Population differentiation and clustering
After stringent filtering, the average number of SNPs reduced from
52,693 to 3,729 for Carlia (N=135 across four lineages), from
150,178 to 7,472 for Diporiphora (N=147 across eight lineages),
from 182,688 to 11,531 for Gehyra (N=214 across ten lineages) and
from 185,704 to 10,017 for Heteronotia (N=83; three lineages).
Values per lineage, the region of occurrence and habitat specialization
are given in Table 1. After partitioning samples into major lineages,
mean sample size was 23 individuals and, post-filtering, no lineages had
more than 6% of missing data. As expected from prior studies, most
species had deeply divergent intraspecific lineages, reflected in
largely coincident patterns across the PCo A, fastStructureand either of the spatial or non-spatial ConStruct graphs (see
Figure 2 for an example with Carlia amax; data for the other
species are available in the Suppl. Mat. Figure S5-S8). The number of
discrete lineages identified per species varied from one to three and
these supported historically isolated lineages recognized in previous
studies, mostly using different datasets (Suppl. Mat. S1). Our
subsequent landscape genetic studies focused on variation within these
lineages. However, some of these lineages as defined here could still
comprise multiple less divergent but historically isolated populations
that could confound some landscape genetic analyses but could not
confidently resolved with the sampling here. These includeDiporiphora bilineata and D. perplexa (Fenker et al,unpublished data ), Gehyra gemina and G. koira(Oliver et al., 2020), G. nana 4 (Moritz et al., 2018), H.
binoei TE (Moritz et al., 2016) and Carlia munda (Potter et al.,
2018) (Suppl. Mat. S1).