Comparative phylogeography of three skink species (Oligosoma moco, O. smithi, O. suteri; Reptilia: Scincidae) in northeastern New Zealand

On the sand and among the crowds: a new species of Woodworthia gecko (Reptilia: Diplodactylidae) from Auckland, Aotearoa/ New Zealand

Woodworthia is a diverse genus of diplodactylid geckos found in Aotearoa/ New Zealand, with 17 likely species. Despite this diversity, only two species have been formally described: Woodworthia maculata (Gray, 1845) and W. chrysosiretica (Robb, 1980). In this paper, we use an integrated taxonomic approach to describe a new species of Woodworthia gecko, Woodworthia korowai sp. nov., found along the western coastline of the Auckland Region, New Zealand. Although this species occurs in duneland habitat behind a popular beach near New Zealands most populated city, it was only recognised as a distinct taxon in 2016. We describe W. korowai sp. nov. based on a suite of morphological character states and substantial genetic divergence, based on the mitochondrial NADH dehydrogenase subunit 2 (ND2) gene, that distinguish it from W. maculata sensu stricto and all other known species of Woodworthia. Phylogenetic reconstruction and molecular dating place it sister to the W. maculata group, with an estimated time of divergence in the mid to late Pliocene. This gecko is one of the most geographically restricted of all Woodworthia geckos, occupying an area of less than 500 km2 within the Auckland Region. Its narrow range and coastal association make it susceptible to environmental and genetic stochasticity. Furthermore, the popularity and recreational usage of the dune system threaten its habitat. Therefore, we hope that this description will bring attention to the value of coastal environments and the unique and sensitive duneland of Te Korowai-o-Te-Tonga/ South Kaipara Peninsula and Te Oneone Rangatira/ Muriwai Beach in particular and encourage conservation efforts to protect this newly described species and its habitat.

Oligosoma aureocola sp. nov. (Reptilia: Scincidae) from the northern Southland high country of Aotearoa/New Zealand

A species of diurnal skink from the Mataura Range and Mid Dome in central northern Southland, Aotearoa/New Zealand is described as Oligosoma aureocola sp. nov. It is a small species, coloured mid- to dark brown with smooth longitudinal stripes, and lives along rocky alpine ridges, low-stature shrublands, and tussock grasslands. This skink is a conspicuous species, easily sighted basking and foraging in talus or alpine plants such as golden spear grass (Aciphylla aurea).

Genetic divergence between isolated populations of the North Island New Zealand Rifleman (Acanthisitta chloris granti) implicates ancient biogeographic impacts rather than recent habitat fragmentation

This research investigates the extent and causal mechanisms of genetic population divergence in a poorly flighted passerine, the North Island Rifleman or Titipounamu (Acanthisitta chloris granti). While this species has a historically widespread distribution, anthropogenic forest clearance has resulted in a highly fragmented current distribution. We conducted analyses of mitochondrial DNA (COI and Control Region) and 12 nuclear DNA microsatellites to test for population divergence and estimate times of divergence. diyabc and biogeobears were then used to assess likely past dispersal scenarios based on both mtDNA and nDNA. The results reveal several significantly divergent lineages across the North Island of New Zealand and indicate that some populations have been isolated for extensive periods of time (0.7-4.9 mya). Modeling indicated a dynamic history of population connectivity, with a drastic restriction in gene flow between three geographic regions, followed by a more recent re-establishment of connectivity. Our analyses indicate the dynamic influence of key geological and climatological events on the distribution of genetic diversity in this species, including support for the genetic impact of old biogeographic boundaries such as the Taupo Line and Cockayne's Line, rather than recent anthropogenic habitat fragmentation. These findings present a rare example of an avian species with a genetic history more like that of flightless taxa and so provide new general insights into vicariant processes affecting populations of passerines with limited dispersal.

The role of ecological factors in determining phylogeographic and population genetic structure of two sympatric island skinks (Plestiodon kishinouyei and P. stimpsonii)

We conducted comparative phylogeographic and population genetic analyses of Plestiodon kishinouyei and P. stimpsonii, two sympatric skinks endemic to islands in the southern Ryukyus, to explore different factors that have influenced population structure. Previous phylogenetic studies using partial mitochondrial DNA indicate similar divergence times from their respective closest relatives, suggesting that differences in population structure are driven by intrinsic attributes of either species rather than the common set of extrinsic factors that both presumably have been exposed to throughout their history. In this study, analysis of mtDNA sequences and microsatellite polymorphism demonstrate contrasting patterns of phylogeography and population structure: P. kishinouyei exhibits a lower genetic variability and lower genetic differentiation among islands than P. stimpsonii, consistent with recent population expansion. However, historical demographic analyses indicate that the relatively high genetic uniformity in P. kishinouyei is not attributable to recent expansion. We detected significant isolation-by-distance patterns among P. kishinouyei populations on the land bridge islands, but not among P. stimpsonii populations occurring on those same islands. Our results suggest that P. kishinouyei populations have maintained gene flows across islands until recently, probably via ephemeral Quaternary land bridges. The lower genetic variability in P. kishinouyei may also indicate smaller effective population sizes on average than that of P. stimpsonii. We interpret these differences as a consequence of ecological divergence between the two species, primarily in trophic level and habitat preference.

Nest-site selection and the factors influencing hatching success and offspring phenotype in a nocturnal skink

Nest-site selection in ectothermic animals influences hatching success and offspring phenotype, and it is predicted that females should choose nesting sites that maximise their reproductive fitness, ultimately through the reproductive success of their offspring. We completed nest-site choice experiments on a nocturnal lizard, the egg-laying skink (Oligosoma suteri), to determine whether eggs (and subsequent hatchlings) from cooler nests do better at cooler incubation temperatures, and conversely if those laid in warmer nests perform better at warmer incubation temperatures. We provided a simple nest-choice experiment, with oviposition-retreat sites available in either a hot or a cool sector of the enclosure; in the wild females nest under objects. Female O. suteri laid eggs both during the day and night, and nested more in the hot than cool sector. Eggs from each clutch were split across three egg incubation temperatures (18°C, 22°C, 26°C) to decouple the impact of initial nest-site choice from the subsequent incubation temperature regime. Whether eggs were initially laid in the hot or cool sector was not related to hatching success, offspring phenotype or offspring locomotor performance. We conclude that offspring phenotype and performance is primarily influenced by the temperature during incubation, rather than the initial thermal environment of the nest location. Thus, female O. suteri may select warmer nesting sites to ensure higher incubation temperature and enhanced offspring fitness.

A retrospective approach to testing the DNA barcoding method

A decade ago, DNA barcoding was proposed as a standardised method for identifying existing species and speeding the discovery of new species. Yet, despite its numerous successes across a range of taxa, its frequent failures have brought into question its accuracy as a short-cut taxonomic method. We use a retrospective approach, applying the method to the classification of New Zealand skinks as it stood in 1977 (primarily based upon morphological characters), and compare it to the current taxonomy reached using both morphological and molecular approaches. For the 1977 dataset, DNA barcoding had moderate-high success in identifying specimens (78-98%), and correctly flagging specimens that have since been confirmed as distinct taxa (77-100%). But most matching methods failed to detect the species complexes that were present in 1977. For the current dataset, there was moderate-high success in identifying specimens (53-99%). For both datasets, the capacity to discover new species was dependent on the methodological approach used. Species delimitation in New Zealand skinks was hindered by the absence of either a local or global barcoding gap, a result of recent speciation events and hybridisation. Whilst DNA barcoding is potentially useful for specimen identification and species discovery in New Zealand skinks, its error rate could hinder the progress of documenting biodiversity in this group. We suggest that integrated taxonomic approaches are more effective at discovering and describing biodiversity.

Phylogeography of the endangered Otago skink, Oligosoma otagense: population structure, hybridisation and genetic diversity in captive populations

Climatic cooling and substantial tectonic activity since the late Miocene have had a pronounced influence on the evolutionary history of the fauna of New Zealand's South Island. However, many species have recently experienced dramatic range reductions due to habitat fragmentation and the introduction of mammalian predators and competitors. These anthropogenic impacts have been particularly severe in the tussock grasslands of the Otago region. The Otago skink (Oligosoma otagense), endemic to the region, is one of the most critically endangered vertebrates in New Zealand. We use mitochondrial DNA sequence data to investigate the evolutionary history of the Otago skink, examine its population genetic structure, and assess the level of genetic diversity in the individuals in the captive breeding program. Our data indicate that the Otago skink diverged from its closest relatives in the Miocene, consistent with the commencement of tectonic uplift of the Southern Alps. However, there is evidence for past introgression with the scree skink (O. waimatense) in the northern Otago-southern Canterbury region. The remnant populations in eastern Otago and western Otago are estimated to have diverged in the mid-Pliocene, with no haplotypes shared between these two regions. This divergence accounts for 95% of the genetic diversity in the species. Within both regions there is strong genetic structure among populations, although shared haplotypes are generally evident between adjacent localities. Although substantial genetic diversity is present in the captive population, all individuals originate from the eastern region and the majority had haplotypes that were not evident in the intensively managed populations at Macraes Flat. Our data indicate that eastern and western populations should continue to be regarded as separate management units. Knowledge of the genetic diversity of the breeding stock will act to inform the captive management of the Otago skink and contribute to a key recovery action for the species.

Comparative phylogeography of two closely related Viola species occurring in contrasting habitats in the Japanese archipelago

Similar distribution ranges shared by closely related plant species may have been shaped through different migration histories if those species have differing habitat preference. To test this hypothesis, phylogeographical patterns and population genetic structures were compared between two sister Viola species: Viola eizanensis preferring woodland and V. chaerophylloides var. sieboldiana preferring grassland, both being native to the Japanese Archipelago. Amplified fragment length polymorphism (AFLP) was used for phylogenetic reconstruction, together with Bayesian ancestry analysis, AMOVA, analysis of genetic diversity statistics, and analysis of the relative contribution of each population to total diversity. The results indicated that V. eizanensis had two distinct lineages occurring in the western and eastern part of Japan, but such lineages are not distinct in V. chaerophylloides var. sieboldiana. Both species exhibited the low genetic diversity and high between-population differentiation typical of selfing plants. In V. chaerophylloides var. sieboldiana, one particular population made a significantly higher contribution to the total heterozygosity (H (T)), whereas in V. eizanensis, no population was identified as making a particularly higher contribution to H (T). These findings suggest that V. eizanensis had been isolated in two large glacial refugia, whereas populations of V. chaerophylloides var. sieboldiana were restricted to a single small refuge. Different light requirements between these two closely related species probably caused these differing responses to climatic change during the last ice age.

Evolution of New Zealand's terrestrial fauna: a review of molecular evidence

New Zealand biogeography has been dominated by the knowledge that its geophysical history is continental in nature. The continental crust (Zealandia) from which New Zealand is formed broke from Gondwanaland ca 80 Ma, and there has existed a pervading view that the native biota is primarily a product of this long isolation. However, molecular studies of terrestrial animals and plants in New Zealand indicate that many taxa arrived since isolation of the land, and that diversification in most groups is relatively recent. This is consistent with evidence for species turnover from the fossil record, taxonomic affinity, tectonic evidence and observations of biological composition and interactions. Extinction, colonization and speciation have yielded a biota in New Zealand which is, in most respects, more like that of an oceanic archipelago than a continent.

A SINE of restricted gene flow across the Alpine Fault: phylogeography of the New Zealand common skink (Oligosoma nigriplantare polychroma)

New Zealand has experienced a complex climatic and geological history since the Pliocene. Thus, identifying the processes most important in having driven the evolution of New Zealand's biota has proven difficult. Here we examine the phylogeography of the New Zealand common skink (Oligosoma nigriplantare polychroma) which is distributed throughout much of New Zealand and crosses many putative biogeographical boundaries. Using mitochondrial DNA sequence data, we revealed five geographically distinct lineages that are highly differentiated (pairwise Phi(ST) 0.54-0.80). The phylogeographical pattern and inferred age of the lineages suggests Pliocene mountain building along active fault lines promoted their divergence 3.98-5.45 million years ago. A short interspersed nuclear element (SINE) polymorphism in the myosin gene intron (MYH-2) confirmed a pattern of restricted gene flow between lineages on either side of the mountain ranges associated with the Alpine Fault that runs southwest to northeast across the South Island of New Zealand. An analysis of molecular variance confirmed that approximately 40% of the genetic differentiation in O. n. polychroma is distributed across this major fault line. The straits between the main islands of New Zealand accounted for much less of the variation found within O. n. polychroma, most likely due to the repeated existence of landbridges between islands during periods of the Pleistocene that allowed migration. Overall, our findings reveal the relative roles of different climatic and geological processes, and in particular, demonstrate the importance of the Alpine Fault in the evolution of New Zealand's biota.

Origin and post-colonization evolution of the Chatham Islands skink (Oligosoma nigriplantare nigriplantare)

Island ecosystems provide an opportunity to examine a range of evolutionary and ecological processes. The Chatham Islands are an isolated archipelago situated approximately 800 km east of New Zealand. Geological evidence indicates that the Chatham Islands re-emerged within the last 1-4 million years, following a prolonged period of marine inundation, and therefore the resident flora and fauna is the result of long-distance overwater dispersal. We examine the origin and post-colonization evolution of the Chatham Islands skink, Oligosoma nigriplantare nigriplantare, the sole reptile species occurring on the archipelago. We sampled O. n. nigriplantare from across nine islands within the Chatham Islands group, and representative samples from across the range of its closest relative, the New Zealand mainland common skink (Oligosoma nigriplantare polychroma). Our mitochondrial sequence data indicate that O. n. nigriplantare diverged from O. n. polychroma 5.86-7.29 million years ago. This pre-dates the emergence date for the Chatham Islands, but indicates that O. n. nigriplantare colonized the Chatham Islands via overwater dispersal on a single occasion. Despite the substantial morphological variability evident in O. n. nigriplantare, only relatively shallow genetic divergences (maximum divergence approximately 2%) were found across the Chatham Islands. Our analyses (haplotypic diversity, Phi(ST), analysis of molecular variance, and nested clade phylogeographical analysis) indicated restricted gene flow in O. n. nigriplantare resulting in strong differentiation between islands. However, the restrictions to gene flow might have only arisen recently as there was also a significant pattern of isolation by distance, possibly from when the Chatham Islands were a single landmass during Pleistocene glacial maxima when sea levels were lower. The level of genetic and morphological divergence between O. n. nigriplantare and O. n. polychroma might warrant their recognition as distinct species.