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

A global biogeographic regionalization for butterflies

The partitioning of global biodiversity into biogeographic regions is critical for understanding the impacts of global-scale ecological and evolutionary processes on species assemblages as well as prioritizing areas for conservation. However, the lack of globally comprehensive data on species distributions precludes fine-scale estimation of biogeographical regionalization for numerous taxa of ecological, economic and conservation interest. Using a recently published phylogeny and novel curated native range maps for over 10 000 species of butterflies around the world, we delineated biogeographic regions for the world's butterflies using phylogenetic dissimilarity. We uncovered 19 distinct phylogenetically delimited regions (phyloregions) nested within 6 realms. Regional boundaries were predicted by spatial turnover in modern-day temperature and precipitation seasonality, but historical climate change also left a pronounced fingerprint on deeper- (realm-) level boundaries. We use a culturally and ecologically important group of insects to expand our understanding of how historical and contemporary factors drive the distribution of organismal lineages on the Earth. As insects and global biodiversity more generally face unprecedented challenges from anthropogenic factors, our research provides the groundwork for prioritizing regions and taxa for conservation, especially with the goal of preserving the legacies of our biosphere's evolutionary history.This article is part of the discussion meeting issue 'Bending the curve towards nature recovery: building on Georgina Mace's legacy for a biodiverse future'.

Fossil-calibrated phylogenies of Southern cave wētā show dispersal and extinction confound biogeographic signal

The biota of continents and islands are commonly considered to have a source-sink relationship, but small islands can harbour distinctive taxa. The distribution of four monotypic genera of Orthoptera on young subantarctic islands indicates a role for long-distance dispersal and extinction. Phylogenetic relationships were inferred from whole mtDNA genomes and nuclear sequences (45S cassette; four histones). We used a fossil and one palaeogeographic event to calibrate molecular clock analysis. We confirm that neither the Australian nor Aotearoa-New Zealand Rhaphidophoridae faunas are monophyletic. The radiation of Macropathinae may have begun in the late Jurassic, but trans-oceanic dispersal is required to explain the current distribution of some lineages within this subfamily. Dating the most recent common ancestor of seven island endemic species with their nearest mainland relative suggests that each existed long before their island home was available. Time estimates from our fossil-calibrated molecular clock analysis suggest several lineages have not been detected on mainland New Zealand, Australia, or elsewhere most probably due to their extinction, providing evidence that patterns of extinction, which are not consistently linked to range size or lineage age, confound biogeographic signal.

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.

A National Catalogue of Viruses Associated with Indigenous Species Reveals High-Throughput Sequencing as a Driver of Indigenous Virus Discovery

Viruses are important constituents of ecosystems, with the capacity to alter host phenotype and performance. However, virus discovery cued by disease symptoms overlooks latent or beneficial viruses, which are best detected using targeted virus detection or discovered by non-targeted methods, e.g., high-throughput sequencing (HTS). To date, in 64 publications, 701 viruses have been described associated with indigenous species of Aotearoa New Zealand. Viruses were identified in indigenous birds (189 viruses), bats (13 viruses), starfish (4 viruses), insects (280 viruses), and plants (126 viruses). HTS gave rise to a 21.9-fold increase in virus discovery rate over the targeted methods, and 72.7-fold over symptom-based methods. The average number of viruses reported per publication has also increased proportionally over time. The use of HTS has driven the described national virome recently by 549 new-to-science viruses; all are indigenous. This report represents the first catalogue of viruses associated with indigenous species of a country. We provide evidence that the application of HTS to samples of Aotearoa New Zealand's unique fauna and flora has driven indigenous virus discovery, a key step in the process to understand the role of viruses in the biological diversity and ecology of the land, sea, and air environments of a country.

Genome-wide patterns of genetic diversity, population structure and demographic history in mānuka (Leptospermum scoparium) growing on indigenous Māori land

Leptospermum scoparium J. R. Forst et G. Forst, known as mānuka by Māori, the indigenous people of Aotearoa (New Zealand), is a culturally and economically significant shrub species, native to New Zealand and Australia. Chemical, morphological and phylogenetic studies have indicated geographical variation of mānuka across its range in New Zealand, and genetic differentiation between New Zealand and Australia. We used pooled whole genome re-sequencing of 76 L. scoparium and outgroup populations from New Zealand and Australia to compile a dataset totalling ~2.5 million SNPs. We explored the genetic structure and relatedness of L. scoparium across New Zealand, and between populations in New Zealand and Australia, as well as the complex demographic history of this species. Our population genomic investigation suggests there are five geographically distinct mānuka gene pools within New Zealand, with evidence of gene flow occurring between these pools. Demographic modelling suggests three of these gene pools have undergone expansion events, whilst the evolutionary histories of the remaining two have been subjected to contractions. Furthermore, mānuka populations in New Zealand are genetically distinct from populations in Australia, with coalescent modelling suggesting these two clades diverged ~9-12 million years ago. We discuss the evolutionary history of this species and the benefits of using pool-seq for such studies. Our research will support the management and conservation of mānuka by landowners, particularly Māori, and the development of a provenance story for the branding of mānuka based products.

Patterns of diversification of the operculate land snail genus Cyclophorus (Caenogastropoda: Cyclophoridae) on the Ryukyu Islands, Japan

The Ryukyu Islands, an island chain in southwestern Japan, originated from land masses that separated from the Eurasian continent due to the formation of sea barriers about 1.55 million years ago. In this study, we investigated the phylogenetic relationships of the operculate land snail genus Cyclophorus (Caenogastropoda: Cyclophoridae) in the Ryukyu Archipelago and surrounding regions based on DNA sequence data. According to our results, all studied Cyclophorus specimens from Japan form a monophyletic group containing eight subclades. Six of these subclades were found only on the Ryukyu Islands. On most islands of the Ryukyu Archipelago, no more than one Cyclophorus subclade was recorded, which may be due to limited ecological niche space and competition. No subclade was found to occur on both sides of the Watase Line, a regional zoogeographical boundary. Divergence times were estimated based on a time-calibrated phylogeny. We found that multiple splits among the Japanese Cyclophorus subclades predate the emergence of major sea barriers in the Ryukyu Archipelago. Vicariance due to sea barrier formation, as assumed for many other taxa from the region, was thus likely not the main driver for subclade divergence in these snails. Instead, certain geographical features might have shaped the diversification of subclades prior to sea barrier formation. Given that Cyclophorus populations were also present on islands that have never been connected to other land masses, the snails must have colonized them via oversea dispersal. As not all nominal taxa corresponded to monophyletic groups, our molecular phylogenetic approach revealed that a taxonomic revision of the Japanese Cyclophorus fauna is necessary. The eight subclades may be regarded as potential species-level groups based on COI p-distances. A canonical discriminant analysis using shell morphological data revealed slight differences among the subclades.

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.

Phylogeny, systematics and rarity assessment of New Zealand endemic Saphydrus beetles and related enigmatic larvae (Coleoptera : Hydrophilidae : Cylominae)

The New Zealand endemic beetle genus Saphydrus Sharp, 1884 (Coleoptera:Hydrophilidae:Cylominae) is studied in order to understand its phylogenetic position, species-level systematics, biology and distribution, and to reveal reasons for its rarity. The first complete genus-level phylogeny of Cylominae based on two mitochondrial (cox1, 16S) and two nuclear genes (18S, 28S) covering 18 of 19 genera of the subfamily reveals Saphydrus as an isolated lineage situated in a clade with Cylorygmus (South America), Relictorygmus (South Africa) and Eurygmus (Australia). DNA is used to associate two larval morphotypes with Saphydrus: one of them represents the larvae of S. suffusus Sharp, 1884; the other, characterised by unique characters of the head and prothorax morphology, is revealed as sister but not closely related to Saphydrus. It is described here as Enigmahydrus, gen. nov. with a single species, E. larvalis, sp. nov., whose adult stage remains unknown. Saphydrus includes five species, two of which (S. moeldnerae, sp. nov. and S. tanemahuta, sp. nov.) are described as new. Larvae of Enigmahydrus larvalis and Saphydrus suffusus are described and illustrated in detail based on DNA-identified specimens. Candidate larvae for Saphydrus obesus Sharp, 1884 and S. tanemahuta are illustrated and diagnosed. Specimen data are used to evaluate the range, altitudinal distribution, seasonality and population dynamics over time for all species. Strongly seasonal occurrence of adults combined with other factors (winter occurrence in S. obesus, occurrence at high altitudes in S. tanemahuta) is hypothesised as the primary reason of the rarity for Saphydrus species. By contrast, Enigmahydrus larvalis underwent a strong decline in population number and size since the 1970s and is currently known from a single, locally limited population; we propose the ‘nationally threatened’ status for this species. http://zoobank.org/urn:lsid:zoobank.org:pub:28D87163-29E8-418C-9380-262D3038023A

Phase change and flowering in woody plants of the New Zealand flora

Heteroblastic and homoblastic woody plants from the New Zealand flora provide a rich playground for testing hypotheses relating to phase change and flowering.

Insights into the molecular phylogeny of Rhaphidophoridae, an ancient, worldwide lineage of Orthoptera

We investigated the molecular phylogenetic divergence and historical biogeography of cave crickets belonging to the family Rhaphidophoridae (Orthoptera, Ensifera). We used taxa representative of most of the regions embraced by the family, considering samples of Macropathinae from Gondwana land (i.e., Tasmania, Australia, New Zealand, South Africa, and South America); Aemodogryllinae and Rhaphidophorinae from Southern-eastern Asia (i.e., India, Bhutan, China, Philippines and the Sulawesi islands); Dolichopodainae and Troglophilinae from the Mediterranean region and Ceuthophilinae from North America. Based on previous papers, we carried out an analysis of both mitochondrial and nuclear DNA sequences considering the ribosomal RNA units 12S, 16S, 18S, and 28S. To reconstruct phylogeny, we use cladistics, Maximum Likelihood (ML), and Bayesian analyses. All phylogenetic analyses showed the same highly supported topology generally congruent with the classical systematic arrangement at the level of each sub-family but strongly disagree with previous affinity hypotheses between sub-families based on morphological characters. Our results reveal a close affinity between Asiatic and Gondwanian taxa from one hand and between North American and Mediterranean ones from the other hand. Dating estimates indicated that Rhaphidophoridae originated in the Cretaceous period during the Mesozoic era with the ancestral area located both in the northern and southern hemisphere. A possible biogeographic scenario, reconstructed using S-DEC with RASP software, suggested that the current distribution of Rhaphidophoridae might be explained by a combination of both dispersal and vicariance events occurred especially in the ancestral populations. The radiation of Rhaphidophoridae started within the Pangaea, where the ancestor of Rhaphidophoridae occurred throughout an ancestral area including Australia, North America, and the Mediterranean region. The opening of the Atlantic Ocean promoted the divergence of North American and Mediterranean lineages while the differentiation of the southern lineages, spread from Australia, appears to be related to the fragmentation of Gondwana land.

DNA barcoding a unique avifauna: an important tool for evolution, systematics and conservation

BACKGROUND

DNA barcoding utilises a standardised region of the cytochrome c oxidase I (COI) gene to identify specimens to the species level. It has proven to be an effective tool for identification of avian samples. The unique island avifauna of New Zealand is taxonomically and evolutionarily distinct. We analysed COI sequence data in order to determine if DNA barcoding could accurately identify New Zealand birds.

RESULTS

We sequenced 928 specimens from 180 species. Additional Genbank sequences expanded the dataset to 1416 sequences from 211 of the estimated 236 New Zealand species. Furthermore, to improve the assessment of genetic variation in non-endemic species, and to assess the overall accuracy of our approach, sequences from 404 specimens collected outside of New Zealand were also included in our analyses. Of the 191 species represented by multiple sequences, 88.5% could be successfully identified by their DNA barcodes. This is likely a conservative estimate of the power of DNA barcoding in New Zealand, given our extensive geographic sampling. The majority of the 13 groups that could not be distinguished contain recently diverged taxa, indicating incomplete lineage sorting and in some cases hybridisation. In contrast, 16 species showed evidence of distinct intra-species lineages, some of these corresponding to recognised subspecies. For species identification purposes a character-based method was more successful than distance and phylogenetic tree-based methods.

CONCLUSIONS

DNA barcodes accurately identify most New Zealand bird species. However, low levels of COI sequence divergence in some recently diverged taxa limit the identification power of DNA barcoding. A small number of currently recognised species would benefit from further systematic investigations. The reference database and analysis presented will provide valuable insights into the evolution, systematics and conservation of New Zealand birds.

Unintentional rewilding: lessons for trophic rewilding from other forms of species introductions

Trophic rewilding involves adding species into ecosystems to restore extinct, top-down interactions, but limited quantitative data have prevented a systematic attempt to quantify its outcomes. Here, we exploit species introductions that have occurred for purposes other than restoration to inform trophic rewilding. We compiled 51 studies with 158 different responses of lower trophic levels to a species introduction that restored an extinct interaction, whether it intended to do so or not. Unintentional introductions were compared with checklists of extinct animals to identify potential analogues. Using the latest meta-analysis techniques, we found that the few cases of intentional rewilding had similar effects to unintentional rewilding, though there were large taxonomic and geographical biases. We also tested predictions from studies on trophic cascades about the factors that should influence rewilding. Unintentional rewilding was stronger where introduced consumers were non-invasive, but there was no effect of time that compared sites differed in introduction status, latitude or coevolution of responses with a taxonomically related analogue. Our study now shows that rewilding can reinstate extinct trophic interactions and highlights remaining data gaps that need closure to restore ecosystems across larger scales than has been previously possible.This article is part of the theme issue 'Trophic rewilding: consequences for ecosystems under global change'.

First detection of Wolbachia in the New Zealand biota

Wolbachia is one of the most widespread intracellular bacteria on earth, estimated to infect between 40 and 66% of arthropod species in most ecosystems that have been surveyed. Their significance rests not only in their vast distribution, but also in their ability to modify the reproductive biology of their hosts, which can ultimately affect genetic diversity and speciation of infected populations. Wolbachia has yet to be formally identified in the fauna of New Zealand which has high levels of endemic biodiversity and this represents a gap in our understanding of the global biology of Wolbachia. Using High Throughput Sequencing (HTS) of host DNA in conjunction with traditional molecular techniques we identified six endemic Orthoptera species that were positive for Wolbachia infection. In addition, short-sequence amplification with Wolbachia specific primers applied to New Zealand and introduced invertebrates detected a further 153 individuals positive for Wolbachia. From these short-range DNA amplification products sequence data was obtained for the ftsZ gene region from 86 individuals representing 10 host species. Phylogenetic analysis using the sequences obtained in this study reveals that there are two distinct Wolbachia bacteria lineages in New Zealand hosts belonging to recognised Wolbachia supergroups (A and B). These represent the first described instances of Wolbachia in the New Zealand native fauna, including detection in putative parasitoids of infected Orthoptera suggesting a possible transmission path. Our detection of Wolbachia infections of New Zealand species provides the opportunity to study local transmission of Wolbachia and explore their role in the evolution of New Zealand invertebrates.

A revised phylogeny of macropathine cave crickets (Orthoptera: Rhaphidophoridae) uncovers a paraphyletic Australian fauna

Australian cave crickets are members of the subfamily Macropathinae (Orthoptera: Rhaphidophoridae). The subfamily is thought to have originated prior to the tectonic separation of the supercontinent Gondwana based on distributions of extant lineages and molecular phylogenetic evidence, although the Australian fauna have been underrepresented in previous studies. The current study augments existing multigene data (using 12S, 16S, and 28S rRNA genes) to investigate the placement of the Australian representatives within the Macropathinae and to assess divergence dates of select clades. Results suggest that the endemic Tasmanian genus Parvotettix is the sister lineage to the remaining members of the subfamily, an outcome that presents a paraphyletic Australian fauna in contrast to previous studies. All other Australian taxa represented in this study (Micropathus and Novotettix) emerged as a sister group to the New Zealand and South American macropathine lineages. Estimation of phylogenetic divergence ages among the aforementioned clades were calibrated using two methods, in absence of suitable fossil records: (i) tectonic events depicting the fragmentation of Gondwanan landmasses that invoke vicariant scenarios of present day geographic distributions; and (ii) molecular evolutionary rates. Geological calibrations place the median age of the most recent common ancestor of extant macropathines at ∼125 to ∼165 Ma, whereas analyses derived from molecular substitution rates suggest a considerably younger origin of ∼32 Ma. This phylogenetic study represents the most rigorous taxonomic sampling of the Australian cave cricket fauna to date and stresses the influence of lineage representation on biogeographic inference.

Was Charles Darwin right in his explanation of the ‘abominable mystery’?

The site and time of origin of angiosperms are still debated. The co-occurrence of many of the early branching lineages of flowering plants in a region somewhere between Australia and the SW Pacific islands suggests a possible Gondwanan origin of angiosperms. The recent recognition of Zealandia, a 94% submerged continent in the east of Australia, could explain the discrepancy between molecular clocks and fossil records about the age of angiosperms, supporting the old Darwinian hypothesis of a “lost continent” to explain the “abominable mystery” regarding the origin and rapid radiation of flowering plants.

Was Charles Darwin right in his explanation of the ‘abominable mystery’?

The site and time of origin of angiosperms are still debated. The co-occurrence of many of the early branching lineages of flowering plants in a region somewhere between Australia and the SW Pacific islands suggests a possible Gondwanan origin of angiosperms. The recent recognition of Zealandia, a 94% submerged continent in the east of Australia, could explain the discrepancy between molecular clocks and fossil records about the age of angiosperms, supporting the old Darwinian hypothesis of a “lost continent” to explain the “abominable mystery” regarding the origin and rapid radiation of flowering plants.

A new, large-bodied omnivorous bat (Noctilionoidea: Mystacinidae) reveals lost morphological and ecological diversity since the Miocene in New Zealand

A new genus and species of fossil bat is described from New Zealand's only pre-Pleistocene Cenozoic terrestrial fauna, the early Miocene St Bathans Fauna of Central Otago, South Island. Bayesian total evidence phylogenetic analysis places this new Southern Hemisphere taxon among the burrowing bats (mystacinids) of New Zealand and Australia, although its lower dentition also resembles Africa's endemic sucker-footed bats (myzopodids). As the first new bat genus to be added to New Zealand's fauna in more than 150 years, it provides new insight into the original diversity of chiropterans in Australasia. It also underscores the significant decline in morphological diversity that has taken place in the highly distinctive, semi-terrestrial bat family Mystacinidae since the Miocene. This bat was relatively large, with an estimated body mass of ~40 g, and its dentition suggests it had an omnivorous diet. Its striking dental autapomorphies, including development of a large hypocone, signal a shift of diet compared with other mystacinids, and may provide evidence of an adaptive radiation in feeding strategy in this group of noctilionoid bats.

Does wing reduction influence the relationship between altitude and insect body size? A case study using New Zealand's diverse stonefly fauna

Researchers have long been intrigued by evolutionary processes that explain biological diversity. Numerous studies have reported strong associations between animal body size and altitude, but insect analyses have often yielded equivocal results. Here, we analyze a collection database of New Zealand's diverse endemic stonefly fauna (106 species across 21 genera) to test for relationships between altitude and plecopteran body size. This insect assemblage includes a variety of wing-reduced (26 spp) and fully winged (80 spp) taxa and covers a broad range of altitudes (0-2,000 m). We detected significant relationships between altitude and body size for wing-reduced, but not fully winged, stonefly taxa. These results suggest that, while the maintenance of flight apparatus might place a constraint on body size in some fully winged species, the loss of flight may free insects from this evolutionary constraint. We suggest that rapid switches in insect dispersal ability may facilitate rapid evolutionary shifts across a number of biological attributes and may explain the inconsistent results from previous macroecological analyses of insect assemblages.

Closing the gap: Avian lineage splits at a young, narrow seaway imply a protracted history of mixed population response

The evolutionary significance of spatial habitat gaps has been well recognized since Alfred Russel Wallace compared the faunas of Bali and Lombok. Gaps between islands influence population structuring of some species, and flightless birds are expected to show strong partitioning even where habitat gaps are narrow. We examined the population structure of the most numerous living flightless land bird in New Zealand, Weka (Gallirallus australis). We surveyed Weka and their feather lice in native and introduced populations using genetic data gathered from DNA sequences of mitochondrial genes and nuclear β-fibrinogen and five microsatellite loci. We found low genetic diversity among extant Weka population samples. Two genetic clusters were evident in the mtDNA from Weka and their lice, but partitioning at nuclear loci was less abrupt. Many formerly recognized subspecies/species were not supported; instead, we infer one subspecies for each of the two main New Zealand islands. Although currently range restricted, North Island Weka have higher mtDNA diversity than the more wide-ranging southern Weka. Mismatch and neutrality statistics indicate North Island Weka experienced rapid and recent population reduction, while South Island Weka display the signature of recent expansion. Similar haplotype data from a widespread flying relative of Weka and other New Zealand birds revealed instances of North Island-South Island partitioning associated with a narrow habitat gap (Cook Strait). However, contrasting patterns indicate priority effects and other ecological factors have a strong influence on spatial exchange at this scale.

Cryptic diversity and multiple origins of the widespread mayfly species group Baetis rhodani (Ephemeroptera: Baetidae) on northwestern Mediterranean islands

How the often highly endemic biodiversity of islands originated has been debated for decades, and it remains a fervid research ground. Here, using mitochondrial and nuclear gene sequence analyses, we investigate the diversity, phylogenetic relationships, and evolutionary history of the mayfly Baetis gr. rhodani on the three largest northwestern Mediterranean islands (Sardinia, Corsica, Elba). We identify three distinct, largely co‐distributed, and deeply differentiated lineages, with divergences tentatively dated back to the Eocene–Oligocene transition. Bayesian population structure analyses reveal a lack of gene exchange between them, even at sites where they are syntopic, indicating that these lineages belong to three putative species. Their phylogenetic relationships with continental relatives, together with the dating estimates, support a role for three processes contributing to this diversity: (1) vicariance, primed by microplate disjunction and oceanic transgression; (2) dispersal from the continent; and (3) speciation within the island group. Thus, our results do not point toward a prevailing role for any of the previously invoked processes. Rather, they suggest that a variety of processes equally contributed to shape the diverse and endemic biota of this group of islands.

The importance of replicating genomic analyses to verify phylogenetic signal for recently evolved lineages

Genomewide SNP data generated by nontargeted methods such as RAD and GBS are increasingly being used in phylogenetic and phylogeographic analyses. When these methods are used in the absence of a reference genome, however, little is known about the locations and evolution of the SNPs. In using such data to address phylogenetic questions, researchers risk drawing false conclusions, particularly if a representative number of SNPs is not obtained. Here, we empirically test the robustness of phylogenetic inference based on SNP data for closely related lineages. We conducted a genomewide analysis of 75 712 SNPs, generated via GBS, of southern bull-kelp (Durvillaea). Durvillaea chathamensis co-occurs with D. antarctica on Chatham Island, but the two species have previously been found to be so genetically similar that the status of the former has been questioned. Our results show that D. chathamensis, which differs from D. antarctica ecologically as well as morphologically, is indeed a reproductively isolated species. Furthermore, our replicated analyses show that D. chathamensis cannot be reliably distinguished phylogenetically from closely related D. antarctica using subsets (ranging in size from 400 to 10 000 sites) of the 40 912 parsimony-informative SNPs in our data set and that bootstrap values alone can give misleading impressions of the strength of phylogenetic inferences. These results highlight the importance of independently replicating SNP analyses to verify that phylogenetic inferences based on nontargeted SNP data are robust. Our study also demonstrates that modern genomic approaches can be used to identify cases of recent or incipient speciation that traditional approaches (e.g. Sanger sequencing of a few loci) may be unable to detect or resolve.

New alphacoronavirus in Mystacina tuberculata bats, New Zealand

Because of recent interest in bats as reservoirs of emerging diseases, we investigated the presence of viruses in Mystacina tuberculata bats in New Zealand. A novel alphacoronavirus sequence was detected in guano from roosts of M. tuberculata bats in pristine indigenous forest on a remote offshore island (Codfish Island).

Species radiation of carabid beetles (broscini: mecodema) in new zealand

New Zealand biodiversity has often been viewed as Gondwanan in origin and age, but it is increasingly apparent from molecular studies that diversification, and in many cases origination of lineages, postdate the break-up of Gondwanaland. Relatively few studies of New Zealand animal species radiations have as yet been reported, and here we consider the species-rich genus of carabid beetles, Mecodema. Constrained stratigraphic information (emergence of the Chatham Islands) and a substitution rate for Coleoptera were separately used to calibrate Bayesian relaxed molecular clock date estimates for diversification of Mecodema. The inferred timings indicate radiation of these beetles no earlier than the mid-Miocene with most divergences being younger, dating to the Plio-Pleistocene. A shallow age for the radiation along with a complex spatial distribution of these taxa involving many instances of sympatry implicates recent ecological speciation rather than a simplistic allopatric model. This emphasises the youthful and dynamic nature of New Zealand evolution that will be further elucidated with detailed ecological and population genetic analyses.

Colliding fragment islands transport independent lineages of endemic rock-crawlers (Grylloblattodea: Grylloblattidae) in the Japanese archipelago

Fragment islands, viewed from the paradigm of island biogeographic theory, depend on continual immigration from continental sources to maintain levels of species diversity, or otherwise undergo a period of relaxation where species diversity declines to a lower equilibrium. Japan is a recently derived fragment island with a rich endemic flora and fauna. These endemic species have been described as paleoendemics, and conversely as recently derived Pleistocene colonists. Geological events in the Miocene period, notably the fragmentation and collision of islands, and the subsequent uplift of mountains in central Japan, provided opportunities for genetic isolation. More recently, cyclical climatic change during the Pliocene and Pleistocene periods led to intermittent land bridge connections to continental Asia. Here we investigate the pattern and timing of diversification in a diverse endemic lineage in order to test whether ongoing migration has sustained species diversity, whether there is evidence of relaxation, and how geological and climatic events are associated with lineage diversification. Using multi-locus genetic data, we test these hypotheses in a poorly dispersing, cold-adapted terrestrial insect lineage (Grylloblattodea: Grylloblattidae) sampled from Japan, Korea, and Russia. In phylogenetic analyses of concatenated data and a species tree approach, we find evidence of three deeply divergent lineages of rock-crawlers in Japan consistent with the pattern of island fragmentation from continental Asia. Tests of lineage diversification rates suggest that relaxation has not occurred and instead endemism has increased in the Japanese Grylloblattidae following mountain-building events in the Miocene. Although the importance of climate change in generating species diversity is a commonly held paradigm in Japanese biogeography, our analyses, including analyses of demographic change and phylogeographic range shifts in putative species, suggests that Pleistocene climatic change has had a limited effect on the diversification of rock-crawlers.

Phylogeny, biogeography, and evolution of sex expression in the southern hemisphere genus Leptinella (Compositae, Anthemideae)

Leptinella is exceptional in the Anthemideae (Compositae) in its evolution of dimorphic sex expression. A molecular phylogeny including 40 of its 42 described taxa based on nucleotide sequences from two plastid regions (psbA-trnH and trnC-petN spacers) and one nuclear marker (nrDNA ITS) is presented. Phylogenetic reconstruction was hampered by inadequate phylogenetic signal indicating recent radiation of species during the last 5 Ma and high level of reticulate evolution presumably caused by hybridisation and polyploidisation. Nevertheless, Leptinella is nested within a paraphyletic genus Cotula that also engulfs the South American genus Soliva. Within Leptinella, the highly polyploid and sexually polymorphic subgenus Leptinella is monophyletic, while subgenus Oligoleima as well as subgenus Radiata are polyphyletic. We found a basal split between a lineage of Australian and New Guinean taxa and one of largely New Zealand taxa. At least five long-distance dispersal events have to be assumed in order to explain the distribution pattern in Leptinella. Among those, one is from New Zealand to Australia, while the others are dispersals to South America and to several subantarctic islands. The phylogeny presented here indicates that the ancestral sex expression in Leptinella is monoecy and that dioecy and paradioecy are derived conditions. High ploidy is especially common in the dioica-group, where dioecy is also common. However, the occurrence of a dioecious sex expression in tetraploid representatives of this group and of polyploidy in other clades that only exhibit monoecious or paradioecious conditions indicate that there is no consistent correlation between these two characters.

Towards a dynamic analysis of weighted networks in biogeography

An improvement to the Network Analysis Method (NAM) in Biogeography based on weighted inference and dynamic exploration of sympatry networks is proposed. Intricate distributions of species result in a reticulated structure of spatial associations. Species are geographically connected through sympatry links forming an overall natural network in biogeography. Spatial records are the signals that provide evidence to infer these sympatry links in the network. Punctual data are independent of a priori area determination. NAM is oriented to detect groups of species embedded into the global network that are internally sustained by sympatric cohesiveness but weakly connected (or disconnected) to outgroup entities. These groups, called units of co-occurrence (UCs), are segregated through the iterative removal of intermediary species according to their betweenness scores. Instances of analysis of the original NAM are improved through the following changes and extensions: (i) inference of weighted sympatry networks using new measures sensitive to the strength of overlap and topological resemblance between set of points; (ii) construction of a basal network discriminating major from minor sympatry associations; (iii) evaluation of the entire process of iterative removal of intermediary species for the selection of UCs found on different subnetworks; (iv) network partitioning based on the intrinsic cohesiveness of the UCs; (v) production of a graphical tool (cleavogram) depicting the structural changes of the network along the removal process. Improvements are tested using real and hypothetical data sets. Resolution of patterns is notably increased due to a more accurate recognition of allopatric patterns and the possibility of segregating spatially overlapped UCs. As in original NAM, spatial expressions of UCs are building blocks for biogeography supported by strictly endemic and connected species through sympatry paths.

Exploring Phylogeographic Congruence in a Continental Island System

A prediction in phylogeographic studies is that patterns of lineage diversity and timing will be similar within the same landscape under the assumption that these lineages have responded to past environmental changes in comparable ways. Eight invertebrate taxa from four different orders were included in this study of mainland New Zealand and Chatham Islands lineages to explore outcomes of island colonization. These comprised two orthopteran genera, one an endemic forest-dwelling genus of cave weta (Rhaphidophoridae, Talitropsis) and the other a grasshopper (Acrididae, Phaulacridum) that inhabits open grassland; four genera of Coleoptera including carabid beetles (Mecodema), stag beetles (Geodorcus), weevils (Hadramphus) and clickbeetles (Amychus); the widespread earwig genus Anisolabis (Dermaptera) that is common on beaches in New Zealand and the Chatham Islands, and an endemic and widespread cockroach genus Celatoblatta (Blattodea). Mitochondrial DNA data were used to reconstruct phylogeographic hypotheses to compare among these taxa. Strikingly, despite a maximum age of the Chathams of ∼4 million years there is no concordance among these taxa, in the extent of genetic divergence and partitioning between Chatham and Mainland populations. Some Chatham lineages are represented by insular endemics and others by haplotypes shared with mainland populations. These diverse patterns suggest that combinations of intrinsic (taxon ecology) and extrinsic (extinction and dispersal) factors can result in apparently very different biogeographic outcomes.

The Invertebrate Life of New Zealand: A Phylogeographic Approach

Phylogeography contributes to our knowledge of regional biotas by integrating spatial and genetic information. In New Zealand, comprising two main islands and hundreds of smaller ones, phylogeography has transformed the way we view our biology and allowed comparison with other parts of the world. Here we review studies on New Zealand terrestrial and freshwater invertebrates. We find little evidence of congruence among studies of different taxa; instead there are signatures of partitioning in many different regions and expansion in different directions. A number of studies have revealed unusually high genetic distances within putative species, and in those where other data confirm this taxonomy, the revealed phylogeographic structure contrasts with northern hemisphere continental systems. Some taxa show a signature indicative of Pliocene tectonic events encompassing land extension and mountain building, whereas others are consistent with range expansion following the last glacial maximum (LGM) of the Pleistocene. There is some indication that montane taxa are more partitioned than lowland ones, but this observation is obscured by a broad range of patterns within the sample of lowland/forest taxa. We note that several geophysical processes make similar phylogeographic predictions for the same landscape, rendering confirmation of the drivers of partitioning difficult. Future multi-gene analyses where applied to testable alternative hypotheses may help resolve further the rich evolutionary history of New Zealand's invertebrates.