Spatial Phylogenetics of Florida Vascular Plants: The Effects of Calibration and Uncertainty on Diversity Estimates.

Recent availability of biodiversity data resources has enabled an unprecedented ability to estimate phylogenetically based biodiversity metrics over broad scales. Such approaches elucidate ecological and evolutionary processes yielding a biota and help guide conservation efforts. However, the choice of appropriate phylogenetic resources and underlying input data uncertainties may affect interpretation. Here, we address how differences among phylogenetic source trees and levels of phylogenetic uncertainty affect these metrics and test existing hypotheses regarding geographic biodiversity patterns across the diverse vascular plant flora of Florida, US. Ecological niche models for 1,490 Florida species were combined with a "purpose-built" phylogenetic tree (phylogram and chronogram), as well as with trees derived from community resources (Phylomatic and Open Tree of Life). There were only modest differences in phylodiversity metrics given the phylogenetic source tree and taking into account the level of phylogenetic uncertainty; we identify similar areas of conservation interest across Florida regardless of the method used.

Niche divergence between diploid and autotetraploid Tolmiea.

PREMISE OF STUDY: Polyploidy is common in eukaryotes and is of major evolutionary importance over both short and long time-scales. Compared to allopolyploids, autopolyploids remain understudied; they are often morphologically cryptic and frequently remain taxonomically unrecognized, although there is increasing recognition of the high frequency of autopolyploidy in angiosperms. While autopolyploidy can serve as an instant speciation mechanism, little is known about the ecological consequences of this process. We describe the ecological divergence of a diploid-autotetraploid species pair in Tolmiea. METHODS: We investigated whether abiotic niche divergence has shaped the current allopatric distribution of diploid T. diplomenziesii and its autotetraploid derivative, T. menziesii, in the Pacific Northwest of North America. We employed field measures of light availability, as well as niche modeling and a principal component analysis of environmental space. Within a common garden, we also investigated physiological responses to changes in soil moisture. KEY RESULTS: Diploid and autotetraploid Tolmiea inhabit significantly different climatic niche spaces. The climatic niche divergence between these two species is best explained by a shift in precipitation availability, and we found evidence of differing physiological response to water availability between these species. CONCLUSIONS: We found that spatial segregation of T. diplomenziesii and T. menziesii was accompanied by adaptation to changes in climatic regime. Tolmiea menziesii is not a nascent autotetraploid, having persisted long enough to be established throughout the Pacific Northwest, and therefore both polyploidization and subsequent evolution have contributed to the observed differences between T. menziesii and T. diplomenziesii.

A new resource for the development of SSR markers: Millions of loci from a thousand plant transcriptomes.

PREMISE OF THE STUDY: The One Thousand Plant Transcriptomes Project (1KP, 1000+ assembled plant transcriptomes) provides an enormous resource for developing microsatellite loci across the plant tree of life. We developed loci from these transcriptomes and tested their utility. METHODS AND RESULTS: Using software packages and custom scripts, we identified microsatellite loci in 1KP transcriptomes. We assessed the potential for cross-amplification and whether loci were biased toward exons, as compared to markers derived from genomic DNA. We characterized over 5.7 million simple sequence repeat (SSR) loci from 1334 plant transcriptomes. Eighteen percent of loci substantially overlapped with open reading frames (ORFs), and electronic PCR revealed that over half the loci would amplify successfully in conspecific taxa. Transcriptomic SSRs were approximately three times more likely to map to translated regions than genomic SSRs. CONCLUSIONS: We believe microsatellites still have a place in the genomic age-they remain effective and cost-efficient markers. The loci presented here are a valuable resource for researchers.

The report of my death was an exaggeration: A review for researchers using microsatellites in the 21st century.

Microsatellites, or simple sequence repeats (SSRs), have long played a major role in genetic studies due to their typically high polymorphism. They have diverse applications, including genome mapping, forensics, ascertaining parentage, population and conservation genetics, identification of the parentage of polyploids, and phylogeography. We compare SSRs and newer methods, such as genotyping by sequencing (GBS) and restriction site associated DNA sequencing (RAD-Seq), and offer recommendations for researchers considering which genetic markers to use. We also review the variety of techniques currently used for identifying microsatellite loci and developing primers, with a particular focus on those that make use of next-generation sequencing (NGS). Additionally, we review software for microsatellite development and report on an experiment to assess the utility of currently available software for SSR development. Finally, we discuss the future of microsatellites and make recommendations for researchers preparing to use microsatellites. We argue that microsatellites still have an important place in the genomic age as they remain effective and cost-efficient markers.

Are microsatellite fragment lengths useful for population-level studies? The case of Polygala lewtonii (Polygalaceae).

PREMISE OF THE STUDY: Microsatellites, despite being commonly used population-level markers, contain biases because scoring relies solely on fragment length. Their complexity can lead to homoplasy, the effects of which are poorly understood. We investigated the impact of using fragment lengths, repeats, or flanking region sequences on common population-level analyses. METHODS: Five polymorphic microsatellite markers amplified across the central Florida scrub endemic Polygala lewtonii (Polygalaceae) and its close, widespread congener P. polygama. We genotyped 147 individuals of P. lewtonii and 156 of P. polygama, and sequenced the amplicons of four markers across all individuals. We ran basic statistics, spatial clustering analysis, historical demographics, and migration tests. RESULTS: One population of intermediate morphology was genetically clearly identified as P. polygama, making it the southernmost population of this species. Statistics were comparable between the fragment length and repeat numbers, with some notable differences. Flanking regions exhibited surprisingly high polymorphism between species, and between geographically distant conspecific populations. DISCUSSION: The increasing use of markers developed in one species and amplified in another is only a good practice if precautions are taken, notably the sequencing of the fragments between species and populations. Flanking region sequences are a useful marker at the interspecific level.

Digitization workflows for flat sheets and packets of plants, algae, and fungi.

Effective workflows are essential components in the digitization of biodiversity specimen collections. To date, no comprehensive, community-vetted workflows have been published for digitizing flat sheets and packets of plants, algae, and fungi, even though latest estimates suggest that only 33% of herbarium specimens have been digitally transcribed, 54% of herbaria use a specimen database, and 24% are imaging specimens. In 2012, iDigBio, the U.S. National Science Foundation's (NSF) coordinating center and national resource for the digitization of public, nonfederal U.S. collections, launched several working groups to address this deficiency. Here, we report the development of 14 workflow modules with 7-36 tasks each. These workflows represent the combined work of approximately 35 curators, directors, and collections managers representing more than 30 herbaria, including 15 NSF-supported plant-related Thematic Collections Networks and collaboratives. The workflows are provided for download as Portable Document Format (PDF) and Microsoft Word files. Customization of these workflows for specific institutional implementation is encouraged.

Microsatellite marker development for the federally listed Prunus geniculata (Rosaceae).

PREMISE OF THE STUDY: Prunus geniculata is a federally listed species endemic to the central Florida scrub. To investigate levels and geographic partitioning of genetic variation in this species, we developed microsatellite markers for P. geniculata and its sister species, P. maritima. METHODS AND RESULTS: Following a protocol optimized in our laboratory, we designed 36 primer pairs, of which 8 amplified across both species and showed informative polymorphism. Product size varied from 163 to 370 bp, and the number of alleles ranged from 5 to 27. He across all populations ranged from 0.604 to 0.9155. CONCLUSIONS: Eight loci were useful at the population level and will be used for conservation genetic and phylogeographic studies of Prunus geniculata and P. maritima. Furthermore, from five to all eight of these loci can also be amplified in several other North American Prunus species.