Gustavo A. Silva-Arias

Multilocus phylogeny reconstruction: new insights into the evolutionary history of the genus Petunia.

The phylogeny of Petunia species has been difficult to resolve, primarily due to the recent diversification of the genus. Several studies have included molecular data in phylogenetic reconstructions of this genus, but all of them have failed to include all taxa and/or analyzed few genetic markers. In the present study, we employed the most inclusive genetic and taxonomic datasets for the genus, aiming to reconstruct the evolutionary history of Petunia based on molecular phylogeny, biogeographic distribution, and character evolution. We included all 20 Petunia morphological species or subspecies in these analyses. Based on nine nuclear and five plastid DNA markers, our phylogenetic analysis reinforces the monophyly of the genus Petunia and supports the hypothesis that the basal divergence is more related to the differentiation of corolla tube length, whereas the geographic distribution of species is more related to divergences within these main clades. Ancestral area reconstructions suggest the Pampas region as the area of origin and earliest divergence in Petunia. The state reconstructions suggest that the ancestor of Petunia might have had a short corolla tube and a bee pollination floral syndrome.

Novel microsatellites for Calibrachoa heterophylla (Solanaceae) endemic to the South Atlantic Coastal Plain of South America

Premise of the study: Calibrachoa heterophylla (Solanaceae) is a petunia species restricted to the South Atlantic Coastal Plain of South America and presents a recent history of colonization from continental to coastal environments and diversification following the formation of the Coastal Plain during the Quaternary period. Methods and Results: This study reports a suite of 16 microsatellite loci for C. heterophylla. The applicability of these markers was assessed by genotyping 57 individuals from two natural populations. Of the 16 described loci, 12 were found to be polymorphic. Successful cross-amplification tests were obtained using 12 Calibrachoa species. Conclusions: The development of microsatellite markers will be useful to recover the contemporary history of the colonization of the Coastal Plain and to provide information for the conservation of this endemic species.

A small subset of NLR genes drives local adaptation to pathogens in wild tomato

In plants, defence-associated genes including the NLR gene family are under constant evolutionary pressure to adapt to pathogens. It is still unknown how many NLRs contribute to adaptation, and if the involved loci vary within a species across habitats. We use a three-pronged approach to reveal and quantify selection signatures at over 90 NLR genes over 14 populations of Solanum chilense a wild tomato species endemic to Peru and Chile found in different habitats. First, we generated a de novo genome of S. chilense. Second, by whole genome resequencing of three geographically distant individuals we infer the species past demographic history of habitat colonisation. Finally, using targeted resequencing we show that a small subset of NLRs, 7%, show signs of positive or balancing selection. We demonstrate that 13 NLRs change direction of selection during the colonisation of new habitats and form a mosaic pattern of adaptation to pathogens. We estimate that the turn over time of selection (birth-and-death rate) on NLRs is 18,000 years. Finally, our work identifies new NLRs under strong selective pressure between habitats, thus providing novel opportunities for R-gene identification.Nucleotide binding site, Leucine-rich repeat Receptors (NLRs), are canonical resistance (R) genes in plants, fungi and animals, functioning as central (helper) and peripheral (sensor) genes in a signalling network. We investigate NLR evolution during the colonisation of novel habitats in a model tomato species, Solanum chilense. We used R-gene enrichment sequencing (RENSeq) to obtain polymorphism data at NLRs of 140 plants sampled across 14 populations covering the whole species range. We inferred the past demographic history of habitat colonisation by resequencing whole genomes from three S. chilense plants from three key populations, and performing Approximate Bayesian Computation using data from the 14 populations. Using these parameters we simulated the genetic differentiation statistics distribution expected under neutral NLR evolution, and identified small subsets of outlier NLRs exhibiting signatures of selection across populations. NLRs under selection between habitats are more often helper genes, while those showing signatures of adaptation in single populations are more often sensor-NLRs. Thus, centrality in the NLR network does not constrain NLR evolvability, and new mutations in central genes in the network are key for R gene adaptation during colonisation of different habitats.