Going under down under? Lineage ages argue for extensive survival of the Oligocene marine transgression on Zealandia

New records of immature aquatic Diptera from the Foulden Maar Fossil-Lagerstätte, New Zealand, and their biogeographic implications

Background

The biogeographical and ecological history of true flies (Diptera) in New Zealand is little known due to a scarcity of fossil specimens. Here, we report a fauna of immature aquatic dipterans from freshwater diatomites of the early Miocene Foulden Maar Fossil-Lagerstätte in southern New Zealand.

Methods

We document 30 specimens of immature dipterans, mostly pupae, and compare their external morphology to extant aquatic Diptera. Based on the reconstructed paleoenvironment of Foulden Maar, we discuss taxonomic, ecological and taphonomic implications of this early Miocene fauna.

Results

Among Chironomidae, one pupal morphotype is attributed to Tanypodinae, one pupal morphotype and one larval morphotype are placed into Chironomus (Chironominae) and a further morphotype into Chironominae incertae sedis. Chaoboridae are represented by a pupal morphotype congeneric or very close to the extant Chaoborus, today globally distributed except for New Zealand. Additional immature specimens are likely larvae and puparia of brachyceran flies but cannot be identified to a narrower range. These finds document an aquatic dipteran fauna in New Zealand in the earliest Miocene and highlight Neogene extinction as a factor in shaping the extant Diptera fauna in New Zealand. Immature aquatic dipterans were a common and likely ecologically important component of the early Miocene Foulden Maar lake. Preservation of larvae and pupae may have been promoted by diatomaceous microbial mats and the light colour of the diatomite likely facilitated spotting of these minute fossils in the field.

Novel chromosomes and genomes provide new insights into evolution and adaptation of the whole genome duplicated yeast-like fungus TN3-1 isolated from natural honey

Aureobasidium melanogenum TN3-1 strain and A. melanogenum P16 strain were isolated from the natural honey and the mangrove ecosystem, respectively. The former can produce much higher pullulan from high concentration of glucose than the latter. In order to know what happened to their genomes, the PacBio sequencing and Hi-C technologies were used to create the first high-quality chromosome-level reference genome assembly of A. melanogenum TN3-1 (51.61 Mb) and A. melanogenum P16 (25.82 Mb) with the contig N50 of 2.19 Mb and 2.26 Mb, respectively. Based on the Hi-C results, a total of 93.33% contigs in the TN3-1 strain and 92.31% contigs in the P16 strain were anchored onto 24 and 12 haploid chromosomes, respectively. The genomes of the TN3-1 strain had two subgenomes A and B. Synteny analysis showed that the genomic contents of the two subgenomes were asymmetric with many structural variations. Intriguingly, the TN3-1 strain was revealed as a recent hybrid/fusion between the ancestor of A. melanogenum CBS105.22/CBS110374 and the ancestor of another unidentified strain of A. melanogenum similar to P16 strain. We estimated that the two ancient progenitors diverged around 18.38 Mya and merged around 10.66-9.98 Mya. It was found that in the TN3-1 strain, telomeres of each chromosome contained high level of long interspersed nuclear elements (LINEs), but had low level of the telomerase encoding gene. Meanwhile, there were high level of transposable elements (TEs) inserted in the chromosomes of the TN3-1 strain. In addition, the positively selected genes of the TN3-1 strain were mainly enriched in the metabolic processes related to harsh environmental adaptability. Most of the stress-related genes were found to be related to the adjacent LTRs, and the glucose derepression was caused by the mutation of the Glc7-2 in the Snf-Mig1 system. All of these could contribute to its genetic instability, genome evolution, high stress resistance, and high pullulan production from glucose.

Northern Richness, Southern Dead End-Origin and Dispersal Events of Pseudolycoriella (Sciaridae, Diptera) between New Zealand's Main Islands

Sciaridae (Diptera) is a widespread insect family of which some species can reach high abundances in arboreal habitats. This trait, together with their (passive) mobility, enables them to quickly colonise suitable habitats. To reveal the biogeographic history of the New Zealand members of the sciarid genus Pseudolycoriella, we analysed three molecular markers of selected species and populations in a Bayesian approach. At the intra- and interspecific levels, we detected a pattern of northern richness vs. southern purity, which has probably developed as a result of Pleistocene glacial cycles. Since the late Miocene, we identified 13 dispersal events across the sea strait separating New Zealand's main islands. As nine of these dispersal events were south-directed, North Island can be considered the centre of radiation for this genus. An unequivocal re-colonisation of North Island was only observed once. Based on the inclusion of three undescribed species from Tasmania and on previously published data, three colonisations of New Zealand are likely, all of them assumed to be of Australian origin. One of these most probably took place during the late Miocene, and the other two during the late Pliocene or at the Pliocene-Pleistocene boundary.

Mitogenomes resolve the phylogeography and divergence times within the endemic New Zealand Callaeidae (Aves: Passerida)

The biogeographical origins of the endemic birds of New Zealand (Aotearoa) are of great interest, particularly Palaeogene lineages such as Callaeidae, a passerine family characterized by brightly coloured wattles behind the beak and, in some cases, extreme sexual dimorphism in bill size and shape. Ancestral representatives of Callaeidae are thought to have split from their closest relatives outside New Zealand in the Oligocene, but little is known about the timing of divergences within the family. We present a fully dated molecular phylogeny of Callaeidae mitogenomes and discuss the biogeographical implications. Our results suggest that formation of Pliocene marine seaways, such as the Manawatu Strait, are likely to have played a significant role in the differentiation of North Island and South Island kōkako (Callaeas spp.) and saddlebacks/tīeke (Philesturnus spp.).

A dated phylogeny shows Plio-Pleistocene climates spurred evolution of antibrowsing defences in the New Zealand flora

Some plant traits may be legacies of coevolution with extinct megafauna. One example is the convergent evolution of 'divaricate' cage architectures in many New Zealand lineages, interpreted as a response to recently extinct flightless avian browsers whose ancestors arrived during the Paleogene period. Although experiments have confirmed that divaricate habit deters extant browsers, its abundance on frosty, droughty sites appears consistent with an earlier interpretation as a response to cold, dry Plio-Pleistocene climates. We used 45 protein-coding sequences from plastid genomes to reconstruct the evolutionary history of the divaricate habit in extant New Zealand lineages. Our dated phylogeny of 215 species included 91% of New Zealand eudicot divaricate species. We show that 86% of extant divaricate plants diverged from non-divaricate sisters within the last 5 Ma, implicating Plio-Pleistocene climates in the proliferation of cage architectures in New Zealand. Our results, combined with other recent findings, are consistent with the synthetic hypothesis that the browser-deterrent effect of cage architectures was strongly selected only when Plio-Pleistocene climatic constraints prevented woody plants from growing quickly out of reach of browsers. This is consistent with the abundance of cage architectures in other regions where plant growth is restricted by aridity or short frost-free periods.

The Contribution of Kurī (Polynesian Dog) to the Ecological Impacts of the Human Settlement of Aotearoa New Zealand

The pre-human Aotearoa New Zealand fauna was dominated by avian and reptilian species. Prior to first human settlement by East Polynesian colonists, the top predators were two giant raptorial birds. Aside from humans themselves, colonisation also resulted in the simultaneous introduction of two novel mammalian predators into this naive ecosystem, the kiore (Pacific rat) and kurī (Polynesian dog). While the ecological impacts of kiore are relatively well understood, those of kurī are difficult to assess, and as such kurī have frequently been disregarded as having any meaningful impact on New Zealand’s biodiversity. Here we use the archaeological and palaeoecological record to reassess the potential impacts of kurī on this ecosystem. We argue that far from being confined to villages, kurī could have had a significant widespread but relatively localised impact on New Zealand’s avian, reptilian and marine mammal (seals and sea lions) fauna as a novel predator of medium-sized species. In this way, kurī potentially amplified the already significant impacts of Polynesian colonists and their descendants on New Zealand’s ecosystem, prior to European arrival. As such, kurī should be included in models of human impact in addition to over-hunting, environmental modification and predation by kiore.

Global dispersal and diversification in ground beetles of the subfamily Carabinae

The origin and diversification process of lineages of organisms that are currently widely distributed among continents is an interesting subject for exploring the evolutionary history of global species diversity. Ground beetles of the subfamily Carabinae are flightless except for one lineage, but nevertheless occur on all continents except Antarctica. Here, we used sequence data from ultraconserved elements to reconstruct the phylogeny, divergence time, biogeographical history, ancestral state of hind wings and changes in the speciation rate of Carabinae. Our results show that Carabinae originated in the Americas and diversified into four tribes during the period from the late Jurassic to the late Cretaceous, with two in South America (Celoglossini) and Australasia (Pamborini) and two in Laurasia (Cychrini and Carabini). The ancestral Carabinae were inferred to be winged; three of four tribes (Cychrini, Ceglossini and Pamborini) have completely lost their hind wings and flight capability. The remaining tribe, Carabini, diverged into the subtribes Carabina (wingless) and Calosomina (winged) in the Oligocene. Carabina originated in Europe, spread over Eurasia and diversified into approximately 1000 species, accounting for around 60% of all Carabinae species. Calosomina that were flight-capable dispersed from North America or Eurasia to South America, Australia, and Africa, and then flightless lineages evolved on oceanic islands and continental highlands. The speciation rate increased in the Cychrini and Carabini clades in Eurasia. Within Carabini, the speciation rate was higher for wingless than winged states. Our study showed that the global distribution of Carabinae resulted from ancient dispersal before the breakup of Gondwana and more recent dispersal through flight around the world. These patterns consequently illustrate the causal relationships of geographical history, evolution of flightlessness, and the global distribution and species diversity of Carabinae.

Phylogeography of the endemic red-tailed cicadas of New Zealand (Hemiptera: Cicadidae: Rhodopsalta), and molecular, morphological and bioacoustical confirmation of the existence of Hudson’s Rhodopsalta microdora

Why do some genera radiate, whereas others do not? The genetic structure of present-day populations can provide clues for developing hypotheses. In New Zealand, three Cicadidae genera are depauperate [Amphipsalta (three species), Notopsalta (one species) and Rhodopsalta (three species)], whereas two have speciated extensively [Kikihia (~30 species/subspecies) and Maoricicada (~20 species/subspecies). Here, we examine the evolution of Rhodopsalta, the last New Zealand genus to be studied phylogenetically and phylogeographically. We use Bayesian and maximum-likelihood analyses of mitochondrial cox1 and nuclear EF1α gene sequences. Concatenated and single-gene phylogenies for 70 specimens (58 localities) support its monophyly and three described species: Rhodopsalta cruentata, Rhodopsalta leptomera and Rhodopsalta microdora, the last taxon previously regarded as uncertain. We provide distribution maps, biological notes and the first descriptions of diagnostic songs. We show that both R. cruentata and R. microdora exhibit northern and southern genetic subclades. Subclades of the dry-adapted R. microdora clade show geographical structure, whereas those of the mesic R. cruentata and sand-dune specialist R. leptomera have few discernible patterns. Genetic, bioacoustical and detailed distributional evidence for R. microdora add to the known biodiversity of New Zealand. We designate a lectotype for Tettigonia cruentata  Fabricius, 1775, the type species of Rhodopsalta.

Comparative phylogeography of two Agarophyton species in the New Zealand archipelago

Molecular studies have reported the coexistence of two species of Agarophyton in New Zealand: the newly described A.transtasmanicum with an apparently restricted distribution to some sites in the North Island, and the more widespread A.chilense. Here, we compared the distribution, genetic diversity, and structure of both Agarophyton species throughout the archipelago using sequences of the nuclear Internal Transcribed Spacer 2 (ITS2) marker. Agarophyton chilense's distribution was continuous and extensive along the North and South Islands, Stewart Island, and Chatham Island, and the genetic clusters were mostly concordant with boundaries between biogeographic regions. In contrast, specimens of A.transtasmanicum were collected in four sites broadly distributed in both the North and South Islands, with no clear spatial structure of the genetic diversity. Populations, where the species co-occurred, tended to display similar levels in genetic diversity for the two species. Demographic inferences supported a postglacial demographic expansion for two A.chilense genetic clusters, one present in the South Island and the eastern coast of the North Island, and the other present in northern South Island. A third genetic cluster located on the western coast of the North Island had a signature of long-term demographic stability. For A.transtasmanicum, the skyline plot also suggested a postglacial demographic expansion. Last, we developed a new molecular tool to quickly and easily distinguish between the two Agarophyton species, which could be used to ease future fine-scale population studies, especially in areas where the two species coexist.

Deep Macroevolutionary Impact of Humans on New Zealand's Unique Avifauna

Islands are at the frontline of the anthropogenic extinction crisis [1]. A vast number of island birds have gone extinct since human colonization [2], and an important proportion is currently threatened with extinction [3]. While the number of lost or threatened avian species has often been quantified [4], the macroevolutionary consequences of human impact on island biodiversity have rarely been measured [5]. Here, we estimate the amount of evolutionary time that has been lost or is under threat due to anthropogenic activity in a classic example, New Zealand. Half of its bird taxa have gone extinct since humans arrived [6, 7] and many are threatened [8], including lineages forming highly distinct branches in the avian tree of life [9-11]. Using paleontological and ancient DNA information, we compiled a dated phylogenetic dataset for New Zealand's terrestrial avifauna. We extend the method DAISIE developed for island biogeography [12] to allow for the fact that many of New Zealand's birds are evolutionarily isolated and use it to estimate natural rates of speciation, extinction, and colonization. Simulating under a range of human-induced extinction scenarios, we find that it would take approximately 50 million years (Ma) to recover the number of species lost since human colonization of New Zealand and up to 10 Ma to return to today's species numbers if currently threatened species go extinct. This study puts into macroevolutionary perspective the impact of humans in an isolated fauna and reveals how conservation decisions we take today will have repercussions for millions of years.

How ‘Gondwanan’ is Riethia? Molecular phylogenetics elucidates the mode and tempo of diversification in Austro-Pacific Chironominae (Diptera)

Riethia Kieffer, a genus of the non-biting midge subfamily Chironominae (Diptera: Chironomidae) is distributed in Australia, New Zealand, New Caledonia and South America. This austral distribution could be due to earth history (vicariance) or from Southern Hemisphere dispersal(s). We obtained samples from each area, most intensively from throughout Australia. We included putative sister genus Pseudochironomus Malloch, many genera from tribe Tanytarsini, enigmatic taxa in Chironomini and conventional outgroups from other subfamilies. We assembled a multilocus molecular dataset for four genetic regions from 107 individuals to reconstruct the first dated molecular phylogeny for the group. Four terminal clusters corresponded to unreared (thus unassociated) larvae. Monophyly was supported for ‘core’ Riethia, Pseudochironomus, putative tribe Pseudochironomini, tribe Tanytarsini (including enigmatic Nandeva Wiedenbrug, Reiss & Fittkau) and subfamily Chironominae. All species are monophyletic except for R. cinctipes Freeman, which includes R. neocaledonica Cranston. Riethia zeylandica Freeman, previously thought to be widespread in eastern Australia, now is a New Zealand endemic with Australian specimens allocated now to several regionally restricted species. The origin of Riethia was at 60.6 Ma (‘core’) or 52.1 Ma depending on the relationship of two South American species. Both dates are before the break-up of South America and Australia. Diversification within crown group Riethia started before the Cretaceous–Paleogene boundary, with subsequent separation at 52 Ma of an Australian ‘clade I’ from its sister ‘clade II’, which comprises Australian, New Zealand and New Caledonian species. Inferred dates for species origins of New Caledonia and New Zealand taxa imply transoceanic dispersals from eastern Australia. Western Australian species diverged during the mid to late Miocene from their eastern Australian sister taxa. This correlates with the onset of drying of Australia and the separation of mesic east from west by the formation of an arid proto-Nullarbor. Taken together, the inferred tempo of diversification in the group included both older ages reflecting earth history, yet with suggested recent intra-Pacific separations due to transoceanic dispersals.

Molecular phylogeny and biogeography of the temperate Gondwanan family Triaenonychidae (Opiliones : Laniatores) reveals pre-Gondwanan regionalisation, common vicariance, and rare dispersal

Triaenonychidae Sørensen in L. Koch, 1886 is a large family of Opiliones with ~480 described species broadly distributed across temperate forests in the Southern Hemisphere. However, it remains poorly understood taxonomically, as no comprehensive phylogenetic work has ever been undertaken. In this study we capitalise on samples largely collected by us during the last two decades and use Sanger DNA-sequencing techniques to produce a large phylogenetic tree with 300 triaenonychid terminals representing nearly 50% of triaenonychid genera and including representatives from all the major geographic areas from which they are known. Phylogenetic analyses using maximum likelihood and Bayesian inference methods recover the family as diphyletic, placing Lomanella Pocock, 1903 as the sister group to the New Zealand endemic family Synthetonychiidae Forster, 1954. With the exception of the Laurasian representatives of the family, all landmasses contain non-monophyletic assemblages of taxa. To determine whether this non-monophyly was the result of Gondwanan vicariance, ancient cladogenesis due to habitat regionalisation, or more recent over-water dispersal, we inferred divergence times. We found that most divergence times between landmasses predate Gondwanan breakup, though there has been at least one instance of transoceanic dispersal – to New Caledonia. In all, we identify multiple places in the phylogeny where taxonomic revision is needed, and transfer Lomanella outside of Triaenonychidae in order to maintain monophyly of the family.

Mesozoic sooty mould beetles as living relicts in New Zealand

New Zealand is an island continent that completed its split from the Gondwanan continent at 52 Ma, harbouring an iconic biota of tuatara, kiwi and weta. The sooty mould community is a distinctive trophic element of New Zealand forest ecosystems that is driven by plant-feeding sternorrhynchan Hemiptera. These produce honeydew, which supports fungal growth, which in turn supports numerous endemic invertebrates, including endemic New Zealand beetle families. Ancient New Zealand insect fossils are rare but a single fossil of a sooty mould cyclaxyrid was recently described from Cretaceous Burmese amber, a family that was previously known from two extant New Zealand species. Well-preserved fossils like this one are recasting Earth history, and, based on a wealth of additional specimens, we re-evaluate the taxonomy of Cretaceous cyclaxyrids and one Eocene species here transferred to Cyclaxyridae. Cyclaxyridae are highly tied to the sooty mould community and have now been discovered to occur in disparate biogeographic realms in deep time. Our discovery indicates that the family, and perhaps the sooty mould community in general, was widespread in Pangaea from at least the Cretaceous and survived as a relict in New Zealand. Persistence of a sooty mould ecosystem in New Zealand and fungal specialization may not necessarily be an evolutionary 'dead-end' for cyclaxyrids and other insects.

Phylogenetic divergence of island biotas: Molecular dates, extinction, and "relict" lineages

Island formation is a key driver of biological evolution, and several studies have used geological ages of islands to calibrate rates of DNA change. However, many islands are home to "relict" lineages whose divergence apparently pre-dates island age. The geologically dynamic New Zealand (NZ) archipelago sits upon the ancient, largely submerged continent Zealandia, and the origin and age of its distinctive biota have long been contentious. While some researchers have interpreted NZ's biota as equivalent to that of a post-Oligocene island, a recent review of genetic studies identified a sizeable proportion of pre-Oligocene "relict" lineages, concluding that much of the biota survived an incomplete drowning event. Here, we assemble comparable genetic divergence data sets for two recently formed South Pacific archipelagos (Lord Howe; Chatham Islands) and demonstrate similarly substantial proportions of relict lineages. Similar to the NZ biota, our island reviews provide surprisingly little evidence for major genetic divergence "pulses" associated with island emergence. The dominance of Quaternary divergence estimates in all three biotas may highlight the importance of rapid biological turnover and new arrivals in response to recent climatic and/or geological disturbance and change. We provide a schematic model to help account for discrepancies between expected versus observed divergence-date distributions for island biotas, incorporating the effects of both molecular dating error and lineage extinction. We conclude that oceanic islands can represent both evolutionary "cradles" and "museums" and that the presence of apparently archaic island lineages does not preclude dispersal origins.