101
|
Kjer KM, Ware JL, Rust J, Wappler T, Lanfear R, Jermiin LS, Zhou X, Aspöck H, Aspöck U, Beutel RG, Blanke A, Donath A, Flouri T, Frandsen PB, Kapli P, Kawahara AY, Letsch H, Mayer C, McKenna DD, Meusemann K, Niehuis O, Peters RS, Wiegmann BM, Yeates DK, von Reumont BM, Stamatakis A, Misof B. Response to Comment on “Phylogenomics resolves the timing and pattern of insect evolution”. Science 2015; 349:487. [DOI: 10.1126/science.aaa7136] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Affiliation(s)
- K. M. Kjer
- University of California, Davis, CA, USA
| | - J. L. Ware
- Rutgers University, New Brunswick, NJ, USA
| | | | | | | | - L. S. Jermiin
- Commonwealth Scientific and Industrial Research Organization, Canberra, ACT, Australia
| | - X. Zhou
- China National GeneBank, BGI–Shenzhen, China
- BGI-Shenzhen, China
| | | | - U. Aspöck
- Universität Wien, Vienna, Austria
- Naturhistorisches Museum Wien, Vienna, Austria
| | - R. G. Beutel
- Phyletischem Museum Jena, Friedrich-Schiller-Universität Jena, Germany
| | | | - A. Donath
- Universität Bonn, Germany
- Zoologisches Forschungsmuseum Alexander Koenig (ZFMK), Bonn, Germany
| | - T. Flouri
- Heidelberg Institute for Theoretical Studies (HITS), Heidelberg, Germany
| | - P. B. Frandsen
- Rutgers University, New Brunswick, NJ, USA
- Smithsonian Institution, Washington, DC, USA
| | - P. Kapli
- Heidelberg Institute for Theoretical Studies (HITS), Heidelberg, Germany
| | | | | | - C. Mayer
- Universität Bonn, Germany
- Zoologisches Forschungsmuseum Alexander Koenig (ZFMK), Bonn, Germany
| | | | - K. Meusemann
- Commonwealth Scientific and Industrial Research Organization, Canberra, ACT, Australia
- Zoologisches Forschungsmuseum Alexander Koenig (ZFMK), Bonn, Germany
| | - O. Niehuis
- Zoologisches Forschungsmuseum Alexander Koenig (ZFMK), Bonn, Germany
- Arizona State University, Tempe, AZ, USA
| | - R. S. Peters
- Universität Bonn, Germany
- Zoologisches Forschungsmuseum Alexander Koenig (ZFMK), Bonn, Germany
| | | | - D. K. Yeates
- Commonwealth Scientific and Industrial Research Organization, Canberra, ACT, Australia
| | - B. M. von Reumont
- Zoologisches Forschungsmuseum Alexander Koenig (ZFMK), Bonn, Germany
- Natural History Museum London, London, UK
| | - A. Stamatakis
- Heidelberg Institute for Theoretical Studies (HITS), Heidelberg, Germany
| | - B. Misof
- Zoologisches Forschungsmuseum Alexander Koenig (ZFMK), Bonn, Germany
| |
Collapse
|
102
|
De Baets K, Dentzien-Dias P, Upeniece I, Verneau O, Donoghue PCJ. Constraining the Deep Origin of Parasitic Flatworms and Host-Interactions with Fossil Evidence. ADVANCES IN PARASITOLOGY 2015; 90:93-135. [PMID: 26597066 DOI: 10.1016/bs.apar.2015.06.002] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Novel fossil discoveries have contributed to our understanding of the evolutionary appearance of parasitism in flatworms. Furthermore, genetic analyses with greater coverage have shifted our views on the coevolution of parasitic flatworms and their hosts. The putative record of parasitic flatworms is consistent with extant host associations and so can be used to put constraints on the evolutionary origin of the parasites themselves. The future lies in new molecular clock analyses combined with additional discoveries of exceptionally preserved flatworms associated with hosts and coprolites. Besides direct evidence, the host fossil record and biogeography have the potential to constrain their evolutionary history, albeit with caution needed to avoid circularity, and a need for calibrations to be implemented in the most conservative way. This might result in imprecise, but accurate divergence estimates for the evolution of parasitic flatworms.
Collapse
Affiliation(s)
- Kenneth De Baets
- Fachgruppe PaläoUmwelt, GeoZentrum Nordbayern, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Paula Dentzien-Dias
- Núcleo de Oceanografia Geológica, Instituto de Oceanografia, Universidade Federal do Rio Grande, Rio Grande, Brazil
| | - Ieva Upeniece
- Department of Geology, University of Latvia, Riga, Latvia
| | - Olivier Verneau
- Centre de Formation et de Recherche sur les Environnements Méditerranéens, University of Perpignan Via Domitia, Perpignan, France; CNRS, Centre de Formation et de Recherche sur les Environnements Méditerranéens, Perpignan, France; Unit for Environmental Sciences and Management, North-West University, Potchefstroom, South Africa
| | - Philip C J Donoghue
- School of Earth Sciences, University of Bristol, Life Science Building, Bristol, UK
| |
Collapse
|
103
|
van Tuinen M, Torres CR. Potential for bias and low precision in molecular divergence time estimation of the Canopy of Life: an example from aquatic bird families. Front Genet 2015; 6:203. [PMID: 26106406 PMCID: PMC4459087 DOI: 10.3389/fgene.2015.00203] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2015] [Accepted: 05/25/2015] [Indexed: 11/13/2022] Open
Abstract
Uncertainty in divergence time estimation is frequently studied from many angles but rarely from the perspective of phylogenetic node age. If appropriate molecular models and fossil priors are used, a multi-locus, partitioned analysis is expected to equally minimize error in accuracy and precision across all nodes of a given phylogeny. In contrast, if available models fail to completely account for rate heterogeneity, substitution saturation and incompleteness of the fossil record, uncertainty in divergence time estimation may increase with node age. While many studies have stressed this concern with regard to deep nodes in the Tree of Life, the inference that molecular divergence time estimation of shallow nodes is less sensitive to erroneous model choice has not been tested explicitly in a Bayesian framework. Because of available divergence time estimation methods that permit fossil priors across any phylogenetic node and the present increase in efficient, cheap collection of species-level genomic data, insight is needed into the performance of divergence time estimation of shallow (<10 MY) nodes. Here, we performed multiple sensitivity analyses in a multi-locus data set of aquatic birds with six fossil constraints. Comparison across divergence time analyses that varied taxon and locus sampling, number and position of fossil constraint and shape of prior distribution showed various insights. Deviation from node ages obtained from a reference analysis was generally highest for the shallowest nodes but determined more by temporal placement than number of fossil constraints. Calibration with only the shallowest nodes significantly underestimated the aquatic bird fossil record, indicating the presence of saturation. Although joint calibration with all six priors yielded ages most consistent with the fossil record, ages of shallow nodes were overestimated. This bias was found in both mtDNA and nDNA regions. Thus, divergence time estimation of shallow nodes may suffer from bias and low precision, even when appropriate fossil priors and best available substitution models are chosen. Much care must be taken to address the possible ramifications of substitution saturation across the entire Tree of Life.
Collapse
Affiliation(s)
- Marcel van Tuinen
- Department of Biology and Marine Biology, University of North Carolina at WilmingtonWilmington, NC, USA
- Centre of Evolutionary and Ecological Studies, Marine Evolution and Conservation Group, University of GroningenGroningen, Netherlands
| | - Christopher R. Torres
- Department of Biology and Marine Biology, University of North Carolina at WilmingtonWilmington, NC, USA
- National Evolutionary Synthesis CenterDurham, NC, USA
- Department of Integrative Biology, University of Texas at AustinAustin, TX, USA
| |
Collapse
|
104
|
Ksepka DT, Parham JF, Allman JF, Benton MJ, Carrano MT, Cranston KA, Donoghue PCJ, Head JJ, Hermsen EJ, Irmis RB, Joyce WG, Kohli M, Lamm KD, Leehr D, Patané JL, Polly PD, Phillips MJ, Smith NA, Smith ND, Van Tuinen M, Ware JL, Warnock RCM. The Fossil Calibration Database—A New Resource for Divergence Dating. Syst Biol 2015; 64:853-9. [DOI: 10.1093/sysbio/syv025] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2014] [Accepted: 04/22/2015] [Indexed: 01/10/2023] Open
|
105
|
Condamine FL, Nagalingum NS, Marshall CR, Morlon H. Origin and diversification of living cycads: a cautionary tale on the impact of the branching process prior in Bayesian molecular dating. BMC Evol Biol 2015; 15:65. [PMID: 25884423 PMCID: PMC4449600 DOI: 10.1186/s12862-015-0347-8] [Citation(s) in RCA: 118] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2015] [Accepted: 04/02/2015] [Indexed: 01/21/2023] Open
Abstract
Background Bayesian relaxed-clock dating has significantly influenced our understanding of the timeline of biotic evolution. This approach requires the use of priors on the branching process, yet little is known about their impact on divergence time estimates. We investigated the effect of branching priors using the iconic cycads. We conducted phylogenetic estimations for 237 cycad species using three genes and two calibration strategies incorporating up to six fossil constraints to (i) test the impact of two different branching process priors on age estimates, (ii) assess which branching prior better fits the data, (iii) investigate branching prior impacts on diversification analyses, and (iv) provide insights into the diversification history of cycads. Results Using Bayes factors, we compared divergence time estimates and the inferred dynamics of diversification when using Yule versus birth-death priors. Bayes factors were calculated with marginal likelihood estimated with stepping-stone sampling. We found striking differences in age estimates and diversification dynamics depending on prior choice. Dating with the Yule prior suggested that extant cycad genera diversified in the Paleogene and with two diversification rate shifts. In contrast, dating with the birth-death prior yielded Neogene diversifications, and four rate shifts, one for each of the four richest genera. Nonetheless, dating with the two priors provided similar age estimates for the divergence of cycads from Ginkgo (Carboniferous) and their crown age (Permian). Of these, Bayes factors clearly supported the birth-death prior. Conclusions These results suggest the choice of the branching process prior can have a drastic influence on our understanding of evolutionary radiations. Therefore, all dating analyses must involve a model selection process using Bayes factors to select between a Yule or birth-death prior, in particular on ancient clades with a potential pattern of high extinction. We also provide new insights into the history of cycad diversification because we found (i) periods of extinction along the long branches of the genera consistent with fossil data, and (ii) high diversification rates within the Miocene genus radiations. Electronic supplementary material The online version of this article (doi:10.1186/s12862-015-0347-8) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Fabien L Condamine
- CNRS, UMR 7641 Centre de Mathématiques Appliquées (École Polytechnique), Route de Saclay, 91128, Palaiseau, France. .,Department of Biological and Environmental Sciences, University of Gothenburg, Box 461, SE-405 30, Göteborg, Sweden.
| | - Nathalie S Nagalingum
- National Herbarium of New South Wales, Royal Botanic Gardens & Domain Trust, Mrs Macquaries Road, Sydney, NSW, 2000, Australia.
| | - Charles R Marshall
- Department of Integrative Biology and Museum of Paleontology, University of California, 1101 Valley Life Sciences Building, Berkeley, CA, 94720-4780, USA.
| | - Hélène Morlon
- CNRS, UMR 8197 Institut de Biologie de l'École Normale Supérieure, 46 rue d'Ulm, 75005, Paris, France.
| |
Collapse
|
106
|
Battistuzzi FU, Billing-Ross P, Murillo O, Filipski A, Kumar S. A Protocol for Diagnosing the Effect of Calibration Priors on Posterior Time Estimates: A Case Study for the Cambrian Explosion of Animal Phyla. Mol Biol Evol 2015; 32:1907-12. [PMID: 25808541 DOI: 10.1093/molbev/msv075] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
We present a procedure to test the effect of calibration priors on estimated times, which applies a recently developed calibration-free approach (RelTime) method that produces relative divergence times for all nodes in the tree. We illustrate this protocol by applying it to a timetree of metazoan diversification (Erwin DH, Laflamme M, Tweedt SM, Sperling EA, Pisani D, Peterson KJ. 2011. The Cambrian conundrum: early divergence and later ecological success in the early history of animals. Science 334:1091-1097.), which placed the divergence of animal phyla close to the time of the Cambrian explosion inferred from the fossil record. These analyses revealed that the two maximum-only calibration priors in the pre-Cambrian are the primary determinants of the young divergence times among animal phyla in this study. In fact, these two maximum-only calibrations produce divergence times that severely violate minimum boundaries of almost all of the other 22 calibration constraints. The use of these 22 calibrations produces dates for metazoan divergences that are hundreds of millions of years earlier in the Proterozoic. Our results encourage the use of calibration-free approaches to identify most influential calibration constraints and to evaluate their impact in order to achieve biologically robust interpretations.
Collapse
Affiliation(s)
| | - Paul Billing-Ross
- Department of Molecular Biology and Genetics, College of Human Ecology, Cornell University
| | - Oscar Murillo
- Institute for Genomics and Evolutionary Medicine, Temple University
| | - Alan Filipski
- Institute for Genomics and Evolutionary Medicine, Temple University
| | - Sudhir Kumar
- Institute for Genomics and Evolutionary Medicine, Temple University Department of Biology, Temple University Center for Genomic Medicine and Research, King Abdulaziz University, Jddah, Saudi Arabia
| |
Collapse
|
107
|
Massoni J, Couvreur TLP, Sauquet H. Five major shifts of diversification through the long evolutionary history of Magnoliidae (angiosperms). BMC Evol Biol 2015; 15:49. [PMID: 25887386 PMCID: PMC4377182 DOI: 10.1186/s12862-015-0320-6] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2014] [Accepted: 02/24/2015] [Indexed: 11/13/2022] Open
Abstract
Background With 10,000 species, Magnoliidae are the largest clade of flowering plants outside monocots and eudicots. Despite an ancient and rich fossil history, the tempo and mode of diversification of Magnoliidae remain poorly known. Using a molecular data set of 12 markers and 220 species (representing >75% of genera in Magnoliidae) and six robust, internal fossil age constraints, we estimate divergence times and significant shifts of diversification across the clade. In addition, we test the sensitivity of magnoliid divergence times to the choice of relaxed clock model and various maximum age constraints for the angiosperms. Results Compared with previous work, our study tends to push back in time the age of the crown node of Magnoliidae (178.78-126.82 million years, Myr), and of the four orders, Canellales (143.18-125.90 Myr), Piperales (158.11-88.15 Myr), Laurales (165.62-112.05 Myr), and Magnoliales (164.09-114.75 Myr). Although families vary in crown ages, Magnoliidae appear to have diversified into most extant families by the end of the Cretaceous. The strongly imbalanced distribution of extant diversity within Magnoliidae appears to be best explained by models of diversification with 6 to 13 shifts in net diversification rates. Significant increases are inferred within Piperaceae and Annonaceae, while the low species richness of Calycanthaceae, Degeneriaceae, and Himantandraceae appears to be the result of decreases in both speciation and extinction rates. Conclusions This study provides a new time scale for the evolutionary history of an important, but underexplored, part of the tree of angiosperms. The ages of the main clades of Magnoliidae (above the family level) are older than previously thought, and in several lineages, there were significant increases and decreases in net diversification rates. This study is a new robust framework for future investigations of trait evolution and of factors influencing diversification in this group as well as angiosperms as a whole. Electronic supplementary material The online version of this article (doi:10.1186/s12862-015-0320-6) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Julien Massoni
- Laboratoire Ecologie, Systématique, Evolution, Université Paris-Sud, CNRS UMR 8079, 91405, Orsay, France.
| | - Thomas L P Couvreur
- Institut de Recherche pour le Développement (IRD), UMR-DIADE, 911, avenue Agropolis, BP 64501, Cedex 5, F-34394, Montpellier, France. .,Département des Sciences Biologiques, Université de Yaoundé I, Ecole Normale Supérieure, Laboratoire de Botanique systématique et d'Ecologie, B.P. 047, Yaoundé, Cameroon.
| | - Hervé Sauquet
- Laboratoire Ecologie, Systématique, Evolution, Université Paris-Sud, CNRS UMR 8079, 91405, Orsay, France.
| |
Collapse
|
108
|
De Baets K, Littlewood DTJ. The Importance of Fossils in Understanding the Evolution of Parasites and Their Vectors. ADVANCES IN PARASITOLOGY 2015; 90:1-51. [PMID: 26597064 DOI: 10.1016/bs.apar.2015.07.001] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Knowledge concerning the diversity of parasitism and its reach across our current understanding of the tree of life has benefitted considerably from novel molecular phylogenetic methods. However, the timing of events and the resolution of the nature of the intimate relationships between parasites and their hosts in deep time remain problematic. Despite its vagaries, the fossil record provides the only direct evidence of parasites and parasitism in the fossil record of extant and extinct lineages. Here, we demonstrate the potential of the fossil record and other lines of geological evidence to calibrate the origin and evolution of parasitism by combining different kinds of dating evidence with novel molecular clock methodologies. Other novel methods promise to provide additional evidence for the presence or the life habit of pathogens and their vectors, including the discovery and analysis of ancient DNA and other biomolecules, as well as computed tomographic methods.
Collapse
|