1
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Didier G, Laurin M. Testing extinction events and temporal shifts in diversification and fossilization rates through the skyline Fossilized Birth-Death (FBD) model: The example of some mid-Permian synapsid extinctions. Cladistics 2024; 40:282-306. [PMID: 38651531 DOI: 10.1111/cla.12577] [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: 12/31/2023] [Revised: 02/23/2024] [Accepted: 03/07/2024] [Indexed: 04/25/2024] Open
Abstract
In the last decade, the Fossilized Birth-Death (FBD) process has yielded interesting clues about the evolution of biodiversity through time. To facilitate such studies, we extend our method to compute the probability density of phylogenetic trees of extant and extinct taxa in which the only temporal information is provided by the fossil ages (i.e. without the divergence times) in order to deal with the piecewise constant FBD process, known as the "skyline FBD", which allows rates to change between pre-defined time intervals, as well as modelling extinction events at the bounds of these intervals. We develop approaches based on this method to assess hypotheses about the diversification process and to answer questions such as "Does a mass extinction occur at this time?" or "Is there a change in the fossilization rate between two given periods?". Our software can also yield Bayesian and maximum-likelihood estimates of the parameters of the skyline FBD model under various constraints. These approaches are applied to a simulated dataset in order to test their ability to answer the questions above. Finally, we study an updated dataset of Permo-Carboniferous synapsids to get additional insights into the dynamics of biodiversity change in three clades (Ophiacodontidae, Edaphosauridae and Sphenacodontidae) in the Pennsylvanian (Late Carboniferous) and Cisuralian (Early Permian), and to assess support for end-Sakmarian (or Artinskian) and end-Cisuralian mass extinction events discussed in previous studies.
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Affiliation(s)
| | - Michel Laurin
- CR2P ("Centre de Recherches sur la Paléobiodiversité et les Paléoenvironnements"; UMR 7207), CNRS/MNHN/UPMC, Sorbonne Université, Muséum National d'Histoire Naturelle, Paris, France
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2
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Tejada JV, Antoine PO, Münch P, Billet G, Hautier L, Delsuc F, Condamine FL. Bayesian Total-Evidence Dating Revisits Sloth Phylogeny and Biogeography: A Cautionary Tale on Morphological Clock Analyses. Syst Biol 2024; 73:125-139. [PMID: 38041854 PMCID: PMC11129595 DOI: 10.1093/sysbio/syad069] [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: 03/22/2023] [Revised: 11/06/2023] [Accepted: 11/14/2023] [Indexed: 12/04/2023] Open
Abstract
Combining morphological and molecular characters through Bayesian total-evidence dating allows inferring the phylogenetic and timescale framework of both extant and fossil taxa, while accounting for the stochasticity and incompleteness of the fossil record. Such an integrative approach is particularly needed when dealing with clades such as sloths (Mammalia: Folivora), for which developmental and biomechanical studies have shown high levels of morphological convergence whereas molecular data can only account for a limited percentage of their total species richness. Here, we propose an alternative hypothesis of sloth evolution that emphasizes the pervasiveness of morphological convergence and the importance of considering the fossil record and an adequate taxon sampling in both phylogenetic and biogeographic inferences. Regardless of different clock models and morphological datasets, the extant sloth Bradypus is consistently recovered as a megatherioid, and Choloepus as a mylodontoid, in agreement with molecular-only analyses. The recently extinct Caribbean sloths (Megalocnoidea) are found to be a monophyletic sister-clade of Megatherioidea, in contrast to previous phylogenetic hypotheses. Our results contradict previous morphological analyses and further support the polyphyly of "Megalonychidae," whose members were found in five different clades. Regardless of taxon sampling and clock models, the Caribbean colonization of sloths is compatible with the exhumation of islands along Aves Ridge and its geological time frame. Overall, our total-evidence analysis illustrates the difficulty of positioning highly incomplete fossils, although a robust phylogenetic framework was recovered by an a posteriori removal of taxa with high percentages of missing characters. Elimination of these taxa improved topological resolution by reducing polytomies and increasing node support. However, it introduced a systematic and geographic bias because most of these incomplete specimens are from northern South America. This is evident in biogeographic reconstructions, which suggest Patagonia as the area of origin of many clades when taxa are underrepresented, but Amazonia and/or Central and Southern Andes when all taxa are included. More generally, our analyses demonstrate the instability of topology and divergence time estimates when using different morphological datasets and clock models and thus caution against making macroevolutionary inferences when node support is weak or when uncertainties in the fossil record are not considered.
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Affiliation(s)
- Julia V Tejada
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, CA 91125, USA
- Institut des Sciences de l’Évolution de Montpellier, UMR 5554, Université de Montpellier, CNRS, IRD, Place Eugène Bataillon, 34095 Montpellier Cedex 5, France
| | - Pierre-Olivier Antoine
- Institut des Sciences de l’Évolution de Montpellier, UMR 5554, Université de Montpellier, CNRS, IRD, Place Eugène Bataillon, 34095 Montpellier Cedex 5, France
| | - Philippe Münch
- Géosciences Montpellier, UMR 5243, Université de Montpellier, CNRS, Université des Antilles, Place Eugène Bataillon, 34095 Montpellier, France
| | - Guillaume Billet
- Centre de Recherche en Paléontologie—Paris, CR2P—UMR 7207, Muséum National d’Histoire Naturelle, CNRS, Sorbonne Université, 8 rue Buffon 75005, Paris
| | - Lionel Hautier
- Institut des Sciences de l’Évolution de Montpellier, UMR 5554, Université de Montpellier, CNRS, IRD, Place Eugène Bataillon, 34095 Montpellier Cedex 5, France
| | - Frédéric Delsuc
- Institut des Sciences de l’Évolution de Montpellier, UMR 5554, Université de Montpellier, CNRS, IRD, Place Eugène Bataillon, 34095 Montpellier Cedex 5, France
| | - Fabien L Condamine
- Institut des Sciences de l’Évolution de Montpellier, UMR 5554, Université de Montpellier, CNRS, IRD, Place Eugène Bataillon, 34095 Montpellier Cedex 5, France
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3
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Poust AW, Barrett PZ, Tomiya S. An early nimravid from California and the rise of hypercarnivorous mammals after the middle Eocene climatic optimum. Biol Lett 2022. [PMCID: PMC9554728 DOI: 10.1098/rsbl.2022.0291] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Carnivoraforms (crown carnivorans and their closest relatives) first occupied hypercarnivorous niches near the dawn of the late Eocene, 40–37 Ma. This followed the decline or extinction of earlier carnivorous groups, Mesonychia and Oxyaenodonta, leaving carnivoraforms and hyaenodontan meat-eaters as high trophic level consumers. The pattern of this change and the relative contributions of the taxonomic groups has hitherto been unclear. We report a new genus and species of the sabretoothed mammalian carnivore family Nimravidae, Pangurban egiae, from the Eocene Pomerado Conglomerate of southern California, with strongly derived hypercarnivorous features. While geochronologically the oldest named nimravid in North America, Pangurban egiae is recovered as phylogenetically derived, with affinities to Hoplophoneus. This provides unequivocal evidence for rapid radiation and spread of nimravid carnivores across Asia and North America and constrains the timing of early divergences within the family. Pangurban egiae narrows the gap between convergent iterations of sabretoothed mammalian carnivores and demonstrates swift diversification of the hypercarnivorous nimravids during a period of global climatic instability. Furthermore, it highlights the top-to-bottom restructuring North American ecosystems underwent during the Eocene–Oligocene transition, resulting in carnivoraforms taking positions as trophic specialists for the first time, a niche they still occupy today.
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Affiliation(s)
- Ashley W. Poust
- Department of Paleontology, San Diego Natural History Museum, San Diego, CA 92101, USA,University of California Museum of Paleontology, Berkeley, CA 94720, USA
| | - Paul Z. Barrett
- Department of Earth Sciences, University of Oregon, Eugene, OR 97403, USA
| | - Susumu Tomiya
- University of California Museum of Paleontology, Berkeley, CA 94720, USA,Center for International Collaboration and Advanced Studies in Primatology, Kyoto University Primate Research Institute, Inuyama, Aichi 484-8506, Japan,Center for the Evolutionary Origins of Human Behavior, Kyoto University, Inuyama, Aichi 484-8506, Japan,Negaunee Integrative Research Center, Field Museum of Natural History, Chicago, IL 60605, USA
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4
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Morlon H, Robin S, Hartig F. Studying speciation and extinction dynamics from phylogenies: addressing identifiability issues. Trends Ecol Evol 2022; 37:497-506. [PMID: 35246322 DOI: 10.1016/j.tree.2022.02.004] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Revised: 12/20/2021] [Accepted: 02/07/2022] [Indexed: 11/18/2022]
Abstract
A lot of what we know about past speciation and extinction dynamics is based on statistically fitting birth-death processes to phylogenies of extant species. Despite their wide use, the reliability of these tools is regularly questioned. It was recently demonstrated that vast 'congruent' sets of alternative diversification histories cannot be distinguished (i.e., are not identifiable) using extant phylogenies alone, reanimating the debate about the limits of phylogenetic diversification analysis. Here, we summarize what we know about the identifiability of the birth-death process and how identifiability issues can be addressed. We conclude that extant phylogenies, when combined with appropriate prior hypotheses and regularization techniques, can still tell us a lot about past diversification dynamics.
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Affiliation(s)
- Hélène Morlon
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, CNRS, INSERM, PSL Research University, Paris, France.
| | - Stéphane Robin
- UMR MIA-Paris, AgroParisTech, INRA, Paris-Saclay University, 75005 Paris, France; Centre d'Ecologie et des Sciences de la Conservation (CESCO), Muséum National d'Histoire Naturelle, CNRS, Sorbonne University, Paris, France
| | - Florian Hartig
- Theoretical Ecology, University of Regensburg, Regensburg, Germany
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5
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Didier G, Laurin M. Distributions of extinction times from fossil ages and tree topologies: the example of mid-Permian synapsid extinctions. PeerJ 2021; 9:e12577. [PMID: 34966586 PMCID: PMC8667717 DOI: 10.7717/peerj.12577] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Accepted: 11/09/2021] [Indexed: 11/20/2022] Open
Abstract
Given a phylogenetic tree that includes only extinct, or a mix of extinct and extant taxa, where at least some fossil data are available, we present a method to compute the distribution of the extinction time of a given set of taxa under the Fossilized-Birth-Death model. Our approach differs from the previous ones in that it takes into account (i) the possibility that the taxa or the clade considered may diversify before going extinct and (ii) the whole phylogenetic tree to estimate extinction times, whilst previous methods do not consider the diversification process and deal with each branch independently. Because of this, our method can estimate extinction times of lineages represented by a single fossil, provided that they belong to a clade that includes other fossil occurrences. We assess and compare our new approach with a standard previous one using simulated data. Results show that our method provides more accurate confidence intervals. This new approach is applied to the study of the extinction time of three Permo-Carboniferous synapsid taxa (Ophiacodontidae, Edaphosauridae, and Sphenacodontidae) that are thought to have disappeared toward the end of the Cisuralian (early Permian), or possibly shortly thereafter. The timing of extinctions of these three taxa and of their component lineages supports the idea that the biological crisis in the late Kungurian/early Roadian consisted of a progressive decline in biodiversity throughout the Kungurian.
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Affiliation(s)
| | - Michel Laurin
- CNRS/MNHN/UPMC, Sorbonne Université, Muséum National d’Histoire Naturelle, CR2P (“Centre de Recherches sur la Paléobiodiversité et les Paléoenvironnements” UMR 7207), Paris, France
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6
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Welt RS, Raxworthy CJ. Dispersal, not vicariance, explains the biogeographic origin of iguanas on Madagascar. Mol Phylogenet Evol 2021; 167:107345. [PMID: 34748875 DOI: 10.1016/j.ympev.2021.107345] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Revised: 09/23/2021] [Accepted: 11/02/2021] [Indexed: 11/19/2022]
Abstract
Lizards of the clade Iguanidae (sensu lato) are primarily a New World group. Thus, the remarkable presence of an endemic lineage of iguanas (family Opluridae) on the isolated Indian Ocean island of Madagascar has long been considered a biogeographic anomaly. Previous work attributed this disjunct extant distribution to: (1) vicariance at about 140-165 Ma, caused by the breakup of Gondwana and the separation of South America, Africa, and Madagascar (with subsequent extinction of iguanas on Africa, and potentially other Gondwanan landmasses), (2) vicariance at about 80-90 Ma, caused by the sundering of hypothesized land-bridge connections between South America, Antarctica, India, and Madagascar, or (3) long-distance overwater dispersal from South America to Madagascar. Each hypothesis has been supported with molecular divergence dating analyses, and thus the biogeographic origin of the Opluridae is not yet well resolved. Here we utilize genetic sequences of ultraconserved elements for all Iguania families and the majority of Iguanidae (s.l.) genera, and morphological data for extant and fossil taxa (used for divergence dating analyses), to produce the most comprehensive dataset applied to date to test these origin hypotheses. We find strong support for a sister relationship between the Opluridae (Madagascar) and Leiosauridae (South America). Divergence of the Opluridae from Leiosauridae is dated to between the late Cretaceous and mid-Paleogene, at a time when Madagascar was already an island and was isolated from all other Gondwanan landmasses. Consequently, our results support a hypothesis of long-distance overwater dispersal of the Opluridae lineage, either directly from South America to Madagascar or potentially via Antarctica or Africa, leading to this radiation of iguanas in the Indian Ocean.
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Affiliation(s)
- Rachel S Welt
- Department of Herpetology, American Museum of Natural History, USA.
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7
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Barrett PZ. The largest hoplophonine and a complex new hypothesis of nimravid evolution. Sci Rep 2021; 11:21078. [PMID: 34702935 PMCID: PMC8548586 DOI: 10.1038/s41598-021-00521-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Accepted: 10/11/2021] [Indexed: 11/24/2022] Open
Abstract
Nimravids were the first carnivorans to evolve saberteeth, but previously portrayed as having a narrow evolutionary trajectory of increasing degrees of sabertooth specialization. Here I present a novel hypothesis about the evolution of this group, including a description of Eusmilus adelos, the largest known hoplophonine, which forces a re-evaluation of not only their relationships, but perceived paleoecology. Using a tip-dated Bayesian analysis with sophisticated evolutionary models, nimravids can now be viewed as following two paths of evolution: one led to numerous early dirk-tooth forms, including E. adelos, while the other converged on living feline morphology, tens of millions of years before its appearance in felids.
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8
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Silvestro D, Bacon CD, Ding W, Zhang Q, Donoghue PCJ, Antonelli A, Xing Y. Fossil data support a pre-Cretaceous origin of flowering plants. Nat Ecol Evol 2021; 5:449-457. [PMID: 33510432 DOI: 10.1038/s41559-020-01387-8] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Accepted: 12/17/2020] [Indexed: 01/30/2023]
Abstract
Flowering plants (angiosperms) are the most diverse of all land plants, becoming abundant in the Cretaceous and achieving dominance in the Cenozoic. However, the exact timing of their origin remains a controversial topic, with molecular clocks generally placing their origin much further back in time than the oldest unequivocal fossils. To resolve this discrepancy, we developed a Bayesian method to estimate the ages of angiosperm families on the basis of the fossil record (a newly compiled dataset of ~15,000 occurrences in 198 families) and their living diversity. Our results indicate that several families originated in the Jurassic, strongly rejecting a Cretaceous origin for the group. We report a marked increase in lineage accumulation from 125 to 72 million years ago, supporting Darwin's hypothesis of a rapid Cretaceous angiosperm diversification. Our results demonstrate that a pre-Cretaceous origin of angiosperms is supported not only by molecular clock approaches but also by analyses of the fossil record that explicitly correct for incomplete sampling.
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Affiliation(s)
- Daniele Silvestro
- Department of Biology, University of Fribourg, Fribourg, Switzerland.
- Swiss Institute of Bioinformatics, Fribourg, Switzerland.
- Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden.
- Gothenburg Global Biodiversity Centre, Gothenburg, Sweden.
| | - Christine D Bacon
- Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden
- Gothenburg Global Biodiversity Centre, Gothenburg, Sweden
| | - Wenna Ding
- CAS Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla, China
| | - Qiuyue Zhang
- Department of Biology, University of Fribourg, Fribourg, Switzerland
- CAS Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla, China
- Department of Computational Biology, University of Lausanne, Lausanne, Switzerland
| | | | - Alexandre Antonelli
- Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden
- Gothenburg Global Biodiversity Centre, Gothenburg, Sweden
- Royal Botanic Gardens, Kew, Richmond, UK
- Department of Plant Sciences, University of Oxford, Oxford, UK
| | - Yaowu Xing
- CAS Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla, China
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9
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Guindon S. Rates and Rocks: Strengths and Weaknesses of Molecular Dating Methods. Front Genet 2020; 11:526. [PMID: 32536940 PMCID: PMC7267027 DOI: 10.3389/fgene.2020.00526] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2019] [Accepted: 04/30/2020] [Indexed: 12/19/2022] Open
Abstract
I present here an in-depth, although non-exhaustive, review of two topics in molecular dating. Clock models, which describe the evolution of the rate of evolution, are considered first. Some of the shortcomings of popular approaches-uncorrelated clock models in particular-are presented and discussed. Autocorrelated models are shown to be more reasonable from a biological perspective. Some of the most recent autocorrelated models also rely on a coherent treatment of instantaneous and average substitution rates while previous models are based on implicit approximations. Second, I provide a brief overview of the processes involved in collecting and preparing fossil data. I then review the main techniques that use this data for calibrating the molecular clock. I argue that, in its current form, the fossilized birth-death process relies on assumptions about the mechanisms underlying fossilization and the data collection process that may negatively impact the date estimates. Node-dating approaches make better use of the data available, even though they rest on paleontologists' intervention to prepare raw fossil data. Altogether, this study provides indications that may help practitioners in selecting appropriate methods for molecular dating. It will also hopefully participate in defining the contour of future methodological developments in the field.
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Affiliation(s)
- Stéphane Guindon
- Laboratoire d'Informatique de Robotique et de Microélectronique de Montpellier, CNRS and Université Montpellier (UMR 5506), Montpellier, France
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10
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Didier G, Laurin M. Exact Distribution of Divergence Times from Fossil Ages and Tree Topologies. Syst Biol 2020; 69:1068-1087. [DOI: 10.1093/sysbio/syaa021] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2018] [Revised: 01/15/2020] [Accepted: 02/27/2020] [Indexed: 12/22/2022] Open
Abstract
Abstract
Being given a phylogenetic tree of both extant and extinct taxa in which the fossil ages are the only temporal information (namely, in which divergence times are considered unknown), we provide a method to compute the exact probability distribution of any divergence time of the tree with regard to any speciation (cladogenesis), extinction, and fossilization rates under the Fossilized Birth–Death model. We use this new method to obtain a probability distribution for the age of Amniota (the synapsid/sauropsid or bird/mammal divergence), one of the most-frequently used dating constraints. Our results suggest an older age (between about 322 and 340 Ma) than has been assumed by most studies that have used this constraint (which typically assumed a best estimate around 310–315 Ma) and provide, for the first time, a method to compute the shape of the probability density for this divergence time. [Divergence times; fossil ages; fossilized birth–death model; probability distribution.]
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Affiliation(s)
| | - Michel Laurin
- CR2P (“Centre de Recherches de Paléontologie – Paris; UMR 7207), CNRS/MNHN/Sorbonne Université, Muséum National d’Histoire Naturelle, Paris, France
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11
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Šmíd J, Tolley KA. Calibrating the tree of vipers under the fossilized birth-death model. Sci Rep 2019; 9:5510. [PMID: 30940820 PMCID: PMC6445296 DOI: 10.1038/s41598-019-41290-2] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2018] [Accepted: 02/15/2019] [Indexed: 11/09/2022] Open
Abstract
Scaling evolutionary trees to time is essential for understanding the origins of clades. Recently developed methods allow including the entire fossil record known for the group of interest and eliminated the need for specifying prior distributions for node ages. Here we apply the fossilized birth-death (FBD) approach to reconstruct the diversification timeline of the viperines (subfamily Viperinae). Viperinae are an Old World snake subfamily comprising 102 species from 13 genera. The fossil record of vipers is fairly rich and well assignable to clades due to the unique vertebral and fang morphology. We use an unprecedented sampling of 83 modern species and 13 genetic markers in combination with 197 fossils representing 28 extinct taxa to reconstruct a time-calibrated phylogeny of the Viperinae. Our results suggest a late Eocene-early Oligocene origin with several diversification events following soon after the group's establishment. The age estimates inferred with the FBD model correspond to those from previous studies that were based on node dating but FBD provides notably narrower credible intervals around the node ages. Viperines comprise two African and an Eurasian clade, but the ancestral origin of the subfamily is ambiguous. The most parsimonious scenarios require two transoceanic dispersals over the Tethys Sea during the Oligocene.
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Affiliation(s)
- Jiří Šmíd
- South African National Biodiversity Institute, Kirstenbosch Research Centre, Cape Town, South Africa. .,Department of Botany and Zoology, University of Stellenbosch, Stellenbosch, Private Bag X1, South Africa. .,Department of Zoology, National Museum, Cirkusová, 1740, Prague, Czech Republic. .,Department of Zoology, Faculty of Science, Charles University in Prague, Viničná 7, Prague, Czech Republic.
| | - Krystal A Tolley
- South African National Biodiversity Institute, Kirstenbosch Research Centre, Cape Town, South Africa.,Centre for Ecological Genomics and Wildlife Conservation, Department of Zoology, University of Johannesburg, Auckland Park, 2000, Johannesburg, South Africa
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12
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Mitchell JS, Etienne RS, Rabosky DL. Inferring Diversification Rate Variation From Phylogenies With Fossils. Syst Biol 2018; 68:1-18. [PMID: 29788398 DOI: 10.1093/sysbio/syy035] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2017] [Accepted: 05/09/2018] [Indexed: 12/18/2022] Open
Abstract
Time-calibrated phylogenies of living species have been widely used to study the tempo and mode of species diversification. However, it is increasingly clear that inferences about species diversification-extinction rates in particular-can be unreliable in the absence of paleontological data. We introduce a general framework based on the fossilized birth-death process for studying speciation-extinction dynamics on phylogenies of extant and extinct species. The model assumes that phylogenies can be modeled as a mixture of distinct evolutionary rate regimes and that a hierarchical Poisson process governs the number of such rate regimes across a tree. We implemented the model in BAMM, a computational framework that uses reversible jump Markov chain Monte Carlo to simulate a posterior distribution of macroevolutionary rate regimes conditional on the branching times and topology of a phylogeny. The implementation, we describe can be applied to paleontological phylogenies, neontological phylogenies, and to phylogenies that include both extant and extinct taxa. We evaluate performance of the model on data sets simulated under a range of diversification scenarios. We find that speciation rates are reliably inferred in the absence of paleontological data. However, the inclusion of fossil observations substantially increases the accuracy of extinction rate estimates. We demonstrate that inferences are relatively robust to at least some violations of model assumptions, including heterogeneity in preservation rates and misspecification of the number of occurrences in paleontological data sets.
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Affiliation(s)
- Jonathan S Mitchell
- Museum of Zoology and Department of Ecology and Evolutionary Biology, University of Michigan, 1105 North University Avenue, Ann Arbor, Michigan 48109 USA
- Department of Biology, West Virginia University Institute of Technology, 410 Neville Street, Beckley, WV 25801, USA
| | - Rampal S Etienne
- Groningen Institute for Evolutionary Life Sciences, University of Groningen, Box 11103, 9700 CC Groningen, The Netherlands
| | - Daniel L Rabosky
- Museum of Zoology and Department of Ecology and Evolutionary Biology, University of Michigan, 1105 North University Avenue, Ann Arbor, Michigan 48109 USA
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13
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Guindon S. Accounting for Calibration Uncertainty: Bayesian Molecular Dating as a "Doubly Intractable" Problem. Syst Biol 2018; 67:651-661. [PMID: 29385558 DOI: 10.1093/sysbio/syy003] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2017] [Accepted: 01/23/2018] [Indexed: 11/13/2022] Open
Abstract
This study introduces a new Bayesian technique for molecular dating that explicitly accommodates for uncertainty in the phylogenetic position of calibrated nodes derived from the analysis of fossil data. The proposed approach thus defines an adequate framework for incorporating expert knowledge and/or prior information about the way fossils were collected in the inference of node ages. Although it belongs to the class of "node-dating" approaches, this method shares interesting properties with "tip-dating" techniques. Yet, it alleviates some of the computational and modeling difficulties that hamper tip-dating approaches. The influence of fossil data on the probabilistic distribution of trees is the crux of the matter considered here. More specifically, among all the phylogenies that a tree model (e.g., the birth-death process) generates, only a fraction of them "agree" with the fossil data. Bayesian inference under the new model requires taking this fraction into account. However, evaluating this quantity is difficult in practice. A generic solution to this issue is presented here. The proposed approach relies on a recent statistical technique, the so-called exchange algorithm, dedicated to drawing samples from "doubly intractable" distributions. A small example illustrates the problem of interest and the impact of uncertainty in the placement of calibration constraints in the phylogeny given fossil data. An analysis of land plant sequences and multiple fossils further highlights the pertinence of the proposed approach.
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Affiliation(s)
- Stéphane Guindon
- Laboratoire d'Informatique, de Robotique et de Microélectronique de Montpellier, UMR 5506, CNRS, Université de Montpellier, Montpellier, France
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14
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Alignment-based and alignment-free methods converge with experimental data on amino acids coded by stop codons at split between nuclear and mitochondrial genetic codes. Biosystems 2018; 167:33-46. [DOI: 10.1016/j.biosystems.2018.03.002] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2018] [Revised: 03/18/2018] [Accepted: 03/19/2018] [Indexed: 12/11/2022]
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15
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Stadler T, Gavryushkina A, Warnock RCM, Drummond AJ, Heath TA. The fossilized birth-death model for the analysis of stratigraphic range data under different speciation modes. J Theor Biol 2018; 447:41-55. [PMID: 29550451 PMCID: PMC5931795 DOI: 10.1016/j.jtbi.2018.03.005] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2017] [Revised: 09/15/2017] [Accepted: 03/05/2018] [Indexed: 10/26/2022]
Abstract
A birth-death-sampling model gives rise to phylogenetic trees with samples from the past and the present. Interpreting "birth" as branching speciation, "death" as extinction, and "sampling" as fossil preservation and recovery, this model - also referred to as the fossilized birth-death (FBD) model - gives rise to phylogenetic trees on extant and fossil samples. The model has been mathematically analyzed and successfully applied to a range of datasets on different taxonomic levels, such as penguins, plants, and insects. However, the current mathematical treatment of this model does not allow for a group of temporally distinct fossil specimens to be assigned to the same species. In this paper, we provide a general mathematical FBD modeling framework that explicitly takes "stratigraphic ranges" into account, with a stratigraphic range being defined as the lineage interval associated with a single species, ranging through time from the first to the last fossil appearance of the species. To assign a sequence of fossil samples in the phylogenetic tree to the same species, i.e., to specify a stratigraphic range, we need to define the mode of speciation. We provide expressions to account for three common speciation modes: budding (or asymmetric) speciation, bifurcating (or symmetric) speciation, and anagenetic speciation. Our equations allow for flexible joint Bayesian analysis of paleontological and neontological data. Furthermore, our framework is directly applicable to epidemiology, where a stratigraphic range is the observed duration of infection of a single patient, "birth" via budding is transmission, "death" is recovery, and "sampling" is sequencing the pathogen of a patient. Thus, we present a model that allows for incorporation of multiple observations through time from a single patient.
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Affiliation(s)
- Tanja Stadler
- Department of Biosystems Science & Engineering, Eidgenössische Technische Hochschule Zürich, Basel 4058, Switzerland; Swiss Institute of Bioinformatics (SIB), Switzerland.
| | - Alexandra Gavryushkina
- Department of Biosystems Science & Engineering, Eidgenössische Technische Hochschule Zürich, Basel 4058, Switzerland; Swiss Institute of Bioinformatics (SIB), Switzerland
| | - Rachel C M Warnock
- Department of Biosystems Science & Engineering, Eidgenössische Technische Hochschule Zürich, Basel 4058, Switzerland; Swiss Institute of Bioinformatics (SIB), Switzerland
| | - Alexei J Drummond
- Department of Computer Science, Centre for Computational Evolution, University of Auckland, Auckland 1010, New Zealand
| | - Tracy A Heath
- Department of Ecology, Evolution, & Organismal Biology, Iowa State University, Ames, Iowa 50011, USA
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16
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Stadler T, Smrckova J. Estimating shifts in diversification rates based on higher-level phylogenies. Biol Lett 2017; 12:rsbl.2016.0273. [PMID: 27703054 PMCID: PMC5095187 DOI: 10.1098/rsbl.2016.0273] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2016] [Accepted: 09/09/2016] [Indexed: 11/27/2022] Open
Abstract
Macroevolutionary studies recently shifted from only reconstructing the past state, i.e. the species phylogeny, to also infer the past speciation and extinction dynamics that gave rise to the phylogeny. Methods for estimating diversification dynamics are sensitive towards incomplete species sampling. We introduce a method to estimate time-dependent diversification rates from phylogenies where clades of a particular age are represented by only one sampled species. A popular example of this type of data is phylogenies on the genus- or family-level, i.e. phylogenies where one species per genus or family is included. We conduct a simulation study to validate our method in a maximum-likelihood framework. Further, this method has already been introduced into the Bayesian package MrBayes, which led to new insights into the evolution of Hymenoptera.
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Affiliation(s)
- Tanja Stadler
- Department of Biosystems Science and Engineering, ETH Zürich, 4058 Basel, Switzerland Swiss Institute of Bioinformatics (SIB), 1015 Lausanne, Switzerland
| | - Jana Smrckova
- Department of Zoology, Faculty of Science, University of South Bohemia, 37005 Ceske Budejovice, Czech Republic
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17
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Rabosky DL, Mitchell JS, Chang J. Is BAMM Flawed? Theoretical and Practical Concerns in the Analysis of Multi-Rate Diversification Models. Syst Biol 2017; 66:477-498. [PMID: 28334223 PMCID: PMC5790138 DOI: 10.1093/sysbio/syx037] [Citation(s) in RCA: 152] [Impact Index Per Article: 21.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2016] [Revised: 02/13/2017] [Accepted: 02/14/2017] [Indexed: 11/13/2022] Open
Abstract
Bayesian analysis of macroevolutionary mixtures (BAMM) is a statistical framework that uses reversible jump Markov chain Monte Carlo to infer complex macroevolutionary dynamics of diversification and phenotypic evolution on phylogenetic trees. A recent article by Moore et al. (MEA) reported a number of theoretical and practical concerns with BAMM. Major claims from MEA are that (i) BAMM's likelihood function is incorrect, because it does not account for unobserved rate shifts; (ii) the posterior distribution on the number of rate shifts is overly sensitive to the prior; and (iii) diversification rate estimates from BAMM are unreliable. Here, we show that these and other conclusions from MEA are generally incorrect or unjustified. We first demonstrate that MEA's numerical assessment of the BAMM likelihood is compromised by their use of an invalid likelihood function. We then show that "unobserved rate shifts" appear to be irrelevant for biologically plausible parameterizations of the diversification process. We find that the purportedly extreme prior sensitivity reported by MEA cannot be replicated with standard usage of BAMM v2.5, or with any other version when conventional Bayesian model selection is performed. Finally, we demonstrate that BAMM performs very well at estimating diversification rate variation across the ${\sim}$20% of simulated trees in MEA's data set for which it is theoretically possible to infer rate shifts with confidence. Due to ascertainment bias, the remaining 80% of their purportedly variable-rate phylogenies are statistically indistinguishable from those produced by a constant-rate birth-death process and were thus poorly suited for the summary statistics used in their performance assessment. We demonstrate that inferences about diversification rates have been accurate and consistent across all major previous releases of the BAMM software. We recognize an acute need to address the theoretical foundations of rate-shift models for phylogenetic trees, and we expect BAMM and other modeling frameworks to improve in response to mathematical and computational innovations. However, we remain optimistic that that the imperfect tools currently available to comparative biologists have provided and will continue to provide important insights into the diversification of life on Earth.
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Affiliation(s)
- Daniel L. Rabosky
- Department of Ecology and Evolutionary Biology and Museum of Zoology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Jonathan S. Mitchell
- Department of Ecology and Evolutionary Biology and Museum of Zoology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Jonathan Chang
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA 90095, USA
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18
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Álvarez A, Arévalo RLM, Verzi DH. Diversification patterns and size evolution in caviomorph rodents. Biol J Linn Soc Lond 2017. [DOI: 10.1093/biolinnean/blx026] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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19
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Gavryushkina A, Heath TA, Ksepka DT, Stadler T, Welch D, Drummond AJ. Bayesian Total-Evidence Dating Reveals the Recent Crown Radiation of Penguins. Syst Biol 2017; 66:57-73. [PMID: 28173531 PMCID: PMC5410945 DOI: 10.1093/sysbio/syw060] [Citation(s) in RCA: 89] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2015] [Revised: 06/08/2016] [Accepted: 06/09/2016] [Indexed: 01/08/2023] Open
Abstract
The total-evidence approach to divergence time dating uses molecular and morphological data from extant and fossil species to infer phylogenetic relationships, species divergence times, and macroevolutionary parameters in a single coherent framework. Current model-based implementations of this approach lack an appropriate model for the tree describing the diversification and fossilization process and can produce estimates that lead to erroneous conclusions. We address this shortcoming by providing a total-evidence method implemented in a Bayesian framework. This approach uses a mechanistic tree prior to describe the underlying diversification process that generated the tree of extant and fossil taxa. Previous attempts to apply the total-evidence approach have used tree priors that do not account for the possibility that fossil samples may be direct ancestors of other samples, that is, ancestors of fossil or extant species or of clades. The fossilized birth–death (FBD) process explicitly models the diversification, fossilization, and sampling processes and naturally allows for sampled ancestors. This model was recently applied to estimate divergence times based on molecular data and fossil occurrence dates. We incorporate the FBD model and a model of morphological trait evolution into a Bayesian total-evidence approach to dating species phylogenies. We apply this method to extant and fossil penguins and show that the modern penguins radiated much more recently than has been previously estimated, with the basal divergence in the crown clade occurring at ∼12.7 ∼12.7 Ma and most splits leading to extant species occurring in the last 2 myr. Our results demonstrate that including stem-fossil diversity can greatly improve the estimates of the divergence times of crown taxa. The method is available in BEAST2 (version 2.4) software www.beast2.org with packages SA (version at least 1.1.4) and morph-models (version at least 1.0.4) installed.
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Affiliation(s)
- Alexandra Gavryushkina
- Centre for Computational Evolution, University of Auckland, Auckland, New Zealand
- Department of Computer Science, University of Auckland, Auckland 1010, New Zealand
| | - Tracy A. Heath
- Department of Ecology, Evolution, & Organismal Biology, Iowa State University, Ames, IA 50011, USA
| | | | - Tanja Stadler
- Department of Biosystems Science & Engineering, Eidgenössische Technische Hochschule Zürich, 4058 Basel, Switzerland
| | - David Welch
- Centre for Computational Evolution, University of Auckland, Auckland, New Zealand
- Department of Computer Science, University of Auckland, Auckland 1010, New Zealand
| | - Alexei J. Drummond
- Centre for Computational Evolution, University of Auckland, Auckland, New Zealand
- Department of Computer Science, University of Auckland, Auckland 1010, New Zealand
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20
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Sakamoto M, Venditti C, Benton MJ. ‘Residual diversity estimates’ do not correct for sampling bias in palaeodiversity data. Methods Ecol Evol 2016. [DOI: 10.1111/2041-210x.12666] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Manabu Sakamoto
- School of Biological Sciences University of Reading Reading RG6 6AJ UK
| | - Chris Venditti
- School of Biological Sciences University of Reading Reading RG6 6AJ UK
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21
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Bernardi M, Angielczyk KD, Mitchell JS, Ruta M. Phylogenetic Stability, Tree Shape, and Character Compatibility: A Case Study Using Early Tetrapods. Syst Biol 2016; 65:737-58. [PMID: 27288479 DOI: 10.1093/sysbio/syw049] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2014] [Accepted: 05/19/2016] [Indexed: 11/13/2022] Open
Abstract
Phylogenetic tree shape varies as the evolutionary processes affecting a clade change over time. In this study, we examined an empirical phylogeny of fossil tetrapods during several time intervals, and studied how temporal constraints manifested in patterns of tree imbalance and character change. The results indicate that the impact of temporal constraints on tree shape is minimal and highlights the stability through time of the reference tetrapod phylogeny. Unexpected values of imbalance for Mississippian and Pennsylvanian time slices strongly support the hypothesis that the Carboniferous was a period of explosive tetrapod radiation. Several significant diversification shifts take place in the Mississippian and underpin increased terrestrialization among the earliest limbed vertebrates. Character incompatibility is relatively high at the beginning of tetrapod history, but quickly decreases to a relatively stable lower level, relative to a null distribution based on constant rates of character change. This implies that basal tetrapods had high, but declining, rates of homoplasy early in their evolutionary history, although the origin of Lissamphibia is an exception to this trend. The time slice approach is a powerful method of phylogenetic analysis and a useful tool for assessing the impact of combining extinct and extant taxa in phylogenetic analyses of large and speciose clades.
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Affiliation(s)
- Massimo Bernardi
- MUSE-Museo delle Scienze, Corso del Lavoro e della Scienza, 3, 38122 Trento, Italy; School of Earth Sciences, University of Bristol, Wills Memorial Building, Queens Road, Bristol BS8 1RJ, UK;
| | - Kenneth D Angielczyk
- Integrative Research Center, Field Museum of Natural History, 1400 South Lake Shore Drive, Chicago, IL 60605-2496, USA
| | - Jonathan S Mitchell
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48103, USA; and
| | - Marcello Ruta
- School of Life Sciences, Joseph Banks Laboratories, University of Lincoln, Green Lane, Lincoln LN6 7DL, UK
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22
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Sanmartín I, Meseguer AS. Extinction in Phylogenetics and Biogeography: From Timetrees to Patterns of Biotic Assemblage. Front Genet 2016; 7:35. [PMID: 27047538 PMCID: PMC4802293 DOI: 10.3389/fgene.2016.00035] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2015] [Accepted: 02/29/2016] [Indexed: 01/03/2023] Open
Abstract
Global climate change and its impact on biodiversity levels have made extinction a relevant topic in biological research. Yet, until recently, extinction has received less attention in macroevolutionary studies than speciation; the reason is the difficulty to infer an event that actually eliminates rather than creates new taxa. For example, in biogeography, extinction has often been seen as noise, introducing homoplasy in biogeographic relationships, rather than a pattern-generating process. The molecular revolution and the possibility to integrate time into phylogenetic reconstructions have allowed studying extinction under different perspectives. Here, we review phylogenetic (temporal) and biogeographic (spatial) approaches to the inference of extinction and the challenges this process poses for reconstructing evolutionary history. Specifically, we focus on the problem of discriminating between alternative high extinction scenarios using time trees with only extant taxa, and on the confounding effect introduced by asymmetric spatial extinction – different rates of extinction across areas – in biogeographic inference. Finally, we identify the most promising avenues of research in both fields, which include the integration of additional sources of evidence such as the fossil record or environmental information in birth–death models and biogeographic reconstructions, the development of new models that tie extinction rates to phenotypic or environmental variation, or the implementation within a Bayesian framework of parametric non-stationary biogeographic models.
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Affiliation(s)
| | - Andrea S Meseguer
- INRA, UMR 1062, Centre de Biologie pour la Gestion des Populations - INRA- IRD-CIRAD-Montpellier SupAgro Montferrier-sur-Lez, France
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23
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Zhang C, Stadler T, Klopfstein S, Heath TA, Ronquist F. Total-Evidence Dating under the Fossilized Birth-Death Process. Syst Biol 2016; 65:228-49. [PMID: 26493827 PMCID: PMC4748749 DOI: 10.1093/sysbio/syv080] [Citation(s) in RCA: 198] [Impact Index Per Article: 24.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2015] [Accepted: 10/12/2015] [Indexed: 11/16/2022] Open
Abstract
Bayesian total-evidence dating involves the simultaneous analysis of morphological data from the fossil record and morphological and sequence data from recent organisms, and it accommodates the uncertainty in the placement of fossils while dating the phylogenetic tree. Due to the flexibility of the Bayesian approach, total-evidence dating can also incorporate additional sources of information. Here, we take advantage of this and expand the analysis to include information about fossilization and sampling processes. Our work is based on the recently described fossilized birth-death (FBD) process, which has been used to model speciation, extinction, and fossilization rates that can vary over time in a piecewise manner. So far, sampling of extant and fossil taxa has been assumed to be either complete or uniformly at random, an assumption which is only valid for a minority of data sets. We therefore extend the FBD process to accommodate diversified sampling of extant taxa, which is standard practice in studies of higher-level taxa. We verify the implementation using simulations and apply it to the early radiation of Hymenoptera (wasps, ants, and bees). Previous total-evidence dating analyses of this data set were based on a simple uniform tree prior and dated the initial radiation of extant Hymenoptera to the late Carboniferous (309 Ma). The analyses using the FBD prior under diversified sampling, however, date the radiation to the Triassic and Permian (252 Ma), slightly older than the age of the oldest hymenopteran fossils. By exploring a variety of FBD model assumptions, we show that it is mainly the accommodation of diversified sampling that causes the push toward more recent divergence times. Accounting for diversified sampling thus has the potential to close the long-discussed gap between rocks and clocks. We conclude that the explicit modeling of fossilization and sampling processes can improve divergence time estimates, but only if all important model aspects, including sampling biases, are adequately addressed.
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Affiliation(s)
- Chi Zhang
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, SE-104 05 Stockholm, Sweden
| | - Tanja Stadler
- Department of Biosystems Science and Engineering, Eidgenössische Technische Hochschule Zürich, 4053 Basel, Switzerland; Swiss Institute of Bioinformatics (SIB), Switzerland
| | - Seraina Klopfstein
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, SE-104 05 Stockholm, Sweden; Department of Invertebrates, Natural History Museum Bern, CH-3005 Bern, Switzerland
| | - Tracy A Heath
- Department of Integrative Biology, University of California, Berkeley, CA 94720 USA; Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, KS 66045, USA; Department of Ecology, Evolution & Organismal Biology, Iowa State University, Ames, IA 50011, USA
| | - Fredrik Ronquist
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, SE-104 05 Stockholm, Sweden;
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24
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Bokma F, Godinot M, Maridet O, Ladevèze S, Costeur L, Solé F, Gheerbrant E, Peigné S, Jacques F, Laurin M. Testing for Depéret's Rule (Body Size Increase) in Mammals using Combined Extinct and Extant Data. Syst Biol 2015; 65:98-108. [PMID: 26508768 PMCID: PMC4678255 DOI: 10.1093/sysbio/syv075] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2014] [Accepted: 09/23/2015] [Indexed: 11/25/2022] Open
Abstract
Whether or not evolutionary lineages in general show a tendency to increase in body size has often been discussed. This tendency has been dubbed “Cope's rule” but because Cope never hypothesized it, we suggest renaming it after Depéret, who formulated it clearly in 1907. Depéret's rule has traditionally been studied using fossil data, but more recently a number of studies have used present-day species. While several paleontological studies of Cenozoic placental mammals have found support for increasing body size, most studies of extant placentals have failed to detect such a trend. Here, we present a method to combine information from present-day species with fossil data in a Bayesian phylogenetic framework. We apply the method to body mass estimates of a large number of extant and extinct mammal species, and find strong support for Depéret's rule. The tendency for size increase appears to be driven not by evolution toward larger size in established species, but by processes related to the emergence of new species. Our analysis shows that complementary data from extant and extinct species can greatly improve inference of macroevolutionary processes.
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Affiliation(s)
- Folmer Bokma
- Department of Ecology and Environmental Science, Umeå University, SE-901 87 Umeå, Sweden;
| | - Marc Godinot
- UMR 7207, CNRS/MNHN/UPMC, Ecole Pratique des Hautes Etudes, Paris, France
| | - Olivier Maridet
- Jurassica Museum, route de Fontenais 21, 2900 Porrentruy, Switzerland
| | - Sandrine Ladevèze
- UMR 7207, CNRS/MNHN/UPMC, Centre de Recherche sur la Paléodiversité et les Paléoenvironments (CR2P), Muséum national d'Histoire naturelle, Département Histoire de la Terre, 57 rue Cuvier, F-75231 Paris Cedex 05, France
| | - Loïc Costeur
- Naturhistorisches Museum Basel, Augustinergasse 2, 4001 Basel, Switzerland; and
| | - Floréal Solé
- Department of Palaeontology, Royal Belgian Institute of Natural Sciences, 29, rue Vautier, 1000 Brussels, Belgium
| | - Emmanuel Gheerbrant
- UMR 7207, CNRS/MNHN/UPMC, Centre de Recherche sur la Paléodiversité et les Paléoenvironments (CR2P), Muséum national d'Histoire naturelle, Département Histoire de la Terre, 57 rue Cuvier, F-75231 Paris Cedex 05, France
| | - Stéphane Peigné
- UMR 7207, CNRS/MNHN/UPMC, Centre de Recherche sur la Paléodiversité et les Paléoenvironments (CR2P), Muséum national d'Histoire naturelle, Département Histoire de la Terre, 57 rue Cuvier, F-75231 Paris Cedex 05, France
| | - Florian Jacques
- UMR 7207, CNRS/MNHN/UPMC, Centre de Recherche sur la Paléodiversité et les Paléoenvironments (CR2P), Muséum national d'Histoire naturelle, Département Histoire de la Terre, 57 rue Cuvier, F-75231 Paris Cedex 05, France
| | - Michel Laurin
- UMR 7207, CNRS/MNHN/UPMC, Centre de Recherche sur la Paléodiversité et les Paléoenvironments (CR2P), Muséum national d'Histoire naturelle, Département Histoire de la Terre, 57 rue Cuvier, F-75231 Paris Cedex 05, France
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25
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Gavryushkina A, Welch D, Stadler T, Drummond AJ. Bayesian inference of sampled ancestor trees for epidemiology and fossil calibration. PLoS Comput Biol 2014; 10:e1003919. [PMID: 25474353 PMCID: PMC4263412 DOI: 10.1371/journal.pcbi.1003919] [Citation(s) in RCA: 183] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2014] [Accepted: 09/08/2014] [Indexed: 12/22/2022] Open
Abstract
Phylogenetic analyses which include fossils or molecular sequences that are sampled through time require models that allow one sample to be a direct ancestor of another sample. As previously available phylogenetic inference tools assume that all samples are tips, they do not allow for this possibility. We have developed and implemented a Bayesian Markov Chain Monte Carlo (MCMC) algorithm to infer what we call sampled ancestor trees, that is, trees in which sampled individuals can be direct ancestors of other sampled individuals. We use a family of birth-death models where individuals may remain in the tree process after sampling, in particular we extend the birth-death skyline model [Stadler et al., 2013] to sampled ancestor trees. This method allows the detection of sampled ancestors as well as estimation of the probability that an individual will be removed from the process when it is sampled. We show that even if sampled ancestors are not of specific interest in an analysis, failing to account for them leads to significant bias in parameter estimates. We also show that sampled ancestor birth-death models where every sample comes from a different time point are non-identifiable and thus require one parameter to be known in order to infer other parameters. We apply our phylogenetic inference accounting for sampled ancestors to epidemiological data, where the possibility of sampled ancestors enables us to identify individuals that infected other individuals after being sampled and to infer fundamental epidemiological parameters. We also apply the method to infer divergence times and diversification rates when fossils are included along with extant species samples, so that fossilisation events are modelled as a part of the tree branching process. Such modelling has many advantages as argued in the literature. The sampler is available as an open-source BEAST2 package (https://github.com/CompEvol/sampled-ancestors). A central goal of phylogenetic analysis is to estimate evolutionary relationships and the dynamical parameters underlying the evolutionary branching process (e.g. macroevolutionary or epidemiological parameters) from molecular data. The statistical methods used in these analyses require that the underlying tree branching process is specified. Standard models for the branching process which were originally designed to describe the evolutionary past of present day species do not allow one sampled taxon to be the ancestor of another. However the probability of sampling a direct ancestor is not negligible for many types of data. For example, when fossil and living species are analysed together to infer species divergence times, fossil species may or may not be direct ancestors of living species. In epidemiology, a sampled individual (a host from which a pathogen sequence was obtained) can infect other individuals after sampling, which then go on to be sampled themselves. The models that account for direct ancestors produce phylogenetic trees with a different structure from classic phylogenetic trees and so using these models in inference requires new computational methods. Here we developed a method for phylogenetic analysis that accounts for the possibility of direct ancestors.
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Affiliation(s)
- Alexandra Gavryushkina
- Department of Computer Science, University of Auckland, Auckland, New Zealand
- Allan Wilson Centre for Molecular Ecology and Evolution, Massey University, Palmerston North, New Zealand
- * E-mail: (AJD); (AG)
| | - David Welch
- Department of Computer Science, University of Auckland, Auckland, New Zealand
| | - Tanja Stadler
- Department of Biosystems Science and Engineering, ETH Zürich, Switzerland
| | - Alexei J. Drummond
- Department of Computer Science, University of Auckland, Auckland, New Zealand
- Allan Wilson Centre for Molecular Ecology and Evolution, Massey University, Palmerston North, New Zealand
- * E-mail: (AJD); (AG)
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26
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Ho SYW, Duchêne S. Molecular-clock methods for estimating evolutionary rates and timescales. Mol Ecol 2014; 23:5947-65. [DOI: 10.1111/mec.12953] [Citation(s) in RCA: 225] [Impact Index Per Article: 22.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2014] [Revised: 09/29/2014] [Accepted: 09/30/2014] [Indexed: 11/29/2022]
Affiliation(s)
- Simon Y. W. Ho
- School of Biological Sciences; University of Sydney; Sydney NSW 2006 Australia
| | - Sebastián Duchêne
- School of Biological Sciences; University of Sydney; Sydney NSW 2006 Australia
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27
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Arcila D, Alexander Pyron R, Tyler JC, Ortí G, Betancur-R R. An evaluation of fossil tip-dating versus node-age calibrations in tetraodontiform fishes (Teleostei: Percomorphaceae). Mol Phylogenet Evol 2014; 82 Pt A:131-45. [PMID: 25462998 DOI: 10.1016/j.ympev.2014.10.011] [Citation(s) in RCA: 80] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2014] [Accepted: 10/14/2014] [Indexed: 10/24/2022]
Abstract
Time-calibrated phylogenies based on molecular data provide a framework for comparative studies. Calibration methods to combine fossil information with molecular phylogenies are, however, under active development, often generating disagreement about the best way to incorporate paleontological data into these analyses. This study provides an empirical comparison of the most widely used approach based on node-dating priors for relaxed clocks implemented in the programs BEAST and MrBayes, with two recently proposed improvements: one using a new fossilized birth-death process model for node dating (implemented in the program DPPDiv), and the other using a total-evidence or tip-dating method (implemented in MrBayes and BEAST). These methods are applied herein to tetraodontiform fishes, a diverse group of living and extinct taxa that features one of the most extensive fossil records among teleosts. Previous estimates of time-calibrated phylogenies of tetraodontiforms using node-dating methods reported disparate estimates for their age of origin, ranging from the late Jurassic to the early Paleocene (ca. 150-59Ma). We analyzed a comprehensive dataset with 16 loci and 210 morphological characters, including 131 taxa (95 extant and 36 fossil species) representing all families of fossil and extant tetraodontiforms, under different molecular clock calibration approaches. Results from node-dating methods produced consistently younger ages than the tip-dating approaches. The older ages inferred by tip dating imply an unlikely early-late Jurassic (ca. 185-119Ma) origin for this order and the existence of extended ghost lineages in their fossil record. Node-based methods, by contrast, produce time estimates that are more consistent with the stratigraphic record, suggesting a late Cretaceous (ca. 86-96Ma) origin. We show that the precision of clade age estimates using tip dating increases with the number of fossils analyzed and with the proximity of fossil taxa to the node under assessment. This study suggests that current implementations of tip dating may overestimate ages of divergence in calibrated phylogenies. It also provides a comprehensive phylogenetic framework for tetraodontiform systematics and future comparative studies.
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Affiliation(s)
- Dahiana Arcila
- Department of Biological Sciences, The George Washington University, 2023 G St. NW, Washington, DC 20052, United States; Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, P.O. Box 37012, MRC 159, Washington, DC 20013, United States.
| | - R Alexander Pyron
- Department of Biological Sciences, The George Washington University, 2023 G St. NW, Washington, DC 20052, United States
| | - James C Tyler
- Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, P.O. Box 37012, MRC 159, Washington, DC 20013, United States
| | - Guillermo Ortí
- Department of Biological Sciences, The George Washington University, 2023 G St. NW, Washington, DC 20052, United States
| | - Ricardo Betancur-R
- Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, P.O. Box 37012, MRC 159, Washington, DC 20013, United States; Department of Biology, University of Puerto Rico - Río Piedras, P.O. Box 23360, San Juan 00931, Puerto Rico
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Heath TA, Huelsenbeck JP, Stadler T. The fossilized birth-death process for coherent calibration of divergence-time estimates. Proc Natl Acad Sci U S A 2014; 111:E2957-66. [PMID: 25009181 PMCID: PMC4115571 DOI: 10.1073/pnas.1319091111] [Citation(s) in RCA: 360] [Impact Index Per Article: 36.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Time-calibrated species phylogenies are critical for addressing a wide range of questions in evolutionary biology, such as those that elucidate historical biogeography or uncover patterns of coevolution and diversification. Because molecular sequence data are not informative on absolute time, external data--most commonly, fossil age estimates--are required to calibrate estimates of species divergence dates. For Bayesian divergence time methods, the common practice for calibration using fossil information involves placing arbitrarily chosen parametric distributions on internal nodes, often disregarding most of the information in the fossil record. We introduce the "fossilized birth-death" (FBD) process--a model for calibrating divergence time estimates in a Bayesian framework, explicitly acknowledging that extant species and fossils are part of the same macroevolutionary process. Under this model, absolute node age estimates are calibrated by a single diversification model and arbitrary calibration densities are not necessary. Moreover, the FBD model allows for inclusion of all available fossils. We performed analyses of simulated data and show that node age estimation under the FBD model results in robust and accurate estimates of species divergence times with realistic measures of statistical uncertainty, overcoming major limitations of standard divergence time estimation methods. We used this model to estimate the speciation times for a dataset composed of all living bears, indicating that the genus Ursus diversified in the Late Miocene to Middle Pliocene.
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Affiliation(s)
- Tracy A Heath
- Department of Integrative Biology, University of California, Berkeley, CA 94720;Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, KS 66045
| | - John P Huelsenbeck
- Department of Integrative Biology, University of California, Berkeley, CA 94720;Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - Tanja Stadler
- Department of Environmental Systems Science, Eidgenössische Technische Hochschule Zürich, 8092 Zurich, Switzerland; andDepartment of Biosystems Science and Engineering, Eidgenössische Technische Hochschule Zürich, 4058 Basel, Switzerland
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29
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Rabosky DL. Automatic detection of key innovations, rate shifts, and diversity-dependence on phylogenetic trees. PLoS One 2014; 9:e89543. [PMID: 24586858 PMCID: PMC3935878 DOI: 10.1371/journal.pone.0089543] [Citation(s) in RCA: 661] [Impact Index Per Article: 66.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2013] [Accepted: 01/22/2014] [Indexed: 11/18/2022] Open
Abstract
A number of methods have been developed to infer differential rates of species diversification through time and among clades using time-calibrated phylogenetic trees. However, we lack a general framework that can delineate and quantify heterogeneous mixtures of dynamic processes within single phylogenies. I developed a method that can identify arbitrary numbers of time-varying diversification processes on phylogenies without specifying their locations in advance. The method uses reversible-jump Markov Chain Monte Carlo to move between model subspaces that vary in the number of distinct diversification regimes. The model assumes that changes in evolutionary regimes occur across the branches of phylogenetic trees under a compound Poisson process and explicitly accounts for rate variation through time and among lineages. Using simulated datasets, I demonstrate that the method can be used to quantify complex mixtures of time-dependent, diversity-dependent, and constant-rate diversification processes. I compared the performance of the method to the MEDUSA model of rate variation among lineages. As an empirical example, I analyzed the history of speciation and extinction during the radiation of modern whales. The method described here will greatly facilitate the exploration of macroevolutionary dynamics across large phylogenetic trees, which may have been shaped by heterogeneous mixtures of distinct evolutionary processes.
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Affiliation(s)
- Daniel L. Rabosky
- Department of Ecology and Evolutionary Biology and Museum of Zoology, University of Michigan, Ann Arbor, Michigan, United States of America
- * E-mail:
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30
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Silvestro D, Schnitzler J, Liow LH, Antonelli A, Salamin N. Bayesian estimation of speciation and extinction from incomplete fossil occurrence data. Syst Biol 2014; 63:349-67. [PMID: 24510972 DOI: 10.1093/sysbio/syu006] [Citation(s) in RCA: 100] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The temporal dynamics of species diversity are shaped by variations in the rates of speciation and extinction, and there is a long history of inferring these rates using first and last appearances of taxa in the fossil record. Understanding diversity dynamics critically depends on unbiased estimates of the unobserved times of speciation and extinction for all lineages, but the inference of these parameters is challenging due to the complex nature of the available data. Here, we present a new probabilistic framework to jointly estimate species-specific times of speciation and extinction and the rates of the underlying birth-death process based on the fossil record. The rates are allowed to vary through time independently of each other, and the probability of preservation and sampling is explicitly incorporated in the model to estimate the true lifespan of each lineage. We implement a Bayesian algorithm to assess the presence of rate shifts by exploring alternative diversification models. Tests on a range of simulated data sets reveal the accuracy and robustness of our approach against violations of the underlying assumptions and various degrees of data incompleteness. Finally, we demonstrate the application of our method with the diversification of the mammal family Rhinocerotidae and reveal a complex history of repeated and independent temporal shifts of both speciation and extinction rates, leading to the expansion and subsequent decline of the group. The estimated parameters of the birth-death process implemented here are directly comparable with those obtained from dated molecular phylogenies. Thus, our model represents a step towards integrating phylogenetic and fossil information to infer macroevolutionary processes.
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Affiliation(s)
- Daniele Silvestro
- Department of Ecology and Evolution, University of Lausanne, 1015 Lausanne, Switzerland
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31
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Morlon H. Phylogenetic approaches for studying diversification. Ecol Lett 2014; 17:508-25. [PMID: 24533923 DOI: 10.1111/ele.12251] [Citation(s) in RCA: 226] [Impact Index Per Article: 22.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2013] [Revised: 10/03/2013] [Accepted: 12/30/2013] [Indexed: 12/17/2022]
Abstract
Estimating rates of speciation and extinction, and understanding how and why they vary over evolutionary time, geographical space and species groups, is a key to understanding how ecological and evolutionary processes generate biological diversity. Such inferences will increasingly benefit from phylogenetic approaches given the ever-accelerating rates of genetic sequencing. In the last few years, models designed to understand diversification from phylogenetic data have advanced significantly. Here, I review these approaches and what they have revealed about diversification in the natural world. I focus on key distinctions between different models, and I clarify the conclusions that can be drawn from each model. I identify promising areas for future research. A major challenge ahead is to develop models that more explicitly take into account ecology, in particular the interaction of species with each other and with their environment. This will not only improve our understanding of diversification; it will also present a new perspective to the use of phylogenies in community ecology, the science of interaction networks and conservation biology, and might shift the current focus in ecology on equilibrium biodiversity theories to non-equilibrium theories recognising the crucial role of history.
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Affiliation(s)
- Hélène Morlon
- Center for Applied Mathematics, Ecole Polytechnique, Palaiseau, Essonne, France
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32
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Pyron RA, Burbrink FT. Phylogenetic estimates of speciation and extinction rates for testing ecological and evolutionary hypotheses. Trends Ecol Evol 2013; 28:729-36. [PMID: 24120478 DOI: 10.1016/j.tree.2013.09.007] [Citation(s) in RCA: 73] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2013] [Revised: 09/03/2013] [Accepted: 09/15/2013] [Indexed: 10/26/2022]
Abstract
Phylogenies are used to estimate rates of speciation and extinction, reconstruct historical diversification scenarios, and link these to ecological and evolutionary factors, such as climate or organismal traits. Recent models can now estimate the effects of binary, multistate, continuous, and biogeographic characters on diversification rates. Others test for diversity dependence (DD) in speciation and extinction, which has become recognized as an important process in numerous clades. A third class incorporates flexible time-dependent functions, enabling reconstruction of major periods of both expanding and contracting diversity. Although there are some potential problems (particularly for estimating extinction), these methods hold promise for answering many classic questions in ecology and evolution, such as the origin of adaptive radiations, and the latitudinal gradient in species richness.
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Affiliation(s)
- R Alexander Pyron
- Department of Biological Sciences, The George Washington University, 2023 G St. NW, Washington, DC 20052, USA.
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Paradis E, Tedesco PA, Hugueny B. QUANTIFYING VARIATION IN SPECIATION AND EXTINCTION RATES WITH CLADE DATA. Evolution 2013; 67:3617-27. [DOI: 10.1111/evo.12256] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2013] [Accepted: 08/14/2013] [Indexed: 11/30/2022]
Affiliation(s)
- Emmanuel Paradis
- Institut de Recherche pour le Développement; ISEM UMR 226/5554 - UM2/CNRS/IRD; Jl. Taman Kemang 32B Jakarta 12730 Indonesia
| | - Pablo A. Tedesco
- UMR Biologie des ORganismes et des Écosystémes Aquatiques (UMR BOREA, IRD 207-CNRS 7208-UPMC-MNHN); Département Milieux et Peuplements Aquatiques; Muséum National d'Histoire Naturelle; 43 rue Cuvier 75231 Paris cedex France
| | - Bernard Hugueny
- UMR Biologie des ORganismes et des Écosystémes Aquatiques (UMR BOREA, IRD 207-CNRS 7208-UPMC-MNHN); Département Milieux et Peuplements Aquatiques; Muséum National d'Histoire Naturelle; 43 rue Cuvier 75231 Paris cedex France
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34
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Slater GJ, Harmon LJ. Unifying fossils and phylogenies for comparative analyses of diversification and trait evolution. Methods Ecol Evol 2013. [DOI: 10.1111/2041-210x.12091] [Citation(s) in RCA: 72] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Affiliation(s)
- Graham J. Slater
- Department of Paleobiology and Division of Mammals; National Museum of Natural History; Smithsonian Institution; MRC 121, P.O. Box 37012; Washington; DC; 20013-7012; USA
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35
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Slater GJ. Phylogenetic evidence for a shift in the mode of mammalian body size evolution at the Cretaceous-Palaeogene boundary. Methods Ecol Evol 2013. [DOI: 10.1111/2041-210x.12084] [Citation(s) in RCA: 156] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- Graham J. Slater
- Department of Paleobiology; National Museum of Natural History; Smithsonian Institution; MRC 121, P.O. Box 37012; Washington; DC; 20013-7012; USA
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36
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Pennell MW, Harmon LJ. An integrative view of phylogenetic comparative methods: connections to population genetics, community ecology, and paleobiology. Ann N Y Acad Sci 2013; 1289:90-105. [DOI: 10.1111/nyas.12157] [Citation(s) in RCA: 170] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
| | - Luke J. Harmon
- Department of Biological Sciences and Institute for Bioinformatics and Evolutionary Studies; University of Idaho; Moscow; Idaho
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37
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Condamine FL, Rolland J, Morlon H. Macroevolutionary perspectives to environmental change. Ecol Lett 2013; 16 Suppl 1:72-85. [DOI: 10.1111/ele.12062] [Citation(s) in RCA: 183] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2012] [Revised: 10/10/2012] [Accepted: 12/04/2012] [Indexed: 11/28/2022]
Affiliation(s)
- Fabien L. Condamine
- CNRS; UMR 7641 Centre de Mathématiques Appliquées (École Polytechnique); Route de Saclay; 91128 Palaiseau; France
| | - Jonathan Rolland
- CNRS; UMR 7641 Centre de Mathématiques Appliquées (École Polytechnique); Route de Saclay; 91128 Palaiseau; France
| | - Hélène Morlon
- CNRS; UMR 7641 Centre de Mathématiques Appliquées (École Polytechnique); Route de Saclay; 91128 Palaiseau; France
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