Abstract Detail


Skibicki, Sam [1], Barrett, Craig [2].

Creating genomic libraries from herbarium specimens for phylogenomics in the subtribe Zinniinae (Asteraceae; Heliantheae).

Herbaria are tremendous resources for botanists interested in taxonomy, biogeography, ecology, conservation, and the effects of climate change on species distributions. However, the plant tissue itself is a repository of genomic information as well. While considering best practices for tissue sampling, these specimens will continue to have multifaceted uses to biologists, especially when field collection of fresh material is not feasible. The Zinniinae are a New World subtribe within the family Asteraceae with roughly 54 species ranging from southern Canada to Paraguay, with Mexico being the center of diversity. Phylogenetic relationships, taxonomy, morphological trait variation, and biogeographic patterns of diversification are poorly studied in this subtribe, despite their ecological and economic importance (e.g. Echinacea, Zinnia). Due to logistical challenges of collecting in Mexico and Central America at this time, ‘herbariomics’ is the best way to accomplish a phylogenetic revision of this subtribe. Since high throughput sequencing machines use shorter fragments of DNA than Sanger methods we have chosen this approach for our project. We have extracted DNA from 118 specimens from the sister subtribes Zinniinae (all species) and Spilanthinae (~half of the species) and successfully created 116 genomic libraries. These libraries were created with herbarium material ranging in age from two days old to 98 years old. While the older samples were obviously more degraded by examining total DNA agarose gel smears, the final libraries were similar to newer samples while comparing Qubit scores. These libraries will be used as templates for Target Sequence Capture. We have chosen the myBaits Compositae probe set which has been shown to successfully capture 800-1000 single or low copy loci from throughout the Asteraceae family. The data generated will allow for the robust estimation of phylogenetic trees using methods that account for gene tree discordance, which will be used as a phylogenomic framework to study speciation rates, morphological variation, chromosome number evolution, and biogeography in the clade within the larger context of Asteraceae.   

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Genomic Libraries

Presentation Type: Oral Paper
Session: SYS3, Systematics III: Cooley Award presentations
Location: Virtual/Virtual
Date: Wednesday, July 29th, 2020
Time: 10:45 AM
Number: SYS3004
Abstract ID:408
Candidate for Awards:George R. Cooley Award

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