17 Works

Data from: Causes and consequences of large clonal assemblies in a poplar hybrid zone

David Macaya-Sanz, Myriam Heuertz, Dorothea Lindtke, Giovanni G. Vendramin, Christian Lexer & Santiago C. Gonzalez-Martinez
Asexual reproduction is a common and fundamental mode of reproduction in plants. Although persistence in adverse conditions underlies most known cases of clonal dominance, proximal genetic drivers remain unclear, in particular for populations dominated by a few large clones. In this study, we studied a clonal population of the riparian tree Populus alba in the Douro river basin (northwestern Iberian Peninsula) where it hybridizes with Populus tremula, a species that grows in highly contrasted ecological...

Data from: The extent and meaning of hybridization and introgression between Siberian spruce (Picea obovata) and Norway spruce (Picea abies): cryptic refugia as stepping stones to the west?

Yoshiaki Tsuda, Jun Chen, Michael Stocks, Thomas Källman, Jørn Henrik Sønstebø, Laura Parducci, Vladimir Semerikov, Christoph Sperisen, Dmitry Politov, Tiina Ronkainen, Minna Väliranta, Giovanni Giuseppe Vendramini, Mari Mette Tollefsrud, Martin Lascoux & Giovanni Giuseppe Vendramin
Boreal species were repeatedly exposed to ice ages and went through cycles of contraction and expansion while sister species alternated periods of contact and isolation. The resulting genetic structure is consequently complex, and demographic inferences are intrinsically challenging. The range of Norway spruce (Picea abies) and Siberian spruce (Picea obovata) covers most of northern Eurasia; yet their geographical limits and histories remain poorly understood. To delineate the hybrid zone between the two species and reconstruct...

Data from: Assessing early fitness consequences of exotic gene flow in the wild: a field study with Iberian pine relicts

Gregor M. Unger, Myriam Heuertz, Giuseppe G. Vendramin & Juan J. Robledo-Arnuncio
Gene flow from plantations of nonlocal (genetically exotic) tree provenances into natural stands of the same species is probably a widespread phenomenon, but its effects remain largely unexamined. We investigated early fitness consequences of intraspecific exotic gene flow in the wild by assessing differences in survival among native, nonlocal, and F1 intraspecific hybrid seedlings naturally established within two native pine relicts (one of Pinus pinaster and the other of P. sylvestris) surrounded by nonlocal plantations....

Data from: Estimating exotic gene flow into native pine stands: zygotic versus gametic components

Gregor M. Unger, Giovanni G. Vendramin & Juan J. Robledo-Arnuncio
Monitoring contemporary gene flow from widespread exotic plantations is becoming an important problem in forest conservation genetics. In plants, where both seed and pollen disperse, three components of exotic gene flow with potentially unequal consequences should be, but have not been, explicitly distinguished: zygotic, male gametic and female gametic. Building on a previous model for estimating contemporary rates of zygotic and male gametic gene flow among plant populations, we present here an approach that additionally...

Data from: Inferring selection in instances of long‐range colonization: the Aleppo pine (Pinus halepensis) in the Mediterranean Basin

Rose Ruiz Daniels, Richard S. Taylor, María Jesús Serra-Varela, Giovanni G. Vendramin, Santiago C. González-Martínez & Delphine Grivet
Teasing apart the effects of natural selection and demography on current allele frequencies is challenging, due to both processes leaving a similar molecular footprint. In particular, when attempting to identify selection in species that have undergone a recent range expansion, the increase of genetic drift at the edges of range expansions (“allele surfing”) can be a confounded factor. To address this potential issue, we first assess the long-range colonisation history of the Aleppo pine across...

Data from: SNP genotyping elucidates the genetic diversity of Magna Graecia grapevine germplasm and its historical origin and dissemination

Gabriella De Lorenzis, Francesco Mercati, Carlo Bergamini, Maria Francesca Cardone, Antonio Lupini, Antonio Mauceri, Angelo Raffale Caputo, Loredana Abbate, Maria Gabriella Barbagallo, Donato Antonacci, Francesco Sunseri & Lucio Brancadoro
Background: Magna Graecia is the ancient name used to label the area of South of Italy extensively populated by Greek colonizers. Archeological and historical evidences identified in this region the oldest winegrowing area in Italy, pointing out its importance in the spread of high specialized viticulture around the Mediterranean Sea shores. In this work, the genetic diversity of Magna Graecia grape germplasm was assessed and its role in the grapevine propagation around the Mediterranean basin...

Data from: Development of chloroplast genomic resources for Cynara

Pasquale L. Curci, Domenico De Paola & Gabriella Sonnante
In this study, new chloroplast (cp) resources were developed for the genus Cynara, using whole cp genomes from 20 genotypes, by means of high-throughput sequencing technologies. Our target species included seven globe artichokes, two cultivated cardoons, eight wild artichokes, and three other wild Cynara species (C. baetica, C. cornigera, and C. syriaca). One complete cp genome was isolated using short reads from a whole genome sequencing project, while the others were obtained by means of...

Data from: Halfway encounters: meeting points of colonization routes among the southern beeches Nothofagus pumilio and N. antarctica

Carolina Soliani, Yoshiaki Tsuda, Francesca Bagnoli, Leonardo A. Gallo, Giovanni G. Vendramin & Paula Marchelli
The Patagonian region is characterized by a complex biogeographic history, with evidence of deep phylogeographic breaks shared among species. Of particular interest to conservation is the nature of colonization and settlement patterns after the last glacial period, including the detection of secondary contact between different lineages and/or hybridization among related species around phylogeographic breaks. Here we studied population demography and past hybridization of two widespread tree species endemic to South America, Nothofagus pumilio and N....

Data from: Multispecies genetic structure and hybridization in the Betula genus across Eurasia

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 genetic 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...

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: Sex-biased gene expression in dioecious garden asparagus (Asparagus officinalis)

Alex Harkess, Francesco Mercati, Hong-Yan Shan, Francesco Sunseri, Agostino Falavigna & Jim Leebens-Mack
Sex chromosomes have evolved independently in phylogenetically diverse flowering plant lineages. The genes governing sex determination in dioecious species remain unknown, but theory predicts that the linkage of genes influencing male and female function will spur the origin and early evolution of sex chromosomes. For example, in an XY system, the origin of an active Y may be spurred by the linkage of female suppressing and male promoting genes. Garden asparagus (Asparagus officinalis) serves as...

Data from: Molecular proxies for climate maladaptation in a long-lived tree (Pinus pinaster Aiton, Pinaceae)

Juan Pablo Jaramilo-Correa, Isabel Rodríguez-Quilón, Delphine Grivet, Camille Lepoittevin, Federico Sebastiani, Myriam Heuertz, Pauline H. Garnier-Géré, Ricardo Alía, Christophe Plomion, Giovanni G. Vendramin, Santiago C. González-Martínez, J.-P. Jaramillo-Correa, S. C. Gonzalez-Martinez & P. H. Garnier-Gere
Understanding adaptive genetic responses to climate change is a main challenge for preserving biological diversity. Successful predictive models for climate-driven range shifts of species depend on the integration of information on adaptation, including that derived from genomic studies. Long-lived forest trees can experience substantial environmental change across generations, which results in a much more prominent adaptation lag than in annual species. Here, we show that candidate-gene SNPs (Single Nucleotide Polymorphisms) can be used as predictors...

Data from: Genomic exploration and molecular marker development in a large and complex conifer genome using RADseq and mRNAseq

Marie-Joe Karam, François Lefèvre, Magda Bou Dagher-Kharrat, Sara Pinosio & Giovanni Vendramin
We combined restriction site associated DNA sequencing (RADseq) using a hypomethylation-sensitive enzyme and messenger RNA sequencing (mRNAseq) to develop molecular markers for the 16 gigabase genome of Cedrus atlantica, a conifer tree species. With each method, Illumina® reads from one individual were used to generate de novo assemblies. SNPs from the RADseq data set were detected in a panel of one single individual and three pools of three individuals each. We developed a flexible script...

Data from: First insights into the transcriptome and development of new genomic tools of a widespread circum-Mediterranean tree species, Pinus halepensis Mill.

Sara Pinosio, Santiago C. González-Martínez, Francesca Bagnoli, Federica Cattonaro, Delphine Grivet, Fabio Marroni, Zaida Lorenzo, Juli G. Pausas, Miguel Verdú & Giovanni G. Vendramin
Pinus halepensis is a relevant conifer species for studying adaptive responses to drought and fire regimes in the Mediterranean region. Deciphering the molecular basis of Aleppo pine to the Mediterranean environment is therefore needed. In this study we performed Illumina next-generation sequencing of two phenotypically divergent Pinus halepensis accessions with the aims of i) characterizing the transcriptome through Illumina RNA-Seq of two accessions, phenotypically divergent for adaptive traits link to fire adaptation and drought, ii)...

Data from: Evidence of divergent selection for drought and cold tolerance at landscape and local scales in Abies alba Mill. in the French Mediterranean Alps

Anna M. Roschanski, Katalin Csilléry, Sascha Liepelt, Sylvie Oddou-Muratorio, Birgit Ziegenhagen, Frédéric Huard, Kristian K. Ullrich, Dragos Postolache, Giovanni G. Vendramin & Bruno Fady
Understanding local adaptation in forest trees is currently a key research and societal priority. Geographically and ecologically marginal populations provide ideal case studies, because environmental stress along with reduced gene flow can facilitate the establishment of locally adapted populations. We sampled European silver fir (Abies alba Mill.) trees in the French Mediterranean Alps, along the margin of its distribution range, from pairs of high and low elevation plots on four different mountains situated along a...

Data from: Local effects drive heterozygosity-fitness correlations in an outcrossing long-lived tree

Isabel Rodriguez-Quilon, Luis Santos-Del-Blanco, Delphine Grivet, Juan Pablo Jaramillo-Correa, Juan Majada, Giovanni Vendramin, Ricardo Alía & Santiago Gonzalez-Martinez
Heterozygosity-fitness correlations (HFCs) have been used to understand the complex interactions between inbreeding, genetic diversity and evolution. Although frequently reported for decades, evidence for HFCs was often based on underpowered studies or inappropriate methods, and hence their underlying mechanisms are still under debate. Here, we used 6,100 genome-wide Single Nucleotide Polymorphisms (SNPs) to test for general and local effect HFCs in maritime pine (Pinus pinaster Ait.), an iconic Mediterranean forest tree. Survival was used as...

Evolutionary rate and genetic load in an emblematic Mediterranean tree following an ancient and prolonged population collapse

Santiago C Gonzalez-Martinez, Juan Jaramillo-Correa, Francesca Bagnoli, Delphine Grivet, Bruno Fady, Filippos Aravanopoulos & Giovanni Vendramin
Severe bottlenecks significantly diminish the amount of genetic diversity and the speed at which it accumulates (i.e. evolutionary rate). They further compromise the efficiency of natural selection to eliminate deleterious variants, which may reach fixation in the surviving populations. Consequently, expanding and adapting to new environments may pose a significant challenge when strong bottlenecks result in genetic pauperization. Herein, we surveyed the patterns of nucleotide diversity, molecular adaptation and genetic load across hundreds of loci...

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