Tracing evolutionary trajectories in the presence of gene flow in South American temperate lizards (Squamata: Liolaemus kingii group)

Evolutionary processes behind lineage divergence often involve multidimensional differentiation. However, in the context of recent divergences, the signals exhibited by each dimension may not converge. In such scenarios, incomplete lineage sorting, gene flow, and scarce phenotypic differentiation are pervasive. Here, we integrated genomic (RAD loci of 90 individuals), phenotypic (linear and geometric traits of 823 and 411 individuals, respectively), spatial, and climatic data to reconstruct the evolutionary history of a speciation continuum of liolaemid lizards (Liolaemus kingii group). Specifically, we (i) inferred the population structure of the group and contrasted it with the phenotypic variability; (ii) assessed the role of post-divergence gene flow in shaping phylogeographic and phenotypic patterns; and (iii) explored eco-geographic drivers of diversification across time and space. We inferred eight genomic clusters exhibiting leaky genetic borders coincident with geographic trans..., , , # Tracing evolutionary trajectories in the presence of gene flow in South American temperate lizards (Squamata: *Liolaemus kingii* group)

## Notes

Specimens and tissues are hosted in the herpetological collection LJAMM-CNP (IPEEC-CONICET, Puerto Madryn, Argentina). Field trips were conducted in the Patagonia Steppe during the years 2000-2022.

## Usage

Uncompress the data and follow the steps provided in the scripts to replicate the results presented in the manuscript

## File structure

* `bpp_A00_MSci.zip`: bpp estimates of Multispecies Coalescent + introgression parameters. The script `phylogeography.R` includes the code used to estimate the support for the different introgression models through the Savage-Dickey density ratio. The rationale behind the analysis is detailed in the Supplementary Material.

* `step1/`: Step 1 of the protocol implemented to reconstruct introgression events.

* `bid_bag-sou/`: parameters of the `baguali` ⇄ `south` introgression mode...