Recent range expansion in Australian hummock grasses (Triodia) inferred using genotyping-by-sequencing

Abstract

The Australian arid zone (AAZ) has undergone aridification and the formation of vast sandy deserts since the mid-Miocene. Studies on AAZ organisms, particularly animals, have shown patterns of mesic ancestry, persistence in rocky refugia and range expansions in arid lineages. There has been limited molecular investigation of plants in the AAZ, particularly of taxa that arrived in Australia after the onset of aridification. Here we investigate populations of the widespread AAZ grass Triodia basedowii to determine whether there is evidence for a recent range expansion, and if so, its source and direction. We also undertake a dating analysis for the species complex to which T. basedowii belongs, in order to place its diversification in relation to changes in AAZ climate and landscapes. We analyse a genomic single nucleotide polymorphism data set from 17 populations of T. basedowii in a recently developed approach for detecting the signal and likely origin of a range expansion. We also use alignments from existing and newly sequenced plastomes from across Poaceae for analysis in BEAST to construct fossil-calibrated phylogenies. Across a range of sampling parameters and outgroups, we detected a consistent signal of westward expansion for T. basedowii , originating in central or eastern Australia. Divergence time estimation indicates that Triodia began to diversify in the late Miocene (crown 7.0–8.8 million years (Ma)), and the T. basedowii complex began to radiate during the Pleistocene (crown 1.4–2.0 Ma). This evidence for range expansion in an arid-adapted plant is consistent with similar patterns in AAZ animals and likely reflects a general response to the opening of new habitat during aridification. Radiation of the T. basedowii complex through the Pleistocene has been associated with preferences for different substrates, providing an explanation why only one lineage is widespread across sandy deserts.

Multi-Species Phylogeography of Arid-Zone Sminthopsinae (Marsupialia: Dasyuridae) Reveals Evidence of Refugia and Population Expansion in Response to Quaternary Change

“…This expansion coincides with increasing aridity during peak climate oscillations of the mid-late Pleistocene and is comparable to butcherbirds [ 6 ], monsoonal/savannah occurring macropods [ 72 ], and clades of a widespread arid-adapted lineage of geckos [ 11 ], which experienced population expansion that also began during the mid-late Pleistocene. Our results are concordant with a growing number of studies that suggest population expansions of arid-adapted taxa occurred during the high amplitude climate cycles of the mid-late Pleistocene, coinciding with periods of intense aridification [ 14 , 15 , 23 , 67 , 73 , 74 ].…”

Large scale genome skimming from herbarium material for accurate plant identification and phylogenomics

“…Applying this phylogeny as a topological constraint on a larger (more species-complete) phylogeny based on Sanger sequencing of a limited set of markers provided substantially improved backbone resolution and support. Finally, cpDNA genomes from this study have also been combined with existing chloroplast genomic sequences to examine the diversification timing of an Australian arid zone grass species complex ( Tridoia basedowii ) [19].…”

“…However, there are many other potential uses of extensive plastid sequence data beyond species identification [22]. Like the Ptilotus [18] and Triodia [19] studies, the sequences from this project could be used to improve the resolution of plant phylogenies, which are increasingly based on the integration of samples, some with short marker sequences and others complete genomes. A third potential use of the data is studies of the evolution of plastid genome function, including understanding adaptive changes (e.g.…”

The geography of speciation in dasyurid marsupials

“…For example the widespread xeric‐adapted Dunnart, Sminthopsis crassicaudata , is usually associated with cracking clay soils, whereas its close relative Sminthopsis douglasi is limited to alluvial plain Mitchell grass pastures in central‐northern Queensland (Woolley, 1992). Likewise, spinifex ( Triodia ) grasses have been integral to the radiation of many arid‐zone dasyurid lineages (Anderson et al, 2019), including the tiny rodent‐like Ningauis ( Ningaui ), which primarily inhabit spinifex hummocks (Dickman, 2003).…”