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Pozzi L, Penna A. Rocks and clocks revised: New promises and challenges in dating the primate tree of life. Evol Anthropol 2022; 31:138-153. [PMID: 35102633 DOI: 10.1002/evan.21940] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Revised: 10/04/2021] [Accepted: 01/12/2022] [Indexed: 01/14/2023]
Abstract
In recent years, multiple technological and methodological advances have increased our ability to estimate phylogenies, leading to more accurate dating of the primate tree of life. Here we provide an overview of the limitations and potentials of some of these advancements and discuss how dated phylogenies provide the crucial temporal scale required to understand primate evolution. First, we review new methods, such as the total-evidence dating approach, that promise a better integration between the fossil record and molecular data. We then explore how the ever-increasing availability of genomic-level data for more primate species can impact our ability to accurately estimate timetrees. Finally, we discuss more recent applications of mutation rates to date divergence times. We highlight example studies that have applied these approaches to estimate divergence dates within primates. Our goal is to provide a critical overview of these new developments and explore the promises and challenges of their application in evolutionary anthropology.
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Affiliation(s)
- Luca Pozzi
- Department of Anthropology, The University of Texas at San Antonio, San Antonio, Texas, USA
| | - Anna Penna
- Department of Anthropology, The University of Texas at San Antonio, San Antonio, Texas, USA
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2
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Pardo JD, Lennie K, Anderson JS. Can We Reliably Calibrate Deep Nodes in the Tetrapod Tree? Case Studies in Deep Tetrapod Divergences. Front Genet 2020; 11:506749. [PMID: 33193596 PMCID: PMC7596322 DOI: 10.3389/fgene.2020.506749] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2019] [Accepted: 09/03/2020] [Indexed: 12/12/2022] Open
Abstract
Recent efforts have led to the development of extremely sophisticated methods for incorporating tree-wide data and accommodating uncertainty when estimating the temporal patterns of phylogenetic trees, but assignment of prior constraints on node age remains the most important factor. This depends largely on understanding substantive disagreements between specialists (paleontologists, geologists, and comparative anatomists), which are often opaque to phylogeneticists and molecular biologists who rely on these data as downstream users. This often leads to misunderstandings of how the uncertainty associated with node age minima arises, leading to inappropriate treatments of that uncertainty by phylogeneticists. In order to promote dialogue on this subject, we here review factors (phylogeny, preservational megabiases, spatial and temporal patterns in the tetrapod fossil record) that complicate assignment of prior node age constraints for deep divergences in the tetrapod tree, focusing on the origin of crown-group Amniota, crown-group Amphibia, and crown-group Tetrapoda. We find that node priors for amphibians and tetrapods show high phylogenetic lability and different phylogenetic treatments identifying disparate taxa as the earliest representatives of these crown groups. This corresponds partially to the well-known problem of lissamphibian origins but increasingly reflects deeper instabilities in early tetrapod phylogeny. Conversely, differences in phylogenetic treatment do not affect our ability to recognize the earliest crown-group amniotes but do affect how diverse we understand the earliest amniote faunas to be. Preservational megabiases and spatiotemporal heterogeneity of the early tetrapod fossil record present unrecognized challenges in reliably estimating the ages of tetrapod nodes; the tetrapod record throughout the relevant interval is spatially restricted and disrupted by several major intervals of minimal sampling coincident with the emergence of all three crown groups. Going forward, researchers attempting to calibrate the ages for these nodes, and other similar deep nodes in the metazoan fossil record, should consciously consider major phylogenetic uncertainty, preservational megabias, and spatiotemporal heterogeneity, preferably examining the impact of working hypotheses from multiple research groups. We emphasize a need for major tetrapod collection effort outside of classic European and North American sections, particularly from the southern hemisphere, and suggest that such sampling may dramatically change our timelines of tetrapod evolution.
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Affiliation(s)
- Jason D. Pardo
- Department of Comparative and Experimental Biology, Faculty of Veterinary Medicine, University of Calgary, Calgary, AB, Canada
- McCaig Institute for Bone and Joint Health, University of Calgary, Calgary, AB, Canada
| | - Kendra Lennie
- McCaig Institute for Bone and Joint Health, University of Calgary, Calgary, AB, Canada
- Department of Biological Sciences, University of Calgary, Calgary, AB, Canada
| | - Jason S. Anderson
- Department of Comparative and Experimental Biology, Faculty of Veterinary Medicine, University of Calgary, Calgary, AB, Canada
- McCaig Institute for Bone and Joint Health, University of Calgary, Calgary, AB, Canada
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3
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Cascini M, Mitchell KJ, Cooper A, Phillips MJ. Reconstructing the Evolution of Giant Extinct Kangaroos: Comparing the Utility of DNA, Morphology, and Total Evidence. Syst Biol 2018; 68:520-537. [DOI: 10.1093/sysbio/syy080] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2018] [Revised: 11/20/2018] [Accepted: 11/20/2018] [Indexed: 11/12/2022] Open
Affiliation(s)
- Manuela Cascini
- School of Earth, Environmental and Biological Sciences, Queensland University of Technology, 2, George Street, Brisbane, QLD 4000, Australia
| | - Kieren J Mitchell
- Australian Centre for Ancient DNA, School of Biological Sciences, University of Adelaide, North Terrace Campus, South Australia 5005, Australia
| | - Alan Cooper
- Australian Centre for Ancient DNA, School of Biological Sciences, University of Adelaide, North Terrace Campus, South Australia 5005, Australia
| | - Matthew J Phillips
- School of Earth, Environmental and Biological Sciences, Queensland University of Technology, 2, George Street, Brisbane, QLD 4000, Australia
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4
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Field DJ, Hsiang AY. A North American stem turaco, and the complex biogeographic history of modern birds. BMC Evol Biol 2018; 18:102. [PMID: 29936914 PMCID: PMC6016133 DOI: 10.1186/s12862-018-1212-3] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2017] [Accepted: 06/06/2018] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Earth's lower latitudes boast the majority of extant avian species-level and higher-order diversity, with many deeply diverging clades restricted to vestiges of Gondwana. However, palaeontological analyses reveal that many avian crown clades with restricted extant distributions had stem group relatives in very different parts of the world. RESULTS Our phylogenetic analyses support the enigmatic fossil bird Foro panarium Olson 1992 from the early Eocene (Wasatchian) of Wyoming as a stem turaco (Neornithes: Pan-Musophagidae), a clade that is presently endemic to sub-Saharan Africa. Our analyses offer the first well-supported evidence for a stem musophagid (and therefore a useful fossil calibration for avian molecular divergence analyses), and reveal surprising new information on the early morphology and biogeography of this clade. Total-clade Musophagidae is identified as a potential participant in dispersal via the recently proposed 'North American Gateway' during the Palaeogene, and new biogeographic analyses illustrate the importance of the fossil record in revealing the complex historical biogeography of crown birds across geological timescales. CONCLUSIONS In the Palaeogene, total-clade Musophagidae was distributed well outside the range of crown Musophagidae in the present day. This observation is consistent with similar biogeographic observations for numerous other modern bird clades, illustrating shortcomings of historical biogeographic analyses that do not incorporate information from the avian fossil record.
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Affiliation(s)
- Daniel J. Field
- Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, Claverton Down, Bath, BA2 7AY UK
- Department of Geology and Geophysics, Yale University, 210 Whitney Avenue, New Haven, CT 06511 USA
| | - Allison Y. Hsiang
- Department of Geology and Geophysics, Yale University, 210 Whitney Avenue, New Haven, CT 06511 USA
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, 10405 Stockholm, Sweden
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5
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Karanovic I, Sitnikova TY. Phylogenetic position and age of Lake Baikal candonids (Crustacea, Ostracoda) inferred from multigene sequence analyzes and molecular dating. Ecol Evol 2017; 7:7091-7103. [PMID: 28904786 PMCID: PMC5587501 DOI: 10.1002/ece3.3159] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2017] [Revised: 05/19/2017] [Accepted: 05/23/2017] [Indexed: 11/23/2022] Open
Abstract
With 104 endemic species family Candonidae is one of the most diverse crustacean groups in Lake Baikal, yet their phylogenetic relationships and position in the family have not been addressed so far. Here, we study the phylogenetic position of Baikal candonids within the family and their evolutionary history using molecular markers for the first time since their original description. We choose 10 Baikal and 28 species from around the world, and three ribosomal RNA‐s (18S, 28S, and 16S), and analyze individual and concatenated datasets using Bayesian Inference in MrBayes and BEAST. For molecular divergence time estimates, four fossil records are used to calibrate the root and three internal nodes. The 28S dataset is tested under the strict molecular clock, while for other data we use relaxed clocks. Resulting trees show incongruence between molecular and fossil divergence time estimates, with the former suggesting older ages. Strict molecular clock analysis results in narrower node age confidence intervals and younger time estimates than other analysis. All trees support at least two candonid lineages in Baikal, with two independent colonization events, and 28S suggests a major radiation between 12 and 5 Mya. This divergence time estimate mostly agrees with another, unrelated, ostracod group in the lake and other lake animals as well. Baikal candonid clades show a close phylogenetic relationship with Palearctic lineages, but their deep divergence is indicative of separate genera. Results also suggest a monophyly of tribes that today live exclusively in subterranean waters, and we offer several hypotheses of their evolutionary history.
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Affiliation(s)
- Ivana Karanovic
- Department of Life Science College of Natural Science Hanyang University Seoul South Korea.,Institute for Marine and Antarctic Studies University of Tasmania Hobart Tas Australia
| | - Tatiana Ya Sitnikova
- Limnological Institute Siberian Branch Russian Academy of Sciences Irkutsk Russia
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6
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Turner AH, Pritchard AC, Matzke NJ. Empirical and Bayesian approaches to fossil-only divergence times: A study across three reptile clades. PLoS One 2017; 12:e0169885. [PMID: 28187191 PMCID: PMC5302793 DOI: 10.1371/journal.pone.0169885] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2016] [Accepted: 12/23/2016] [Indexed: 11/19/2022] Open
Abstract
Estimating divergence times on phylogenies is critical in paleontological and neontological studies. Chronostratigraphically-constrained fossils are the only direct evidence of absolute timing of species divergence. Strict temporal calibration of fossil-only phylogenies provides minimum divergence estimates, and various methods have been proposed to estimate divergences beyond these minimum values. We explore the utility of simultaneous estimation of tree topology and divergence times using BEAST tip-dating on datasets consisting only of fossils by using relaxed morphological clocks and birth-death tree priors that include serial sampling (BDSS) at a constant rate through time. We compare BEAST results to those from the traditional maximum parsimony (MP) and undated Bayesian inference (BI) methods. Three overlapping datasets were used that span 250 million years of archosauromorph evolution leading to crocodylians. The first dataset focuses on early Sauria (31 taxa, 240 chars.), the second on early Archosauria (76 taxa, 400 chars.) and the third on Crocodyliformes (101 taxa, 340 chars.). For each dataset three time-calibrated trees (timetrees) were calculated: a minimum-age timetree with node ages based on earliest occurrences in the fossil record; a 'smoothed' timetree using a range of time added to the root that is then averaged over zero-length internodes; and a tip-dated timetree. Comparisons within datasets show that the smoothed and tip-dated timetrees provide similar estimates. Only near the root node do BEAST estimates fall outside the smoothed timetree range. The BEAST model is not able to overcome limited sampling to correctly estimate divergences considerably older than sampled fossil occurrence dates. Conversely, the smoothed timetrees consistently provide node-ages far older than the strict dates or BEAST estimates for morphologically conservative sister-taxa when they sit on long ghost lineages. In this latter case, the relaxed-clock model appears to be correctly moderating the node-age estimate based on the limited morphological divergence. Topologies are generally similar across analyses, but BEAST trees for crocodyliforms differ when clades are deeply nested but contain very old taxa. It appears that the constant-rate sampling assumption of the BDSS tree prior influences topology inference by disfavoring long, unsampled branches.
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Affiliation(s)
- Alan H. Turner
- Department of Anatomical Sciences, Stony Brook University, Stony Brook, New York, United States of America
| | - Adam C. Pritchard
- Department of Geology, Yale University, New Haven, Connecticut, United States of America
| | - Nicholas J. Matzke
- Division of Ecology, Evolution, and Genetics, Research School of Biology, The Australian National University, Canberra, Australia
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7
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Spinks PQ, Thomson RC, McCartney-Melstad E, Shaffer HB. Phylogeny and temporal diversification of the New World pond turtles (Emydidae). Mol Phylogenet Evol 2016; 103:85-97. [DOI: 10.1016/j.ympev.2016.07.007] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2015] [Revised: 06/03/2016] [Accepted: 07/07/2016] [Indexed: 11/16/2022]
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Warnock RCM, Parham JF, Joyce WG, Lyson TR, Donoghue PCJ. Calibration uncertainty in molecular dating analyses: there is no substitute for the prior evaluation of time priors. Proc Biol Sci 2015; 282:20141013. [PMID: 25429012 PMCID: PMC4262156 DOI: 10.1098/rspb.2014.1013] [Citation(s) in RCA: 108] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Calibration is the rate-determining step in every molecular clock analysis and, hence, considerable effort has been expended in the development of approaches to distinguish good from bad calibrations. These can be categorized into a priori evaluation of the intrinsic fossil evidence, and a posteriori evaluation of congruence through cross-validation. We contrasted these competing approaches and explored the impact of different interpretations of the fossil evidence upon Bayesian divergence time estimation. The results demonstrate that a posteriori approaches can lead to the selection of erroneous calibrations. Bayesian posterior estimates are also shown to be extremely sensitive to the probabilistic interpretation of temporal constraints. Furthermore, the effective time priors implemented within an analysis differ for individual calibrations when employed alone and in differing combination with others. This compromises the implicit assumption of all calibration consistency methods, that the impact of an individual calibration is the same when used alone or in unison with others. Thus, the most effective means of establishing the quality of fossil-based calibrations is through a priori evaluation of the intrinsic palaeontological, stratigraphic, geochronological and phylogenetic data. However, effort expended in establishing calibrations will not be rewarded unless they are implemented faithfully in divergence time analyses.
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Affiliation(s)
- Rachel C M Warnock
- School of Earth Sciences, University of Bristol, Bristol, UK National Evolutionary Synthesis Center, Durham, NC, USA Department of Paleobiology, Smithsonian Institution, Washington DC, USA
| | - James F Parham
- John D. Cooper Archaeological and Paleontological Center, Department of Geological Sciences, California State University, Fullerton, CA, USA
| | - Walter G Joyce
- Department of Geosciences, University of Fribourg/Freiburg, Switzerland
| | - Tyler R Lyson
- Denver Museum of Nature and Science, Denver, CO, USA
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9
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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
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Grimm GW, Kapli P, Bomfleur B, McLoughlin S, Renner SS. Using More Than the Oldest Fossils: Dating Osmundaceae with Three Bayesian Clock Approaches. Syst Biol 2014; 64:396-405. [DOI: 10.1093/sysbio/syu108] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2014] [Accepted: 12/01/2014] [Indexed: 11/13/2022] Open
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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: 82] [Impact Index Per Article: 8.2] [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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Eme L, Sharpe SC, Brown MW, Roger AJ. On the age of eukaryotes: evaluating evidence from fossils and molecular clocks. Cold Spring Harb Perspect Biol 2014; 6:6/8/a016139. [PMID: 25085908 DOI: 10.1101/cshperspect.a016139] [Citation(s) in RCA: 116] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Our understanding of the phylogenetic relationships among eukaryotic lineages has improved dramatically over the few past decades thanks to the development of sophisticated phylogenetic methods and models of evolution, in combination with the increasing availability of sequence data for a variety of eukaryotic lineages. Concurrently, efforts have been made to infer the age of major evolutionary events along the tree of eukaryotes using fossil-calibrated molecular clock-based methods. Here, we review the progress and pitfalls in estimating the age of the last eukaryotic common ancestor (LECA) and major lineages. After reviewing previous attempts to date deep eukaryote divergences, we present the results of a Bayesian relaxed-molecular clock analysis of a large dataset (159 proteins, 85 taxa) using 19 fossil calibrations. We show that for major eukaryote groups estimated dates of divergence, as well as their credible intervals, are heavily influenced by the relaxed molecular clock models and methods used, and by the nature and treatment of fossil calibrations. Whereas the estimated age of LECA varied widely, ranging from 1007 (943-1102) Ma to 1898 (1655-2094) Ma, all analyses suggested that the eukaryotic supergroups subsequently diverged rapidly (i.e., within 300 Ma of LECA). The extreme variability of these and previously published analyses preclude definitive conclusions regarding the age of major eukaryote clades at this time. As more reliable fossil data on eukaryotes from the Proterozoic become available and improvements are made in relaxed molecular clock modeling, we may be able to date the age of extant eukaryotes more precisely.
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Affiliation(s)
- Laura Eme
- Centre for Comparative Genomics and Evolutionary Bioinformatics, Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax B3H 4R2, Canada
| | - Susan C Sharpe
- Centre for Comparative Genomics and Evolutionary Bioinformatics, Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax B3H 4R2, Canada
| | - Matthew W Brown
- Centre for Comparative Genomics and Evolutionary Bioinformatics, Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax B3H 4R2, Canada
| | - Andrew J Roger
- Centre for Comparative Genomics and Evolutionary Bioinformatics, Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax B3H 4R2, Canada
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Noonan BP, Pramuk JB, Bezy RL, Sinclair EA, Queiroz KD, Sites JW. Phylogenetic relationships within the lizard clade Xantusiidae: Using trees and divergence times to address evolutionary questions at multiple levels. Mol Phylogenet Evol 2013; 69:109-22. [DOI: 10.1016/j.ympev.2013.05.017] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2012] [Revised: 05/15/2013] [Accepted: 05/21/2013] [Indexed: 11/25/2022]
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14
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Bibi F. A multi-calibrated mitochondrial phylogeny of extant Bovidae (Artiodactyla, Ruminantia) and the importance of the fossil record to systematics. BMC Evol Biol 2013; 13:166. [PMID: 23927069 PMCID: PMC3751017 DOI: 10.1186/1471-2148-13-166] [Citation(s) in RCA: 141] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2013] [Accepted: 08/06/2013] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Molecular phylogenetics has provided unprecedented resolution in the ruminant evolutionary tree. However, molecular age estimates using only one or a few (often misapplied) fossil calibration points have produced a diversity of conflicting ages for important evolutionary events within this clade. I here identify 16 fossil calibration points of relevance to the phylogeny of Bovidae and Ruminantia and use these, individually and together, to construct a dated molecular phylogeny through a reanalysis of the full mitochondrial genome of over 100 ruminant species. RESULTS The new multi-calibrated tree provides ages that are younger overall than found in previous studies. Among these are young ages for the origin of crown Ruminantia (39.3-28.8 Ma), and crown Bovidae (17.3-15.1 Ma). These are argued to be reasonable hypotheses given that many basal fossils assigned to these taxa may in fact lie on the stem groups leading to the crown clades, thus inflating previous age estimates. Areas of conflict between molecular and fossil dates do persist, however, especially with regard to the base of the rapid Pecoran radiation and the sister relationship of Moschidae to Bovidae. Results of the single-calibrated analyses also show that a very wide range of molecular age estimates are obtainable using different calibration points, and that the choice of calibration point can influence the topology of the resulting tree. Compared to the single-calibrated trees, the multi-calibrated tree exhibits smaller variance in estimated ages and better reflects the fossil record. CONCLUSIONS The use of a large number of vetted fossil calibration points with soft bounds is promoted as a better approach than using just one or a few calibrations, or relying on internal-congruency metrics to discard good fossil data. This study also highlights the importance of considering morphological and ecological characteristics of clades when delimiting higher taxa. I also illustrate how phylogeographic and paleoenvironmental hypotheses inferred from a tree containing only extant taxa can be problematic without consideration of the fossil record. Incorporating the fossil record of Ruminantia is a necessary step for future analyses aiming to reconstruct the evolutionary history of this clade.
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Affiliation(s)
- Faysal Bibi
- Museum für Naturkunde, Leibniz Institute for Research on Evolution and Biodiversity at the Humboldt University Berlin, Invalidenstrasse 43, Berlin 10115, Germany
- Current address: Department of Mammalogy, American Museum of Natural History, 200 Central Park West, New York, NY 10024, USA
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15
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Nowak MD, Smith AB, Simpson C, Zwickl DJ. A simple method for estimating informative node age priors for the fossil calibration of molecular divergence time analyses. PLoS One 2013; 8:e66245. [PMID: 23755303 PMCID: PMC3673923 DOI: 10.1371/journal.pone.0066245] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2012] [Accepted: 05/03/2013] [Indexed: 11/19/2022] Open
Abstract
Molecular divergence time analyses often rely on the age of fossil lineages to calibrate node age estimates. Most divergence time analyses are now performed in a Bayesian framework, where fossil calibrations are incorporated as parametric prior probabilities on node ages. It is widely accepted that an ideal parameterization of such node age prior probabilities should be based on a comprehensive analysis of the fossil record of the clade of interest, but there is currently no generally applicable approach for calculating such informative priors. We provide here a simple and easily implemented method that employs fossil data to estimate the likely amount of missing history prior to the oldest fossil occurrence of a clade, which can be used to fit an informative parametric prior probability distribution on a node age. Specifically, our method uses the extant diversity and the stratigraphic distribution of fossil lineages confidently assigned to a clade to fit a branching model of lineage diversification. Conditioning this on a simple model of fossil preservation, we estimate the likely amount of missing history prior to the oldest fossil occurrence of a clade. The likelihood surface of missing history can then be translated into a parametric prior probability distribution on the age of the clade of interest. We show that the method performs well with simulated fossil distribution data, but that the likelihood surface of missing history can at times be too complex for the distribution-fitting algorithm employed by our software tool. An empirical example of the application of our method is performed to estimate echinoid node ages. A simulation-based sensitivity analysis using the echinoid data set shows that node age prior distributions estimated under poor preservation rates are significantly less informative than those estimated under high preservation rates.
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Affiliation(s)
- Michael D Nowak
- Institute of Systematic Botany, University of Zürich, Zürich, Switzerland.
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Angielczyk KD, Feldman CR. Are diminutive turtles miniaturized? The ontogeny of plastron shape in emydine turtles. Biol J Linn Soc Lond 2013. [DOI: 10.1111/bij.12010] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Affiliation(s)
- Kenneth D. Angielczyk
- Department of Geology; Field Museum of Natural History; 1400 South Lake Shore Drive; Chicago; IL; 60605; USA
| | - Chris R. Feldman
- Department of Biology; University of Nevada, Reno; 1664 North Virginia Street; Reno; NV; 89557; USA
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DNA and morphology unite two species and 10 million year old fossils. PLoS One 2012; 7:e52083. [PMID: 23284880 PMCID: PMC3527379 DOI: 10.1371/journal.pone.0052083] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2012] [Accepted: 11/08/2012] [Indexed: 11/25/2022] Open
Abstract
Species definition and delimitation is a non-trivial problem in evolutionary biology that is particularly problematic for fossil organisms. This is especially true when considering the continuity of past and present species, because species defined in the fossil record are not necessarily equivalent to species defined in the living fauna. Correctly assigned fossil species are critical for sensitive downstream analysis (e.g., diversification studies and molecular-clock calibration). The marine snail genus Alcithoe exemplifies many of the problems with species identification. The paucity of objective diagnostic characters, prevalence of morphological convergence between species and considerable variability within species that are observed in Alcithoe are typical of a broad range of fossilised organisms. Using a synthesis of molecular and morphometric approaches we show that two taxa currently recognised as distinct are morphological variants of a single species. Furthermore, we validate the fossil record for one of these morphotypes by finding a concordance between the palaeontological record and divergence time of the lineage inferred using molecular-clock analysis. This work demonstrates the utility of living species represented in the fossil record as candidates for molecular-clock calibration, as the veracity of fossil species assignment can be more rigorously tested.
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Krosch MN, Schutze MK, Armstrong KF, Graham GC, Yeates DK, Clarke AR. A molecular phylogeny for the Tribe Dacini (Diptera: Tephritidae): Systematic and biogeographic implications. Mol Phylogenet Evol 2012; 64:513-23. [DOI: 10.1016/j.ympev.2012.05.006] [Citation(s) in RCA: 64] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2011] [Revised: 05/01/2012] [Accepted: 05/10/2012] [Indexed: 11/16/2022]
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19
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Marine turtle mitogenome phylogenetics and evolution. Mol Phylogenet Evol 2012; 65:241-50. [PMID: 22750111 DOI: 10.1016/j.ympev.2012.06.010] [Citation(s) in RCA: 70] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2012] [Revised: 06/11/2012] [Accepted: 06/13/2012] [Indexed: 11/21/2022]
Abstract
The sea turtles are a group of cretaceous origin containing seven recognized living species: leatherback, hawksbill, Kemp's ridley, olive ridley, loggerhead, green, and flatback. The leatherback is the single member of the Dermochelidae family, whereas all other sea turtles belong in Cheloniidae. Analyses of partial mitochondrial sequences and some nuclear markers have revealed phylogenetic inconsistencies within Cheloniidae, especially regarding the placement of the flatback. Population genetic studies based on D-Loop sequences have shown considerable structuring in species with broad geographic distributions, shedding light on complex migration patterns and possible geographic or climatic events as driving forces of sea-turtle distribution. We have sequenced complete mitogenomes for all sea-turtle species, including samples from their geographic range extremes, and performed phylogenetic analyses to assess sea-turtle evolution with a large molecular dataset. We found variation in the length of the ATP8 gene and a highly variable site in ND4 near a proton translocation channel in the resulting protein. Complete mitogenomes show strong support and resolution for phylogenetic relationships among all sea turtles, and reveal phylogeographic patterns within globally-distributed species. Although there was clear concordance between phylogenies and geographic origin of samples in most taxa, we found evidence of more recent dispersal events in the loggerhead and olive ridley turtles, suggesting more recent migrations (<1 Myr) in these species. Overall, our results demonstrate the complexity of sea-turtle diversity, and indicate the need for further research in phylogeography and molecular evolution.
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20
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Parham JF, Donoghue PCJ, Bell CJ, Calway TD, Head JJ, Holroyd PA, Inoue JG, Irmis RB, Joyce WG, Ksepka DT, Patané JSL, Smith ND, Tarver JE, van Tuinen M, Yang Z, Angielczyk KD, Greenwood JM, Hipsley CA, Jacobs L, Makovicky PJ, Müller J, Smith KT, Theodor JM, Warnock RCM, Benton MJ. Best practices for justifying fossil calibrations. Syst Biol 2012; 61:346-59. [PMID: 22105867 PMCID: PMC3280042 DOI: 10.1093/sysbio/syr107] [Citation(s) in RCA: 378] [Impact Index Per Article: 31.5] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2011] [Revised: 09/22/2011] [Accepted: 11/14/2011] [Indexed: 11/30/2022] Open
Affiliation(s)
- James F Parham
- Alabama Museum of Natural History, University of Alabama, 427 6th Avenue, Smith Hall, Box 870340, Tuscaloosa, AL 35487, USA.
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21
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Dating cryptodiran nodes: origin and diversification of the turtle superfamily Testudinoidea. Mol Phylogenet Evol 2011; 62:496-507. [PMID: 22100825 DOI: 10.1016/j.ympev.2011.10.022] [Citation(s) in RCA: 55] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2011] [Revised: 10/19/2011] [Accepted: 10/25/2011] [Indexed: 11/20/2022]
Abstract
The superfamily Testudinoidea is the most diverse and widely distributed clade of extant turtles. Surprisingly, despite an extensive fossil record, and increasing amount of molecular data available, the temporal origin of this group is still largely unknown. To address this issue, we used a comprehensive molecular dataset to perform phylogenetic and molecular dating analyses, as well as seven fossil constraints to calibrate the ages of the nodes in the phylogeny. The molecular dataset includes the complete mitochondrial genomes of 37 turtle species, including newly sequenced mitochondrial genomes of Phrynops hilarii, Emys orbicularis, Rhinoclemmys punctularia, and Chelonoidis nigra, and four nuclear markers. Our results revealed that the earliest divergences within crown testudinoids occurred around 95.0 Mya, in the early Late Cretaceous, earlier than previously reported, raising new questions about the historical biogeography of this group.
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22
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Macroevolutionary patterns in the Aphidini aphids (Hemiptera: Aphididae): diversification, host association, and biogeographic origins. PLoS One 2011; 6:e24749. [PMID: 21935453 PMCID: PMC3174202 DOI: 10.1371/journal.pone.0024749] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2011] [Accepted: 08/16/2011] [Indexed: 11/19/2022] Open
Abstract
Background Due to its biogeographic origins and rapid diversification, understanding the tribe Aphidini is key to understanding aphid evolution. Major questions about aphid evolution include origins of host alternation as well as age and patterns of diversification in relation to host plants. To address these questions, we reconstructed the phylogeny of the Aphidini which contains Aphis, the most diverse genus in the family. We used a combined dataset of one nuclear and four mitochondrial DNA regions. A molecular dating approach, calibrated with fossil records, was used to estimate divergence times of these taxa. Principal Findings Most generic divergences in Aphidini occurred in the Middle Tertiary, and species-level divergences occurred between the Middle and Late Tertiary. The ancestral state of host use for Aphidini was equivocal with respect to three states: monoecy on trees, heteroecy, and monoecy on grasses. The ancestral state of Rhopalosiphina likely included both heteroecy and monoecy, whereas that of Aphidina was most likely monoecy. The divergence times of aphid lineages at the generic or subgeneric levels are close to those of their primary hosts. The species-level divergences in aphids are consistent with the diversification of the secondary hosts, as a few examples suggest. The biogeographic origin of Aphidini as a whole was equivocal, but the major lineages within Aphidina likely separated into Nearctic, Western Palearctic, and Eastern Palearctic regions. Conclusions Most generic divergences in Aphidini occurred in the Middle Tertiary when primary hosts, mainly in the Rosaceae, were diverging, whereas species-level divergences were contemporaneous with diversification of the secondary hosts such as Poaceae in the Middle to Late Tertiary. Our results suggest that evolution of host alternation within Aphidini may have occurred during the Middle Tertiary (Oligocene) when the secondary hosts emerged.
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Pyron RA. Divergence time estimation using fossils as terminal taxa and the origins of Lissamphibia. Syst Biol 2011; 60:466-81. [PMID: 21540408 DOI: 10.1093/sysbio/syr047] [Citation(s) in RCA: 223] [Impact Index Per Article: 17.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Were molecular data available for extinct taxa, questions regarding the origins of many groups could be settled in short order. As this is not the case, various strategies have been proposed to combine paleontological and neontological data sets. The use of fossil dates as node age calibrations for divergence time estimation from molecular phylogenies is commonplace. In addition, simulations suggest that the addition of morphological data from extinct taxa may improve phylogenetic estimation when combined with molecular data for extant species, and some studies have merged morphological and molecular data to estimate combined evidence phylogenies containing both extinct and extant taxa. However, few, if any, studies have attempted to estimate divergence times using phylogenies containing both fossil and living taxa sampled for both molecular and morphological data. Here, I infer both the phylogeny and the time of origin for Lissamphibia and a number of stem tetrapods using Bayesian methods based on a data set containing morphological data for extinct taxa, molecular data for extant taxa, and molecular and morphological data for a subset of extant taxa. The results suggest that Lissamphibia is monophyletic, nested within Lepospondyli, and originated in the late Carboniferous at the earliest. This research illustrates potential pitfalls for the use of fossils as post hoc age constraints on internal nodes and highlights the importance of explicit phylogenetic analysis of extinct taxa. These results suggest that the application of fossils as minima or maxima on molecular phylogenies should be supplemented or supplanted by combined evidence analyses whenever possible.
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Affiliation(s)
- R Alexander Pyron
- Department of Ecology and Evolution, Stony Brook University, Stony Brook, NY 11794-5245, USA.
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Ksepka DT, Benton MJ, Carrano MT, Gandolfo MA, Head JJ, Hermsen EJ, Joyce WG, Lamm KS, Patané JSL, Phillips MJ, Polly PD, Van Tuinen M, Ware JL, Warnock RCM, Parham JF. Synthesizing and databasing fossil calibrations: divergence dating and beyond. Biol Lett 2011; 7:801-3. [PMID: 21525049 DOI: 10.1098/rsbl.2011.0356] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Divergence dating studies, which combine temporal data from the fossil record with branch length data from molecular phylogenetic trees, represent a rapidly expanding approach to understanding the history of life. National Evolutionary Synthesis Center hosted the first Fossil Calibrations Working Group (3-6 March, 2011, Durham, NC, USA), bringing together palaeontologists, molecular evolutionists and bioinformatics experts to present perspectives from disciplines that generate, model and use fossil calibration data. Presentations and discussions focused on channels for interdisciplinary collaboration, best practices for justifying, reporting and using fossil calibrations and roadblocks to synthesis of palaeontological and molecular data. Bioinformatics solutions were proposed, with the primary objective being a new database for vetted fossil calibrations with linkages to existing resources, targeted for a 2012 launch.
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Affiliation(s)
- Daniel T Ksepka
- Department of Marine, Earth and Atmospheric Sciences, North Carolina State University, Raleigh, NC 27695, USA.
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Dornburg A, Beaulieu JM, Oliver JC, Near TJ. Integrating Fossil Preservation Biases in the Selection of Calibrations for Molecular Divergence Time Estimation. Syst Biol 2011; 60:519-27. [DOI: 10.1093/sysbio/syr019] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Alex Dornburg
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT 06520, USA
| | - Jeremy M. Beaulieu
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT 06520, USA
| | - Jeffrey C. Oliver
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT 06520, USA
| | - Thomas J. Near
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT 06520, USA
- Peabody Museum of Natural History, Yale University, New Haven, CT 06520, USA
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26
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Smith ND. Phylogenetic analysis of pelecaniformes (aves) based on osteological data: implications for waterbird phylogeny and fossil calibration studies. PLoS One 2010; 5:e13354. [PMID: 20976229 PMCID: PMC2954798 DOI: 10.1371/journal.pone.0013354] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2010] [Accepted: 09/21/2010] [Indexed: 01/08/2023] Open
Abstract
BACKGROUND Debate regarding the monophyly and relationships of the avian order Pelecaniformes represents a classic example of discord between morphological and molecular estimates of phylogeny. This lack of consensus hampers interpretation of the group's fossil record, which has major implications for understanding patterns of character evolution (e.g., the evolution of wing-propelled diving) and temporal diversification (e.g., the origins of modern families). Relationships of the Pelecaniformes were inferred through parsimony analyses of an osteological dataset encompassing 59 taxa and 464 characters. The relationships of the Plotopteridae, an extinct family of wing-propelled divers, and several other fossil pelecaniforms (Limnofregata, Prophaethon, Lithoptila, ?Borvocarbo stoeffelensis) were also assessed. The antiquity of these taxa and their purported status as stem members of extant families makes them valuable for studies of higher-level avian diversification. METHODOLOGY/PRINCIPAL FINDINGS Pelecaniform monophyly is not recovered, with Phaethontidae recovered as distantly related to all other pelecaniforms, which are supported as a monophyletic Steganopodes. Some anatomical partitions of the dataset possess different phylogenetic signals, and partitioned analyses reveal that these discrepancies are localized outside of Steganopodes, and primarily due to a few labile taxa. The Plotopteridae are recovered as the sister taxon to Phalacrocoracoidea, and the relationships of other fossil pelecaniforms representing key calibration points are well supported, including Limnofregata (sister taxon to Fregatidae), Prophaethon and Lithoptila (successive sister taxa to Phaethontidae), and ?Borvocarbo stoeffelensis (sister taxon to Phalacrocoracidae). These relationships are invariant when 'backbone' constraints based on recent avian phylogenies are imposed. CONCLUSIONS/SIGNIFICANCE Relationships of extant pelecaniforms inferred from morphology are more congruent with molecular phylogenies than previously assumed, though notable conflicts remain. The phylogenetic position of the Plotopteridae implies that wing-propelled diving evolved independently in plotopterids and penguins, representing a remarkable case of convergent evolution. Despite robust support for the placement of fossil taxa representing key calibration points, the successive outgroup relationships of several "stem fossil + crown family" clades are variable and poorly supported across recent studies of avian phylogeny. Thus, the impact these fossils have on inferred patterns of temporal diversification depends heavily on the resolution of deep nodes in avian phylogeny.
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Affiliation(s)
- Nathan D Smith
- University of Chicago, Chicago, Illinois, United States of America.
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27
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Angielczyk KD, Feldman CR, Miller GR. ADAPTIVE EVOLUTION OF PLASTRON SHAPE IN EMYDINE TURTLES. Evolution 2010; 65:377-94. [DOI: 10.1111/j.1558-5646.2010.01118.x] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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Forest F. Calibrating the Tree of Life: fossils, molecules and evolutionary timescales. ANNALS OF BOTANY 2009; 104:789-94. [PMID: 19666901 PMCID: PMC2749537 DOI: 10.1093/aob/mcp192] [Citation(s) in RCA: 73] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2009] [Revised: 06/11/2009] [Accepted: 07/09/2009] [Indexed: 05/09/2023]
Abstract
BACKGROUND Molecular dating has gained ever-increasing interest since the molecular clock hypothesis was proposed in the 1960s. Molecular dating provides detailed temporal frameworks for divergence events in phylogenetic trees, allowing diverse evolutionary questions to be addressed. The key aspect of the molecular clock hypothesis, namely that differences in DNA or protein sequence between two species are proportional to the time elapsed since they diverged, was soon shown to be untenable. Other approaches were proposed to take into account rate heterogeneity among lineages, but the calibration process, by which relative times are transformed into absolute ages, has received little attention until recently. New methods have now been proposed to resolve potential sources of error associated with the calibration of phylogenetic trees, particularly those involving use of the fossil record. SCOPE AND CONCLUSIONS The use of the fossil record as a source of independent information in the calibration process is the main focus of this paper; other sources of calibration information are also discussed. Particularly error-prone aspects of fossil calibration are identified, such as fossil dating, the phylogenetic placement of the fossil and the incompleteness of the fossil record. Methods proposed to tackle one or more of these potential error sources are discussed (e.g. fossil cross-validation, prior distribution of calibration points and confidence intervals on the fossil record). In conclusion, the fossil record remains the most reliable source of information for the calibration of phylogenetic trees, although associated assumptions and potential bias must be taken into account.
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Affiliation(s)
- Félix Forest
- Jodrell Laboratory, Royal Botanic Gardens, Kew, Richmond, Surrey TW9 3DS, UK.
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Ho SYW, Phillips MJ. Accounting for Calibration Uncertainty in Phylogenetic Estimation of Evolutionary Divergence Times. Syst Biol 2009; 58:367-80. [PMID: 20525591 DOI: 10.1093/sysbio/syp035] [Citation(s) in RCA: 521] [Impact Index Per Article: 34.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Affiliation(s)
- Simon Y. W. Ho
- Centre for Macroevolution and Macroecology, Research School of Biology, Australian National University, Canberra, ACT 0200, Australia
| | - Matthew J. Phillips
- Centre for Macroevolution and Macroecology, Research School of Biology, Australian National University, Canberra, ACT 0200, Australia
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Ksepka DT. Broken gears in the avian molecular clock: new phylogenetic analyses support stem galliform status forGallinuloides wyomingensisand rallid affinities forAmitabha urbsinterdictensis. Cladistics 2009; 25:173-197. [DOI: 10.1111/j.1096-0031.2009.00250.x] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
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32
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Marshall CR. A Simple Method for Bracketing Absolute Divergence Times on Molecular Phylogenies Using Multiple Fossil Calibration Points. Am Nat 2008; 171:726-42. [PMID: 18462127 DOI: 10.1086/587523] [Citation(s) in RCA: 158] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Affiliation(s)
- Charles R Marshall
- Museum of Comparative Zoology, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts 02138, USA.
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33
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Parham JF, Papenfuss TJ. High genetic diversity among fossorial lizard populations (Anniella pulchra) in a rapidly developing landscape (Central California). CONSERV GENET 2008. [DOI: 10.1007/s10592-008-9544-y] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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34
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Near T, Meylan P, Shaffer H. Caveats on the Use of Fossil Calibrations for Molecular Dating: A Reply to Parham and Irmis. Am Nat 2008. [DOI: 10.1086/524201] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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