1
|
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.
Collapse
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
| |
Collapse
|
2
|
Höhna S, Kopperud BT, Magee AF. CRABS: Congruent rate analyses in birth–death scenarios. Methods Ecol Evol 2022. [DOI: 10.1111/2041-210x.13997] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- Sebastian Höhna
- GeoBio‐Center LMU Ludwig‐Maximilians‐Universität München Munich Germany
- Department of Earth and Environmental Sciences, Paleontology & Geobiology Ludwig‐Maximilians‐Universität München Munich Germany
| | - Bjørn T. Kopperud
- GeoBio‐Center LMU Ludwig‐Maximilians‐Universität München Munich Germany
- Department of Earth and Environmental Sciences, Paleontology & Geobiology Ludwig‐Maximilians‐Universität München Munich Germany
| | - Andrew F. Magee
- Department of Human Genetics University of California Los Angeles California USA
| |
Collapse
|
3
|
Cornuault J, Sanmartín I. A road map for phylogenetic models of species trees. Mol Phylogenet Evol 2022; 173:107483. [DOI: 10.1016/j.ympev.2022.107483] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2021] [Revised: 03/09/2022] [Accepted: 04/05/2022] [Indexed: 10/18/2022]
|
4
|
Riggs K, Chen HS, Rotunno M, Li B, Simonds NI, Mechanic LE, Peng B. On the application, reporting, and sharing of in silico simulations for genetic studies. Genet Epidemiol 2020; 45:131-141. [PMID: 33063887 PMCID: PMC7984380 DOI: 10.1002/gepi.22362] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2020] [Revised: 09/11/2020] [Accepted: 09/14/2020] [Indexed: 12/31/2022]
Abstract
In silico simulations play an indispensable role in the development and application of statistical models and methods for genetic studies. Simulation tools allow for the evaluation of methods and investigation of models in a controlled manner. With the growing popularity of evolutionary models and simulation‐based statistical methods, genetic simulations have been applied to a wide variety of research disciplines such as population genetics, evolutionary genetics, genetic epidemiology, ecology, and conservation biology. In this review, we surveyed 1409 articles from five journals that publish on major application areas of genetic simulations. We identified 432 papers in which genetic simulations were used and examined the targets and applications of simulation studies and how these simulation methods and simulated data sets are reported and shared. Whereas a large proportion (30%) of the surveyed articles reported the use of genetic simulations, only 28% of these genetic simulation studies used existing simulation software, 2% used existing simulated data sets, and 19% and 12% made source code and simulated data sets publicly available, respectively. Moreover, 15% of articles provided no information on how simulation studies were performed. These findings suggest a need to encourage sharing and reuse of existing simulation software and data sets, as well as providing more information regarding the performance of simulations.
Collapse
Affiliation(s)
- Kaleigh Riggs
- Department of Statistics, Rice University, Houston, Texas, USA
| | - Huann-Sheng Chen
- Division of Cancer Control and Population Sciences, Statistical Research and Applications Branch, Surveillance Research Program, National Cancer Institute (NCI), National Institutes of Health (NIH), Bethesda, Maryland, USA
| | - Melissa Rotunno
- Division of Cancer Control and Population Sciences, Genomic Epidemiology Branch, Epidemiology and Genomics Research Program, NCI, NIH, Bethesda, Maryland, USA
| | - Bing Li
- Department of Biostatistics, Brown University, Providence, Rhode Island, USA
| | | | - Leah E Mechanic
- Division of Cancer Control and Population Sciences, Genomic Epidemiology Branch, Epidemiology and Genomics Research Program, NCI, NIH, Bethesda, Maryland, USA
| | - Bo Peng
- Department of Medicine, Baylor College of Medicine, Houston, Texas, USA
| |
Collapse
|
5
|
Condamine FL, Nel A, Grandcolas P, Legendre F. Fossil and phylogenetic analyses reveal recurrent periods of diversification and extinction in dictyopteran insects. Cladistics 2020; 36:394-412. [PMID: 34619806 DOI: 10.1111/cla.12412] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/23/2020] [Indexed: 01/22/2023] Open
Abstract
Variations of speciation and extinction rates determine the fate of clades through time. Periods of high diversification and extinction (possibly mass-extinction events) can punctuate the evolutionary history of various clades, but they remain loosely defined for many biological groups, especially nonmarine invertebrates like insects. Here, we examine whether the cockroaches, mantises and termites (altogether included in Dictyoptera) have experienced episodic pulses of speciation or extinction and how these pulses may be associated with environmental fluctuations or mass extinctions. We relied on molecular phylogeny and fossil data to shed light on the times and rates at which dictyopterans diversified. The diversification of Dictyoptera has alternated between (i) periods of high diversification in the late Carboniferous, Early-Middle Triassic, Early Cretaceous and middle Palaeogene, and (ii) periods of high extinction rates particularly at the Permian-Triassic boundary, but not necessarily correlated with the major global biodiversity crises as in the mid-Cretaceous. This study advocates the importance of analyzing, when possible, both molecular phylogeny and fossil data to unveil diversification and extinction periods for a given group. The causes and consequences of extinction must be studied beyond mass-extinction events alone to gain a broader understanding of how clades wax and wane.
Collapse
Affiliation(s)
- Fabien L Condamine
- CNRS, UMR 5554 Institut des Sciences de l'Évolution de Montpellier (Université de Montpellier
- CNRS
- IRD
- EPHE), Place Eugène Bataillon, 34095, Montpellier, France
| | - André Nel
- Institut de Systématique, Évolution, Biodiversité (ISYEB), Muséum national d'Histoire naturelle, CNRS, SU, EPHE, UA, 57 rue Cuvier, 75231, Paris Cedex 05, France
| | - Philippe Grandcolas
- Institut de Systématique, Évolution, Biodiversité (ISYEB), Muséum national d'Histoire naturelle, CNRS, SU, EPHE, UA, 57 rue Cuvier, 75231, Paris Cedex 05, France
| | - Frédéric Legendre
- Institut de Systématique, Évolution, Biodiversité (ISYEB), Muséum national d'Histoire naturelle, CNRS, SU, EPHE, UA, 57 rue Cuvier, 75231, Paris Cedex 05, France
| |
Collapse
|