing to ecological dominance of leafcutter ants, we estimate the phylogeny of fungi cultivated by fungus-growing (attine) ants, including fungal cultivars from (i) the entire leafcutter range from southern South America to southern North America, (ii) all higher-attine ant lineages (leafcutting genera Atta, Acromyrmex; nonleafcutting genera Trachymyrmex, Sericomyrmex) and (iii) all lower-attine lineages. Higher-attine fungi form two clades, Clade-A fungi (Leucocoprinus gongylophorus, formerly Attamyces) previously thought to be cultivated only by leafcutter ants, and a sister clade, Clade-B fungi, previously thought to be cultivated only by Trachymyrmex and Sericomyrmex ants...
May 9, 2018: Molecular Ecology
https://www.readbyqxmd.com/read/29729657/genome-wide-evidence-for-divergent-selection-between-populations-of-a-major-agricultural-pathogen
#11
Fanny E Hartmann, Bruce A McDonald, Daniel Croll
The genetic and environmental homogeneity in agricultural ecosystems is thought to impose strong and uniform selection pressures. However, the impact of this selection on plant pathogen genomes remains largely unknown. We aimed to identify the proportion of the genome and the specific gene functions under positive selection in populations of the fungal wheat pathogen Zymoseptoria tritici. First, we performed genome scans in four field populations that were sampled from different continents and on distinct wheat cultivars to test which genomic regions are under recent selection...
May 5, 2018: Molecular Ecology
https://www.readbyqxmd.com/read/29729049/population-structure-of-guyanagaster-necrorhizus-supports-termite-dispersal-for-this-enigmatic-fungus
#12
Rachel A Koch, M Catherine Aime
Understanding how species accomplish dispersal of their propagules can shed light on how they are adapted for their ecosystem. Guyanagaster necrorhizus is a sequestrate fungus, meaning its dispersal propagules, or spores, are entirely enclosed within a fruiting body, termed a sporocarp. This fungus is most closely related to Armillaria and its allies. While Armillaria species form mushrooms and have forcibly discharged spores, G. necrorhizus spores have lost this ability, and by necessity, must be passively dispersed...
May 4, 2018: Molecular Ecology
https://www.readbyqxmd.com/read/29726053/feather-mites-play-a-role-in-cleaning-host-feathers-new-insights-from-dna-metabarcoding-and-microscopy
#13
Jorge Doña, Heather Proctor, David Serrano, Kevin P Johnson, Arnika Oddy-van Oploo, Jose C Huguet-Tapia, Marina S Ascunce, Roger Jovani
Parasites and other symbionts are crucial components of ecosystems, regulating host populations and supporting food webs. However, most symbiont systems, especially those involving commensals and mutualists, are relatively poorly understood. In this study, we have investigated the nature of the symbiotic relationship between birds and their most abundant and diverse ectosymbionts: the vane-dwelling feather mites. For this purpose, we studied the diet of feather mites using two complementary methods. First, we used light microscopy to examine the gut contents of 1,300 individual feather mites representing 100 mite genera (18 families) from 190 bird species belonging to 72 families and 19 orders...
May 3, 2018: Molecular Ecology
https://www.readbyqxmd.com/read/29717553/faster-x-evolution-of-gene-expression-is-driven-by-recessive-adaptive-cis-regulatory-variation-in-drosophila
#14
Ana Llopart
The hemizygosity of the X (Z) chromosome fully exposes the fitness effects of mutations on that chromosome, and has evolutionary consequences on the relative rates of evolution of X and autosomes. Specifically, several population genetics models predict increased rates of evolution in X-linked loci relative to autosomal loci. This prediction of faster-X evolution has been evaluated and confirmed for both protein coding sequences and gene expression. In the case of faster-X evolution for gene expression divergence, it is often assumed that variation in 5' noncoding sequences is associated with variation in transcript abundance between species but a formal, genome-wide test of this hypothesis is still missing...
May 1, 2018: Molecular Ecology
https://www.readbyqxmd.com/read/29717521/evolution-of-interspecies-unilateral-incompatibility-in-the-relatives-of-arabidopsis-thaliana
#15
Ling Li, Bo Liu, Xiaomei Deng, Hainan Zhao, Hongyan Li, Shilai Xing, Della D Fetzer, Mengya Li, Mikhail E Nasrallah, June B Nasrallah, Pei Liu
The evolutionary concurrence of intraspecies self-incompatibility (SI) and explosive angiosperm radiation in the Cretaceous has led to the hypothesis that SI was one of the predominant drivers of rapid speciation in angiosperms. Interspecies unilateral incompatibility (UI) usually occurs when pollen from a self-compatible (SC) species is rejected by the pistils of a SI species, while the reciprocal pollination is compatible (UC). Although this SI x SC type UI is most prevalent and viewed as a prezygotic isolation barrier to promote incipient speciation of angiosperms, comparative evidence to support such a role is lacking...
May 1, 2018: Molecular Ecology
https://www.readbyqxmd.com/read/29707847/signatures-of-local-adaptation-along-environmental-gradients-in-a-range-expanding-damselfly-ischnura-elegans
#16
Rachael Y Dudaniec, Chuan Ji Yong, Lesley T Lancaster, Erik I Svensson, Bengt Hansson
Insect distributions are shifting rapidly in response to climate change and are undergoing rapid evolutionary change. We investigate the molecular signatures underlying local adaptation in the range-expanding damselfly, Ischnura elegans. Using a landscape genomic approach combined with generalized dissimilarity modelling (GDM), we detect selection signatures on loci via allelic frequency change along environmental gradients. We analyse 13,612 Single Nucleotide Polymorphisms (SNPs), derived from Restriction site-Associated DNA sequencing (RADseq), in 426 individuals from 25 sites spanning the I...
April 29, 2018: Molecular Ecology
https://www.readbyqxmd.com/read/29701315/incongruence-in-molecular-species-delimitation-schemes-what-to-do-when-adding-more-data-is-difficult
#17
Sarah J Jacobs, Casey Kristoferson, Simon Uribe-Convers, Maribeth Latvis, David C Tank
Using multiple, independent approaches to molecular species delimitation is advocated to accommodate limitations and assumptions of a single approach. Incongruence in delimitation schemes is a potential byproduct of employing multiple methods on the same data, and little attention has been paid to its reconciliation. Instead, a particular scheme is prioritized and/or molecular delimitations are coupled with additional, independent lines of evidence that mitigate incongruence. We advocate that incongruence within a line of evidence should be accounted for before comparing across lines of evidence, that can themselves be incongruent...
April 27, 2018: Molecular Ecology
https://www.readbyqxmd.com/read/29693314/mhc-mediated-sexual-selection-on-bird-song-generic-polymorphism-particular-alleles-and-acoustic-signals
#18
László Zsolt Garamszegi, Magdalena Zagalska-Neubauer, David Canal, György Blázi, Miklós Laczi, Gergely Nagy, Eszter Szöllősi, Éva Vaskuti, János Török, Sándor Zsebők
Several hypotheses predict that the major histocompatibility complex (MHC) drives mating preference in females. Olfactory, color or morphological traits are often found as reliable signals of the MHC profile, but the role of avian song mediating MHC-based female choice remains largely unexplored. We investigated the relationship between several MHC and acoustic features in the collared flycatcher (Ficedula albicollis) a European passerine with complex songs. We screened a fragment of the class IIB 2nd exon of the MHC molecule, of which individuals harbor 4-15 alleles, while considerable sequence diversity is maintained at the population level...
April 25, 2018: Molecular Ecology
https://www.readbyqxmd.com/read/29693300/adaptive-population-divergence-and-directional-gene-flow-across-steep-elevational-gradients-in-a-climate-sensitive-mammal
#19
Matthew D Waterhouse, Liesl P Erb, Erik A Beever, Michael A Russello
The ecological effects of climate change have been shown in most major taxonomic groups; however, the evolutionary consequences are less well-documented. Adaptation to new climatic conditions offers a potential long-term mechanism for species to maintain viability in rapidly changing environments, but mammalian examples remain scarce. The American pika (Ochotona princeps) has been impacted by recent climate-associated extirpations and range-wide reductions in population sizes, establishing it as a sentinel mammalian species for climate change...
April 25, 2018: Molecular Ecology
https://www.readbyqxmd.com/read/29693297/host-targeted-rad-seq-reveals-genetic-changes-in-the-coral-oculina-patagonica-associated-with-range-expansion-along-the-spanish-mediterranean-coast
#20
Karine Posbic Leydet, Carsten G B Grupstra, Rafel Coma, Marta Ribes, Michael E Hellberg
Many organisms are expanding their ranges in response to changing environmental conditions. Understanding the patterns of genetic diversity and adaptation along an expansion front is crucial to assessing a species' long-term success. While next-generation sequencing techniques can reveal these changes in fine detail, ascribing them to a particular species can be difficult for organisms that live in close association with symbionts. Using a novel modified restriction-site associated DNA sequencing (RAD-Seq) protocol to target coral DNA, we collected 595 coral-specific single nucleotide polymorphisms (SNPs) from 189 colonies of the invasive coral Oculina patagonica from the Spanish Mediterranean coast, including established core populations and two expansion fronts...
April 25, 2018: Molecular Ecology
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