Genetic and morphological evidence for two species ofLeucocarboshag (Aves, Pelecaniformes, Phalacrocoracidae) from southern South Island of New Zealand

Large-scale genetic investigation of nematode diversity and their phylogenetic patterns in New Zealand's marine animals

Nematodes constitute one of the most speciose metazoan groups on earth, and a significant proportion of them have parasitic life styles. Zooparasitic nematodes have zoonotic, commercial and ecological significance within natural systems. Due to their generally small size and hidden nature within their hosts, and the fact that species discrimination using traditional morphological characteristics is often challenging, their biodiversity is not well known, especially within marine ecosystems. For instance, the majority of New Zealand's marine animals have never been the subject of nematode studies, and many currently known nematodes in New Zealand await confirmation of their species identity with modern taxonomic techniques. In this study, we present the results of an extensive biodiversity survey and phylogenetic analyses of parasitic nematodes infecting New Zealand's marine animals. We used genetic data to differentiate nematodes to the lowest taxonomic level possible and present phylogenies of the dominant clades to illustrate their genetic diversity in New Zealand. Our findings reveal a high diversity of parasitic nematodes (23 taxa) infecting New Zealand's marine animals (62 of 94 free-living animal species investigated). The novel data collected here provide a solid baseline for future assessments of change in diversity and distribution of parasitic nematodes.

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.).

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.

EcoQBNs: First Application of Ecological Modeling with Quantum Bayesian Networks

A recent advancement in modeling was the development of quantum Bayesian networks (QBNs). QBNs generally differ from BNs by substituting traditional Bayes calculus in probability tables with the quantum amplification wave functions. QBNs can solve a variety of problems which are unsolvable by, or are too complex for, traditional BNs. These include problems with feedback loops and temporal expansions; problems with non-commutative dependencies in which the order of the specification of priors affects the posterior outcomes; problems with intransitive dependencies constituting the circular dominance of the outcomes; problems in which the input variables can affect each other, even if they are not causally linked (entanglement); problems in which there may be >1 dominant probability outcome dependent on small variations in inputs (superpositioning); and problems in which the outcomes are nonintuitive and defy traditional probability calculus (Parrondo’s paradox and the violation of the Sure Thing Principle). I present simple examples of these situations illustrating problems in prediction and diagnosis, and I demonstrate how BN solutions are infeasible, or at best require overly-complex latent variable structures. I then argue that many problems in ecology and evolution can be better depicted with ecological QBN (EcoQBN) modeling. The situations that fit these kinds of problems include noncommutative and intransitive ecosystems responding to suites of disturbance regimes with no specific or single climax condition, or that respond differently depending on the specific sequence of the disturbances (priors). Case examples are presented on the evaluation of habitat conditions for a bat species, representing state-transition models of a boreal forest under disturbance, and the entrainment of auditory signals among organisms. I argue that many current ecological analysis structures—such as state-and-transition models, predator–prey dynamics, the evolution of symbiotic relationships, ecological disturbance models, and much more—could greatly benefit from a QBN approach. I conclude by presenting EcoQBNs as a nascent field needing the further development of the quantum mathematical structures and, eventually, adjuncts to existing BN modeling shells or entirely new software programs to facilitate model development and application.

Helminth parasites of shags (Phalacrocoracidae) from the Otago region of southern New Zealand

A total of 61 specimens representing five species of shag - Auckland Island shag Leucocarbo colensoi, little pied shag Microcarbo melanoleucos brevirostris, black shag Phalacrocorax carbo novaehollandiae, Otago shag Leucocarbo chalconotus and spotted shag Phalacrocorax punctatus - from the coast around Otago, South Island, New Zealand, were examined for helminths. A total of 18 helminth species was found: six nematodes (Anisakis pegreffi, Contracaecum rudolphii E, Baruscapillaria sp., Cosmocephalus jaenschi, Ingliseria cirrohamata, Desmidocercella australis), four trematodes (Apatemon sp. 'jamiesoni', Cardiocephaloides ovicorpus, Apophallus sp., Microphallidae gen. sp.), four cestodes (Microsomacanthus cormoranti, Microsomacanthus sp., Paradilepis urceina, Tetrabothrius sp.) and four acanthocephalans (Andracantha leucocarboi, A. sigma, Corynosoma hannae, Profilicollis novaezelandensis). Descriptions are provided for females of C. jaenschi and D. australis, which were previously undescribed. The data include 20 new host records and seven new locality records. New 18S ribosomal DNA and internal transcribed spacer (ITS1 and ITS2) DNA sequences have been provided where specimen conditions permitted. These data add considerably to our sparse knowledge of helminths in New Zealand shags, and provide a baseline for observations of change in the future.

Analyses of phenotypic differentiations among South Georgian Diving Petrel (Pelecanoides georgicus) populations reveal an undescribed and highly endangered species from New Zealand

Unresolved taxonomy of threatened species is problematic for conservation as the field relies on species being distinct taxonomic units. Differences in breeding habitat and results from a preliminary molecular analysis indicated that the New Zealand population of the South Georgian Diving Petrel (Pelecanoides georgicus) was a distinct, yet undescribed, species. We measured 11 biometric characters and scored eight plumage characters in 143 live birds and 64 study skins originating from most populations of P. georgicus, to assess their taxonomic relationships. We analysed differences with principal component analyses (PCA), factorial ANOVAs, and Kruskal-Wallis rank sum tests. Results show that individuals from New Zealand differ significantly from P. georgicus from all other populations as following: 1) longer wings, 2) longer outer tail feathers, 3) deeper bills, 4) longer heads, 5) longer tarsi, 6) limited collar extent, 7) greater extent of contrasting scapulars, 8) larger contrasting markings on the secondaries, 9) paler ear coverts, 10) paler collars, and 11) paler flanks. Furthermore, we used a species delimitation test with quantitative phenotypic criteria; results reveal that the New Zealand population of P. georgicus indeed merits species status. We hereby name this new species Pelecanoides whenuahouensis sp. nov. Due to severe reductions in its range and the very low number of remaining birds (~150 individuals limited to a single breeding colony on Codfish Island/Whenua Hou) the species warrants listing as ‘Critically Endangered’. An abstract in the Māori language/Te Reo Māori can be found in S1 File.

Ancient DNA and morphometric analysis reveal extinction and replacement of New Zealand's unique black swans

Prehistoric human impacts on megafaunal populations have dramatically reshaped ecosystems worldwide. However, the effects of human exploitation on smaller species, such as anatids (ducks, geese, and swans) are less clear. In this study we apply ancient DNA and osteological approaches to reassess the history of Australasia's iconic black swans (Cygnus atratus) including the palaeo-behaviour of prehistoric populations. Our study shows that at the time of human colonization, New Zealand housed a genetically, morphologically, and potentially ecologically distinct swan lineage (C. sumnerensis, Poūwa), divergent from modern (Australian) C. atratus Morphological analyses indicate C. sumnerensis exhibited classic signs of the 'island rule' effect, being larger, and likely flight-reduced compared to C. atratus Our research reveals sudden extinction and replacement events within this anatid species complex, coinciding with recent human colonization of New Zealand. This research highlights the role of anthropogenic processes in rapidly reshaping island ecosystems and raises new questions for avian conservation, ecosystem re-wilding, and de-extinction.

Time to Spread Your Wings: A Review of the Avian Ancient DNA Field

Ancient DNA (aDNA) has the ability to inform the evolutionary history of both extant and extinct taxa; however, the use of aDNA in the study of avian evolution is lacking in comparison to other vertebrates, despite birds being one of the most species-rich vertebrate classes. Here, we review the field of “avian ancient DNA” by summarising the past three decades of literature on this topic. Most studies over this time have used avian aDNA to reconstruct phylogenetic relationships and clarify taxonomy based on the sequencing of a few mitochondrial loci, but recent studies are moving toward using a comparative genomics approach to address developmental and functional questions. Applying aDNA analysis with more practical outcomes in mind (such as managing conservation) is another increasingly popular trend among studies that utilise avian aDNA, but the majority of these have yet to influence management policy. We find that while there have been advances in extracting aDNA from a variety of avian substrates including eggshell, feathers, and coprolites, there is a bias in the temporal focus; the majority of the ca. 150 studies reviewed here obtained aDNA from late Holocene (100–1000 yBP) material, with few studies investigating Pleistocene-aged material. In addition, we identify and discuss several other issues within the field that require future attention. With more than one quarter of Holocene bird extinctions occurring in the last several hundred years, it is more important than ever to understand the mechanisms driving the evolution and extinction of bird species through the use of aDNA.