Abstract Detail

Phylogenomics

Anderson, Benjamin [1], Grierson, Pauline [1], Krauss, Siegfried [1], Thiele, Kevin [1], Barrett, Matthew [2].

Genotyping by sequencing in a 'spiny' species complex of Australian arid zone grasses (Triodia).

Next-generation sequencing approaches are becoming increasingly accessible to researchers interested in systematics, although best practice for addressing systematic questions is not yet established. One approach suitable for non-model systems is genotyping by sequencing (GBS), which involves generating a reduced representation of the genome using restriction enzymes. We applied GBS to resolve evolutionary relationships in a species complex of hummock grasses in the genus Triodia, which forms a dominant component of the vegetation over c. 18% of Australia. As ecologically important primary producers and habitat providers for animals, Triodia grasses are critical targets for restoration in regions impacted by large-scale mining, but taxonomically unresolved species complexes make identifications and correct provenance seed sourcing difficult. The Triodia basedowii species complex comprises two named taxa, five informally named taxa and at least two additional taxa awaiting recognition. Morphological overlap between, and variability within, taxa in the complex make identifications challenging. Previous sequencing of ITS was unable to clearly distinguish between some taxa. GBS raw reads were processed using Stacks and PEAR and assembled into loci using PyRAD, including optimising assembly parameters using replicates and genetic distances within populations. SNPs were analysed with distance-based clustering, assembled loci were concatenated for phylogenetic analysis in RAxML and TNT, and individual loci were used to create gene trees for summary species tree approaches (e.g. ASTRAL). While species tree approaches were relatively robust to variation in PyRAD assembly parameters, our RAxML analyses recovered well-supported but conflicting topologies for two different sets of parameters. Despite this conflict, multiple clades were consistently supported across analyses. GBS and the analyses we implemented provided support for the distinction of multiple new species, improved resolution of relationships between taxa compared to ITS, and both corroborated and contradicted ITS evidence for hybridisation between taxa. Our results will inform future taxonomic revision of the Triodia basedowii species complex, and facilitate the testing of hypotheses regarding the evolution of the Australian arid zone biota. Our approach to assembly and analysis of GBS data should be helpful for researchers hoping to resolve systematic challenges at this evolutionary scale.

1 - The University of Western Australia, School of Plant Biology, 35 Stirling Hwy, Crawley, WA, 6009, Australia
2 - Botanic Gardens and Parks Authority, Kings Park and Botanic Garden, Fraser Ave, Kings Park, WA, 6005, Australia

Keywords:
ASTRAL
Australia
Genotyping by sequencing (GBS)
PyRAD
Species complex
Triodia.

Presentation Type: Oral Paper
Session: 1, Phylogenomics I
Location: 101/Savannah International Trade and Convention Center
Date: Monday, August 1st, 2016
Time: 8:00 AM
Number: 1001
Abstract ID:55
Candidate for Awards:None