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Miskelly, Colin M., Shepherd, Lara D., Tennyson, Alan J.D. (2023): Designation of a neotype for Eudyptula minor (Aves: Spheniscidae). Zootaxa 5228 (1): 92-96, DOI: https://doi.org/10.11646/zootaxa.5228.1.6

Phormium tenax (harakeke) and P. cookianum (wharariki) are important plants for Māori, particularly as weaving materials. At least 60 different cultivars were selected for specific purposes; most are harakeke, but some are suspected hybrids between the two species. We used next-generation sequencing to examine the relationships of wild and cultivated Phormium. We found that the two species could be distinguished genetically, despite evidence of hybridization and introgression. We observed genetic structuring within harakeke and most of the cultivars clustered with wild North Island samples. Our results indicate that it is possible that the populations of harakeke on offshore islands (Norfolk Island, the Kermadec Archipelago, Rēkohu and the subantarctic islands) are all introduced, either by Māori or early European settlers.

Despite the absence of cuttlefish in Aotearoa New Zealand waters, cuttlebones and cuttlebone fragments have been reported and collected in the country since the early twentieth century. Not all could be reliably identified. As such, here we review all cuttlebone material collected from New Zealand shores available in natural history collections, as well as literature and online records. Species were identified, through morphological features and, for the first time, DNA barcoding, as: the Australian endemic Sepia apama Gray, 1849 (and possibly S. grahami A. Reid, 2001) and the widely distributed Indo-Pacific S. latimanus Quoy & Gaimard, 1832. In addition, the predation/scavenging marks (praedichnia) left on the cuttlebones by other organisms are assigned to four major types and attributed to albatrosses, sharks, and dolphins. The successful extraction of DNA from cuttlebones has potential future applications, including the examination of type specimens, since species were described based only on cuttlebones.

International audience; Understanding the movements of animals that spend much of their life at sea is difficult but important for effective conservation. Determining the at-sea distributions of Macaroni (Eudyptes chrysolophus) and Royal (Eudyptes schlegeli) Penguins poses particular challenges, including their occurrence in remote locations and difficulties in species identification owing to overlap in morphological characters, particularly in immature birds. Here we use DNA sequencing to examine vagrant Macaroni and Royal Penguins from Antarctica and New Zealand in order to improve understanding of their non-breeding distributions. Our sampling included samples from living birds, museum specimens and scavenged penguin remains recovered from the stomachs of Antarctic toothfish (Dissostichus mawsoni) caught north of the Ross Sea. Mitochondrial control region (HVRI) sequences indicated that the two samples from New Zealand were likely Royal Penguins as were the scavenged penguins. Both Macaroni and Royal Penguins were detected at Terre Adélie, Antarctica, despite the nearest breeding colony of Macaroni Penguins being 4000 km away. We provide the first evidence of Royal Penguins reaching the Ross Dependency. All but one of the vagrants were immature birds, supporting suggestions that this age group is the most likely to disperse large distances from the breeding colonies. Our study demonstrates how DNA sequences can assist in identifying taxa with similar or overlapping morphologies, as well as fragmentary bird remains.

Past studies of Sophora sect. Edwardsia using traditional phylogenetic and population genetic markers have been unable to produce a resolved species phylogeny of this recent radiation of shrubs and...

Little Spotted Kiwi (LSK; Apteryx owenii) have the lowest genetic diversity of five currently recognised kiwi species apparently due to a bottleneck when at most five individuals were translocated to Kapiti Island in 1912. Ancient DNA analyses show that LSK also had the lowest genetic diversity of kiwi species historically, possibly due to population bottlenecks during Pleistocene glaciation. We compare genetic diversity between LSK from Kapiti Island (extant), D’Urville Island (extinct) and the South Island of mainland New Zealand (extinct) at 495 bp of the mitochondrial control region (mtDNA) and 15 nuclear microsatellite loci (nDNA). Despite higher sample sizes in extant (n = 31 mtDNA, 97 nDNA) than recently extinct (n = 10 mtDNA, 9 nDNA) populations, extant LSK have at least 78% fewer mtDNA haplotypes and 52% fewer microsatellite alleles than recently extinct LSK. Extant LSK were strongly divergent from historical LSK for both mtDNA and nDNA (FST = 0.237 to 0.480), but showed greatest similarity with historical samples from Fiordland near the putative source population of Kapiti founders. Microsatellite data suggest that Kapiti LSK could have arisen from as few as three birds and our mtDNA data show that at least two of the founders were female. Our results indicate that substantial genetic diversity has been lost with the recent extinctions of remnant populations. Locating and protecting any last surviving individuals in presumed extinct populations will require intensive conservation efforts, but could also provide an invaluable source of genetic diversity for the species.

Blechnum opacum is a small forest fern indigenous to New Caledonia and Vanuatu. After examining the considerable morphological variation in New Caledonian populations, along with phylogenetic analy...

The fern genus Lastreopsis has been recently re-circumscribed to include about 19 species. It occurs from southern Asia through the Pacific to the Neotropics, with Australasia having the most speci...

The study of material culture is increasingly including techniques based on DNA sequencing. This article describes the use of mitochondrial DNA (mtDNA) sequencing to identify mammal skins in a Mala...

Pycnolejeunea glauca, originally described by Stephani based on a collection in New Zealand by William Colenso, was placed by Grolle into the synonymy of the paleotropical species Cheilolejeunea intertexta with a type from Micronesia. In this study, we generated DNA sequences from a recently-collected sample of P. glauca and compared them with published sequences of C. intertexta from China. Pycnolejeunea glauca was recovered in the phylogenetic analyses as sister to C. nipponica, whereas C. intertexta grouped in another clade with C. vittata and C. streimannii. The analysis justifies the reinstatement of P. glauca as the new combination Cheilolejeunea glauca, a New Zealand endemic. Descriptions and illustrations are provided of key features of this species together with data on its position in the phylogeny of the genus.

SummaryCook’s Petrel Pterodroma cookii is an endemic New Zealand seabird that has experienced a large range decline since the arrival of humans and now only breeds on two offshore islands (Te Hauturu-o-Toi/Little Barrier Island and Whenua Hou/Codfish Island) at the extreme ends of its former distribution. Morphological, behavioural, and mitochondrial cytochrome oxidase 1 (CO1) sequence data led a previous study to recognise the two extant populations as distinct conservation management units. Here, we further examine the genetic relationship between the extant populations using two nuclear introns (β-fibint7 and PAX). Using one mitochondrial locus (CO1), we also investigate the past distribution of a single nucleotide polymorphism (SNP) that differentiates the modern populations using bone and museum skins sourced from within its former range across New Zealand’s North and South Islands. We found significant population genetic structure between the two extant Cook’s Petrel populations for one of the two nuclear introns (β-fibint7). The mitochondrial DNA CO1 analysis indicated that the SNP variant found in the Codfish Island population was formerly widely distributed across both the North and South Islands, whereas the Little Barrier Island variant was detected only in North Island samples. We argue that these combined data support the recognition of the extant populations as different subspecies. Previous names for these taxa exist, thus Cook’s Petrel from Little Barrier Island becomes Pterodroma cookii cookii and Cook’s Petrel from Codfish Island becomes P. c. orientalis. Furthermore, we suggest that both genetic and non-genetic data should be taken into consideration when planning future mainland translocations. Namely, any translocations on the South Island should be sourced from Codfish Island and future translocations on the North Island should continue to be sourced from Little Barrier Island only.

This study examines the taxonomic rank of the New Zealand endemic sedge Schoenus caespitans. This taxon has been alternatively recognised as a separate species or as a variety of Schoenus apogon an...

Pyrrosia serpens is recorded here for the first time from the New Zealand Botanical Region, based on a single collection from Dayrell Island in the Kermadec Islands. This is a significant southern ...

The largest anthropogenic extinction events during the Holocene occurred on Pacific islands, where thousands of bird populations were lost. Although ancient DNA approaches have become widely used to monitor the genetic variability of species through time, few studies have been conducted to identify the potential cryptic loss of genetic and species diversity within Pacific seabird species. Here we used heterochronous sampling of mitochondrial DNA (Cytochrome b) in the genus Pterodroma from Norfolk Island to quantify potential loss of genetic and species diversity. We particularly focused on the providence petrel P. solandri whose main breeding colony (~ 1,000,000 breeding pairs) became extirpated from Norfolk Island following European settlement circa 1800. We sampled subfossil bones consistent with Pterodroma spp. from Norfolk Island, and performed genetic comparisons with other populations of P. solandri and congeneric species. The majority of subfossil Norfolk Island individuals exhibited the most common mitochondrial haplotype from Lord Howe Island P. solandri, suggesting no appreciable loss of genetic variation as a consequence of the Norfolk Island extirpation. Our findings provide an example where a large seabird population was rapidly extirpated by humans without loss of species-level genetic diversity, probably as a consequence of high connectivity with other populations. However, past connectivity was insufficient to prevent the extirpation itself, which has conservation implications for predicting the resilience of threatened seabirds. In contrast, ancient DNA analyses of smaller Pterodroma bones from Norfolk Island indicate the loss of a second species, potentially P. pycrofti, P. brevipes or another closely related, possibly undescribed taxon, from the Tasman Sea.

Sophora sect. Edwardsia is a group of 19 species largely confined to the South Pacific, with New Zealand the centre of species diversity. We used DNA and morphological analyses to investigate the o...

16 pages, 5 figures, 5 tables, supplementary information https://doi.org/10.1007/s00438-021-01845-3.-- Availability of data and material: DNA sequences: GenBank accession numbers are provided in Table 1. All data are available in the manuscript or in the Supplementary information file, Interspecific introgression can occur between species that evolve rapidly within an adaptive radiation. Pachyptila petrels differ in bill size and are characterised by incomplete reproductive isolation, leading to interspecific gene flow. Salvin’s prion (Pachyptila salvini), whose bill width is intermediate between broad-billed (P. vittata) and Antarctic (P. desolata) prions, evolved through homoploid hybrid speciation. MacGillivray’s prion (P. macgillivrayi), known from a single population on St Paul (Indian Ocean), has a bill width intermediate between salvini and vittata and could also be the product of interspecies introgression or hybrid speciation. Recently, another prion population phenotypically similar to macgillivrayi was discovered on Gough (Atlantic Ocean), where it breeds 3 months later than vittata. The similarity in bill width between the medium-billed birds on Gough and macgillivrayi suggest that they could be closely related. In this study, we used genetic and morphological data to infer the phylogenetic position and evolutionary history of P. macgillivrayi and the Gough medium-billed prion relative other Pachyptila taxa, to determine whether species with medium bill widths evolved through common ancestry or convergence. We found that Gough medium-billed prions belong to the same evolutionary lineage as macgillivrayi, representing a new population of MacGillivray’s prion that originated through a colonisation event from St Paul. We show that macgillivrayi’s medium bill width evolved through divergence (genetic drift) and independently from that of salvini, which evolved through hybridisation (gene flow). This represents the independent convergence towards a similarly medium-billed phenotype. The newly discovered MacGillivray’s prion population on Gough is of utmost conservation relevance, as the relict macgillivrayi population in the Indian Ocean is very small, Open Access funding enabled and organized by Projekt DEAL. PQ, JFM, TLC and LC were supported by the Deutsche Forschungsgemeinschaft (Germany), Heisenberg program (grant number DFG, Qu 148-5 to P.Q.). Logistical and financial support was obtained from the South African Department of Environmental Affairs, through the South African National Antarctic Programme. LDS was supported by a Rutherford Discovery Fellowship from the Royal Society of New Zealand, With the institutional support of the ‘Severo Ochoa Centre of Excellence’ accreditation (CEX2019-000928-S)

Cheilolejeunea rodneyi Bever. & Glenny, a new species of liverwort from lowland indigenous forest reserves in the Tararua Ecological District near Wellington in the North Island of New Zealand is described and illustrated. In both morphology and phylogeny, it is closest to the recently-described C. morganii Bever. & Glenny, with which it shares monoicy, pycnolejeuneoid innovation leaf sequences, a pentacarinate perianth with long rostrum and absence of large botryoidal oil-bodies, but differs in having a single or two-celled uniseriate second tooth, a large extal lobule papilla, a cylindrical rostrum, oil-bodies with large, usually homogeneous segments, and the common presence of cladia. Its addition to the New Zealand flora brings the total species of Cheilolejeunea to 11, four of which are endemic.

The New Zealand wattlebirds (Callaeidae) are an endemic New Zealand passerine family whose species show extreme variation in bill morphology. In particular, the extinct huia (Heteralocha acutirostris) has attracted considerable attention because it exhibited extreme sexual dimorphism in bill morphology. However, the phylogenetic relationships within the Callaeidae, crucial for understanding bill evolution in the family, have not been resolved to date. Here we present phylogenies based on complete mitochondrial genome sequences and nuclear ultraconserved elements. Kōkako (Callaeas spp.) is strongly supported as sister taxon to saddleback/tīeke (Philesturnus spp.) and huia, diverging around 6.8 Ma. Saddleback and huia are estimated to have split from each other 5 Ma, indicating that the extreme sexual bill dimorphism in huia has evolved within this time frame. Our estimates for the divergences within the Callaetidae are similar to, or younger than, those of most other endemic New Zealand avian families, therefore the observed bill variation is not a consequence of a longer divergence time. Instead, the expansion of the huia into the wood-foraging niche, combined with the sexual dimorphism it evolved in order to optimise feeding on this resource, has been the main contributor to the large variation of bill morphologies within this family.

Allopolyploids arise when two or more species hybridise to form an entirely new species with a duplicated genome. Although initially met with an array of potentially catastrophic challenges trigger...

Recent treatments have recognised seven species indigenous to New Zealand in the fern genus Adiantum. Most of these species display dimorphism with respect to the presence or absence of hai...

Phlegmariurus varius is an Australasian species of lycophyte that has long been recognised as morphologically and ecologically variable. A recent study reported incongruence between morphological and genetic variation within New Zealand samples. However, a reappraisal and repeat of the genetic analyses of chloroplast DNA sequence data, and a more detailed examination of morphological variation, strongly supports the recognition of two species that are sympatric in New Zealand. The combination Phlegmariurus billardierei (Spring) Brownsey & Perrie is made here for plants with distinct strobili. The other species, Phlegmariurus varius (R.Br.) A.R.Field & Bostock sensu stricto, has comparatively indistinct strobili, and remains morphologically and ecologically variable even after the segregation of P. billardierei. Phlegmariurus varius is indigenous to both Australia and New Zealand, while P. billardierei is the only species of Lycopodiaceae endemic to New Zealand.

We review the biology and ecology of the endemic New Zealand genus Alseuosmia A. Cunn. The taxonomy of the genus has a complicated history with considerable debate about both its relationsh...

Introduction. Cheilolejeunea morganii Bever. & Glenny, a new species of Cheilolejeunea from a lowland forest habitat in eastern Taranaki in the North Island of New Zealand, is described and illustr...

We investigated the phylogeography of the New Zealand endemic monotypic coastal tree Entelea arborescens (whau; Malvaceae). The distribution of whau in the southern North Island and South I...

Diving petrels (genus Pelecanoides) are a group of small Southern Ocean seabirds whose taxonomy has remained problematic due to a lack of morphological diversity between species and limited availability of genetic data. Here we examine the phylogenetic relationships of the Pelecanoides diving petrels with analyses of the mitochondrial cytochrome b gene, focusing in particular, on the recently described and critically endangered Whenua Hou Diving Petrel (P. whenuahouensis). Pelecanoides whenuahouensis showed only minor sequence divergence from its sister species, the South Georgian Diving Petrel (P. georgicus), comparable to divergence levels observed between subspecies of the Common Diving Petrel (P. urinatrix). The paratype of P. whenuahouensis, which was collected from the now extinct population on the Auckland Islands, is genetically indistinguishable from P. georgicus raising the question of which species formerly bred on these subantarctic islands. Our genetic analyses provide insights into the phylogeography and evolutionary history of Pelecanoides and will help inform the conservation of the critically endangered Whenua Hou Diving Petrel.

Lycopods are tracheophytes in the Kingdom Plantae and represent one of the oldest lineages of living vascular plants. Symbiotic interactions between these plants with fungi and bacteria, including fine root endophytes in Endogonales, have been hypothesized to have helped early diverging plant lineages colonize land. However, attempts to study the lycopod rhizobiome in its natural environment are still limited. In this study, we used Illumina amplicon sequencing to characterize fungal and bacterial diversity in nine Lycopodiaceae (club moss) species collected in New Zealand. This was done with generic fungal ITS rDNA primers, as well as Endogonales- and arbuscular mycorrhizal fungi (AMF)-selective primer sets targeting the 18S rDNA, and generic bacterial primers targeting the V4 region of the 16S rDNA. We found that the Lycopodiaceae rhizobiome was comprised of an unexpected high frequency of Basidiomycota and Ascomycota coincident with a low abundance of Endogonales and Glomerales. The distribution and abundance of Endogonales varied with host lycopod, and included a novel taxon as well as a single operational taxonomic unit (OTU) that was detected across all plant species. The Lycopodiaceae species with the greatest number and also most unique OTUs was Phlegmariurus varius, while the plant species that shared the most fungal OTUs were Lycopodiella fastigiatum and Lycopodium scariosum. The bacterial OTU distribution was generally not consistent with fungal OTU distribution. For example, community dissimilarity analysis revealed strong concordance between the evolutionary histories of host plants with the fungal community but not with the bacterial community, indicating that Lycopodiaceae have evolved specific relationships with their fungal symbionts. Notably, nearly 16% of the ITS rDNA fungal diversity detected in the Lycopodiaceae rhizobiome remained poorly classified, indicating there is much plant-associated fungal diversity left to describe in New Zealand.

Asplenium flabellifolium Cav. is a cytologically variable Australian and New Zealand fern. Here, we sequence chloroplast trnL-trnF and rps4-trnS from samples throughout its range to provide the first phylogeographic investigation of a fern common in both countries. Twenty-three haplotypes were detected, which formed six haplogroups in a network. Australian specimens were placed in all haplogroups. The placement of New Zealand haplotypes in five of the haplogroups suggests that this species has dispersed across the Tasman Sea at least five times. Sexually reproducing plants of lower ploidy, detected only in south-eastern Australia, contained haplotypes from the two haplogroups that are successive sisters to the remaining diversity in the phylogeny. This likely suggests that A. flabellifolium was originally a sexually reproducing species in south-eastern Australia and spread to the rest of its distribution where apomictic plants dominate. More than one haplogroup was detected in several areas across its distribution, suggesting that these areas were colonised several times. Other areas harboured several haplotypes from a single haplogroup or haplogroups not recovered elsewhere, indicating possible long-term persistence in these areas. Haplotypes and morphological features were not found to be exclusive to either breeding system or ploidy and no taxonomic revision is proposed.

Five indigenous species of Pellaea in Australasia belong to section Platyloma. Their taxonomic history is outlined, morphological, cytological and genetic evidence for their recognition reviewed, and new morphological and chloroplast DNA-sequence data provided. Australian plants of P. falcata (R.Br.) Fée are diploid and have longer, narrower pinnae than do New Zealand plants previously referred to P. falcata, which are tetraploid. Evidence indicates that P. falcata does not occur in New Zealand, and that collections so-named are P. rotundifolia (G.Forst.) Hook. Chloroplast DNA sequences are uninformative in distinguishing Australian P. falcata from New Zealand P. rotundifolia, but show that Australian P. nana is distinct from both. Sequence data also show that Australian and New Zealand populations of P. calidirupium Brownsey & Lovis are closely related, and that Australian P. paradoxa (R.Br.) Hook. is distinct from other Australian species. Although P. falcata is diploid and P. rotundifolia tetraploid, P. calidirupium, P. nana (Hook.) Bostock and P. paradoxa each contain multiple ploidy levels. Diploid populations of Pellaea species are confined to Australia, and only tetraploids are known in New Zealand. Evolution of the group probably involved hybridisation, autoploidy, alloploidy, and possibly apomixis. Further investigation is required to resolve the status of populations from Mount Maroon, Queensland and the Kermadec Islands.

Three tropical fern species previously treated in the Dennstaedtiaceae genus Hypolepis were recently segregated in a new genus, Hiya, based on phylogenetic analysis of chloroplast DNA sequences and assessment of their morphology. That study specifically mentioned the uncertain placement of the Australasian species Hypolepis distans, which has long been regarded as anomalous within Hypolepis. Using phylogenetic analysis of rbcL and rpl16 sequences, along with morphological and cytological characters, we show that Hypolepis distans is best placed in Hiya, and make the new combination Hiya distans. However, this requires a significant adjustment in the morphological characterisation of Hiya. It can be recognised by the adaxial sulcus of the primary pinnae being confluent with the rachis, veins which reach the lamina margin at an indentation, and the primary pinnae arising at ± 90° from the rachis. It is also a significant ecological extension of Hiya, from the tropical highlands of Malesia and Centra...

Significance The mode and tempo of extinctions and extirpations after the first contact phase of human settlements is a widely debated topic. As the last major landmass to be settled by humans, New Zealand offers a unique lens through which to study interactions of people and biota. By analyzing ancient DNA from more than 5,000 nondiagnostic and fragmented bones from 38 subfossil assemblages, we describe species and patterns that have been missed by morphological approaches. We report the identification of five species of whale from an archaeological context in New Zealand and describe the prehistoric kākāpō population structure. Taken together, this study demonstrates insights into subsistence practices and extinction processes and demonstrates the value of genetic analyses of fossil assemblages., New Zealand’s geographic isolation, lack of native terrestrial mammals, and Gondwanan origins make it an ideal location to study evolutionary processes. However, since the archipelago was first settled by humans 750 y ago, its unique biodiversity has been under pressure, and today an estimated 49% of the terrestrial avifauna is extinct. Current efforts to conserve the remaining fauna rely on a better understanding of the composition of past ecosystems, as well as the causes and timing of past extinctions. The exact temporal and spatial dynamics of New Zealand’s extinct fauna, however, can be difficult to interpret, as only a small proportion of animals are preserved as morphologically identifiable fossils. Here, we conduct a large-scale genetic survey of subfossil bone assemblages to elucidate the impact of humans on the environment in New Zealand. By genetically identifying more than 5,000 nondiagnostic bone fragments from archaeological and paleontological sites, we reconstruct a rich faunal record of 110 species of birds, fish, reptiles, amphibians, and marine mammals. We report evidence of five whale species rarely reported from New Zealand archaeological middens and characterize extinct lineages of leiopelmatid frog (Leiopelma sp.) and kākāpō (Strigops habroptilus) haplotypes lost from the gene pool. Taken together, this molecular audit of New Zealand’s subfossil record not only contributes to our understanding of past biodiversity and precontact Māori subsistence practices but also provides a more nuanced snapshot of anthropogenic impacts on native fauna after first human arrival.

Knowledge about the diets of New Zealand's extinct moa (Aves: Dinornithiformes) is heavily biased towards just three species (Dinornis robustus, Megalapteryx didinus and Pachyornis elephantopus), which represent about 90% of all identified coprolites and gizzard content samples. By comparison, the diets of the other six moa species are poorly known. Here, we report the discovery of a new coprolite deposit attributed to little bush moa (Anomalopteryx didiformis) based on DNA barcoding and former moa species distributions. The deposit is the southernmost site from which moa coprolites have been recovered and just the second to contain mid-Holocene specimens. Moreover, the deposit provides the longest known temporal span (∼2200 years) of moa coprolites within a stratigraphic context. Pollen and plant DNA from the coprolites, as well as associated plant macrofossils, indicate that the deposit spans a period when the forest canopy was transitioning from Podocarpaceae to silver beech (Lophozonia menziesii) dominance about 6800–4600 years ago. Our analysis of coprolite content supports the current hypothesis that little bush moa browsed trees and shrubs within the forest understorey, but provides new evidence that ferns were also an important part of their diet. Based on this finding, we suggest that moa might once have played a previously unrecognised role in the dispersal of ground fern spores throughout New Zealand forests.