Phylogeographic evidence for two mesic refugia in a biodiversity hotspot

Abstract

Phylogeographic studies of flora in species-rich south-western Australia point to complex evolutionary histories, reflecting patterns of persistence and resilience to climatic changes during the Pleistocene. We asked whether coastal areas of the mid-west and south, as well as granite outcrops and inland ranges, have acted as major refugia within this region during Pleistocene climatic fluctuations by analysing phylogeographic patterns in the shrub Calothamnus quadrifidus R.Br. (Myrtaceae). We determined variation in chloroplast DNA data for 41 populations across the geographic range. Relationships and major clades were resolved using parsimony and Bayesian analyses. We tested for demographic and spatial expansion of the major clades and estimated clade divergence dates using an uncorrelated, lognormal relaxed clock based on two conservative chloroplast mutation rates. Two distinct phylogeographic clades were identified showing divergence during the Pleistocene, consistent with other phylogeographic studies of south-west Australian flora, emphasising the impact of climatic oscillations in driving divergence in this landscape. The southern clade was more diverse, having higher haplotype diversity and greater genetic structure, while the northern clade showed evidence of fluctuation in population size. Regions of high haplotype diversity with adjacent areas of low diversity observed in each clade indicated the locations of two coastal refugia: one on the south coast and another along the mid-west coast. This is the first evidence for major Pleistocene refugia using chloroplast genetic data in a common, widespread species from this region.

Landscape genetics indicate recently increased habitat fragmentation in African forest‐associated chafers

“…More northern occurring species, such as P. nelshoogteensis and P. fasciatipennis , appeared to have persisted in northern refugia (Figs S5 and S17). Such potential long‐term refugia (Ibrahim et al ., ; Nistelberger et al ., ) of Pleophylla in the northern parts of the Great Escarpment were also supported by the high haplotype diversity that was recovered for the northern species in this study (Figs e, g and e, g) as well as the occurrence of locally endemic species (e.g., P. warnockae , P. pseudopilosa , P. ruthae ; Eberle et al ., ).…”

Biogeography and speciation of terrestrial fauna in the south‐western Australian biodiversity hotspot

“…Dated phylogeographies are available for species in at least five families of plants (see Table 1), and many studies on widespread species have identified divergent lineages that separated during the mid-Pleistocene, e.g. Eucalyptus loxophleba (Byrne & Hines, 2004), Acacia acuminata (Byrne et al, 2002), Santalum spicatum (Byrne, Macdonald & Brand, 2003) and Calothamnus quadrifidus (Nistelberger et al, 2014). Older intraspecific divergences in the late Pliocene have also been noted in the widespread E. marginata (Wheeler & Byrne, 2006) and the restricted and disjunct Lambertia orbifolia (Byrne, Macdonald & Coates, 1999).…”

Cryptic species in an ancient flowering‐plant lineage (Hydatellaceae, Nymphaeales) revealed by molecular and micromorphological data

“…Parallel divergences between northern and southern clades of other species in the Western Australian Floristic Region have been shown in plant and animal biogeographic studies, and may be driven by climatic change from the early to late Pleistocene (Byrne & al., , ; Fujioka & al., ; Murphy & al., ; Nistelberger & al., ). The microsatellite data show the greatest difference between the southern populations (group IV) and all other accessions (Fig.…”