ORCID Profile
0000-0001-8008-6083
Current Organisations
University of Adelaide
,
Manaaki Whenua - Landcare Research
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Publisher: Wiley
Date: 11-2017
DOI: 10.1002/ECS2.1997
Publisher: Public Library of Science (PLoS)
Date: 06-01-2021
DOI: 10.1371/JOURNAL.PONE.0243363
Abstract: Globally, wetlands are in decline due to anthropogenic modification and climate change. Knowledge about the spatial distribution of bio ersity and biological processes within wetlands provides essential baseline data for predicting and mitigating the effects of present and future environmental change on these critical ecosystems. To explore the potential for environmental DNA (eDNA) to provide such insights, we used 16S rRNA metabarcoding to characterise prokaryote communities and predict the distribution of prokaryote metabolic pathways in peats and sediments up to 4m below the surface across seven New Zealand wetlands. Our results reveal distinct vertical structuring of prokaryote communities and metabolic pathways in these wetlands. We also find evidence for differences in the relative abundance of certain metabolic pathways that may correspond to the degree of anthropogenic modification the wetlands have experienced. These patterns, specifically those for pathways related to aerobic respiration and the carbon cycle, can be explained predominantly by the expected effects of wetland drainage. Our study demonstrates that eDNA has the potential to be an important new tool for the assessment and monitoring of wetland health.
Publisher: Elsevier BV
Date: 03-2017
Publisher: Public Library of Science (PLoS)
Date: 25-02-2013
Publisher: New Zealand Ecological Society
Date: 2018
Publisher: Elsevier BV
Date: 12-2008
Publisher: Elsevier BV
Date: 02-2016
Publisher: Public Library of Science (PLoS)
Date: 05-11-2014
Publisher: Elsevier BV
Date: 06-2016
Publisher: American Association for the Advancement of Science (AAAS)
Date: 23-05-2014
Abstract: The evolution of the ratite birds has been widely attributed to vicariant speciation, driven by the Cretaceous breakup of the supercontinent Gondwana. The early isolation of Africa and Madagascar implies that the ostrich and extinct Madagascan elephant birds (Aepyornithidae) should be the oldest ratite lineages. We sequenced the mitochondrial genomes of two elephant birds and performed phylogenetic analyses, which revealed that these birds are the closest relatives of the New Zealand kiwi and are distant from the basal ratite lineage of ostriches. This unexpected result strongly contradicts continental vicariance and instead supports flighted dispersal in all major ratite lineages. We suggest that convergence toward gigantism and flightlessness was facilitated by early Tertiary expansion into the diurnal herbivory niche after the extinction of the dinosaurs.
Publisher: Informa UK Limited
Date: 03-07-2019
Publisher: Oxford University Press (OUP)
Date: 05-2017
DOI: 10.1111/ZOJ.12432
Publisher: Informa UK Limited
Date: 18-08-2022
Publisher: Elsevier BV
Date: 10-2013
Publisher: Springer Science and Business Media LLC
Date: 04-02-2015
Publisher: Wiley
Date: 15-01-2019
DOI: 10.1111/AEN.12384
Publisher: Elsevier BV
Date: 04-2018
Publisher: Wiley
Date: 22-05-2020
DOI: 10.1111/JVS.12887
Publisher: The Royal Society
Date: 08-2016
DOI: 10.1098/RSOS.160258
Abstract: Human settlers transported chickens ( Gallus gallus domesticus ) to most East Polynesian archipelagos between AD 1000 and 1300 however, it has long been assumed that New Zealand was an exception. Despite the fact that chicken bones have been recovered from localities of early archaeological middens in New Zealand, their age and genetic relationships have never been critically assessed. Here, we test the assumption that chickens were not introduced to New Zealand during prehistory through ancient DNA and radiocarbon analyses of chicken bones from sites of Māori middens containing prehistoric material. The chickens belong to the widespread mitochondrial control region haplogroup E. Radiocarbon dating reveals that the bones are not prehistoric, but are still the earliest chicken remains known from New Zealand. Two of the bones pre-date permanent European settlement ( ca 1803s onwards) but overlap with the arrival of James Cook's second voyage (1773–1774), and, therefore, they are likely to be chickens, or progeny thereof, liberated during that voyage. Our results support the idea that chickens were first introduced to New Zealand by Europeans, and provide new insights into Māori uptake and integration of resources introduced during the early post-European period.
Publisher: MDPI AG
Date: 07-11-2019
DOI: 10.3390/F10110998
Abstract: C bell Island, which is 600 km south of New Zealand, has the southernmost tree line in this ocean sector. Directly under the maximum of the westerlies, the island is sensitive to changes in wind strength and direction. Pollen records from three peat cores spanning the tree line ecotone provide a 17,000-year history of vegetation change, temperature, and site moisture. With postglacial warming, tundra was replaced by tussock grassland 12,500 years ago. A subsequent increase of shrubland was reversed at 10,500 years ago and wetland-grassland communities became dominant. Around 9000 years ago, trees spread, with maximum tree line elevation reached around 6500 to 3000 years ago. This sequence is out of step with Southern Ocean sea surface temperatures, which were warmer than 12,500 to 9000 years ago, and, subsequently, cooled. C bell Island tree lines were decoupled from temperature trends in the adjacent ocean by weaker westerlies from 12,500 to 9000 years ago, which leads to the intrusion of warmer, cloudier northern airmasses. This reduced solar radiation and evapotranspiration while increasing atmospheric humidity and substrate wetness, which suppressed tree growth. Cooler, stronger westerlies in the Holocene brought clearer skies, drier air, increased evapotranspiration, and rising tree lines. Future global warming will not necessarily lead to rising tree lines in oceanic regions.
Publisher: Wiley
Date: 25-12-2019
DOI: 10.1002/MBO3.780
Publisher: Wiley
Date: 25-02-2019
DOI: 10.1111/GCB.14583
Abstract: Comprehending ecological dynamics requires not only knowledge of modern communities but also detailed reconstructions of ecosystem history. Ancient DNA (aDNA) metabarcoding allows bio ersity responses to major climatic change to be explored at different spatial and temporal scales. We extracted aDNA preserved in fossil rodent middens to reconstruct late Quaternary vegetation dynamics in the hyperarid Atacama Desert. By comparing our paleo-informed millennial record with contemporary observations of interannual variations in ersity, we show local plant communities behave differentially at different timescales. In the interannual (years to decades) time frame, only annual herbaceous expand and contract their distributional ranges (emerging from persistent seed banks) in response to precipitation, whereas perennials distribution appears to be extraordinarily resilient. In contrast, at longer timescales (thousands of years) many perennial species were displaced up to 1,000 m downslope during pluvial events. Given ongoing and future natural and anthropogenically induced climate change, our results not only provide baselines for vegetation in the Atacama Desert, but also help to inform how these and other high mountain plant communities may respond to fluctuations of climate in the future.
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: Elsevier BV
Date: 12-2014
Publisher: Cambridge University Press (CUP)
Date: 20-03-2018
DOI: 10.1017/S0031182018000380
Abstract: Ancient s les present a number of technical challenges for DNA barcoding, including damaged DNA with low endogenous copy number and short fragment lengths. Nevertheless, techniques are available to overcome these issues, and DNA barcoding has now been used to successfully recover parasite DNA from a wide variety of ancient substrates, including coprolites, cesspit sediment, mummified tissues, burial sediments and permafrost soils. The study of parasite DNA from ancient s les can provide a number of unique scientific insights, for ex le: (1) into the parasite communities and health of prehistoric human populations (2) the ability to reconstruct the natural parasite faunas of rare or extinct host species, which has implications for conservation management and de-extinction and (3) the ability to view in ‘real-time’ processes that may operate over century- or millenial-timescales, such as how parasites responded to past climate change events or how they co-evolved alongside their hosts. The application of DNA metabarcoding and high-throughput sequencing to ancient specimens has so far been limited, but in future promises great potential for gaining empirical data on poorly understood processes such as parasite co-extinction.
Publisher: Elsevier BV
Date: 04-2019
DOI: 10.1016/J.EJOP.2018.12.002
Abstract: Methodological advances are essential for robust ecological research. Quantitative reconstructions of environmental conditions using testate amoebae rely on sound taxonomy. While the taxonomy of large species is relatively well resolved, this is not the case for most small taxa (typically <45 μm long). In New Zealand, peatlands contain a ersity of both cosmopolitan and characteristic large southern endemic taxa, but also have a high abundance of small taxa. The latter are often lumped into morphotypes reducing their value as ecological indicators. In this study, we demonstrate how (a) lumping small taxa versus splitting them into unique types, and (b) including or excluding them from community analysis influenced their ecological inference. We assessed testate amoeba composition in six peat bogs from New Zealand, three that were moderately-to-highly impacted, and three that were non-impacted. Environmental variables were measured at each s ling site and the surface testate amoeba community patterns and community-environment relationships compared. We found a clear ision between impacted and non-impacted sites. Several distinct small taxa were more strongly related to water-table depth and conductivity, while the larger taxa were more correlated to pH. These results show that improved taxonomic resolution of small taxa can provide more informed environmental assessment.
Publisher: Wiley
Date: 08-2019
DOI: 10.1111/MEC.15177
Abstract: Little is known about the ersity patterns of plant pathogens and how they change with land use at a broad scale. We employed DNA metabarcoding to describe the ersity and composition of putative plant pathogen communities in three substrates (soil, roots, and leaves) across five major land uses at a national scale. Almost all plant pathogen communities (fungi, oomycetes, and bacteria) showed strong responses to land use and substrate type. Land use category could explain up to 24% of the variance in composition between communities. Alpha- ersity (richness) of plant pathogens was consistently lower in natural forests than in agricultural systems. In planted forests, there was also generally low pathogen alpha- ersity in soil and roots, but alpha- ersity in leaves was high compared with most other land uses. In contrast to alpha- ersity, differences in within-land use beta- ersity of plant pathogens (the predictability of plant pathogen communities within land use) were subtle. Our results show that large-scale patterns and distributions of putative plant pathogens can be determined using metabarcoding, allowing some of the first landscape level insights into these critically important communities.
Publisher: Elsevier BV
Date: 04-2011
Publisher: The Royal Society
Date: 18-04-2018
Abstract: Often the mutualistic roles of extinct species are inferred based on plausible assumptions, but sometimes palaeoecological evidence can overturn such inferences. We present an ex le from New Zealand, where it has been widely assumed that some of the largest-seeded plants were dispersed by the giant extinct herbivorous moa (Dinornithiformes). The presence of large seeds in preserved moa gizzard contents supported this hypothesis, and five slow-germinating plant species ( Elaeocarpus dentatus, E. hookerianus, Prumnopitys ferruginea, P. taxifolia, Vitex lucens ) with thick seedcoats prompted speculation about whether these plants were adapted for moa dispersal. However, we demonstrate that all these assumptions are incorrect. While large seeds were present in 48% of moa gizzards analysed, analysis of 152 moa coprolites (subfossil faeces) revealed a very fine-grained consistency unparalleled in extant herbivores, with no intact seeds larger than 3.3 mm diameter. Secondly, prolonged experimental mechanical scarification of E. dentatus and P. ferruginea seeds did not reduce time to germination, providing no experimental support for the hypothesis that present-day slow germination results from the loss of scarification in moa guts. Paradoxically, although moa were New Zealand's largest native herbivores, the only seeds to survive moa gut passage intact were those of small-seeded herbs and shrubs.
Publisher: Informa UK Limited
Date: 07-09-2022
Publisher: Wiley
Date: 15-12-2014
Publisher: Cold Spring Harbor Laboratory
Date: 10-02-2023
DOI: 10.1101/2023.02.09.526923
Abstract: The drivers and dynamics of initial human migrations across in idual islands and archipelagos are poorly understood, affecting assessments of human-modification of island bio ersity. Here, we describe and test a process-explicit approach for reconstructing human arrival and expansion on islands, which combines archaeological and climate records with high-resolution spatial population models. Using Polynesian colonisation of New Zealand as an ex le, we show that our new method can generate information crucial for assessing how humans affected bio ersity on islands. The transition of islands from prehuman to human dominated ecosystems has typically been assessed by comparing bio ersity before and after time of first arrival, without considering the potential importance of the spatiotemporal dynamics of the human expansion event. Our new approach, which uses pattern-oriented modelling methods to combine inferences of human colonisation dynamics from dated archaeological material with spatially explicit population models, produces validated reconstructions of the pattern and pace of human migration across islands at high spatiotemporal resolutions. From these reconstructions, demographic and environmental drivers of human colonization can be identified, and the role that people had on bio ersity established. Using this technique, we show that closely reconciling inferences of Polynesian colonisation of New Zealand requires there to have been a single founding population of approximately 500 people, arriving between 1233 and 1257 AD, settling multiple areas, and expanding quickly over both North and South islands. The resultant maps of Māori colonisation dynamics provide new opportunities to better determine how human activities transformed bio ersity of New Zealand in space and time. Process-explicit models can reconstruct human migration across large islands, producing validated, high resolution spatiotemporal projections of human occupancy and abundance that account for dispersal and population dynamics. This modelling framework should prove effective across any islands and archipelagos where climate and archaeological records are available.
Publisher: Proceedings of the National Academy of Sciences
Date: 13-02-2018
Abstract: Over the past 50,000 y, biotic extinctions and declines have left a legacy of vacant niches and broken ecological interactions across global terrestrial ecosystems. Reconstructing the natural, unmodified ecosystems that preceded these events relies on high-resolution analyses of paleoecological deposits. Coprolites are a source of uniquely detailed information about trophic interactions and the behaviors, gut parasite communities, and microbiotas of prehistoric animal species. Such insights are critical for understanding the legacy effects of extinctions on ecosystems, and can help guide contemporary conservation and ecosystem restoration efforts. Here we use high-throughput sequencing (HTS) of ancient eukaryotic DNA from coprolites to reconstruct aspects of the biology and ecology of four species of extinct moa and the critically endangered kakapo parrot from New Zealand (NZ). Importantly, we provide evidence that moa and prehistoric kakapo consumed ectomycorrhizal fungi, suggesting these birds played a role in dispersing fungi that are key to NZ’s natural forest ecosystems. We also provide the first DNA-based evidence that moa frequently supplemented their broad diets with ferns and mosses. Finally, we also find parasite taxa that provide insight into moa behavior, and present data supporting the hypothesis of coextinction between moa and several parasite species. Our study demonstrates that HTS sequencing of coprolites provides a powerful tool for resolving key aspects of ancient ecosystems and may rapidly provide information not obtainable by conventional paleoecological techniques, such as fossil analyses.
Publisher: Wiley
Date: 10-2012
DOI: 10.1111/J.1523-1739.2012.01931.X
Abstract: Late Quaternary extinctions and population fragmentations have severely disrupted animal‐plant interactions globally. Detection of disrupted interactions often relies on anachronistic plant characteristics, such as spines in the absence of large herbivores or large fruit without dispersers. However, obvious anachronisms are relatively uncommon, and it can be difficult to prove a direct link between the anachronism and a particular faunal taxon. Analysis of coprolites (fossil feces) provides a novel way of exposing lost interactions between animals (depositors) and consumed organisms. We analyzed ancient DNA to show that a coprolite from the South Island of New Zealand was deposited by the rare and threatened kakapo ( Strigops habroptilus ), a large, nocturnal, flightless parrot. When we analyzed the pollen and spore content of the coprolite, we found pollen from the cryptic root‐parasite Dactylanthus taylorii . The relatively high abundance (8.9% of total pollen and spores) of this zoophilous pollen type in the coprolite supports the hypothesis of a former direct feeding interaction between kakapo and D. taylorii . The ranges of both species have contracted substantially since human settlement, and their present distributions no longer overlap. Currently, the lesser short‐tailed bat ( Mystacina tuberculata ) is the only known native pollinator of D. taylorii, but our finding raises the possibility that birds, and other small fauna, could have once fed on and pollinated the plant. If confirmed, through experimental work and observations, this finding may inform conservation of the plant. For ex le, it may be possible to translocate D. taylorii to predator‐free offshore islands that lack bats but have thriving populations of endemic nectar‐feeding birds. The study of coprolites of rare or extinct taxonomic groups provides a unique way forward to expand existing knowledge of lost plant and animal interactions and to identify pollination and dispersal syndromes. This approach of linking paleobiology with neoecology offers significant untapped potential to help inform conservation and restoration plans . Un Eslabón Perdido entre un Loro No Volador y una Planta Parásita y el Papel Potencial de Coprolitos en Paleobiología de la Conservación
Publisher: Proceedings of the National Academy of Sciences
Date: 13-08-2014
Publisher: Informa UK Limited
Date: 12-2011
Publisher: Informa UK Limited
Date: 11-07-2022
Publisher: Elsevier BV
Date: 04-2016
Publisher: Informa UK Limited
Date: 09-2008
Publisher: Wiley
Date: 02-11-2016
DOI: 10.1111/JVS.12469
Publisher: Elsevier BV
Date: 02-2019
DOI: 10.1016/J.YMPEV.2018.10.025
Abstract: Human impacts have substantially reduced avian bio ersity in many parts of the world, particularly on isolated islands of the Pacific Ocean. The New Zealand archipelago, including its five subantarctic island groups, holds breeding grounds for a third of the world's penguin species, including several representatives of the erse crested penguin genus Eudyptes. While this species-rich genus has been little studied genetically, recent population estimates indicate that several Eudyptes taxa are experiencing demographic declines. Although crested penguins are currently limited to southern regions of the New Zealand archipelago, prehistoric fossil and archaeological deposits suggest a wider distribution during prehistoric times, with breeding ranges perhaps extending to the North Island. Here, we analyse ancient, historic and modern DNA sequences to explore two hypotheses regarding the recent history of Eudyptes in New Zealand, testing for (1) human-driven extinction of Eudyptes lineages and (2) reduced genetic ersity in surviving lineages. From 83 prehistoric bone s les, each tentatively identified as 'Eudyptes spp.', we genetically identified six prehistoric penguin taxa from mainland New Zealand, including one previously undescribed genetic lineage. Moreover, our Bayesian coalescent analyses indicated that, while the range of Fiordland crested penguin (E. pachyrhynchus) may have contracted markedly over the last millennium, genetic DNA ersity within this lineage has remained relatively constant. This result contrasts with human-driven bio ersity reductions previously detected in several New Zealand coastal vertebrate taxa.
Publisher: Elsevier BV
Date: 09-2012
Publisher: Wiley
Date: 19-06-2018
DOI: 10.1111/ENS.12316
Publisher: Proceedings of the National Academy of Sciences
Date: 30-09-2013
Abstract: Coprolites provide unique insights into the plant taxa consumed over a discrete time period by extinct herbivores and have typically been used to reconstruct the diets of single herbivore species. Through ancient DNA, pollen, and plant macrofossil analyses of 51 coprolites deposited by four species of extinct herbivore (the large avian moa of New Zealand) in a single rock shelter, we show the potential for coprolites to also resolve broader paleoecological questions around niche partitioning of extinct sympatric herbivore species and prehistoric herbivore community structure. Such information can help in our understanding of late Quaternary ecosystem functioning and the ecological consequences of prehistoric extinctions, as well as helping to inform rewilding efforts.
Publisher: New Zealand Ecological Society
Date: 18-01-2019
Publisher: Informa UK Limited
Date: 12-2013
Publisher: Informa UK Limited
Date: 09-2011
Publisher: Springer Science and Business Media LLC
Date: 21-11-2018
DOI: 10.1038/S41598-018-35299-2
Abstract: Future climate change has the potential to alter the distribution and prevalence of plant pathogens, which may have significant implications for both agricultural crops and natural plant communities. However, there are few long-term datasets against which modelled predictions of pathogen responses to climate change can be tested. Here, we use 18S metabarcoding of 28 rodent middens (solidified deposits of rodent coprolites and nesting material) from the Central Atacama, spanning the last ca. 49 ka, to provide the first long-term late Quaternary record of change in plant pathogen communities in response to changing climate. Plant pathogen richness was significantly greater in middens deposited during the Central Andean Pluvial Event (CAPE) a period of increased precipitation between 17.5–8.5 ka. Moreover, the occurrence frequency of Pucciniaceae (rust fungi) was significantly greater during the CAPE, and the highest relative abundances for five additional potentially pathogenic taxa also occurred during this period. The results demonstrate the promising potential for ancient DNA analysis of late Quaternary s les to reveal insights into how plant pathogens responded to past climatic and environmental change, which could help predict how pathogens may responded to future change.
Publisher: Wiley
Date: 12-2020
DOI: 10.1111/ECOG.04917
Publisher: Elsevier BV
Date: 12-2019
Publisher: Elsevier BV
Date: 09-2016
DOI: 10.1016/J.YMPEV.2016.05.038
Abstract: The New Zealand acanthisittid wrens are the sister-taxon to all other "perching birds" (Passeriformes) and - including recently extinct species - represent the most erse endemic passerine family in New Zealand. Consequently, they are important for understanding both the early evolution of Passeriformes and the New Zealand biota. However, five of the seven species have become extinct since the arrival of humans in New Zealand, complicating evolutionary analyses. The results of morphological analyses have been largely equivocal, and no comprehensive genetic analysis of Acanthisittidae has been undertaken. We present novel mitochondrial genome sequences from four acanthisittid species (three extinct, one extant), allowing us to resolve the phylogeny and revise the taxonomy of acanthisittids. Reanalysis of morphological data in light of our genetic results confirms a close relationship between the extant rifleman (Acanthisitta chloris) and an extinct Miocene wren (Kuiornis indicator), making Kuiornis a useful calibration point for molecular dating of passerines. Our molecular dating analyses reveal that the stout-legged wrens (Pachyplichas) erged relatively recently from a more gracile (Xenicus-like) ancestor. Further, our results suggest a possible Early Oligocene origin of the basal Lyall's wren (Traversia) lineage, which would imply that Acanthisittidae survived the Oligocene marine inundation of New Zealand and therefore that the inundation was not complete.
Publisher: Magnolia Press
Date: 11-2018
DOI: 10.11646/PHYTOTAXA.374.1.8
Abstract: We report a partial cpDNA trnL sequence of 203 base pairs from the extinct legume Streblorrhiza speciosa that was obtained from herbarium specimens collected from Phillip Island, south-western Pacific Ocean, in 1836. Bayesian phylogenetic analysis of the trnL sequence of S. speciosa and those of other Fabaceae species placed S. speciosa as a member of the tribe Coluteae, along with the Australian and New Zealand genera Carmichaelia, Clianthus, Montigena and Swainsona. Smaller genetic distances and shared morphological features indicate stronger links within this group may exist between S. speciosa and Carmichaelia.
Publisher: Springer Science and Business Media LLC
Date: 31-03-2021
Publisher: Wiley
Date: 02-04-2018
DOI: 10.1002/ECE3.3998
Publisher: eLife Sciences Publications, Ltd
Date: 19-05-2020
DOI: 10.7554/ELIFE.52787
Abstract: The effects of land use on soil invertebrates – an important ecosystem component – are poorly understood. We investigated land-use impacts on a comprehensive range of soil invertebrates across New Zealand, measured using DNA metabarcoding and six bio ersity metrics. Rarity and phylogenetic rarity – direct measures of the number of species or the portion of a phylogeny unique to a site – showed stronger, more consistent responses across taxa to land use than widely used metrics of species richness, effective species numbers, and phylogenetic ersity. Overall, phylogenetic rarity explained the highest proportion of land use-related variance. Rarity declined from natural forest to planted forest, grassland, and perennial cropland for most soil invertebrate taxa, demonstrating pervasive impacts of agricultural land use on soil invertebrate communities. Commonly used ersity metrics may underestimate the impacts of land use on soil invertebrates, whereas rarity provides clearer and more consistent evidence of these impacts.
Publisher: Informa UK Limited
Date: 02-04-2016
Publisher: Wiley
Date: 03-04-2017
DOI: 10.1111/NPH.14470
Abstract: Contents Summary 924 I. Introduction 925 II. Environmental and temporal limits for survival of aDNA 925 III. Lake sediments 927 IV. Perspective for plant aDNA research 929 V. Perspective for plant aDNA research 930 VI. Pollen DNA 930 VII. Sedimentary aDNA 931 VIII. Recent key findings and future methods using HTS techniques 933 IX. Challenges when studying aDNA from lake sediments 935 X. Bioinformatic processing 936 XI. Conclusions and directions for future research 938 Acknowledgements 938 References 938 Recent advances in sequencing technologies now permit the analyses of plant DNA from fossil s les (ancient plant DNA , plant aDNA ), and thus enable the molecular reconstruction of palaeofloras. Hitherto, ancient frozen soils have proved excellent in preserving DNA molecules, and have thus been the most commonly used source of plant aDNA . However, DNA from soil mainly represents taxa growing a few metres from the s ling point. Lakes have larger catchment areas and recent studies have suggested that plant aDNA from lake sediments is a more powerful tool for palaeofloristic reconstruction. Furthermore, lakes can be found globally in nearly all environments, and are therefore not limited to perennially frozen areas. Here, we review the latest approaches and methods for the study of plant aDNA from lake sediments and discuss the progress made up to the present. We argue that aDNA analyses add new and additional perspectives for the study of ancient plant populations and, in time, will provide higher taxonomic resolution and more precise estimation of abundance. Despite this, key questions and challenges remain for such plant aDNA studies. Finally, we provide guidelines on technical issues, including lake selection, and we suggest directions for future research on plant aDNA studies in lake sediments.
Publisher: Public Library of Science (PLoS)
Date: 29-06-2012
Publisher: Elsevier BV
Date: 07-2016
Publisher: New Zealand Ecological Society
Date: 2017
Publisher: Cambridge University Press (CUP)
Date: 24-07-2017
DOI: 10.1017/S037689291700039X
Abstract: Extinctions have altered island ecosystems throughout the late Quaternary. Here, we review the main historic drivers of extinctions on islands, patterns in extinction chronologies between islands, and the potential for restoring ecosystems through reintroducing extirpated species. While some extinctions have been caused by climatic and environmental change, most have been caused by anthropogenic impacts. We propose a general model to describe patterns in these anthropogenic island extinctions. Hunting, habitat loss and the introduction of invasive predators accompanied prehistoric settlement and caused declines of endemic island species. Later settlement by European colonists brought further land development, a different suite of predators and new drivers, leading to more extinctions. Extinctions alter ecological networks, causing ripple effects for islands through the loss of ecosystem processes, functions and interactions between species. Reintroduction of extirpated species can help restore ecosystem function and processes, and can be guided by palaeoecology. However, reintroduction projects must also consider the cultural, social and economic needs of humans now inhabiting the islands and ensure resilience against future environmental and climate change.
Publisher: Elsevier BV
Date: 2014
DOI: 10.1016/J.YMPEV.2013.08.017
Abstract: The Chatham duck (Pachyanas chathamica) represented one of just three modern bird genera endemic to the Chatham archipelago (situated ~850 km east of New Zealand) but became extinct soon after humans first settled the islands (c. 13th-15th centuries AD). The taxonomic affinity of the Chatham duck remains largely unresolved previous studies have tentatively suggested placements within both Tadornini (shelducks) and Anatini (dabbling ducks). Herein, we sequence a partial mitochondrial genome (excluding the D-loop) from the Chatham duck and discover that it was a phenotypically- ergent species within the genus Anas (Anatini). This conclusion is further supported by a re-examination of osteological characters. Our molecular analyses convincingly demonstrate that the Chatham duck is the most basal member of a sub-clade comprising the New Zealand and sub-Antarctic brown teals (the brown teal [A. chlorotis], Auckland Island teal [A. aucklandica] and C bell Island teal [A. nesiotis]). Molecular clock calculations based on an ingroup fossil calibration support a ergence between the Chatham duck and its sister-taxa that is consistent with the estimated time of emergence of the Chatham Islands. Additionally, we find that mtDNA ergence between the two sub-Antarctic teal species (A. aucklandica and A. nesiotis) significantly pre-dates the last few glacial cycles, raising interesting questions about the timing of their dispersal to these islands, and the recent phylogeographic history of brown teal lineages in the region.
Publisher: Wiley
Date: 19-12-2015
Publisher: Wiley
Date: 20-10-2016
Publisher: New Zealand Ecological Society
Date: 2017
Publisher: Oxford University Press (OUP)
Date: 28-08-2014
DOI: 10.1111/ZOJ.12164
Publisher: Oxford University Press (OUP)
Date: 08-2017
DOI: 10.1111/ZOJ.12483
Publisher: Wiley
Date: 24-10-2012
DOI: 10.1002/JQS.1539
Publisher: Wiley
Date: 11-09-2013
DOI: 10.1111/COBI.12150
Abstract: Islands play a key role globally in the conservation of endemic species. Many island reserves have been highly modified since human colonization, and their restoration and management usually occur without knowledge of their prehuman state. However, conservation paleoecology is increasingly being recognized as a tool that can help to inform both restoration and conservation of island reserves by providing prehuman vegetation baselines. Many of New Zealand's mammal‐free offshore islands are foci for biological ersity conservation and, like many islands in the Polynesian region, were deforested following initial human settlement. Therefore, their current restoration, replanting, and management are guided either by historic vegetation descriptions or the occurrence of species on forested islands. We analyzed pollen and ancient DNA in soil cores from an offshore island in northern New Zealand. The result was a 2000‐year record of vegetation change that began years before human settlement and spanned 550 years of human occupation and 180 years of forest succession since human occupation ceased. Between prehuman and contemporary forests there was nearly a complete species turnover including the extirpation of a dominant conifer and a palm tree. The podocarp‐dominated forests were replaced by a native but novel angiosperm‐dominated forest. There is no modern analog of the prehuman forests on any northern New Zealand island, and those islands that are forested are dominated by angiosperms which are assumed to be climax forests. The pollen and DNA evidence for conifer‐ and palm‐rich forests in the prehuman era challenge this climax forest assumption. Prehuman vegetation records can thus help to inform future restoration of degraded offshore islands by informing the likely rate and direction of successional change helping to determine whether natural rates of succession are preferable to more costly replanting programs and providing past species lists if restoration replanting is desired. Uso de Polen y ADN Antiguo como Líneas de Base de Conservación en Islas Litorales en Nueva Zelanda
Publisher: Elsevier BV
Date: 2017
DOI: 10.1016/J.YMPEV.2016.09.022
Abstract: The relationships of the extinct New Zealand ravens (Corvus spp.) are poorly understood. We sequenced the mitogenomes of the two currently recognised species and found they were sister-taxa to a clade comprising the Australian raven, little raven, and forest raven (C.coronoides, C. mellori and C. tasmanicus respectively). The ergence between the New Zealand ravens and Australian raven clade occurred in the latest Pliocene, which coincides with the onset of glacial deforestation. We also found that the ergence between the two putative New Zealand species C. antipodum and C. moriorum probably occurred in the late Pleistocene making their separation as species untenable. Consequently, we consider Corax antipodum (Forbes, 1893) to be a subspecies of Corvus moriorum Forbes, 1892. We re-examine the osteological evidence that led 19th century researchers to assign the New Zealand taxa to a separate genus, and re-assess these features in light of our new phylogenetic hypotheses. Like previous researchers, we conclude that the morphology of the palate of C. moriorum is unique among the genus Corvus, and suggest this may be an adaptation for a specialist diet.
Publisher: Wiley
Date: 10-2014
DOI: 10.1002/JQS.2740
Publisher: Informa UK Limited
Date: 25-09-2018
Publisher: Elsevier BV
Date: 08-2014
Publisher: Elsevier BV
Date: 04-2016
Publisher: Elsevier BV
Date: 02-2018
Publisher: Oxford University Press (OUP)
Date: 04-2015
DOI: 10.1642/AUK-14-257.1
Publisher: Proceedings of the National Academy of Sciences
Date: 17-03-2014
Abstract: Ancient DNA sequences from chickens provide an opportunity to study their human-mediated dispersal across the Pacific due to the significant genetic ersity and range of archaeological material available. We analyze ancient and modern material and reveal that previous studies have been impacted by contamination with modern chicken DNA and, that as a result, there is no evidence for Polynesian dispersal of chickens to pre-Columbian South America. We identify genetic markers of authentic ancient Polynesian chickens and use them to model early chicken dispersals across the Pacific. We find connections between chickens in the Micronesian and Bismarck Islands, but no evidence these were involved in dispersals further east. We also find clues about the origins of Polynesian chickens in the Philippines.
Publisher: SAGE Publications Ltd
Date: 2012
Publisher: New Zealand Ecological Society
Date: 07-02-2020
Publisher: Public Library of Science (PLoS)
Date: 04-04-2019
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: Informa UK Limited
Date: 09-2013
Publisher: New Zealand Ecological Society
Date: 2021
Publisher: New Zealand Ecological Society
Date: 11-2022
Publisher: Springer Science and Business Media LLC
Date: 30-09-2015
Publisher: The Royal Society
Date: 07-2009
Abstract: Feathers are known to contain lifiable DNA at their base (calamus) and have provided an important genetic source from museum specimens. However, feathers in subfossil deposits generally only preserve the upper shaft and feather ‘vane’ which are thought to be unsuitable for DNA analysis. We analyse subfossil moa feathers from Holocene New Zealand rockshelter sites and demonstrate that both ancient DNA and plumage information can be recovered from their upper portion, allowing species identification and a means to reconstruct the appearance of extinct taxa. These ancient DNA sequences indicate that the distal portions of feathers are an untapped resource for studies of museum, palaeontological and modern specimens. We investigate the potential to reconstruct the plumage of pre-historically extinct avian taxa using subfossil remains, rather than assuming morphological uniformity with closely related extant taxa. To test the notion of colour persistence in subfossil feathers, we perform digital comparisons of feathers of the red-crowned parakeet ( Cyanor hus novaezelandiae novaezelandiae ) excavated from the same horizons as the moa feathers, with modern s les. The results suggest that the coloration of the moa feathers is authentic, and computer software is used to perform plumage reconstructions of moa based on subfossil remains.
Publisher: Wiley
Date: 29-10-2022
DOI: 10.1111/NPH.17797
Abstract: Interactions between in idual plant pathogens and their environment have been described many times. However, the relative contribution of different environmental parameters as controls of pathogen communities remains largely unknown. Here we investigate the importance of environmental factors, including geomorphology, climate, land use, soil and plant community composition, for a broad range of aboveground and belowground fungal, oomycete and bacterial plant pathogens. We found that plant community composition is the main driver of the composition and richness of plant pathogens after taking into account all other tested parameters, especially those related to climate and soil. In the face of future changes in climate and land use, our results suggest that changes in plant pathogen community composition and richness will primarily be mediated through changes in plant communities, rather than the direct effects of climate or soils.
Publisher: Oxford University Press (OUP)
Date: 09-08-2018
Publisher: Informa UK Limited
Date: 06-2008
Publisher: eLife Sciences Publications, Ltd
Date: 04-03-2020
Start Date: 2017
End Date: 2020
Funder: Marsden Fund
View Funded ActivityStart Date: 2020
End Date: 2023
Funder: Marsden Fund
View Funded Activity