Community-level phylogenetic diversity does not differ between rare and common lineages across tallgrass prairies in the northern Great Plains.

Niche differentiation has served as one explanation for species coexistence, and phylogenetic relatedness provides a means to approximate how ecologically similar species are to each other. To explore the contribution of rare species to community phylogenetic diversity, we sampled 21 plant communities across the Prairie Coteau ecoregion, an area of high conservation concern. We used breakpoint analysis through the iterative addition of less abundant species to the phylogenetic tree for each community to assess the contribution of rare species to community phylogenetic diversity.

Digitized collections elucidate invasion history and patterns of awn polymorphism in Microstegium vimineum.

Premise: Digitized collections can help illuminate the mechanisms behind the establishment and spread of invasive plants. These databases provide a record of traits in space and time that allows for investigation of abiotic and biotic factors that influence invasive species.

Methods: Over 1100 digitized herbarium records were examined to investigate the invasion history and trait variation of Microstegium vimineum.

Examining the utility of DNA barcodes for the identification of tallgrass prairie flora.

Premise: The tallgrass prairies of North America are one of the most threatened ecosystems in the world, making efficient species identification essential for understanding and managing diversity. Here, we assess DNA barcoding with high-throughput sequencing as a method for rapid plant species identification.

Methods: Using herbarium collections representing the tallgrass prairie flora of Oak Lake Field Station, South Dakota, USA, we amplified and examined four common nuclear and plastid barcode regions (ITS, , , and ), individually and in combination, to test their success in identifying samples to family, genus, and species levels using BLAST searches of three databases of varying size.

Fluidigm2PURC: Automated processing and haplotype inference for double-barcoded PCR amplicons.

Premise Of The Study: Targeted enrichment strategies for phylogenomic inference are a time- and cost-efficient way to collect DNA sequence data for large numbers of individuals at multiple, independent loci. Automated and reproducible processing of these data is a crucial step for researchers conducting phylogenetic studies.

Methods And Results: We present Fluidigm2PURC, an open source Python utility for processing paired-end Illumina data from double-barcoded PCR amplicons.

Incongruence in molecular species delimitation schemes: What to do when adding more data is difficult.

Using multiple, independent approaches to molecular species delimitation is advocated to accommodate limitations and assumptions of a single approach. Incongruence in delimitation schemes is a potential by-product of employing multiple methods on the same data, and little attention has been paid to its reconciliation. Instead, a particular scheme is prioritized, and/or molecular delimitations are coupled with additional, independent lines of evidence that mitigate incongruence.

Primers for and their utility across Orobanchaceae: II. Single-copy nuclear loci.

Premise Of The Study: We developed primers targeting nuclear loci in with the goal of reconstructing the evolutionary history of this challenging clade. These primers were tested across other major clades in Orobanchaceae to assess their broader utility.

Methods And Results: We assembled low-coverage genomes for three taxa in and developed primer combinations for the single-copy conserved ortholog set (COSII) and the pentatricopeptide repeat (PPR) gene family.

Primers for and their utility across Orobanchaceae: I. Chloroplast primers.

Premise Of The Study: Chloroplast primers were developed from genomic data for the taxonomically challenging genus . We further tested the broader utility of these primers across Orobanchaceae, identifying a core set of chloroplast primers amplifying across the clade.

Methods And Results: Using a combination of three low-coverage genomes and sequence data from 12 plastomes, 76 primer combinations were specifically designed and tested for .

Phylogenetic relationships and character evolution analysis of Saxifragales using a supermatrix approach.

Premise Of The Study: We sought novel evolutionary insights for the highly diverse Saxifragales by constructing a large phylogenetic tree encompassing 36.8% of the species-level biodiversity. •

Methods: We built a phylogenetic tree for 909 species of Saxifragales and used this hypothesis to examine character evolution for annual or perennial habit, woody or herbaceous habit, ovary position, petal number, carpel number, and stamen to petal ratio.

Angiosperm phylogeny: 17 genes, 640 taxa.

Premise Of The Study: Recent analyses employing up to five genes have provided numerous insights into angiosperm phylogeny, but many relationships have remained unresolved or poorly supported. In the hope of improving our understanding of angiosperm phylogeny, we expanded sampling of taxa and genes beyond previous analyses.

Methods: We conducted two primary analyses based on 640 species representing 330 families.

Rosid radiation and the rapid rise of angiosperm-dominated forests.

The rosid clade (70,000 species) contains more than one-fourth of all angiosperm species and includes most lineages of extant temperate and tropical forest trees. Despite progress in elucidating relationships within the angiosperms, rosids remain the largest poorly resolved major clade; deep relationships within the rosids are particularly enigmatic. Based on parsimony and maximum likelihood (ML) analyses of separate and combined 12-gene (10 plastid genes, 2 nuclear; >18,000 bp) and plastid inverted repeat (IR; 24 genes and intervening spacers; >25,000 bp) datasets for >100 rosid species, we provide a greatly improved understanding of rosid phylogeny.

Floral variation and floral genetics in basal angiosperms.

Recent advances in phylogeny reconstruction and floral genetics set the stage for new investigations of the origin and diversification of the flower. We review the current state of angiosperm phylogeny, with an emphasis on basal lineages. With the surprising inclusion of Hydatellaceae with Nymphaeales, recent studies support the topology of Amborella sister to all other extant angiosperms, with Nymphaeales and then Austrobaileyales as subsequent sisters to all remaining angiosperms.

Floral gigantism in Rafflesiaceae.

Species of Rafflesiaceae possess the world's largest flowers (up to 1 meter in diameter), yet their precise evolutionary relationships have been elusive, hindering our understanding of the evolution of their extraordinary reproductive morphology. We present results of phylogenetic analyses of mitochondrial, nuclear, and plastid data showing that Rafflesiaceae are derived from within Euphorbiaceae, the spurge family. Most euphorbs produce minute flowers, suggesting that the enormous flowers of Rafflesiaceae evolved from ancestors with tiny flowers.