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Molecular Ecology

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https://www.readbyqxmd.com/read/28628257/contrasting-gene-expression-programs-correspond-with-predator-induced-phenotypic-plasticity-within-and-across-generations-in-daphnia
#1
Nicole R Hales, Drew R Schield, Audra L Andrew, Daren C Card, Matthew R Walsh, Todd A Castoe
Research has shown that a change in environmental conditions can alter the expression of traits during development (i.e., 'within-generation phenotypic plasticity') as well as induce heritable phenotypic responses that persist for multiple generations (i.e., 'transgenerational plasticity'). It has long been assumed that shifts in gene expression are tightly linked to observed trait responses at the phenotypic level. Yet, the manner in which organisms couple within- and trans-generational plasticity at the molecular level is unclear...
June 19, 2017: Molecular Ecology
https://www.readbyqxmd.com/read/28627128/signatures-of-soft-sweeps-across-the-dt1-locus-underlying-determinate-growth-habit-in-soybean-glycine-max-l-merr
#2
Limei Zhong, Qiaomei Yang, Xin Yan, Chao Yu, Liu Su, Xifeng Zhang, Youlin Zhu
Determinate growth habit is an agronomically important trait associated with domestication in soybean. Previous studies have demonstrated that the emergence of determinacy is correlated with artificial selection on four non-synonymous mutations in the Dt1 gene. To better understand the signatures of the soft sweeps across the Dt1 locus and track the origins of the determinate alleles, we examined patterns of nucleotide variation in Dt1 and the surrounding genomic region of approximately 800 kb. Four local, asymmetrical hard sweeps on four determinate alleles, sized approximately 660, 120, 220 and 150 kb were identified, which constitute the soft sweeps for the adaptation...
June 19, 2017: Molecular Ecology
https://www.readbyqxmd.com/read/28626973/role-of-parasite-transmission-in-promoting-inbreeding-ii-pedigree-reconstruction-reveals-sib-transmission-and-consequent-kin-mating
#3
Jillian T Detwiler, Charles D Criscione
Even though parasitic flatworms are one of the most species rich groups of hermaphroditic organisms, we know virtually nothing of their mating systems (selfing or kin-mating rates) in nature. Hence, we lack an understanding of the role of inbreeding in parasite evolution. The natural mating systems of parasitic flatworms have remained elusive due to the inherent difficulty in generating progeny-array data in many parasite systems. New developments in pedigree reconstruction allow direct inference of realized selfing rates in nature by simply using a sample of genotyped individuals...
June 19, 2017: Molecular Ecology
https://www.readbyqxmd.com/read/28626971/genetics-and-developmental-biology-of-cooperation
#4
Claudia Kasper, Maddalena Vierbuchen, Ulrich Ernst, Stefan Fischer, Reinder Radersma, Aura Raulo, Filipa Cunha-Saraiva, Min Wu, Kenyon Mobley, Barbara Taborsky
Despite essential progress towards understanding the evolution of cooperative behaviour, we still lack detailed knowledge about its underlying molecular mechanisms, genetic basis, evolutionary dynamics and ontogeny. An international workshop 'Genetics and Development of Cooperation', organized by the University of Bern (Switzerland), aimed at discussing the current progress in this research field and suggesting avenues for future research. This review uses the major themes of the meeting as a springboard to synthesize the concepts of genetic and non-genetic inheritance of cooperation, and to review a quantitative genetic framework that allows for the inclusion of indirect genetic effects...
June 19, 2017: Molecular Ecology
https://www.readbyqxmd.com/read/28626946/do-changes-in-gene-expression-contribute-to-sexual-isolation-and-reinforcement-in-the-house-mouse
#5
Etienne Loire, Sergio Tusso, Pierre Caminade, Dany Severac, Pierre Boursot, Guila Ganem, Carole M Smadja
Expression divergence, rather than sequence divergence, has been shown to be important in speciation, particularly in the early stages of divergence of traits involved in reproductive isolation. In the two European subspecies of house mice, Mus musculus musculus and M. m. domesticus, earlier studies have demonstrated olfactory-based assortative mate preference in populations close to their hybrid zone. It has been suggested that this behaviour evolved following the recent secondary contact between the two taxa (~3,000 years ago) in response to selection against hybridisation...
June 19, 2017: Molecular Ecology
https://www.readbyqxmd.com/read/28626938/role-of-parasite-transmission-in-promoting-inbreeding-i-infection-intensities-drive-individual-parasite-selfing-rates
#6
Jillian T Detwiler, Isabel C Caballero, Charles D Criscione
Among parasitic organisms, inbreeding has been implicated as a potential driver of host-parasite coevolution, drug-resistance evolution, and parasite diversification. Yet, fundamental topics about how parasite life histories impact inbreeding remain to be addressed. In particular, there are no direct selfing-rate estimates for hermaphroditic parasites in nature. Our objectives were to elucidate the mating system of a parasitic flatworm in nature and to understand how aspects of parasite transmission could influence the selfing rates of individual parasites...
June 19, 2017: Molecular Ecology
https://www.readbyqxmd.com/read/28626905/genome-architecture-enables-local-adaptation-of-atlantic-cod-despite-high-connectivity
#7
Julia M I Barth, Paul R Berg, Per R Jonsson, Sara Bonanomi, Hanna Corell, Jakob Hemmer-Hansen, Kjetill S Jakobsen, Kerstin Johannesson, Per Erik Jorde, Halvor Knutsen, Per-Olav Moksnes, Bastiaan Star, Nils Chr Stenseth, Henrik Svedäng, Sissel Jentoft, Carl André
Adaptation to local conditions is a fundamental process in evolution; however, mechanisms maintaining local adaptation despite high gene flow are still poorly understood. Marine ecosystems provide a wide array of diverse habitats that frequently promote ecological adaptation even in species characterized by strong levels of gene flow. As one example, populations of the marine fish Atlantic cod (Gadus morhua) are highly connected due to immense dispersal capabilities but nevertheless show local adaptation in several key traits...
June 19, 2017: Molecular Ecology
https://www.readbyqxmd.com/read/28614601/genome-wide-transcriptional-reprogramming-in-the-seagrass-cymodocea-nodosa-under-experimental-ocean-acidification
#8
Miriam Ruocco, Francesco Musacchia, Irene Olivé, Monya M Costa, Isabel Barrote, Rui Santos, Remo Sanges, Gabriele Procaccini, João Silva
Here we report the first use of massive scale RNA-Sequencing to explore seagrass response to CO2 -driven ocean acidification (OA). Large-scale gene expression changes in the seagrass Cymodocea nodosa occurred at CO2 levels projected by the end of the century. C. nodosa transcriptome was obtained using Illumina RNA-Seq technology and de novo assembly, and differential gene expression was explored in plants exposed to short-term high CO2 / low pH conditions. At high pCO2 , there was a significant increased expression of transcripts associated to photosynthesis, including light reaction functions and CO2 fixation, and also to respiratory pathways, specifically for enzymes involved in glycolysis, in the tricarboxylic acid cycle and in the energy metabolism of the mitochondrial electron transport...
June 14, 2017: Molecular Ecology
https://www.readbyqxmd.com/read/28614599/investigating-the-genomic-basis-of-discrete-phenotypes-using-a-pool-seq-only-approach-new-insights-into-the-genetics-underlying-color-variation-in-diverse-taxa
#9
Ramprasad Neethiraj, Emily Anne Hornett, Jason Hill, Christopher W Wheat
While large-scale genomics approaches are increasingly revealing the genetic basis of polymorphic phenotypes such as color morphs, such approaches are almost exclusively conducted in species with high quality genomes and annotations. Here we use Pool-Seq data for both genome assembly and SNP frequency estimation, followed by scanning for FST outliers to identify divergent genomic regions. Using paired-end, short-read sequencing data from two groups of individuals expressing divergent phenotypes, we generate a de novo rough draft genome, identify SNPs, and calculate genome wide FST differences between phenotypic groups...
June 14, 2017: Molecular Ecology
https://www.readbyqxmd.com/read/28612961/genome-wide-analysis-of-allele-frequency-change-in-sunflower-crop-wild-hybrid-populations-evolving-under-natural-conditions
#10
Jonathan Corbi, Eric J Baack, Jennifer M Dechaine, Gerald Seiler, John M Burke
Crop-wild hybridization occurs in numerous plant species, and could alter the genetic structure and evolutionary dynamics of wild populations. Studying crop-derived alleles in wild populations is also relevant to assessing/mitigating the risks associated with transgene escape. To date, crop-wild hybridization has generally been examined via short-term studies, typically within a single generation, focusing on few traits or genetic markers. Little is known about patterns of selection on crop-derived alleles over multiple generations, particularly at a genome-wide scale...
June 14, 2017: Molecular Ecology
https://www.readbyqxmd.com/read/28612956/connecting-genomic-patterns-of-local-adaptation-and-niche-suitability-in-teosintes
#11
J A Aguirre-Liguori, M I Tenaillon, A Vázquez-Lobo, B S Gaut, J P Jaramillo-Correa, S Montes-Hernandez, V Souza, L E Eguiarte
The central-abundance hypothesis predicts that local adaptation is a function of the distance to the center of a species' geographic range. To test this hypothesis, we gathered genomic diversity data from 49 populations, 646 individuals and 33,464 SNPs of two wild relatives of maize, the teosintes Zea mays ssp. parviglumis and Zea. mays. ssp. mexicana. We examined the association between the distance to their climatic and geographic centroids and the enrichment of SNPs bearing signals of adaptation. We identified candidate adaptive SNPs in each population by combining neutrality tests and cline analyzes...
June 14, 2017: Molecular Ecology
https://www.readbyqxmd.com/read/28605149/increase-in-multiple-paternity-across-the-reproductive-lifespan-in-a-sperm-storing-hermaphroditic-freshwater-snail
#12
Anja Bürkli, Jukka Jokela
Polyandry is a common phenomenon and challenges the traditional view of stronger sexual selection in males than in females. In simultaneous hermaphrodites, the physical proximity of both sex functions was long thought to preclude the operation of sexual selection. Laboratory studies suggest that multiple mating and polyandry in hermaphrodites may actually be common, but data from natural populations are sparse. We therefore estimated the rate of multiple paternity and its seasonal variability in the annual, sperm-storing, simultaneously hermaphroditic freshwater snail Radix balthica for the entire duration of the reproductive lifespan...
June 12, 2017: Molecular Ecology
https://www.readbyqxmd.com/read/28600900/screening-of-duplicated-loci-reveals-hidden-divergence-patterns-in-a-complex-salmonid-genome
#13
Morten T Limborg, Wesley A Larson, Lisa W Seeb, James E Seeb
A whole genome duplication (WGD) doubles the entire genomic content of a species and is thought to have catalyzed adaptive radiation in some polyploid-origin lineages. However, little is known about general consequences of a WGD since gene duplicates (i.e. paralogs) are commonly filtered in genomic studies; such filtering may remove substantial portions of the genome in data sets from polyploid-origin species. We demonstrate a new method that enables genome-wide scans for signatures of selection at both non-duplicated and duplicated loci by taking locus-specific copy number into account...
June 10, 2017: Molecular Ecology
https://www.readbyqxmd.com/read/28599072/zooplankton-community-structure-along-a-pollution-gradient-at-fine-geographical-scales-in-river-ecosystems-the-importance-of-species-sorting-over-dispersal
#14
Wei Xiong, Ping Ni, Yiyong Chen, Yangchun Gao, Baoqing Shan, Aibin Zhan
The release of anthropogenic pollution into freshwater ecosystems has largely transformed biodiversity and its geographical distribution patterns globally. However, for many communities including ecologically crucial ones such as zooplankton, it is largely unknown how different communities respond to environmental pollution. Collectively, dispersal and species sorting are two competing processes in determining the structure and geographical distribution of zooplankton communities in running water ecosystems such as rivers...
June 9, 2017: Molecular Ecology
https://www.readbyqxmd.com/read/28598519/complexities-of-gene-expression-patterns-in-natural-populations-of-an-extremophile-fish-poecilia-mexicana-poeciliidae
#15
Courtney N Passow, Anthony P Brown, Lenin Arias-Rodriquez, M-C Yee, Alexandra Sockell, Manfred Schartl, Wesley C Warren, Carlos Bustamante, Joanna L Kelley, Michael Tobler
Variation in gene expression can provide insights into organismal responses to environmental stress and physiological mechanisms mediating adaptation to habitats with contrasting environmental conditions. We performed an RNA-sequencing experiment to quantify gene expression patterns in fish adapted to habitats with different combinations of environmental stressors, including the presence of toxic hydrogen sulfide (H2 S) and the absence of light in caves. We specifically asked how gene expression varies among populations living in different habitats, whether population differences were consistent among organs, and whether there is evidence for shared expression responses in populations exposed to the same stressors...
June 9, 2017: Molecular Ecology
https://www.readbyqxmd.com/read/28597534/whole-genome-patterns-of-linkage-disequilibrium-across-flycatcher-populations-clarify-the-causes-and-consequences-of-fine-scale-recombination-rate-variation-in-birds
#16
Takeshi Kawakami, Carina F Mugal, Alexander Suh, Alexander Nater, Reto Burri, Linnéa Smeds, Hans Ellegren
Recombination rate is heterogeneous across the genome of various species, and so are genetic diversity and differentiation as a consequence of linked selection. However, we still lack a clear picture of the underlying mechanisms for regulating recombination. Here we estimated fine-scale population recombination rate based on the patterns of linkage disequilibrium (LD) across the genomes of multiple populations of two closely related flycatcher species (Ficedula albicollis and F. hypoleuca). This revealed an overall conservation of the recombination landscape between these species at the scale of 200-kb, but we also identified differences in the local rate of recombination despite their recent divergence (<1 million years)...
June 8, 2017: Molecular Ecology
https://www.readbyqxmd.com/read/28570031/evolution-of-sociality-in-spiders-leads-to-depleted-genomic-diversity-at-both-population-and-species-level
#17
V Settepani, M F Schou, M Greve, L Grinsted, J Bechsgaard, T Bilde
Across several animal taxa, the evolution of sociality involves a suite of characteristics, a 'social syndrome', that includes cooperative breeding, reproductive skew, primary female biased sex-ratio, and the transition from outcrossing to inbreeding mating system, factors that are expected to reduce effective population size (Ne). This social syndrome may be favoured by short-term benefits but come with long-term costs, because the reduction in Ne amplifies loss of genetic diversity by genetic drift, ultimately restricting the potential of populations to respond to environmental change...
June 1, 2017: Molecular Ecology
https://www.readbyqxmd.com/read/28570029/plasticity-contributes-to-a-fine-scale-depth-gradient-in-sticklebacks-visual-system
#18
Thor Veen, Chad Brock, Diana Rennison, Daniel Bolnick
The light environment influences an animal's ability to forage, evade predators, and find mates, and consequently is known to drive local adaptation of visual systems. However, the light environment may also vary over fine spatial scales at which genetic adaptation is difficult. For instance, in aquatic systems the available wavelengths of light change over a few meters depth. Do animals plastically adjust their visual system to such small-scale environmental light variation? Here, we show that in threespine stickleback (Gasterosteus aculeatus), opsin gene expression (an important determinant of colour vision) changes over a 2-meter vertical gradient in nest depth...
June 1, 2017: Molecular Ecology
https://www.readbyqxmd.com/read/28570016/divergent-taxonomic-and-functional-responses-of-microbial-communities-to-field-simulation-of-aeolian-soil-erosion-and-deposition
#19
Xingyu Ma, Cancan Zhao, Ying Gao, Bin Liu, Tengxu Wang, Tong Yuan, Lauren Hale, Joy D Van Nostrand, Shiqiang Wan, Jizhong Zhou, Yunfeng Yang
Aeolian soil erosion and deposition have worldwide impacts on agriculture, air quality and public health. However, ecosystem responses to soil erosion and deposition remain largely unclear in regard to microorganisms, which are the crucial drivers of biogeochemical cycles. Using integrated metagenomics technologies, we analyzed microbial communities subjected to simulated soil erosion and deposition in a semiarid grassland of Inner Mongolia, China. As expected, soil total organic carbon and plant coverage were decreased by soil erosion, and soil dissolved organic carbon (DOC) was increased by soil deposition, demonstrating that field simulation was reliable...
June 1, 2017: Molecular Ecology
https://www.readbyqxmd.com/read/28570015/genome-wide-patterns-of-variation-in-genetic-diversity-are-shared-among-populations-species-and-higher-order-taxa
#20
Nagarjun Vijay, Matthias Weissensteiner, Reto Burri, Takeshi Kawakami, Hans Ellegren, Jochen B W Wolf
Genome-wide screens of genetic variation within and between populations can reveal signatures of selection implicated in adaptation and speciation. Genomic regions with low genetic diversity and elevated differentiation reflective of locally reduced effective population sizes (Ne ) are candidates for barrier loci contributing to population divergence. Yet, such candidate genomic regions need not arise as a result of selection promoting adaptation or advancing reproductive isolation. Linked selection unrelated to lineage-specific adaptation or population divergence can generate comparable signatures...
June 1, 2017: Molecular Ecology
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