ORCID Profile
0000-0002-7136-0017
Current Organisations
Museum of New Zealand Te Papa Tongarewa
,
Massey University
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Publisher: Frontiers Media SA
Date: 15-01-2020
Publisher: Elsevier BV
Date: 07-2008
DOI: 10.1016/J.YMPEV.2008.02.023
Abstract: A previous study of the relationships amongst three subgroups of the Austral Asplenium ferns found conflicting signal between the two chloroplast loci investigated. Because organelle genomes like those of chloroplasts and mitochondria are thought to be non-recombining, with a single evolutionary history, we sequenced four additional chloroplast loci with the expectation that this would resolve these relationships. Instead, the conflict was only magnified. Although tree-building analyses favoured one of the three possible trees, one of the alternative trees actually had one more supporting site (six versus five) and received greater support in spectral and neighbor-net analyses. Simulations suggested that chance alone was unlikely to produce strong support for two of the possible trees and none for the third. Likelihood permutation tests indicated that the concatenated chloroplast sequence data appeared to have experienced recombination. However, recombination between the chloroplast genomes of different species would be highly atypical, and corollary supporting observations, like chloroplast heteroplasmy, are lacking. Wider taxon s ling clarified the composition of the Austral group, but the conflicting signal meant analyses (e.g., morphological evolution, biogeographic) conditional on a well-supported phylogeny could not be performed.
Publisher: Oxford University Press (OUP)
Date: 26-04-2019
Abstract: Speciation through homoploid hybridization (HHS) is considered extremely rare in animals. This is mainly because the establishment of reproductive isolation as a product of hybridization is uncommon. Additionally, many traits are underpinned by polygeny and/or incomplete dominance, where the hybrid phenotype is an additive blend of parental characteristics. Phenotypically intermediate hybrids are usually at a fitness disadvantage compared with parental species and tend to vanish through backcrossing with parental population(s). It is therefore unknown whether the additive nature of hybrid traits in itself could lead successfully to HHS. Using a multi-marker genetic data set and a meta-analysis of diet and morphology, we investigated a potential case of HHS in the prions (Pachyptila spp.), seabirds distinguished by their bills, prey choice, and timing of breeding. Using approximate Bayesian computation, we show that the medium-billed Salvin’s prion (Pachyptila salvini) could be a hybrid between the narrow-billed Antarctic prion (Pachyptila desolata) and broad-billed prion (Pachyptila vittata). Remarkably, P. salvini’s intermediate bill width has given it a feeding advantage with respect to the other Pachyptila species, allowing it to consume a broader range of prey, potentially increasing its fitness. Available metadata showed that P. salvini is also intermediate in breeding phenology and, with no overlap in breeding times, it is effectively reproductively isolated from either parental species through allochrony. These results provide evidence for a case of HHS in nature, and show for the first time that additivity of ergent parental traits alone can lead directly to increased hybrid fitness and reproductive isolation.
Publisher: Informa UK Limited
Date: 04-10-2022
Publisher: Wiley
Date: 08-2014
DOI: 10.12705/634.13
Publisher: CSIRO Publishing
Date: 2020
DOI: 10.1071/SB20001
Abstract: Asplenium flabellifolium Cav. is a cytologically variable Australian and New Zealand fern. Here, we sequence chloroplast trnL-trnF and rps4-trnS from s les 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 ersity 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.
Publisher: Springer Science and Business Media LLC
Date: 2005
Publisher: Springer Science and Business Media LLC
Date: 18-12-2021
DOI: 10.1007/S00438-021-01845-3
Abstract: 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 ergence (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.
Publisher: CSIRO Publishing
Date: 2014
DOI: 10.1071/SB14047
Abstract: Asplenium listeri C.Chr. has been considered endemic to Christmas Island and is one of only two fern species listed as Critically Endangered under Australia’s Environment Protection and Bio ersity Conservation Act. Its status as a distinct species has been questioned because of morphological similarity to the widespread A. polyodon G.Forst., which also occurs on Christmas Island. Molecular analyses revealed that A. listeri and plants attributed to A. polyodon from coastal limestone in New Caledonia and Vanuatu share the same rbcL, trnL–trnF and rps4–trnS haplotype and that other s les of A. polyodon in Australia and the south-western Pacific belong to three separate molecular lineages. One of these lineages is formed by epiphytic A. polyodon from Christmas Island and has a chloroplast haplotype closely related to that of A. listeri, differing by four mutations. The A. listeri haplotype and each of the three A. polyodon lineages are associated with morphological characters and are all worthy of recognition as separate species. Asplenium listeri is here expanded to include limestone dwelling populations in the Pacific previously assigned to A. polyodon. This greatly extends the geographic range of A. listeri, and its conservation status should be revised accordingly. Application of correct names to all species in the A. polyodon complex requires further molecular s ling throughout its geographic range and clarification of how type material relates to each of the molecular groups.
Publisher: Proceedings of the National Academy of Sciences
Date: 09-07-2018
Abstract: 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.
Publisher: Informa UK Limited
Date: 18-08-2022
Publisher: CSIRO Publishing
Date: 2014
DOI: 10.1071/SB14024
Abstract: Species boundaries and relationships were investigated in the Asplenium paleaceum (Aspleniaceae) species complex from eastern Australia, using AFLP fingerprinting and chloroplast trnL–trnF and rps4–trnS and nuclear pgiC DNA sequences. Phenetic analyses of AFLP data resulted in the following five distinct groups: (1) A. carnarvonense, (2) A. bicentenniale (including nearby collections originally identified as A. paleaceum), (3) A. paleaceum with both aborted and normal spores, (4) one population of putative tetraploid A. attenuatum var. in isum from south Queensland, and (5) remaining octoploid A. attenuatum populations and several putative hybrids. Taxonomic revision of this complex will require morphological re-circumscription of the current species and recognition of a new species if these AFLP groups are taken to represent separate species. The chloroplast regions, morphology and pgiC together provide good evidence that an Asplenium of unconfirmed identity, A. sp. ‘Kroombit Tops’, is an allopolyploid with a species of the A. paleaceum chloroplast clade, probably A. paleaceum, and distantly related A. polyodon as parents. Further study is required to determine the complete ancestry of the other species of the A. paleaceum complex.
Publisher: Informa UK Limited
Date: 03-2009
Publisher: Public Library of Science (PLoS)
Date: 02-08-2012
Publisher: Cambridge University Press (CUP)
Date: 05-10-2020
DOI: 10.1017/S0959270920000350
Abstract: Cook’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 s les. 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.
Publisher: CSIRO Publishing
Date: 2014
DOI: 10.1071/SB14043
Abstract: Aspleniaceae is one of the largest fern families. It is species-rich in Australasia and the south-western Pacific (ASWP), where approximately 115 species occur. In the current study, the chloroplast regions rbcL, trnL–trnF and rps4–trnS were sequenced for 100 Aspleniaceae s les from ASWP. These data were combined with published sequences for species from New Zealand and other regions for phylogenetic analyses. Species of Aspleniaceae from ASWP were placed in six of the eight previously identified inter-continental clades. The majority of species from ASWP were placed in two of these clades, with the remaining four clades each being represented by three or fewer species. Strong biogeographic affinities with South-east Asia were observed and immigration, rather than local radiations of endemic taxa, appears to have made a more important contribution to patterns of ersity in ASWP. This study supports the current taxonomic practice of recognising two genera, Asplenium L. and Hymenasplenium Hayata, in Aspleniaceae, and identifies future taxonomic work required for the family in this region, including potential synonymising of species, and revision of species complexes or widespread species that are demonstrably non-monophyletic.
Publisher: Wiley
Date: 10-04-2008
Publisher: Springer Science and Business Media LLC
Date: 21-03-2016
Publisher: Proceedings of the National Academy of Sciences
Date: 07-11-2005
Abstract: Microevolution is regarded as changes in the frequencies of genes in populations over time. Ancient DNA technology now provides an opportunity to demonstrate evolution over a geological time frame and to possibly identify the causal factors in any such evolutionary event. Using nine nuclear microsatellite DNA loci, we genotyped an ancient population of Adélie penguins ( Pygoscelis adeliae ) aged ≈6,000 years B.P. Subfossil bones from this population were excavated by using an accurate stratigraphic method that allowed the identification of in iduals even within the same layer. We compared the allele frequencies in the ancient population with those recorded from the modern population at the same site in Antarctica. We report significant changes in the frequencies of alleles between these two time points, hence demonstrating microevolutionary change. This study demonstrates a nuclear gene-frequency change over such a geological time frame. We discuss the possible causes of such a change, including the role of mutation, genetic drift, and the effects of gene mixing among different penguin populations. The latter is likely to be precipitated by mega-icebergs that act to promote migration among penguin colonies that typically show strong natal return.
Publisher: Oxford University Press (OUP)
Date: 03-2020
Publisher: Informa UK Limited
Date: 09-2013
Publisher: Public Library of Science (PLoS)
Date: 25-11-2009
Publisher: Springer Science and Business Media LLC
Date: 19-07-2022
DOI: 10.1038/S41467-022-31508-9
Abstract: Penguins lost the ability to fly more than 60 million years ago, subsequently evolving a hyper-specialized marine body plan. Within the framework of a genome-scale, fossil-inclusive phylogeny, we identify key geological events that shaped penguin ersification and genomic signatures consistent with widespread refugia/recolonization during major climate oscillations. We further identify a suite of genes potentially underpinning adaptations related to thermoregulation, oxygenation, ing, vision, diet, immunity and body size, which might have facilitated their remarkable secondary transition to an aquatic ecology. Our analyses indicate that penguins and their sister group (Procellariiformes) have the lowest evolutionary rates yet detected in birds. Together, these findings help improve our understanding of how penguins have transitioned to the marine environment, successfully colonizing some of the most extreme environments on Earth.
Publisher: Public Library of Science (PLoS)
Date: 10-10-2022
DOI: 10.1371/JOURNAL.PONE.0266430
Abstract: Kiwi are a unique and emblematic group of birds endemic to New Zealand. Deep-time evolutionary relationships among the five extant kiwi species have been difficult to resolve, in part due to the absence of pre-Quaternary fossils to inform speciation events. Here, we utilise single representative nuclear genomes of all five extant kiwi species (great spotted kiwi, little spotted kiwi, Okarito brown kiwi, North Island brown kiwi, and southern brown kiwi) and investigate their evolutionary histories with phylogenomic, genetic ersity, and deep-time (past million years) demographic analyses. We uncover relatively low levels of gene-tree phylogenetic discordance across the genomes, suggesting clear distinction between species. However, we also find indications of post- ergence gene flow, concordant with recent reports of interspecific hybrids. The four species for which unbiased levels of genetic ersity could be calculated, due to the availability of reference assemblies (all species except the southern brown kiwi), show relatively low levels of genetic ersity, which we suggest reflects a combination of older environmental as well as more recent anthropogenic influence. In addition, we suggest hypotheses regarding the impact of known past environmental events, such as volcanic eruptions and glacial periods, on the similarities and differences observed in the demographic histories of the five kiwi species over the past million years.
Publisher: Oxford University Press (OUP)
Date: 07-2005
Abstract: Analysis of nucleotide sequence variation at a microsatellite DNA locus revealed extensive size homoplasy of alleles in Adélie penguins (Pygoscelis adeliae). Variation in the flanking regions at this locus allowed discrimination between mechanisms proposed for length changes in microsatellite DNA alleles. We further examined the structure of alleles for the same microsatellite DNA locus across 11 additional species of penguin (Spheniscidae) by mapping allele sequences onto an independent penguin phylogeny. Our analysis indicated that the repeat motifs appear to have evolved independently on several occasions. We observed sequence instability in the region bordering the repeat tract with a transversional bias predominating. We propose that this bias results from inaccurate DNA replication owing to the sequence context of this repeat tract. Because we show that regions flanking repeat sequences exhibit this mutational bias, this cautions against the use of such regions for phylogeny reconstruction.
Publisher: CSIRO Publishing
Date: 2010
DOI: 10.1071/SB10028
Abstract: The fern Asplenium hookerianum Colenso (Aspleniaceae) is indigenous to New Zealand and Australia. In New Zealand, it is widespread and genetically erse, with 26 haplotypes previously identified for the chloroplast trnL–trnF locus. In Australia, A. hookerianum is currently known only from two small populations in Victoria and two in Tasmania. The present study assessed the ersity, relationships and biogeographic history of the Australian populations. A single trnL–trnF haplotype was identified in Tasmanian populations, and it was shared with populations in south-western New Zealand. The single haplotype found in Victorian populations was unique and most similar to a haplotype found in populations from central and eastern North Island, New Zealand. Relationships among haplotypes suggest that the two Australian haplotypes are derived within the group (not close to the root of the haplotype network) and only distantly related. This pattern is consistent with two independent dispersals of A. hookerianum from New Zealand to Australia. These findings are unique in providing evidence for more than one trans-Tasman dispersal event in a species of vascular plant.
Publisher: Wiley
Date: 21-12-2005
Publisher: Elsevier BV
Date: 07-2021
Publisher: Springer Science and Business Media LLC
Date: 03-04-2020
Publisher: Informa UK Limited
Date: 17-11-2023
Publisher: CSIRO Publishing
Date: 2020
DOI: 10.1071/SB20006
Abstract: 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.
Publisher: Springer Science and Business Media LLC
Date: 10-06-2209
Publisher: Proceedings of the National Academy of Sciences
Date: 17-01-2006
Publisher: Elsevier BV
Date: 05-2007
DOI: 10.1016/J.YMPEV.2006.12.008
Abstract: The monophyly of the endemic New Zealand wattlebirds (Callaeatidae) was examined through the sequencing of nuclear RAG-1 and c-mos genes and comparison to other passerine sequences. The New Zealand wattlebirds were strongly supported to be monophyletic and were nested within Corvida. An estimate for the time of ergence of the New Zealand wattlebirds indicated that the ancestors of this family arrived via transoceanic dispersal after the separation of New Zealand from Gondwana. Long branches separated the three New Zealand wattlebird genera from one another and relationships among them were unresolved, even in analyses including a further 1.5 kb of mitochondrial DNA sequences. However, most of the analyses supported either a basally erging huia or kokako.
Publisher: Informa UK Limited
Date: 12-2013
Publisher: Oxford University Press (OUP)
Date: 05-02-2019
Abstract: The emergence of islands has been linked to spectacular radiations of erse organisms. Although penguins spend much of their lives at sea, they rely on land for nesting, and a high proportion of extant species are endemic to geologically young islands. Islands may thus have been crucial to the evolutionary ersification of penguins. We test this hypothesis using a fossil-calibrated phylogeny of mitochondrial genomes (mitogenomes) from all extant and recently extinct penguin taxa. Our temporal analysis demonstrates that numerous recent island-endemic penguin taxa erged following the formation of their islands during the Plio-Pleistocene, including the Galápagos (Galápagos Islands), northern rockhopper (Gough Island), erect-crested (Antipodes Islands), Snares crested (Snares) and royal (Macquarie Island) penguins. Our analysis also reveals two new recently extinct island-endemic penguin taxa from New Zealand’s Chatham Islands: Eudyptes warhami sp. nov. and a dwarf subspecies of the yellow-eyed penguin, Megadyptes antipodes richdalei ssp. nov. Eudyptes warhami erged from the Antipodes Islands erect-crested penguin between 1.1 and 2.5 Ma, shortly after the emergence of the Chatham Islands (∼3 Ma). This new finding of recently evolved taxa on this young archipelago provides further evidence that the radiation of penguins over the last 5 Ma has been linked to island emergence. Mitogenomic analyses of all penguin species, and the discovery of two new extinct penguin taxa, highlight the importance of island formation in the ersification of penguins, as well as the extent to which anthropogenic extinctions have affected island-endemic taxa across the Southern Hemisphere’s isolated archipelagos.
Publisher: Oxford University Press (OUP)
Date: 09-08-2018
No related grants have been discovered for Lara Shepherd.