Identifying Climatic Drivers of Hybridization with a New Ancestral Niche Reconstruction Method.

Applications of molecular phylogenetic approaches have uncovered evidence of hybridization across numerous clades of life, yet the environmental factors responsible for driving opportunities for hybridization remain obscure. Verbal models implicating geographic range shifts that brought species together during the Pleistocene have often been invoked, but quantitative tests using paleoclimatic data are needed to validate these models. Here, we produce a phylogeny for Heuchereae, a clade of 15 genera and 83 species in Saxifragaceae, with complete sampling of recognized species, using 277 nuclear loci and nearly complete chloroplast genomes. We then employ an improved framework with a coalescent simulation approach to test and confirm previous hybridization hypotheses and identify one new intergeneric hybridization event. Focusing on the North American distribution of Heuchereae, we introduce and implement a newly developed approach to reconstruct potential past distributions for ancestral lineages across all species in the clade and across a paleoclimatic record extending from the late Pliocene. Time calibration based on both nuclear and chloroplast trees recovers a mid- to late-Pleistocene date for most inferred hybridization events, a timeframe concomitant with repeated geographic range restriction into overlapping refugia. Our results indicate an important role for past episodes of climate change, and the contrasting responses of species with differing ecological strategies, in generating novel patterns of range contact among plant communities and therefore new opportunities for hybridization. The new ancestral niche method flexibly models the shape of niche while incorporating diverse sources of uncertainty and will be an important addition to the current comparative methods toolkit. [Ancestral niche reconstruction; hybridization; paleoclimate; pleistocene.].

Impact of genome duplication on secondary metabolite composition in non-cultivated species: a systematic meta-analysis.

BACKGROUND AND AIMS: Whole-genome duplication is known to influence ecological interactions and plant physiology; however, despite abundant case studies, much is still unknown about the typical impact of genome duplication on plant secondary metabolites (PSMs). In this study, we assessed the impact of polyploidy events on PSM characteristics in non-cultivated plants. METHODS: We conducted a systematic review and meta-analysis to compare composition and concentration of PSMs among closely related plant species or species complexes differing in ploidy level. KEY RESULTS: We assessed 53 studies that focus on PSMs among multiple cytotypes, of which only 14 studies compared concentration quantitatively among cytotypes. We found that whole-genome duplication can have a significant effect on PSM concentration; however, these effects are highly inconsistent. CONCLUSION: Overall, there was no consistent effect of whole-genome duplication on PSM concentrations or profiles.

Climatic niche comparison among ploidal levels in the classic autopolyploid system, Galax urceolata.

PREMISE OF THE STUDY: Autopolyploidy, or whole-genome duplication within a species, leads to closely related cytotypes in one geographic location. One hypothesized mechanism by which autopolyploids become established is climatic niche divergence from their diploid progenitor. Here we tested this hypothesis in diploid, triploid, and tetraploid Galax urceolata (Diapensiaceae) and predicted the effects of climate change on the relative distributions of these cytotypes. METHODS: We investigated whether climatic niche divergence has shaped the current distributions of Galax urceolata cytotypes in eastern North America using climatic niche modeling, multivariate analyses of environmental space, and geographic range analyses. We then projected the models of the three cytotypes onto an ensemble of future climate maps to determine how the distributions might be altered over time. KEY RESULTS: All cytotypes are geographically sympatric; however, climatic niche contraction and a slight niche shift of the tetraploids was observed relative to that of the diploids. Climate projections for all diploid and tetraploid cytotypes showed substantial range contraction without much, or any, range shift, suggesting that Galax urceolata will likely go extinct in nature as mountain refugia become warmer. CONCLUSIONS: Galax urceolata tetraploids occupy a slightly wetter habitat than that of their diploid progenitors. While we cannot take into account future adaptation, our models suggest extensive decreases in range distributions for both diploid and tetraploid G. urceolata based on climate change projections. Galax urceolata may therefore be under extreme threat due to loss of suitable habitat, and conservation efforts will be needed.

Geographic And Taxonomic Occurrence R-based Scrubbing (gatoRs): An R package and workflow for processing biodiversity data.

Premise: Digitized biodiversity data offer extensive information; however, obtaining and processing biodiversity data can be daunting. Complexities arise during data cleaning, such as identifying and removing problematic records. To address these issues, we created the R package Geographic And Taxonomic Occurrence R-based Scrubbing (gatoRs). Methods and Results: The gatoRs workflow includes functions that streamline downloading records from the Global Biodiversity Information Facility (GBIF) and Integrated Digitized Biocollections (iDigBio). We also created functions to clean downloaded specimen records. Unlike previous R packages, gatoRs accounts for differences in download structure between GBIF and iDigBio and allows for user control via interactive cleaning steps. Conclusions: Our pipeline enables the scientific community to process biodiversity data efficiently and is accessible to the R coding novice. We anticipate that gatoRs will be useful for both established and beginning users. Furthermore, we expect our package will facilitate the introduction of biodiversity-related concepts into the classroom via the use of herbarium specimens.

Transcriptome and organellar sequencing highlights the complex origin and diversification of allotetraploid Brassica napus.

Brassica napus, an allotetraploid crop, is hypothesized to be a hybrid from unknown varieties of Brassica rapa and Brassica oleracea. Despite the economic importance of B. napus, much is unresolved regarding its phylogenomic relationships, genetic structure, and diversification. Here we conduct a comprehensive study among diverse accessions from 183 B. napus (including rapeseed, rutabaga, and Siberian kale), 112 B. rapa, and 62 B. oleracea and its wild relatives. Using RNA-seq of B. napus accessions, we define the genetic diversity and sub-genome variance of six genetic clusters. Nuclear and organellar phylogenies for B. napus and its progenitors reveal varying patterns of inheritance and post-formation introgression. We discern regions with signatures of selective sweeps and detect 8,187 differentially expressed genes with implications for B. napus diversification. This study highlights the complex origin and evolution of B. napus providing insights that can further facilitate B. napus breeding and germplasm preservation.