Contextualizing enigmatic extinctions using genomic DNA from fluid-preserved museum specimens of Desmognathus salamanders

Candidate‐species delimitation in Desmognathus salamanders reveals gene flow across lineage boundaries, confounding phylogenetic estimation and clarifying hybrid zones

“…Intriguingly, the sNMF admixture analysis suggested a non‐zero percentage of fuscus C ancestry in USNM 468094 (16%) and 468095 (25%), the existence of which was hypothesized in our previous study (Pyron et al, 2020). However, we also noted long terminal branches for these specimens in the concatenated ML phylogenetic estimate (see SI) and a large number of unique, apparently homozygous SNP calls in these specimens (Pyron et al, 2022), potentially driven by DNA degradation from fixatives or preservatives (O’Connell et al, 2021). Thus, the branch lengths and “ fuscus C” ancestry may be noise arising from template or sequencing errors misleading the sNMF algorithm.…”

“…We, therefore, divided the dataset into fully sampled SNP matrices for each specimen, yielding 1176 SNPs from 56 loci for USNM 468094 and 1605 from 79 for USNM 468095. The phylogenetic and clustering analyses both strongly estimated membership of these specimens in auriculatus A (Pyron et al, 2022). Both analyses also estimated the same general clusters and relationships as the primary analysis of the Lowland fuscus clade, with auriculatus B/C supported as a single candidate species along with fuscus D, and three admixed phylogeographic lineages in fuscus C (Figure 15; see full results in Dryad repository https://doi.org/10.5061/dryad.f4qrfj6x8).…”

“…However, we also noted that the extinction of numerous auriculatus A populations (such as the former fuscus subspecies “ carri ”) may have limited our ability to recover this signal (Pyron et al, 2022). Therefore, the signal of fuscus C ancestry in extirpated peninsular populations of auriculatus A may indeed be a real pattern reflecting historical evolutionary relationships and hybridization.…”

“…For further analysis, we created a reduced secondary alignment with all 896 terminals, pruned to the 27,763 bp from 129 loci called for these two individuals, that was 94.4% complete overall. We applied a limited set of the gene-tree and SNP-based analyses described below to confirm the placement of these samples in corroboration of their previously estimated genetic identity as auriculatus A (Pyron et al, 2022).…”

“…This includes nearly every known geographic population segment of Desmognathus , excepting a few marginal populations that are presumed extirpated. We also sequenced two formalin‐fixed, fluid‐preserved museum specimens (see Pyron et al, 2022) and only included these in a subset of analyses. Consequently, our primary sampling consisted of 894 specimens representing 49 mito‐nuclear candidate species.…”