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)

Sminthopsis youngsoni

mtDNA data

Sminthopsis ooldea

Atypical sampling approach

S. ooldea S. youngsoni

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

Sminthopsis ooldea

K=2PCA n=47

Sminthopsis youngsoni

K=3Narrowing of suitable habitat

PCA

n=44Tissue

sample gap

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