Ancient DNA from the extinct New Zealand grayling (Prototroctes oxyrhynchus) reveals evidence for Miocene marine dispersal

The evolutionary history of Southern Hemisphere graylings (Retropinnidae) in New Zealand (NZ), including their relationship to the Australian grayling, is poorly understood. The NZ grayling (Prototroctes oxyrhynchus) is the only known fish in NZ to have gone extinct since human arrival there. Despite its historical abundance, only 23 wet and dried, formalin-fixed specimens exist in museums. We used high-throughput DNA sequencing to generate mitogenomes from formalin-fixed P. oxyrhynchus specimens, and analysed these in a temporal phylogenetic framework of retropinnids and osmerids. We recovered a strong sister-relationship between NZ and Australian grayling (P. mareana), with a common ancestor ~13.8 Mya [95% highest posterior density (HPD): 6.1–23.2 Mya], after the height of Oligocene marine inundation in NZ. Our temporal phylogenetic analysis suggests a single marine dispersal between NZ and Australia, although the direction of dispersal is equivocal, followed by divergence into genetically and morphologically distinguishable species through isolation by distance. This study provides further insights into the possible extinction drivers of the NZ grayling, informs discussion regarding reintroduction of Prototroctes to NZ and highlights how advances in palaeogenetics can be used to test evolutionary hypotheses in fish, which, until relatively recently, have been comparatively neglected in ancient-DNA research.

Application of palaeogenetic techniques to historic mollusc shells reveals phylogeographic structure in a New Zealand abalone

Natural history collections worldwide contain a plethora of mollusc shells. Recent studies have detailed the sequencing of DNA extracted from shells up to thousands of years old and from various taphonomic and preservational contexts. However, previous approaches have largely addressed methodological rather than evolutionary research questions. Here we report the generation of DNA sequence data from mollusc shells using such techniques, applied to Haliotis virginea Gmelin, 1791, a New Zealand abalone, in which morphological variation has led to the recognition of several forms and subspecies. We successfully recovered near-complete mitogenomes from 22 specimens including 12 dry-preserved shells up to 60 years old. We used a combination of palaeogenetic techniques that have not previously been applied to shell, including DNA extraction optimized for ultra-short fragments and hybridization-capture of single-stranded DNA libraries. Phylogenetic analyses revealed three major, well-supported clades comprising samples from: 1) the Three Kings Islands; 2) the Auckland, Chatham and Antipodes Islands; and 3) mainland New Zealand and Campbell Island. This phylogeographic structure does not correspond to the currently recognized forms. Critically, our non-reliance on freshly collected or ethanol-preserved samples enabled inclusion of topotypes of all recognized subspecies as well as additional difficult-to-sample populations. Broader application of these comparatively cost-effective and reliable methods to modern, historical, archaeological and palaeontological shell samples has the potential to revolutionize invertebrate genetic research.

Skeletal variation in extant species enables systematic identification of New Zealand's large, subfossil diplodactylids

New Zealand’s diplodactylid geckos exhibit high species-level diversity, largely independent of discernible osteological changes. Consequently, systematic affinities of isolated skeletal elements (fossils) are primarily determined by comparisons of size, particularly in the identification of Hoplodactylus duvaucelii, New Zealand’s largest extant gecko species. Here, three-dimensional geometric morphometrics of maxillae (a common fossilized element) was used to determine whether consistent shape and size differences exist between genera, and if cryptic extinctions have occurred in subfossil ‘Hoplodactylus cf. duvaucelii’. Sampling included 13 diplodactylid species from five genera, and 11 Holocene subfossil ‘H. cf. duvaucelii’ individuals. We found phylogenetic history was the most important predictor of maxilla morphology among extant diplodactylid genera. Size comparisons could only differentiate Hoplodactylus from other genera, with the remaining genera exhibiting variable degrees of overlap. Six subfossils were positively identified as H. duvaucelii, confirming their proposed Holocene distribution throughout New Zealand. Conversely, five subfossils showed no clear affinities with any modern diplodactylid genera, implying either increased morphological diversity in mainland ‘H. cf. duvaucelii’ or the presence of at least one extinct, large, broad-toed diplodactylid species.