First attempts using NGS in Senecio (Asteraceae) Building a robust phylogeny of Culcitium group: a baseline for addressing further evolutionary questions for the genus in the Andes

1. First attempts using NGS in Senecio (Asteraceae)
Building a robust phylogeny of Culcitium group: a
baseline for addressing further evolutionary
questions for the genus in the Andes
Luciana Salomón1, 2 & Petr Sklenář1
1 Faculty of Science, Charles University
2 email: salomonl@natur.cuni.cz

2. Why do the Andes hold the highest plant species diversity in the world? This is one of the most intriguing ques;ons in studies
addressing the mechanisms of the origin and pa<erning of plant diversity worldwide. Several studies 1,2,3 have recently pointed to
the explosive adap;ve radia;ons found in high Andean groups as triggers to this spectacular diversity. In this way, my project aims to
contribute to be<er knowledge of the mechanisms shaping the hyperdiverse Andean region, focusing on an endemic Senecio
(Asteraceae) group, which has recently been recircumscribed4 and iden;fied as a lineage with rapid adap;ve radia;on5: Senecio ser.
Culci*um.
Previous phylogenies6: species missing, no
support or resolu;on
Introduc)on
The phylogeny as first step to accomplish these aims for the group:
*1st to obtain and date the phylogeny for the entire group, applying highly variable
genome-wide molecular markers, never used so far in Senecio (Objective I).
I will share with you some result for this first objective
*2nd analyze congruence/incongruence patterns together with other data (e.g. flow
cytometry) in order to detect mechanisms associated with the explosive radiation of
the group (Objective II).
*3rd reconstruct the ancestral states of morphological features to evaluate the
morphological changes accompanied the evolution of the group along the Andes
(Objective III).

3. Materials & Methods
Senecio series Culcitium: a well defined and variable group
with 43 sp along Northern and Central Andes.
At the moment 69 samples Hyb-seq data: 9 outgroups, 60
samples (30 species) ingroup. Asteraceae COS baits
enrichment + not enriched material.
2 workflow on Metacentrum portal: HybPhyloMaker7(HPM)
and HybPiper8 (HP). A 3rd one in development (HybWizard-
HW) to combine both of them using multiple references and
selecting just orthologous. RAxML9 for gene trees, species
tree recontruction using Astral10
HPM
Reference: 1 (Sunflower)
Only works with orthologous
HP
Reference: multiple
Paralogs warning
HW
Reference: mulSple
Selected orthologous
Nodding capitula
Microechinate
pollen

4. Exons-HPM Exons-HP
0.86
0.87
0.93
Low support
Mul9ple samples same species split along the tree
(Preliminary) Results
Exons-HP+HW+HPM
Low support
Some samples same species split in the tree
Some groups make sense from morphology
More loci recovered
Paralogs detected
Better support
Few samples same species still split in the tree (MD)
Some groups make sense from morphology (circle)
More loci recovered
Paralogs discarded
*Same shade color represent
same sp splitted along the trees
*Bars on the side shows groups
making sense from morphology

5. *Preliminary results: more samples nedded to complete sampling (cancelled field trip, pues
COVID)
*Promising results increasing support and resolu>on
*Best coverage using mul>ple references
*Paralogs detected (a clue to tackle the next objec>ves of my work)
*Re-sequencing some samples because missing data
Final considerations & future work
Thanks to Lenka Flašková for lab assistance, Roswitha Schmickl & Tomáš Fér for training in HPM, Roman Ufimov for training in HP
and HW. Founding from European Structural and Investment Funds OperaKonal Programme Research, Development & EducaKon
trough the Ministry of EducaKon, Youth and Sports Czech Republic is acknowledge.
References 1Bell, C. D., & Donoghue, M. J. (2005). Phylogeny and biogeography of Valerianaceae (Dipsacales) with special reference to the South American valerians. Organisms Diversity & Evolu>on, 5(2), 147-159. 2Hughes, C., & Eastwood, R. (2006). Island radia>on on a con>nental scale: excep>onal rates of plant diversifica>on a[er
upli[ of the Andes. 3Vargas, O. M., Or>z, E. M., & Simpson, B. B. (2017). Conflic>ng phylogenomic signals reveal a pa_ern of re>culate evolu>on in a recent high-Andean diversifica>on (Asteraceae: Astereae: Diplostephium). New Phytologist, 214 (4), 1736-1750. 4Salomón L., P. Sklenář & S.E. Freire. 2018. Synopsis of Senecio series
Culci>um (Asteraceae: Senecioneae, Senecioninae) in the Andean region of South America. Phytotaxa 340 (1): 001–047.5Dušková, E., Sklenář, P., Kolář, F., Vásquez, D. L., Romoleroux, K., Fér, T., & Marhold, K. (2017). Growth form evolu>on and hybridiza>on in Senecio(Asteraceae) from the high equatorial Andes. Ecology and Evolu>on, 7
(16), 6455-6468.6Salomón L., S.M. Sede & S.E. Freire. 2019. Phylogene>c posi>on of Argen>nian and Chilean endemic species of Senecio ser. Culci>um (Asteraceae) with an evolu>onary analysis of morphological characters. Phytotaxa 387 (3): 177–209.7Fér, T., & Schmickl, R. E. (2018). HybPhyloMaker: Target Enrichment Data Analysis
From Raw Reads to Species Trees. Evolu>onary Bioinforma>cs, 14, 1176934317742613.8Johnson, Ma_hew G., et al. "HybPiper: Extrac>ng coding sequence and introns for phylogene>cs from high-throughput sequencing reads using target enrichment." Applica>ons in plant sciences 4.7 (2016): 1600016. 9Stamatakis, A. (2014). RAxML
version 8: a tool for phylogene>c analysis and post-analysis of large phylogenies. Bioinforma>cs, 30(9), 1312-1313. 10Mirarab, S., Reaz, R., Bayzid, M. S., Zimmermann, T., Swenson, M. S., & Warnow, T. (2014). ASTRAL: genome-scale coalescent-based species tree es>ma>on. Bioinforma>cs, 30(17), i541-i548.