Insights into the population genetic structure of desert-dwelling marsupials using RAD sequencingLinette Umbrello, Jose Carvajal, Raphael Didham, Ric How, Joel Huey
Dasyurids in the arid zone
¨ High diversity (for mammals!) & adapted to infrequent rainfall events
¨ Sparse sampling = unknowns; species declines, pop structure/gene flow
¨ Next-gen sequencing to answer pop-gen questions
From Gibson & McKenzie 2009, WAM RecordsFrom Mitchell et al. 2014, MBE
¨ Pop expansion from refuge areas since LGM¨ Presence of hummock grasslands essential for dasyurids
From Byrne et al. 2008 Molecular Ecology
Arid zone refuges
Hummock grassland (Triodia) after rain
Sminthopsis
¨ Mega-diverse ~18 spp¨ 8 species in arid zone
¨ 9-14g¨ Sandy substrates
¨ Hairy footpads
(www.flickr.com/photos/angusmcnab)
S. youngsoni
¨ 10-18g¨ Loamy substrates
¨ Granulated footpads
S. ooldea
(Photo: WAM)
Double-digest RAD-seq¨ Cost effective outsourced to AGRF¨ High quality DNA required -80°C liver 3mm2
¨ ipyRAD pipeline used à ipyrad.readthedocs.io
Species Sample No. No. SNPs No. Loci Avg coverage of loci
S. ooldea 47 27607 11815 70.1
S. youngsoni 44 35301 14678 42.6
Conclusions
¨ RADseq results clearer than mtDNA¨ Population structure present
¤ Pleistocene refuge areas à Pilbara, Carnarvon¤ Isolation by distance¤ Population expansion
¨ Species biology drives patterns¨ Complex arid zone = complex species responses
Acknowledgements¨ Travel funding: CBA travel grant, AMS John Seebeck award
¨ Sequencing: NCB project
¨ Lab assistance: Mia Hillyer and Gaynor Dolman
¨ Supervisors: Joel, Raph and Ric
¨ Bioinfor“magician”: Jose github.com/ignacio3437/wambam
¨ Samples: WAM, SAM (ABTC; Leanne and Steve D), Mark Cowan (DBCA), Roy Teale (Biota), Traditional Owners