Museum specimens of endangered species are important to determine pre-decline population structure and to characterise loss of diversity in surviving populations. Kākāpō (Strigops habroptilus), the critically endangered New Zealand ground parrot, suffered massive population declines in the nineteenth and twentieth centuries resulting in a genetic bottleneck and adverse inbreeding effects. The University of Sydney Chau Chak Wing Museum (formerly the Macleay Museum) holds several Kākāpō study skins in the Macleay Collections (Australia’s oldest natural history collection), obtained in the mid1800s prior to population declines, but with unknown provenance. Here, we used ancient DNA (aDNA) methods to sequence mitochondrial DNA (mtDNA) from nine Macleay skins and compared them to published sequences of North and South Island Kākāpō to establish the provenance of each skin. Phylogeography suggests the skins were collected on the southern west coast of the South Island, excluding the North Island as a source. Genetic results corroborate historical records of scientific field trips in the mid1800s taken by museum directors Sir James Hector and Sir Julius von Haast, who sent the skins to the Macleay from New Zealand. All nine Macleay specimens yielded unique mtDNA genome sequences consistent with previous findings of high mtDNA haplotype diversity in pre-decline Kākāpō, especially within southern South Island populations. The Macleay Collection’s skins are some of the oldest historical museum specimens of Kākāpō to have been genetically analysed and are an important genetic resource for future studies of Kākāpō genomic diversity.

Museum specimens of endangered species are important to determine pre-decline population structure and to characterise loss of diversity in surviving populations. Kākāpō (Strigops habroptilus), the critically endangered New Zealand ground parrot, suffered massive population declines in the nineteenth and twentieth centuries resulting in a genetic bottleneck and adverse inbreeding effects. The University of Sydney Chau Chak Wing Museum (formerly the Macleay Museum) holds several Kākāpō study skins in the Macleay Collections (Australia’s oldest natural history collection), obtained in the mid1800s prior to population declines, but with unknown provenance. Here, we used ancient DNA (aDNA) methods to sequence mitochondrial DNA (mtDNA) from nine Macleay skins and compared them to published sequences of North and South Island Kākāpō to establish the provenance of each skin. Phylogeography suggests the skins were collected on the southern west coast of the South Island, excluding the North Island as a source. Genetic results corroborate historical records of scientific field trips in the mid1800s taken by museum directors Sir James Hector and Sir Julius von Haast, who sent the skins to the Macleay from New Zealand. All nine Macleay specimens yielded unique mtDNA genome sequences consistent with previous findings of high mtDNA haplotype diversity in pre-decline Kākāpō, especially within southern South Island populations. The Macleay Collection’s skins are some of the oldest historical museum specimens of Kākāpō to have been genetically analysed and are an important genetic resource for future studies of Kākāpō genomic diversity.

Input and output from phylogenetic analyses of Camelops sequences in "Evidence for Pleistocene gene flow through the ice-free corridor from extinct horses and camels from Natural Trap Cave, Wyoming" (https://doi.org/10.1016/j.quaint.2021.11.017).

Input and output from phylogenetic analyses of Camelops sequences in "Evidence for Pleistocene gene flow through the ice-free corridor from extinct horses and camels from Natural Trap Cave, Wyoming" (https://doi.org/10.1016/j.quaint.2021.11.017).

Input and output from phylogenetic analyses of Equus sequences in "Evidence for Pleistocene gene flow through the ice-free corridor from extinct horses and camels from Natural Trap Cave, Wyoming" (https://doi.org/10.1016/j.quaint.2021.11.017).

All mitochondrial consensus sequences from "Evidence for Pleistocene gene flow through the ice-free corridor from extinct horses and camels from Natural Trap Cave, Wyoming" (https://doi.org/10.1016/j.quaint.2021.11.017).

Input and output from phylogenetic analyses of Haringtonhippus sequences in "Evidence for Pleistocene gene flow through the ice-free corridor from extinct horses and camels from Natural Trap Cave, Wyoming" (https://doi.org/10.1016/j.quaint.2021.11.017).

Input and output from phylogenetic analyses of Haringtonhippus sequences in "Evidence for Pleistocene gene flow through the ice-free corridor from extinct horses and camels from Natural Trap Cave, Wyoming" (https://doi.org/10.1016/j.quaint.2021.11.017).

Input and output from phylogenetic analyses of Equus sequences in "Evidence for Pleistocene gene flow through the ice-free corridor from extinct horses and camels from Natural Trap Cave, Wyoming" (https://doi.org/10.1016/j.quaint.2021.11.017).

All mitochondrial consensus sequences from "Evidence for Pleistocene gene flow through the ice-free corridor from extinct horses and camels from Natural Trap Cave, Wyoming" (https://doi.org/10.1016/j.quaint.2021.11.017).