Abstract Detail

Systematics

Garcia, Nicolas [1], Folk, Ryan [2].

Progress in elucidating the phylogeny and species delimitation in a Chilean endemic clade of lilies.

Phycella (Amaryllidaceae) is a clade of lilies comprising approximately 13 species. It is endemic to the mediterranean-type ecosystem (MTE) of Chile and appears to represent a rapid radiation with significant diversity in ecology and distribution; the group is also of conservation interest. An unclear taxonomy at the species level makes it a priority to clarify the number and range of species before addressing questions about speciation in this clade. To approach the evolutionary history and species delimitation of Phycella, we designed single-copy nuclear markers covering 893 genes and designed a custom hybrid target enrichment for Illumina HiSeq sequencing. We sampled a total of 137 individuals from 47 populations of Phycella, including all described taxa throughout the geographic range of the group. We used aTRAM 2.2 for assembly of nuclear loci. To reduce ambiguity of species tree inferences in ASTRAL 2 and *BEAST, we treated populations as tips and individuals as allelic variations. Additionally, we conducted a concatenated analysis of nuclear loci in RAxML.
Near-complete plastomes were assembled for all samples to compare with the nuclear framework. Chloroplast reads were extracted with BLAT and a custom Python script, and plastomes were assembled for each sample using the Geneious Prime reference-based assembler. Plastome sequences were aligned with MAFFT and manually curated. The final plastome alignment (excluding one Inverted Repeat region), consists of 132374 bp with ~2% of missing data, and was analyzed using RAxML and MrBayes.
Our results show 1) widespread cytonuclear discordance, 2) strong geographical structure in the plastome tree, and 3) at least three species are non-monophyletic in the nuclear species tree, suggesting cryptic species. Nuclear and chloroplast signals were integrated through phylogenetic network analyses in SplitsTree4. Molecular-based species delimitation was explored through the coalescent Bayesian species validation approach implemented in BPP. Preliminary results indicate that the consideration of morphological variation may be critical to propose a reasonable taxonomic scheme in Phycella. This robust systematic and taxonomic framework will set the stage for addressing biogeography and speciation within an exemplary radiation of the Chilean MTE.

1 - Universidad de Chile, Herbario EIF & Laboratorio de Sistemática y Evolución de Plantas, Av. Santa Rosa 11315, La Pintana, Santiago, 8820808, Chile
2 - Mississippi State University, 295 E. Lee Blvd., P.O. Box GY, 295 E. Lee Blvd., P.O. Box GY, Mississippi State, MS, 39762, United States

Keywords:
phylogenomics
phylogeography
monocots
Asparagales
Amaryllidaceae
species tree
species boundaries
networks
Taxonomy.

Presentation Type: Oral Paper
Session: SYS5, Systematics V: Gymnosperms to Monocots part A
Location: Virtual/Virtual
Date: Friday, July 31st, 2020
Time: 12:45 PM
Number: SYS5002
Abstract ID:258
Candidate for Awards:None