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Abstract Detail

Revolutionizing systematics: Herbaria in the Genomics Age

Lagomarsino, Laura [1], Uribe-Convers, Simon [2], Carlsen, Monica [3], Antonelli, Alexandre [4], Muchhala, Nathan [5].

The promises and pitfalls of herbarium phylogenomics: A case study in a Neotropical plant radiation.

The field of phylogenetics has undergone a data revolution in the last decade as high-throughput sequencing datasets have become, increasingly, the norm. This methodological improvement is also associated with the increasing utility of DNA from herbarium and other museum specimens. In particular, target enrichment sequence capture, a reduced representation genome sequencing method that is robust to low quality, low quantity DNA typical of herbarium specimens, allows the inclusion of historical specimens in genomic-scale analyses. Moreover, this approach requires minimal destructive sampling of the physical specimens. Here, we apply sequence capture to the centropogonid clade of Neotropical bellflowers (Campanulaceae: Lobelioideae), a recent, rapid plant radiation with a primarily Andean distribution, to infer phylogenetic relationships. Sequences for RNA baits to capture putatively low copy nuclear loci were designed using a combination of transcriptome and low-coverage genome sequencing data. Herbarium specimens and field-collected tissue were both important sources of DNA for sequence capture in our study. Comparisons of sequence capture efficiency of field-collected and herbarium specimens suggest that phylogenetic distance from taxa on which probes were designed is a more important predictor of efficiency than degraded input DNA. Phylogenomic analyses that incorporate gene tree-species tree incongruence due to incomplete lineage sorting greatly improved our knowledge of relationships in this group, particularly at deeper nodes in the phylogeny, and confirmed that concatenation analyses are perhaps overly simplistic for this clade. Using the inferred species tree, we performed a biogeographic analysis incorporating a key biological trait, fruit type, to explore the role of bird dispersal in structuring geographical patterns in this large clade. By incorporating herbarium specimens into our analyses, we were able to expand our sampling to include taxa that would otherwise be absent, either due to prohibitively expensive fieldwork, occurrence in difficult to access localities, or logistical issues. In other studies, this can be expanded to include endangered species, small populations where sampling would be ecologically detrimental, and even recently extinct lineages. Sequence capture effectively "opens the treasure chest," allowing even the oldest, most degraded herbarium specimens from remote parts of the world to be included in genome-scale phylogenetic and/or evolutionary analyses.

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1 - Louisiana State University, Dept Of Biological Sciences, 103 Life Sciences Building, Louisiana State University, Baton Rouge, LA, 70803, United States
2 - University Of Missouri - St. Louis, Biology Department, One University Blvd, R323 Research Hall, St. Louis, MO, 63121, United States
3 - Missouri Botanical Garden, P.O. Box 299, Saint Louis, MO, 63166, United States
4 - University of Gothenburg, Goteborg, Sweden
5 - University of Missouri-St. Louis, Department of Biology, St Louis, MO, 63110

Sequence capture

Presentation Type: Colloquium Presentations
Session: C10, Revolutionizing Systematics: Herbaria in the Genomics Age
Location: 103/Mayo Civic Center
Date: Wednesday, July 25th, 2018
Time: 9:30 AM
Number: C10007
Abstract ID:499
Candidate for Awards:None

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