Data from: Lineage range estimation method reveals fine-scale endemism linked to Pleistocene stability in Australian rainforest herpetofauna

Areas of suitable habitat for species and communities have arisen,
shifted, and disappeared with Pleistocene climate cycles, and through this
shifting landscape, current biodiversity has found paths to the present.
Evolutionary refugia, areas of relative habitat stability in this shifting
landscape, support persistence of lineages through time, and are thus
crucial to the accumulation and maintenance of biodiversity. Areas of
endemism are indicative of refugial areas where diversity has persisted,
and endemism of intraspecific lineages in particular is strongly
associated with late-Pleistocene habitat stability. However, it remains a
challenge to consistently estimate the geographic ranges of intraspecific
lineages and thus infer phylogeographic endemism, because spatial sampling
for genetic analyses is typically sparse relative to species records. We
present a novel technique to model the geographic distribution of
intraspecific lineages, which is informed by the ecological niche of a
species and known locations of its constituent lineages. Our approach
allows for the effects of isolation by unsuitable habitat, and captures
uncertainty in the extent of lineage ranges. Applying this method to the
arc of rainforest areas spanning 3500 km in eastern Australia, we
estimated lineage endemism for 53 species of rainforest dependent
herpetofauna with available phylogeographic data. We related endemism to
the stability of rainforest habitat over the past 120,000 years and
identified distinct concentrations of lineage endemism that can be
considered putative refugia. These areas of lineage endemism are strongly
related to historical stability of rainforest habitat, after controlling
for the effects of current environment. In fact, a dynamic stability model
that allows movement to track suitable habitat over time was the most
important factor in explaining current patterns of endemism. The
techniques presented here provide an objective, practical method for
estimating geographic ranges below the species level, and including them
in spatial analyses of biodiversity.