Matthew Phillips

Identifying Complex DNA Contamination in Pig-Footed Bandicoots Helps to Clarify an Anomalous Ecological Transition

Publisher: MDPI AG

Date: 29-04-2022

DOI: 10.3390/D14050352

Abstract: Our understanding of the biology of the extinct pig-footed bandicoots (Chaeropus) has been substantially revised over the past two decades by both molecular and morphological research. Resolving the systematic and temporal contexts of Chaeropus evolution has relied heavily on sequencing DNA from century-old specimens. We have used sliding window BLASTs and phylogeny reconstruction, as well as cumulative likelihood and apomorphy distributions, to identify contamination in sequences from both species of pig-footed bandicoot. The sources of non-target DNA that were identified range from other bandicoot species to a bird—emphasizing the importance of sequence authentication for historical museum specimens, as has become standard for ancient DNA studies. Upon excluding the putatively contaminated fragments, Chaeropus was resolved as the sister to all other bandicoots (Peramelidae), to the exclusion of bilbies (Macrotis). The estimated ergence time between the two Chaeropus species also decreases in better agreement with the fossil record. This study provides evolutionary context for testing hypotheses on the ecological transition of pig-footed bandicoots from semi-fossorial omnivores towards cursorial grazers, which in turn may represent the only breach of deeply conserved ecospace partitioning between modern Australo-Papuan marsupial orders.

The soft explosive model of placental mammal evolution

Publisher: Springer Science and Business Media LLC

Date: 03-07-2018

DOI: 10.1186/S12862-018-1218-X

The evolutionary relationships of Diprotodontia and improving the accuracy of phylogenetic inference from morphological data

Publisher: Informa UK Limited

Date: 19-03-2023

DOI: 10.1080/03115518.2023.2184492

Australian rodents reveal conserved Cranial Evolutionary Allometry across 10 million years of murid evolution

Publisher: Cold Spring Harbor Laboratory

Date: 05-2020

DOI: 10.1101/2020.04.30.071308

Abstract: Among vertebrates, placental mammals are particularly variable in the covariance between their cranial shapes and body size (allometry), with the notable exception of rodents. Australian murid rodents present an opportunity to assess the cause of this anomaly because they radiated on an ecologically erse continent unique for lacking other terrestrial placentals. Here we used 3D geometric morphometrics to quantify species-level and evolutionary allometries in 38 species (317 crania) from all Australian murid genera. We ask if ecological opportunity resulted in greater allometric ersity conversely, we test if intrinsic constraints and/or stabilizing selection conserved allometry. To increase confidence in species-level allometric slopes, we introduce a new phylogeny-based method of bootstrapping and randomly res ling across the whole s le. We found exceedingly conserved allometry across the 10 million year split between Mus and the clade containing Australian murids. Cranial shapes followed craniofacial evolutionary allometry (CREA) patterns, with larger species having relatively longer snouts and smaller braincases. CREA is consistent with both intrinsic constraints and stabilizing selection hypotheses for conserved allometry. However, large-bodied frugivores evolved faster, while carnivorous specialists showed skull modifications known to conflict with masticatory efficiency. These results suggest a strong role of stabilizing selection on the masticatory apparatus of murid rodents.

Closing the gap between rocks and clocks using total-evidence dating

Publisher: The Royal Society

Date: 19-07-2016

DOI: 10.1098/RSTB.2015.0136

Abstract: Total-evidence dating (TED) allows evolutionary biologists to incorporate a wide range of dating information into a unified statistical analysis. One might expect this to improve the agreement between rocks and clocks but this is not necessarily the case. We explore the reasons for such discordance using a mammalian dataset with rich molecular, morphological and fossil information. There is strong conflict in this dataset between morphology and molecules under standard stochastic models. This causes TED to push ergence events back in time when using inadequate models or vague priors, a phenomenon we term ‘deep root attraction’ (DRA). We identify several causes of DRA. Failure to account for ersified s ling results in dramatic DRA, but this can be addressed using existing techniques. Inadequate morphological models also appear to be a major contributor to DRA. The major reason seems to be that current models do not account for dependencies among morphological characters, causing distorted topology and branch length estimates. This is particularly problematic for huge morphological datasets, which may contain large numbers of correlated characters. Finally, ersification and fossil s ling priors that do not incorporate all the available background information can contribute to DRA, but these priors can also be used to compensate for DRA. Specifically, we show that DRA in the mammalian dataset can be addressed by introducing a modest extra penalty for ghost lineages that are unobserved in the fossil record, for instance by assuming rapid ersification, rare extinction or high fossil s ling rate any of these assumptions produces highly congruent ergence time estimates with a minimal gap between rocks and clocks. Under these conditions, fossils have a stabilizing influence on ergence time estimates and significantly increase the precision of those estimates, which are generally close to the dates suggested by palaeontologists. This article is part of the themed issue ‘Dating species ergences using rocks and clocks’.

The soft explosive model of placental mammal evolution

Publisher: Cold Spring Harbor Laboratory

Date: 22-01-2018

DOI: 10.1101/251520

Abstract: Recent molecular dating estimates for placental mammals echo fossil inferences for an explosive interordinal ersification, but typically place this event some 10-20 million years earlier than the Paleocene fossils, among apparently more “primitive” mammal faunas. However, current models of molecular evolution do not adequately account for parallel rate changes, and result in dramatic ergence underestimates for large, long-lived mammals such as whales and hominids. Calibrating among these taxa shifts the rate model errors deeper in the tree, inflating interordinal ergence estimates. We employ simulations based on empirical rate variation, which show that this “error-shift inflation” can explain previous molecular dating overestimates relative to fossil inferences. Molecular dating accuracy is substantially improved in the simulations by focusing on calibrations for taxa that retain plesiomorphic life-history characteristics. Applying this strategy to the empirical data favours the soft explosive model of placental evolution, in line with traditional palaeontological interpretations – a few Cretaceous placental lineages give rise to a rapid interordinal ersification following the 66 Ma Cretaceous-Paleogene boundary mass extinction. Our soft explosive model for the ersification of placental mammals brings into agreement previously incongruous molecular, fossil, and ancestral life history estimates, and closely aligns with a growing consensus for a similar model for bird evolution. We show that recent criticism of the soft explosive model relies on ignoring both experimental controls and statistical confidence, as well as misrepresentation, and inconsistent interpretations of morphological phylogeny. More generally, we suggest that the evolutionary properties of adaptive radiations may leave current molecular dating methods susceptible to overestimating the timing of major ersification events.

Using 3D geometric morphometrics to aid taxonomic and ecological understanding of a recent speciation event within a small Australian marsupial (genus Antechinus)

Publisher: Cold Spring Harbor Laboratory

Date: 28-04-2021

DOI: 10.1101/2021.04.28.441717

Abstract: Taxonomic distinction of species forms the foundation of bio ersity assessments and conservation priorities. However, traditional morphological and/or genetics-based taxonomic assessments frequently miss the opportunity of elaborating on the ecological and functional context of species ersification. Here, we used 3D geometric morphometrics of the cranium to improve taxonomic differentiation and add eco-morphological characterisation of a young cryptic ergence within the marsupial carnivorous genus Antechinus . Specifically, we used 168 museum specimens to characterise the recently proposed clades A. stuartii “south”, A. stuartii “north” and A. subtropicus . Beyond slight differences attributable to overall size (and therefore not necessarily diagnostic), we also found clear allometry-independent shape variation. This allowed us to define new, easily measured diagnostic traits in the palate, which differentiate the three clades. Contrary to previous suggestions, we found no support for a latitudinal gradient as causing the differentiation between the clades. However, skull shape co-varied with temperature and precipitation seasonality, suggesting that the clades may be adapted to environmental variables that are likely to be impacted by climate change. Our study demonstrates the use of 3D geometric morphometrics to improve taxonomic diagnosis of cryptic mammalian species, while providing perspectives on the adaptive origins and potential future threats of mammalian ersity.

A mixed relaxed clock model

Publisher: The Royal Society

Date: 19-07-2016

DOI: 10.1098/RSTB.2015.0132

Abstract: Over recent years, several alternative relaxed clock models have been proposed in the context of Bayesian dating. These models fall in two distinct categories: uncorrelated and autocorrelated across branches. The choice between these two classes of relaxed clocks is still an open question. More fundamentally, the true process of rate variation may have both long-term trends and short-term fluctuations, suggesting that more sophisticated clock models unfolding over multiple time scales should ultimately be developed. Here, a mixed relaxed clock model is introduced, which can be mechanistically interpreted as a rate variation process undergoing short-term fluctuations on the top of Brownian long-term trends. Statistically, this mixed clock represents an alternative solution to the problem of choosing between autocorrelated and uncorrelated relaxed clocks, by proposing instead to combine their respective merits. Fitting this model on a dataset of 105 placental mammals, using both node-dating and tip-dating approaches, suggests that the two pure clocks, Brownian and white noise, are rejected in favour of a mixed model with approximately equal contributions for its uncorrelated and autocorrelated components. The tip-dating analysis is particularly sensitive to the choice of the relaxed clock model. In this context, the classical pure Brownian relaxed clock appears to be overly rigid, leading to biases in ergence time estimation. By contrast, the use of a mixed clock leads to more recent and more reasonable estimates for the crown ages of placental orders and superorders. Altogether, the mixed clock introduced here represents a first step towards empirically more adequate models of the patterns of rate variation across phylogenetic trees. This article is part of the themed issue ‘Dating species ergences using rocks and clocks’.

Genomic, Functional and Structural Analyses Reveal Mechanisms of Evolutionary Innovation within the Sea Anemone 8 Toxin Family

Publisher: Cold Spring Harbor Laboratory

Date: 10-12-2022

DOI: 10.1101/2022.12.08.518931

Abstract: ShK from Stichodactyla helianthus has established the therapeutic potential of sea anemone venom peptides, but many lineage-specific toxin families in actinarians remain uncharacterised. One such peptide family, sea anemone 8 (SA8), is present in all five sea anemone superfamilies. We explored the genomic arrangement and evolution of the SA8 gene family in Actinia tenebrosa and Telmatactis stephensoni , characterised the expression patterns of SA8 sequences, and examined the structure and function of SA8 from the venom of T . stephensoni . We identified ten SA8 genes in two clusters and six SA8 genes in five clusters for T. stephensoni and A. tenebrosa , respectively. Nine SA8 T. stephensoni genes were found in a single cluster and an SA8 peptide encoded by an inverted SA8 gene from this cluster was recruited to venom. We show that SA8 genes in both species are expressed in a tissue-specific manner and the inverted SA8 gene has a unique tissue distribution. While functional activity of the SA8 putative toxin encoded by the inverted gene was inconclusive, its tissue localisation is similar to toxins used for predator deterrence. We demonstrate that, although mature SA8 putative toxins have similar cysteine spacing to ShK, SA8 peptides are distinct from ShK peptides based on structure and disulfide connectivity. Our results provide the first demonstration that SA8 is a unique gene family in actiniarians, evolving through a variety of structural changes including tandem and proximal gene duplication and an inversion event that together allowed SA8 to be recruited into the venom of T . stephensoni .

Multiple modes of inference reveal less phylogenetic signal in marsupial basicranial shape compared with the rest of the cranium

Publisher: The Royal Society

Date: 15-05-2023

DOI: 10.1098/RSTB.2022.0085

Abstract: Incorporating morphological data into modern phylogenies allows integration of fossil evidence, facilitating ergence dating and macroevolutionary inferences. Improvements in the phylogenetic utility of morphological data have been sought via Procrustes-based geometric morphometrics (GMM), but with mixed success and little clarity over what anatomical areas are most suitable. Here, we assess GMM-based phylogenetic reconstructions in a heavily s led source of discrete characters for mammalian phylogenetics—the basicranium—in 57 species of marsupial mammals, compared with the remainder of the cranium. We show less phylogenetic signal in the basicranium compared with a ‘Rest of Cranium’ partition, using erse metrics of phylogenetic signal ( K mult , phylogenetically aligned principal components analysis, comparisons of UPGMA/neighbour-joining arsimony trees and cophenetic distances to a reference phylogeny) for scaled, Procrustes-aligned landmarks and allometry-corrected residuals. Surprisingly, a similar pattern emerged from parsimony-based analyses of discrete cranial characters. The consistent results across methods suggest that easily computed metrics such as K mult can provide good guidance on phylogenetic information in a landmarking configuration. In addition, GMM data may be less informative for intricate but conservative anatomical regions such as the basicranium, while better—but not necessarily novel—phylogenetic information can be expected for broadly characterized shapes such as entire bones. This article is part of the theme issue ‘The mammalian skull: development, structure and function’.

Australian National University

Location: Australia

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Dames And Moore

Location: Australia

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Queensland University Of Technology

Location: Australia

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Massey University

Location: New Zealand

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University Of Oxford

Location: United Kingdom of Great Britain and Northern Ireland

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Discovery Projects - Grant ID: DP0774015

Start Date: 07-2007

End Date: 11-2010

Amount: $320,000.00

Funder: Australian Research Council

Discovery Projects - Grant ID: DP150104659

Start Date: 2015

End Date: 04-2019

Amount: $392,700.00

Funder: Australian Research Council

Discovery Projects - Grant ID: DP220103234

Start Date: 06-2022

End Date: 05-2025

Amount: $475,000.00

Funder: Australian Research Council

Discovery Projects - Grant ID: DP190103636

Start Date: 04-2019

End Date: 04-2022

Amount: $445,000.00

Funder: Australian Research Council

Discovery Projects - Grant ID: DP170103227

Start Date: 2017

End Date: 12-2020

Amount: $298,000.00

Funder: Australian Research Council