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1. A basic dd RAD seq two‐enzyme protocol performs well with herbarium and silica‐dried tissues across four genera

   https://doi.org/10.1002/aps3.11344  

   Jordon‐Thaden, Ingrid E. ; Beck, James B. ; Rushworth, Catherine A. ; Windham, Michael D. ; Diaz, Nicolas ; Cantley, Jason T. ; Martine, Christopher T. ; Rothfels, Carl J. ( April 2020 , Applications in Plant Sciences)

   The ability to sequence genome‐scale data from herbarium specimens would allow for the economical development of data sets with broad taxonomic and geographic sampling that would otherwise not be possible. Here, we evaluate the utility of a basic double‐digest restriction site–associatedDNAsequencing (ddRADseq) protocol usingDNAs from four genera extracted from both silica‐dried and herbarium tissue.

   DNAs fromDraba,Boechera,Solidago, andIlexwere processed with a ddRADseq protocol. The effects ofDNAdegradation, taxon, and specimen age were assessed.

   Although taxon, preservation method, and specimen age affected data recovery, large phylogenetically informative data sets were obtained from the majority of samples.

   These results suggest that herbarium samples can be incorporated into ddRADseq project designs, and that specimen age can be used as a rapid on‐site guide for sample choice. The detailed protocol we provide will allow users to pursue herbarium‐based ddRADseq projects that minimize the expenses associated with fieldwork and sample evaluation.

    

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2. Differences in flowering time maintain species boundaries in a continental radiation of Viburnum

   https://doi.org/10.1002/ajb2.1292  

   Spriggs, Elizabeth L. ; Schlutius, Caroline ; Eaton, Deren A. ; Park, Brian ; Sweeney, Patrick W. ; Edwards, Erika J. ; Donoghue, Michael J. ( May 2019 , American Journal of Botany)

   We take an integrative approach in assessing how introgression and Pleistocene climate fluctuations have shaped the diversification of the coreLentagoclade ofViburnum, a group of five interfertile species with broad areas of sympatry. We specifically tested whether flowering time plays a role in maintaining species isolation.

   RAD‐seq data for 103 individuals were used to infer the species relationships and the genetic structure within each species. Flowering times were compared among species on the basis of historical flowering dates documented by herbarium specimens.

   Within each species, we found a strong relationship between flowering date and latitude, such that southern populations flower earlier than northern ones. In areas of sympatry, the species flower in sequence rather than simultaneously, with flowering dates offset by ≥9 d for all species pairs. In two cases it appears that the offset in flowering times is an incidental consequence of adaptation to differing climates, but in the recently diverged sister speciesV. prunifoliumandV. rufidulum, we find evidence that reinforcement led to reproductive character displacement. Long‐term trends suggest that the two northern‐most species are flowering earlier in response to recent climate change.

   We argue that speciation in theLentagoclade has primarily occurred through ecological divergence of allopatric populations, but differences in flowering time were essential to maintain separation of incipient species when they came into secondary contact. This combination of factors may underlie diversification in many other plant clades.

    

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3. Integrating herbarium specimen observations into global phenology data systems

   https://doi.org/10.1002/aps3.1231  

   Brenskelle, Laura ; Stucky, Brian J. ; Deck, John ; Walls, Ramona ; Guralnick, Rob P. ( March 2019 , Applications in Plant Sciences)

   The Plant Phenology Ontology (PPO) was originally developed to integrate phenology observations of whole plants across different global observation networks. Here we describe a new release of thePPOand associated data pipelines that supports integration of phenology observations from herbarium specimens, which provide historical and modern phenology data.

   Critical changes to thePPOinclude key terms that describe how measurements from parts of plants, which are captured in most imaged herbarium specimens, relate to whole plants. We provide proof of concept for ingesting annotations from imaged herbarium sheets ofPrunus serotina, the common black cherry. We then provide an example analysis of changes in flowering timing over the past 125 years, demonstrating the value of integrating herbarium and observational phenology data sets.

   These conceptual and technical advances will support the addition of phenology data from herbaria, but also could be expanded upon to facilitate the inclusion of data from photograph‐based citizen science platforms. With the incorporation of herbarium phenology data, new historical baseline data will strengthen the capability to monitor, model, and forecast plant phenology changes.

    

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4. Extreme copy number variation at a tRNA ligase gene affecting phenology and fitness in yellow monkeyflowers

   https://doi.org/10.1111/mec.14904  

   Nelson, Thomas C. ; Monnahan, Patrick J. ; McIntosh, Mariah K. ; Anderson, Kayli ; MacArthur‐Waltz, Evan ; Finseth, Findley R. ; Kelly, John K. ; Fishman, Lila ( December 2018 , Molecular Ecology)

   Copy number variation (CNV) is a major part of the genetic diversity segregating within populations, but remains poorly understood relative to single nucleotide variation. Here, we report on atRNAligase gene (Migut.N02091;RLG1a) exhibiting unprecedented, and fitness‐relevant,CNVwithin an annual population of the yellow monkeyflowerMimulus guttatus.RLG1a variation was associated with multiple traits in pooled population sequencing (PoolSeq) scans of phenotypic and phenological cohorts. Resequencing of inbred lines revealed intermediate‐frequency three‐copy variants ofRLG1a (trip+;5/35 = 14%), andtrip+lines exhibited elevatedRLG1a expression under multiple conditions.trip+carriers, in addition to being over‐represented in late‐flowering and large‐flowered PoolSeq populations, flowered later under stressful conditions in a greenhouse experiment (p < 0.05). In wild population samples, we discovered an additional rareRLG1a variant (high+) that carries 250–300 copies ofRLG1a totalling ~5.7 Mb (20–40% of a chromosome). In the progeny of ahigh+carrier, Mendelian segregation of diagnostic alleles andqPCR‐based copy counts indicate thathigh+is a single tandem array unlinked to the single‐copyRLG1a locus. In the wild,high+carriers had highest fitness in two particularly dry and/or hot years (2015 and 2017; bothp < 0.01), while single‐copy individuals were twice as fecund as eitherCNVtype in a lush year (2016:p < 0.005). Our results demonstrate fluctuating selection onCNVs affecting phenological traits in a wild population, suggest that planttRNAligases mediate stress‐responsive life‐history traits, and introduce a novel system for investigating the molecular mechanisms of gene amplification.

    

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5. The compounding consequences of wildfire and climate change for a high‐elevation wildflower ( Saxifraga austromontana )

   https://doi.org/10.1111/jbi.13441  

   Bloom, Trevor D. S. ; Flower, Aquila ; Medler, Michael ; DeChaine, Eric G. ( October 2018 , Journal of Biogeography)

   High‐elevation plants are disproportionally affected by climate change. As temperatures rise, the amount of available alpine habitat in the Rocky Mountains will decrease resulting in potential local extinctions of plant species. In addition to the direct effects of climate‐driven habitat loss, alpine plants must also respond to indirect effects, such as changes in disturbance regimes. One notable shift is the increase of wildfire frequency in regions where fire was previously rare or absent, including the alpine. We hypothesized that direct climatic changes compounded with increased wildfire frequency will reduce the future suitable habitat of high‐elevation plants more than if climate was considered alone.

   Rocky Mountain Floristic Region, western North America.

   Saxifraga austromontana(Saxifragaceae), a wildflower endemic to high elevations of the Rocky Mountain Floristic Region.

   Our approach integrated historical herbarium records, field surveys, remote sensing, species distribution models, historic wildfire data, and predictive models.

   Our results indicate wildfire has significantly reduced the abundance and increased the likelihood of extirpation forS. austromontana. Increased fire frequency compounded with direct climatic changes will likely reduce the range of the species by approximately 43% by 2050 compared to 38% due to climate alone, under a moderateCO₂emissions scenario. The influence of wildfire varies regionally. For instance, the Middle Rockies will likely lose 74% of its suitable habitat of which 16% may be lost due to fire, while other regions, such as the northern range, will be less negatively affected by direct and indirect effects.

   Our evidence that increased wildfire frequency will compound the impacts of climate change on alpine taxa in North America led to the development of a new, general hypothesis on the fundamental interaction between direct and indirect effects of climate change on species range reductions.

    

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