ORCID Profile
0000-0003-4454-2576
Current Organisation
The University of Auckland
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Publisher: Wiley
Date: 08-04-2019
DOI: 10.1002/EAP.1877
Abstract: Invertebrates are a major component of terrestrial ecosystems, however, estimating their bio ersity is challenging. We compiled an inventory of invertebrate bio ersity along an elevation gradient on the temperate forested island of Hauturu, New Zealand, by DNA barcoding of specimens obtained from leaf litter s les and pitfall traps. We compared the barcodes and bio ersity estimates from this data set with those from a parallel DNA metabarcoding analysis of soil from the same locations, and with pre-existing sequences in reference databases, before exploring the use of combined data sets as a basis for estimating total invertebrate bio ersity. We obtained 1,282 28S and 1,610 COI barcodes from a total of 1,947 invertebrate specimens, which were clustered into 247 (28S) and 366 (COI) OTUs, of which ≤ 10% were represented in GenBank. Coleoptera were most abundant (730 sequenced specimens), followed by Hymenoptera, Diptera, Lepidoptera, and Amphipoda. The most abundant OTU from both the 28S (153 sequences) and COI (140 sequences) data sets was an undescribed beetle from the family Salpingidae. Based on the occurrences of COI OTUs along the elevation gradient, we estimated there are ~1,000 arthropod species (excluding mites) on Hauturu, including 770 insects, of which 344 are beetles. A DNA metabarcoding analysis of soil DNA from the same sites resulted in the identification of similar numbers of OTUs in most invertebrate groups compared with the DNA barcoding, but less than 10% of the DNA barcoding COI OTUs were also detected by the metabarcoding analysis of soil DNA. A mark-recapture analysis based on the overlap between these data sets estimated the presence of approximately 6,800 arthropod species (excluding mites) on the island, including ~3,900 insects. Estimates of New Zealand-wide bio ersity for selected arthropod groups based on matching of the COI DNA barcodes with pre-existing reference sequences suggested over 13,200 insect species are present, including 4,000 Coleoptera, 2,200 Diptera, and 2,700 Hymenoptera species, and 1,000 arachnid species (excluding mites). These results confirm that metabarcoding analyses of soil DNA tends to recover different components of terrestrial invertebrate bio ersity compared to traditional invertebrate s ling, but the combined methods provide a novel basis for estimating invertebrate bio ersity.
Publisher: Wiley
Date: 27-09-2018
Publisher: Elsevier BV
Date: 07-2005
Publisher: Oxford University Press (OUP)
Date: 28-01-2016
Publisher: American Association for the Advancement of Science (AAAS)
Date: 24-08-2012
Abstract: English is part of the large Indo-European language family, which includes Celtic, Germanic, Italic, Balto-Slavic, and Indo-Iranian languages. The origin of this family is hotly debated: one hypothesis places the origin north of the Caspian Sea in the Pontic steppes, from where it was disseminated by Kurgan semi-nomadic pastoralists a second suggests that Anatolia, in modern-day Turkey, is the source, and the language radiated with the spread of agriculture. Bouckaert et al. (p. 957 ) used phylogenetic methods and modeling to assess the geographical spread of the Indo-European language group. The findings support the suggestion that the origin of the language family was indeed Anatolia 7 to 10 thousand years ago—contemporaneous with the spread of agriculture.
Publisher: American Association for the Advancement of Science (AAAS)
Date: 22-03-2002
Abstract: Well-preserved subfossil bones of Adélie penguins, Pygoscelis adeliae , underlie existing and abandoned nesting colonies in Antarctica. These bones, dating back to more than 7000 years before the present, harbor some of the best-preserved ancient DNA yet discovered. From 96 radiocarbon-aged bones, we report large numbers of mitochondrial haplotypes, some of which appear to be extinct, given the 380 living birds s led. We demonstrate DNA sequence evolution through time and estimate the rate of evolution of the hypervariable region I using a Markov chain Monte Carlo integration and a least-squares regression analysis. Our calculated rates of evolution are approximately two to seven times higher than previous indirect phylogenetic estimates.
Publisher: Springer Science and Business Media LLC
Date: 09-2003
DOI: 10.1038/NATURE01871
Publisher: Oxford University Press (OUP)
Date: 06-2007
Publisher: Public Library of Science (PLoS)
Date: 10-03-2010
Publisher: Springer Berlin Heidelberg
Date: 2007
Publisher: Elsevier BV
Date: 11-2005
DOI: 10.1016/J.YMPEV.2005.03.020
Abstract: The resolution of higher level phylogeny of the coleoid cephalopods (octopuses, squids, and cuttlefishes) has been hindered by homoplasy among morphological characters in conjunction with a very poor fossil record. Initial molecular studies, based primarily on small fragments of single mitochondrial genes, have produced little resolution of the deep relationships amongst coleoid cephalopod families. The present study investigated this issue using 3415 base pairs (bp) from three nuclear genes (octopine dehydrogenase, pax-6, and rhodopsin) and three mitochondrial genes (12S rDNA, 16S rDNA, and cytochrome oxidase I) from a total of 35 species (including representatives of each of the higher level taxa). Bayesian analyses were conducted on mitochondrial and nuclear genes separately and also all six genes together. Separate analyses were conducted with the data partitioned by gene, codon/rDNA, gene+codon/rDNA or not partitioned at all. In the majority of analyses partitioning the data by gene+codon was the appropriate model with partitioning by codon the second most selected model. In some instances the topology varied according to the model used. Relatively high posterior probabilities and high levels of congruence were present between the topologies resulting from the analysis of all Octopodiform (octopuses and v ire "squid") taxa for all six genes, and independently for the datasets of mitochondrial and nuclear genes. In contrast, the highest levels of resolution within the Decapodiformes (squids and cuttlefishes) resulted from analysis of nuclear genes alone. Different higher level Decapodiform topologies were obtained through the analysis of only the 1st+2nd codon positions of nuclear genes and of all three codon positions. It is notable that there is strong evidence of saturation among the 3rd codon positions within the Decapodiformes and this may contribute spurious signal. The results suggest that the Decapodiformes may have radiated earlier and/or had faster rates of evolution than the Octopodiformes. The following taxonomic conclusions are drawn from our analyses: (1) the order Octopoda and suborders Cirrata, Incirrata, and Oegopsida are monophyletic groups (2) the family Spirulidae (Ram's horn squids) are the sister taxon to the family Sepiidae (cuttlefishes) (3) the family Octopodidae, as currently defined, is paraphyletic (4) the superfamily Argonautoidea are basal within the suborder Incirrata and (5) the benthic octopus genera Benthoctopus and Enteroctopus are sister taxa.
Publisher: Oxford University Press (OUP)
Date: 04-12-2009
Publisher: Public Library of Science (PLoS)
Date: 08-04-2019
Publisher: Oxford University Press (OUP)
Date: 14-04-2017
Publisher: Wiley
Date: 31-01-2006
DOI: 10.1111/J.1096-0031.2006.00086.X
Abstract: This is the first study to use both molecular and fossil data to date the ergence of taxa within the coleoid cephalopods (octopus, squid, cuttlefish). A dataset including sequences from three nuclear and three mitochondrial genes (3415 bp in total) was used to investigate the evolutionary ergences within the group. Divergence time analyses were performed using the Thorne/Kishino method of analysis which allows multiple constraints from the fossil record and permits rates of molecular evolution to vary on different branches of a phylogenetic tree. The data support a Paleozoic origin of the Orders V yromorpha, Octopoda and the majority of the extant higher level decapodiform taxa. These estimated ergence times are considerably older than paleontological estimates. The major lineages within the Order Octopoda were estimated to have erged in the Mesozoic, with a radiation of many taxa around the Cretaceous/Cenozoic boundary. Higher level decapodiform phylogenetic relationships appear to have been obscured due to an ancient ersification of this group.
Publisher: Springer Science and Business Media LLC
Date: 23-03-2006
Abstract: Genetic ersity of the human immunodeficiency virus type 1 (HIV-1) population within an in idual is lost during transmission to a new host. The demography of transmission is an important determinant of evolutionary dynamics, particularly the relative impact of natural selection and genetic drift immediately following HIV-1 infection. Despite this, the magnitude of this population bottleneck is unclear. We use coalescent methods to quantify the bottleneck in a single case of homosexual transmission and find that over 99% of the env and gag ersity present in the donor is lost. This was consistent with the ersity present at seroconversion in nine other horizontally infected in iduals. Furthermore, we estimated viral ersity at birth in 27 infants infected through vertical transmission and found there to be no difference between the two modes of transmission. Assuming the bottleneck at transmission is selectively neutral, such a severe reduction in genetic ersity has important implications for adaptation in HIV-1, since beneficial mutations have a reduced chance of transmission.
Publisher: Springer Science and Business Media LLC
Date: 11-12-2020
DOI: 10.1038/S41467-020-20235-8
Abstract: New Zealand, a geographically remote Pacific island with easily sealable borders, implemented a nationwide ‘lockdown’ of all non-essential services to curb the spread of COVID-19. Here, we generate 649 SARS-CoV-2 genome sequences from infected patients in New Zealand with s les collected during the ‘first wave’, representing 56% of all confirmed cases in this time period. Despite its remoteness, the viruses imported into New Zealand represented nearly all of the genomic ersity sequenced from the global virus population. These data helped to quantify the effectiveness of public health interventions. For ex le, the effective reproductive number, R e of New Zealand’s largest cluster decreased from 7 to 0.2 within the first week of lockdown. Similarly, only 19% of virus introductions into New Zealand resulted in ongoing transmission of more than one additional case. Overall, these results demonstrate the utility of genomic pathogen surveillance to inform public health and disease mitigation.
Publisher: Oxford University Press (OUP)
Date: 06-04-2005
Abstract: Studies of molecular evolutionary rates have yielded a wide range of rate estimates for various genes and taxa. Recent studies based on population-level and pedigree data have produced remarkably high estimates of mutation rate, which strongly contrast with substitution rates inferred in phylogenetic (species-level) studies. Using Bayesian analysis with a relaxed-clock model, we estimated rates for three groups of mitochondrial data: avian protein-coding genes, primate protein-coding genes, and primate d-loop sequences. In all three cases, we found a measurable transition between the high, short-term (< 1-2 Myr) mutation rate and the low, long-term substitution rate. The relationship between the age of the calibration and the rate of change can be described by a vertically translated exponential decay curve, which may be used for correcting molecular date estimates. The phylogenetic substitution rates in mitochondria are approximately 0.5% per million years for avian protein-coding sequences and 1.5% per million years for primate protein-coding and d-loop sequences. Further analyses showed that purifying selection offers the most convincing explanation for the observed relationship between the estimated rate and the depth of the calibration. We rule out the possibility that it is a spurious result arising from sequence errors, and find it unlikely that the apparent decline in rates over time is caused by mutational saturation. Using a rate curve estimated from the d-loop data, several dates for last common ancestors were calculated: modern humans and Neandertals (354 ka 222-705 ka), Neandertals (108 ka 70-156 ka), and modern humans (76 ka 47-110 ka). If the rate curve for a particular taxonomic group can be accurately estimated, it can be a useful tool for correcting ergence date estimates by taking the rate decay into account. Our results show that it is invalid to extrapolate molecular rates of change across different evolutionary timescales, which has important consequences for studies of populations, domestication, conservation genetics, and human evolution.
Publisher: Oxford University Press (OUP)
Date: 11-2006
DOI: 10.1534/GENETICS.105.052019
Abstract: The evolution of the human immunodeficiency virus (HIV-1) during chronic infection involves the rapid, continuous turnover of genetic ersity. However, the role of natural selection, relative to random genetic drift, in governing this process is unclear. We tested a stochastic model of genetic drift using partial envelope sequences s led longitudinally in 28 infected children. In each case the Bayesian posterior (empirical) distribution of coalescent genealogies was estimated using Markov chain Monte Carlo methods. Posterior predictive simulation was then used to generate a null distribution of genealogies assuming neutrality, with the null and empirical distributions compared using four genealogy-based summary statistics sensitive to nonneutral evolution. Because both null and empirical distributions were generated within a coalescent framework, we were able to explicitly account for the confounding influence of demography. From the distribution of corrected P-values across patients, we conclude that empirical genealogies are more asymmetric than expected if evolution is driven by mutation and genetic drift only, with an excess of low-frequency polymorphisms in the population. This indicates that although drift may still play an important role, natural selection has a strong influence on the evolution of HIV-1 envelope. A negative relationship between effective population size and substitution rate indicates that as the efficacy of selection increases, a smaller proportion of mutations approach fixation in the population. This suggests the presence of deleterious mutations. We therefore conclude that intrahost HIV-1 evolution in envelope is dominated by purifying selection against low-frequency deleterious mutations that do not reach fixation.
Publisher: Public Library of Science (PLoS)
Date: 29-08-2013
Publisher: Cold Spring Harbor Laboratory
Date: 17-06-2018
DOI: 10.1101/348391
Abstract: When populations become isolated, members of these populations can erge genetically over time. This leads to genetic differences between these populations that increase over time if the isolation persists. This process can be counteracted by gene flow, i.e. when genes are exchanged between populations. In order to study the speciation processes when gene flow is present, isolation-with-migration methods have been developed. These methods typically assume that the ranked topology of the species history is already known. However, this is often not the case and the species tree is therefore of interest itself. For the inference of species trees, it is in turn often necessary to assume that there is no gene flow between co-existing species. This assumption, however, can lead to wrongly inferred speciation times and species tree topologies. We here introduce a new method that allows inference of the species tree while explicitly modelling the flow of genes between coexisting species. By using Markov chain Monte Carlo s ling, we co-infer the species tree alongside evolutionary parameters of interest. By using simulations, we show that our newly introduced approach is able to reliably infer the species trees and parameters of the isolation-with-migration model from genetic sequence data. We then use this approach to infer the species history of the mosquitoes from the Anopheles gambiae species complex. Accounting for gene flow when inferring the species history suggests a slightly different speciation order and gene flow than previously suggested.
Publisher: Proceedings of the National Academy of Sciences
Date: 08-12-2009
Abstract: The ratite moa (Aves: Dinornithiformes) were a speciose group of massive graviportal avian herbivores that dominated the New Zealand (NZ) ecosystem until their extinction ≈600 years ago. The phylogeny and evolutionary history of this morphologically erse order has remained controversial since their initial description in 1839. We synthesize mitochondrial phylogenetic information from 263 subfossil moa specimens from across NZ with morphological, ecological, and new geological data to create the first comprehensive phylogeny, taxonomy, and evolutionary timeframe for all of the species of an extinct order. We also present an important new geological aleogeographical model of late Cenozoic NZ, which suggests that terrestrial biota on the North and South Island landmasses were isolated for most of the past 20–30 Ma. The data reveal that the patterns of genetic ersity within and between different moa clades reflect a complex history following a major marine transgression in the Oligocene, affected by marine barriers, tectonic activity, and glacial cycles. Surprisingly, the remarkable morphological radiation of moa appears to have occurred much more recently than previous early Miocene ( ca. 15 Ma) estimates, and was coincident with the accelerated uplift of the Southern Alps just ca. 5–8.5 Ma. Together with recent fossil evidence, these data suggest that the recent evolutionary history of nearly all of the iconic NZ terrestrial biota occurred principally on just the South Island.
Publisher: Cold Spring Harbor Laboratory
Date: 19-11-2018
DOI: 10.1101/474296
Abstract: Elaboration of Bayesian phylogenetic inference methods has continued at pace in recent years with major new advances in nearly all aspects of the joint modelling of evolutionary data. It is increasingly appreciated that some evolutionary questions can only be adequately answered by combining evidence from multiple independent sources of data, including genome sequences, s ling dates, phenotypic data, radiocarbon dates, fossil occurrences, and biogeographic range information among others. Including all relevant data into a single joint model is very challenging both conceptually and computationally. Advanced computational software packages that allow robust development of compatible (sub-)models which can be composed into a full model hierarchy have played a key role in these developments. Developing such software frameworks is increasingly a major scientific activity in its own right, and comes with specific challenges, from practical software design, development and engineering challenges to statistical and conceptual modelling challenges. BEAST 2 is one such computational software platform, and was first announced over 4 years ago. Here we describe a series of major new developments in the BEAST 2 core platform and model hierarchy that have occurred since the first release of the software, culminating in the recent 2.5 release. Bayesian phylogenetic inference methods have undergone considerable development in recent years, and joint modelling of rich evolutionary data, including genomes, phenotypes and fossil occurrences is increasingly common. Advanced computational software packages that allow robust development of compatible (sub-)models which can be composed into a full model hierarchy have played a key role in these developments. Developing scientific software is increasingly crucial to advancement in many fields of biology. The challenges range from practical software development and engineering, distributed team coordination, conceptual development and statistical modelling, to validation and testing. BEAST 2 is one such computational software platform for phylogenetics, population genetics and phylodynamics, and was first announced over 4 years ago. Here we describe the full range of new tools and models available on the BEAST 2.5 platform, which expand joint evolutionary inference in many new directions, especially for joint inference over multiple data types, non-tree models and complex phylodynamics.
Publisher: Oxford University Press (OUP)
Date: 06-10-2015
Publisher: Elsevier BV
Date: 06-2004
Publisher: Pleiades Publishing Ltd
Date: 08-2019
Publisher: Oxford University Press (OUP)
Date: 11-01-2007
Abstract: Populations of RNA viruses are often characterized by abundant genetic variation. However, the relative fitness of these mutations is largely unknown, although this information is central to our understanding of viral emergence, immune evasion, and drug resistance. Here we develop a phylogenetic method, based on the distribution of nonsynonymous and synonymous changes, to assess the relative fitness of polymorphisms in the structural genes of 143 RNA viruses. This reveals that a substantial proportion of the amino acid variation observed in natural populations of RNA viruses comprises transient deleterious mutations that are later purged by purifying selection, potentially limiting virus adaptability. We also demonstrate, for the first time, the existence of a relationship between amino acid variability and the phylogenetic distribution of polymorphisms. From this relationship, we propose an empirical threshold for the maximum viable deleterious mutation load in RNA viruses.
Publisher: Elsevier BV
Date: 04-2004
Publisher: Cold Spring Harbor Laboratory
Date: 07-01-2018
DOI: 10.1101/242875
Abstract: Evolutionary models account for either population- or species-level processes, but usually not both. We introduce a new model, the FBD-MSC, which makes it possible for the first time to integrate both the genealogical and fossilization phenomena, by means of the multispecies coalescent (MSC) and the fossilized birth-death (FBD) processes. Using this model, we reconstruct the phylogeny representing all extant and many fossil Caninae, recovering both the relative and absolute time of speciation events. We quantify known inaccuracy issues with ergence time estimates using the popular strategy of concatenating molecular alignments, and show that the FBD-MSC solves them. Our new integrative method and empirical results advance the paradigm and practice of probabilistic total evidence analyses in evolutionary biology.
Publisher: Oxford University Press (OUP)
Date: 09-02-2005
Abstract: In recent years, a number of phylogenetic methods have been developed for estimating molecular rates and ergence dates under models that relax the molecular clock constraint by allowing rate change throughout the tree. These methods are being used with increasing frequency, but there have been few studies into their accuracy. We tested the accuracy of several relaxed-clock methods (penalized likelihood and Bayesian inference using various models of rate change) using nucleotide sequences simulated on a nine-taxon tree. When the sequences evolved with a constant rate, the methods were able to infer rates accurately, but estimates were more precise when a molecular clock was assumed. When the sequences evolved under a model of auto-correlated rate change, rates were accurately estimated using penalized likelihood and by Bayesian inference using lognormal and exponential models of rate change, while other models did not perform as well. When the sequences evolved under a model of uncorrelated rate change, only Bayesian inference using an exponential rate model performed well. Collectively, the results provide a strong recommendation for using the exponential model of rate change if a conservative approach to ergence time estimation is required. A case study is presented in which we use a simulation-based approach to examine the hypothesis of elevated rates in the Cambrian period, and it is found that these high rate estimates might be an artifact of the rate estimation method. If this bias is present, then the ages of metazoan ergences would be systematically underestimated. The results of this study have implications for studies of molecular rates and ergence dates.
No related grants have been discovered for Alexei Drummond.