Investigating historical drivers of latitudinal gradients in polyploid plant biogeography: A multi-clade perspective

Premise of the Study
The proportion of polyploid plants in a community increases with latitude, and different hypotheses have been proposed about which factors drive this pattern. Here, we aim to understand the historical causes of the latitudinal polyploidy gradient using a combination of ancestral state reconstruction methods. Specifically, we assess whether (1) polyploidization enables movement to higher latitudes (i.e., polyploidization precedes occurrences in higher latitudes) or (2) higher latitudes facilitate polyploidization (i.e., occurrence in higher latitudes precedes polyploidization).
Methods
We reconstruct the ploidy states and ancestral niches of 1,032 angiosperm species at four paleoclimatic time slices ranging from 3.3 million years ago to the present, comprising taxa from four well-represented clades: Onagraceae, Primulaceae, Solanum (Solanaceae), and Pooideae (Poaceae). We use ancestral niche reconstruction models alongside a customized discrete character evolution mo..., Phylogenies were collected from the following sources: Onagraceae (Freyman and Höhna 2019), Primulaceae (De Vos et al. 2014), Solanaceae (Särkinen et al. 2013), and Poaceae (Spriggs et al. 2014). The phylogenies of Solanaceae and Poaceae were pruned to retain just those species in Solanum and Pooideae respectively. Occurrence points for species in each clade were downloaded from GBIF, and were cleaned for inaccuracies following protocols similar to those in Boyko et al. (2023). Ploidy data were gathered from the supplementary data of Rice et al. (2019).
The ancestral ranges of taxa in each clade were reconstructed using the program machuruku (Guillory and Brown 2021) to time periods available from PaleoClim data (Brown et al. 2018): the Last Interglacial (LIG, c. 130 ka), Marine Isotope Stage 19 (MIS19, c. 787 ka), the mid-Pliocene Warm Period (mPWP, c. 3.205 Ma), and Marine Isotope Stage M2 (M2, c. 3.3 Ma). Ploidy was reconstructed using corHMM (Beaulieu et al. 2013; Boyko and Beaulieu..., , The proportion of polyploid plants in a community increases with latitude, and different hypotheses have been proposed about which factors drive this pattern. Here, we aim to understand the historical causes of the latitudinal polyploidy gradient using a combination of ancestral state reconstruction methods. Specifically, we assess whether (1) polyploidization enables movement to higher latitudes (i.e., polyploidization precedes occurrences in higher latitudes) or (2) higher latitudes facilitate polyploidization (i.e., occurrence in higher latitudes precedes polyploidization). We reconstruct the ploidy states and ancestral niches of 1,032 angiosperm species at four paleoclimatic time slices ranging from 3.3 million years ago to the present, comprising taxa from four well-represented clades: Onagraceae, Primulaceae, Solanum (Solanaceae), and Pooideae (Poaceae). We use ancestral niche reconstruction models alongside a customized discrete character evolution model to allow reconstruction o...