SignificanceThe mode and tempo of extinctions and extirpations after the first contact phase of human settlements is a widely debated topic. As the last major landmass to be settled by humans, New Zealand offers a unique lens through which to study interactions of people and biota. By analyzing ancient DNA from more than 5,000 nondiagnostic and fragmented bones from 38 subfossil assemblages, we describe species and patterns that have been missed by morphological approaches. We report the identification of five species of whale from an archaeological context in New Zealand and describe the prehistoric kākāpō population structure. Taken together, this study demonstrates insights into subsistence practices and extinction processes and demonstrates the value of genetic analyses of fossil assemblages.

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Prehistoric human impacts on megafaunal populations have dramatically reshaped ecosystems worldwide. However, the effects of human exploitation on smaller species, such as anatids (ducks, geese, and swans) are less clear. In this study we apply ancient DNA and osteological approaches to reassess the history of Australasia's iconic black swans () including the palaeo-behaviour of prehistoric populations. Our study shows that at the time of human colonization, New Zealand housed a genetically, morphologically, and potentially ecologically distinct swan lineage (, Poūwa), divergent from modern (Australian) Morphological analyses indicate exhibited classic signs of the 'island rule' effect, being larger, and likely flight-reduced compared to Our research reveals sudden extinction and replacement events within this anatid species complex, coinciding with recent human colonization of New Zealand. This research highlights the role of anthropogenic processes in rapidly reshaping island ecosystems and raises new questions for avian conservation, ecosystem re-wilding, and de-extinction.

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The decline of amphibians has been of international concern for more than two decades, and the global spread of introduced fauna is a major factor in this decline. Conservation management decisions to implement control of introduced fauna are often based on diet studies. One of the most common metrics to report in diet studies is Frequency of Occurrence (FO), but this can be difficult to interpret, as it does not include a temporal perspective. Here, we examine the potential for FO data derived from molecular diet analysis to inform invasive species management, using invasive ship rats ( Rattus rattus ) and endemic frogs ( Leiopelma spp.) in New Zealand as a case study. Only two endemic frog species persist on the mainland. One of these, Leiopelma archeyi , is Critically Endangered (IUCN 2017) and ranked as the world's most evolutionarily distinct and globally endangered amphibian (EDGE, 2018). Ship rat stomach contents were collected by kill‐trapping and subjected to three methods of diet analysis (one morphological and two DNA‐based). A new primer pair was developed targeting all anuran species that exhibits good coverage, high taxonomic resolution, and reasonable specificity. Incorporating a temporal parameter allowed us to calculate the minimum number of ingestion events per rat per night, providing a more intuitive metric than the more commonly reported FO. We are not aware of other DNA‐based diet studies that have incorporated a temporal parameter into FO data. The usefulness of such a metric will depend on the study system, in particular the feeding ecology of the predator. Ship rats are consuming both species of native frogs present on mainland New Zealand, and this study provides the first detections of remains of these species in mammalian stomach contents.