ORCID Profile
0000-0002-8698-7656
Current Organisation
The University of Auckland
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In Research Link Australia (RLA), "Research Topics" refer to ANZSRC FOR and SEO codes. These topics are either sourced from ANZSRC FOR and SEO codes listed in researchers' related grants or generated by a large language model (LLM) based on their publications.
Phylogeny and Comparative Analysis | Molecular Evolution | Ecological Impacts of Climate Change | Biogeography and Phylogeography | Genetics | Evolutionary Biology | Bacteriology
Expanding Knowledge in the Biological Sciences | Expanding Knowledge in the Environmental Sciences | Effects of Climate Change and Variability on Australia (excl. Social Impacts) |
Publisher: Springer Science and Business Media LLC
Date: 02-03-2011
DOI: 10.1038/NATURE09678
Abstract: Palaeontologists characterize mass extinctions as times when the Earth loses more than three-quarters of its species in a geologically short interval, as has happened only five times in the past 540 million years or so. Biologists now suggest that a sixth mass extinction may be under way, given the known species losses over the past few centuries and millennia. Here we review how differences between fossil and modern data and the addition of recently available palaeontological information influence our understanding of the current extinction crisis. Our results confirm that current extinction rates are higher than would be expected from the fossil record, highlighting the need for effective conservation measures.
Publisher: Proceedings of the National Academy of Sciences
Date: 17-06-2013
Abstract: Chloroplasts and mitochondria descended from bacterial ancestors, but the dating of these primary endosymbiosis events remains very uncertain, despite their importance for our understanding of the evolution of both bacteria and eukaryotes. All phylogenetic dating in the Proterozoic and before is difficult: Significant debates surround potential fossil calibration points based on the interpretation of the Precambrian microbial fossil record, and strict molecular clock methods cannot be expected to yield accurate dates over such vast timescales because of strong heterogeneity in rates. Even with more sophisticated relaxed-clock analyses, nodes that are distant from fossil calibrations will have a very high uncertainty in dating. However, endosymbiosis events and gene duplications provide some additional information that has never been exploited in dating namely, that certain nodes on a gene tree must represent the same events, and thus must have the same or very similar dates, even if the exact date is uncertain. We devised techniques to exploit this information: cross-calibration, in which node date calibrations are reused across a phylogeny, and cross-bracing, in which node date calibrations are formally linked in a hierarchical Bayesian model. We apply these methods to proteins with ancient duplications that have remained associated and originated from plastid and mitochondrial endosymbionts: the α and β subunits of ATP synthase and its relatives, and the elongation factor thermo unstable. The methods yield reductions in dating uncertainty of 14–26% while only using date calibrations derived from phylogenetically unambiguous Phanerozoic fossils of multicellular plants and animals. Our results suggest that primary plastid endosymbiosis occurred ∼900 Mya and mitochondrial endosymbiosis occurred ∼1,200 Mya.
Publisher: National Academies Press
Date: 28-11-2007
DOI: 10.17226/11790
Publisher: Springer Science and Business Media LLC
Date: 2011
Publisher: Springer Science and Business Media LLC
Date: 15-05-2010
Publisher: Oxford University Press (OUP)
Date: 2023
Abstract: The bacterial flagellar motor (BFM) is a rotary nanomachine powered by the translocation of ions across the inner membrane through the stator complex. The stator complex consists of two membrane proteins: MotA and MotB (in H+-powered motors), or PomA and PomB (in Na+-powered motors). In this study, we used ancestral sequence reconstruction (ASR) to probe which residues of MotA correlate with function and may have been conserved to preserve motor function. We reconstructed 10 ancestral sequences of MotA and found four of them were motile in combination with contemporary Escherichia coli MotB and in combination with our previously published functional ancestral MotBs. Sequence comparison between wild-type (WT) E. coli MotA and MotA-ASRs revealed 30 critical residues across multiple domains of MotA that were conserved among all motile stator units. These conserved residues included pore-facing, cytoplasm-facing, and MotA–MotA intermolecular facing sites. Overall, this work demonstrates the role of ASR in assessing conserved variable residues in a subunit of a molecular complex.
Publisher: Geological Society of America
Date: 2016
Publisher: Elsevier BV
Date: 12-2013
DOI: 10.1016/J.YMPEV.2013.07.026
Abstract: Multiple rounds of whole genome duplication have repeatedly marked the evolution of vertebrates, and correlate strongly with morphological innovation. However, less is known about the behavioral, physiological and ecological consequences of genome duplication, and whether these events coincide with major transitions in vertebrate complexity. The complex behavior of anadromy - where adult fishes migrate up rivers from the sea to their natal site to spawn - is well known in salmonid fishes. Some hypotheses suggest that migratory behavior evolved as a consequence of an ancestral genome duplication event, which permitted salinity tolerance and osmoregulatory plasticity. Here we test whether anadromy evolved multiple times within salmonids, and whether genome duplication coincided with the evolution of anadromy. We present a method that uses ancestral character simulation data to plot the frequency of character transitions over a time calibrated phylogenetic tree to provide estimates of the absolute timing of character state transitions. Furthermore, we incorporate extinct and extant taxa to improve on previous estimates of ergence times. We present the first phylogenetic evidence indicating that anadromy evolved at least twice from freshwater salmonid ancestors. Results suggest that genome duplication did not coincide in time with changes in migratory behavior, but preceded a transition to anadromy by 55-50 million years. Our study represents the first attempt to estimate the absolute timing of a complex behavioral trait in relation to a genome duplication event.
Publisher: Springer Science and Business Media LLC
Date: 10-01-2015
Publisher: The Royal Society
Date: 08-2016
Abstract: Tip-dating methods are becoming popular alternatives to traditional node calibration approaches for building time-scaled phylogenetic trees, but questions remain about their application to empirical datasets. We compared the performance of the most popular methods against a dated tree of fossil Canidae derived from previously published monographs. Using a canid morphology dataset, we performed tip-dating using BEAST v. 2.1.3 and M r B ayes v. 3.2.5. We find that for key nodes ( Canis, approx. 3.2 Ma, Caninae approx. 11.7 Ma) a non-mechanistic model using a uniform tree prior produces estimates that are unrealistically old (27.5, 38.9 Ma). Mechanistic models (incorporating lineage birth, death and s ling rates) estimate ages that are closely in line with prior research. We provide a discussion of these two families of models (mechanistic versus non-mechanistic) and their applicability to fossil datasets.
Publisher: Wiley
Date: 09-2014
DOI: 10.1111/ECOG.00783
Publisher: Cold Spring Harbor Laboratory
Date: 31-12-2018
DOI: 10.1101/507533
Abstract: The bacterial flagellar motor (BFM) powers the rotation that propels swimming bacteria. Rotational torque is generated by harnessing the flow of ions through ion channels known as stators which couple the energy from the ion gradient across the inner membrane to rotation of the rotor. Here we used error-prone PCR to introduce single point mutations into the sodium-powered Vibrio alginolyticus / Escherichia coli chimeric stator PotB and selected for motors that exhibited motility in the presence of the sodium-channel inhibitor phenamil. We found single mutations that enable motility under phenamil occurred at two sites: 1) the transmembrane domain of PotB, corresponding to the TM region of the PomB stator from V. alginolyticus , and 2) near the peptidoglycan (PG) binding region that corresponds to the C-terminal region of the MotB stator from E. coli. Single cell rotation assays confirmed that in idual flagellar motors could rotate in up to 100 µM phenamil. Using phylogenetic logistic regression, we found correlation between natural residue variation and ion source at positions corresponding to PotB F22Y, but not at other sites. Our results demonstrate that it is not only the pore region of the stator that moderates motility in the presence of ion-channel blockers.
Publisher: Springer Science and Business Media LLC
Date: 05-09-2006
DOI: 10.1038/NRMICRO1493
Abstract: In the recent Dover trial, and elsewhere, the 'Intelligent Design' movement has ch ioned the bacterial flagellum as an irreducibly complex system that, it is claimed, could not have evolved through natural selection. Here we explore the arguments in favour of viewing bacterial flagella as evolved, rather than designed, entities. We dismiss the need for any great conceptual leaps in creating a model of flagellar evolution and speculate as to how an experimental programme focused on this topic might look.
Publisher: Wiley
Date: 16-07-2014
DOI: 10.1111/NPH.12929
Abstract: Climate refugia, locations where taxa survive periods of regionally adverse climate, are thought to be critical for maintaining bio ersity through the glacial–interglacial climate changes of the Q uaternary. A critical research need is to better integrate and reconcile the three major lines of evidence used to infer the existence of past refugia – fossil records, species distribution models and phylogeographic surveys – in order to characterize the complex spatiotemporal trajectories of species and populations in and out of refugia. Here we review the complementary strengths, limitations and new advances for these three approaches. We provide case studies to illustrate their combined application, and point the way towards new opportunities for synthesizing these disparate lines of evidence. Case studies with E uropean beech, Q inghai spruce and D ouglas‐fir illustrate how the combination of these three approaches successfully resolves complex species histories not attainable from any one approach. Promising new statistical techniques can capitalize on the strengths of each method and provide a robust quantitative reconstruction of species history. Studying past refugia can help identify contemporary refugia and clarify their conservation significance, in particular by elucidating the fine‐scale processes and the particular geographic locations that buffer species against rapidly changing climate. Contents Summary 38 I. Climate refugia: biogeographical and conservation significance 38 II. Approaches for reconstructing refugia: strengths, limitations and recent advances 39 III. Climate refugia of the past: three case studies 46 IV. New integrative approaches to reconstructing refugia 47 V. How can historical refugia inform us about future refugia? 48 VI. Concluding thoughts 49 Acknowledgements 49 References 49
Publisher: Wiley
Date: 03-03-2016
DOI: 10.1111/JBI.12727
Publisher: Cambridge University Press (CUP)
Date: 2019
DOI: 10.1017/S0007680519000643
Abstract: The ability to combine technological innovation with innovation in product design has been recognized by business historians as an important characteristic of a successful business. This article examines the use of product design as a source of competitive advantage by leading firms in the Manchester cotton, Macclesfield silk, and Staffordshire pottery sectors in the period 1750–1860. Four design strategies are identified: copying (direct imitation and adaptation), commissioning, capacity building, and collaboration. Distinction is made between proactive firms, which innovated whenever there was an opportunity, and reactive firms, which innovated only when necessary.
Publisher: Elsevier BV
Date: 2018
Publisher: Wiley
Date: 09-08-2022
DOI: 10.1111/JBI.14346
Abstract: Statistical model comparison has become common in historical biogeography, enabled by the R package BioGeoBEARS , which implements several models in a common framework, allowing models to be compared with standard likelihood‐based methods of statistical model comparison. Ree and Sanmartín ( Journal of Biogeography , 45, 741–749, 2018) critiqued the comparison of Dispersal–Extinction–Cladogenesis (DEC) and a modification of it, DEC+J, which adds the process of jump dispersal at speciation. DEC+J provides highly significant improvements in model fit on most (although not all) datasets. They claim that the comparison is statistically invalid for a variety of reasons. I analyse the key claims made by the critique. Simulated data. Simulated data. Likelihood calculations are checked by comparison between programs and by‐hand calculations, and by summing likelihoods across all possible datasets. Model adequacy of DEC versus DEC+J is checked by a simulation/inference experiment. Mistakes in the critique's ex le likelihood calculations are demonstrated. DEC+J fits better on datasets because the DEC model is statistically inadequate in the common situation when most species have geographical ranges of single areas the DEC model requires long residence times of multi‐area ranges, and when these are not observed, a model that does produce such data patterns, such as DEC+J, prevails. More fundamentally, statistical comparison of DEC and DEC+J produces identical log‐likelihood differences to statistical comparison of two submodels of ClaSSE where extinction rates are fixed to 0. DEC fails a basic model adequacy check for understandable reasons, while DEC+J does not. As Ree and Sanmartín recommend ClaSSE models as valid for comparison, the comparison of DEC and DEC+J is statistically valid according to their own criteria.
Publisher: Cold Spring Harbor Laboratory
Date: 06-02-2017
DOI: 10.1101/106302
Abstract: • The Andean mountains of South America are the most species-rich bio ersity hotspot worldwide with about 15% of the world’s plant species, in only 1% of the world’s land surface. Orchids are a key element of the Andean flora, and one of the most prominent components of the Neotropical epiphyte ersity, yet very little is known about their origin and ersification. • We address this knowledge gap by inferring the biogeographical history and evolutionary dynamics of the two largest Neotropical orchid groups (Cymbidieae and Pleurothallidinae), using two unparalleled, densely-s led orchid phylogenies (including 400+ newly generated DNA sequences), comparative phylogenetic methods, geological and biological datasets. • We find that the majority of Andean orchid lineages only originated in the last 15 million years. Most Andean lineages are derived from lowland Amazonian ancestors, with additional contributions from Central America and the Antilles. Species ersification is correlated with Andean orogeny, and multiple migrations and re-colonizations across the Andes indicate that mountains do not constrain orchid dispersal over long timescales. • Our study sheds new light on the timing and geography of a major Neotropical radiation, and suggests that mountain uplift promotes species ersification across all elevational zones.
Publisher: The Royal Society
Date: 05-06-2019
Abstract: The importance of long-distance dispersal (LDD) in shaping geographical distributions has been debated since the nineteenth century. In terrestrial vertebrates, LDD events across large water bodies are considered highly improbable, but organismal traits affecting dispersal capacity are generally not taken into account. Here, we focus on a recent lizard radiation and combine a summary-coalescent species tree based on 1225 exons with a probabilistic model that links dispersal capacity to an evolving trait, to investigate whether ecological specialization has influenced the probability of trans-oceanic dispersal. Cryptoblepharus species that occur in coastal habitats have on average dispersed 13 to 14 times more frequently than non-coastal species and coastal specialization has, therefore, led to an extraordinarily widespread distribution that includes multiple continents and distant island archipelagoes. Furthermore, their presence across the Pacific substantially predates the age of human colonization and we can explicitly reject the possibility that these patterns are solely shaped by human-mediated dispersal. Overall, by combining new analytical methods with a comprehensive phylogenomic dataset, we use a quantitative framework to show how coastal specialization can influence dispersal capacity and eventually shape geographical distributions at a macroevolutionary scale.
Publisher: Elsevier BV
Date: 03-2004
Publisher: Wiley
Date: 06-06-2019
DOI: 10.1111/GEB.12929
Publisher: Wiley
Date: 06-12-2012
DOI: 10.1111/ELE.12039
Abstract: Although clouds are the most recognisable and defining feature of tropical montane cloud forests, little research has focussed on how clouds affect plant functioning. We used satellite and ground-based observations to study cloud and leaf wetting patterns in contrasting tropical montane and pre-montane cloud forests. We then studied the consequences of leaf wetting for the direct uptake of water accumulated on leaf surfaces into the leaves themselves. During the dry season, the montane forest experienced higher precipitation, cloud cover and leaf wetting events of longer duration than the pre-montane forest. Leaf wetting events resulted in foliar water uptake in all species studied. The capacity for foliar water uptake differed significantly between the montane and pre-montane forest plant communities, as well as among species within a forest. Our results indicate that foliar water uptake is common in these forest plants and improves plant water status during the dry season.
Publisher: Oxford University Press (OUP)
Date: 10-06-2016
Abstract: True frogs of the genus Rana are widely used as model organisms in studies of development, genetics, physiology, ecology, behavior, and evolution. Comparative studies among the more than 100 species of Rana rely on an understanding of the evolutionary history and patterns of ersification of the group. We estimate a well-resolved, time-calibrated phylogeny from sequences of six nuclear and three mitochondrial loci s led from most species of Rana, and use that phylogeny to clarify the group's ersification and global biogeography. Our analyses consistently support an "Out of Asia" pattern with two independent dispersals of Rana from East Asia to North America via Beringian land bridges. The more species-rich lineage of New World Rana appears to have experienced a rapid radiation following its colonization of the New World, especially with its expansion into montane and tropical areas of Mexico, Central America, and South America. In contrast, Old World Rana exhibit different trajectories of ersification ersification in the Old World began very slowly and later underwent a distinct increase in speciation rate around 29-18 Ma. Net ersification is associated with environmental changes and especially intensive tectonic movements along the Asian margin from the Oligocene to early Miocene. Our phylogeny further suggests that previous classifications were misled by morphological homoplasy and plesiomorphic color patterns, as well as a reliance primarily on mitochondrial genes. We provide a phylogenetic taxonomy based on analyses of multiple nuclear and mitochondrial gene loci. [Amphibians biogeography ersification rate Holarctic transcontinental dispersal.
Publisher: Elsevier BV
Date: 11-2007
Publisher: Elsevier BV
Date: 03-2017
Publisher: Oxford University Press (OUP)
Date: 29-12-2013
Abstract: Incorporation of fossils into biogeographic studies can have a profound effect on the conclusions that result, particularly when fossil ranges are nonoverlapping with extant ranges. This is the case in archaeid spiders, where there are known fossils from the Northern Hemisphere, yet all living members are restricted to the Southern Hemisphere. To better understand the biogeographic patterns of archaeid spiders and their palpimanoid relatives, we estimate a dated phylogeny using a relaxed clock on a combined molecular and morphological data set. Dating information is compared with treating the archaeid fossil taxa as both node calibrations and as noncontemporaneous terminal tips, both with and without additional calibration points. Estimation of ancestral biogeographic ranges is then performed, using likelihood and Bayesian methods to take into account uncertainty in phylogeny and in dating. We find that treating the fossils as terminal tips within a Bayesian framework, as opposed to dating the phylogeny based only on molecular data with the dates coming from node calibrations, removes the subjectivity involved in assigning priors, which has not been possible with previous methods. Our analyses suggest that the ersification of the northern and southern archaeid lineages was congruent with the breakup of Pangaea into Laurasia and Gondwanaland. This analysis provides a rare ex le, and perhaps the most strongly supported, where a dated phylogeny confirms a biogeographical hypothesis based on vicariance due to the breakup of the ancient continental plates.
Publisher: The Royal Society
Date: 07-2016
Abstract: Dated phylogenies of fossil taxa allow palaeobiologists to estimate the timing of major ergences and placement of extinct lineages, and to test macroevolutionary hypotheses. Recently developed Bayesian ‘tip-dating’ methods simultaneously infer and date the branching relationships among fossil taxa, and infer putative ancestral relationships. Using a previously published dataset for extinct theropod dinosaurs, we contrast the dated relationships inferred by several tip-dating approaches and evaluate potential downstream effects on phylogenetic comparative methods. We also compare tip-dating analyses to maximum-parsimony trees time-scaled via alternative a posteriori approaches including via the probabilistic cal3 method. Among tip-dating analyses, we find opposing but strongly supported relationships, despite similarity in inferred ancestors. Overall, tip-dating methods infer ergence dates often millions (or tens of millions) of years older than the earliest stratigraphic appearance of that clade. Model-comparison analyses of the pattern of body-size evolution found that the support for evolutionary mode can vary across and between tree s les from cal3 and tip-dating approaches. These differences suggest that model and software choice in dating analyses can have a substantial impact on the dated phylogenies obtained and broader evolutionary inferences.
Publisher: Wiley
Date: 19-01-2021
DOI: 10.1111/ECOG.05485
Abstract: The ENMTools software package was introduced in 2008 as a platform for making measurements on environmental niche models (ENMs, frequently referred to as species distribution models or SDMs), and for using those measurements in the context of newly developed Monte Carlo tests to evaluate hypotheses regarding niche evolution. Additional functionality was later added for model selection and simulation from ENMs, and the software package has been quite widely used. ENMTools was initially implemented as a Perl script, which was also compiled into an executable file for various platforms. However, the package had a number of significant limitations it was only designed to fit models using Maxent, it relied on a specific Perl distribution to function, and its internal structure made it difficult to maintain and expand. Subsequently, the R programming language became the platform of choice for most ENM studies, making ENMTools less usable for many practitioners. Here we introduce a new R version of ENMTools that implements much of the functionality of its predecessor as well as numerous additions that simplify the construction, comparison and evaluation of niche models. These additions include new metrics for model fit, methods of measuring ENM overlap, and methods for testing evolutionary hypotheses. The new version of ENMTools is also designed to work within the expanding universe of R tools for ecological biogeography, and as such includes greatly simplified interfaces for analyses from several other R packages.
Publisher: Frontiers Media SA
Date: 23-12-2020
DOI: 10.3389/FMICB.2020.625837
Abstract: The bacterial flagellar motor (BFM) is a nanomachine that rotates the flagellum to propel many known bacteria. The BFM is powered by ion transit across the cell membrane through the stator complex, a membrane protein. Different bacteria use various ions to run their BFM, but the majority of BFMs are powered by either proton (H + ) or sodium (Na + ) ions. The transmembrane (TM) domain of the B-subunit of the stator complex is crucial for ion selectivity, as it forms the ion channel in complex with TM3 and TM4 of the A-subunit. In this study, we reconstructed and engineered thirteen ancestral sequences of the stator B-subunit to evaluate the functional properties and ionic power source of the stator proteins at reconstruction nodes to evaluate the potential of ancestral sequence reconstruction (ASR) methods for stator engineering and to test specific motifs previously hypothesized to be involved in ion-selectivity. We found that all thirteen of our reconstructed ancient B-subunit proteins could assemble into functional stator complexes in combination with the contemporary Escherichia coli MotA-subunit to restore motility in stator deleted E. coli strains. The flagellar rotation of the thirteen ancestral MotBs was found to be Na + independent which suggested that the F30/Y30 residue was not significantly correlated with sodium roton phenotype, in contrast to what we had reported previously. Additionally, four among the thirteen reconstructed B-subunits were compatible with the A-subunit of Aquifex aeolicus and able to function in a sodium-independent manner. Overall, this work demonstrates the use of ancestral reconstruction to generate novel stators and quantify which residues are correlated with which ionic power source.
Publisher: Springer Science and Business Media LLC
Date: 06-06-2012
DOI: 10.1038/NATURE11018
Abstract: Localized ecological systems are known to shift abruptly and irreversibly from one state to another when they are forced across critical thresholds. Here we review evidence that the global ecosystem as a whole can react in the same way and is approaching a planetary-scale critical transition as a result of human influence. The plausibility of a planetary-scale 'tipping point' highlights the need to improve biological forecasting by detecting early warning signs of critical transitions on global as well as local scales, and by detecting feedbacks that promote such transitions. It is also necessary to address root causes of how humans are forcing biological changes.
Publisher: Wiley
Date: 02-08-2018
DOI: 10.1111/ZSC.12299
Publisher: Wiley
Date: 26-11-2017
DOI: 10.1111/JBI.12898
Publisher: Cold Spring Harbor Laboratory
Date: 17-05-2016
DOI: 10.1101/053611
Abstract: Statistical historical biogeographical methods rely on the use of models that assume various biogeographic processes. Until recently model selection remains an explored topic and the impacts of using different models on inferring biogeographic history are poorly understood. Focusing on the Neotropical weevils in the Exophthalmus genus complex (Insecta: Curculionidae: Entiminae), we compare three commonly used biogeographic models – DIVA (Dispersal-Vicariance Analysis), DEC (Dispersal-Extinction-Cladogenesis) and BayArea (Bayesian Analysis of Biogeography), and examine the impact of modeling founder-event jump dispersal on biogeographic history estimation. We also investigate the biogeographic events that have shaped patterns of distributions, ersification, and endemism in this group of weevils. We s le representatives of 65 species of the Exophthalmus genus complex and 26 outgroup terminals from the Neotropics including Caribbean islands and mainland. We reconstruct a molecular phylogeny based on six genes and performed molecular dating using a relaxed clock with three fossil calibration points. We conduct biogeographic history estimations and compare alternative biogeographic models with the R package BioGeoBEARS. Model selection strongly favors biogeographic models that include founder-event jump dispersal. Without modeling jump dispersal, estimations based on the three biogeographic models are dramatically different, especially at early erging nodes. When jump dispersal is modeled, however, the three biogeographic models perform similarly. Accordingly, we show that the Neotropical mainland was colonized by Caribbean species in the early Miocene, and that in situ ersification accounts for a majority (~75%) of the biogeographic events in the Exophthalmus genus complex. Our study highlights the need for testing for wide-ranging historical biogeographic processes in the study of Caribbean biogeography and the importance of comparing and selecting the best-fitting model in statistical biogeographic inferences. We demonstrate that modeling founder-event jump dispersal significantly improves the fit of the biogeographic history estimation of Caribbean and Neotropical mainland weevils. We establish that in situ ersification acts as a dominant biogeographic force in the evolution of the Exophthalmus genus complex. The colonization of the Neotropical mainland from Caribbean islands reinforces the notion that islands can be an important source of continental ersity.
Publisher: The Royal Society
Date: 07-08-2015
Abstract: The phylogenetic relationships of several hominin species remain controversial. Two methodological issues contribute to the uncertainty—use of partial, inconsistent datasets and reliance on phylogenetic methods that are ill-suited to testing competing hypotheses. Here, we report a study designed to overcome these issues. We first compiled a supermatrix of craniodental characters for all widely accepted hominin species. We then took advantage of recently developed Bayesian methods for building trees of serially s led tips to test among hypotheses that have been put forward in three of the most important current debates in hominin phylogenetics—the relationship between Australopithecus sediba and Homo , the taxonomic status of the Dmanisi hominins, and the place of the so-called hobbit fossils from Flores, Indonesia, in the hominin tree. Based on our results, several published hypotheses can be statistically rejected. For ex le, the data do not support the claim that Dmanisi hominins and all other early Homo specimens represent a single species, nor that the hobbit fossils are the remains of small-bodied modern humans, one of whom had Down syndrome. More broadly, our study provides a new baseline dataset for future work on hominin phylogeny and illustrates the promise of Bayesian approaches for understanding hominin phylogenetic relationships.
Publisher: Wiley
Date: 20-09-2020
DOI: 10.1111/JBI.13705
Publisher: Elsevier BV
Date: 04-2017
DOI: 10.1016/J.YMPEV.2016.12.039
Abstract: Statistical historical biogeographic methods rely on models that represent various biogeographic processes. Until recently model selection in this domain was not widely used, and the impact of differential model selection on inferring biogeographic scenarios was not well understood. Focusing on Neotropical weevils in the Exophthalmus genus complex (EGC) (Insecta: Curculionidae: Entiminae), we compare three commonly used biogeographic models - DIVA (Dispersal-Vicariance Analysis), DEC (Dispersal-Extinction-Cladogenesis) and BayArea (Bayesian Analysis of Biogeography), and examine the impact of modeling founder-event jump dispersal on historical biogeographic reconstructions. We also investigate the biogeographic events that have shaped patterns of distribution, ersification, and endemism in this weevil lineage. We s le representatives of 65 species of the EGC and 26 outgroup terminals from the Neotropics, including Caribbean islands and the mainland. We reconstruct a molecular phylogeny based on six genes and apply molecular dating using a relaxed clock with three fossil calibration points. Historical biogeographic estimations and alternative biogeographic models are computed and compared with the R package BioGeoBEARS. Model selection strongly favors biogeographic models that include founder-event jump dispersal. Without modeling jump dispersal, estimations based on the three biogeographic models are dramatically different, especially for early- erging nodes. When jump dispersal is included, the three biogeographic models perform similarly. Accordingly, we show that the Neotropical mainland was colonized by Caribbean species in the early Miocene, and that in situ ersification accounts for a majority (∼75%) of the biogeographic events in the EGC. Our study highlights the need to assess wide-ranging historical biogeographic processes - including founder-event jump dispersal - for best-fitting statistical Caribbean biogeographic reconstructions. Moreover, colonization of the Neotropical mainland from the Caribbean reinforces the notion that islands can be an important source of continental ersity.
Publisher: Proceedings of the National Academy of Sciences
Date: 04-01-2012
Abstract: The pigmentation patterns of shells in the genus Conus can be generated by a neural-network model of the mantle. We fit model parameters to the shell pigmentation patterns of 19 living Conus species for which a well resolved phylogeny is available. We infer the evolutionary history of these parameters and use these results to infer the pigmentation patterns of ancestral species. The methods we use allow us to characterize the evolutionary history of a neural network, an organ that cannot be preserved in the fossil record. These results are also notable because the inferred patterns of ancestral species sometimes lie outside the range of patterns of their living descendants, and illustrate how development imposes constraints on the evolution of complex phenotypes.
Publisher: Wiley
Date: 16-05-2021
Abstract: We report evidence further supporting homology between proteins in the F 1 F O ‐ATP synthetase and the bacterial flagellar motor (BFM). BFM proteins FliH, FliI, and FliJ have been hypothesized to be homologous to F O ‐b + F 1 ‐δ, F 1 ‐α/β, and F 1 ‐γ, with similar structure and interactions. We conduct a further test by constructing a gene order dataset, examining the order of fliH , fliI , and fliJ genes across the phylogenetic breadth of flagellar and nonflagellar type 3 secretion systems, and comparing this to published surveys of gene order in the F 1 F O ‐ATP synthetase, its N‐ATPase relatives, and the bacterial/archaeal V‐ and A‐type ATPases. Strikingly, the fliHIJ gene order was deeply conserved, with the few exceptions appearing derived, and exactly matching the widely conserved F‐ATPase gene order atpFHAG , coding for subunits b‐δ‐α‐γ. The V/A‐type ATPases have a similar conserved gene order. Our results confirm homology between these systems, and suggest a rare case of synteny conserved over billions of years, predating the Last Universal Common Ancestor (LUCA).
Publisher: Proceedings of the National Academy of Sciences
Date: 15-05-2007
Abstract: Although evolutionary biology is replete with explanations for complex biological structures, scientists concerned about evolution education have been forced to confront “intelligent design” (ID), which rejects a natural origin for biological complexity. The content of ID is a subset of the claims made by the older “creation science” movement. Both creationist views contend that highly complex biological adaptations and even organisms categorically cannot result from natural causes but require a supernatural creative agent. Historically, ID arose from efforts to produce a form of creationism that would be less vulnerable to legal challenges and that would not overtly rely upon biblical literalism. Scientists do not use ID to explain nature, but because it has support from outside the scientific community, ID is nonetheless contributing substantially to a long-standing assault on the integrity of science education.
Publisher: Cold Spring Harbor Laboratory
Date: 21-04-2016
DOI: 10.1101/049643
Abstract: Tip-dating methods are becoming popular alternatives to traditional node calibration approaches for building time-scaled phylogenetic trees, but questions remain about their application to empirical datasets. We compared the performance of the most popular methods against a dated tree of fossil Canidae derived from previously published monographs. Using a canid morphology dataset, we performed tip-dating using Beast 2.1.3 and MrBayes 3.2.5. We find that for key nodes ( Canis , ~3.2 Ma, Caninae ~11.7 Ma) a non-mechanistic model using a uniform tree prior produces estimates that are unrealistically old (27.5, 38.9 Ma). Mechanistic models (incorporating lineage birth, death, and s ling rates) estimate ages that are closely in line with prior research. We provide a discussion of these two families of models (mechanistic vs. non-mechanistic) and their applicability to fossil datasets.
Publisher: Springer Science and Business Media LLC
Date: 05-2006
DOI: 10.1038/NI0506-433
Publisher: American Association for the Advancement of Science (AAAS)
Date: 2016
Abstract: A phylogeny identifies ancestors of modern creationist legislation
Publisher: Cambridge University Press (CUP)
Date: 14-07-2020
DOI: 10.1017/PAB.2020.24
Abstract: Echinoderms make up a substantial component of Ordovician marine invertebrates, yet their speciation and dispersal history as inferred within a rigorous phylogenetic and statistical framework is lacking. We use biogeographic stochastic mapping (BSM implemented in the R package BioGeoBEARS) to infer ancestral area relationships and the number and type of dispersal events through the Ordovician for diploporan blastozoans and related species. The BSM analysis was ided into three time slices to analyze how dispersal paths changed before and during the great Ordovician bio ersification event (GOBE) and within the Late Ordovician mass extinction intervals. The best-fit biogeographic model incorporated jump dispersal, indicating this was an important speciation strategy. Reconstructed areas within the phylogeny indicate the first diploporan blastozoans likely originated within Baltica or Gondwana. Dispersal, jump dispersal, and sympatry dominated the BSM inference through the Ordovician, while dispersal paths varied in time. Long-distance dispersal events in the Early Ordovician indicate distance was not a significant predictor of dispersal, whereas increased dispersal events between Baltica and Laurentia are apparent during the GOBE, indicating these areas were important to blastozoan speciation. During the Late Ordovician, there is an increase in dispersal events among all paleocontinents. The drivers of dispersal are attributed to oceanic and epicontinental currents. Speciation events plotted against geochemical data indicate that blastozoans may not have responded to climate cooling events and other geochemical perturbations, but additional data will continue to shed light on the drivers of early Paleozoic blastozoan speciation and dispersal patterns.
Publisher: Oxford University Press (OUP)
Date: 12-12-2015
Publisher: Public Library of Science (PLoS)
Date: 10-02-2017
Publisher: Cold Spring Harbor Laboratory
Date: 02-01-2021
DOI: 10.1101/2021.01.01.425057
Abstract: Evidence of homology between proteins in the ATP synthetase and the bacterial flagellar motor (BFM) has been accumulating since the 1980s. Specifically, the BFM’s Type 3 Secretion System (T3SS) export apparatus FliH, FliI, and FliJ are considered homologous to F O -b + F 1 -δ, F 1 -α/β, and F 1 -γ, and have similar structure and interactions. We review the discoveries that advanced the homology hypothesis and then conduct a further test by examining gene order in the two systems and their relatives. Conservation of gene order, or synteny, is often observed between closely related prokaryote species, but usually degrades with phylogenetic distance. As a result, observed conservation of synteny over vast phylogenetic distances can be evidence of shared ancestral coexpression, interaction, and function. We constructed a gene order dataset by examining the order of fliH , fliI , and fliJ genes across the phylogenetic breadth of flagellar and nonflagellar T3SS. We compared this to published surveys of gene order in the F 1 F O -ATP synthetase, its N-ATPase relatives, and the bacterial/archaeal V- and A-type ATPases. Strikingly, the fliHIJ gene order was deeply conserved, with the few exceptions appearing derived, and exactly matching the widely conserved F-ATPase gene order atpFHAG , coding for subunits b - δ - α - γ . The V/A-type ATPases have a similar conserved gene order shared for homologous components. Our results further strengthen the argument for homology between these systems, and suggest a rare case of synteny conserved over billions of years, dating back to well before the Last Universal Common Ancestor (LUCA).
Publisher: Cold Spring Harbor Laboratory
Date: 18-10-2022
DOI: 10.1101/2022.10.17.512626
Abstract: The bacterial flagellar motor (BFM) is a rotary nanomachine powered by the translocation of ions across the inner membrane through the stator complex. The stator complex consists of two membrane proteins: MotA and MotB (in H + powered motors), or PomA and PomB (in Na + powered motors). In this study we used ancestral sequence reconstruction (ASR) to probe which residues of MotA correlate with function and may have been conserved to preserve motor function. We reconstructed ten ancestral sequences of MotA and found four of them were motile in combination with contemporary E. coli MotB and in combination with our previously published functional ancestral MotBs. Sequence comparison between wild-type (WT) E. coli MotA and MotA-ASRs revealed 30 critical residues across multiple domains of MotA that were conserved among all motile stator units. These conserved residues included pore-facing, cytoplasm-facing and MotA-MotA intermolecular facing sites. Overall, this work demonstrates the role of ASR in assessing conserved variable residues in a subunit of a molecular complex.
Publisher: The Royal Society
Date: 09-2021
Abstract: The role of whole-genome duplication (WGD) in facilitating shifts into novel biomes remains unknown. Focusing on two erse woody plant groups in New Zealand, Coprosma (Rubiaceae) and Veronica (Plantaginaceae), we investigate how biome occupancy varies with ploidy level, and test the hypothesis that WGD increases the rate of biome shifting. Ploidy levels and biome occupancy (forest, open and alpine) were determined for indigenous species in both clades. The distribution of low-ploidy ( Coprosma : 2 x , Veronica : 6 x ) versus high-ploidy ( Coprosma : 4–10 x , Veronica : 12–18 x ) species across biomes was tested statistically. Estimation of the phylogenetic history of biome occupancy and WGD was performed using time-calibrated phylogenies and the R package BioGeoBEARS. Trait-dependent dispersal models were implemented to determine support for an increased rate of biome shifting among high-ploidy lineages. We find support for a greater than random portion of high-ploidy species occupying multiple biomes. We also find strong support for high-ploidy lineages showing a three- to eightfold increase in the rate of biome shifts. These results suggest that WGD promotes ecological expansion into new biomes.
Publisher: Portland Press Ltd.
Date: 12-12-2009
DOI: 10.1042/BJ20081534
Abstract: ID (‘intelligent design’) is not science, but a form of creationism both are very different from the simple theological proposition that a ine Creator is responsible for the natural patterns and processes of the Universe. Its current version maintains that a ‘Designer’ must intervene miraculously to accomplish certain natural scientific events. The verdict in the 2005 case Kitzmiller, et al. v. Dover School District, et al. (in Harrisburg, PA, U.S.A.) was a landmark of American jurisprudence that prohibited the teaching of ID as science, identified it as religiously based, and forbade long-refuted ‘criticisms of evolution’ from introduction into public school classes. Much of the science of the trial was based on biochemistry biochemists and other scientists have several important opportunities to improve scientific literacy and science education in American public schools (‘state schools’) by working with teachers, curriculum developers and textbook writers.
Publisher: Oxford University Press (OUP)
Date: 27-07-2013
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: Springer Science and Business Media LLC
Date: 16-07-2010
Abstract: For Google Summer of Code 2009/NESCENT Phyloinformatics Summer of Code 2009, I built a Geography module for Biopython. The purpose of the module is to search, download, and process biogeographical data from GBIF, much as Biopython currently accesses Genbank. Application of the tool to a historical biogeography study on bivalves will be illustrated.As required by Google Summer of Code and Biopython, the code is open access and is released under the Biopython License:"www.biopython.org/DIST/LICENSE":www.biopython.org/DIST/LICENSEThe module is described, and a tutorial is presented, on the Biopython wiki:iki/BioGeographyThe page contains links to the source hosted on Github here is the direct link:"matzke/biopython/tree/Geography":matzke/biopython/tree/Geography
Publisher: Oxford University Press (OUP)
Date: 14-08-2014
Abstract: Founder-event speciation, where a rare jump dispersal event founds a new genetically isolated lineage, has long been considered crucial by many historical biogeographers, but its importance is disputed within the vicariance school. Probabilistic modeling of geographic range evolution creates the potential to test different biogeographical models against data using standard statistical model choice procedures, as long as multiple models are available. I re-implement the Dispersal-Extinction-Cladogenesis (DEC) model of LAGRANGE in the R package BioGeoBEARS, and modify it to create a new model, DEC + J, which adds founder-event speciation, the importance of which is governed by a new free parameter, [Formula: see text]. The identifiability of DEC and DEC + J is tested on data sets simulated under a wide range of macroevolutionary models where geography evolves jointly with lineage birth/death events. The results confirm that DEC and DEC + J are identifiable even though these models ignore the fact that molecular phylogenies are missing many cladogenesis and extinction events. The simulations also indicate that DEC will have substantially increased errors in ancestral range estimation and parameter inference when the true model includes + J. DEC and DEC + J are compared on 13 empirical data sets drawn from studies of island clades. Likelihood-ratio tests indicate that all clades reject DEC, and AICc model weights show large to overwhelming support for DEC + J, for the first time verifying the importance of founder-event speciation in island clades via statistical model choice. Under DEC + J, ancestral nodes are usually estimated to have ranges occupying only one island, rather than the widespread ancestors often favored by DEC. These results indicate that the assumptions of historical biogeography models can have large impacts on inference and require testing and comparison with statistical methods.
Publisher: Public Library of Science (PLoS)
Date: 21-01-2014
Publisher: Wiley
Date: 08-07-2016
DOI: 10.1111/GBI.12200
Abstract: The rise of oxygen ca. 2.3 billion years ago (Ga) is the most distinct environmental transition in Earth history. This event was enabled by the evolution of oxygenic photosynthesis in the ancestors of Cyanobacteria. However, long-standing questions concern the evolutionary timing of this metabolism, with conflicting answers spanning more than one billion years. Recently, knowledge of the Cyanobacteria phylum has expanded with the discovery of non-photosynthetic members, including a closely related sister group termed Melainabacteria, with the known oxygenic phototrophs restricted to a clade recently designated Oxyphotobacteria. By integrating genomic data from the Melainabacteria, cross-calibrated Bayesian relaxed molecular clock analyses show that crown group Oxyphotobacteria evolved ca. 2.0 billion years ago (Ga), well after the rise of atmospheric dioxygen. We further estimate the ergence between Oxyphotobacteria and Melainabacteria ca. 2.5-2.6 Ga, which-if oxygenic photosynthesis is an evolutionary synapomorphy of the Oxyphotobacteria-marks an upper limit for the origin of oxygenic photosynthesis. Together, these results are consistent with the hypothesis that oxygenic photosynthesis evolved relatively close in time to the rise of oxygen.
Location: United States of America
Location: United States of America
Location: United States of America
Start Date: 2020
End Date: 2023
Funder: Royal Society of New Zealand
View Funded ActivityStart Date: 2020
End Date: 2021
Funder: University of Auckland
View Funded ActivityStart Date: 2017
End Date: 2020
Funder: Marsden Fund
View Funded ActivityStart Date: 2022
End Date: 2027
Funder: Rutherford Discovery Fellowship
View Funded ActivityStart Date: 2018
End Date: 2021
Funder: Australian Research Council
View Funded ActivityStart Date: 07-2015
End Date: 04-2018
Amount: $369,536.00
Funder: Australian Research Council
View Funded ActivityStart Date: 2019
End Date: 07-2022
Amount: $405,000.00
Funder: Australian Research Council
View Funded Activity