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Dunne EM, Thompson SED, Butler RJ, Rosindell J, Close RA. Mechanistic neutral models show that sampling biases drive the apparent explosion of early tetrapod diversity. Nat Ecol Evol 2023; 7:1480-1489. [PMID: 37500908 PMCID: PMC10482683 DOI: 10.1038/s41559-023-02128-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 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: 03/01/2022] [Accepted: 06/20/2023] [Indexed: 07/29/2023]
Abstract
Estimates of deep-time biodiversity typically rely on statistical methods to mitigate the impacts of sampling biases in the fossil record. However, these methods are limited by the spatial and temporal scale of the underlying data. Here we use a spatially explicit mechanistic model, based on neutral theory, to test hypotheses of early tetrapod diversity change during the late Carboniferous and early Permian, critical intervals for the diversification of vertebrate life on land. Our simulations suggest that apparent increases in early tetrapod diversity were not driven by local endemism following the 'Carboniferous rainforest collapse'. Instead, changes in face-value diversity can be explained by variation in sampling intensity through time. Our results further demonstrate the importance of accounting for sampling biases in analyses of the fossil record and highlight the vast potential of mechanistic models, including neutral models, for testing hypotheses in palaeobiology.
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Affiliation(s)
- Emma M Dunne
- GeoZentrum Nordbayern, Friedrich-Alexander University Erlangen-Nürnberg (FAU), Erlangen, Germany.
- School of Geography, Earth and Environmental Sciences, University of Birmingham, Birmingham, UK.
| | - Samuel E D Thompson
- Department of Life Sciences, Imperial College London, Ascot, UK
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
| | - Richard J Butler
- School of Geography, Earth and Environmental Sciences, University of Birmingham, Birmingham, UK
| | - James Rosindell
- Department of Life Sciences, Imperial College London, Ascot, UK
| | - Roger A Close
- Department of Earth Sciences, University of Oxford, Oxford, UK
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Thompson SED, Chisholm RA, Rosindell J. pycoalescence and rcoalescence: Packages for simulating spatially explicit neutral models of biodiversity. Methods Ecol Evol 2020. [DOI: 10.1111/2041-210x.13451] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Affiliation(s)
- Samuel E. D. Thompson
- Department of Life Sciences, Silwood Park Campus Imperial College London Ascot UK
- Faculty of Science Department of Biological Sciences National University of Singapore Singapore
| | - Ryan A. Chisholm
- Department of Life Sciences, Silwood Park Campus Imperial College London Ascot UK
| | - James Rosindell
- Faculty of Science Department of Biological Sciences National University of Singapore Singapore
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Thompson SED, Chisholm RA, Rosindell J. Characterising extinction debt following habitat fragmentation using neutral theory. Ecol Lett 2019; 22:2087-2096. [PMID: 31612627 DOI: 10.1111/ele.13398] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [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: 07/31/2019] [Revised: 08/25/2019] [Accepted: 09/09/2019] [Indexed: 01/13/2023]
Abstract
Habitat loss leads to species extinctions, both immediately and over the long term as 'extinction debt' is repaid. The same quantity of habitat can be lost in different spatial patterns with varying habitat fragmentation. How this translates to species loss remains an open problem requiring an understanding of the interplay between community dynamics and habitat structure across temporal and spatial scales. Here we develop formulas that characterise extinction debt in a spatial neutral model after habitat loss and fragmentation. Central to our formulas are two new metrics, which depend on properties of the taxa and landscape: 'effective area', measuring the remaining number of individuals and 'effective connectivity', measuring individuals' ability to disperse through fragmented habitat. This formalises the conventional wisdom that habitat area and habitat connectivity are the two critical requirements for long-term preservation of biodiversity. Our approach suggests that mechanistic fragmentation metrics help resolve debates about fragmentation and species loss.
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Affiliation(s)
- Samuel E D Thompson
- Department of Biological Sciences, Faculty of Science, National University of Singapore, 14 Science Drive 4, Singapore, 117543, Singapore.,Department of Life Sciences, Imperial College London, Silwood Park campus, Buckhurst Road, Ascot, Berkshire, SL5 7PY, UK
| | - Ryan A Chisholm
- Department of Biological Sciences, Faculty of Science, National University of Singapore, 14 Science Drive 4, Singapore, 117543, Singapore
| | - James Rosindell
- Department of Life Sciences, Imperial College London, Silwood Park campus, Buckhurst Road, Ascot, Berkshire, SL5 7PY, UK
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Bongalov B, Burslem DFRP, Jucker T, Thompson SED, Rosindell J, Swinfield T, Nilus R, Clewley D, Phillips OL, Coomes DA. Reconciling the contribution of environmental and stochastic structuring of tropical forest diversity through the lens of imaging spectroscopy. Ecol Lett 2019; 22:1608-1619. [PMID: 31347263 PMCID: PMC6852337 DOI: 10.1111/ele.13357] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [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: 02/07/2019] [Revised: 03/08/2019] [Accepted: 07/01/2019] [Indexed: 11/29/2022]
Abstract
Both niche and stochastic dispersal processes structure the extraordinary diversity of tropical plants, but determining their relative contributions has proven challenging. We address this question using airborne imaging spectroscopy to estimate canopy β-diversity for an extensive region of a Bornean rainforest and challenge these data with models incorporating niches and dispersal. We show that remotely sensed and field-derived estimates of pairwise dissimilarity in community composition are closely matched, proving the applicability of imaging spectroscopy to provide β-diversity data for entire landscapes of over 1000 ha containing contrasting forest types. Our model reproduces the empirical data well and shows that the ecological processes maintaining tropical forest diversity are scale dependent. Patterns of β-diversity are shaped by stochastic dispersal processes acting locally whilst environmental processes act over a wider range of scales.
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Affiliation(s)
- Boris Bongalov
- Forest Ecology and Conservation Group, Department of Plant Sciences, University of Cambridge, Cambridge, CB2 3EA, UK
| | - David F R P Burslem
- School of Biological Sciences, University of Aberdeen, Cruickshank Building, St Machar Drive, Aberdeen, UK
| | - Tommaso Jucker
- Forest Ecology and Conservation Group, Department of Plant Sciences, University of Cambridge, Cambridge, CB2 3EA, UK.,School of Biological Sciences, University of Bristol, 24 Tyndall Avenue, Bristol, BS8 1TQ, UK
| | - Samuel E D Thompson
- Imperial College London, Silwood Park Campus, Buckhurst Road, Ascot, Berkshire, SL5 7PY, UK.,National University of Singapore, 21 Lower Kent Ridge Road, 119077, Singapore
| | - James Rosindell
- Imperial College London, Silwood Park Campus, Buckhurst Road, Ascot, Berkshire, SL5 7PY, UK
| | - Tom Swinfield
- Forest Ecology and Conservation Group, Department of Plant Sciences, University of Cambridge, Cambridge, CB2 3EA, UK.,Centre for Conservation Science, Royal Society for Protection of Birds, David Attenborough Building, Cambridge, CB2 3QZ, UK
| | - Reuben Nilus
- Forest Research Centre, Sabah Forestry Department, Sandakan, Malaysia
| | | | | | - David A Coomes
- Forest Ecology and Conservation Group, Department of Plant Sciences, University of Cambridge, Cambridge, CB2 3EA, UK
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