1
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Marion AFP, Condamine FL, Guinot G. Sequential trait evolution did not drive deep-time diversification in sharks. Evolution 2024; 78:1405-1425. [PMID: 38745524 DOI: 10.1093/evolut/qpae070] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Revised: 04/23/2024] [Accepted: 05/13/2024] [Indexed: 05/16/2024]
Abstract
Estimating how traits evolved and impacted diversification across the tree of life represents a critical topic in ecology and evolution. Although there has been considerable research in comparative biology, large parts of the tree of life remain underexplored. Sharks are an iconic clade of marine vertebrates, and key components of marine ecosystems since the early Mesozoic. However, few studies have addressed how traits evolved or whether they impacted their extant diversity patterns. Our study aimed to fill this gap by reconstructing the largest time-calibrated species-level phylogeny of sharks and compiling an exhaustive database for ecological (diet, habitat) and biological (reproduction, maximum body length) traits. Using state-of-the-art models of evolution and diversification, we outlined the major character shifts and modes of trait evolution across shark species. We found support for sequential models of trait evolution and estimated a small to medium-sized lecithotrophic and coastal-dwelling most recent common ancestor for extant sharks. However, our exhaustive hidden traits analyses do not support trait-dependent diversification for any examined traits, challenging previous works. This suggests that the role of traits in shaping sharks' diversification dynamics might have been previously overestimated and should motivate future macroevolutionary studies to investigate other drivers of diversification in this clade.
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Affiliation(s)
- Alexis F P Marion
- Institut des Sciences de l'Evolution de Montpellier (ISEM), CNRS, IRD, EPHE, Université de Montpellier, Montpellier, France
| | - Fabien L Condamine
- Institut des Sciences de l'Evolution de Montpellier (ISEM), CNRS, IRD, EPHE, Université de Montpellier, Montpellier, France
| | - Guillaume Guinot
- Institut des Sciences de l'Evolution de Montpellier (ISEM), CNRS, IRD, EPHE, Université de Montpellier, Montpellier, France
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2
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Guo Z, Benton MJ, Stubbs TL, Chen ZQ. Morphological innovation did not drive diversification in Mesozoic-Cenozoic brachiopods. Nat Ecol Evol 2024:10.1038/s41559-024-02491-9. [PMID: 39054349 DOI: 10.1038/s41559-024-02491-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2024] [Accepted: 06/28/2024] [Indexed: 07/27/2024]
Abstract
Over long spans of geological time, various groups of organisms may wax and wane, experiencing times of apparent success and contraction. These rises and falls are often said to reflect either opportunities created by climate change or the relative success of innovative characteristics. Phylum Brachiopoda was one of the most successful marine clades before the Permian/Triassic mass extinction (PTME), but after this event, they became marginal components of marine communities through to the present day. How brachiopod morphological innovations reacted to swiftly declining diversity has long remained poorly understood. Here we analyse morphological evolution over the 300 Myr (Permian-Quaternary) history of the four major Mesozoic-Cenozoic brachiopod orders (Terebratulida, Rhynchonellida, Spiriferinida, Athyridida). Unexpectedly, their disparities reached or exceeded pre-PTME levels, but were decoupled from generic richness, which was generally low. Distribution of taxa in morphospace and shifts in centroid indicate that all four orders exploited new morphospaces when adapting to post-Permian environments. A comparison of morphospace occupation and diversity evolution suggests that the high extinction rate of brachiopods and the limited diversification of new forms may have accounted for the depauperate nature of modern-day brachiopods.
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Affiliation(s)
- Zhen Guo
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences (Wuhan), Wuhan, China
| | | | - Thomas L Stubbs
- School of Life, Health and Chemical Sciences, The Open University, Milton Keynes, UK
| | - Zhong-Qiang Chen
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences (Wuhan), Wuhan, China.
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3
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Park T, Burin G, Lazo-Cancino D, Rees JPG, Rule JP, Slater GJ, Cooper N. Charting the course of pinniped evolution: insights from molecular phylogeny and fossil record integration. Evolution 2024; 78:1212-1226. [PMID: 38644688 DOI: 10.1093/evolut/qpae061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Revised: 04/02/2024] [Accepted: 04/19/2024] [Indexed: 04/23/2024]
Abstract
Pinnipeds (seals, sea lions, walruses, and their fossil relatives) are one of the most successful mammalian clades to live in the oceans. Despite a well-resolved molecular phylogeny and a global fossil record, a complete understanding of their macroevolutionary dynamics remains hampered by a lack of formal analyses that combine these 2 rich sources of information. We used a meta-analytic approach to infer the most densely sampled pinniped phylogeny to date (36 recent and 93 fossil taxa) and used phylogenetic paleobiological methods to study their diversification dynamics and biogeographic history. Pinnipeds mostly diversified at constant rates. Walruses, however, experienced rapid turnover in which extinction rates ultimately exceeded speciation rates from 12 to 6 Ma, possibly due to changing sea levels and/or competition with otariids (eared seals). Historical biogeographic analyses, including fossil data, allowed us to confidently identify the North Pacific and the North Atlantic (plus or minus Paratethys) as the ancestral ranges of Otarioidea (eared seals + walrus) and crown phocids (earless seals), respectively. Yet, despite the novel addition of stem pan-pinniped taxa, the region of origin for Pan-Pinnipedia remained ambiguous. These results suggest further avenues of study in pinnipeds and provide a framework for investigating other groups with substantial extinct and extant diversity.
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Affiliation(s)
- Travis Park
- School of Biological Sciences, Monash University, Melbourne, Australia
- Science Group, Natural History Museum London, London, United Kingdom
- Sciences, Museums Victoria, Melbourne, Australia
| | - Gustavo Burin
- Science Group, Natural History Museum London, London, United Kingdom
| | - Daniela Lazo-Cancino
- Laboratorio de Mastozoología, Departamento de Zoología, Facultad de Ciencias Naturales y Oceanográficas, Universidad de Concepción, Concepción, Chile
| | - Joseph P G Rees
- Science Group, Natural History Museum London, London, United Kingdom
- Department of Life Sciences, Imperial College London, London, United Kingdom
| | - James P Rule
- School of Biological Sciences, Monash University, Melbourne, Australia
- Science Group, Natural History Museum London, London, United Kingdom
| | - Graham J Slater
- Department of the Geophysical Sciences, University of Chicago, Chicago, IL, United States
| | - Natalie Cooper
- Science Group, Natural History Museum London, London, United Kingdom
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4
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Wilson CJ, Reitan T, Liow LH. Unveiling the underlying drivers of Phanerozoic marine diversification. Proc Biol Sci 2024; 291:20240165. [PMID: 38889777 DOI: 10.1098/rspb.2024.0165] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2024] [Accepted: 03/26/2024] [Indexed: 06/20/2024] Open
Abstract
In investigating global patterns of biodiversity through deep time, many large-scale drivers of diversification have been proposed, both biotic and abiotic. However, few robust conclusions about these hypothesized effectors or their roles have been drawn. Here, we use a linear stochastic differential equation (SDE) framework to test for the presence of underlying drivers of diversification patterns before examining specific hypothesized drivers. Using a global dataset of observations of skeletonized marine fossils, we infer origination, extinction and sampling rates (collectively called fossil time series) throughout the Phanerozoic using a capture-mark-recapture approach. Using linear SDEs, we then compare models including and excluding hidden (i.e. unmeasured) drivers of these fossil time series. We find evidence of large-scale underlying drivers of marine Phanerozoic diversification rates and present quantitative characterizations of these. We then test whether changing global temperature, sea-level, marine sediment area or continental fragmentation could act as drivers of the fossil time series. We show that it is unlikely any of these four abiotic factors are the hidden drivers we identified, though there is evidence for correlative links between sediment area and origination/extinction rates. Our characterization of the hidden drivers of Phanerozoic diversification and sampling will aid in the search for their ultimate identities.
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Affiliation(s)
- Connor J Wilson
- Natural History Museum, University of Oslo, 0562 Oslo, Norway
- School of Geography and the Environment, University of Oxford, Oxford OX1 3QY, UK
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ 85719, USA
| | - Trond Reitan
- Natural History Museum, University of Oslo, 0562 Oslo, Norway
- Centre for Planetary Habitability, Department of Geosciences, University of Oslo, 0562 Oslo, Norway
| | - Lee Hsiang Liow
- Natural History Museum, University of Oslo, 0562 Oslo, Norway
- Centre for Planetary Habitability, Department of Geosciences, University of Oslo, 0562 Oslo, Norway
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5
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Jouault C, Condamine FL, Legendre F, Perrichot V. The Angiosperm Terrestrial Revolution buffered ants against extinction. Proc Natl Acad Sci U S A 2024; 121:e2317795121. [PMID: 38466878 PMCID: PMC10990090 DOI: 10.1073/pnas.2317795121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Accepted: 02/08/2024] [Indexed: 03/13/2024] Open
Abstract
With ~14,000 extant species, ants are ubiquitous and of tremendous ecological importance. They have undergone remarkable diversification throughout their evolutionary history. However, the drivers of their diversity dynamics are not well quantified or understood. Previous phylogenetic analyses have suggested patterns of diversity dynamics associated with the Angiosperm Terrestrial Revolution (ATR), but these studies have overlooked valuable information from the fossil record. To address this gap, we conducted a comprehensive analysis using a large dataset that includes both the ant fossil record (~24,000 individual occurrences) and neontological data (~14,000 occurrences), and tested four hypotheses proposed for ant diversification: co-diversification, competitive extinction, hyper-specialization, and buffered extinction. Taking into account biases in the fossil record, we found three distinct diversification periods (the latest Cretaceous, Eocene, and Oligo-Miocene) and one extinction period (Late Cretaceous). The competitive extinction hypothesis between stem and crown ants is not supported. Instead, we found support for the co-diversification, buffered extinction, and hyper-specialization hypotheses. The environmental changes of the ATR, mediated by the angiosperm radiation, likely played a critical role in buffering ants against extinction and favoring their diversification by providing new ecological niches, such as forest litter and arboreal nesting sites, and additional resources. We also hypothesize that the decline and extinction of stem ants during the Late Cretaceous was due to their hyper-specialized morphology, which limited their ability to expand their dietary niche in changing environments. This study highlights the importance of a holistic approach when studying the interplay between past environments and the evolutionary trajectories of organisms.
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Affiliation(s)
- Corentin Jouault
- Institut de Systématique Évolution, Biodiversité, UMR 7205, Muséum national d’Histoire naturelle, CNRS, Sorbonne Université, EPHE-PSL, Université des Antilles, Paris75005, France
- Institut des Sciences de l’Évolution de Montpellier, Université de Montpellier, CNRS, Montpellier34095, France
- Géosciences Rennes, UMR 6118, Univ. Rennes, CNRS, Rennes35000, France
| | - Fabien L. Condamine
- Institut des Sciences de l’Évolution de Montpellier, Université de Montpellier, CNRS, Montpellier34095, France
| | - Frédéric Legendre
- Institut de Systématique Évolution, Biodiversité, UMR 7205, Muséum national d’Histoire naturelle, CNRS, Sorbonne Université, EPHE-PSL, Université des Antilles, Paris75005, France
| | - Vincent Perrichot
- Géosciences Rennes, UMR 6118, Univ. Rennes, CNRS, Rennes35000, France
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6
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Payne ARD, Mannion PD, Lloyd GT, Davis KE. Decoupling speciation and extinction reveals both abiotic and biotic drivers shaped 250 million years of diversity in crocodile-line archosaurs. Nat Ecol Evol 2024; 8:121-132. [PMID: 38049481 PMCID: PMC10781641 DOI: 10.1038/s41559-023-02244-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Accepted: 09/26/2023] [Indexed: 12/06/2023]
Abstract
Whereas living representatives of Pseudosuchia, crocodylians, number fewer than 30 species, more than 700 pseudosuchian species are known from their 250-million-year fossil record, displaying far greater ecomorphological diversity than their extant counterparts. With a new time-calibrated tree of >500 species, we use a phylogenetic framework to reveal that pseudosuchian evolutionary history and diversification dynamics were directly shaped by the interplay of abiotic and biotic processes over hundreds of millions of years, supported by information theory analyses. Speciation, but not extinction, is correlated with higher temperatures in terrestrial and marine lineages, with high sea level associated with heightened extinction in non-marine taxa. Low lineage diversity and increased speciation in non-marine species is consistent with opportunities for niche-filling, whereas increased competition may have led to elevated extinction rates. In marine lineages, competition via increased lineage diversity appears to have driven both speciation and extinction. Decoupling speciation and extinction, in combination with ecological partitioning, reveals a more complex picture of pseudosuchian evolution than previously understood. As the number of species threatened with extinction by anthropogenic climate change continues to rise, the fossil record provides a unique window into the drivers that led to clade success and those that may ultimately lead to extinction.
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Affiliation(s)
- Alexander R D Payne
- Department of Biology, University of York, York, UK
- Leverhulme Centre for Anthropocene Biodiversity, University of York, York, UK
| | - Philip D Mannion
- Department of Earth Sciences, University College London, London, UK
| | | | - Katie E Davis
- Department of Biology, University of York, York, UK.
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7
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Weppe R, Condamine FL, Guinot G, Maugoust J, Orliac MJ. Drivers of the artiodactyl turnover in insular western Europe at the Eocene-Oligocene Transition. Proc Natl Acad Sci U S A 2023; 120:e2309945120. [PMID: 38109543 PMCID: PMC10756263 DOI: 10.1073/pnas.2309945120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Accepted: 11/10/2023] [Indexed: 12/20/2023] Open
Abstract
Simultaneously investigating the effects of abiotic and biotic factors on diversity dynamics is essential to understand the evolutionary history of clades. The Grande Coupure corresponds to a major faunal turnover at the Eocene-Oligocene transition (EOT) (~34.1 to 33.55 Mya) and is defined in western Europe as an extinction of insular European mammals coupled with the arrival of crown clades from Asia. Here, we focused on the species-rich group of endemic European artiodactyls to determine the drivers of the Grande Coupure during the major environmental disruptions at the EOT. Using Bayesian birth-death models, we analyzed an original high-resolution fossil dataset (90 species, >2,100 occurrences) from southwestern France (Quercy area) and estimated the regional diversification and diversity dynamics of endemic and immigrant artiodactyls. We show that the endemic artiodactyl radiation was mainly related to the Eocene tropical conditions, combined with biotic controls on speciation and clade-related diversity dependence. We further highlight that the major environmental changes at the transition (77% of species became extinct) and the concurrent increase in seasonality in Europe during the Oligocene were likely the main drivers of their decline. Surprisingly, our results do not support the widely-held hypothesis of active competition between endemic and immigrant artiodactyls but rather suggest a passive or opportunistic replacement by immigrants, which is further supported by morphological clustering of specific ecological traits across the Eocene-Oligocene transition. Our analyses provide insights into the evolutionary and ecological processes driving the diversification and decline of mammalian clades during a major biological and climatic crisis.
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Affiliation(s)
- Romain Weppe
- Institut des Sciences de l’Evolution de Montpellier, Univ Montpellier, CNRS, IRD, Montpellier Cedex 534095, France
| | - Fabien L. Condamine
- Institut des Sciences de l’Evolution de Montpellier, Univ Montpellier, CNRS, IRD, Montpellier Cedex 534095, France
| | - Guillaume Guinot
- Institut des Sciences de l’Evolution de Montpellier, Univ Montpellier, CNRS, IRD, Montpellier Cedex 534095, France
| | - Jacob Maugoust
- Institut des Sciences de l’Evolution de Montpellier, Univ Montpellier, CNRS, IRD, Montpellier Cedex 534095, France
| | - Maëva J. Orliac
- Institut des Sciences de l’Evolution de Montpellier, Univ Montpellier, CNRS, IRD, Montpellier Cedex 534095, France
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8
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Sun J, Liu X, Huang Y, Wang F, Sun Y, Chen J, Chu D, Song H. Automatic identification and morphological comparison of bivalve and brachiopod fossils based on deep learning. PeerJ 2023; 11:e16200. [PMID: 37842038 PMCID: PMC10576495 DOI: 10.7717/peerj.16200] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Accepted: 09/07/2023] [Indexed: 10/17/2023] Open
Abstract
Fossil identification is an essential and fundamental task for conducting palaeontological research. Because the manual identification of fossils requires extensive experience and is time-consuming, automatic identification methods are proposed. However, these studies are limited to a few or dozens of species, which is hardly adequate for the needs of research. This study enabled the automatic identification of hundreds of species based on a newly established fossil dataset. An available "bivalve and brachiopod fossil image dataset" (BBFID, containing >16,000 "image-label" data pairs, taxonomic determination completed) was created. The bivalves and brachiopods contained in BBFID are closely related in morphology, ecology and evolution that have long attracted the interest of researchers. We achieved >80% identification accuracy at 22 genera and ∼64% accuracy at 343 species using EfficientNetV2s architecture. The intermediate output of the model was extracted and downscaled to obtain the morphological feature space of fossils using t-distributed stochastic neighbor embedding (t-SNE). We found a distinctive boundary between the morphological feature points of bivalves and brachiopods in fossil morphological feature distribution maps. This study provides a possible method for studying the morphological evolution of fossil clades using computer vision in the future.
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Affiliation(s)
- Jiarui Sun
- State Key Laboratory of Biogeology and Environmental Geology, School of Earth Sciences, China University of Geosciences, Wuhan, Hubei, China
| | - Xiaokang Liu
- State Key Laboratory of Biogeology and Environmental Geology, School of Earth Sciences, China University of Geosciences, Wuhan, Hubei, China
- Department of Biology, University of Fribourg, Fribourg, Switzerland
| | - Yunfei Huang
- School of Geosciences, Yangtze University, Wuhan, Hubei, China
| | - Fengyu Wang
- State Key Laboratory of Biogeology and Environmental Geology, School of Earth Sciences, China University of Geosciences, Wuhan, Hubei, China
| | - Yongfang Sun
- State Key Laboratory of Biogeology and Environmental Geology, School of Earth Sciences, China University of Geosciences, Wuhan, Hubei, China
| | - Jing Chen
- Yifu Museum, China University of Geosciences, Wuhan, Hubei, China
| | - Daoliang Chu
- State Key Laboratory of Biogeology and Environmental Geology, School of Earth Sciences, China University of Geosciences, Wuhan, Hubei, China
| | - Haijun Song
- State Key Laboratory of Biogeology and Environmental Geology, School of Earth Sciences, China University of Geosciences, Wuhan, Hubei, China
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9
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Guo Z, Flannery-Sutherland JT, Benton MJ, Chen ZQ. Bayesian analyses indicate bivalves did not drive the downfall of brachiopods following the Permian-Triassic mass extinction. Nat Commun 2023; 14:5566. [PMID: 37689772 PMCID: PMC10492784 DOI: 10.1038/s41467-023-41358-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Accepted: 08/29/2023] [Indexed: 09/11/2023] Open
Abstract
Certain times of major biotic replacement have often been interpreted as broadly competitive, mediated by innovation in the succeeding clades. A classic example was the switch from brachiopods to bivalves as major seabed organisms following the Permian-Triassic mass extinction (PTME), ~252 million years ago. This was attributed to competitive exclusion of brachiopods by the better adapted bivalves or simply to the fact that brachiopods had been hit especially hard by the PTME. The brachiopod-bivalve switch is emblematic of the global turnover of marine faunas from Palaeozoic-type to Modern-type triggered by the PTME. Here, using Bayesian analyses, we find that unexpectedly the two clades displayed similar large-scale trends of diversification before the Jurassic. Insight from a multivariate birth-death model shows that the extinction of major brachiopod clades during the PTME set the stage for the brachiopod-bivalve switch, with differential responses to high ocean temperatures post-extinction further facilitating their displacement by bivalves. Our study strengthens evidence that brachiopods and bivalves were not competitors over macroevolutionary time scales, with extinction events and environmental stresses shaping their divergent fates.
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Affiliation(s)
- Zhen Guo
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences (Wuhan), Wuhan, 430074, China
| | | | - Michael J Benton
- School of Earth Sciences, University of Bristol, Bristol, BS8 1RJ, UK.
| | - Zhong-Qiang Chen
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences (Wuhan), Wuhan, 430074, China.
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10
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Rolland J, Henao-Diaz LF, Doebeli M, Germain R, Harmon LJ, Knowles LL, Liow LH, Mank JE, Machac A, Otto SP, Pennell M, Salamin N, Silvestro D, Sugawara M, Uyeda J, Wagner CE, Schluter D. Conceptual and empirical bridges between micro- and macroevolution. Nat Ecol Evol 2023; 7:1181-1193. [PMID: 37429904 DOI: 10.1038/s41559-023-02116-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Accepted: 06/13/2023] [Indexed: 07/12/2023]
Abstract
Explaining broad molecular, phenotypic and species biodiversity patterns necessitates a unifying framework spanning multiple evolutionary scales. Here we argue that although substantial effort has been made to reconcile microevolution and macroevolution, much work remains to identify the links between biological processes at play. We highlight four major questions of evolutionary biology whose solutions require conceptual bridges between micro and macroevolution. We review potential avenues for future research to establish how mechanisms at one scale (drift, mutation, migration, selection) translate to processes at the other scale (speciation, extinction, biogeographic dispersal) and vice versa. We propose ways in which current comparative methods to infer molecular evolution, phenotypic evolution and species diversification could be improved to specifically address these questions. We conclude that researchers are in a better position than ever before to build a synthesis to understand how microevolutionary dynamics unfold over millions of years.
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Affiliation(s)
- Jonathan Rolland
- CNRS, UMR5174, Laboratoire Evolution et Diversité Biologique, Université Toulouse 3 Paul Sabatier, Toulouse, France.
| | - L Francisco Henao-Diaz
- Department of Zoology, and Biodiversity Research Centre, University of British Columbia, Vancouver, British Columbia, Canada
- Department of Ecology and Evolution, University of Chicago, Chicago, IL, USA
| | - Michael Doebeli
- Department of Zoology, and Department of Mathematics, University of British Columbia, Vancouver, British Columbia, Canada
| | - Rachel Germain
- Department of Zoology, and Biodiversity Research Centre, University of British Columbia, Vancouver, British Columbia, Canada
| | - Luke J Harmon
- Dept. of Biological Sciences, University of Idaho, Moscow, ID, USA
| | - L Lacey Knowles
- Department of Ecology and Evolutionary Biology, Museum of Zoology, University of Michigan, Ann Arbor, MI, USA
| | | | - Judith E Mank
- Department of Zoology, and Biodiversity Research Centre, University of British Columbia, Vancouver, British Columbia, Canada
| | - Antonin Machac
- Department of Zoology, and Biodiversity Research Centre, University of British Columbia, Vancouver, British Columbia, Canada
- Laboratory of Environmental Microbiology, Institute of Microbiology of the CAS, Prague, Czech Republic
| | - Sarah P Otto
- Department of Zoology, and Biodiversity Research Centre, University of British Columbia, Vancouver, British Columbia, Canada
| | - Matt Pennell
- Departments of Quantitative and Computational Biology and Biological Sciences, University of Southern California, Los Angeles, CA, USA
| | - Nicolas Salamin
- Department of Computational Biology, University of Lausanne, Lausanne, Switzerland
| | - Daniele Silvestro
- Department of Biology, University of Fribourg, Fribourg, Switzerland
- Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden
- Gothenburg Global Biodiversity Centre, University of Gothenburg, Gothenburg, Sweden
| | - Mauro Sugawara
- Department of Zoology, and Biodiversity Research Centre, University of British Columbia, Vancouver, British Columbia, Canada
- Mário Schenberg Institute, São Paulo, Brazil
| | - Josef Uyeda
- Department of Biological Sciences, Virginia Tech, Blacksburg, VA, USA
| | - Catherine E Wagner
- Department of Botany, and Program in Ecology and Evolution, University of Wyoming, Laramie, WY, USA
| | - Dolph Schluter
- Department of Zoology, and Biodiversity Research Centre, University of British Columbia, Vancouver, British Columbia, Canada
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11
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Strotz LC, Lieberman BS. The end of the line: competitive exclusion and the extinction of historical entities. ROYAL SOCIETY OPEN SCIENCE 2023; 10:221210. [PMID: 36844802 PMCID: PMC9943885 DOI: 10.1098/rsos.221210] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Accepted: 02/06/2023] [Indexed: 06/18/2023]
Abstract
Identifying competitive exclusion at the macroevolutionary scale has typically relied on demonstrating a reciprocal, contradictory response by two co-occurring, functionally similar clades. Finding definitive examples of such a response in fossil time series has proven challenging, however, as has controlling for the effects of a changing physical environment. We take a novel approach to this issue by quantifying variation in trait values that capture almost the entirety of function for steam locomotives (SL), a known example of competitive exclusion from material culture, with the goal of identifying patterns suitable for assessing clade replacement in the fossil record. Our analyses find evidence of an immediate, directional response to the first appearance of a direct competitor, with subsequent competitors further reducing the realized niche of SLs, until extinction was the inevitable outcome. These results demonstrate when interspecific competition should lead to extinction and suggest that clade replacement may only occur when niche overlap between an incumbent and its competitors is near absolute and where the incumbent is incapable of transitioning to a new adaptive zone. Our findings provide the basis for a new approach to analyse putative examples of competitive exclusion that is largely free of a priori assumptions.
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Affiliation(s)
- Luke C. Strotz
- State Key Laboratory of Continental Dynamics, Shaanxi Key Laboratory of Early Life & Environments and Department of Geology, Northwest University, Xi'an 710069, People's Republic of China
- Biodiversity Institute and Department of Ecology & Evolutionary Biology, University of Kansas, Lawrence, KS 66045, USA
- Department of Palaeontology, University of Vienna, Althanstrasse 14, 1090 Vienna, Austria
| | - Bruce S. Lieberman
- Biodiversity Institute and Department of Ecology & Evolutionary Biology, University of Kansas, Lawrence, KS 66045, USA
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12
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Hodge JR, Price SA. Biotic Interactions and the Future of Fishes on Coral Reefs: The Importance of Trait-Based Approaches. Integr Comp Biol 2022; 62:1734-1747. [PMID: 36138511 DOI: 10.1093/icb/icac147] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Revised: 08/24/2022] [Accepted: 09/06/2022] [Indexed: 01/05/2023] Open
Abstract
Biotic interactions govern the structure and function of coral reef ecosystems. As environmental conditions change, reef-associated fish populations can persist by tracking their preferred niche or adapting to new conditions. Biotic interactions will affect how these responses proceed and whether they are successful. Yet, our understanding of these effects is currently limited. Ecological and evolutionary theories make explicit predictions about the effects of biotic interactions, but many remain untested. Here, we argue that large-scale functional trait datasets enable us to investigate how biotic interactions have shaped the assembly of contemporary reef fish communities and the evolution of species within them, thus improving our ability to predict future changes. Importantly, the effects of biotic interactions on these processes have occurred simultaneously within dynamic environments. Functional traits provide a means to integrate the effects of both ecological and evolutionary processes, as well as a way to overcome some of the challenges of studying biotic interactions. Moreover, functional trait data can enhance predictive modeling of future reef fish distributions and evolvability. We hope that our vision for an integrative approach, focused on quantifying functionally relevant traits and how they mediate biotic interactions in different environmental contexts, will catalyze new research on the future of reef fishes in a changing environment.
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Affiliation(s)
- Jennifer R Hodge
- Department of Biological Sciences, Clemson University, Clemson, SC 29634, USA
| | - Samantha A Price
- Department of Biological Sciences, Clemson University, Clemson, SC 29634, USA
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Jouault C, Nel A, Perrichot V, Legendre F, Condamine FL. Multiple drivers and lineage-specific insect extinctions during the Permo-Triassic. Nat Commun 2022; 13:7512. [PMID: 36473862 PMCID: PMC9726944 DOI: 10.1038/s41467-022-35284-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2022] [Accepted: 11/25/2022] [Indexed: 12/12/2022] Open
Abstract
The Permo-Triassic interval encompasses three extinction events including the most dramatic biological crisis of the Phanerozoic, the latest Permian mass extinction. However, their drivers and outcomes are poorly quantified and understood for terrestrial invertebrates, which we assess here for insects. We find a pattern with three extinctions: the Roadian/Wordian (≈266.9 Ma; extinction of 64.5% insect genera), the Permian/Triassic (≈252 Ma; extinction of 82.6% insect genera), and the Ladinian/Carnian boundaries (≈237 Ma; extinction of 74.8% insect genera). We also unveil a heterogeneous effect of these extinction events across the major insect clades. Because extinction events have impacted Permo-Triassic ecosystems, we investigate the influence of abiotic and biotic factors on insect diversification dynamics and find that changes in floral assemblages are likely the strongest drivers of insects' responses throughout the Permo-Triassic. We also assess the effect of diversity dependence between three insect guilds; an effect ubiquitously found in current ecosystems. We find that herbivores held a central position in the Permo-Triassic interaction network. Our study reveals high levels of insect extinction that profoundly shaped the evolutionary history of the most diverse non-microbial lineage.
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Affiliation(s)
- Corentin Jouault
- grid.462844.80000 0001 2308 1657Institut de Systématique, Évolution, Biodiversité (ISYEB), Muséum national d’Histoire naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, CP50, 57 rue Cuvier, 75005 Paris, France ,grid.462934.e0000 0001 1482 4447Univ. Rennes, CNRS, Géosciences Rennes, UMR 6118, F-35000 Rennes, France ,grid.4444.00000 0001 2112 9282CNRS, UMR 5554 Institut des Sciences de l’Évolution de Montpellier, Place Eugène Bataillon, 34095 Montpellier, France
| | - André Nel
- grid.462844.80000 0001 2308 1657Institut de Systématique, Évolution, Biodiversité (ISYEB), Muséum national d’Histoire naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, CP50, 57 rue Cuvier, 75005 Paris, France
| | - Vincent Perrichot
- grid.462934.e0000 0001 1482 4447Univ. Rennes, CNRS, Géosciences Rennes, UMR 6118, F-35000 Rennes, France
| | - Frédéric Legendre
- grid.462844.80000 0001 2308 1657Institut de Systématique, Évolution, Biodiversité (ISYEB), Muséum national d’Histoire naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, CP50, 57 rue Cuvier, 75005 Paris, France
| | - Fabien L. Condamine
- grid.4444.00000 0001 2112 9282CNRS, UMR 5554 Institut des Sciences de l’Évolution de Montpellier, Place Eugène Bataillon, 34095 Montpellier, France
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14
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Kopperud BT, Lidgard S, Liow LH. Enhancing georeferenced biodiversity inventories: automated information extraction from literature records reveal the gaps. PeerJ 2022; 10:e13921. [PMID: 35999848 PMCID: PMC9393005 DOI: 10.7717/peerj.13921] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Accepted: 07/29/2022] [Indexed: 01/19/2023] Open
Abstract
We use natural language processing (NLP) to retrieve location data for cheilostome bryozoan species (text-mined occurrences (TMO)) in an automated procedure. We compare these results with data combined from two major public databases (DB): the Ocean Biodiversity Information System (OBIS), and the Global Biodiversity Information Facility (GBIF). Using DB and TMO data separately and in combination, we present latitudinal species richness curves using standard estimators (Chao2 and the Jackknife) and range-through approaches. Our combined DB and TMO species richness curves quantitatively document a bimodal global latitudinal diversity gradient for extant cheilostomes for the first time, with peaks in the temperate zones. A total of 79% of the georeferenced species we retrieved from TMO (N = 1,408) and DB (N = 4,549) are non-overlapping. Despite clear indications that global location data compiled for cheilostomes should be improved with concerted effort, our study supports the view that many marine latitudinal species richness patterns deviate from the canonical latitudinal diversity gradient (LDG). Moreover, combining online biodiversity databases with automated information retrieval from the published literature is a promising avenue for expanding taxon-location datasets.
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Affiliation(s)
- Bjørn Tore Kopperud
- Natural History Museum, University of Oslo, Oslo, Norway,GeoBio-Center, Ludwig-Maximilians-Universität München, München, Germany,Department of Earth and Environmental Sciences, Ludwig-Maximilians-Universität München, München, Germany
| | - Scott Lidgard
- Negaunee Integrative Research Center, Field Museum of Natural History, Chicago, Illinois, U.S.A.
| | - Lee Hsiang Liow
- Natural History Museum, University of Oslo, Oslo, Norway,Centre for Ecological and Evolutionary Synthesis, University of Oslo, Oslo, Norway
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15
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Cogni R, Quental TB, Guimarães PR. Ehrlich and Raven escape and radiate coevolution hypothesis at different levels of organization: Past and future perspectives. Evolution 2022; 76:1108-1123. [PMID: 35262199 DOI: 10.1111/evo.14456] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2021] [Revised: 02/02/2022] [Accepted: 02/22/2022] [Indexed: 01/21/2023]
Abstract
The classic paper by Ehrlich and Raven on coevolution will soon be 60 years old. Although they were not the first to develop the idea of coevolution, their thought-provoking paper certainly popularized this idea and inspired several generations of scientists interested in coevolution. Here, we describe some of their main contributions, quantitatively measure the impact of their seminal paper on different fields of research, and discuss how ideas related to their original paper might push the study of coevolution forward. To guide our discussion, we explore their original hypothesis into three research fields that are associated with distinct scales/levels of organization: (1) the genetic mechanisms underlying coevolutionary interactions; (2) the potential association between coevolutionary diversification and the organization of ecological networks; and (3) the micro- and macroevolutionary mechanisms and expected patterns under their hypothesis. By doing so, we discuss potentially overlooked aspects and future directions for the study of coevolutionary dynamics and diversification.
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Affiliation(s)
- Rodrigo Cogni
- Department of Ecology, University of São Paulo, São Paulo, SP, 05508-900, Brazil
| | - Tiago B Quental
- Department of Ecology, University of São Paulo, São Paulo, SP, 05508-900, Brazil
| | - Paulo R Guimarães
- Department of Ecology, University of São Paulo, São Paulo, SP, 05508-900, Brazil
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16
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Christison BE, Gaidies F, Pineda-Munoz S, Evans AR, Gilbert MA, Fraser D. Dietary niches of creodonts and carnivorans of the late Eocene Cypress Hills Formation. J Mammal 2022; 103:2-17. [PMID: 35087328 PMCID: PMC8789764 DOI: 10.1093/jmammal/gyab123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2019] [Accepted: 10/09/2021] [Indexed: 11/14/2022] Open
Abstract
Modern North American carnivorous mammal assemblages consist of species from a single clade: the Carnivora. Carnivorans once coexisted with members of other meat-eating clades, including the creodonts (Hyaenodontida and Oxyaenida). Creodonts, however, went extinct in North America during the late Eocene and early Oligocene, potentially due to niche overlap and resource competition with contemporary carnivorans. In this study, we employ a community ecology approach to understand whether the dietary niches of coexisting creodonts and carnivorans overlapped during the late Eocene (Chadronian North American Land Mammal Age), a time when creodonts were dwindling and carnivorans were diversifying. We quantify niche overlap based on inferences of diet from carnassial tooth shape estimated using Orientation Patch Count, Dirichlet's Normal Surface Energy, and linear dental measurements as well as from body mass for all species in the Calf Creek Local Fauna of Cypress Hills, Saskatchewan (Treaty 4 land). Although creodonts and carnivorans shared characteristics of their carnassial tooth shape, suggesting similar chewing mechanics and feeding habits, we find that marked differences in body size likely facilitated niche partitioning, at least between the largest creodonts and carnivorans. Calculations of prey focus masses and prey mass spectra indicate that only the smallest creodont may have experienced significant competition for prey with the coeval carnivorans. We suggest that the ultimate extinction of creodonts from North America during the late Eocene and Oligocene was unlikely to have been driven by factors related to niche overlap with carnivorans.
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Affiliation(s)
| | - Fred Gaidies
- Department of Earth Sciences, Carleton University, Ottawa, Ontario, Canada
| | - Silvia Pineda-Munoz
- Department of Earth and Atmospheric Sciences, Indiana University, Bloomington, IN, USA
- Department of Paleobiology, Smithsonian National Museum of Natural History, Washington, District of Columbia, USA
| | - Alistair R Evans
- School of Biological Sciences, Monash University, Melbourne, Victoria, Australia
- Geosciences, Museums Victoria, Melbourne, Victoria, Australia
| | - Marisa A Gilbert
- Palaeobiology, Canadian Museum of Nature, Ottawa, Ontario, Canada
| | - Danielle Fraser
- Department of Biology, Carleton University, Ottawa, Ontario, Canada
- Department of Earth Sciences, Carleton University, Ottawa, Ontario, Canada
- Department of Paleobiology, Smithsonian National Museum of Natural History, Washington, District of Columbia, USA
- Palaeobiology, Canadian Museum of Nature, Ottawa, Ontario, Canada
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17
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Ye F, Shi GR, Bitner MA. Global biogeography of living brachiopods: Bioregionalization patterns and possible controls. PLoS One 2021; 16:e0259004. [PMID: 34748573 PMCID: PMC8575269 DOI: 10.1371/journal.pone.0259004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Accepted: 10/08/2021] [Indexed: 11/19/2022] Open
Abstract
The global distribution patterns of 14918 geo-referenced occurrences from 394 living brachiopod species were mapped in 5° grid cells, which enabled the visualization and delineation of distinct bioregions and biodiversity hotspots. Further investigation using cluster and network analyses allowed us to propose the first systematically and quantitatively recognized global bioregionalization framework for living brachiopods, consisting of five bioregions and thirteen bioprovinces. No single environmental or ecological variable is accountable for the newly proposed global bioregionalization patterns of living brachiopods. Instead, the combined effects of large-scale ocean gyres, climatic zonation as well as some geohistorical factors (e.g., formation of land bridges and geological recent closure of ancient seaways) are considered as the main drivers at the global scale. At the regional scale, however, the faunal composition, diversity and biogeographical differentiation appear to be mainly controlled by seawater temperature variation, regional ocean currents and coastal upwelling systems.
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Affiliation(s)
- Facheng Ye
- School of Earth, Atmospheric and Life Sciences, Faculty of Science, Medicine and Health, University of Wollongong, Wollongong, New South Wales, Australia
| | - G. R. Shi
- School of Earth, Atmospheric and Life Sciences, Faculty of Science, Medicine and Health, University of Wollongong, Wollongong, New South Wales, Australia
- * E-mail:
| | - Maria Aleksandra Bitner
- Department of Evolutionary Paleobiology, Institute of Paleobiology, Polish Academy of Sciences, Warsaw, Poland
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18
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Bush AM, Payne JL. Biotic and Abiotic Controls on the Phanerozoic History of Marine Animal Biodiversity. ANNUAL REVIEW OF ECOLOGY, EVOLUTION, AND SYSTEMATICS 2021. [DOI: 10.1146/annurev-ecolsys-012021-035131] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
During the past 541 million years, marine animals underwent three intervals of diversification (early Cambrian, Ordovician, Cretaceous–Cenozoic) separated by nondirectional fluctuation, suggesting diversity-dependent dynamics with the equilibrium diversity shifting through time. Changes in factors such as shallow-marine habitat area and climate appear to have modulated the nondirectional fluctuations. Directional increases in diversity are best explained by evolutionary innovations in marine animals and primary producers coupled with stepwise increases in the availability of food and oxygen. Increasing intensity of biotic interactions such as predation and disturbance may have led to positive feedbacks on diversification as ecosystems became more complex. Important areas for further research include improving the geographic coverage and temporal resolution of paleontological data sets, as well as deepening our understanding of Earth system evolution and the physiological and ecological traits that modulated organismal responses to environmental change.
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Affiliation(s)
- Andrew M. Bush
- Department of Geosciences and Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, Connecticut 06269, USA
| | - Jonathan L. Payne
- Department of Geological Sciences, Stanford University, Stanford, California 94305, USA
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19
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Lidgard S, Di Martino E, Zágoršek K, Liow LH. When fossil clades 'compete': local dominance, global diversification dynamics and causation. Proc Biol Sci 2021; 288:20211632. [PMID: 34547910 PMCID: PMC8456135 DOI: 10.1098/rspb.2021.1632] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Accepted: 08/26/2021] [Indexed: 01/14/2023] Open
Abstract
Examining the supposition that local-scale competition drives macroevolutionary patterns has become a familiar goal in fossil biodiversity studies. However, it is an elusive goal, hampered by inadequate confirmation of ecological equivalence and interactive processes between clades, patchy sampling, few comparative analyses of local species assemblages over long geological intervals, and a dearth of appropriate statistical tools. We address these concerns by reevaluating one of the classic examples of clade displacement in the fossil record, in which cheilostome bryozoans surpass the once dominant cyclostomes. Here, we analyse a newly expanded and vetted compilation of 40 190 fossil species occurrences to estimate cheilostome and cyclostome patterns of species proportions within assemblages, global genus richness and genus origination and extinction rates while accounting for sampling. Comparison of time-series models using linear stochastic differential equations suggests that inter-clade genus origination and extinction rates are causally linked to each other in a complex feedback relationship rather than by simple correlations or unidirectional relationships, and that these rates are not causally linked to changing within-assemblage proportions of cheilostome versus cyclostome species.
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Affiliation(s)
- Scott Lidgard
- Negaunee Integrative Research Center, Field Museum, 1400 S. Lake Shore Drive, Chicago, IL 60605 USA
| | | | - Kamil Zágoršek
- Department of Geography, Technical University of Liberec, Studentská 2, CZ-461 Liberec, Czech Republic
| | - Lee Hsiang Liow
- Natural History Museum, University of Oslo, Oslo, Norway
- Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, Oslo, Norway
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20
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Condamine FL, Guinot G, Benton MJ, Currie PJ. Dinosaur biodiversity declined well before the asteroid impact, influenced by ecological and environmental pressures. Nat Commun 2021; 12:3833. [PMID: 34188028 PMCID: PMC8242047 DOI: 10.1038/s41467-021-23754-0] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2019] [Accepted: 05/10/2021] [Indexed: 02/05/2023] Open
Abstract
The question why non-avian dinosaurs went extinct 66 million years ago (Ma) remains unresolved because of the coarseness of the fossil record. A sudden extinction caused by an asteroid is the most accepted hypothesis but it is debated whether dinosaurs were in decline or not before the impact. We analyse the speciation-extinction dynamics for six key dinosaur families, and find a decline across dinosaurs, where diversification shifted to a declining-diversity pattern ~76 Ma. We investigate the influence of ecological and physical factors, and find that the decline of dinosaurs was likely driven by global climate cooling and herbivorous diversity drop. The latter is likely due to hadrosaurs outcompeting other herbivores. We also estimate that extinction risk is related to species age during the decline, suggesting a lack of evolutionary novelty or adaptation to changing environments. These results support an environmentally driven decline of non-avian dinosaurs well before the asteroid impact.
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Affiliation(s)
- Fabien L Condamine
- Institut des Sciences de l'Evolution de Montpellier (Université de Montpellier | CNRS|IRD|EPHE), Montpellier, France.
| | - Guillaume Guinot
- Institut des Sciences de l'Evolution de Montpellier (Université de Montpellier | CNRS|IRD|EPHE), Montpellier, France
| | - Michael J Benton
- Department of Earth Sciences, University of Bristol, Bristol, UK
| | - Philip J Currie
- Department of Biological Sciences, University of Alberta, Edmonton, AB, Canada
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21
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Weppe R, Orliac MJ, Guinot G, Condamine FL. Evolutionary drivers, morphological evolution and diversity dynamics of a surviving mammal clade: cainotherioids at the Eocene-Oligocene transition. Proc Biol Sci 2021; 288:20210173. [PMID: 34074121 PMCID: PMC8170207 DOI: 10.1098/rspb.2021.0173] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Accepted: 05/10/2021] [Indexed: 11/12/2022] Open
Abstract
The Eocene-Oligocene transition (EOT) represents a period of global environmental changes particularly marked in Europe and coincides with a dramatic biotic turnover. Here, using an exceptional fossil preservation, we document and analyse the diversity dynamics of a mammal clade, Cainotherioidea (Artiodactyla), that survived the EOT and radiated rapidly immediately after. We infer their diversification history from Quercy Konzentrat-Lagerstätte (south-west France) at the species level using Bayesian birth-death models. We show that cainotherioid diversity fluctuated through time, with extinction events at the EOT and in the late Oligocene, and a major speciation burst in the early Oligocene. The latter is in line with our finding that cainotherioids had a high morphological adaptability following environmental changes throughout the EOT, which probably played a key role in the survival and evolutionary success of this clade in the aftermath. Speciation is positively associated with temperature and continental fragmentation in a time-continuous way, while extinction seems to synchronize with environmental change in a punctuated way. Within-clade interactions negatively affected the cainotherioid diversification, while inter-clade competition might explain their final decline during the late Oligocene. Our results provide a detailed dynamic picture of the evolutionary history of a mammal clade in a context of global change.
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Affiliation(s)
- R. Weppe
- Institut des Sciences de l’évolution de Montpellier, Université de Montpellier, CNRS, IRD, EPHE, Place Eugène Bataillon, 34095 Montpellier Cedex 5, France
| | - M. J. Orliac
- Institut des Sciences de l’évolution de Montpellier, Université de Montpellier, CNRS, IRD, EPHE, Place Eugène Bataillon, 34095 Montpellier Cedex 5, France
| | - G. Guinot
- Institut des Sciences de l’évolution de Montpellier, Université de Montpellier, CNRS, IRD, EPHE, Place Eugène Bataillon, 34095 Montpellier Cedex 5, France
| | - F. L. Condamine
- Institut des Sciences de l’évolution de Montpellier, Université de Montpellier, CNRS, IRD, EPHE, Place Eugène Bataillon, 34095 Montpellier Cedex 5, France
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22
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Tomiya S, Miller LK. Why aren't rabbits and hares larger? Evolution 2021; 75:847-860. [PMID: 33599290 PMCID: PMC8252017 DOI: 10.1111/evo.14187] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Revised: 11/28/2020] [Accepted: 02/03/2021] [Indexed: 11/28/2022]
Abstract
Macroevolutionary consequences of competition among large clades have long been sought in patterns of lineage diversification. However, mechanistically clear examples of such effects remain elusive. Here, we postulated that the limited phenotypic diversity and insular gigantism in lagomorphs could be explained at least in part by an evolutionary constraint placed on them by potentially competing ungulate-type herbivores (UTHs). Our analyses yielded three independent lines of evidence supporting this hypothesis: (1) the minimum UTH body mass is the most influential predictor of the maximum lagomorph body mass in modern ecoregions; (2) the scaling patterns of local-population energy use suggest universal competitive disadvantage of lagomorphs weighing over approximately 6.3 kg against artiodactyls, closely matching their observed upper size limit in continental settings; and (3) the trajectory of maximum lagomorph body mass in North America from the late Eocene to the Pleistocene (37.5-1.5 million years ago) was best modeled by the body mass ceiling placed by the smallest contemporary perissodactyl or artiodactyl. Body size evolution in lagomorphs has likely been regulated by the forces of competition within the clade, increased predation in open habitats, and importantly, competition from other ungulate-type herbivores. Our findings suggest conditionally-coupled dynamics of phenotypic boundaries among multiple clades within an adaptive zone, and highlight the synergy of biotic and abiotic drivers of diversity.
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Affiliation(s)
- Susumu Tomiya
- Center for International Collaboration and Advanced Studies in Primatology, Kyoto University Primate Research Institute, Inuyama, Aichi, 484-8506, Japan.,Negaunee Integrative Research and Gantz Family Collections Centers, Field Museum of Natural History, Chicago, IL, 60605, USA.,Museums of Paleontology and Vertebrate Zoology, University of California, Berkeley, CA, 94720, USA.,Department of Integrative Biology, University of California, Berkeley, CA, 94720, USA
| | - Lauren K Miller
- Department of Integrative Biology, University of California, Berkeley, CA, 94720, USA
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24
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Condamine FL, Silvestro D, Koppelhus EB, Antonelli A. The rise of angiosperms pushed conifers to decline during global cooling. Proc Natl Acad Sci U S A 2020; 117:28867-28875. [PMID: 33139543 PMCID: PMC7682372 DOI: 10.1073/pnas.2005571117] [Citation(s) in RCA: 48] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Competition among species and entire clades can impact species diversification and extinction, which can shape macroevolutionary patterns. The fossil record shows successive biotic turnovers such that a dominant group is replaced by another. One striking example involves the decline of gymnosperms and the rapid diversification and ecological dominance of angiosperms in the Cretaceous. It is generally believed that angiosperms outcompeted gymnosperms, but the macroevolutionary processes and alternative drivers explaining this pattern remain elusive. Using extant time trees and vetted fossil occurrences for conifers, we tested the hypotheses that clade competition or climate change led to the decline of conifers at the expense of angiosperms. Here, we find that both fossil and molecular data show high congruence in revealing 1) low diversification rates, punctuated by speciation pulses, during warming events throughout the Phanerozoic and 2) that conifer extinction increased significantly in the Mid-Cretaceous (100 to 110 Ma) and remained high ever since. Their extinction rates are best explained by the rise of angiosperms, rejecting alternative models based on either climate change or time alone. Our results support the hypothesis of an active clade replacement, implying that direct competition with angiosperms increased the extinction of conifers by pushing their remaining species diversity and dominance out of the warm tropics. This study illustrates how entire branches on the Tree of Life may actively compete for ecological dominance under changing climates.
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Affiliation(s)
- Fabien L Condamine
- CNRS, UMR 5554 Institut des Sciences de l'Evolution de Montpellier (Université de Montpellier), 34095 Montpellier, France;
- Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E9, Canada
| | - Daniele Silvestro
- Department of Biology, University of Fribourg, 1700 Fribourg, Switzerland
- Department of Biological and Environmental Sciences, University of Gothenburg, SE-405 30 Gothenburg, Sweden
- Gothenburg Global Biodiversity Centre, SE-405 30 Gothenburg, Sweden
| | - Eva B Koppelhus
- Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E9, Canada
| | - Alexandre Antonelli
- Department of Biological and Environmental Sciences, University of Gothenburg, SE-405 30 Gothenburg, Sweden
- Gothenburg Global Biodiversity Centre, SE-405 30 Gothenburg, Sweden
- Department of Plant Sciences, University of Oxford, South Parks Road, Oxford OX1 3RB, United Kingdom
- Royal Botanic Gardens, Kew, Richmond, Surrey TW9 3AE, United Kingdom
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25
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Comparison of Approaches for Data Analysis of Multi-Parametric Monitoring Systems: Insights from the Acuto Test-Site (Central Italy). APPLIED SCIENCES-BASEL 2020. [DOI: 10.3390/app10217658] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
This paper deals with monitoring systems to manage the risk due to fast slope failures that involve rock masses, in which important elements (such as infrastructures or cultural heritages, among the others) are exposed. Three different approaches for data analysis were here compared to evaluate their suitability for detecting mutual relations among destabilising factors, acting on different time windows, and induced strain effects on rock masses: (i) an observation-based approach (OBA), (ii) a statistics-based approach (SBA) and (iii) a semi-empirical approach (SEA). For these purposes, a test-site has been realised in an abandoned quarry in Central Italy by installing a multi-parametric monitoring sensor network on a rock wall able to record strain effects induced by natural and anthropic forcing actions (like as temperature, rainfall, wind and anthropic vibrations). The comparison points out that the considered approaches allow one to identify forcing actions, responsible for the strain effects on the rock mass over several time windows, regarding a specific size (i.e., rock block dimensional scale). The OBA was more suitable for computing the relations over short- to medium time windows, as well as the role of impulsive actions (i.e., hourly to seasonal and/or instantaneous). The SBA was suitable for computing the relations over medium- to long time windows (i.e., daily to seasonal), also returning the time lag between forcing actions and induced strains using the cross-correlation statistical function. Last, the SEA was highly suitable for detecting irreversible strain effects over long- to very long-time windows (i.e., plurennial).
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26
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Fraser D, Soul LC, Tóth AB, Balk MA, Eronen JT, Pineda-Munoz S, Shupinski AB, Villaseñor A, Barr WA, Behrensmeyer AK, Du A, Faith JT, Gotelli NJ, Graves GR, Jukar AM, Looy CV, Miller JH, Potts R, Lyons SK. Investigating Biotic Interactions in Deep Time. Trends Ecol Evol 2020; 36:61-75. [PMID: 33067015 DOI: 10.1016/j.tree.2020.09.001] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Revised: 08/31/2020] [Accepted: 09/02/2020] [Indexed: 11/16/2022]
Abstract
Recent renewed interest in using fossil data to understand how biotic interactions have shaped the evolution of life is challenging the widely held assumption that long-term climate changes are the primary drivers of biodiversity change. New approaches go beyond traditional richness and co-occurrence studies to explicitly model biotic interactions using data on fossil and modern biodiversity. Important developments in three primary areas of research include analysis of (i) macroevolutionary rates, (ii) the impacts of and recovery from extinction events, and (iii) how humans (Homo sapiens) affected interactions among non-human species. We present multiple lines of evidence for an important and measurable role of biotic interactions in shaping the evolution of communities and lineages on long timescales.
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Affiliation(s)
- Danielle Fraser
- Palaeobiology, Canadian Museum of Nature, Ottawa, ON, Canada; Biology and Earth Sciences, Carleton University, Ottawa, ON, Canada; Department of Paleobiology and Evolution of Terrestrial Ecosystems Program, Smithsonian Institution, National Museum of Natural History, Washington, DC , USA.
| | - Laura C Soul
- Department of Paleobiology and Evolution of Terrestrial Ecosystems Program, Smithsonian Institution, National Museum of Natural History, Washington, DC , USA
| | - Anikó B Tóth
- Centre for Ecosystem Science, School of Biological, Earth and Environmental Sciences, UNSW, Sydney, NSW, Australia
| | - Meghan A Balk
- Department of Paleobiology and Evolution of Terrestrial Ecosystems Program, Smithsonian Institution, National Museum of Natural History, Washington, DC , USA; BIO5 Institute, University of Arizona, Tucson, AZ, USA
| | - Jussi T Eronen
- Ecosystems and Environment Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland; Helsinki Institute of Sustainability Science, Faculty of Biological and Environmental Sciences, Ecosystems and Environment Research Programme, University of Helsinki, Helsinki, Finland; BIOS research Unit, Helsinki, Finland
| | - Silvia Pineda-Munoz
- Department of Earth and Atmospheric Sciences, Georgia Institute of Technology, Atlanta, GA, USA
| | | | - Amelia Villaseñor
- Department of Anthropology, University of Arkansas, Fayetteville, AR, USA
| | - W Andrew Barr
- Department of Paleobiology and Evolution of Terrestrial Ecosystems Program, Smithsonian Institution, National Museum of Natural History, Washington, DC , USA; Center for the Advanced Study of Human Paleobiology, Department of Anthropology, The George Washington University, Washington, DC, USA
| | - Anna K Behrensmeyer
- Department of Paleobiology and Evolution of Terrestrial Ecosystems Program, Smithsonian Institution, National Museum of Natural History, Washington, DC , USA
| | - Andrew Du
- Department of Anthropology and Geography, Colorado State University, Fort Collins, CO, USA
| | - J Tyler Faith
- Natural History Museum of Utah, University of Utah, Salt Lake City, UT,USA; Department of Anthropology, University of Utah, Salt Lake City, UT, USA
| | | | - Gary R Graves
- Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, DC, USA; Center for Macroecology, Evolution and Climate, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Advait M Jukar
- Department of Paleobiology and Evolution of Terrestrial Ecosystems Program, Smithsonian Institution, National Museum of Natural History, Washington, DC , USA
| | - Cindy V Looy
- Department of Integrative Biology, Museum of Paleontology, University and Jepson Herbaria, University of California-Berkeley, Berkeley, CA , USA
| | - Joshua H Miller
- Department of Geology, University of Cincinnati, Cincinnati, OH, USA
| | - Richard Potts
- Human Origins Program, National Museum of Natural History, Smithsonian Institution, Washington, DC , USA
| | - S Kathleen Lyons
- School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, NE, USA
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27
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Payne JL, Bachan A, Heim NA, Hull PM, Knope ML. The evolution of complex life and the stabilization of the Earth system. Interface Focus 2020; 10:20190106. [PMID: 32642051 PMCID: PMC7333899 DOI: 10.1098/rsfs.2019.0106] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/25/2020] [Indexed: 11/12/2022] Open
Abstract
The half-billion-year history of animal evolution is characterized by decreasing rates of background extinction. Earth's increasing habitability for animals could result from several processes: (i) a decrease in the intensity of interactions among species that lead to extinctions; (ii) a decrease in the prevalence or intensity of geological triggers such as flood basalt eruptions and bolide impacts; (iii) a decrease in the sensitivity of animals to environmental disturbance; or (iv) an increase in the strength of stabilizing feedbacks within the climate system and biogeochemical cycles. There is no evidence that the prevalence or intensity of interactions among species or geological extinction triggers have decreased over time. There is, however, evidence from palaeontology, geochemistry and comparative physiology that animals have become more resilient to an environmental change and that the evolution of complex life has, on the whole, strengthened stabilizing feedbacks in the climate system. The differential success of certain phyla and classes appears to result, at least in part, from the anatomical solutions to the evolution of macroscopic size that were arrived at largely during Ediacaran and Cambrian time. Larger-bodied animals, enabled by increased anatomical complexity, were increasingly able to mix the marine sediment and water columns, thus promoting stability in biogeochemical cycles. In addition, body plans that also facilitated ecological differentiation have tended to be associated with lower rates of extinction. In this sense, Cambrian solutions to Cambrian problems have had a lasting impact on the trajectory of complex life and, in turn, fundamental properties of the Earth system.
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Affiliation(s)
- Jonathan L. Payne
- Department of Geological Sciences, Stanford University, 450 Serra Mall, Building 320, Stanford, CA 94305, USA
| | - Aviv Bachan
- Department of Geological Sciences, Stanford University, 450 Serra Mall, Building 320, Stanford, CA 94305, USA
| | - Noel A. Heim
- Department of Earth and Ocean Sciences, Tufts University, Medford, MA 02155, USA
| | - Pincelli M. Hull
- Department of Geology and Geophysics, Yale University, 210 Whitney Avenue, New Haven, CT 06511, USA
| | - Matthew L. Knope
- Department of Biology, University of Hawaii-Hilo, 200 West Kawili Street, Hilo, HI 96720, USA
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28
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Kröger B, Penny A. Skeletal marine animal biodiversity is built by families with long macroevolutionary lag times. Nat Ecol Evol 2020; 4:1410-1415. [PMID: 32747774 DOI: 10.1038/s41559-020-1265-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Accepted: 06/26/2020] [Indexed: 11/09/2022]
Abstract
The clade dynamics of marine animals have changed markedly over the Phanerozoic. Long-term diversification is associated with decreasing origination and extinction rates, and with increasing taxon longevity. Here we use the diversification trajectories of skeletal non-colonial marine families to infer the mechanisms that generated these trends. Suggested mechanisms behind these trends include stochastic extinction of taxa with high evolutionary volatility and selection for traits that buffer against extinction. We find an increasing predominance of Phanerozoic families with long lag times between first appearance and peak diversity, over those with 'early burst' diversification trajectories. Long-lag families persisted for longer and had lower evolutionary volatilities, higher genus-level occupancies and genera with larger niche breadths than early burst families. However, they do not preferentially show ecological modes known to protect against extinction. We interpret the rise of the long-lag families as reflecting an intensification of ecosystem-level mechanisms supporting both long-term coexistence and transient dynamics, which increased the capacity of marine ecosystems to accommodate highly diverse communities.
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Affiliation(s)
- Björn Kröger
- Finnish Museum of Natural History, University of Helsinki, Helsinki, Finland.
| | - Amelia Penny
- Finnish Museum of Natural History, University of Helsinki, Helsinki, Finland
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29
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Abstract
AbstractHuman-mediated species invasion and climate change are leading to global extinctions and are predicted to result in the loss of important axes of phylogenetic and functional diversity. However, the long-term robustness of modern communities to invasion is unknown, given the limited timescales over which they can be studied. Using the fossil record of the Paleocene-Eocene thermal maximum (PETM; ∼56 Ma) in North America, we evaluate mammalian community-level response to a rapid global warming event (5°-8°C) and invasion by three Eurasian mammalian orders and by species undergoing northward range shifts. We assembled a database of 144 species body sizes and created a time-scaled composite phylogeny. We calculated the phylogenetic and functional diversity of all communities before, during, and after the PETM. Despite increases in the phylogenetic diversity of the regional species pool, phylogenetic diversity of mammalian communities remained relatively unchanged, a pattern that is invariant to the tree dating method, uncertainty in tree topology, and resolution. Similarly, body size dispersion and the degree of spatial taxonomic turnover of communities remained similar across the PETM. We suggest that invasion by new taxa had little impact on Paleocene-Eocene mammal communities because niches were not saturated. Our findings are consistent with the numerous studies of modern communities that record little change in community-scale richness despite turnover in taxonomic composition during invasion. What remains unknown is whether long-term robustness to biotic and abiotic perturbation are retained by modern communities given global anthropogenic landscape modification.
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30
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Close RA, Benson RBJ, Saupe EE, Clapham ME, Butler RJ. The spatial structure of Phanerozoic marine animal diversity. Science 2020; 368:420-424. [PMID: 32327597 DOI: 10.1126/science.aay8309] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2019] [Accepted: 03/09/2020] [Indexed: 11/02/2022]
Abstract
The global fossil record of marine animals has fueled long-standing debates about diversity change through time and the drivers of this change. However, the fossil record is not truly global. It varies considerably in geographic scope and in the sampling of environments among intervals of geological time. We account for this variability using a spatially explicit approach to quantify regional-scale diversity through the Phanerozoic. Among-region variation in diversity is comparable to variation through time, and much of this is explained by environmental factors, particularly the extent of reefs. By contrast, influential hypotheses of diversity change through time, including sustained long-term increases, have little explanatory power. Modeling the spatial structure of the fossil record transforms interpretations of Phanerozoic diversity patterns and their macroevolutionary explanations. This necessitates a refocus of deep-time diversification studies.
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Affiliation(s)
- R A Close
- School of Geography, Earth and Environmental Sciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK.
| | - R B J Benson
- Department of Earth Sciences, University of Oxford, Oxford OX1 3AN, UK
| | - E E Saupe
- Department of Earth Sciences, University of Oxford, Oxford OX1 3AN, UK
| | - M E Clapham
- Department of Earth and Planetary Sciences, UC Santa Cruz, Santa Cruz, CA 95064, USA
| | - R J Butler
- School of Geography, Earth and Environmental Sciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
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31
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Billaud O, Moen DS, Parsons TL, Morlon H. Estimating Diversity Through Time Using Molecular Phylogenies: Old and Species-Poor Frog Families are the Remnants of a Diverse Past. Syst Biol 2020; 69:363-383. [PMID: 31682272 DOI: 10.1093/sysbio/syz057] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2017] [Revised: 07/08/2019] [Accepted: 08/26/2019] [Indexed: 01/27/2023] Open
Abstract
Estimating how the number of species in a given group varied in the deep past is of key interest to evolutionary biologists. However, current phylogenetic approaches for obtaining such estimates have limitations, such as providing unrealistic diversity estimates at the origin of the group. Here, we develop a robust probabilistic approach for estimating diversity through time curves and uncertainty around these estimates from phylogenetic data. We show with simulations that under various realistic scenarios of diversification, this approach performs better than previously proposed approaches. We also characterize the effect of tree size and undersampling on the performance of the approach. We apply our method to understand patterns of species diversity in anurans (frogs and toads). We find that Archaeobatrachia-a species-poor group of old frog clades often found in temperate regions-formerly had much higher diversity and net diversification rate, but the group declined in diversity as younger, nested clades diversified. This diversity decline seems to be linked to a decline in speciation rate rather than an increase in extinction rate. Our approach, implemented in the R package RPANDA, should be useful for evolutionary biologists interested in understanding how past diversity dynamics have shaped present-day diversity. It could also be useful in other contexts, such as for analyzing clade-clade competitive effects or the effect of species richness on phenotypic divergence.
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Affiliation(s)
- O Billaud
- Institut de Biologie de l'École Normale Supérieure (IBENS), CNRS UMR 8197, INSERM U1024, École Normale Supérieure, Paris Sciences et Lettres (PSL) Research University, F-75005 Paris, France
| | - D S Moen
- Department of Integrative Biology, Oklahoma State University, 517 Life Sciences West, Stillwater, OK 74078, USA
| | - T L Parsons
- Laboratoire de Probabilités, Statistique et Modélisation (LPSM), Sorbonne Université, CNRS UMR 8001, Paris, France
| | - H Morlon
- Institut de Biologie de l'École Normale Supérieure (IBENS), CNRS UMR 8197, INSERM U1024, École Normale Supérieure, Paris Sciences et Lettres (PSL) Research University, F-75005 Paris, France
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32
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Guinot G, Cavin L. Distinct Responses of Elasmobranchs and Ray-Finned Fishes to Long-Term Global Change. Front Ecol Evol 2020. [DOI: 10.3389/fevo.2019.00513] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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33
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Antell GT, Kiessling W, Aberhan M, Saupe EE. Marine Biodiversity and Geographic Distributions Are Independent on Large Scales. Curr Biol 2020; 30:115-121.e5. [PMID: 31839449 DOI: 10.1016/j.cub.2019.10.065] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2019] [Revised: 10/17/2019] [Accepted: 10/30/2019] [Indexed: 02/05/2023]
Abstract
Fundamental ecological and evolutionary theories, such as community saturation and diversity-dependent diversification, assume that biotic competition restricts resource use, and thus limits realized niche breadth and geographic range size [1-3]. This principle is called competitive exclusion. The corollary (ecological release) posits that, after competitors disappear from a region, species that were previously excluded will invade. Hundreds of field experiments have demonstrated ecological release in living populations. However, few of these studies were conducted in marine environments, and almost no work extended beyond 10 years and 1,000 km2 [4, 5]. In limited investigation of marine taxa at larger spatiotemporal scales, macroecologists and paleobiologists have observed little evidence of competitive exclusion [6-9]. Here, we quantified spatial trends in the rich and densely sampled fossil history of brachiopods and bivalves, while accounting for inconsistent sampling coverage through time using a new method of spatial standardization. The number of potential competitors in a region did not explain the geographic distribution of constituent species or genera. Furthermore, although ecological release predicts species to expand after extinction events, survivors of intervals with net species loss expanded as rarely as species in other intervals. Regression model estimates indicated different spatial responses of brachiopods and bivalves, and of habitat specialists and generalists, but no effect from changes in number of potential competitors. Biotic competition may control the distribution of populations, but, on larger spatiotemporal scales, non-competitive factors may have driven biogeographic patterns of brachiopods and bivalves.
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Affiliation(s)
- Gawain T Antell
- Department of Earth Sciences, University of Oxford, Oxford OX1 3AN, UK.
| | - Wolfgang Kiessling
- Section Paleobiology, Friedrich-Alexander Universität Erlangen-Nürnberg, Loewenichstraße 28, Erlangen 91054, Germany
| | - Martin Aberhan
- Museum für Naturkunde, Invalidenstraße 43, Berlin 10115, Germany
| | - Erin E Saupe
- Department of Earth Sciences, University of Oxford, Oxford OX1 3AN, UK.
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34
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Schachat SR, Labandeira CC, Clapham ME, Payne JL. A Cretaceous peak in family-level insect diversity estimated with mark-recapture methodology. Proc Biol Sci 2019; 286:20192054. [PMID: 31847775 PMCID: PMC6939917 DOI: 10.1098/rspb.2019.2054] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2019] [Accepted: 11/22/2019] [Indexed: 12/20/2022] Open
Abstract
The history of insects' taxonomic diversity is poorly understood. The two most common methods for estimating taxonomic diversity in deep time yield conflicting results: the 'range through' method suggests a steady, nearly monotonic increase in family-level diversity, whereas 'shareholder quorum subsampling' suggests a highly volatile taxonomic history with family-level mass extinctions occurring repeatedly, even at the midpoints of geological periods. The only feature shared by these two diversity curves is a steep increase in standing diversity during the Early Cretaceous. This apparent diversification event occurs primarily during the Aptian, the pre-Cenozoic interval with the most described insect occurrences, raising the possibility that this feature of the diversity curves reflects preservation and sampling biases rather than insect evolution and extinction. Here, the capture-mark-recapture (CMR) approach is used to estimate insects' family-level diversity. This method accounts for the incompleteness of the insect fossil record as well as uneven sampling among time intervals. The CMR diversity curve shows extinctions at the Permian/Triassic and Cretaceous/Palaeogene boundaries but does not contain any mass extinctions within geological periods. This curve also includes a steep increase in diversity during the Aptian, which appears not to be an artefact of sampling or preservation bias because this increase still appears when time bins are standardized by the number of occurrences they contain rather than by the amount of time that they span. The Early Cretaceous increase in family-level diversity predates the rise of angiosperms by many millions of years and can be better attributed to the diversification of parasitic and especially parasitoid insect lineages.
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Affiliation(s)
- Sandra R. Schachat
- Department of Geological Sciences, Stanford University, Stanford, CA 94305, USA
| | - Conrad C. Labandeira
- Department of Paleobiology, Smithsonian Institution, Washington, DC 20013, USA
- Department of Entomology, University of Maryland, College Park, MD 20742, USA
- College of Life Sciences, Capital Normal University, Beijing 100048, People’s Republic of China
| | - Matthew E. Clapham
- Department of Earth and Planetary Sciences, University of California, Santa Cruz, CA 95064, USA
| | - Jonathan L. Payne
- Department of Geological Sciences, Stanford University, Stanford, CA 94305, USA
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35
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Reitan T, Liow LH. layeranalyzer: Inferring correlative and causal connections from time series data inr. Methods Ecol Evol 2019. [DOI: 10.1111/2041-210x.13299] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Affiliation(s)
- Trond Reitan
- Department of Biosciences Centre for Ecological and Evolutionary Synthesis University of Oslo Oslo Norway
- Natural History Museum University of Oslo Oslo Norway
| | - Lee Hsiang Liow
- Department of Biosciences Centre for Ecological and Evolutionary Synthesis University of Oslo Oslo Norway
- Natural History Museum University of Oslo Oslo Norway
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36
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Climate cooling and clade competition likely drove the decline of lamniform sharks. Proc Natl Acad Sci U S A 2019; 116:20584-20590. [PMID: 31548392 DOI: 10.1073/pnas.1902693116] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Understanding heterogeneity in species richness between closely related clades is a key research question in ecology and evolutionary biology. Multiple hypotheses have been proposed to interpret such diversity contrasts across the tree of life, with most studies focusing on speciation rates to explain clades' evolutionary radiations, while often neglecting extinction rates. Here we study a notorious biological model as exemplified by the sister relationships between mackerel sharks (Lamniformes, 15 extant species) and ground sharks (Carcharhiniformes, ∼290 extant species). Using a comprehensive fossil dataset, we found that the diversity dynamics of lamniforms waxed and waned following repeated cycles of radiation phases and declining phases. Radiation phases peaked up to 3 times the current diversity in the early Late Cretaceous. In the last 20 million years, the group declined to its present-day diversity. Along with a higher extinction risk for young species, we further show that this declining pattern is likely attributed to a combination of abiotic and biotic factors, with a cooling-driven extinction (negative correlation between temperature and extinction) and clade competition with some ground sharks. Competition from multiple clades successively drove the demise and replacement of mackerel sharks due to a failure to originate facing the rise of ground sharks, particularly since the Eocene. These effects came from ecologically similar carcharhiniform species inhibiting diversification of medium- and large-sized lamniforms. These results imply that the interplay between abiotic and biotic drivers had a substantial role in extinction and speciation, respectively, which determines the sequential rise and decline of marine apex predators.
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37
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Aristide L, Morlon H. Understanding the effect of competition during evolutionary radiations: an integrated model of phenotypic and species diversification. Ecol Lett 2019; 22:2006-2017. [PMID: 31507039 DOI: 10.1111/ele.13385] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Revised: 06/12/2019] [Accepted: 08/19/2019] [Indexed: 02/05/2023]
Abstract
Competition can drive macroevolutionary change, for example during adaptive radiations. However, we still lack a clear understanding of how it shapes diversification processes and patterns. To better understand the macroevolutionary consequences of competition, as well as the signal left on phylogenetic data, we developed a model linking trait evolution and species diversification in an ecological context. We find four main results: first, competition spurs trait diversity but not necessarily species richness; second, competition produces slowdowns in species diversification even in the absence of explicit ecological limits, but not in phenotypic diversification even in the presence of such limits; third, early burst patterns do not provide a reliable way of testing for adaptive radiations; and fourth, looking for phylogenetic signal in trait data and support for phenotypic models incorporating competition is a better alternative. Our results clarify the macroevolutionary consequences of competition and could help design more powerful tests of adaptive radiations in nature.
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Affiliation(s)
- Leandro Aristide
- École Normale Supérieure, Paris Sciences et Lettres (PSL) Research University, Institut de Biologie de l'École Normale Supérieure (IBENS), CNRS, UMR 8197, INSERM U1024, 46 rue d'Ulm, F-75005, Paris, France
| | - Hélène Morlon
- École Normale Supérieure, Paris Sciences et Lettres (PSL) Research University, Institut de Biologie de l'École Normale Supérieure (IBENS), CNRS, UMR 8197, INSERM U1024, 46 rue d'Ulm, F-75005, Paris, France
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38
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Kröger B, Franeck F, Rasmussen CMØ. The evolutionary dynamics of the early Palaeozoic marine biodiversity accumulation. Proc Biol Sci 2019; 286:20191634. [PMID: 31455187 PMCID: PMC6732384 DOI: 10.1098/rspb.2019.1634] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
The early Palaeozoic Era records the initial biodiversification of the Phanerozoic. The increase in biodiversity involved drastic changes in taxon longevity, and in rates of origination and extinction. Here, we calculate these variables in unprecedented temporal resolution. We find that highly volatile origination and extinction rates are associated with short genus longevities during the Cambrian Period. During the Ordovician and Silurian periods, evolutionary rates were less volatile and genera persisted for increasingly longer intervals. The 90%-genus life expectancy doubled from 5 Myr in the late Cambrian to more than 10 Myr in the Ordovician–Silurian periods. Intervals with widespread ecosystem disruption are associated with short genus longevities during the Cambrian and with exceptionally high longevities during the Ordovician and Silurian periods. The post-Cambrian increase in persistence of genera, therefore, indicates an elevated ability of the changing early Palaeozoic marine ecosystems to sustainably maintain existing genera. This is evidence of a new level of ecosystem resilience which evolved during the Ordovician Period.
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Affiliation(s)
- Björn Kröger
- Finnish Museum of Natural History, University of Helsinki, Helsinki, Finland
| | | | - Christian M Ø Rasmussen
- Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark.,Center for Macroecology, Evolution and Climate, University of Copenhagen, Copenhagen, Denmark
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39
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Strotz LC, Simões M, Girard MG, Breitkreuz L, Kimmig J, Lieberman BS. Getting somewhere with the Red Queen: chasing a biologically modern definition of the hypothesis. Biol Lett 2019; 14:rsbl.2017.0734. [PMID: 29720444 DOI: 10.1098/rsbl.2017.0734] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2017] [Accepted: 04/13/2018] [Indexed: 01/24/2023] Open
Abstract
The Red Queen hypothesis (RQH) is both familiar and murky, with a scope and range that has broadened beyond its original focus. Although originally developed in the palaeontological arena, it now encompasses many evolutionary theories that champion biotic interactions as significant mechanisms for evolutionary change. As such it de-emphasizes the important role of abiotic drivers in evolution, even though such a role is frequently posited to be pivotal. Concomitant with this shift in focus, several studies challenged the validity of the RQH and downplayed its propriety. Herein, we examine in detail the assumptions that underpin the RQH in the hopes of furthering conceptual understanding and promoting appropriate application of the hypothesis. We identify issues and inconsistencies with the assumptions of the RQH, and propose a redefinition where the Red Queen's reign is restricted to certain types of biotic interactions and evolutionary patterns occurring at the population level.
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Affiliation(s)
- Luke C Strotz
- Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, KS 66045, USA .,Biodiversity Institute, University of Kansas, Lawrence, KS 66045, USA
| | - Marianna Simões
- Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, KS 66045, USA.,Biodiversity Institute, University of Kansas, Lawrence, KS 66045, USA
| | - Matthew G Girard
- Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, KS 66045, USA.,Biodiversity Institute, University of Kansas, Lawrence, KS 66045, USA
| | - Laura Breitkreuz
- Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, KS 66045, USA.,Biodiversity Institute, University of Kansas, Lawrence, KS 66045, USA
| | - Julien Kimmig
- Biodiversity Institute, University of Kansas, Lawrence, KS 66045, USA
| | - Bruce S Lieberman
- Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, KS 66045, USA.,Biodiversity Institute, University of Kansas, Lawrence, KS 66045, USA
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40
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Edie SM, Huang S, Collins KS, Roy K, Jablonski D. Loss of Biodiversity Dimensions through Shifting Climates and Ancient Mass Extinctions. Integr Comp Biol 2019; 58:1179-1190. [PMID: 30204879 DOI: 10.1093/icb/icy111] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Many aspects of climate affect the deployment of biodiversity in time and space, and so changes in climate might be expected to drive regional and global extinction of both taxa and their ecological functions. Here we examine the association of past climate changes with extinction in marine bivalves, which are increasingly used as a model system for macroecological and macroevolutionary analysis. Focusing on the Cenozoic Era (66 Myr ago to the present), we analyze extinction patterns in shallow-water marine bivalve genera relative to temperature dynamics as estimated from isotopic data in microfossils. When the entire Cenozoic timeseries is considered, extinction intensity is not significantly associated with the mean temperature or the detrended variance in temperature within a given time interval (stratigraphic stage). However, extinction increases significantly with both the rate of temperature change within the stage of extinction and the absolute change in mean temperature from the preceding stage to the stage of extinction. Thus, several extinction events, particularly the extinction pulse near the Pliocene-Pleistocene boundary, do appear to have climatic drivers. Further, the latitudinal diversity gradient today and the Cenozoic history of polar faunas suggest that long-term, regional extinctions associated with cooling removed not just taxa but a variety of ecological functions from high-latitude seas. These dynamics of biodiversity loss contrast with the two mass extinctions bracketing the Mesozoic Era, which had negligible effects on the diversity of ecological functions despite removing nearly as many taxa as the latitudinal gradient does today. Thus, the fossil record raises a key issue: whether the biotic consequences of present-day stresses will more closely resemble the long-term effects of past climate changes or those that cascaded from the mass extinctions.
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Affiliation(s)
- Stewart M Edie
- Department of the Geophysical Sciences, University of Chicago, 5734 South Ellis Avenue, Chicago, IL 60637, USA
| | - Shan Huang
- Senckenberg Biodiversity and Climate Research Center (BiK-F), Senckenberganlage 25, Frankfurt (Main) 60325, Germany
| | - Katie S Collins
- Department of the Geophysical Sciences, University of Chicago, 5734 South Ellis Avenue, Chicago, IL 60637, USA
| | - Kaustuv Roy
- Section of Ecology, Behavior and Evolution, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0116, USA
| | - David Jablonski
- Department of the Geophysical Sciences, University of Chicago, 5734 South Ellis Avenue, Chicago, IL 60637, USA
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41
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Kopperud BT, Lidgard S, Liow LH. Text-mined fossil biodiversity dynamics using machine learning. Proc Biol Sci 2019; 286:20190022. [PMID: 31014224 PMCID: PMC6501925 DOI: 10.1098/rspb.2019.0022] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2019] [Accepted: 04/02/2019] [Indexed: 01/08/2023] Open
Abstract
Documented occurrences of fossil taxa are the empirical foundation for understanding large-scale biodiversity changes and evolutionary dynamics in deep time. The fossil record contains vast amounts of understudied taxa. Yet the compilation of huge volumes of data remains a labour-intensive impediment to a more complete understanding of Earth's biodiversity history. Even so, many occurrence records of species and genera in these taxa can be uncovered in the palaeontological literature. Here, we extract observations of fossils and their inferred ages from unstructured text in books and scientific articles using machine-learning approaches. We use Bryozoa, a group of marine invertebrates with a rich fossil record, as a case study. Building on recent advances in computational linguistics, we develop a pipeline to recognize taxonomic names and geologic time intervals in published literature and use supervised learning to machine-read whether the species in question occurred in a given age interval. Intermediate machine error rates appear comparable to human error rates in a simple trial, and resulting genus richness curves capture the main features of published fossil diversity studies of bryozoans. We believe our automated pipeline, that greatly reduced the time required to compile our dataset, can help others compile similar data for other taxa.
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Affiliation(s)
- Bjørn Tore Kopperud
- Natural History Museum, University of Oslo, PO Box 1172, Blindern, 0318 Oslo, Norway
| | - Scott Lidgard
- Integrative Research Center, Field Museum, 1400 South Lake Shore Drive, Chicago IL, 60605, USA
| | - Lee Hsiang Liow
- Natural History Museum, University of Oslo, PO Box 1172, Blindern, 0318 Oslo, Norway
- Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, PO Box 1066, Blindern, 0316 Oslo, Norway
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42
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Adams NF, Rayfield EJ, Cox PG, Cobb SN, Corfe IJ. Functional tests of the competitive exclusion hypothesis for multituberculate extinction. ROYAL SOCIETY OPEN SCIENCE 2019; 6:181536. [PMID: 31032010 PMCID: PMC6458384 DOI: 10.1098/rsos.181536] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/11/2018] [Accepted: 02/21/2019] [Indexed: 05/08/2023]
Abstract
Multituberculate mammals thrived during the Mesozoic, but their diversity declined from the mid-late Paleocene onwards, becoming extinct in the late Eocene. The radiation of superficially similar, eutherian rodents has been linked to multituberculate extinction through competitive exclusion. However, characteristics providing rodents with a supposed competitive advantage are currently unknown and comparative functional tests between the two groups are lacking. Here, a multifaceted approach to craniomandibular biomechanics was taken to test the hypothesis that superior skull function made rodents more effective competitors. Digital models of the skulls of four extant rodents and the Upper Cretaceous multituberculate Kryptobaatar were constructed and used (i) in finite-element analysis to study feeding-induced stresses, (ii) to calculate metrics of bite force production and (iii) to determine mechanical resistances to bending and torsional forces. Rodents exhibit higher craniomandibular stresses and lower resistances to bending and torsion than the multituberculate, apparently refuting the competitive exclusion hypothesis. However, rodents optimize bite force production at the expense of higher skull stress and we argue that this is likely to have been more functionally and selectively important. Our results therefore provide the first functional lines of evidence for potential reasons behind the decline of multituberculates in the changing environments of the Paleogene.
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Affiliation(s)
- Neil F. Adams
- School of Earth Sciences, University of Bristol, Bristol BS8 1RJ, UK
- Author for correspondence: Neil F. Adams e-mail:
| | - Emily J. Rayfield
- School of Earth Sciences, University of Bristol, Bristol BS8 1RJ, UK
- Author for correspondence: Emily J. Rayfield e-mail:
| | - Philip G. Cox
- Department of Archaeology, University of York, York YO1 7EP, UK
- Centre for Anatomical and Human Sciences, Hull York Medical School, University of York, York YO10 5DD, UK
| | - Samuel N. Cobb
- Department of Archaeology, University of York, York YO1 7EP, UK
- Centre for Anatomical and Human Sciences, Hull York Medical School, University of York, York YO10 5DD, UK
| | - Ian J. Corfe
- Institute of Biotechnology, University of Helsinki, 00014 Helsinki, Finland
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43
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Size, weapons, and armor as predictors of competitive outcomes in fossil and contemporary marine communities. ECOL MONOGR 2019. [DOI: 10.1002/ecm.1354] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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45
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Bastide P, Ané C, Robin S, Mariadassou M. Inference of Adaptive Shifts for Multivariate Correlated Traits. Syst Biol 2018; 67:662-680. [PMID: 29385556 DOI: 10.1093/sysbio/syy005] [Citation(s) in RCA: 52] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2017] [Accepted: 01/23/2018] [Indexed: 11/14/2022] Open
Abstract
To study the evolution of several quantitative traits, the classical phylogenetic comparative framework consists of a multivariate random process running along the branches of a phylogenetic tree. The Ornstein-Uhlenbeck (OU) process is sometimes preferred to the simple Brownian motion (BM) as it models stabilizing selection toward an optimum. The optimum for each trait is likely to be changing over the long periods of time spanned by large modern phylogenies. Our goal is to automatically detect the position of these shifts on a phylogenetic tree, while accounting for correlations between traits, which might exist because of structural or evolutionary constraints. We show that, in the presence of shifts, phylogenetic Principal Component Analysis fails to decorrelate traits efficiently, so that any method aiming at finding shifts needs to deal with correlation simultaneously. We introduce here a simplification of the full multivariate OU model, named scalar OU, which allows for noncausal correlations and is still computationally tractable. We extend the equivalence between the OU and a BM on a rescaled tree to our multivariate framework. We describe an Expectation-Maximization (EM) algorithm that allows for a maximum likelihood estimation of the shift positions, associated with a new model selection criterion, accounting for the identifiability issues for the shift localization on the tree. The method, freely available as an R-package (PhylogeneticEM) is fast, and can deal with missing values. We demonstrate its efficiency and accuracy compared to another state-of-the-art method ($\ell$1ou) on a wide range of simulated scenarios and use this new framework to reanalyze recently gathered data sets on New World Monkeys and Anolis lizards.
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Affiliation(s)
- Paul Bastide
- Unité Mixte de Recherche Mathématiques et Informatique Appliquées (MIA - Paris), AgroParisTech, Institut National de la Recherche Agronomique (INRA), Université Paris-Saclay, 16 rue Claude Bernard, 75005 Paris, France.,Unité de Recherche Mathématiques et Informatique Appliquées du Génome à l'Environnement (MaIAGE), Institut National de la Recherche Agronomique (INRA), Université Paris-Saclay, Domaine de Vilvert, 78352 Jouy-en-Josas, France
| | - Cécile Ané
- Department of Statistics, University of Wisconsin-Madison, 1300 University Avenue, Madison, WI 53706, USA.,Department of Botany, University of Wisconsin-Madison, 430 Lincoln Drive, Madison, WI 53706, USA
| | - Stéphane Robin
- Unité Mixte de Recherche Mathématiques et Informatique Appliquées (MIA - Paris), AgroParisTech, Institut National de la Recherche Agronomique (INRA), Université Paris-Saclay, 16 rue Claude Bernard, 75005 Paris, France
| | - Mahendra Mariadassou
- Unité de Recherche Mathématiques et Informatique Appliquées du Génome à l'Environnement (MaIAGE), Institut National de la Recherche Agronomique (INRA), Université Paris-Saclay, Domaine de Vilvert, 78352 Jouy-en-Josas, France
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46
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Legendre F, Condamine FL. When Darwin's Special Difficulty Promotes Diversification in Insects. Syst Biol 2018; 67:873-887. [PMID: 29481653 DOI: 10.1093/sysbio/syy014] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2017] [Accepted: 02/14/2018] [Indexed: 01/22/2023] Open
Abstract
Eusociality, Darwin's special difficulty, has been widely investigated but remains a topic of great debate in organismal biology. Eusocial species challenge existing theories, and the impact of highly integrated societies on diversification dynamics is controversial with opposing assertions and hypotheses in the literature. Here, using phylogenetic approaches in termites-the first group that has evolved eusociality-we assessed the fundamental prediction that eusocial lineages have higher diversification rates than non-eusocial clades. We found multiple lines of evidence that eusociality provided higher diversification as compared to non-eusociality. This is particularly exacerbated for eusocial species with "true" workers as compared to species with "false" workers. Because most species with "true" workers have an entirely prokaryotic microbiota, the latter feature is also related to higher diversification rates, but it should be investigated further, notably in relation to angiosperm diversification. Overall, this study suggests that societies with "true" workers are not only more successful at ecological timescales but also over millions of years, which further implies that both organism- and species-level traits act on species selection.
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Affiliation(s)
- Frédéric Legendre
- Muséum national d'Histoire naturelle, UMR 7205 Institut de Systématique, Evolution, Biodiversité ISYEB - UMR 7205 - MNHN CNRS UPMC EPHE, Sorbonne Universités, 57 rue Cuvier, 75231 Paris Cedex 05, France
| | - Fabien L Condamine
- CNRS, UMR 5554 Institut des Sciences de l'Evolution (Université de Montpellier), Place Eugène Bataillon, 34095 Montpellier, France
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47
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Lewitus E, Morlon H. Detecting Environment-Dependent Diversification From Phylogenies: A Simulation Study and Some Empirical Illustrations. Syst Biol 2018; 67:576-593. [PMID: 29272547 DOI: 10.1093/sysbio/syx095] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2017] [Accepted: 12/11/2017] [Indexed: 01/30/2023] Open
Abstract
Understanding the relative influence of various abiotic and biotic variables on diversification dynamics is a major goal of macroevolutionary studies. Recently, phylogenetic approaches have been developed that make it possible to estimate the role of various environmental variables on diversification using time-calibrated species trees, paleoenvironmental data, and maximum-likelihood techniques. These approaches have been effectively employed to estimate how speciation and extinction rates vary with key abiotic variables, such as temperature and sea level, and we can anticipate that they will be increasingly used in the future. Here we compile a series of biotic and abiotic paleodatasets that can be used as explanatory variables in these models and use simulations to assess the statistical properties of the approach when applied to these paleodatasets. We demonstrate that environment-dependent models perform well in recovering environment-dependent speciation and extinction parameters, as well as in correctly identifying the simulated environmental model when speciation is environment-dependent. We explore how the strength of the environment-dependency, tree size, missing taxa, and characteristics of the paleoenvironmental curves influence the performance of the models. Finally, using these models, we infer environment-dependent diversification in two empirical phylogenies: temperature-dependence in Cetacea and $\delta^{13}C$-dependence in Ruminantia. We illustrate how to evaluate the relative importance of abiotic and biotic variables in these two clades and interpret these results in light of macroevolutionary hypotheses. Given the important role paleoenvironments are presumed to have played in species evolution, our statistical assessment of how environment-dependent models behave is crucial for their utility in macroevolutionary analysis.
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Affiliation(s)
- Eric Lewitus
- IBENS, Département de Biologie, Ecole Normale Supérieure, CNRS, Inserm, PSL Research University, F-75005 Paris, France
| | - Hélène Morlon
- IBENS, Département de Biologie, Ecole Normale Supérieure, CNRS, Inserm, PSL Research University, F-75005 Paris, France
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48
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Burin G, Alencar LRV, Chang J, Alfaro ME, Quental TB. How Well Can We Estimate Diversity Dynamics for Clades in Diversity Decline? Syst Biol 2018; 68:47-62. [DOI: 10.1093/sysbio/syy037] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2016] [Accepted: 05/09/2018] [Indexed: 01/13/2023] Open
Affiliation(s)
- Gustavo Burin
- Departamento de Ecologia, Instituto de Biociências, Universidade de São Paulo, Rua do Matão, Travessa 14, São Paulo - SP 05508-900, Brazil
| | - Laura R V Alencar
- Departamento de Ecologia, Instituto de Biociências, Universidade de São Paulo, Rua do Matão, Travessa 14, São Paulo - SP 05508-900, Brazil
| | - Jonathan Chang
- Department of Ecology and Evolutionary Biology, University of California, 610 Young Drive South, Los Angeles, CA 90095, USA
| | - Michael E Alfaro
- Department of Ecology and Evolutionary Biology, University of California, 610 Young Drive South, Los Angeles, CA 90095, USA
| | - Tiago B Quental
- Departamento de Ecologia, Instituto de Biociências, Universidade de São Paulo, Rua do Matão, Travessa 14, São Paulo - SP 05508-900, Brazil
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49
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Olivares I, Karger DN, Kessler M. Assessing species saturation: conceptual and methodological challenges. Biol Rev Camb Philos Soc 2018; 93:1874-1890. [PMID: 29733121 DOI: 10.1111/brv.12424] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2017] [Revised: 04/04/2018] [Accepted: 04/10/2018] [Indexed: 11/29/2022]
Abstract
Is there a maximum number of species that can coexist? Intuitively, we assume an upper limit to the number of species in a given assemblage, or that a lineage can produce, but defining and testing this limit has proven problematic. Herein, we first outline seven general challenges of studies on species saturation, most of which are independent of the actual method used to assess saturation. Among these are the challenge of defining saturation conceptually and operationally, the importance of setting an appropriate referential system, and the need to discriminate among patterns, processes and mechanisms. Second, we list and discuss the methodological approaches that have been used to study species saturation. These approaches vary in time and spatial scales, and in the variables and assumptions needed to assess saturation. We argue that assessing species saturation is possible, but that many studies conducted to date have conceptual and methodological flaws that prevent us from currently attaining a good idea of the occurrence of species saturation.
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Affiliation(s)
- Ingrid Olivares
- Department of Systematic and Evolutionary Botany, University of Zurich, Zollikerstrasse 107, 8008 Zurich, Switzerland
| | - Dirk N Karger
- Department of Systematic and Evolutionary Botany, University of Zurich, Zollikerstrasse 107, 8008 Zurich, Switzerland.,Swiss Federal Research Institute WSL, Zürcherstrasse 111, 8903 Birmensdorf, Switzerland
| | - Michael Kessler
- Department of Systematic and Evolutionary Botany, University of Zurich, Zollikerstrasse 107, 8008 Zurich, Switzerland
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50
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Hagen O, Andermann T, Quental TB, Antonelli A, Silvestro D. Estimating Age-Dependent Extinction: Contrasting Evidence from Fossils and Phylogenies. Syst Biol 2018; 67:458-474. [PMID: 29069434 PMCID: PMC5920349 DOI: 10.1093/sysbio/syx082] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2016] [Revised: 03/03/2017] [Accepted: 10/15/2017] [Indexed: 01/12/2023] Open
Abstract
The estimation of diversification rates is one of the most vividly debated topics in modern systematics, with considerable controversy surrounding the power of phylogenetic and fossil-based approaches in estimating extinction. Van Valen's seminal work from 1973 proposed the "Law of constant extinction," which states that the probability of extinction of taxa is not dependent on their age. This assumption of age-independent extinction has prevailed for decades with its assessment based on survivorship curves, which, however, do not directly account for the incompleteness of the fossil record, and have rarely been applied at the species level. Here, we present a Bayesian framework to estimate extinction rates from the fossil record accounting for age-dependent extinction (ADE). Our approach, unlike previous implementations, explicitly models unobserved species and accounts for the effects of fossil preservation on the observed longevity of sampled lineages. We assess the performance and robustness of our method through extensive simulations and apply it to a fossil data set of terrestrial Carnivora spanning the past 40 myr. We find strong evidence of ADE, as we detect the extinction rate to be highest in young species and declining with increasing species age. For comparison, we apply a recently developed analogous ADE model to a dated phylogeny of extant Carnivora. Although the phylogeny-based analysis also infers ADE, it indicates that the extinction rate, instead, increases with increasing taxon age. The estimated mean species longevity also differs substantially, with the fossil-based analyses estimating 2.0 myr, in contrast to 9.8 myr derived from the phylogeny-based inference. Scrutinizing these discrepancies, we find that both fossil and phylogeny-based ADE models are prone to high error rates when speciation and extinction rates increase or decrease through time. However, analyses of simulated and empirical data show that fossil-based inferences are more robust. This study shows that an accurate estimation of ADE from incomplete fossil data is possible when the effects of preservation are jointly modeled, thus allowing for a reassessment of Van Valen's model as a general rule in macroevolution.
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Affiliation(s)
- Oskar Hagen
- Swiss Federal Research Institute WSL, 8903 Birmensdorf, Switzerland
- Landscape Ecology, Institute of Terrestrial Ecosystems, ETH Zurich, 8092 Zurich, Switzerland
- Department of Biological and Environmental Sciences, University of Gothenburg, SE-405 30 Göteborg, Sweden
| | - Tobias Andermann
- Department of Biological and Environmental Sciences, University of Gothenburg, SE-405 30 Göteborg, Sweden
- Gothenburg Global Biodiversity Centre, Box 461, SE-405 30 Göteborg, Sweden
| | - Tiago B Quental
- Departamento de Ecologia, Universidade de São Paulo, 05508-900 São Paulo, Brazil
| | - Alexandre Antonelli
- Department of Biological and Environmental Sciences, University of Gothenburg, SE-405 30 Göteborg, Sweden
- Gothenburg Global Biodiversity Centre, Box 461, SE-405 30 Göteborg, Sweden
- Gothenburg Botanical Garden, Carl Skottsbergs gata 22A, SE-413 19 Göteborg, Sweden
| | - Daniele Silvestro
- Department of Biological and Environmental Sciences, University of Gothenburg, SE-405 30 Göteborg, Sweden
- Gothenburg Global Biodiversity Centre, Box 461, SE-405 30 Göteborg, Sweden
- Department of Computational Biology, University of Lausanne, 1015 Lausanne, Switzerland
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