Abstract
The dynamic geology and climate of the New Zealand archipelago has had pronounced effects on the evolution of its endemic flora and fauna. However, contemporary biodiversity is depauperate, with previous studies revealing complex extinction-recolonization dynamics and cryptic extinctions following both Polynesian and European arrival. Hoplodactylus duvaucelii (Duvaucel’s gecko) is a large Diplodactylidae species, previously widespread throughout New Zealand (based on relative-size identification of Holocene subfossils), with extant populations restricted to predator-free offshore islands. This thesis uses integrated morphological and genetic approaches to reconstruct the taxonomic and phylogeographic diversity of New Zealand’s large geckos (‘H. cf. duvaucelii’) prior to Polynesian and European arrival. Geometric morphometrics (of three-dimensional micro-CT scans) was used to characterise and describe maxillae shape and size variation between extant genera (Dactylocnemis, Hoplodactylus, Mokopirirakau, Naultinus and Woodworthia), and to determine the taxonomic affinities of Holocene ‘H. cf. duvaucelii’ subfossils. All genera were morphologically distinct, with shape variation in the nasal and orbital margins primarily reflecting ecomorphological adaptation. However relative-size comparisons were only effective in distinguishing Hoplodactylus. Additionally, while some ‘H. cf. duvaucelii’ subfossils exhibited strong affinities towards H. duvaucelii, others possessed morphological variation not encompassed by extant representatives. Furthermore, ancient mitochondrial genomes recovered from Holocene ‘H. cf. duvaucelii’ subfossils using a minimally destructive DNA extraction method, were used to test for cryptic extinctions of large Holocene geckos, and to reconstruct phylogeographic structure in H. duvaucelii. All recovered ancient mitochondrial genomes were identified as H. duvaucelii, confirming their once widespread mainland distribution. Absence of large Holocene representatives outside Hoplodactylus implies gigantism evolved only once within the New Zealand Diplodactylidae radiation. Pronounced phylogeographic structure was identified within H. duvaucelii, with extant populations comprising two deeply divergent and morphologically distinct species: H. duvaucelii ‘North’ and H. duvaucelii ‘South’. This thesis provides the most comprehensive study of New Zealand’s Holocene subfossil geckos and highlights the applications of integrated geometric morphometric and ancient DNA analyses in taxonomy, biogeography and conservation of understudied fauna.