11 Works

Data from: \"Discovery and characterization of 80 SNPs and 1,624 SSRs in the transcriptome of Atlantic mackerel (Scomber scombrus, L)\" in Genomic Resources Notes Accepted 1 June 2015 to 31 July 2015

Iratxe Montes, Jorge Langa, César Vilas, Sarah J. Helyar, Paula Álvarez, Darrell Conklin & Andone Estonba
This paper reports on SNP discovery in the Atlantic mackerel transcriptome, using next generation sequencing technologies and applying developed methodology already proven successful for the European anchovy. A total of 9,966 high quality transcriptome contigs were assembled, from which 951 putative SNPs were discovered. In all, 479 putative SNPs and 1,624 simple sequence repeats (SSRs) suitable for genotyping were identified. A subset of 96 was selected for genotyping; from these, 80 SNPs were considered polymorphic...

Data from: Effects of spring temperatures on the strength of selection on timing of reproduction in a long-distance migratory bird

Marcel E. Visser, Phillip Gienapp, Arild Husby, Michael Morrisey, Iván De La Hera, Francisco Pulido & Christiaan Both
Climate change has differentially affected the timing of seasonal events for interacting trophic levels, and this has often led to increased selection on seasonal timing. Yet, the environmental variables driving this selection have rarely been identified, limiting our ability to predict future ecological impacts of climate change. Using a dataset spanning 31 years from a natural population of pied flycatchers (Ficedula hypoleuca), we show that directional selection on timing of reproduction intensified in the first...

Data from: \"Diagnostic SNPs for inferring population structure in American mink (Neovison vison) identified through RAD sequencing\" in Genomic Resources Notes accepted 1 October 2014 to 30 November 2014

Janne Pia Thirstrup, Aritz Ruiz-Gonzalez, Jose Martin Pujolar, Peter Foged Larsen, Rasmus O. Nielsen, Ettore Randi, Andrzej Zalewski, Cino Pertoldi, Mariella Baratti, Tiziana Di Lorenzo, Alessio Iannucci, Diana Maria Paola Galassi, Valentina Iannilli, Just Jensen, Dragos Postolache & Giovanni Giuseppe Vendramin
The article documents the public availability of RAD sequencing data and generated SNPs for the American mink (Neovison vison). 224,095 polymorphic loci were identified from 14 mink from which primers were designed for a subset of 380 SNPs. The panel was tested on 211 mink. Fisher’s F-statistics (Fis, FIT and FST) as well as observed (HO), expected (HE) and unbiased expected (uHE) heterozygosity was calculated for the SNPs and 194 SNPs was validated as being...

Data from: \"De novo assembled transcriptome of organs involved in reproduction in an endangered endemic Iberian cyprinid fish (Squalius pyrenaicus)\" in Genomic Resources Notes Accepted 1 June 2015 to 31 July 2015

Miguel P. Machado, Joana Pinho, Ana R. Grosso, Manfred Schartl, Maria M. Coelho, C. Vilas, Wolfgang Arthofer, Alexander Rief, Birgit C. Schlick-Steiner, Julia Seeber, Florian M. Steiner, D. Conklin, A. Estonba, J. Langa & I. Montes
Sex determination systems are diverse, especially among fish, and include genetic and/or environmental components. Unexpectedly for such a basic aspect of development, sex determination systems change rapidly during evolution and gonadal fate is not ultimate, being actively maintained lifelong. Here, sequences of expressed genes involved in maintenance of gonad identity and reproduction processes were obtained through transcriptome assembly of the brain-gonadal axis tissues of a freshwater fish inhabiting highly variable environments, the gonochoristic Iberian fish...

Data from: Isolation by distance, resistance and/or clusters? Lessons learned from a forest-dwelling carnivore inhabiting a heterogeneous landscape

Aritz Ruiz-González, Samuel A. Cushman, María José Madeira, Benjamín J. Gómez-Moliner & Ettore Randi
Landscape genetics provides a valuable framework to understand how landscape features influence gene flow and to disentangle the factors that lead to discrete and/or clinal population structure. Here, we attempt to differentiate between these processes in a forest-dwelling small carnivore [European pine marten (Martes martes)]. Specifically, we used complementary analytical approaches to quantify the spatially explicit genetic structure and diversity and analyse patterns of gene flow for 140 individuals genotyped at 15 microsatellite loci. We...

Data from: Dissecting the hydrological niche: soil moisture, space and lifespan

Gonzalo García-Baquero, Jonathan Silvertown, David J. Gowing & Cipriano J. Valle
Questions: Are communities structured on a hydrological (soil moisture) gradient? Is there spatial segregation into hydrological niches? What is the shape of the hydrological niches of individual species? Controlling for spatial autocorrelation, how much of the spatial structure in the community is due to variation in hydrology? Do annuals and perennials behave alike with respect to the above questions? Locations: La Mina in Moscosa Farm, Salamanca, western Spain (dehesa community) and Laguna Larga in the...

Data from: \"You are not what you eat: massive parallel sequencing reveals that gut microbiome is not diet-related in larval Dilophus febrilis (Diptera: Bibionidae)\" in Genomic Resources Notes Accepted 1 June 2015 to 31 July 2015

Alexander Rief, Wolfgang Arthofer, Birgit C. Schlick-Steiner, Florian M. Steiner & Julia Seeber
This article documents the public availability of metagenome sequence data from 454 amplicon sequencing of larval dipteran gut (Dilophus febrilis) and their potential food sources dwarf shrub litter (Vaccinium gaultheroides), grass litter (Dactylis glomerata), and cow dung (Bos primigenius taurus).

Data from: Ecological and historical determinants of population genetic structure and diversity in the Mediterranean shrub Rosmarinus officinalis (Lamiaceae)

José Gabriel Segarra-Moragues, Yolanda Carrión Marco, María Clara Castellanos, María José Molina & Patricio García-Fayos
Population genetic studies of widespread Mediterranean shrubs are scarce compared with those of trees and narrow endemics or studies from phylogeographical perspectives, despite the key role these species may play in Mediterranean ecosystems. Knowledge on the effect of ecological factors in shaping their genetic patterns is also limited. In this study we investigate genetic diversity and population structure across 18 populations of Rosmarinus officinalis, a Mediterranean shrubland plant. Populations were sampled along two elevational gradients,...

Data from: Genetic structure and post-glacial expansion of Cornus florida L. (Cornaceae): integrative evidence from phylogeography, population demographic history, and species distribution modeling

Ashley Call, Yan-Xia Sun, Yan Yu, Peter B. Pearman, David T. Thomas, Robert Trigiano, Ignazio Carbone, Qiu-Yun Xiang, Robert N. Trigiano, Yan-Xia Sun & Qiu-Yun Jenny Xiang
Repeated global climatic cooling and warming cycles during the Pleistocene played a major role in the distribution and evolution of the Earth biota. Here, we integrate phylogeography, coalescent-based Bayesian estimation of demographic history, and species distribution modeling (SDM) to understand the genetic patterns and biogeography of the flowering dogwood, Cornus florida subsp. florida L., since the Last Glacial Maximum (LGM). Natural populations of the species are severely threatened by dogwood anthracnose. We genotyped 306 plants...

Data from: Resprouter fraction in Cape Restionaceae assemblages varies with climate and soil type

Rafael O. Wüest, Glenn Litsios, Félix Forest, Christian Lexer, H. Peter Linder, Nicolas Salamin, Niklaus E. Zimmermann & Peter B. Pearman
While fire-induced changes in biodiversity are well documented, less is known about how fire impacts life-history variation and diversity of functional traits that represent distinct strategies for persistence in fire-driven ecosystems. One example is the dichotomy in which ‘resprouter’ species usually survive fires to produce new growth, while ‘reseeder’ species perish and re-establish from seed. Variable relative numbers of reseeder and resprouter species in local assemblages of Restionaceae (Poales) of the Cape Floristic Region (CFR),...

Data from: Dietary overlap and seasonality in three species of mormoopid bats from a tropical dry forest

Valeria B. Salinas-Ramos, Luis Gerardo Herrera Montalvo, Virginia León-Regagnon, Aitor Arrizabalaga-Escudero & Elizabeth L. Clare
Competing hypotheses explaining species’ use of resources have been advanced. Resource limitations in habitat and/or food are factors that affect assemblages of species. These limitations could drive the evolution of morphological and/or behavioural specialization, permitting the coexistence of closely related species through resource partitioning and niche differentiation. Alternatively, when resources are unlimited, fluctuations in resources availability will cause concomitant shifts in resource use regardless of species identity. Here, we used next-generation sequencing to test these...

Registration Year

  • 2015
    11

Resource Types

  • Dataset
    11

Affiliations

  • University of the Basque Country
    11
  • Andalusian Institute of Agricultural and Fisheries Research and Training
    3
  • University of Innsbruck
    3
  • University of Würzburg
    2
  • University of Lisbon
    2
  • Ikerbasque
    2
  • Aalborg University
    2
  • Swiss Institute of Bioinformatics
    1
  • University of Sussex
    1
  • Science Learning Resources (United States)
    1