The ability to predict ancient DNA sequencing success in natural history collections is critical to reducing the amount of destructive sampling of a finite resource. So far, studies investigating such success have predominantly focused on taxa with ranges restricted to temperate or cold environments at northern latitudes which likely aids DNA preservation. Here, we report remarkably high aDNA sequencing success in Sirenia, herbivorous marine mammals of which the distribution is currently constrained to the global tropics. We investigate 91 samples from 85 specimens comprising all four contemporary species and one extinct species, comparing different sample types (cranial/post-cranial bone, skin and cartilage), species, collections, and material age. We obtained remarkably high (e.g. > 20%) endogenous DNA preservation for the majority (e.g. ~57% percent) of samples. Sequencing success was linked to sample type, with cranial bones (including petrous and tympanic bones) yielding significantly higher endogenous DNA. Additionally, we obtained variable, but potentially superior DNA results for preserved cartilage and hide samples that can be associated with historical bone. Although such tissue is not always present, this type of material is easy to sample, with very limited destructive impacts on the associated bones and we therefore highlight its untapped potential as a source of DNA. Overall, our results show the high success of ancient DNA retrieval from historical collections of species with a tropical distribution expanding on the types of specimens that are available for temporal genomic analyses.

The identification of genetically distinct populations is central to the management and conservation of wild populations. Whole-genome-sequencing allows for high-resolution assessment of genetic structure, demographic connectivity and the impacts of selection acting on different parts of the genome. Here, we utilise population genomics to investigate the genetic structure of the Australasian snapper or Tāmure (Chrysophrys auratus), an ecologically, economically, and culturally important (taonga) marine fish. We analysed over four million high-quality SNPs obtained by whole-genome sequencing from 382 individuals collected across its New Zealand range. We identified two genetic clusters (an eastern and western cluster) with genetic disjunctions around on either side of the North Island of New Zealand. These genetic clusters do not match the current fisheries management areas. Pairwise-FST and ADMIXTURE analyses showed the presence of directional gene flow occurring at both genetic disjunctions from the East to the West cluster. We hypothesize that major ocean currents are limiting the dispersal of snapper at these genetic disjunctions. The heterogeneous coastal environment is also likely driving evolutionary change. A genome scan identified four significantly divergent genomic regions between genetic clusters. A diverse pattern of genetic variation in these regions implies that different evolutionary processes drive local adaptation in these clusters. Identification of candidate genes in these regions also provides a tentative connection to which traits may be under selection. Our results provide novel insights into New Zealand’s coastal environment influences evolutionary processes, and valuable information for effective management of the snapper fisheries.