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The first North American RAD Sequencing and Genomics Symposium, sponsored by Floragenex (http://www.floragenex.com/radmeeting/), took place in Portland, Oregon (USA) on 19 April 2011. This symposium was convened to promote and discuss the use of restriction‐site‐associated DNA (RAD) sequencing technologies. RAD sequencing is one of several strategies recently developed to increase the power of data generated via short‐read sequencing technologies by reducing their complexity (Baird et al. 2008; Huang et al. 2009; Andolfatto et al. 2011; Elshire et al. 2011). RAD sequencing, as a form of genotyping by sequencing, has been effectively applied in genetic mapping and quantitative trait loci (QTL) analyses in a range of organisms including nonmodel, genetically highly heterogeneous organisms (Table 1; Baird et al. 2008; Baxter et al. 2011; Chutimanitsakun et al. 2011; Pfender et al. 2011). RAD sequencing has recently found applications in phylogeography (Emerson et al. 2010) and population genomics (Hohenlohe et al. 2010). Considering the diversity of talks presented during this meeting, more developments are to be expected in the very near future.  Published studies using RAD sequencing Organism by application References Genetic mapping Three‐spined stickleback (Gasterosteus aculeatus) Baird et al. (2008)  Diamondback moth (Plutella xylostella) Baxter et al. (2011)  Barley (Hordeum vulgare) Chutimanitsakun et al. (2011)  Perennial Ryegrass (Lolium perenne) Pfender et al. (2011)  Neurospora crassa Baird et al. (2008) Population genomics Three‐spined stickleback (Gasterosteus aculeatus) Hohenlohe et al. (2010) Phylogeography Pitcher plant mosquito (Wyeomyia smithii) Emerson et al. (2010) Whole‐genome sequencing Escherichia coli Etter et al. (2011)

Summary• Primula sect. Aleuritia subsect. Aleuritia ( Aleuritia ) includes diploid, self-incompatible heterostyles and polyploid, self-compatible homostyles, the latter generally occurring at higher latitudes than the former. This study develops a phylogenetic hypothesis for Aleuritia to elucidate the interactions between Pleistocene glacial cycles, biogeographic patterns, ploidy levels and breeding systems.• Sequences from five chloroplast DNA loci were analyzed with parsimony to reconstruct a phylogeny, haplotype network, and ancestral states for ploidy levels and breeding systems.• The results supported the monophyly of Aleuritia and four major biogeographic lineages: an amphi-Pacific, a South American, an amphi-Atlantic and a European/ North American lineage. At least four independent switches to homostyly and five to polyploidy were inferred.• An Asian ancestor probably gave origin to an amphi-Pacific clade and to a lineage that diversified on the European and American continents. Switches to homostyly occurred exclusively in polyploid lineages, which mainly occupy previously glaciated areas. The higher success of the autogamous polyploid species at recolonizing habitats freed by glacial retreat might be explained in terms of selection for reproductive assurance.

Transcriptome sequencing using next-generation platforms has greatly reduced the cost of genomic studies of nonmodel organisms, and the ESTs and microarrays reported here will accelerate evolutionary and molecular investigations of Compositae weeds. Our study also shows how ortholog comparisons can be used to approximately estimate the genome-wide extent of introgression and to identify genes that have been exchanged between hybridizing taxa.

Aim  The presence of numerous reliable fossils and the occurrence of many endemic island species make the Boraginales particularly suitable for integrative biogeographical studies. In this paper we aim to elucidate the time frame and events associated with the origin of selected borages endemic to the Mediterranean climate zone. More specifically, we describe and examine the alternative palaeo‐ and neoendemic hypotheses for their origin. Location  Corsica and Sardinia (continental fragment islands) and the Canary Islands (an oceanic island archipelago). Methods  Eighty‐nine accessions, representing 30 genera from five families ascribed to the Boraginales, were examined for six chloroplast DNA regions. We used an integrative approach including phylogenetic analyses (MrBayes), Bayesian molecular dating (T3 package) with four fossil constraints on nodes, and biogeographical reconstructions (diva) to elucidate the temporal and spatial origins of the Corso‐Sardinian and Canary Island endemics. Results  Species of Echium endemic to the Canary Islands diverged from their continental sister clade during the Miocene (15.3 ± 5.4 Ma), probably after the rise of the oldest islands (c. 20 Ma). Corso‐Sardinian endemics of Borago diverged from their primarily North African sister clade during the late Miocene‐Pliocene (c. 6.9 ± 3.6 Ma), well after the initial fragmentation of the islands (c. 30 Ma). Similarly, Corso‐Sardinian endemics of Anchusa diverged from the South African Anchusa capensis during the Pliocene–Pleistocene (c. 2.7 ± 2.1 Ma). Main conclusions  The present study reveals an Anatolian origin for Anchusa, Borago and Echium and underlines the importance of the Eastern Mediterranean region as a possible reservoir for plant evolution in the Mediterranean Basin. For Anchusa and Borago, the divergence from their respective sister clades on the two types of islands post‐dated the formation of the islands, thus supporting the neo‐endemic hypothesis, whereas the dating results for the origin of Echium endemics were less conclusive.

Although polyploidy plays a fundamental role in plant evolution, the elucidation of polyploid origins is fraught with methodological challenges. For example, allopolyploid species may confound phylogenetic reconstruction because commonly used methods are designed to trace divergent, rather than reticulate patterns. Recently developed techniques of phylogenetic network estimation allow for a more effective identification of incongruence among trees. However, incongruence can also be caused by incomplete lineage sorting, paralogy, concerted evolution, and recombination. Thus, initial hypotheses of hybridization need to be examined via additional sources of evidence, including the partitioning of infraspecific genetic polymorphisms, morphological characteristics, chromosome numbers, crossing experiments, and distributional patterns. Primula sect. Aleuritia subsect. Aleuritia (Aleuritia) represents an ideal case study to examine reticulation because specific hypotheses have been derived from morphology, karyology, interfertility, and distribution to explain the observed variation of ploidy levels, ranging from diploidy to 14-ploidy. Sequences from 5 chloroplast and 1 nuclear ribosomal DNA (nrDNA) markers were analyzed to generate the respective phylogenies and consensus networks. Furthermore, extensive cloning of the nrDNA marker allowed for the identification of shared nucleotides at polymorphic sites, investigation of infraspecific genetic polymorphisms via principal coordinate analyses PCoAs, and detection of recombination between putative progenitor sequences. The results suggest that most surveyed polyploids originated via hybridization and that 2 taxonomic species formed recurrently from different progenitors, findings that are congruent with the expectations of speciation via secondary contact. Overall, the study highlights the importance of using multiple experimental and analytical approaches to disentangle complex patterns of reticulation.

The mustard family (Brassicaceae) is a scientifically and economically important family, containing the model plant Arabidopsis thaliana and numerous crop species that feed billions worldwide. Despite its relevance, most published family phylogenies are incompletely sampled, generally contain massive polytomies, and/or show incongruent topologies between datasets. Here, we present the most complete Brassicaceae genus-level family phylogenies to date (Brassicaceae Tree of Life, or BrassiToL) based on nuclear (>1,000 genes, almost all 349 genera and 53 tribes) and plastome (60 genes, 79% of the genera, all tribes) data. We found cytonuclear discordance between nuclear and plastome-derived phylogenies, which is likely a result of rampant hybridisation among closely and more distantly related species, and highlight rogue taxa. To evaluate the impact of this rampant hybridisation on the nuclear phylogeny reconstruction, we performed four different sampling routines that increasingly removed variable data and likely paralogs. Our resulting cleaned subset of 297 nuclear genes revealed high support for the tribes, while support for the main lineages remained relatively low. Calibration based on the 20 most clock-like nuclear genes suggests a late Eocene to late Oligocene icehouse origin of the family. Finally, we propose five new or re-established tribes, including the recognition of Arabidopsideae, a monotypic tribe to accommodate Arabidopsis. With a worldwide community of thousands of researchers working on this family, our new, densely sampled family phylogeny will be an indispensable tool to further highlight Brassicaceae as an excellent model family for studies on biodiversity and plant biology.

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