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Molecular Ecology

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https://www.readbyqxmd.com/read/28093817/cryptic-inbreeding-depression-in-a-growing-population-of-a-long-lived-species
#1
Helen R Taylor, Rogan M Colbourne, Hugh A Robertson, Nicola J Nelson, Fred W Allendorf, Kristina M Ramstad
Genetic effects are often overlooked in endangered species monitoring, and populations showing positive growth are often assumed to be secure. However, the continued reproductive success of a few individuals may mask issues such as inbreeding depression, especially in long-lived species. Here, we test for inbreeding depression in little spotted kiwi (Apteryx owenii) by comparing a population founded with two birds to one founded with 40 birds, both from the same source population and both showing positive population growth...
January 17, 2017: Molecular Ecology
https://www.readbyqxmd.com/read/28092408/network-structure-and-local-adaptation-in-coevolving-bacteria-phage-interactions
#2
James Gurney, Lafi Aldakak, Alex Betts, Claire Gougat-Barbera, Timothée Poisot, Oliver Kaltz, Michael E Hochberg
Numerous theoretical and experimental studies have investigated antagonistic coevolution between parasites and their hosts. Although experimental tests of theory from a range of biological systems are largely concordant regarding the influence of several driving processes, we know little as to how mechanisms acting at the smallest scales (individual molecular and phenotypic changes) may result in the emergence of structures at larger scales, such as coevolutionary dynamics and local adaptation. We capitalized on methods commonly employed in community ecology to quantify how the structure of community interaction matrices, so called 'bipartite networks', reflected observed coevolutionary dynamics, and how phages from these communities may or may not have adapted locally to their bacterial hosts...
January 16, 2017: Molecular Ecology
https://www.readbyqxmd.com/read/28063192/soft-selective-sweeps-in-fungicide-resistance-adaptation-recurrent-mutations-without-fitness-costs-in-grapevine-downy-mildew
#3
Chloé E L Delmas, Yann Dussert, Laurent Delière, Carole Couture, Isabelle D Mazet, Sylvie Richart Cervera, François Delmotte
Adaptation produces hard or soft selective sweeps depending on the supply of adaptive genetic polymorphism. The evolution of pesticide resistance in parasites is a striking example of rapid adaptation that can shed light on selection processes. Plasmopara viticola, which causes grapevine downy mildew, forms large populations, in which resistance has rapidly evolved due to excessive fungicide use. We investigated the pathways by which fungicide resistance has evolved in this plant pathogen, to determine whether hard or soft selective sweeps were involved...
January 7, 2017: Molecular Ecology
https://www.readbyqxmd.com/read/28052487/the-coexistence-of-generalist-and-specialist-clonal-lineages-in-natural-populations-of-the-irish-famine-pathogen-phytophthora-infestans-explains-local-adaptation-to-potato-and-tomato
#4
Alexander Kröner, Romain Mabon, Roselyne Corbière, Josselin Montarry, Didier Andrivon
Phytophthora infestans, causing late blight on Solanaceae, is a serious threat to potato and tomato crops worldwide. P. infestans populations sampled on either potato or tomato differ in genotypes and pathogenicity, suggesting niche exclusion in the field. We hypothesized that such niche separation can reflect differential host exploitation by different P. infestans genotypes. We thus compared genotypes and phenotypes in 21 isolates sampled on potato (n = 11) or tomato (n = 10). Typing at 12 microsatellite loci assigned potato isolates to the 13_A2, 6_A1 and 1_A1 lineages, and tomato isolates to the 23_A1, 2_A1 and unclassified multi-locus genotypes...
January 4, 2017: Molecular Ecology
https://www.readbyqxmd.com/read/28052431/deciphering-the-genomic-architecture-of-the-stickleback-brain-with-a-novel-multi-locus-gene-mapping-approach
#5
Zitong Li, Baocheng Guo, Jing Yang, Gábor Herczeg, Abigél Gonda, Gergely Balázs, Takahito Shikano, Federico C F Calboli, Juha Merilä
Quantitative traits important to organismal function and fitness, such as brain size, are presumably controlled by many small-effect loci. Deciphering the genetic architecture of such traits with traditional quantitative trait locus (QTL) mapping methods is challenging. Here, we investigated the genetic architecture of brain size (and the size of five different brain parts) in nine-spined sticklebacks (Pungitius pungitius) with the aid of novel multi-locus QTL mapping approaches based on a de-biased LASSO method...
January 4, 2017: Molecular Ecology
https://www.readbyqxmd.com/read/28042895/ecological-genomics-of-tropical-trees-how-local-population-size-and-allelic-diversity-of-resistance-genes-relate-to-immune-responses-co-susceptibility-to-pathogens-and-negative-density-dependence
#6
J H Marden, S A Mangan, M Peterson, E Wafula, H W Fescemyer, J Der, C W dePamphilis, L S Comita
In tropical forests, rarer species show increased sensitivity to species-specific soil pathogens and more negative effects of conspecific density on seedling survival (NDD). These patterns suggest a connection between ecology and immunity, perhaps because small population size disproportionately reduces genetic diversity of hyperdiverse loci such as immunity genes. In an experiment examining seedling roots from six species in one tropical tree community, we found that smaller populations have reduced amino acid diversity in pathogen resistance (R) genes but not the transcriptome in general...
January 2, 2017: Molecular Ecology
https://www.readbyqxmd.com/read/28039963/comment-on-rieux-and-balloux-calibration-from-tip-dating-can-compromise-topological-accuracy-and-evolutionary-inference
#7
Brent C Emerson, Diego F Alvarado-Serrano, Michael J Hickerson
We contribute to the recent review of Rieux & Balloux, 2016, Mol. Ecol., 25, 1911 on inferences from tip-dated phylogenies by developing their discussion on the influence of population size (Ne ) under panmixia for the estimation of substitution rate (μ). We highlight how phylogenetic trees inferred with tip-dated sequences under large panmictic Ne tend to erroneously enforce an age-based coalescent pattern on the posterior distribution of trees, which in turn results in systematically inflated estimates of μ...
December 31, 2016: Molecular Ecology
https://www.readbyqxmd.com/read/28036149/social-dominance-alters-nutrition-related-gene-expression-immediately-transcriptomic-evidence-from-a-monomorphic-queenless-ant
#8
Yasukazu Okada, Yutaka Watanabe, Mandy M Y Tin, Kazuki Tsuji, Alexander S Mikheyev
Queen-worker differentiation in eusocial organisms may have originated from decoupling of maternal care and reproductive behaviors. Recent advances in sequencing techniques have begun to elucidate the molecular basis of queen-worker differentiation. However, current knowledge of the molecular basis of caste differentiation is limited, especially to species with morphological castes. It seems likely that at the dawn of eusociality morphologically undifferentiated, monomorphic females underwent physiological differentiation that yielded egg-laying and caretaking castes...
December 30, 2016: Molecular Ecology
https://www.readbyqxmd.com/read/28036146/behavioral-response-to-song-and-genetic-divergence-in-two-subspecies-of-white-crowned-sparrows-zonotrichia-leucophrys
#9
Sara E Lipshutz, Isaac A Overcast, Michael J Hickerson, Robb T Brumfield, Elizabeth P Derryberry
Divergence in sexual signals may drive reproductive isolation between lineages, but behavioral barriers can weaken in contact zones. Here, we investigate the role of song as a behavioral and genetic barrier in a contact zone between two subspecies of white-crowned sparrows (Zonotrichia leucophrys). We employed a reduced genomic dataset to assess population structure and infer the history underlying divergence, gene flow and hybridization. We also measured divergence in song and tested behavioral responses to song using playback experiments within and outside the contact zone...
December 30, 2016: Molecular Ecology
https://www.readbyqxmd.com/read/28036141/expression-of-eukaryotic-like-protein-in-the-microbiome-of-sponges
#10
C Díez-Vives, L Moitinho-Silva, S Nielsen, D Reynolds, T Thomas
Eukaryotic-like proteins (ELPs) are classes of proteins that are found in prokaryotes, but have a likely evolutionary origin in eukaryotes. ELPs have been postulated to mediate host-microbiome interactions. Recent work has discovered that prokaryotic symbionts of sponges contain abundant and diverse genes for ELPs, which could modulate interactions with their filter-feeding and phagocytic host. However, the extent to which these ELP genes are actually used and expressed by the symbionts is poorly understood...
December 30, 2016: Molecular Ecology
https://www.readbyqxmd.com/read/28035737/high-levels-of-diversity-and-population-structure-in-the-potato-late-blight-pathogen-at-the-mexico-center-of-origin
#11
Jianan Wang, Sylvia P Fernândez-Pavía, Meredith M Larsen, Edith Garay-Serrano, Rosario Gregorio-Cipriano, Gerardo Rodríguez-Alvarado, Niklaus J Grünwald, Erica M Goss
Globally destructive crop pathogens often emerge by migrating out of their native ranges. These pathogens are often diverse at their center of origin, and may exhibit adaptive variation in the invaded range via multiple introductions from different source populations. However, source populations are generally unidentified or poorly studied compared to invasive populations. Phytophthora infestans, the causal agent of late blight, is one of the most costly pathogens of potato and tomato worldwide. Mexico is the center of origin and diversity of P...
December 30, 2016: Molecular Ecology
https://www.readbyqxmd.com/read/28035715/sequence-diversity-patterns-suggesting-balancing-selection-in-partially-sex-linked-genes-of-the-plant-silene-latifolia-are-not-generated-by-demographic-history-or-gene-flow
#12
Sara Guirao-Rico, Alejandro Sánchez-Gracia, Deborah Charlesworth
DNA sequence diversity in genes in the partially sex-linked pseudoautosomal region (PAR) of the sex chromosomes of the plant Silene latifolia is higher than expected from within-species diversity of other genes. This could be the footprint of sexually antagonistic (SA) alleles that are maintained by balancing selection in a PAR gene (or genes) and affect polymorphism in linked genome regions. SA selection is predicted to occur during sex chromosome evolution, but it is important to test whether the unexpectedly high sequence polymorphism could be explained without it, purely by the combined effects of partial linkage with the sex-determining region and the population's demographic history, including possible introgression from S...
December 30, 2016: Molecular Ecology
https://www.readbyqxmd.com/read/28035709/genetic-basis-of-octanoic-acid-resistance-in-drosophila-sechellia-functional-analysis-of-a-fine-mapped-region
#13
J M Andrade López, S M Lanno, J M Auerbach, E C Moskowitz, L A Sligar, P J Wittkopp, J D Coolon
Drosophila sechellia is a species of fruit fly endemic to the Seychelles islands. Unlike its generalist sister species, D. sechellia has evolved to be a specialist on the host plant Morinda citrifolia. This specialization is interesting because the plant's fruit contains secondary defense compounds, primarily octanoic acid (OA), that are lethal to most other Drosophilids. Although ecological and behavioral adaptations to this toxic fruit are known, the genetic basis for evolutionary changes in OA resistance are not...
December 30, 2016: Molecular Ecology
https://www.readbyqxmd.com/read/28029720/genetic-patterns-across-an-invasion-s-history-a-test-of-change-versus-stasis-for-the-eurasian-round-goby-in-north-america
#14
Matthew R Snyder, Carol A Stepien
Biological invasions comprise accidental evolutionary experiments, whose genetic compositions underlie relative success, spread, and persistence in new habitats. However, little is known about whether, or how, their population genetic patterns change temporally and/or spatially across the invasion's history. Theory predicts that most would undergo founder effect, exhibit low genetic divergence across the new range, and gain variation over time via new arriving propagules. To test these predictions, we analyze population genetic diversity and divergence patterns of the Eurasian round goby Neogobius melanostomus across the two decades of its North American invasion in the Laurentian Great Lakes, comparing results from 13 nuclear DNA microsatellite loci and mitochondrial DNA cytochrome b sequences...
December 28, 2016: Molecular Ecology
https://www.readbyqxmd.com/read/28029713/population-genomic-analyses-reveal-a-history-of-range-expansion-and-trait-evolution-across-the-native-and-invaded-range-of-yellow-starthistle-centaurea-solstitialis
#15
Brittany S Barker, Krikor Andonian, Sarah M Swope, Douglas G Luster, Katrina M Dlugosch
Identifying sources of genetic variation and reconstructing invasion routes for non-native introduced species is central to understanding the circumstances under which they may evolve increased invasiveness. In this study, we used genome-wide single nucleotide polymorphisms to study the colonization history of Centaurea solstitialis in its native range in Eurasia and invasions into the Americas. We leveraged this information to pinpoint key evolutionary shifts in plant size, a focal trait associated with invasiveness in this species...
December 28, 2016: Molecular Ecology
https://www.readbyqxmd.com/read/28029196/the-emergence-of-performance-trade-offs-during-local-adaptation-insights-from-experimental-evolution
#16
Lisa M Bono, Leno B Smith, David W Pfennig, Christina L Burch
Environmental heterogeneity is considered a general explanation for phenotypic diversification, particularly when heterogeneity causes populations to diverge via local adaptation. Performance trade-offs, such as those stemming from antagonistic pleiotropy, are thought to contribute to the maintenance of diversity in this scenario. Specifically, alleles that promote adaptation in one environment are expected to promote maladaptation in alternative environments. Contrary to this expectation, however, alleles that underlie locally adaptive traits often fail to exhibit fitness costs in alternative environments...
December 28, 2016: Molecular Ecology
https://www.readbyqxmd.com/read/28028891/a-decade-of-irrigation-transforms-the-soil-microbiome-of-a-semi-arid-pine-forest
#17
Martin Hartmann, Ivano Brunner, Frank Hagedorn, Richard D Bardgett, Beat Stierli, Claude Herzog, Xiamei Chen, Andreas Zingg, Elisabeth Graf-Pannatier, Andreas Rigling, Beat Frey
The impact of climate change on the soil microbiome potentially alters the biogeochemical cycle of terrestrial ecosystems. In semi-arid environments, water availability is a major constraint on biogeochemical cycles due to the combination of high summer temperatures and low rainfall. Here, we explored how ten years of irrigation of a water-limited pine forest in the central European Alps altered the soil microbiome and associated ecosystem functioning. A decade of irrigation stimulated tree growth, resulting in higher crown cover, larger yearly increments of tree biomass, increased litter fall, and greater root biomass...
December 28, 2016: Molecular Ecology
https://www.readbyqxmd.com/read/28028865/endemic-species-may-have-complex-histories-within-refugium-phylogeography-of-an-endangered-iberian-vole
#18
S Barbosa, J Paupério, J S Herman, C M Ferreira, R Pita, H M Vale-Gonçalves, J A Cabral, J A Garrido-García, R C Soriguer, P Beja, A Mira, P C Alves, J B Searle
Glacial refugia protected and promoted biodiversity during the Pleistocene, not only at a broader scale, but also for many endemics that contracted and expanded their ranges within refugial areas. Understanding the evolutionary history of refugial endemics is especially important in the case of endangered species to recognise the origins of their genetic structure and thus produce better informed conservation practices. The Iberian Peninsula is an important European glacial refugium, rich in endemics of conservation concern, including small mammals, such as the Cabrera vole (Microtus cabrerae)...
December 28, 2016: Molecular Ecology
https://www.readbyqxmd.com/read/28028864/genetic-structure-in-the-european-endemic-seabird-phalacrocorax-aristotelis-was-shaped-by-a-complex-interaction-of-historical-and-contemporary-physical-and-non-physical-drivers
#19
Evanthia Thanou, Stefano Sponza, Emily J Nelson, Annika Perry, Sarah Wanless, Francis Daunt, Stephen Cavers
Geographically separated populations tend to be less connected by gene flow, as a result of physical or non-physical barriers preventing dispersal, and this can lead to genetic structure. In this context, highly mobile organisms such as seabirds are interesting because the small effect of physical barriers means non-physical ones may be relatively more important. Here we use microsatellite and mitochondrial data to explore the genetic structure and phylogeography of Atlantic and Mediterranean populations of a European endemic seabird, the European Shag, Phalacrocorax aristotelis, and identify the primary drivers of their diversification...
December 28, 2016: Molecular Ecology
https://www.readbyqxmd.com/read/28028850/history-geography-and-host-use-shape-genome-wide-patterns-of-genetic-variation-in-the-redheaded-pine-sawfly-neodiprion-lecontei
#20
Robin K Bagley, Vitor C Sousa, Matthew L Niemiller, Catherine R Linnen
Divergent host use has long been suspected to drive population differentiation and speciation in plant-feeding insects. Evaluating the contribution of divergent host use to genetic differentiation can be difficult, however, as dispersal limitation and population structure may also influence patterns of genetic variation. In this study, we use double-digest restriction-associated DNA (ddRAD) sequencing to test the hypothesis that divergent host use contributes to genetic differentiation among populations of the redheaded pine sawfly (Neodiprion lecontei), a widespread pest that uses multiple Pinus hosts throughout its range in eastern North America...
December 28, 2016: Molecular Ecology
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