Mitogenomics of historical type specimens of Australasian turtles: clarification of taxonomic confusion and old mitochondrial introgression

Abstract

Diagnosability is central to taxonomy as are type specimens which define taxa. New advances in technologies and the discovery of new informative traits must be matched with previous taxonomic decisions based on name-bearing type specimens. Consequently, the challenge of sequencing highly degraded DNA from historical types becomes an inevitability to resolve the very many taxonomic issues arising from, by modern standards, poor historical species descriptions leading to difficulties to assign names to genetic clusters identified from fresh material. Here we apply high-throughput parallel sequencing and sequence baiting to reconstruct the mitogenomes from 18 type specimens of Australasian side-necked turtles (Chelidae). We resolve a number of important issues that have confused the taxonomy of this family, and analyse the mitogenomes of the types and those of fresh material to improve our understanding of the phylogenetic relationships of this morphologically conservative group. Together with previously published nuclear genomic data, our study provides evidence for multiple old mitochondrial introgressions.

Figure 1

Maximum Likelihood tree for chelid mitogenomes, including historical type specimens using a 16,289-bp-long alignment. For historical type specimens, the original name combinations are shown in bold. Numbers at nodes are bootstrap values and posterior probabilities for a Bayesian tree of the same topology. Asterisks indicate maximum support under both methods. Quotation marks for a GenBank sequence assigned to Emydura subglobosa (KC692462) indicate questionable taxonomic allocation. Lectotype and paralectotype of Hydraspis victoriae were previously erroneously identified. The species description was based only on the putative paralectotype, which is therefore the name-bearing holotype (see Discussion). Snake-necked species of Chelodina in red, long-necked species in black. Icons are derived from photos of Chelodina steindachneri (long-necked Chelodina), C. burrungandjii (snake-necked Chelodina), and Elusor macrurus (short-necked species; from top to bottom). Drawings: U. Fritz. On the right are for Australasian taxa the currently accepted genera shown.

Figure 2

Maximum Likelihood tree for chelids, including historical type specimens using an 11,328-bp-long alignment corresponding to the 13 coding genes of the mitogenome. For historical type specimens, the original name combinations are shown in bold. Quotation marks for a GenBank sequence assigned to Emydura subglobosa (KC692462) indicate questionable taxonomic allocation. Numbers at nodes are bootstrap values and posterior probabilities for a Bayesian tree of the same topology. Asterisks indicate maximum support under both methods. Note the different placement of Chelodina steindachneri compared to Fig. 1. Snake-necked species of Chelodina in red, long-necked species in black. On the right are for Australasian taxa the currently accepted genera shown. Inset: historical type specimen of Testudo longicollis Shaw, 1794 (photo: P. D. Campbell). For further explanation, see Fig. 1.