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Molecular Ecology

Yoshiaki Tsuda, Vladimir Semerikov, Federico Sebastiani, Giovanni Giuseppe Vendramin, Martin Lascoux
Boreal and cool temperate forests are the major land cover of northern Eurasia and information about continental-scale genetic structure and past demographic history of forest species is important from an evolutionary perspective and has conservation implications. However, although many population genetics studies of forest tree species have been conducted in Europe or Eastern Asia, continental-scale genetic structure and past demographic history remain poorly known. Here, we focus on the birch genus Betula, which is commonly distributed in boreal and cool temperate forests, and examine 129 populations of 2 tetraploid and 4 diploid species collected from Iceland to Japan...
October 20, 2016: Molecular Ecology
Eric Capo, Didier Debroas, Fabien Arnaud, Typhaine Guillemot, Vincent Bichet, Laurent Millet, Emilie Gauthier, Charly Massa, Anne-Lise Develle, Cécile Pignol, Franck Lejzerowicz, Isabelle Domaizon
Assessing the extent to which changes in lacustrine biodiversity are affected by anthropogenic or climatic forces requires extensive paleolimnological data. We used high-throughput sequencing to generate time-series data encompassing over 2200 years of microbial eukaryotes (protists and Fungi) diversity changes from the sedimentary DNA record of 2 lakes (Lake Bourget in French Alps and Lake Igaliku in Greenland). From 176 samples, we sequenced a large diversity of microbial eukaryotes, with a total 16 386 Operational Taxonomic Units (OTUs) distributed within 50 phylogenetic groups...
October 20, 2016: Molecular Ecology
Sara Branco, Ke Bi, Hui-Ling Liao, Pierre Gladieux, Hélène Badouin, Christopher E Ellison, Nhu H Nguyen, Rytas Vilgalys, Kabir G Peay, John W Taylor, Thomas D Bruns
Recent advancements in sequencing technology allowed researchers to better address the patterns and mechanisms involved in microbial environmental adaptation at large spatial scales. Here we investigated the genomic basis of adaptation to climate at the continental scale in Suillus brevipes, an ectomycorrhizal fungus symbiotically associated with the roots of pine trees. We used genomic data from 55 individuals in seven locations across North America to perform genome scans to detect signatures of positive selection and assess whether temperature and precipitation were associated with genetic differentiation...
October 20, 2016: Molecular Ecology
Christian Rellstab, Stefan Zoller, Lorenz Walthert, Isabelle Lesur, Andrea R Pluess, René Graf, Catherine Bodénès, Christoph Sperisen, Antoine Kremer, Felix Gugerli
Testing how populations are locally adapted and predicting their response to their future environment is of key importance in view of climate change. Landscape genomics is a powerful approach to investigate genes and environmental factors involved in local adaptation. In a pooled amplicon sequencing approach of 94 genes in 71 populations, we tested if >3'500 single nucleotide polymorphisms (SNPs) in the three most common oak species in Switzerland (Quercus petraea, Q. pubescens, Q. robur) show an association with abiotic factors related to local topography, historical climate, and soil characteristics...
October 19, 2016: Molecular Ecology
R Rebecca Love, Aaron M Steele, Mamadou B Coulibaly, Sékou F Traore, Scott J Emrich, Michael C Fontaine, Nora J Besansky
The molecular mechanisms and genetic architecture that facilitate adaptive radiation of lineages remain elusive. Polymorphic chromosomal inversions, due to their recombination-reducing effect, are proposed instruments of ecotypic differentiation. Here we study an ecologically diversifying lineage of An. gambiae, known as the Bamako chromosomal form based on its unique complement of three chromosomal inversions, to explore the impact of these inversions on ecotypic differentiation. We used pooled and individual genome sequencing of Bamako, typical (non-Bamako) An...
October 19, 2016: Molecular Ecology
Anton Suvorov, Nicholas O Jensen, Camilla R Sharkey, M Stanley Fujimoto, Paul Bodily, Haley M Cahill Wightman, T Heath Ogden, Mark J Clement, Seth M Bybee
Gene duplication plays a central role in adaptation to novel environments by providing new genetic material for functional divergence and evolution of biological complexity. Several evolutionary models have been proposed for gene duplication to explain how new gene copies are preserved by natural selection but these models have rarely been tested using empirical data. Opsin proteins, when combined with a chromophore, form a photopigment that is responsible for the absorption of light, the first step in the phototransduction cascade...
October 18, 2016: Molecular Ecology
Madeleine Berger, Alin Mirel Puinean, Emma Randall, Christoph T Zimmer, Wellington M Silva, Pablo Bielza, Linda M Field, David Hughes, Ian Mellor, Keywan Hassani-Pak, Herbert A A Siqueira, Martin S Williamson, Chris Bass
Many genes increase coding capacity by alternate exon usage. The gene encoding the insect nicotinic acetylcholine receptor (nAChR) α6 subunit, target of the bio-insecticide spinosad, is one example of this and expands protein diversity via alternative splicing of mutually exclusive exons. Here we show that spinosad resistance in the tomato leafminer, Tuta absoluta is associated with aberrant regulation of splicing of Taα6 resulting in a novel form of insecticide resistance mediated by exon skipping. Sequencing of the α6 subunit cDNA from spinosad selected and unselected strains of T...
October 17, 2016: Molecular Ecology
Paul M Hime, Scott Hotaling, Richard E Grewelle, Eric M O'Neill, S Randal Voss, H Bradley Shaffer, David W Weisrock
Perhaps the most important recent advance in species delimitation has been the development of model-based approaches to objectively diagnose species diversity from genetic data. Additionally, the growing accessibility of next-generation sequence datasets provides powerful insights into genome-wide patterns of divergence during speciation. However, applying complex models to large datasets is time consuming and computationally costly, requiring careful consideration of the influence of both individual and population sampling, as well as the number and informativeness of loci on species delimitation conclusions...
October 17, 2016: Molecular Ecology
Schneider Ralf Friedrich, Axel Meyer
There is increasing evidence that phenotypic plasticity can promote population divergence by facilitating phenotypic diversification and, eventually, genetic divergence. When a 'plastic' population colonizes a new habitat it has the possibility to occupy multiple niches by expressing several distinct phenotypes. These initially reflect the population's plastic range but may later become genetically fixed by selection via the process of 'genetic assimilation' (GA). This way multiple specialized sister-lineages can arise that share a common plastic ancestor - the 'flexible stem'...
October 16, 2016: Molecular Ecology
Lars Grossmann, Daniela Beisser, Christina Bock, Antonis Chatzinotas, Manfred Jensen, Angelika Preisfeld, Roland Psenner, Sven Rahmann, Sabina Wodniok, Jens Boenigk
Inferring ecosystem functioning and ecosystem services through inspections of the species inventory is a major aspect of ecological field studies. Ecosystem functions are often stable despite considerable species turnover. Using metatranscriptome analyses, we analyse a thus-far unparalleled freshwater dataset which comprises 21 mainland European freshwater lakes from the Sierra Nevada (Spain) to the Carpathian Mountains (Romania) and from northern Germany to the Apennines (Italy) and covers an altitudinal range from 38 m above sea level (a...
October 16, 2016: Molecular Ecology
Billie A Gould, Yani Chen, David B Lowry
The early stages of speciation are often characterized by the formation of partially reproductively isolated ecotypes, which evolve as a byproduct of divergent selective forces that are endemic to different habitats. Identifying the genomic regions, genes, and ultimately functional polymorphisms that are involved in the processes of ecotype formation is inherently challenging, as there are likely to be many different loci involved in the process. To localize candidate regions of the genome contributing to ecotype formation, we conducted whole genome pooled-sequencing (pool-seq) with 47 coastal perennial and 50 inland annual populations of the yellow monkeyflower, Mimulus guttatus...
October 16, 2016: Molecular Ecology
Rachel A Johnston, Kristina L Paxton, Frank R Moore, Robert K Wayne, Thomas B Smith
The annual migration of a bird can involve thousands of kilometers of non-stop flight, requiring accurately timed seasonal changes in physiology and behavior. Understanding the molecular mechanisms controlling this endogenous programme can provide functional and evolutionary insights into the circannual biological clock and the potential of migratory species to adapt to changing environments. Under naturally-timed photoperiod conditions, we maintained captive Swainson's thrushes (Catharus ustulatus) and performed RNA sequencing (RNA-Seq) of the ventral hypothalamus and optic chiasma to evaluate transcriptome-wide gene expression changes of individuals in migratory condition...
October 16, 2016: Molecular Ecology
Kerri L Coon, Mark R Brown, Michael R Strand
Mosquitoes are insects of interest because several species vector disease-causing pathogens to humans and other vertebrates. We previously reported that mosquitoes from long-term laboratory cultures require living bacteria in their gut to develop, but development does not depend on particular species of bacteria. Here, we focused on three distinct but interrelated areas of study to better understand the role of bacteria in mosquito development by studying field and laboratory populations of Aedes aegypti, Aedes albopictus, and Culex quinquefasciatus from the Southeastern United States...
October 8, 2016: Molecular Ecology
Nicolas Chazot, Keith R Willmott, Fabien L Condamine, Donna Lisa de-Silva, André V L Freitas, Gerardo Lamas, Hélène Morlon, Carlos E Giraldo, Chris D Jiggins, Mathieu Joron, James Mallet, Sandra Uribe, Marianne Elias
Understanding why species richness peaks along the Andes is a fundamental question in the study of Neotropical biodiversity. Several biogeographic and diversification scenarios have been proposed in the literature, but there is confusion about the processes underlying each scenario, and assessing their relative contribution is not straightforward. Here, we propose to refine these scenarios into a framework which evaluates four evolutionary mechanisms: higher speciation rate in the Andes, lower extinction rates in the Andes, older colonization times and higher colonization rates of the Andes from adjacent areas...
October 8, 2016: Molecular Ecology
Nakatada Wachi, Junko Kusumi, Hsy-Yu Tzeng, Zhi-Hui Su
The obligate mutualism of figs and fig pollinating wasps has been one of the classic models used for testing theories of coevolution and cospeciation due to the high species-specificity of these relationships. To investigate the species-specificity between figs and fig pollinators and to further understand the speciation process in obligate mutualisms, we examined the genetic differentiation and phylogenetic relationships of four closely related fig pollinating wasp species (Blastophaga nipponica, B. taiwanensis, B...
October 5, 2016: Molecular Ecology
Makoto Kusakabe, Asano Ishikawa, Mark Ravinet, Kohta Yoshida, Takashi Makino, Atsushi Toyoda, Asao Fujiyama, Jun Kitano
Adaptation to different salinities can drive and maintain divergence between populations of aquatic organisms. Anadromous and stream ecotypes of threespine stickleback (Gasterosteus aculeatus) are an excellent model to explore the genetic mechanisms underlying osmoregulation divergence. Using a parapatric pair of anadromous and stream stickleback ecotypes, we employed an integrated genomic approach to identify candidate genes important for adaptation to different salinity environments. Quantitative trait loci (QTL) mapping of plasma sodium concentrations under a seawater challenge experiment identified a significant QTL on chromosome 16...
October 5, 2016: Molecular Ecology
Zachariah Gompert, Scott P Egan, Rowan Barrett, Jeff Feder, Patrik Nosil
The study of ecological speciation is inherently linked to the study of selection. Methods for estimating phenotypic selection within a generation based on associations between trait values and fitness (e.g., survival) of individuals are established. These methods attempt to disentangle selection acting directly on a trait from indirect selection caused by correlations with other traits via multivariate statistical approaches (i.e., inference of selection gradients). The estimation of selection on genotypic or genomic variation could also benefit from disentangling direct and indirect selection on genetic loci...
October 3, 2016: Molecular Ecology
Lily Khadempour, Kristin E Burnum-Johnson, Erin S Baker, Carrie D Nicora, Bobbie-Jo M Webb-Robertson, Richard A White, Matthew E Monroe, Eric L Huang, Richard D Smith, Cameron R Currie
Herbivores use symbiotic microbes to help derive energy and nutrients from plant material. Leaf-cutter ants are a paradigmatic example, cultivating their mutualistic fungus Leucoagaricus gongylophorus on plant biomass that workers forage from a diverse collection of plant species. Here, we investigate the metabolic flexibility of the ants' fungal cultivar for utilizing different plant biomass. Using feeding experiments and a novel approach in metaproteomics, we examine the enzymatic response of L. gongylophorus to leaves, flowers, oats, or a mixture of all three...
October 1, 2016: Molecular Ecology
T J Poorten, E B Rosenblum
In the past century, recently emerged infectious diseases have become major drivers of species decline and extinction. The fungal disease chytridiomycosis has devastated many amphibian populations and exacerbated the amphibian conservation crisis. Biologists are beginning to understand what host traits contribute to disease susceptibility, but more work is needed to determine why some species succumb to chytridiomycosis while others do not. We conducted an integrative laboratory experiment to examine how two toad species respond to infection with the pathogen Batrachochytrium dendrobatidis in a controlled environment...
October 1, 2016: Molecular Ecology
Christina Bauch, Juliane Riechert, Simon Verhulst, Peter H Becker
Telomere length is a candidate biomarker of ageing and phenotypic quality, but little is known of the (physiological) causes of telomere length variation. We previously showed that individual common terns Sterna hirundo with high reproductive success had short telomeres independent of age, and this pattern was particularly strong in the longer telomeres of the within-individual telomere length distribution. To test whether this relation can be attributed to effects of reproductive effort, we investigated baseline corticosterone in relation to reproductive success (number of fledglings) and telomere length...
October 1, 2016: Molecular Ecology
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