1
|
Guillerme T, Bright JA, Cooney CR, Hughes EC, Varley ZK, Cooper N, Beckerman AP, Thomas GH. Innovation and elaboration on the avian tree of life. Sci Adv 2023; 9:eadg1641. [PMID: 37878701 PMCID: PMC10599619 DOI: 10.1126/sciadv.adg1641] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Accepted: 09/22/2023] [Indexed: 10/27/2023]
Abstract
Widely documented, megaevolutionary jumps in phenotypic diversity continue to perplex researchers because it remains unclear whether these marked changes can emerge from microevolutionary processes. Here, we tackle this question using new approaches for modeling multivariate traits to evaluate the magnitude and distribution of elaboration and innovation in the evolution of bird beaks. We find that elaboration, evolution along the major axis of phenotypic change, is common at both macro- and megaevolutionary scales, whereas innovation, evolution away from the major axis of phenotypic change, is more prominent at megaevolutionary scales. The major axis of phenotypic change among species beak shapes at megaevolutionary scales is an emergent property of innovation across clades. Our analyses suggest that the reorientation of phenotypes via innovation is a ubiquitous route for divergence that can arise through gradual change alone, opening up further avenues for evolution to explore.
Collapse
Affiliation(s)
- Thomas Guillerme
- School of Biosciences, University of Sheffield, Sheffield S10 2TN, UK
| | - Jen A. Bright
- School of Natural Science, University of Hull, Hull HU6 7RX, UK
| | | | - Emma C. Hughes
- School of Biosciences, University of Sheffield, Sheffield S10 2TN, UK
| | - Zoë K. Varley
- Natural History Museum, Cromwell Road, London SW7 5BD, UK
- Bird Group, Department of Life Sciences, the Natural History Museum at Tring, Tring, UK
| | - Natalie Cooper
- Natural History Museum, Cromwell Road, London SW7 5BD, UK
| | | | - Gavin H. Thomas
- School of Biosciences, University of Sheffield, Sheffield S10 2TN, UK
- Bird Group, Department of Life Sciences, the Natural History Museum at Tring, Tring, UK
| |
Collapse
|
2
|
Weisbecker V, Beck RMD, Guillerme T, Harrington AR, Lange-Hodgson L, Lee MSY, Mardon K, Phillips MJ. Multiple modes of inference reveal less phylogenetic signal in marsupial basicranial shape compared with the rest of the cranium. Philos Trans R Soc Lond B Biol Sci 2023; 378:20220085. [PMID: 37183893 PMCID: PMC10184248 DOI: 10.1098/rstb.2022.0085] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/16/2023] Open
Abstract
Incorporating morphological data into modern phylogenies allows integration of fossil evidence, facilitating divergence 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 sampled 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 diverse metrics of phylogenetic signal (Kmult, phylogenetically aligned principal components analysis, comparisons of UPGMA/neighbour-joining/parsimony 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 Kmult 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'.
Collapse
Affiliation(s)
- Vera Weisbecker
- College of Science and Engineering, Flinders University, Adelaide, South Australia 5042, Australia
| | - Robin M D Beck
- School of Science, Engineering and Environment, University of Salford, Salford, M5 4WT, UK
| | - Thomas Guillerme
- School of Biosciences, University of Sheffield, Sheffield, S10 2TN, UK
| | | | - Leonie Lange-Hodgson
- School of Biological Sciences, University of Queensland, Saint Lucia, Queensland, 4072, Australia
| | - Michael S Y Lee
- College of Science and Engineering, Flinders University, Adelaide, South Australia 5042, Australia
- Earth Sciences Section, South Australian Museum, Adelaide, South Australia, 5000 Australia
| | - Karine Mardon
- Centre of Advanced Imaging, University of Queensland, Saint Lucia, Queensland, 4072, Australia
| | - Matthew J Phillips
- School of Biology & Environmental Science, Queensland University of Technology, Brisbane, Queensland, 4000, Australia
| |
Collapse
|
3
|
Affiliation(s)
- Stefano Mammola
- Laboratory for Integrative Biodiversity Research (LIBRe) Finnish Museum of Natural History (Luomus) University of Helsinki Helsinki Finland
- Molecular Ecology Group (MEG) Water Research InstituteNational Research Council (CNR‐IRSA) Verbania Pallanza Italy
| | - Carlos P. Carmona
- Institute of Ecology and Earth Sciences University of Tartu Tartu Estonia
| | - Thomas Guillerme
- Department of Animal and Plant Sciences The University of Sheffield Sheffield UK
| | - Pedro Cardoso
- Laboratory for Integrative Biodiversity Research (LIBRe) Finnish Museum of Natural History (Luomus) University of Helsinki Helsinki Finland
| |
Collapse
|
4
|
Marcy AE, Guillerme T, Sherratt E, Rowe KC, Phillips MJ, Weisbecker V. Australian Rodents Reveal Conserved Cranial Evolutionary Allometry across 10 Million Years of Murid Evolution. Am Nat 2020; 196:755-768. [PMID: 33211559 DOI: 10.1086/711398] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
AbstractAmong vertebrates, placental mammals are particularly variable in the covariance between cranial shape and body size (allometry), with rodents being a major exception. Australian murid rodents allow an assessment of the cause of this anomaly because they radiated on an ecologically diverse continent notably lacking other terrestrial placentals. Here, we use 3D geometric morphometrics to quantify species-level and evolutionary allometries in 38 species (317 crania) from all Australian murid genera. We ask whether ecological opportunity resulted in greater allometric diversity compared with other rodents or whether conserved allometry suggests intrinsic constraints and/or stabilizing selection. We also assess whether cranial shape variation follows the proposed rule of craniofacial evolutionary allometry (CREA), whereby larger species have relatively longer snouts and smaller braincases. To ensure we could differentiate parallel versus nonparallel species-level allometric slopes, we compared the slopes of rarefied samples across all clades. We found exceedingly conserved allometry and CREA-like patterns across the 10-million-year split between Mus and Australian murids. This could support both intrinsic-constraint and stabilizing-selection hypotheses for conserved allometry. Large-bodied frugivores evolved faster than other species along the allometric trajectory, which could suggest stabilizing selection on the shape of the masticatory apparatus as body size changes.
Collapse
|
5
|
Viacava P, Blomberg SP, Sansalone G, Phillips MJ, Guillerme T, Cameron SF, Wilson RS, Weisbecker V. Skull shape of a widely distributed, endangered marsupial reveals little evidence of local adaptation between fragmented populations. Ecol Evol 2020; 10:9707-9720. [PMID: 33005341 PMCID: PMC7520215 DOI: 10.1002/ece3.6593] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Revised: 06/15/2020] [Accepted: 06/17/2020] [Indexed: 11/07/2022] Open
Abstract
The biogeographic distribution of diversity among populations of threatened mammalian species is generally investigated using population genetics. However, intraspecific phenotypic diversity is rarely assessed beyond taxonomy-focused linear measurements or qualitative descriptions. Here, we use a technique widely used in the evolutionary sciences-geometric morphometrics-to characterize shape diversity in the skull of an endangered marsupial, the northern quoll, across its 5,000 km distribution range along Northern Australia. Skull shape is a proxy for feeding, behavior, and phenotypic differentiation, allowing us to ask whether populations can be distinguished and whether patterns of variation indicate adaptability to changing environmental conditions. We analyzed skull shape in 101 individuals across four mainland populations and several islands. We assessed the contribution of population, size, sex, rainfall, temperature, and geography to skull shape variation using principal component analysis, Procrustes ANOVA, and variation partitioning analyses. The populations harbor similar amounts of broadly overlapping skull shape variation, with relatively low geographic effects. Size predicted skull shape best, coinciding with braincase size variation and differences in zygomatic arches. Size-adjusted differences in populations explained less variation with far smaller effect sizes, relating to changes in the insertion areas of masticatory muscles, as well as the upper muzzle and incisor region. Climatic and geographic variables contributed little. Strikingly, the vast majority of shape variation-76%-remained unexplained. Our results suggest a uniform intraspecific scope for shape variation, possibly due to allometric constraints or phenotypic plasticity beyond the relatively strong allometric effect. The lack of local adaptation indicates that cross-breeding between populations will not reduce local morphological skull (and probably general musculoskeletal) adaptation because none exists. However, the potential for heritable morphological variation (e.g., specialization to local diets) seems exceedingly limited. We conclude that 3D geometric morphometrics can provide a comprehensive, statistically rigorous phenomic contribution to genetic-based conservation studies.
Collapse
Affiliation(s)
- Pietro Viacava
- School of Biological Sciences The University of Queensland St. Lucia QLD Australia
| | - Simone P Blomberg
- School of Biological Sciences The University of Queensland St. Lucia QLD Australia
| | - Gabriele Sansalone
- Form, Evolution and Anatomy Research Laboratory, Zoology School of Environmental and Rural Sciences University of New England Armidale NSW Australia
| | - Matthew J Phillips
- Earth, Environmental and Biological Sciences School Queensland University of Technology Brisbane QLD Australia
| | - Thomas Guillerme
- School of Biological Sciences The University of Queensland St. Lucia QLD Australia
| | - Skye F Cameron
- School of Biological Sciences The University of Queensland St. Lucia QLD Australia
| | - Robbie S Wilson
- School of Biological Sciences The University of Queensland St. Lucia QLD Australia
| | - Vera Weisbecker
- College of Science and Engineering Flinders University Adelaide SA Australia
| |
Collapse
|
6
|
Puttick MN, Guillerme T, Wills MA. The complex effects of mass extinctions on morphological disparity. Evolution 2020; 74:2207-2220. [PMID: 32776526 DOI: 10.1111/evo.14078] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2019] [Revised: 07/23/2020] [Accepted: 07/31/2020] [Indexed: 01/01/2023]
Abstract
Studies of biodiversity through deep time have been a staple for biologists and paleontologists for over 60 years. Investigations of species richness (diversity) revealed that at least five mass extinctions punctuated the last half billion years, each seeing the rapid demise of a large proportion of contemporary taxa. In contrast to diversity, the response of morphological diversity (disparity) to mass extinctions is unclear. Generally, diversity and disparity are decoupled, such that diversity may decline as morphological disparity increases, and vice versa. Here, we develop simulations to model disparity changes across mass extinctions using continuous traits and birth-death trees. We find no simple null for disparity change following a mass extinction but do observe general patterns. The range of trait values decreases following either random or trait-selective mass extinctions, whereas variance and the density of morphospace occupation only decline following trait-selective events. General trends may differentiate random and trait-selective mass extinctions, but methods struggle to identify trait selectivity. Long-term effects of mass extinction trait selectivity change support for phylogenetic comparative methods away from the simulated Brownian motion toward Ornstein-Uhlenbeck and Early Burst models. We find that morphological change over mass extinction is best studied by quantifying multiple aspects of morphospace occupation.
Collapse
Affiliation(s)
- Mark N Puttick
- Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, Bath, BA2 7AY, United Kingdom
| | - Thomas Guillerme
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, S10 2TN, United Kingdom
| | - Matthew A Wills
- Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, Bath, BA2 7AY, United Kingdom
| |
Collapse
|
7
|
Guillerme T, Cooper N, Brusatte SL, Davis KE, Jackson AL, Gerber S, Goswami A, Healy K, Hopkins MJ, Jones MEH, Lloyd GT, O'Reilly JE, Pate A, Puttick MN, Rayfield EJ, Saupe EE, Sherratt E, Slater GJ, Weisbecker V, Thomas GH, Donoghue PCJ. Disparities in the analysis of morphological disparity. Biol Lett 2020; 16:20200199. [PMID: 32603646 PMCID: PMC7423048 DOI: 10.1098/rsbl.2020.0199] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Accepted: 06/05/2020] [Indexed: 12/22/2022] Open
Abstract
Analyses of morphological disparity have been used to characterize and investigate the evolution of variation in the anatomy, function and ecology of organisms since the 1980s. While a diversity of methods have been employed, it is unclear whether they provide equivalent insights. Here, we review the most commonly used approaches for characterizing and analysing morphological disparity, all of which have associated limitations that, if ignored, can lead to misinterpretation. We propose best practice guidelines for disparity analyses, while noting that there can be no 'one-size-fits-all' approach. The available tools should always be used in the context of a specific biological question that will determine data and method selection at every stage of the analysis.
Collapse
Affiliation(s)
- Thomas Guillerme
- School of Biological Sciences, University of Queensland, St Lucia, QLD4072, Australia
- Department of Animal and Plant Sciences, The University of Sheffield, Sheffield S10 2TN, UK
| | - Natalie Cooper
- Department of Life Sciences, Natural History Museum London, Cromwell Road, London SW7 5BD, UK
| | - Stephen L. Brusatte
- School of GeoSciences, University of Edinburgh, Grant Institute, Edinburgh EH9 3FE, UK
| | - Katie E. Davis
- Leverhulme Centre for Anthropocene Biodiversity, Department of Biology, University of York, York YO10 5DD, UK
| | - Andrew L. Jackson
- Department of Zoology, School of Natural Sciences, Trinity College Dublin, Dublin 2, Ireland
| | - Sylvain Gerber
- Institut de Systématique, Évolution, Biodiversité (ISYEB), Muséum national d'Histoire naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, 57 rue Cuvier CP39, 75005 Paris, France
| | - Anjali Goswami
- Department of Life Sciences, Natural History Museum London, Cromwell Road, London SW7 5BD, UK
| | - Kevin Healy
- Ryan Institute, School of Natural Sciences, National University of Ireland, Galway, H91YD6H, Ireland
| | - Melanie J. Hopkins
- Division of Paleontology (Invertebrates), American Museum of Natural History, New York, NY 10024, USA
| | - Marc E. H. Jones
- Department of Cell and Developmental Biology, University College London, London WC1E 6BT, UK
| | - Graeme T. Lloyd
- School of Earth and Environment, University of Leeds, Leeds LS2 9JT, UK
| | - Joseph E. O'Reilly
- MRC Institute of Genetic and Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XU, UK
- School of Earth Sciences, University of Bristol, Life Sciences Building, Tyndall Avenue, Bristol BS8 1TQ, UK
| | - Abi Pate
- School of Earth Sciences, University of Bristol, Life Sciences Building, Tyndall Avenue, Bristol BS8 1TQ, UK
| | - Mark N. Puttick
- School of Earth Sciences, University of Bristol, Life Sciences Building, Tyndall Avenue, Bristol BS8 1TQ, UK
- Milner Centre for Evolution, University of Bath, Bath BA2 7AYUK
| | - Emily J. Rayfield
- School of Earth Sciences, University of Bristol, Life Sciences Building, Tyndall Avenue, Bristol BS8 1TQ, UK
| | - Erin E. Saupe
- Department of Earth Sciences, University of Oxford, S Parks Road, Oxford OX1 3AN, UK
| | - Emma Sherratt
- School of Biological Sciences, The University of Adelaide, Adelaide, South Australia 5005, Australia
| | - Graham J. Slater
- Department of the Geophysical Sciences, University of Chicago, Chicago, IL 60637, USA
| | - Vera Weisbecker
- School of Biological Sciences, University of Queensland, St Lucia, QLD4072, Australia
- College of Science and Engineering, Flinders University, Adelaide, South Australia 5042, Australia
| | - Gavin H. Thomas
- Department of Animal and Plant Sciences, The University of Sheffield, Sheffield S10 2TN, UK
| | - Philip C. J. Donoghue
- School of Earth Sciences, University of Bristol, Life Sciences Building, Tyndall Avenue, Bristol BS8 1TQ, UK
| |
Collapse
|
8
|
Guillerme T, Puttick MN, Marcy AE, Weisbecker V. Shifting spaces: Which disparity or dissimilarity measurement best summarize occupancy in multidimensional spaces? Ecol Evol 2020; 10:7261-7275. [PMID: 32760527 PMCID: PMC7391566 DOI: 10.1002/ece3.6452] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Revised: 05/02/2020] [Accepted: 05/06/2020] [Indexed: 01/30/2023] Open
Abstract
Multidimensional analysis of traits are now common in ecology and evolution and are based on trait spaces in which each dimension summarizes the observed trait combination (a morphospace or an ecospace). Observations of interest will typically occupy a subset of this space, and researchers will calculate one or more measures to quantify how organisms inhabit that space. In macroevolution and ecology, these measures called disparity or dissimilarity metrics are generalized as space occupancy measures. Researchers use these measures to investigate how space occupancy changes through time, in relation to other groups of organisms, or in response to global environmental changes. However, the mathematical and biological meaning of most space occupancy measures is vague with the majority of widely used measures lacking formal description. Here, we propose a broad classification of space occupancy measures into three categories that capture changes in size, density, or position. We study the behavior of 25 measures to changes in trait space size, density, and position on simulated and empirical datasets. We find that no measure describes all of trait space aspects but that some are better at capturing certain aspects. Our results confirm the three broad categories (size, density, and position) and allow us to relate changes in any of these categories to biological phenomena. Because the choice of space occupancy measures is specific to the data and question, we introduced https://tguillerme.shinyapps.io/moms/moms, a tool to both visualize and capture changes in space occupancy for any measurement. https://tguillerme.shinyapps.io/moms/moms is designed to help workers choose the right space occupancy measures, given the properties of their trait space and their biological question. By providing guidelines and common vocabulary for space occupancy analysis, we hope to help bridging the gap in multidimensional research between ecology and evolution.
Collapse
Affiliation(s)
- Thomas Guillerme
- School of Biological SciencesUniversity of QueenslandSt. LuciaQLDAustralia
- Department of Animal and Plant SciencesThe University of SheffieldSheffieldUK
| | | | - Ariel E. Marcy
- School of Biological SciencesUniversity of QueenslandSt. LuciaQLDAustralia
| | - Vera Weisbecker
- School of Biological SciencesUniversity of QueenslandSt. LuciaQLDAustralia
- College of Science and EngineeringFlinders UniversityAdelaideSAAustralia
| |
Collapse
|
9
|
Weisbecker V, Guillerme T, Speck C, Sherratt E, Abraha HM, Sharp AC, Terhune CE, Collins S, Johnston S, Panagiotopoulou O. Individual variation of the masticatory system dominates 3D skull shape in the herbivory-adapted marsupial wombats. Front Zool 2019; 16:41. [PMID: 31695725 PMCID: PMC6824091 DOI: 10.1186/s12983-019-0338-5] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2019] [Accepted: 10/04/2019] [Indexed: 12/19/2022] Open
Abstract
Background Within-species skull shape variation of marsupial mammals is widely considered low and strongly size-dependent (allometric), possibly due to developmental constraints arising from the altricial birth of marsupials. However, species whose skulls are impacted by strong muscular stresses – particularly those produced through mastication of tough food items – may not display such intrinsic patterns very clearly because of the known plastic response of bone to muscle activity of the individual. In such cases, allometry may not dominate within-species shape variation, even if it is a driver of evolutionary shape divergence; ordination of shape in a geometric morphometric context through principal component analysis (PCA) should reveal main variation in areas under masticatory stress (incisor region/zygomatic arches/mandibular ramus); but this main variation should emerge from high individual variability and thus have low eigenvalues. Results We assessed the evidence for high individual variation through 3D geometric morphometric shape analysis of crania and mandibles of three species of grazing-specialized wombats, whose diet of tough grasses puts considerable strain on their masticatory system. As expected, we found little allometry and low Principal Component 1 (PC1) eigenvalues within crania and mandibles of all three species. Also as expected, the main variation was in the muzzle, zygomatic arches, and masticatory muscle attachments of the mandibular ramus. We then implemented a new test to ask if the landmark variation reflected on PC1 was reflected in individuals with opposite PC1 scores and with opposite shapes in Procrustes space. This showed that correspondence between individual and ordinated shape variation was limited, indicating high levels of individual variability in the masticatory apparatus. Discussion Our results are inconsistent with hypotheses that skull shape variation within marsupial species reflects a constraint pattern. Rather, they support suggestions that individual plasticity can be an important determinant of within-species shape variation in marsupials (and possibly other mammals) with high masticatory stresses, making it difficult to understand the degree to which intrinsic constraints act on shape variation at the within-species level. We conclude that studies that link micro- and macroevolutionary patterns of shape variation might benefit from a focus on species with low-impact mastication, such as carnivorous or frugivorous species.
Collapse
Affiliation(s)
- Vera Weisbecker
- 1School of Biological Sciences, The University of Queensland, Brisbane, Australia
| | - Thomas Guillerme
- 1School of Biological Sciences, The University of Queensland, Brisbane, Australia
| | - Cruise Speck
- 1School of Biological Sciences, The University of Queensland, Brisbane, Australia
| | - Emma Sherratt
- 2School of Biological Sciences, The University of Adelaide, Adelaide, Australia
| | - Hyab Mehari Abraha
- 3Monash Biomedicine Discovery Institute, Department of Anatomy & Developmental Biology, Monash University, Melbourne, Australia
| | - Alana C Sharp
- 4Department of Cell & Developmental Biology, University College London, London, UK.,5Institute of Ageing and Chronic Disease, University of Liverpool, Liverpool, UK
| | - Claire E Terhune
- 6Department of Anthropology, University of Arkansas, Fayetteville, USA
| | - Simon Collins
- 7School of Agricultural and Food Sciences, The University of Queensland, Brisbane, Australia
| | - Stephen Johnston
- 7School of Agricultural and Food Sciences, The University of Queensland, Brisbane, Australia
| | - Olga Panagiotopoulou
- 3Monash Biomedicine Discovery Institute, Department of Anatomy & Developmental Biology, Monash University, Melbourne, Australia
| |
Collapse
|
10
|
Brazeau MD, Guillerme T, Smith MR. An algorithm for Morphological Phylogenetic Analysis with Inapplicable Data. Syst Biol 2019; 68:619-631. [PMID: 30535172 PMCID: PMC6568014 DOI: 10.1093/sysbio/syy083] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2017] [Revised: 11/27/2018] [Accepted: 11/03/2018] [Indexed: 11/13/2022] Open
Abstract
Morphological data play a key role in the inference of biological relationships and evolutionary history and are essential for the interpretation of the fossil record. The hierarchical interdependence of many morphological characters, however, complicates phylogenetic analysis. In particular, many characters only apply to a subset of terminal taxa. The widely used "reductive coding" approach treats taxa in which a character is inapplicable as though the character's state is simply missing (unknown). This approach has long been known to create spurious tree length estimates on certain topologies, potentially leading to erroneous results in phylogenetic searches-but pratical solutions have yet to be proposed and implemented. Here, we present a single-character algorithm for reconstructing ancestral states in reductively coded data sets, following the theoretical guideline of minimizing homoplasy over all characters. Our algorithm uses up to three traversals to score a tree, and a fourth to fully resolve final states at each node within the tree. We use explicit criteria to resolve ambiguity in applicable/inapplicable dichotomies, and to optimize missing data. So that it can be applied to single characters, the algorithm employs local optimization; as such, the method provides a fast but approximate inference of ancestral states and tree score. The application of our method to published morphological data sets indicates that, compared to traditional methods, it identifies different trees as "optimal." As such, the use of our algorithm to handle inapplicable data may significantly alter the outcome of tree searches, modifying the inferred placement of living and fossil taxa and potentially leading to major differences in reconstructions of evolutionary history.
Collapse
Affiliation(s)
- Martin D Brazeau
- Department of Life Sciences, Imperial College London, Silwood Park Campus, Buckhurst Road, Ascot SL5 7PY, UK
- Department of Earth Sciences, Natural History Museum, Cromwell Road, London SW7 5BD, UK
| | - Thomas Guillerme
- Department of Life Sciences, Imperial College London, Silwood Park Campus, Buckhurst Road, Ascot SL5 7PY, UK
- School of Biological Sciences, The University of Queensland, St. Lucia 4067, Queensland, Australia
| | - Martin R Smith
- Department of Earth Sciences, University of Cambridge, Downing Street, Cambridge CB2 3EQ, UK
- Department of Earth Sciences, Mountjoy Site, Durham University, South Road, Durham DH1 3LE, UK
| |
Collapse
|
11
|
Affiliation(s)
- Thomas Guillerme
- Department of Life SciencesImperial College London Ascot UK
- School of Biological SciencesUniversity of Queensland St. Lucia Queensland Australia
| |
Collapse
|
12
|
Turvey ST, Crees JJ, Hansford J, Jeffree TE, Crumpton N, Kurniawan I, Setiyabudi E, Guillerme T, Paranggarimu U, Dosseto A, van den Bergh GD. Quaternary vertebrate faunas from Sumba, Indonesia: implications for Wallacean biogeography and evolution. Proc Biol Sci 2018; 284:rspb.2017.1278. [PMID: 28855367 PMCID: PMC5577490 DOI: 10.1098/rspb.2017.1278] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2017] [Accepted: 07/21/2017] [Indexed: 12/03/2022] Open
Abstract
Historical patterns of diversity, biogeography and faunal turnover remain poorly understood for Wallacea, the biologically and geologically complex island region between the Asian and Australian continental shelves. A distinctive Quaternary vertebrate fauna containing the small-bodied hominin Homo floresiensis, pygmy Stegodon proboscideans, varanids and giant murids has been described from Flores, but Quaternary faunas are poorly known from most other Lesser Sunda Islands. We report the discovery of extensive new fossil vertebrate collections from Pleistocene and Holocene deposits on Sumba, a large Wallacean island situated less than 50 km south of Flores. A fossil assemblage recovered from a Pleistocene deposit at Lewapaku in the interior highlands of Sumba, which may be close to 1 million years old, contains a series of skeletal elements of a very small Stegodon referable to S. sumbaensis, a tooth attributable to Varanus komodoensis, and fragmentary remains of unidentified giant murids. Holocene cave deposits at Mahaniwa dated to approximately 2000–3500 BP yielded extensive material of two new genera of endemic large-bodied murids, as well as fossils of an extinct frugivorous varanid. This new baseline for reconstructing Wallacean faunal histories reveals that Sumba's Quaternary vertebrate fauna, although phylogenetically distinctive, was comparable in diversity and composition to the Quaternary fauna of Flores, suggesting that similar assemblages may have characterized Quaternary terrestrial ecosystems on many or all of the larger Lesser Sunda Islands.
Collapse
Affiliation(s)
- Samuel T Turvey
- Institute of Zoology, Zoological Society of London, Regent's Park, London NW1 4RY, UK
| | - Jennifer J Crees
- Institute of Zoology, Zoological Society of London, Regent's Park, London NW1 4RY, UK
| | - James Hansford
- Institute of Zoology, Zoological Society of London, Regent's Park, London NW1 4RY, UK.,Ocean and Earth Science, National Oceanography Centre, University of Southampton, Southampton SO14 3ZH, UK
| | - Timothy E Jeffree
- Institute of Zoology, Zoological Society of London, Regent's Park, London NW1 4RY, UK
| | - Nick Crumpton
- Institute of Zoology, Zoological Society of London, Regent's Park, London NW1 4RY, UK
| | | | | | - Thomas Guillerme
- Department of Life Sciences, Imperial College London, Silwood Park, Ascot SL5 7PY, UK
| | | | - Anthony Dosseto
- Wollongong Isotope Geochronology Laboratory, School of Earth and Environmental Sciences, University of Wollongong, Wollongong, New South Wales 2522, Australia
| | - Gerrit D van den Bergh
- Centre for Archaeological Science, School of Earth and Environmental Sciences, University of Wollongong, Wollongong, New South Wales 2522, Australia
| |
Collapse
|
13
|
Guillerme T, Cooper N. Assessment of available anatomical characters for linking living mammals to fossil taxa in phylogenetic analyses. Biol Lett 2016; 12:20151003. [PMID: 27146442 PMCID: PMC4892235 DOI: 10.1098/rsbl.2015.1003] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2015] [Accepted: 04/06/2016] [Indexed: 11/24/2022] Open
Abstract
Analyses of living and fossil taxa are crucial for understanding biodiversity through time. The total evidence method allows living and fossil taxa to be combined in phylogenies, using molecular data for living taxa and morphological data for living and fossil taxa. With this method, substantial overlap of coded anatomical characters among living and fossil taxa is vital for accurately inferring topology. However, although molecular data for living species are widely available, scientists generating morphological data mainly focus on fossils. Therefore, there are fewer coded anatomical characters in living taxa, even in well-studied groups such as mammals. We investigated the number of coded anatomical characters available in phylogenetic matrices for living mammals and how these were phylogenetically distributed across orders. Eleven of 28 mammalian orders have less than 25% species with available characters; this has implications for the accurate placement of fossils, although the issue is less pronounced at higher taxonomic levels. In most orders, species with available characters are randomly distributed across the phylogeny, which may reduce the impact of the problem. We suggest that increased morphological data collection efforts for living taxa are needed to produce accurate total evidence phylogenies.
Collapse
Affiliation(s)
- Thomas Guillerme
- School of Natural Sciences, Trinity College Dublin, Dublin 2, Ireland
| | - Natalie Cooper
- School of Natural Sciences, Trinity College Dublin, Dublin 2, Ireland Department of Life Sciences, Natural History Museum, Cromwell Road, London SW7 5BD, UK
| |
Collapse
|
14
|
Guillerme T, Cooper N. Effects of missing data on topological inference using a Total Evidence approach. Mol Phylogenet Evol 2015; 94:146-58. [PMID: 26335040 DOI: 10.1016/j.ympev.2015.08.023] [Citation(s) in RCA: 57] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2015] [Revised: 08/24/2015] [Accepted: 08/26/2015] [Indexed: 11/25/2022]
Abstract
To fully understand macroevolutionary patterns and processes, we need to include both extant and extinct species in our models. This requires phylogenetic trees with both living and fossil taxa at the tips. One way to infer such phylogenies is the Total Evidence approach which uses molecular data from living taxa and morphological data from living and fossil taxa. Although the Total Evidence approach is very promising, it requires a great deal of data that can be hard to collect. Therefore this method is likely to suffer from missing data issues that may affect its ability to infer correct phylogenies. Here we use simulations to assess the effects of missing data on tree topologies inferred from Total Evidence matrices. We investigate three major factors that directly affect the completeness and the size of the morphological part of the matrix: the proportion of living taxa with no morphological data, the amount of missing data in the fossil record, and the overall number of morphological characters in the matrix. We infer phylogenies from complete matrices and from matrices with various amounts of missing data, and then compare missing data topologies to the "best" tree topology inferred using the complete matrix. We find that the number of living taxa with morphological characters and the overall number of morphological characters in the matrix, are more important than the amount of missing data in the fossil record for recovering the "best" tree topology. Therefore, we suggest that sampling effort should be focused on morphological data collection for living species to increase the accuracy of topological inference in a Total Evidence framework. Additionally, we find that Bayesian methods consistently outperform other tree inference methods. We therefore recommend using Bayesian consensus trees to fix the tree topology prior to further analyses.
Collapse
Affiliation(s)
- Thomas Guillerme
- School of Natural Sciences, Trinity College Dublin, Dublin 2, Ireland; Trinity Centre for Biodiversity Research, Trinity College Dublin, Dublin 2, Ireland.
| | - Natalie Cooper
- School of Natural Sciences, Trinity College Dublin, Dublin 2, Ireland; Trinity Centre for Biodiversity Research, Trinity College Dublin, Dublin 2, Ireland; Department of Life Sciences, Natural History Museum, Cromwell Road, London SW7 5BD, UK
| |
Collapse
|
15
|
Healy K, Guillerme T, Finlay S, Kane A, Kelly SBA, McClean D, Kelly DJ, Donohue I, Jackson AL, Cooper N. Ecology and mode-of-life explain lifespan variation in birds and mammals. Proc Biol Sci 2014; 281:20140298. [PMID: 24741018 DOI: 10.1098/rspb.2014.0298] [Citation(s) in RCA: 167] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Maximum lifespan in birds and mammals varies strongly with body mass such that large species tend to live longer than smaller species. However, many species live far longer than expected given their body mass. This may reflect interspecific variation in extrinsic mortality, as life-history theory predicts investment in long-term survival is under positive selection when extrinsic mortality is reduced. Here, we investigate how multiple ecological and mode-of-life traits that should reduce extrinsic mortality (including volancy (flight capability), activity period, foraging environment and fossoriality), simultaneously influence lifespan across endotherms. Using novel phylogenetic comparative analyses and to our knowledge, the most species analysed to date (n = 1368), we show that, over and above the effect of body mass, the most important factor enabling longer lifespan is the ability to fly. Within volant species, lifespan depended upon when (day, night, dusk or dawn), but not where (in the air, in trees or on the ground), species are active. However, the opposite was true for non-volant species, where lifespan correlated positively with both arboreality and fossoriality. Our results highlight that when studying the molecular basis behind cellular processes such as those underlying lifespan, it is important to consider the ecological selection pressures that shaped them over evolutionary time.
Collapse
Affiliation(s)
- Kevin Healy
- School of Natural Sciences, Trinity College Dublin, , Dublin 2, Republic of Ireland, Trinity Centre for Biodiversity Research, Trinity College Dublin, , Dublin 2, Republic of Ireland
| | | | | | | | | | | | | | | | | | | |
Collapse
|