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Evaluating the impact of scoring parameters on the structure of intra-specific genetic variation using RawGeno, an R package for automating AFLP scoring
- N. Arrigo, Jarek W. Tuszynski, D. Ehrich, T. Gerdes, N. Alvarez
- Biology, Computer Science
- BMC Bioinformatics
- 26 January 2009
A new scoring algorithm, RawGeno, is used, which appears to perform as well as a commercial program in automating AFLP scoring, at least in the context of population genetics or phylogeographic studies. Expand
Restriction site‐associated DNA sequencing, genotyping error estimation and de novo assembly optimization for population genetic inference
- A. Mastretta-Yanes, N. Arrigo, N. Alvarez, T. H. Jorgensen, D. Piñero, B. Emerson
- Biology, Medicine
- Molecular ecology resources
- 1 January 2015
Individual sample replicates are used, under the expectation of identical genotypes, to quantify genotyping error in the absence of a reference genome and optimize de novo assembly parameters within the program Stacks, by minimizing error and maximizing the retrieval of informative loci. Expand
Plastid and nuclear DNA markers reveal intricate relationships at subfamilial and tribal levels in the soapberry family (Sapindaceae).
- S. Buerki, F. Forest, +6 authors N. Alvarez
- Biology, Medicine
- Molecular phylogenetics and evolution
- 1 May 2009
A phylogenetic analysis of Sapindaceae based on eight DNA sequence regions from the plastid and nuclear genomes and including 85 of the 141 genera defined within the family confirms a high level of paraphyly and polyphyly at the subfamilial and tribal levels and even contest the monophyletic status of several genera. Expand
An evaluation of new parsimony‐based versus parametric inference methods in biogeography: a case study using the globally distributed plant family Sapindaceae
By considering lineage divergence times, the DEC method gives more accurate reconstructions that are in agreement with palaeogeographical evidence, and Bayes-DIVA showed the highest decisiveness in unequivocally reconstructing ancestral ranges, probably reflecting its ability to integrate phylogenetic uncertainty. Expand
Broad‐scale adaptive genetic variation in alpine plants is driven by temperature and precipitation
It is shown, for the first time for a large number of species, that the same environmental variables are drivers of plant adaptation at the scale of a whole biome, here the European Alps. Expand
Genetic diversity in widespread species is not congruent with species richness in alpine plant communities.
This work tests whether the genetic and species levels of biodiversity co-vary, using a large-scale and multi-species approach and demonstrates that species richness and genetic diversity are not correlated. Expand
History or ecology? Substrate type as a major driver of spatial genetic structure in Alpine plants.
The relevance of particular ecological factors in shaping genetic patterns, which should be considered when modelling species projective distributions under climate change scenarios, are demonstrated. Expand
Genetic structure and evolution of Alpine polyploid complexes: Ranunculus kuepferi (Ranunculaceae) as a case study
- J. Burnier, S. Buerki, N. Arrigo, P. Küpfer, N. Alvarez
- Biology, Medicine
- Molecular ecology
- 1 September 2009
This 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. Expand
Hybridization Capture Using RAD Probes (hyRAD), a New Tool for Performing Genomic Analyses on Collection Specimens
hyRAD is presented, a novel method that allows sequencing of orthologous loci even from highly degraded DNA samples, opening new avenues of research in the field of museum genomics, and is not sensitive to among-sample loci polymorphisms in the restriction sites that usually causes loci dropout. Expand
Phylogeny and circumscription of Sapindaceae revisited: molecular sequence data, morphology and biogeography support recognition of a new family, Xanthoceraceae.
- S. Buerki, P. Lowry, N. Alvarez, S. Razafimandimbison, P. Küpfer, M. Callmander
- 8 September 2010
The relationships of Xanthoceras are clarified based on phylogenetic analyses using a dataset encompassing nearly 3/4 of sapindaceous genera, comparing the results with information from morphology and biogeography, and support earlier suggestions that Harpullieae are polyphyletic. Expand