Nils Arrigo - Academia.edu (original) (raw)

Papers by Nils Arrigo

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Appendix S1 Sampled populations of Oreina gloriosa and Peucedanum ostruthium with their geographi... more Appendix S1 Sampled populations of Oreina gloriosa and Peucedanum ostruthium with their geographical coordinates and the number of analysed individuals.

Molecular Ecology …, Jan 1, 2012

We briefly introduce R2G2, an R CRAN package to visualize spatially explicit biological data with... more We briefly introduce R2G2, an R CRAN package to visualize spatially explicit biological data within the Google Earth interface. Our package combines a collection of basic graph-editing features, including automated placement of dots, segments, polygons, images (including graphs produced with R), along with several complex three-dimensional (3D) representations such as phylogenies, histograms and pie charts. We briefly present some example data sets and show the immediate benefits in communication gained from using the Google Earth interface to visually explore biological results. The package is distributed with detailed help pages providing examples and annotated source scripts with the hope that users will have an easy time using and further developing this package. R2G2 is distributed on http://cran.r-project.org/web/packages.

Evolutionary history and its relevance in …

Understanding how biodiversity is distributed is central to any conservation effort and has tradi... more Understanding how biodiversity is distributed is central to any conservation effort and has traditionally been based on niche modeling and the causal relationship between spatial distribution of organisms and their environment. More recently, the study of species' evolutionary history and relatedness has permeated the fields of ecology and conservation and, coupled with spatial predictions, provides useful insights to the origin of current biodiversity patterns, community structuring and potential vulnerability to extinction.

Current opinion in plant biology, Jan 1, 2012

Polyploidy, or whole genome duplication, is recognized as an important feature of eukaryotic geno... more Polyploidy, or whole genome duplication, is recognized as an important feature of eukaryotic genome evolution. Among eukaryotes, polyploidy has probably had the largest evolutionary impact on vascular plants where many contemporary species are of recent polyploid origin. Genomic analyses have uncovered evidence of at least one round of polyploidy in the ancestry of most plants, fueling speculation that genome duplications lead to increases in net diversity. In spite of the frequency of ancient polyploidy, recent analyses have found that recently formed polyploid species have higher extinction rates than their diploid relatives. These results suggest that despite leaving a substantial legacy in plant genomes, only rare polyploids survive over the long term and most are evolutionary dead-ends.

BMC evolutionary …, Jan 1, 2011

Background: Within the Coleoptera, the largest order in the animal kingdom, the exclusively herbi... more Background: Within the Coleoptera, the largest order in the animal kingdom, the exclusively herbivorous Chrysomelidae are recognized as one of the most species rich beetle families. The evolutionary processes that have fueled radiation into the more than thirty-five thousand currently recognized leaf beetle species remain partly unresolved. The prominent role of leaf beetles in the insect world, their omnipresence across all terrestrial biomes and their economic importance as common agricultural pest organisms make this family particularly interesting for studying the mechanisms that drive diversification. Here we specifically focus on two ecotypes of the alpine leaf beetle Oreina speciosissima (Scop.), which have been shown to exhibit morphological differences in male genitalia roughly corresponding to the subspecies Oreina speciosissima sensu stricto and Oreina speciosissima troglodytes. In general the two ecotypes segregate along an elevation gradient and by host plants: Oreina speciosissima sensu stricto colonizes high forb vegetation at low altitude and Oreina speciosissima troglodytes is found in stone run vegetation at higher elevations. Both host plants and leaf beetles have a patchy geographical distribution. Through use of gene sequencing and genome fingerprinting (AFLP) we analyzed the genetic structure and habitat use of Oreina speciosissima populations from the Swiss Alps to examine whether the two ecotypes have a genetic basis. By investigating a wide range of altitudes and focusing on the structuring effect of habitat types, we aim to provide answers regarding the factors that drive adaptive radiation in this phytophagous leaf beetle.

Evolutionary …, Jan 1, 2012

Hybridization has played a central role in the evolutionary history of domesticated plants. Notab... more Hybridization has played a central role in the evolutionary history of domesticated plants. Notably, several breeding programs relying on gene introgression from the wild compartment have been performed in fruit tree species within the genus Prunus but few studies investigated spontaneous gene flow among wild and domesticated Prunus species. Consequently, a comprehensive understanding of genetic relationships and levels of gene flow between domesticated and wild Prunus species is needed. Combining nuclear and chloroplastic microsatellites, we investigated the gene flow and hybridization among two key almond tree species, the cultivated Prunus dulcis and one of the most widespread wild relative Prunus orientalis in the Fertile Crescent. We detected high genetic diversity levels in both species along with substantial and symmetric gene flow between the domesticated P. dulcis and the wild P. orientalis. These results were discussed in light of the cultivated species diversity, by outlining the frequent spontaneous genetic contributions of wild species to the domesticated compartment. In addition, crop-to-wild gene flow suggests that ad hoc transgene containment strategies would be required if genetically modified cultivars were introduced in the northwestern Mediterranean.

Molecular Ecology Resources, Jan 1, 2008

The emergence of comparative phylogeography requires tools that allow comparing quantitatively th... more The emergence of comparative phylogeography requires tools that allow comparing quantitatively the genetic structures between species. Whereas numerous methods have been developed to compare trees inferred from two species, comparison methods involving population structures issued from Bayesian inferences or maximum likelihood criterion have been poorly investigated. Here, we present a method implemented in an r (CRAN) scripts collection, SIMIL, based on the mean absolute differences computed from structure 2 outputs. The scripts collection is illustrated by the computation of unweighted and weighted genetic-structure-similarity (GSS) indices in three alpine plants. Different weighting procedures — taking into account the level of overlap between the species sampling areas — are compared among the different species pairs and among the different numbers of gene pools considered in structure.

Evolutionary …, Jan 1, 2011

Gene flow between domesticated species and their wild relatives is receiving growing attention. T... more Gene flow between domesticated species and their wild relatives is receiving growing attention. This study addressed introgression between wheat and natural populations of its wild relatives (Aegilops species). The sampling included 472 individuals, collected from 32 Mediterranean populations of three widespread Aegilops species (Aegilops geniculata, Ae. neglecta and Ae. triuncialis) and compared wheat field borders to areas isolated from agriculture. Individuals were characterized with amplified fragment length polymorphism fingerprinting, analysed through two computational approaches (i.e. Bayesian estimations of admixture and fuzzy clustering), and sequences marking wheat-specific insertions of transposable elements. With this combined approach, we detected substantial gene flow between wheat and Aegilops species. Specifically, Ae. neglecta and Ae. triuncialis showed significantly more admixed individuals close to wheat fields than in locations isolated from agriculture. In contrast, little evidence of gene flow was found in Ae. geniculata. Our results indicated that reproductive barriers have been regularly bypassed during the long history of sympatry between wheat and Aegilops.

Molecular Phylogenetics …, Jan 1, 2011

Aquatic plants, and especially the emblematic genus Baldellia (Alismataceae), are among the most ... more Aquatic plants, and especially the emblematic genus Baldellia (Alismataceae), are among the most threatened organisms, due to unprecedented human-driven habitat destructions. Therefore protection plans are crucially needed and call for thoroughly documenting the genetic diversity and clarifying the taxonomy of this endangered genus. Our sampling included 282 individuals from 42 natural populations and covered the whole geographical range of the genus, across Europe and the Mediterranean. We combined sequencing of nuclear internal transcribed spacer (ITS) and chloroplastic trnL-ndhF regions with amplified fragment length polymorphism (AFLP) genotyping to investigate the Alismataceae phylogeny, and produce a phylogeography of Baldellia. Our phylogeny strongly supported the monophyly of Baldellia and placed it as the sister clade to Luronium and Alisma, therefore excluding, as previously supposed, a close genetic relatedness to the predominantly neotropical genus Echinodorus. The phylogeography of Baldellia outlined patterns consistent with a hypothesis considering glacial refugia located in the Iberian Peninsula and the Italy/Balkan region from which two distinct genetic lineages re-colonized Europe. These two lineages corresponded respectively to Baldellia ranunculoides (Italy/Balkan derived populations) and Baldellia repens (populations recovered from the Iberian Peninsula refuge), therefore supporting differences outlined between the two taxa in previous ecological and morphological studies. These results allowed clarifying taxonomic uncertainties by confirming the genetic distinctness of B. repens according to B. ranunculoides. A third lineage, Baldellia alpestris, originated and remained endemic to the mountainous regions of the Iberian Peninsula. Unexpectedly, B. repens populations collected in northern Africa, appeared to be genetically distinct from their European counterparts, this calls for further investigation to fully address their genetic and conservation status. Finally, we detected a large hybridization zone in northwestern Europe between B. repens and B. ranunculoides. These results were discussed in light of conservation approaches for Baldellia populations.

Molecular …, Jan 1, 2009

The alpine white-flowered buttercup, Ranunculus kuepferi Greuter & Burdet, is a polyploid complex... more The alpine white-flowered buttercup, Ranunculus kuepferi Greuter & Burdet, is a polyploid complex with diploids endemic to the southwestern Alps and polyploids – which have been previously described as apomictic – widespread throughout European mountains. Due to the polymorphic status of both its ploidy level and its reproductive mode, R. kuepferi represents a key species for understanding the evolution of polyploid lineages in alpine habitats. To disentangle the phylogeography of this polyploid taxon, we used cpDNA sequences and AFLP (amplified fragment length polymorphism) markers in 33 populations of R. kuepferi representative of its ploidy level and distribution area. Polyploid individuals were shown to be the result of at least two polyploidization events that may have taken place in the southwestern Alps. From this region, one single main migration of tetraploids colonized the entire Alpine range, the Apennines and Corsica. Genetic recombination among tetraploids was also observed, revealing the facultative nature of the apomictic reproductive mode in R. kuepferi polyploids. Our study shows the contrasting role played by diploid lineages mostly restricted to persistent refugia and by tetraploids, whose dispersal abilities have permitted their range extension all over the previously glaciated Alpine area and throughout neighbouring mountain massifs.

New …, Jan 1, 2010

This study reconstructs the phylogeography of Aegilops geniculata, an allotetraploid relative of ... more This study reconstructs the phylogeography of Aegilops geniculata, an allotetraploid relative of wheat, to discuss the impact of past climate changes and recent human activities (e.g. the early expansion of agriculture) on the genetic diversity of ruderal plant species.

Journal of …, Jan 1, 2011

Aim Recently developed parametric methods in historical biogeography allow researchers to integra... more Aim Recently developed parametric methods in historical biogeography allow researchers to integrate temporal and palaeogeographical information into the reconstruction of biogeographical scenarios, thus overcoming a known bias of parsimony-based approaches. Here, we compare a parametric method, dispersalextinction-cladogenesis (DEC), against a parsimony-based method, dispersalvicariance analysis (DIVA), which does not incorporate branch lengths but accounts for phylogenetic uncertainty through a Bayesian empirical approach (Bayes-DIVA). We analyse the benefits and limitations of each method using the cosmopolitan plant family Sapindaceae as a case study.

Green Gene Technology, Jan 1, 2007

Advances in Biochemical Engineering/Biotechnology reviews actual trends in modern biotechnology. ... more Advances in Biochemical Engineering/Biotechnology reviews actual trends in modern biotechnology. Its aim is to cover all aspects of this interdisciplinary technology where knowledge, methods and expertise are required for chemistry, biochemistry, micro-biology, genetics, chemical engineering and computer science. Special volumes are dedicated to selected topics which focus on new biotechnological products and new processes for their synthesis and purification. They give the state-of-the-art of a topic in a comprehensive way thus being a valuable source for the next 3-5 years.

Plos one, Jan 1, 2007

The genus Vitis is represented by several coexisting species in Europe. Our study focuses on natu... more The genus Vitis is represented by several coexisting species in Europe. Our study focuses on naturalised rootstocks that originate in viticulture. The consequences of their presence to the landscape and to native European species (Vitis vinifera ssp. silvestris) are evaluated. This study compares ecological traits (seven qualitative and quantitative descriptors) and the genetic diversity (10 SSR markers) of populations of naturalised rootstocks and native wild grapevines. 18 large naturalised rootstock populations were studied in the Rhô ne watershed. Wild European grapevines are present in four main habitats (screes, alluvial forests, hedges, and streamside hedges). In contrast, naturalised rootstock populations are mainly located in alluvial forests, but they clearly take advantage of alluvial system dynamics and connectivity at the landscape level. These latter populations appear to reproduce sexually, and show a higher genetic diversity than Vitis vinifera ssp. silvestris. The regrouping of naturalised rootstocks in interconnected populations tends to create active hybrid swarms of rootstocks. The rootstocks show characters of invasive plants. The spread of naturalised rootstocks in the environment, the acceleration of the decline of the European wild grapevine, and the propagation of genes of viticultural interest in natural populations are potential consequences that should be kept in mind when undertaking appropriate management measures.

BMC …, Jan 1, 2009

Since the transfer and application of modern sequencing technologies to the analysis of amplified... more Since the transfer and application of modern sequencing technologies to the analysis of amplified fragment-length polymorphisms (AFLP), evolutionary biologists have included an increasing number of samples and markers in their studies. Although justified in this context, the use of automated scoring procedures may result in technical biases that weaken the power and reliability of further analyses.