25 Works

Speciation in the abyss - genomics and morphology reveal a new species of beaked whale

Emma L. Carroll, Michael R. McGowen, Morgan L. McCarthy, Felix G. Marx, Natacha Aguilar De Soto, Merel L. Dalebout, Sascha Dreyer, Oscar E. Gaggiotti, Sabine S. Hansen, Anton Van Helden, Aubrie B. Onoufriou, Robin W. Baird, C. Scott Baker, Simon Berrow, Danielle Cholewiak, Diane Claridge, Rochelle Constantine, Nicholas J. Davison, Catarina Eira, R. Ewan Fordyce, John Gatesy, G. J. Greg Hofmeyr, Vidal Martin, James G. Mead, Antonio A. Mignucci-Giannoni … & Morten T. Olsen
Earth’s deep oceans remains less well understood than the surface of Mars. Beaked whales (ziphiids) are among the most visible inhabitants of the abyss, due to their large size and worldwide distribution, yet their diversity and ecology remain obscure. We combine genomic and morphometric analyses to reveal a new Southern Hemisphere ziphiid species, Ramari’s beaked whale, Mesoplodon eueu, whose name is linked to the Indigenous people of the lands from which the species holotype and...

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

Steven A. Trewick, Stephen Pilkington, Lara D. Shepherd, Gillian C. Gibb, Mary Morgan-Richards & Steve A. Trewick
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...

Functional beta diversity of New Zealand fishes: characterising morphological turnover along depth and latitude gradients, with derivation of functional bioregions

Elisabeth Myers, David Eme, Libby Liggins, Euan Harvey, Clive Roberts & Marti Anderson
Changes in the functional structures of communities are rarely examined along multiple large-scale environmental gradients. Here, we describe patterns in functional beta diversity for New Zealand marine fishes vs depth and latitude, including broad-scale delineation of functional bioregions. We derived eight functional traits related to food acquisition and locomotion and calculated complementary indices of functional beta diversity for 144 species of marine ray-finned fishes occurring along large-scale depth (50 - 1200 m) and latitudinal gradients...

Changes in key traits versus depth and latitude suggest energy-efficient locomotion, opportunistic feeding and light lead to adaptive morphologies of marine fishes.

Elisabeth Myers, Marti Anderson, David Eme, Libby Liggins & Clive Roberts
1. Understanding patterns and processes governing biodiversity along broad-scale environmental gradients, such as depth or latitude, requires an assessment of not just taxonomic richness, but also morphological and functional traits of organisms. Studies of traits can help to identify major selective forces acting on morphology. Currently, little is known regarding patterns of variation in the traits of fishes at broad spatial scales. 2. The aims of this study were: (i) to identify a suite of...

A framework for mapping the distribution of seabirds by integrating tracking, demography and phenology

Ana P. B. Carneiro, Elizabeth J. Pearmain, Steffen Oppel, Thomas A. Clay, Richard A. Phillips, Anne-Sophie Bonnet-Lebrun, Ross M. Wanless, Edward Abraham, Yvan Richard, Joel Rice, Jonathan Handley, Tammy E. Davies, Ben J. Dilley, Peter G. Ryan, Cleo Small, Javier Arata, John P. Y. Arnould, Elizabeth Bell, Leandro Bugoni, Letizia Campioni, Paulo Catry, Jaimie Cleeland, Lorna Deppe, Graeme Elliott, Amanda Freeman … & Maria P. Dias
1. The identification of geographic areas where the densities of animals are highest across their annual cycles is a crucial step in conservation planning. In marine environments, however, it can be particularly difficult to map the distribution of species, and the methods used are usually biased towards adults, neglecting the distribution of other life-history stages even though they can represent a substantial proportion of the total population. 2. Here we develop a methodological framework for...

Data from: Phylogenetic measures reveal eco-evolutionary drivers of biodiversity along a depth gradient

David Eme, Marti Anderson, Elisabeth Myers, Clive Roberts & Libby Liggins
Energy and environmental stability are positively correlated with species richness along broad-scale spatial gradients in terrestrial ecosystems, so their relative importance in generating and preserving diversity cannot be readily disentangled. This study seeks to exploit the negative correlation between energy and stability along the oceanic depth gradient to better understand their relative contribution in shaping broadscale biodiversity patterns. We develop a conceptual framework by simulating speciation and extinction along energy and stability gradients to generate...

Hybridisation in kiwi (Apteryx; Apterygidae) requires taxonomic revision for great spotted kiwi

Lara Shepherd, Alan Tennyson, Hugh Robertson, Rogan Colbourne & Kristina Ramstad
We review hybridisation in kiwi (Apteryx spp.) and present new genetic data examining the extent of hybridisation between rowi (A. rowi) and little spotted kiwi (A. owenii) at Okarito, the location of the only remaining natural population of the threatened rowi. We find evidence of recurrent hybridisation between these two species over the last 150 years, including one F1 hybrid found in the last 15 years, despite little spotted kiwi’s likely extinction on the mainland...

Westland petrel data combined GPS and accelerometer data 2016 & 2017

Timothee Poupart, Susan Waugh, Akiko Kato & John Arnould
This study investigated the foraging niche of dimorphic males and females Westland petrel during the chick-rearing period. At-sea movements were recorded with GPS, behaviours and foraging behaviour were recorded with accelerometers, and trophic niche was inferred with stable isotopes (carbon, nitrogen). Altogether, these fine-scale data allowed to look at the foraging niche used by males and females.

Pioneering polyploids: the impact of whole-genome duplication on biome shifting in New Zealand Coprosma (Rubiaceae) and Veronica (Plantaginaceae)

Luke Liddell, William Lee, Esther Dale, Heidi Meudt & Nick Matzke
The role of whole-genome duplication in facilitating shifts into novel biomes remains unknown. Focusing on two diverse woody plant groups in New Zealand, Coprosma (Rubiaceae) and Veronica (Plantaginaceae), we investigate how biome occupancy varies with ploidy level, and test the hypothesis that whole-genome duplication increases the rate of biome shifting. Ploidy levels and biome occupancy (forest, open, and alpine) were determined for indigenous species in both clades. The distribution of low ploidy (Coprosma: 2x, Veronica:...

Data from: Parallel polyploid speciation: distinct sympatric gene-pools of recurrently derived allo-octoploid Asplenium ferns

Leon R Perrie
Although polyploidy is widespread, its significance to the generation of biodiversity remains unclear. Many polyploids have been derived recurrently. For a particular polyploid, gene-flow between the products of independent origin is typical where they come into contact. Here, we use AFLP DNA-fingerprinting and chloroplast DNA sequences to demonstrate parallel polyploid speciation within both of the ferns Asplenium cimmeriorum and A. gracillimum. Both of these taxa comprise at least two allopolyploids, recurrently derived from the same...

Data from: Subsistence practices, past biodiversity, and anthropogenic impacts revealed by New Zealand-wide ancient DNA survey

Frederik V. Seersholm, Theresa L. Cole, Alicia Grealy, Nicolas J. Rawlence, Karen Greig, Michael Knapp, Michael Stat, Anders J. Hansen, Luke J. Easton, Lara Shepherd, Alan J. D. Tennyson, R. Paul Scofield, Richard Walter & Michael Bunce
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 (c. 1280 AD), 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...

Lineage identification affects estimates of evolutionary mode in marine snails

Felix Vaux, Michael R Gemmell, Simon F K Hills, Bruce A Marshall, Alan G Beu, James S Crampton, Steve A Trewick & Mary Morgan-Richards
In order to study evolutionary pattern and process we need to be able to accurately identify species and the evolutionary lineages from which they are derived. Determining the concordance between genetic and morphological variation of living populations, and then directly comparing extant and fossil morphological data, provides a robust approach for improving our identification of lineages through time. We investigate genetic and shell morphological variation in extant species of Penion marine snails from New Zealand,...

Data from: Phylogenomic species delimitation dramatically reduces species diversity in an Antarctic adaptive radiation

Elyse Parker, Alex Dornburg, Carl Struthers, Christopher Jones & Thomas Near
Application of genetic data to species delimitation often builds confidence in delimitations previously hypothesized using morphological, ecological, and geographic data and frequently yields recognition of previously-undescribed cryptic diversity. However, a recent critique of genomic data-based species delimitation approaches is that they have the potential to conflate population structure with species diversity, resulting in taxonomic oversplitting. The need for an integrative approach to species delimitation, in which molecular, morphological, ecological, and geographic lines of evidence are...

Temporal and spatial differences in the post-breeding behaviour of a ubiquitous Southern Hemisphere seabird, the common diving petrel

Aymeric Fromant, Charles-Andre Bost, Paco Bustamante, Alice Carravieri, Yves Cherel, Yonina Eizenberg, Colin Miskelly, John Arnould & Karine Delord
The non-breeding period plays a major role in seabird survival and population dynamics. However, our understanding of the migratory behaviour, moulting and feeding strategies of non-breeding seabirds is still very limited, especially for small-sized species. The present study investigated the post-breeding behaviour of three distant populations (Kerguelen Archipelago, south-eastern Australia, New Zealand) of the common diving petrel (Pelecanoides urinatrix), an abundant, widely distributed zooplanktivorous seabird breeding throughout the southern Atlantic, Indian and Pacific oceans. The...

Data from: Earth history and the passerine superradiation

Carl H. Oliveros, Daniel J. Field, Daniel T. Ksepka, F. Keith Barker, Alexandre Aleixo, Michael J. Andersen, Per Alström, Brett W. Benz, Edward L. Braun, Michael J. Braun, Gustavo A. Bravo, Robb T. Brumfield, R. Terry Chesser, Santiago Claramunt, Joel Cracraft, Andrés M. Cuervo, Elizabeth P. Derryberry, Travis C. Glenn, Michael G. Harvey, Peter A. Hosner, Leo Joseph, Rebecca T. Kimball, Andrew L. Mack, Colin M. Miskelly, A. Townsend Peterson … & Brant C. Faircloth
Avian diversification has been influenced by global climate change, plate tectonic movements, and mass extinction events. However, the impact of these factors on the diversification of the hyperdiverse perching birds (passerines) is unclear because family level relationships are unresolved and the timing of splitting events among lineages is uncertain. We analyzed DNA data from 4,060 nuclear loci and 137 passerine families using concatenation and coalescent approaches to infer a comprehensive phylogenetic hypothesis that clarifies relationships...

Data from: Genetic analysis identifies the missing parchment of New Zealand’s founding document, The Treaty of Waitangi.

Lara Shepherd, Peter Whitehead & Anna Whitehead
Genetic analyses provide a powerful tool with which to identify the biological components of historical objects. Te Tiriti o Waitangi | The Treaty of Waitangi is New Zealand’s founding document, intended to be a partnership between the indigenous Māori and the British Crown. Here we focus on an archived piece of blank parchment that has been proposed to be the missing portion of the lower parchment of the Waitangi Sheet of the Treaty. However, its...

Data from: Geographically contrasting biodiversity reductions in a widespread New Zealand seabird

Nicolas J. Rawlence, Martyn Kennedy, Christian N. K. Anderson, Stefan Prost, Charlotte E. Till, Ian Smith, R. Paul Scofield, Alan J. D. Tennyson, Jill Hamel, Chris Lalas, Elizabeth A. Matisoo-Smith, Jonathan M. Waters & Ian W. G. Smith
Unravelling prehistoric anthropogenic impacts on biodiversity represents a key challenge for biologists and archaeologists. New Zealand's endemic Stewart Island Shag (Leucocarbo chalconotus) comprises two distinct phylogeographic lineages, currently restricted to the country's south and southeast. However, fossil and archaeological remains suggest a far more widespread distribution at the time of Polynesian settlement ca. 1280 AD, encompassing much of coastal South Island. We used modern and ancient DNA, radiocarbon dating, and Bayesian modelling, to assess the...

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

Johannes H. Fischer, Igor Debski, Colin M. Miskelly, Charles A. Bost, Aymeric Fromant, Alan J. D. Tennyson, Jake Tessler, Rosalind Cole, Johanna H. Hiscock, Graeme A. Taylor & Heiko U. Wittmer
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,...

Data from: Human-mediated extirpation of the unique Chatham Islands sea lion and implications for the conservation management of remaining New Zealand sea lion populations

Nicolas J. Rawlence, Catherine J. Collins, Christian N. K. Anderson, Justin J. Maxwell, Ian W. G. Smith, Bruce C. Robertson, Michael Knapp, Katherine Ann Horsburgh, Jo-Ann L. Stanton, R. Paul Scofield, Alan J. D. Tennyson, Elizabeth A. Matisoo-Smith & Jonathan M. Waters
While terrestrial megafaunal extinctions have been well characterized worldwide, our understanding of declines in marine megafauna remains limited. Here, we use ancient DNA analyses of prehistoric (<1450–1650 AD) sea lion specimens from New Zealand's isolated Chatham Islands to assess the demographic impacts of human settlement. These data suggest there was a large population of sea lions, unique to the Chatham Islands, at the time of Polynesian settlement. This distinct mitochondrial lineage became rapidly extinct within...

Ancient crested penguin constrains timing of recruitment into seabird hotspot

Daniel Thomas, Alan Tennyson, R. Paul Scofield, Tracy Heath, Walker Pett & Daniel Ksepka
New Zealand is a globally significant hotspot for seabird diversity, but the sparse fossil record for most seabird lineages has impeded our understanding of how and when this hotspot developed. Here, we describe multiple exceptionally well-preserved specimens of a new species of penguin from tightly dated (3.36–3.06 Ma) Pliocene deposits in New Zealand. Bayesian and parsimony analyses place Eudyptes atatu sp. nov. as the sister species to all extant and recently extinct members of the...

Data from: Genetic structure and shell shape variation within a rocky shore whelk suggests both diverging and constraining selection with gene flow

Michael R. Gemmell, Steven A. Trewick, James S. Crampton, Felix Vaux, Simon F.K. Hills, Elizabeth E. Daly, Bruce A. Marshall, Alan G. Beu, Mary Morgan-Richards & Simon F K Hills
Variation in snail shell shape has provided evolutionary biologists with excellent material for the study of local adaptation to local environments. However, assuming shell shape variation is evidence of distinct lineages (species) may have led to taxonomic inflation within some gastropod lineages. Here we compare shell shape variation and genetic structure of two independent lineages of New Zealand rocky shore whelks in order to understand the process that lead to an unusual disjunct distribution. We...

Data from: Convergence and constraint in the cranial evolution of mosasaurid reptiles and early cetaceans

Rebecca Bennion, Jamie MacLaren, Ellen Coombs, Felix Marx, Olivier Lambert & Valentin Fischer
The repeated return of tetrapods to aquatic life provides some of the best-known examples of convergent evolution. One comparison which has received relatively little focus is that of mosasaurids (a group of Late Cretaceous squamates) and archaic cetaceans (the ancestors of modern whales and dolphins), both of which show high levels of craniodental disparity, similar initial trends in locomotory evolution, and global distributions. Here we investigate convergence in skull ecomorphology during the initial aquatic radiations...

Recent extinctions among Little Spotted Kiwi (Apteryx owenii) and the origin of extant populations

Kristina Ramstad, Gillian Gibb, Hugh Robertson, Rogan Colbourne, Erin Doran & Lara Shepherd
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...

High functional diversity in deep-sea fish communities and increasing intra-specific trait variation with increasing latitude

Elisabeth Myers, Marti Anderson, Libby Liggins, Euan Harvey, Clive Roberts & David Eme
Variation in both inter- and intra-specific traits affect community dynamics, yet we know little regarding the relative importance of external environmental filters vs internal biotic interactions that shape the functional space of communities along broad-scale environmental gradients, such as latitude, elevation or depth. We examined changes in several key aspects of functional alpha-diversity for marine fishes along depth and latitude gradients by quantifying intra- and inter-specific richness, dispersion and regularity in functional trait space. We...

Data from: Parallel polyploid speciation: distinct sympatric gene-pools of recurrently derived allo-octoploid Asplenium ferns

Leon R Perrie
Although polyploidy is widespread, its significance to the generation of biodiversity remains unclear. Many polyploids have been derived recurrently. For a particular polyploid, gene-flow between the products of independent origin is typical where they come into contact. Here, we use AFLP DNA-fingerprinting and chloroplast DNA sequences to demonstrate parallel polyploid speciation within both of the ferns Asplenium cimmeriorum and A. gracillimum. Both of these taxa comprise at least two allopolyploids, recurrently derived from the same...

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