Niche modelling supports cryptic diversification in an Andean hemiparasitic herb

Pleistocene climatic fluctuations shaped Andean environments, affecting the geographic and demography of many extant species. <i>Quinchamalium chilense,</i> a hemiparasite monospecific herb is distributed from high elevation Puna in the north, across the Chilean Matorral to alpine environments above the treeline in the temperate Andes. Previous studies have associated these regions with three different lineages: DEPU, MATO and TEMPE. To clarify the taxonomic boundaries we combined ecological niche modelling with demographic analyses based on genetic diversity. We assessed intra-specific genetic structure and predicted lineage distribution under both current and Last Glacial Maximum (LGM) climatic conditions. Additionally, we evaluated geographic range overlap as well as niche equivalency and similarity among lineages. Our results suggest diversification associated to the Great Patagonian Glaciation followed by demographic growth from 800,00 to 200,000 years ago. Our models predict the greatest range extent during LGM with contractions to the present. DEPU shows evidence of southward expansion following glacial retreat, likely tracking the availability of newly suitable habitats. This demography expansion resulted in current geographic contact with MATO, with which it shares moderately overlapping climatic niche. On the other hand, MATO and TEMPE, exhibit demographic stability and limited climatic overlap, suggesting long-term persistence in glacial refugia and expansion of TEMPE to new niches. Notably, DEPU and TEMPE displayed significant niche divergence. Overall, <i>Q. chilense</i> appears to have been affected by Andean orogeny and climate oscillations since the Great Patagonian Glaciation having its greatest suitable range extent during the LGM. The genus undergone postglacial spatial reorganization, shaped by differential responses to climate among lineages. These findings are consistent with a model of cryptic speciation driven by ecological processes, in which climatic niche divergence, demographic history, and range dynamics collectively contributed to the diversification of lineages within <i>Q. chilense</i>, despite limited morphological differentiation.