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Smith SA, Beaulieu JM. Ad fontes: divergence-time estimation and the age of angiosperms. THE NEW PHYTOLOGIST 2024; 244:760-766. [PMID: 39205459 DOI: 10.1111/nph.20076] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2024] [Accepted: 08/06/2024] [Indexed: 09/04/2024]
Abstract
Accurate divergence times are essential for interpreting and understanding the context in which lineages have evolved. Over the past several decades, debates have surrounded the discrepancies between the inferred molecular ages of crown angiosperms, often estimated from the Late Jurassic into the Permian, and the fossil record, placing angiosperms in the Early Cretaceous. That crown angiosperms could have emerged as early as the Permian or even the Triassic would have major implications for the paleoecological context of the origin of one of the most consequential clades in the tree of life. Here, we argue, and demonstrate through simulations, that the older ages inferred from molecular data and relaxed-clock models are misled by lineage-specific rate heterogeneity resulting from life history changes that occurred several times throughout the evolution of vascular plants. To overcome persistent discrepancies in age estimates, more biologically informed and realistic models should be developed, and our results should be considered in the context of their biological implications before we accept inferences that are a major departure from our strongest evidence.
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Affiliation(s)
- Stephen A Smith
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Jeremy M Beaulieu
- Department of Biological Sciences, University of Arkansas, Fayetteville, AR, 72701, USA
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2
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O'Meara BC, Beaulieu JM. Noise leads to the perceived increase in evolutionary rates over short time scales. PLoS Comput Biol 2024; 20:e1012458. [PMID: 39269992 PMCID: PMC11424004 DOI: 10.1371/journal.pcbi.1012458] [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: 07/22/2024] [Revised: 09/25/2024] [Accepted: 09/04/2024] [Indexed: 09/15/2024] Open
Abstract
Across a variety of biological datasets, from genomes to conservation to the fossil record, evolutionary rates appear to increase toward the present or over short time scales. This has long been seen as an indication of processes operating differently at different time scales, even potentially as an indicator of a need for new theory connecting macroevolution and microevolution. Here we introduce a set of models that assess the relationship between rate and time and demonstrate that these patterns are statistical artifacts of time-independent errors present across ecological and evolutionary datasets, which produce hyperbolic patterns of rates through time. We show that plotting a noisy numerator divided by time versus time leads to the observed hyperbolic pattern; in fact, randomizing the amount of change over time generates patterns functionally identical to observed patterns. Ignoring errors can not only obscure true patterns but create novel patterns that have long misled scientists.
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Affiliation(s)
- Brian C O'Meara
- Department of Ecology and Evolutionary Biology, University of Tennessee; Knoxville, Tennessee, United States of America
| | - Jeremy M Beaulieu
- Department of Biological Sciences, University of Arkansas; Fayetteville, Arkansas, United States of America
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3
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Thompson J, Ramírez-Barahona S. The meaning of mass extinctions and what the fossil record tells us about angiosperm survival at K-Pg: a reply to Hagen (2024). Biol Lett 2024; 20:20240265. [PMID: 39192833 DOI: 10.1098/rsbl.2024.0265] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2024] [Revised: 07/10/2024] [Accepted: 07/19/2024] [Indexed: 08/29/2024] Open
Abstract
Last year, we published research using phylogenetic comparative methods (PCMs) to reveal no phylogenetic evidence for elevated lineage-level extinction rates in angiosperms across K-Pg (Thompson JB, Ramírez-Barahona S. 2023 No phylogenetic evidence for angiosperm mass extinction at the Cretaceous-Palaeogene (K-Pg) boundary. Biol. Lett. 19, 20230314. (doi:10.1098/rsbl.2023.0314)), results that are in step with the global angiosperm fossil record. In a critique of our paper (Hagen ER. 2024 A critique of Thompson and Ramírez-Barahona (2023) or: how I learned to stop worrying and love the fossil record. EcoEvoRxiv. (doi:10.32942/X2631W)), simulation work is presented to argue we erred in our methodological choices and interpretations, and that we should have deferred to fossil evidence. In our opinion, underlying this critique are poor methodological choices on simulations and philosophical problems surrounding the definition of a mass extinction event, which leads to incorrect interpretations of both the fossil record and PCMs. We further argue that deferring to one source of evidence in favour of the other shuts the door to important evolutionary and philosophical questions.
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Affiliation(s)
- Jamie Thompson
- School of Biological Sciences, University of Reading, Whiteknights , Reading, Berkshire, UK
- The Milner Centre for Evolution, Department of Life Sciences, University of Bath , Bath, UK
| | - Santiago Ramírez-Barahona
- Departamento de Botánica, Instituto de Biología, Universidad Nacional Autónoma de México , Ciudad de México, México
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4
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Hagen ER. A critique of Thompson and Ramírez-Barahona (2023) or: how I learned to stop worrying and love the fossil record. Biol Lett 2024; 20:20240039. [PMID: 39192834 DOI: 10.1098/rsbl.2024.0039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2024] [Revised: 03/12/2024] [Accepted: 05/02/2024] [Indexed: 08/29/2024] Open
Abstract
A recent study published in Biology Letters by Thompson and Ramírez-Barahona (2023) argued that, according to analyses of diversification on two massive molecular phylogenies comprising thousands of species, there is no evidence that angiosperms (i.e. flowering plants) were affected by the Cretaceous-Paleogene mass extinction. Here, I critique these conclusions from both methodological and philosophical perspectives. I demonstrate that the methods used in their study possess statistical limitations that strongly reduce the power to detect a true mass extinction event using data similar to those analysed by Thompson and Ramírez-Barahona (2023). Additionally, I use their study as a springboard to examine the relationship between phylogenetic and fossil evidence in diversification studies.
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Affiliation(s)
- Eric Robert Hagen
- Department of Ecology & Evolutionary Biology, University of Toronto , Toronto, Ontario, Canada M5S 3B2
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5
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Boom AF, Migliore J, Ojeda Alayon DI, Kaymak E, Hardy OJ. Phylogenomics of Brachystegia: Insights into the origin of African miombo woodlands. AMERICAN JOURNAL OF BOTANY 2024; 111:e16352. [PMID: 38853465 DOI: 10.1002/ajb2.16352] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Revised: 03/29/2024] [Accepted: 04/01/2024] [Indexed: 06/11/2024]
Abstract
PREMISE Phylogenetic approaches can provide valuable insights on how and when a biome emerged and developed using its structuring species. In this context, Brachystegia Benth, a dominant genus of trees in miombo woodlands, appears as a key witness of the history of the largest woodland and savanna biome of Africa. METHODS We reconstructed the evolutionary history of the genus using targeted-enrichment sequencing on 60 Brachystegia specimens for a nearly complete species sampling. Phylogenomic inferences used supermatrix (RAxML-NG) and summary-method (ASTRAL-III) approaches. Conflicts between species and gene trees were assessed, and the phylogeny was time-calibrated in BEAST. Introgression between species was explored using Phylonet. RESULTS The phylogenies were globally congruent regardless of the method used. Most of the species were recovered as monophyletic, unlike previous plastid phylogenetic reconstructions where lineages were shared among geographically close individuals independently of species identity. Still, most of the individual gene trees had low levels of phylogenetic information and, when informative, were mostly in conflict with the reconstructed species trees. These results suggest incomplete lineage sorting and/or reticulate evolution, which was supported by network analyses. The BEAST analysis supported a Pliocene origin for current Brachystegia lineages, with most of the diversification events dated to the Pliocene-Pleistocene. CONCLUSIONS These results suggest a recent origin of species of the miombo, congruently with their spatial expansion documented from plastid data. Brachystegia species appear to behave potentially as a syngameon, a group of interfertile but still relatively well-delineated species, an aspect that deserves further investigations.
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Affiliation(s)
- Arthur F Boom
- Royal Museum for Central Africa, Biology Department, Section Vertebrates, Tervuren, Belgium
- Université Libre de Bruxelles, Faculté des Sciences, Service Evolution Biologique et Ecologie, Bruxelles, Belgium
| | - Jérémy Migliore
- Université Libre de Bruxelles, Faculté des Sciences, Service Evolution Biologique et Ecologie, Bruxelles, Belgium
- Muséum départemental du Var, Toulon, France
| | - Dario I Ojeda Alayon
- Muséum départemental du Var, Toulon, France
- Department of Forest Biodiversity, Norwegian Institute of Bioeconomy Research, Ås, Norway
| | - Esra Kaymak
- Université Libre de Bruxelles, Faculté des Sciences, Service Evolution Biologique et Ecologie, Bruxelles, Belgium
- Institute of Science and Technology (OIST), Okinawa, Japan
| | - Olivier J Hardy
- Université Libre de Bruxelles, Faculté des Sciences, Service Evolution Biologique et Ecologie, Bruxelles, Belgium
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6
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Zhang R, Drummond AJ, Mendes FK. Fast Bayesian Inference of Phylogenies from Multiple Continuous Characters. Syst Biol 2024; 73:102-124. [PMID: 38085256 PMCID: PMC11129596 DOI: 10.1093/sysbio/syad067] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Revised: 03/23/2023] [Accepted: 11/07/2023] [Indexed: 05/28/2024] Open
Abstract
Time-scaled phylogenetic trees are an ultimate goal of evolutionary biology and a necessary ingredient in comparative studies. The accumulation of genomic data has resolved the tree of life to a great extent, yet timing evolutionary events remain challenging if not impossible without external information such as fossil ages and morphological characters. Methods for incorporating morphology in tree estimation have lagged behind their molecular counterparts, especially in the case of continuous characters. Despite recent advances, such tools are still direly needed as we approach the limits of what molecules can teach us. Here, we implement a suite of state-of-the-art methods for leveraging continuous morphology in phylogenetics, and by conducting extensive simulation studies we thoroughly validate and explore our methods' properties. While retaining model generality and scalability, we make it possible to estimate absolute and relative divergence times from multiple continuous characters while accounting for uncertainty. We compile and analyze one of the most data-type diverse data sets to date, comprised of contemporaneous and ancient molecular sequences, and discrete and continuous morphological characters from living and extinct Carnivora taxa. We conclude by synthesizing lessons about our method's behavior, and suggest future research venues.
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Affiliation(s)
- Rong Zhang
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School 169857, Singapore
| | - Alexei J Drummond
- Centre for Computational Evolution, The University of Auckland, Auckland 1010, New Zealand
- School of Biological Sciences, The University of Auckland, Auckland 1010, New Zealand
| | - Fábio K Mendes
- Department of Biology, Washington University in St. Louis, St. Louis, MO 63130, USA
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7
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Henao-Diaz LF, Pennell M. The Major Features of Macroevolution. Syst Biol 2023; 72:1188-1198. [PMID: 37248967 DOI: 10.1093/sysbio/syad032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Revised: 05/02/2023] [Accepted: 05/29/2023] [Indexed: 05/31/2023] Open
Abstract
Evolutionary dynamics operating across deep time leave footprints in the shapes of phylogenetic trees. For the last several decades, researchers have used increasingly large and robust phylogenies to study the evolutionary history of individual clades and to investigate the causes of the glaring disparities in diversity among groups. Whereas typically not the focal point of individual clade-level studies, many researchers have remarked on recurrent patterns that have been observed across many different groups and at many different time scales. Whereas previous studies have documented various such regularities in topology and branch length distributions, they have typically focused on a single pattern and used a disparate collection (oftentimes, of quite variable reliability) of trees to assess it. Here we take advantage of modern megaphylogenies and unify previous disparate observations about the shapes embedded in the Tree of Life to create a catalog of the "major features of macroevolution." By characterizing such a large swath of subtrees in a consistent way, we hope to provide a set of phenomena that process-based macroevolutionary models of diversification ought to seek to explain.
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Affiliation(s)
- L Francisco Henao-Diaz
- Department of Ecology and Evolution, University of Chicago, Chicago, USA
- Department of Zoology and Biodiversity Research Centre, University of British Columbia, Vancouver, Canada
| | - Matt Pennell
- Department of Zoology and Biodiversity Research Centre, University of British Columbia, Vancouver, Canada
- Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, USA
- Department of Biological Sciences, University of Southern California, Los Angeles, USA
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8
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Carlisle E, Janis CM, Pisani D, Donoghue PCJ, Silvestro D. A timescale for placental mammal diversification based on Bayesian modeling of the fossil record. Curr Biol 2023; 33:3073-3082.e3. [PMID: 37379845 DOI: 10.1016/j.cub.2023.06.016] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Revised: 04/21/2023] [Accepted: 06/05/2023] [Indexed: 06/30/2023]
Abstract
The timing of the placental mammal radiation has been the focus of debate over the efficacy of competing methods for establishing evolutionary timescales. Molecular clock analyses estimate that placental mammals originated before the Cretaceous-Paleogene (K-Pg) mass extinction, anywhere from the Late Cretaceous to the Jurassic. However, the absence of definitive fossils of placentals before the K-Pg boundary is compatible with a post-Cretaceous origin. Nevertheless, lineage divergence must occur before it can be manifest phenotypically in descendent lineages. This, combined with the non-uniformity of the rock and fossil records, requires the fossil record to be interpreted rather than read literally. To achieve this, we introduce an extended Bayesian Brownian bridge model that estimates the age of origination and, where applicable, extinction through a probabilistic interpretation of the fossil record. The model estimates the origination of placentals in the Late Cretaceous, with ordinal crown groups originating at or after the K-Pg boundary. The results reduce the plausible interval for placental mammal origination to the younger range of molecular clock estimates. Our findings support both the Long Fuse and Soft Explosive models of placental mammal diversification, indicating that the placentals originated shortly prior to the K-Pg mass extinction. The origination of many modern mammal lineages overlapped with and followed the K-Pg mass extinction.
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Affiliation(s)
- Emily Carlisle
- Bristol Palaeobiology Group, School of Earth Sciences, University of Bristol, Life Sciences Building, Tyndall Avenue, Bristol BS8 1TQ, UK.
| | - Christine M Janis
- Bristol Palaeobiology Group, School of Earth Sciences, University of Bristol, Life Sciences Building, Tyndall Avenue, Bristol BS8 1TQ, UK
| | - Davide Pisani
- Bristol Palaeobiology Group, School of Earth Sciences, University of Bristol, Life Sciences Building, Tyndall Avenue, Bristol BS8 1TQ, UK; Bristol Palaeobiology Group, School of Biological Sciences, University of Bristol, Life Sciences Building, Tyndall Avenue, Bristol BS8 1TQ, UK
| | - Philip C J Donoghue
- Bristol Palaeobiology Group, School of Earth Sciences, University of Bristol, Life Sciences Building, Tyndall Avenue, Bristol BS8 1TQ, UK.
| | - Daniele Silvestro
- Department of Biology, University of Fribourg, 1700 Fribourg, Switzerland; Swiss Institute of Bioinformatics, 1700 Fribourg, Switzerland; Department of Biological and Environmental Sciences, University of Gothenburg, 413 19 Gothenburg, Sweden; Gothenburg Global Biodiversity Centre, 413 19 Gothenburg, Sweden.
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9
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Carruthers T, Scotland RW. Deconstructing age estimates for angiosperms. Mol Phylogenet Evol 2023:107861. [PMID: 37329931 DOI: 10.1016/j.ympev.2023.107861] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Revised: 06/08/2023] [Accepted: 06/13/2023] [Indexed: 06/19/2023]
Abstract
Estimates of the age of angiosperms from molecular phylogenies vary considerably. As in all estimates of evolutionary timescales from phylogenies, generating these estimates requires assumptions about the rate that molecular sequences are evolving (using clock models) and the time duration of the branches in a phylogeny (using fossil calibrations and branching processes). Often, it is difficult to demonstrate that these assumptions reflect current knowledge of molecular evolution or the fossil record. In this study we re-estimate the age of angiosperms using a minimal set of assumptions, therefore avoiding many of the assumptions inherent to other methods. The age estimates we generate are similar for each of the four datasets analysed, ranging from 130 to 400 Ma, but are far less precise than in previous studies. We demonstrate that this reduction in precision results from making less stringent assumptions about both rate and time, and that the analysed molecular dataset has very little effect on age estimates.
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Affiliation(s)
- Tom Carruthers
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, Michigan, 48109, USA
| | - Robert W Scotland
- Department of Biology, University of Oxford, South Parks Road, Oxford OX1 3RB, UK.
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10
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Bryłka K, Alverson AJ, Pickering RA, Richoz S, Conley DJ. Uncertainties surrounding the oldest fossil record of diatoms. Sci Rep 2023; 13:8047. [PMID: 37198388 DOI: 10.1038/s41598-023-35078-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Accepted: 05/12/2023] [Indexed: 05/19/2023] Open
Abstract
Molecular clocks estimate that diatom microalgae, one of Earth's foremost primary producers, originated near the Triassic-Jurassic boundary (200 Ma), which is close in age to the earliest, generally accepted diatom fossils of the genus Pyxidicula. During an extensive search for Jurassic diatoms from twenty-five sites worldwide, three sites yielded microfossils initially recognized as diatoms. After applying stringent safeguards and evaluation criteria, however, the fossils found at each of the three sites were rejected as new diatom records. This led us to systematically reexamine published evidence in support of Lower- and Middle-Jurassic Pyxidicula fossils. Although Pyxidicula resembles some extant radial centric diatoms and has character states that may have been similar to those of ancestral diatoms, we describe numerous sources of uncertainty regarding the reliability of these records. We conclude that the Lower Jurassic Pyxidicula fossils were most likely calcareous nannofossils, whereas the Middle Jurassic Pyxidicula species has been reassigned to the Lower Cretaceous and is likely a testate amoeba, not a diatom. Excluding the Pyxidicula fossils widens the gap between the estimated time of origin and the oldest abundant fossil diatom record to 75 million years. This study underscores the difficulties in discovering and validating ancient microfossils.
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Affiliation(s)
- Karolina Bryłka
- Department of Geology, Lund University, Sölvegatan 12, 223 62, Lund, Sweden.
| | - Andrew J Alverson
- Department of Biological Sciences, University of Arkansas, Fayetteville, AR, 72701, USA
| | | | - Sylvain Richoz
- Department of Geology, Lund University, Sölvegatan 12, 223 62, Lund, Sweden
| | - Daniel J Conley
- Department of Geology, Lund University, Sölvegatan 12, 223 62, Lund, Sweden
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11
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Tyszka AS, Bretz EC, Robertson HM, Woodcock-Girard MD, Ramanauskas K, Larson DA, Stull GW, Walker JF. Characterizing conflict and congruence of molecular evolution across organellar genome sequences for phylogenetics in land plants. FRONTIERS IN PLANT SCIENCE 2023; 14:1125107. [PMID: 37063179 PMCID: PMC10098128 DOI: 10.3389/fpls.2023.1125107] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Accepted: 03/13/2023] [Indexed: 06/19/2023]
Abstract
Chloroplasts and mitochondria each contain their own genomes, which have historically been and continue to be important sources of information for inferring the phylogenetic relationships among land plants. The organelles are predominantly inherited from the same parent, and therefore should exhibit phylogenetic concordance. In this study, we examine the mitochondrion and chloroplast genomes of 226 land plants to infer the degree of similarity between the organelles' evolutionary histories. Our results show largely concordant topologies are inferred between the organelles, aside from four well-supported conflicting relationships that warrant further investigation. Despite broad patterns of topological concordance, our findings suggest that the chloroplast and mitochondrial genomes evolved with significant differences in molecular evolution. The differences result in the genes from the chloroplast and the mitochondrion preferentially clustering with other genes from their respective organelles by a program that automates selection of evolutionary model partitions for sequence alignments. Further investigation showed that changes in compositional heterogeneity are not always uniform across divergences in the land plant tree of life. These results indicate that although the chloroplast and mitochondrial genomes have coexisted for over 1 billion years, phylogenetically, they are still evolving sufficiently independently to warrant separate models of evolution. As genome sequencing becomes more accessible, research into these organelles' evolution will continue revealing insight into the ancient cellular events that shaped not only their history, but the history of plants as a whole.
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Affiliation(s)
- Alexa S. Tyszka
- Department of Biological Sciences, University of Illinois at Chicago, Chicago, IL, United States
| | - Eric C. Bretz
- Department of Biological Sciences, University of Illinois at Chicago, Chicago, IL, United States
| | - Holly M. Robertson
- Sainsbury Laboratory, School of Biological Sciences, University of Cambridge, Cambridge, England, United Kingdom
| | - Miles D. Woodcock-Girard
- Department of Biological Sciences, University of Illinois at Chicago, Chicago, IL, United States
| | - Karolis Ramanauskas
- Department of Biological Sciences, University of Illinois at Chicago, Chicago, IL, United States
| | - Drew A. Larson
- Department of Biology, Indiana University, Bloomington, IN, United States
| | - Gregory W. Stull
- Germplasm Bank of Wild Species in Southwest China, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, China
- Department of Botany, National Museum of Natural History, Smithsonian Institution, Washington, DC, United States
| | - Joseph F. Walker
- Department of Biological Sciences, University of Illinois at Chicago, Chicago, IL, United States
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12
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Schachat SR, Goldstein PZ, Desalle R, Bobo DM, Boyce CK, Payne JL, Labandeira CC. Illusion of flight? Absence, evidence and the age of winged insects. Biol J Linn Soc Lond 2022. [DOI: 10.1093/biolinnean/blac137] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Abstract
The earliest fossils of winged insects (Pterygota) are mid-Carboniferous (latest Mississippian, 328–324 Mya), but estimates of their age based on fossil-calibrated molecular phylogenetic studies place their origin at 440–370 Mya during the Silurian or Devonian. This discrepancy would require that winged insects evaded fossilization for at least the first ~50 Myr of their history. Here, we examine the plausibility of such a gap in the fossil record, and possible explanations for it, based on comparisons with the fossil records of other arthropod groups, the distribution of first occurrence dates of pterygote families, phylogenetically informed simulations of the fossilization of Palaeozoic insects, and re-analysis of data presented by Misof and colleagues using updated fossil calibrations under a variety of prior probability settings. We do not find support for the mechanisms previously suggested to account for such an extended gap in the pterygote fossil record, including sampling bias, preservation bias, and body size. We suggest that inference of an early origin of Pterygota long prior to their first appearance in the fossil record is probably an analytical artefact of taxon sampling and choice of fossil calibration points, possibly compounded by heterogeneity in rates of sequence evolution or speciation, including radiations or ‘bursts’ during their early history.
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Affiliation(s)
- Sandra R Schachat
- Department of Geological Sciences, Stanford University , Stanford, CA , USA
| | - Paul Z Goldstein
- Systematic Entomology Laboratory, USDA, National Museum of Natural History, Smithsonian Institution , Washington, DC , USA
| | - Rob Desalle
- American Museum of Natural History, Sackler Institute for Comparative Genomics , New York, NY , USA
| | - Dean M Bobo
- American Museum of Natural History, Sackler Institute for Comparative Genomics , New York, NY , USA
- Department of Ecology, Evolution, and Environmental Biology, Columbia University , New York, NY , USA
| | - C Kevin Boyce
- Department of Geological Sciences, Stanford University , Stanford, CA , USA
| | - Jonathan L Payne
- Department of Geological Sciences, Stanford University , Stanford, CA , USA
| | - Conrad C Labandeira
- Department of Paleobiology, National Museum of Natural History, Smithsonian Institution , Washington, DC , USA
- Department of Entomology and Behavior, Ecology, Evolution, and Systematics Program, University of Maryland, College Park , MD , USA
- Capital Normal University, School of Life Sciences , Beijing , China
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13
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Beaulieu JM, O'Meara BC. Fossils Do Not Substantially Improve, and May Even Harm, Estimates of Diversification Rate Heterogeneity. Syst Biol 2022; 72:50-61. [PMID: 35861420 DOI: 10.1093/sysbio/syac049] [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: 11/19/2021] [Revised: 07/04/2022] [Accepted: 07/06/2022] [Indexed: 11/14/2022] Open
Abstract
The fossilized birth-death (FBD) model is a naturally appealing way of directly incorporating fossil information when estimating diversification rates. However, an important yet often overlooked property of the original FBD derivation is that it distinguishes between two types of sampled lineages. Here we first discuss and demonstrate the impact of severely undersampling, and even not including fossils that represent samples of lineages that also had sampled descendants. We then explore the benefits of including fossils, generally, by implementing and then testing two-types of FBD models, including one that converts a fossil set into stratigraphic ranges, in more complex likelihood-based models that assume multiple rate classes across the tree. Under various simulation scenarios, including a scenario that exists far outside the set of models we evaluated, including fossils rarely outperforms analyses that exclude them altogether. At best, the inclusion of fossils improves precision but does not influence bias. Similarly, we found that converting the fossil set to stratigraphic ranges, which is one way to remedy the effects of undercounting the number of k-type fossils, results in turnover rates and extinction fraction estimates that are generally underestimated. While fossils remain essential for understanding diversification through time, in the specific case of understanding diversification given an existing, largely modern tree, they are not especially beneficial.
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Affiliation(s)
- Jeremy M Beaulieu
- Department of Biological Sciences, University of Arkansas, Fayetteville, Arkansas, 72701 USA
| | - Brian C O'Meara
- Department of Ecology and Evolutionary Biology, University of Tennessee, Knoxville, Tennessee, 37996-1610 USA
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14
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Pelosi JA, Kim EH, Barbazuk WB, Sessa EB. Phylotranscriptomics Illuminates the Placement of Whole Genome Duplications and Gene Retention in Ferns. FRONTIERS IN PLANT SCIENCE 2022; 13:882441. [PMID: 35909764 PMCID: PMC9330400 DOI: 10.3389/fpls.2022.882441] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Accepted: 06/16/2022] [Indexed: 05/31/2023]
Abstract
Ferns are the second largest clade of vascular plants with over 10,000 species, yet the generation of genomic resources for the group has lagged behind other major clades of plants. Transcriptomic data have proven to be a powerful tool to assess phylogenetic relationships, using thousands of markers that are largely conserved across the genome, and without the need to sequence entire genomes. We assembled the largest nuclear phylogenetic dataset for ferns to date, including 2884 single-copy nuclear loci from 247 transcriptomes (242 ferns, five outgroups), and investigated phylogenetic relationships across the fern tree, the placement of whole genome duplications (WGDs), and gene retention patterns following WGDs. We generated a well-supported phylogeny of ferns and identified several regions of the fern phylogeny that demonstrate high levels of gene tree-species tree conflict, which largely correspond to areas of the phylogeny that have been difficult to resolve. Using a combination of approaches, we identified 27 WGDs across the phylogeny, including 18 large-scale events (involving more than one sampled taxon) and nine small-scale events (involving only one sampled taxon). Most inferred WGDs occur within single lineages (e.g., orders, families) rather than on the backbone of the phylogeny, although two inferred events are shared by leptosporangiate ferns (excluding Osmundales) and Polypodiales (excluding Lindsaeineae and Saccolomatineae), clades which correspond to the majority of fern diversity. We further examined how retained duplicates following WGDs compared across independent events and found that functions of retained genes were largely convergent, with processes involved in binding, responses to stimuli, and certain organelles over-represented in paralogs while processes involved in transport, organelles derived from endosymbiotic events, and signaling were under-represented. To date, our study is the most comprehensive investigation of the nuclear fern phylogeny, though several avenues for future research remain unexplored.
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Affiliation(s)
- Jessie A. Pelosi
- Department of Biology, University of Florida, Gainesville, FL, United States
| | - Emily H. Kim
- Department of Microbiology and Cell Science, University of Florida, Gainesville, FL, United States
| | - W. Brad Barbazuk
- Department of Biology, University of Florida, Gainesville, FL, United States
- Genetics Institute, University of Florida, Gainesville, FL, United States
| | - Emily B. Sessa
- Department of Biology, University of Florida, Gainesville, FL, United States
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15
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Sauquet H, Ramírez-Barahona S, Magallón S. What is the age of flowering plants? JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:3840-3853. [PMID: 35438718 DOI: 10.1093/jxb/erac130] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Accepted: 03/31/2022] [Indexed: 06/14/2023]
Abstract
The origin of flowering plants (angiosperms) was one of the most transformative events in the history of our planet. Despite considerable interest from multiple research fields, numerous questions remain, including the age of the group as a whole. Recent studies have reported a perplexing range of estimates for the crown-group age of angiosperms, from ~140 million years (Ma; Early Cretaceous) to 270 Ma (Permian). Both ends of the spectrum are now supported by both macroevolutionary analyses of the fossil record and fossil-calibrated molecular dating analyses. Here, we first clarify and distinguish among the three ages of angiosperms: the age of their divergence with acrogymnosperms (stem age); the age(s) of emergence of their unique, distinctive features including flowers (morphological age); and the age of the most recent common ancestor of all their living species (crown age). We then demonstrate, based on recent studies, that fossil-calibrated molecular dating estimates of the crown-group age of angiosperms have little to do with either the amount of molecular data or the number of internal fossil calibrations included. Instead, we argue that this age is almost entirely conditioned by its own prior distribution (typically a calibration density set by the user in Bayesian analyses). Lastly, we discuss which future discoveries or novel types of analyses are most likely to bring more definitive answers. In the meantime, we propose that the age of angiosperms is best described as largely unknown (140-270 Ma) and that contrasting age estimates in the literature mostly reflect conflicting prior distributions. We also suggest that future work that depends on the time scale of flowering plant diversification be designed to integrate over this vexing uncertainty.
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Affiliation(s)
- Hervé Sauquet
- National Herbarium of New South Wales (NSW), Royal Botanic Gardens and Domain Trust, Sydney, Australia
- Evolution and Ecology Research Centre, School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, Australia
| | | | - Susana Magallón
- Instituto de Biología, Universidad Nacional Autónoma de México, Ciudad de México, México
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16
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Barba-Montoya J, Tao Q, Kumar S. Assessing rapid relaxed-clock methods for phylogenomic dating. Genome Biol Evol 2021; 13:6423996. [PMID: 34751377 PMCID: PMC8633771 DOI: 10.1093/gbe/evab251] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/04/2021] [Indexed: 11/16/2022] Open
Abstract
Rapid relaxed-clock dating methods are frequently applied to analyze phylogenomic data sets containing hundreds to thousands of sequences because of their accuracy and computational efficiency. However, the relative performance of different rapid dating methods is yet to be compared on the same data sets, and, thus, the power and pitfalls of selecting among these approaches remain unclear. We compared the accuracy, bias, and coverage probabilities of RelTime, treePL, and least-squares dating time estimates by applying them to analyze computer-simulated data sets in which evolutionary rates varied extensively among branches in the phylogeny. RelTime estimates were consistently more accurate than the other two, particularly when evolutionary rates were autocorrelated or shifted convergently among lineages. The 95% confidence intervals (CIs) around RelTime dates showed appropriate coverage probabilities (95% on average), but other methods produced rather low coverage probabilities because of overly narrow CIs of time estimates. Overall, RelTime appears to be a more efficient method for estimating divergence times for large phylogenies.
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Affiliation(s)
- Jose Barba-Montoya
- Institute for Genomics and Evolutionary Medicine, Temple University, Philadelphia, PA, USA.,Department of Biology, Temple University, Philadelphia, PA, USA
| | - Qiqing Tao
- Institute for Genomics and Evolutionary Medicine, Temple University, Philadelphia, PA, USA.,Department of Biology, Temple University, Philadelphia, PA, USA
| | - Sudhir Kumar
- Institute for Genomics and Evolutionary Medicine, Temple University, Philadelphia, PA, USA.,Department of Biology, Temple University, Philadelphia, PA, USA.,Center of Excellence in Genomic Medicine Research, King Abdulaziz University, Jeddah, Saudi Arabia
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17
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Walker JF, Smith SA, Hodel RGJ, Moyroud E. Concordance-based approaches for the inference of relationships and molecular rates with phylogenomic datasets. Syst Biol 2021; 71:943-958. [PMID: 34240209 DOI: 10.1093/sysbio/syab052] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Revised: 06/23/2021] [Accepted: 07/01/2021] [Indexed: 11/12/2022] Open
Abstract
Gene tree conflict is common and finding methods to analyze and alleviate the negative effects that conflict has on species tree analysis is a crucial part of phylogenomics. This study aims to expand the discussion of inferring species trees and molecular branch lengths when conflict is present. Conflict is typically examined in two ways: inferring its prevalence, and inferring the influence of the individual genes (how strongly one gene supports any given topology compared to an alternative topology). Here, we examine a procedure for incorporating both conflict and the influence of genes in order to infer evolutionary relationships. All supported relationships in the gene trees are analyzed and the likelihood of the genes constrained to these relationships is summed to provide a likelihood for the relationship. Consensus tree assembly is conducted based on the sum of likelihoods for a given relationship and choosing relationships based on the most likely relationship assuming it does not conflict with a relationship that has a higher likelihood score. If it is not possible for all most likely relationships to be combined into a single bifurcating tree then multiple trees are produced and a consensus tree with a polytomy is created. This procedure allows for more influential genes to have greater influence on an inferred relationship, does not assume conflict has arisen from any one source, and does not force the dataset to produce a single bifurcating tree. Using this approach on three empirical datasets, we examine and discuss the relationship between influence and prevalence of gene tree conflict. We find that in one of the datasets, assembling a bifurcating consensus tree solely composed of the most likely relationships is impossible. To account for conflict in molecular rate analysis we also introduce a concordance-based approach to the summary and estimation of branch lengths suitable for downstream comparative analyses. We demonstrate through simulation that even under high levels of stochastic conflict, the mean and median of the concordant rates recapitulate the true molecular rate better than using a supermatrix approach. Using a large phylogenomic dataset, we examine rate heterogeneity across concordant genes with a focus on the branch subtending crown angiosperms. Notably, we find highly variable rates of evolution along the branch subtending crown angiosperms. The approaches outlined here have several limitations, but they also represent some alternative methods for harnessing the complexity of phylogenomic datasets and enrich our inferences of both species' relationships and evolutionary processes.
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Affiliation(s)
- Joseph F Walker
- The Sainsbury Laboratory, University of Cambridge, 47 Bateman Street, Cambridge CB2 1LR, UK.,Department of Biological Sciences, University of Illinois at Chicago, Chicago, IL, 60607 U.S.A
| | - Stephen A Smith
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI, USA
| | - Richard G J Hodel
- Department of Botany, National Museum of Natural History, MRC 166, Smithsonian Institution, Washington, DC, 20013-7012, USA
| | - Edwige Moyroud
- The Sainsbury Laboratory, University of Cambridge, 47 Bateman Street, Cambridge CB2 1LR, UK.,Department of Genetics, University of Cambridge, Downing Street, Cambridge CB2 3EH, UK
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18
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Yang Y, Zhang C, Lenton TM, Yan X, Zhu M, Zhou M, Tao J, Phelps TJ, Cao Z. The evolution pathway of ammonia-oxidizing archaea shaped by major geological events. Mol Biol Evol 2021; 38:3637-3648. [PMID: 33993308 PMCID: PMC8382903 DOI: 10.1093/molbev/msab129] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Primordial nitrification processes have been studied extensively using geochemical approaches, but the biological origination of nitrification remains unclear. Ammonia-oxidizing archaea (AOA) are widely distributed nitrifiers and implement the rate-limiting step in nitrification. They are hypothesized to have been important players in the global nitrogen cycle in Earth’s early history. We performed systematic phylogenomic and marker gene analyses to elucidate the diversification timeline of AOA evolution. Our results suggested that the AOA ancestor experienced terrestrial geothermal environments at ∼1,165 Ma (1,928–880 Ma), and gradually evolved into mesophilic soil at ∼652 Ma (767–554 Ma) before diversifying into marine settings at ∼509 Ma (629–412 Ma) and later into shallow and deep oceans, respectively. Corroborated by geochemical evidence and modeling, the timing of key diversification nodes can be linked to the global magmatism and glaciation associated with the assembly and breakup of the supercontinent Rodinia, and the later oxygenation of the deep ocean. Results of this integrated study shed light on the geological forces that may have shaped the evolutionary pathways of the AOA, which played an important role in the ancient global nitrogen cycle.
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Affiliation(s)
- Yiyan Yang
- Department of Gastroenterology, Shanghai 10th People's Hospital, School of Life Sciences and Technology, Tongji University, Shanghai, 200092, China
| | - Chuanlun Zhang
- Shenzhen Key Laboratory of Marine Archaea Geo-Omics, Southern University of Science and Technology, Shenzhen, 518055, P.R. China.,Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, 510000, China.,Shanghai Sheshan National Geophysical Observatory, Shanghai, 201602, China
| | - Timothy M Lenton
- Global Systems Institute, University of Exeter, Exeter, EX4 4QE, United Kingdom
| | - Xinmiao Yan
- Department of Gastroenterology, Shanghai 10th People's Hospital, School of Life Sciences and Technology, Tongji University, Shanghai, 200092, China
| | - Maoyan Zhu
- State Key Laboratory of Palaeobiology and Stratigraphy & Center for Excellence in Life and Paleoenvironment, Nanjing Institute of Geology and Palaeontology, Chinese Academy of Sciences, Nanjing, 210008, P.R. China.,College of Earth and Planetary Sciences, University of Chinese Academy of Sciences, Beijing, 100049, P.R. China
| | - Mengdi Zhou
- Department of Gastroenterology, Shanghai 10th People's Hospital, School of Life Sciences and Technology, Tongji University, Shanghai, 200092, China
| | - Jianchang Tao
- Shenzhen Key Laboratory of Marine Archaea Geo-Omics, Southern University of Science and Technology, Shenzhen, 518055, P.R. China
| | - Tommy J Phelps
- Shenzhen Key Laboratory of Marine Archaea Geo-Omics, Southern University of Science and Technology, Shenzhen, 518055, P.R. China
| | - Zhiwei Cao
- Department of Gastroenterology, Shanghai 10th People's Hospital, School of Life Sciences and Technology, Tongji University, Shanghai, 200092, China
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19
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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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20
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Abstract
Phylogenetic trees inferred from sequence data often have branch lengths measured in the expected number of substitutions and therefore, do not have divergence times estimated. These trees give an incomplete view of evolutionary histories since many applications of phylogenies require time trees. Many methods have been developed to convert the inferred branch lengths from substitution unit to time unit using calibration points, but none is universally accepted as they are challenged in both scalability and accuracy under complex models. Here, we introduce a new method that formulates dating as a nonconvex optimization problem where the variance of log-transformed rate multipliers is minimized across the tree. On simulated and real data, we show that our method, wLogDate, is often more accurate than alternatives and is more robust to various model assumptions.
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Affiliation(s)
- Uyen Mai
- Department of Computer Science and Engineering, UC, San Diego, CA
| | - Siavash Mirarab
- Department of Electrical and Computer Engineering, UC, San Diego, CA
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21
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Spasojevic T, Broad GR, Sääksjärvi IE, Schwarz M, Ito M, Korenko S, Klopfstein S. Mind the Outgroup and Bare Branches in Total-Evidence Dating: a Case Study of Pimpliform Darwin Wasps (Hymenoptera, Ichneumonidae). Syst Biol 2021; 70:322-339. [PMID: 33057674 PMCID: PMC7875445 DOI: 10.1093/sysbio/syaa079] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2019] [Revised: 10/02/2020] [Accepted: 10/02/2020] [Indexed: 01/16/2023] Open
Abstract
Taxon sampling is a central aspect of phylogenetic study design, but it has received limited attention in the context of total-evidence dating, a widely used dating approach that directly integrates molecular and morphological information from extant and fossil taxa. We here assess the impact of commonly employed outgroup sampling schemes and missing morphological data in extant taxa on age estimates in a total-evidence dating analysis under the uniform tree prior. Our study group is Pimpliformes, a highly diverse, rapidly radiating group of parasitoid wasps of the family Ichneumonidae. We analyze a data set comprising 201 extant and 79 fossil taxa, including the oldest fossils of the family from the Early Cretaceous and the first unequivocal representatives of extant subfamilies from the mid-Paleogene. Based on newly compiled molecular data from ten nuclear genes and a morphological matrix that includes 222 characters, we show that age estimates become both older and less precise with the inclusion of more distant and more poorly sampled outgroups. These outgroups not only lack morphological and temporal information but also sit on long terminal branches and considerably increase the evolutionary rate heterogeneity. In addition, we discover an artifact that might be detrimental for total-evidence dating: "bare-branch attraction," namely high attachment probabilities of certain fossils to terminal branches for which morphological data are missing. Using computer simulations, we confirm the generality of this phenomenon and show that a large phylogenetic distance to any of the extant taxa, rather than just older age, increases the risk of a fossil being misplaced due to bare-branch attraction. After restricting outgroup sampling and adding morphological data for the previously attracting, bare branches, we recover a Jurassic origin for Pimpliformes and Ichneumonidae. This first age estimate for the group not only suggests an older origin than previously thought but also that diversification of the crown group happened well before the Cretaceous-Paleogene boundary. Our case study demonstrates that in order to obtain robust age estimates, total-evidence dating studies need to be based on a thorough and balanced sampling of both extant and fossil taxa, with the aim of minimizing evolutionary rate heterogeneity and missing morphological information. [Bare-branch attraction; ichneumonids; fossils; morphological matrix; phylogeny; RoguePlots.].
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Affiliation(s)
- Tamara Spasojevic
- Abteilung Wirbellose Tiere Invertebrates, Naturhistorisches Museum der Burgergemeinde Bern, Bernastrasse 15, 3005 Bern, Switzerland
- Institute of Ecology and Evolution, Department of Biology, University of Bern, 3012 Bern, Switzerland
- Department of Entomology, National Museum of Natural History, Washington, DC 20560, USA
| | - Gavin R Broad
- Department of Life Sciences, Natural History Museum, London SW7 5BD, UK
| | | | | | - Masato Ito
- Graduate School of Agricultural Science, Department of Agrobioscience, Kobe University, 657-8501 Japan
| | - Stanislav Korenko
- Department of Agroecology and Crop Production, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences Prague, 165 21 Prague 6, Suchdol, Czech Republic
| | - Seraina Klopfstein
- Abteilung Wirbellose Tiere Invertebrates, Naturhistorisches Museum der Burgergemeinde Bern, Bernastrasse 15, 3005 Bern, Switzerland
- Institute of Ecology and Evolution, Department of Biology, University of Bern, 3012 Bern, Switzerland
- Abteilung für Biowissenschaften, Naturhistorisches Museum Basel, 4051 Basel, Switzerland
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22
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McFadden CS, Quattrini AM, Brugler MR, Cowman PF, Dueñas LF, Kitahara MV, Paz-García DA, Reimer JD, Rodríguez E. Phylogenomics, Origin, and Diversification of Anthozoans (Phylum Cnidaria). Syst Biol 2021; 70:635-647. [PMID: 33507310 DOI: 10.1093/sysbio/syaa103] [Citation(s) in RCA: 50] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Revised: 12/18/2020] [Accepted: 12/21/2020] [Indexed: 01/19/2023] Open
Abstract
Anthozoan cnidarians (corals and sea anemones) include some of the world's most important foundation species, capable of building massive reef complexes that support entire ecosystems. Although previous molecular phylogenetic analyses have revealed widespread homoplasy of the morphological characters traditionally used to define orders and families of anthozoans, analyses using mitochondrial genes or rDNA have failed to resolve many key nodes in the phylogeny. With a fully resolved, time-calibrated phylogeny for 234 species constructed from hundreds of ultraconserved elements and exon loci, we explore the evolutionary origins of the major clades of Anthozoa and some of their salient morphological features. The phylogeny supports reciprocally monophyletic Hexacorallia and Octocorallia, with Ceriantharia as the earliest diverging hexacorals; two reciprocally monophyletic clades of Octocorallia; and monophyly of all hexacoral orders with the exception of the enigmatic sea anemone Relicanthus daphneae. Divergence dating analyses place Anthozoa in the Cryogenian to Tonian periods (648-894 Ma), older than has been suggested by previous studies. Ancestral state reconstructions indicate that the ancestral anthozoan was a solitary polyp that had bilateral symmetry and lacked a skeleton. Colonial growth forms and the ability to precipitate calcium carbonate evolved in the Ediacaran (578 Ma) and Cambrian (503 Ma) respectively; these hallmarks of reef-building species have subsequently arisen multiple times independently in different orders. Anthozoans formed associations with photosymbionts by the Devonian (383 Ma), and photosymbioses have been gained and lost repeatedly in all orders. Together, these results have profound implications for the interpretation of the Precambrian environment and the early evolution of metazoans.[Bilateral symmetry; coloniality; coral; early metazoans; exon capture; Hexacorallia; Octocorallia photosymbiosis; sea anemone; ultraconserved elements.].
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Affiliation(s)
- Catherine S McFadden
- Department of Biology, Harvey Mudd College, 1250 N. Dartmouth Ave., Claremont, CA 91711 USA
| | - Andrea M Quattrini
- Department of Biology, Harvey Mudd College, 1250 N. Dartmouth Ave., Claremont, CA 91711 USA.,Department of Invertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, DC 20560, USA
| | - Mercer R Brugler
- Division of Invertebrate Zoology, American Museum of Natural History, Central Park West at 79th Street, New York, NY 10024, USA.,Biological Sciences Department, NYC College of Technology, City University of New York, 285 Jay Street, Brooklyn, NY 11201, USA.,Department of Natural Sciences, University of South Carolina Beaufort, 801 Carteret Street, Beaufort, SC 29902, USA
| | - Peter F Cowman
- ARC Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, QLD 4811, Australia.,Biodiversity and Geosciences Program, Museum of Tropical Queensland, Queensland Museum, Townsville, QLD 4810, Australia
| | - Luisa F Dueñas
- Departamento de Biología, Facultad de Ciencias, Universidad Nacional de Colombia-Sede Bogotá, Carrera 30 No.45-03 Edificio 421, Bogotá, D.C., Colombia
| | - Marcelo V Kitahara
- Department of Marine Science, Federal University of São Paulo, Santos, SP 11070-100 Brazil.,Centre for Marine Biology, University of São Paulo, São Sebastião, SP 11612-109 Brazil
| | - David A Paz-García
- CONACyT-Centro de Investigaciones Biológicas del Noroeste (CIBNOR). Laboratorio de Necton y Ecología de Arrecifes. Calle IPN 195, Col. Playa Palo de Santa Rita Sur, 23096 La Paz, B.C.S., México
| | - James D Reimer
- Molecular Invertebrate Systematics and Ecology Laboratory, Department of Marine Science, Chemistry, and Biology, Faculty of Science, University of the Ryukyus, 1 Senbaru, Nishihara, Okinawa 903-0213, Japan.,Tropical Biosphere Research Center, University of the Ryukyus, 1 Senbaru, Nishihara, Okinawa 903-0213, Japan
| | - Estefanía Rodríguez
- Division of Invertebrate Zoology, American Museum of Natural History, Central Park West at 79th Street, New York, NY 10024, USA
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23
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Coiro M, Martínez LCA, Upchurch GR, Doyle JA. Evidence for an extinct lineage of angiosperms from the Early Cretaceous of Patagonia and implications for the early radiation of flowering plants. THE NEW PHYTOLOGIST 2020; 228:344-360. [PMID: 32400897 DOI: 10.1111/nph.16657] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Accepted: 05/05/2020] [Indexed: 06/11/2023]
Abstract
The pinnately lobed Aptian leaf fossil Mesodescolea plicata was originally described as a cycad, but new evidence from cuticle structure suggests that it is an angiosperm. Here we document the morphology and cuticle anatomy of Mesodescolea and explore its significance for early angiosperm evolution. We observed macrofossils and cuticles of Mesodescolea with light, scanning electron and transmission electron microscopy, and used phylogenetic methods to test its relationships among extant angiosperms. Mesodescolea has chloranthoid teeth and tertiary veins forming elongate areoles. Its cuticular morphology and ultrastructure reject cycadalean affinities, whereas its guard cell shape and stomatal ledges are angiospermous. It shares variable stomatal complexes and epidermal oil cells with angiosperm leaves from the lower Potomac Group. Phylogenetic analyses and hypothesis testing support its placement within the basal ANITA grade, most likely in Austrobaileyales, but it diverges markedly in leaf form and venation. Although many Early Cretaceous angiosperms fall within the morphological range of extant taxa, Mesodescolea reveals unexpected early morphological and ecophysiological trends. Its similarity to other Early Cretaceous lobate leaves, many identified previously as eudicots but in some cases pre-dating the appearance of tricolpate pollen, may indicate that Mesodescolea is part of a larger extinct lineage of angiosperms.
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Affiliation(s)
- Mario Coiro
- Department of Systematic and Evolutionary Botany, University of Zurich, Zurich, 8008, Switzerland
| | - Leandro C A Martínez
- Instituto de Botánica Darwinion (ANCEFN - CONICET), Labardén 200, San Isidro, Buenos Aires, Argentina
| | - Garland R Upchurch
- Department of Biology, Texas State University, San Marcos, TX, 78666, USA
| | - James A Doyle
- Department of Evolution and Ecology, University of California Davis, Davis, CA, 95616, USA
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24
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Budd GE, Mann RP. Survival and selection biases in early animal evolution and a source of systematic overestimation in molecular clocks. Interface Focus 2020; 10:20190110. [PMID: 32637066 PMCID: PMC7333906 DOI: 10.1098/rsfs.2019.0110] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/06/2020] [Indexed: 12/21/2022] Open
Abstract
Important evolutionary events such as the Cambrian Explosion have inspired many attempts at explanation: why do they happen when they do? What shapes them, and why do they eventually come to an end? However, much less attention has been paid to the idea of a 'null hypothesis'-that certain features of such diversifications arise simply through their statistical structure. Such statistical features also appear to influence our perception of the timing of these events. Here, we show in particular that study of unusually large clades leads to systematic overestimates of clade ages from some types of molecular clocks, and that the size of this effect may be enough to account for the puzzling mismatches seen between these molecular clocks and the fossil record. Our analysis of the fossil record of the late Ediacaran to Cambrian suggests that it is likely to be recording a true evolutionary radiation of the bilaterians at this time, and that explanations involving various sorts of cryptic origins for the bilaterians do not seem to be necessary.
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Affiliation(s)
- Graham E. Budd
- Department of Earth Sciences, Palaeobiology, Uppsala University, Villavägen 16, Uppsala 752 36, Sweden
| | - Richard P. Mann
- Department of Statistics, School of Mathematics, University of Leeds, Leeds LS2 9JT, UK
- The Alan Turing Institute, London NW1 2DB, UK
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25
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Molecular Clocks without Rocks: New Solutions for Old Problems. Trends Genet 2020; 36:845-856. [PMID: 32709458 DOI: 10.1016/j.tig.2020.06.002] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2020] [Revised: 06/02/2020] [Accepted: 06/11/2020] [Indexed: 02/07/2023]
Abstract
Molecular data have been used to date species divergences ever since they were described as documents of evolutionary history in the 1960s. Yet, an inadequate fossil record and discordance between gene trees and species trees are persistently problematic. We examine how, by accommodating gene tree discordance and by scaling branch lengths to absolute time using mutation rate and generation time, multispecies coalescent (MSC) methods can potentially overcome these challenges. We find that time estimates can differ - in some cases, substantially - depending on whether MSC methods or traditional phylogenetic methods that apply concatenation are used, and whether the tree is calibrated with pedigree-based mutation rates or with fossils. We discuss the advantages and shortcomings of both approaches and provide practical guidance for data analysis when using these methods.
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26
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Affiliation(s)
- Casper J van der Kooi
- Groningen Institute for Evolutionary Life Sciences, University of Groningen, NL-9747AG Groningen, Netherlands.
| | - Jeff Ollerton
- Faculty of Arts, Science and Technology, University of Northampton, Northampton NN1 5PH, UK
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27
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Shafir A, Azouri D, Goldberg EE, Mayrose I. Heterogeneity in the rate of molecular sequence evolution substantially impacts the accuracy of detecting shifts in diversification rates. Evolution 2020; 74:1620-1639. [PMID: 32510165 DOI: 10.1111/evo.14036] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2019] [Accepted: 05/17/2020] [Indexed: 12/01/2022]
Abstract
As species richness varies along the tree of life, there is a great interest in identifying factors that affect the rates by which lineages speciate or go extinct. To this end, theoretical biologists have developed a suite of phylogenetic comparative methods that aim to identify where shifts in diversification rates had occurred along a phylogeny and whether they are associated with some traits. Using these methods, numerous studies have predicted that speciation and extinction rates vary across the tree of life. In this study, we show that asymmetric rates of sequence evolution lead to systematic biases in the inferred phylogeny, which in turn lead to erroneous inferences regarding lineage diversification patterns. The results demonstrate that as the asymmetry in sequence evolution rates increases, so does the tendency to select more complicated models that include the possibility of diversification rate shifts. These results thus suggest that any inference regarding shifts in diversification pattern should be treated with great caution, at least until any biases regarding the molecular substitution rate have been ruled out.
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Affiliation(s)
- Anat Shafir
- School of Plant Sciences and Food security, Tel Aviv University, Ramat Aviv, 69978, Israel
| | - Dana Azouri
- School of Plant Sciences and Food security, Tel Aviv University, Ramat Aviv, 69978, Israel.,School of Molecular Cell Biology & Biotechnology, Tel Aviv University, Ramat Aviv, 69978, Israel
| | | | - Itay Mayrose
- School of Plant Sciences and Food security, Tel Aviv University, Ramat Aviv, 69978, Israel
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28
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Soto Gomez M, Lin Q, Silva Leal E, Gallaher TJ, Scherberich D, Mennes CB, Smith SY, Graham SW. A bi‐organellar phylogenomic study of Pandanales: inference of higher‐order relationships and unusual rate‐variation patterns. Cladistics 2020; 36:481-504. [DOI: 10.1111/cla.12417] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2019] [Revised: 02/20/2020] [Accepted: 02/21/2020] [Indexed: 12/21/2022] Open
Affiliation(s)
- Marybel Soto Gomez
- Department of Botany University of British Columbia 6270 University Boulevard Vancouver BC V6T 1Z4 Canada
- UBC Botanical Garden & Centre for Plant Research University of British Columbia 6804 Marine Drive SW Vancouver BC V6T 1Z4 Canada
| | - Qianshi Lin
- Department of Botany University of British Columbia 6270 University Boulevard Vancouver BC V6T 1Z4 Canada
- UBC Botanical Garden & Centre for Plant Research University of British Columbia 6804 Marine Drive SW Vancouver BC V6T 1Z4 Canada
| | - Eduardo Silva Leal
- Universidade Federal Rural da Amazônia, Campus Capanema Avenida Barão de Capanema s/n Capanema68700-665 PA Brazil
| | | | - David Scherberich
- Jardin Botanique de la Ville de Lyon Mairie de Lyon69205 Lyon Cedex 01 France
| | | | - Selena Y. Smith
- Department of Earth & Environmental Sciences and Museum of Paleontology University of Michigan Ann Arbor MI 48109 USA
| | - Sean W. Graham
- Department of Botany University of British Columbia 6270 University Boulevard Vancouver BC V6T 1Z4 Canada
- UBC Botanical Garden & Centre for Plant Research University of British Columbia 6804 Marine Drive SW Vancouver BC V6T 1Z4 Canada
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29
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Kallal RJ, Dimitrov D, Arnedo MA, Giribet G, Hormiga G. Monophyly, Taxon Sampling, and the Nature of Ranks in the Classification of Orb-Weaving Spiders (Araneae: Araneoidea). Syst Biol 2020; 69:401-411. [PMID: 31165170 DOI: 10.1093/sysbio/syz043] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2019] [Revised: 05/21/2019] [Accepted: 05/24/2019] [Indexed: 12/25/2022] Open
Abstract
We address some of the taxonomic and classification changes proposed by Kuntner et al. (2019) in a comparative study on the evolution of sexual size dimorphism in nephiline spiders. Their proposal to recircumscribe araneids and to rank the subfamily Nephilinae as a family is fundamentally flawed as it renders the family Araneidae paraphyletic. We discuss the importance of monophyly, outgroup selection, and taxon sampling, the subjectivity of ranks, and the implications of the age of origin criterion to assign categorical ranks in biological classifications. We explore the outcome of applying the approach of Kuntner et al. (2019) to the classification of spiders with emphasis on the ecribellate orb-weavers (Araneoidea) using a recently published dated phylogeny. We discuss the implications of including the putative sister group of Nephilinae (the sexually dimorphic genus Paraplectanoides) and the putative sister group of Araneidae (the miniature, monomorphic family Theridiosomatidae). We propose continuation of the phylogenetic classification put forth by Dimitrov et al. (2017), and we formally rank Nephilinae and Phonognathinae as subfamilies of Araneidae. Our classification better reflects the understanding of the phylogenetic placement and evolutionary history of nephilines and phonognathines while maintaining the diagnosability of Nephilinae. It also fulfills the fundamental requirement that taxa must be monophyletic, and thus avoids the paraphyly of Araneidae implied by Kuntner et al. (2019).
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Affiliation(s)
- Robert J Kallal
- Department of Biological Sciences, The George Washington University, 2029 G St. NW, Washington, DC 20052, USA
| | - Dimitar Dimitrov
- Department of Natural History, University Museum of Bergen, University of Bergen, P.O. Box 7800, 5020 Bergen, Norway
| | - Miquel A Arnedo
- Department of Evolutionary Biology, Ecology and Environmental Sciences, & Biodiversity Research Institute (IRBio) Universitat de Barcelona, Avinguda Diagonal 643, Barcelona, Spain.,Museum of Comparative Zoology, Department of Organismic and Evolutionary Biology, Harvard University, 26 Oxford Street, Cambridge, MA 02138, USA
| | - Gonzalo Giribet
- Museum of Comparative Zoology, Department of Organismic and Evolutionary Biology, Harvard University, 26 Oxford Street, Cambridge, MA 02138, USA
| | - Gustavo Hormiga
- Department of Biological Sciences, The George Washington University, 2029 G St. NW, Washington, DC 20052, USA
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30
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Radial or Bilateral? The Molecular Basis of Floral Symmetry. Genes (Basel) 2020; 11:genes11040395. [PMID: 32268578 PMCID: PMC7230197 DOI: 10.3390/genes11040395] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2020] [Revised: 04/01/2020] [Accepted: 04/03/2020] [Indexed: 01/10/2023] Open
Abstract
In the plant kingdom, the flower is one of the most relevant evolutionary novelties. Floral symmetry has evolved multiple times from the ancestral condition of radial to bilateral symmetry. During evolution, several transcription factors have been recruited by the different developmental pathways in relation to the increase of plant complexity. The MYB proteins are among the most ancient plant transcription factor families and are implicated in different metabolic and developmental processes. In the model plant Antirrhinum majus, three MYB transcription factors (DIVARICATA, DRIF, and RADIALIS) have a pivotal function in the establishment of floral dorsoventral asymmetry. Here, we present an updated report of the role of the DIV, DRIF, and RAD transcription factors in both eudicots and monocots, pointing out their functional changes during plant evolution. In addition, we discuss the molecular models of the establishment of flower symmetry in different flowering plants.
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31
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Yang L, Su D, Chang X, Foster CS, Sun L, Huang CH, Zhou X, Zeng L, Ma H, Zhong B. Phylogenomic Insights into Deep Phylogeny of Angiosperms Based on Broad Nuclear Gene Sampling. PLANT COMMUNICATIONS 2020; 1:100027. [PMID: 33367231 PMCID: PMC7747974 DOI: 10.1016/j.xplc.2020.100027] [Citation(s) in RCA: 48] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2019] [Revised: 01/23/2020] [Accepted: 01/25/2020] [Indexed: 05/02/2023]
Abstract
Angiosperms (flowering plants) are the most diverse and species-rich group of plants. The vast majority (∼99.95%) of angiosperms form a clade called Mesangiospermae, which is subdivided into five major groups: eudicots, monocots, magnoliids, Chloranthales, and Ceratophyllales. The relationships among these Mesangiospermae groups have been the subject of long debate. In this study, we assembled a phylogenomic dataset of 1594 genes from 151 angiosperm taxa, including representatives of all five lineages, to investigate the phylogeny of major angiosperm lineages under both coalescent- and concatenation-based methods. We dissected the phylogenetic signal and found that more than half of the genes lack phylogenetic information for the backbone of angiosperm phylogeny. We further removed the genes with weak phylogenetic signal and showed that eudicots, Ceratophyllales, and Chloranthales form a clade, with magnoliids and monocots being the next successive sister lineages. Similar frequencies of gene tree conflict are suggestive of incomplete lineage sorting along the backbone of the angiosperm phylogeny. Our analyses suggest that a fully bifurcating species tree may not be the best way to represent the early radiation of angiosperms. Meanwhile, we inferred that the crown-group angiosperms originated approximately between 255.1 and 222.2 million years ago, and Mesangiospermae diversified into the five extant groups in a short time span (∼27 million years) at the Early to Late Jurassic.
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Affiliation(s)
- Lingxiao Yang
- College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Danyan Su
- College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Xin Chang
- College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Charles S.P. Foster
- School of Life and Environmental Sciences, University of Sydney, Sydney, Australia
| | - Linhua Sun
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
| | - Chien-Hsun Huang
- State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development, Ministry of Education Key Laboratory of Biodiversity Sciences and Ecological Engineering, School of Life Sciences, Fudan University, Shanghai, China
| | - Xiaofan Zhou
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou, China
| | - Liping Zeng
- Institute for Integrative Genome Biology and Department of Botany and Plant Sciences, University of California, Riverside, CA, USA
| | - Hong Ma
- Department of Biology, Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA, USA
| | - Bojian Zhong
- College of Life Sciences, Nanjing Normal University, Nanjing, China
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32
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Budd GE, Mann RP. The dynamics of stem and crown groups. SCIENCE ADVANCES 2020; 6:eaaz1626. [PMID: 32128421 PMCID: PMC7030935 DOI: 10.1126/sciadv.aaz1626] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2019] [Accepted: 12/03/2019] [Indexed: 05/22/2023]
Abstract
The fossil record of the origins of major groups such as animals and birds has generated considerable controversy, especially when it conflicts with timings based on molecular clock estimates. Here, we model the diversity of "stem" (basal) and "crown" (modern) members of groups using a "birth-death model," the results of which qualitatively match many large-scale patterns seen in the fossil record. Typically, the stem group diversifies rapidly until the crown group emerges, at which point its diversity collapses, followed shortly by its extinction. Mass extinctions can disturb this pattern and create long stem groups such as the dinosaurs. Crown groups are unlikely to emerge either cryptically or just before mass extinctions, in contradiction to popular hypotheses such as the "phylogenetic fuse". The patterns revealed provide an essential context for framing ecological and evolutionary explanations for how major groups originate, and strengthen our confidence in the reliability of the fossil record.
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Affiliation(s)
- Graham E. Budd
- Department of Earth Sciences, Palaeobiology Programme, Uppsala University, Uppsala, Sweden
- Corresponding author.
| | - Richard P. Mann
- Department of Statistics, School of Mathematics, University of Leeds, Leeds, UK
- The Alan Turing Institute, London, UK
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33
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Nie Y, Foster CSP, Zhu T, Yao R, Duchêne DA, Ho SYW, Zhong B. Accounting for Uncertainty in the Evolutionary Timescale of Green Plants Through Clock-Partitioning and Fossil Calibration Strategies. Syst Biol 2020; 69:1-16. [PMID: 31058981 DOI: 10.1093/sysbio/syz032] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2018] [Revised: 04/30/2019] [Accepted: 05/02/2019] [Indexed: 11/13/2022] Open
Abstract
Establishing an accurate evolutionary timescale for green plants (Viridiplantae) is essential to understanding their interaction and coevolution with the Earth's climate and the many organisms that rely on green plants. Despite being the focus of numerous studies, the timing of the origin of green plants and the divergence of major clades within this group remain highly controversial. Here, we infer the evolutionary timescale of green plants by analyzing 81 protein-coding genes from 99 chloroplast genomes, using a core set of 21 fossil calibrations. We test the sensitivity of our divergence-time estimates to various components of Bayesian molecular dating, including the tree topology, clock models, clock-partitioning schemes, rate priors, and fossil calibrations. We find that the choice of clock model affects date estimation and that the independent-rates model provides a better fit to the data than the autocorrelated-rates model. Varying the rate prior and tree topology had little impact on age estimates, with far greater differences observed among calibration choices and clock-partitioning schemes. Our analyses yield date estimates ranging from the Paleoproterozoic to Mesoproterozoic for crown-group green plants, and from the Ediacaran to Middle Ordovician for crown-group land plants. We present divergence-time estimates of the major groups of green plants that take into account various sources of uncertainty. Our proposed timeline lays the foundation for further investigations into how green plants shaped the global climate and ecosystems, and how embryophytes became dominant in terrestrial environments.
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Affiliation(s)
- Yuan Nie
- College of Life Sciences, Nanjing Normal University, Nanjing 210046, China
| | - Charles S P Foster
- School of Life and Environmental Sciences, University of Sydney, Sydney, New South Wales 2006, Australia
| | - Tianqi Zhu
- National Center for Mathematics and Interdisciplinary Sciences, Key Laboratory of Random Complex Structures and Data Science, Academy of Mathematics and Systems Science, Chinese Academy of Sciences, Beijing 100000, China
| | - Ru Yao
- College of Life Sciences, Nanjing Normal University, Nanjing 210046, China
| | - David A Duchêne
- School of Life and Environmental Sciences, University of Sydney, Sydney, New South Wales 2006, Australia
| | - Simon Y W Ho
- School of Life and Environmental Sciences, University of Sydney, Sydney, New South Wales 2006, Australia
| | - Bojian Zhong
- College of Life Sciences, Nanjing Normal University, Nanjing 210046, China
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34
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Bateman RM. Hunting the Snark: the flawed search for mythical Jurassic angiosperms. JOURNAL OF EXPERIMENTAL BOTANY 2020; 71:22-35. [PMID: 31538196 DOI: 10.1093/jxb/erz411] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2019] [Accepted: 09/03/2019] [Indexed: 06/10/2023]
Abstract
Several recent palaeobotanical studies claim to have found and described pre-Cretaceous angiosperm macrofossils. With rare exceptions, these papers fail to define a flower, do not acknowledge that fossils require character-based rather than group-based classification, do not explicitly state which morphological features would unambiguously identify a fossil as angiospermous, ignore the modern conceptual framework of phylogeny reconstruction, and infer features in the fossils in question that are interpreted differently by (or even invisible to) other researchers. This unfortunate situation is compounded by the relevant fossils being highly disarticulated two-dimensional compression-impressions lacking anatomical preservation. Given current evidence, all supposed pre-Cretaceous angiosperms are assignable to other major clades among the gymnosperms sensu lato. By any workable morphological definition, flowers are not confined to, and therefore cannot delimit, the angiosperm clade. More precisely defined character states that are potentially diagnostic of angiosperms must by definition originate on the phylogenetic branch that immediately precedes the angiosperm crown group. Although the most reliable candidates for diagnostic characters (triploid endosperm reflecting double fertilization, closed carpel, bitegmic ovule, and phloem companion cells) are rarely preserved and/or difficult to detect unambiguously, similar characters have occasionally been preserved in high-quality permineralized non-angiosperm fossils. The angiosperm radiation documented by Early Cretaceous fossils involves only lineages closely similar to extant taxonomic families, lacks obvious morphological gaps, and (as agreed by both the fossil record and molecular phylogenies) was relatively rapid-all features that suggest a primary radiation. It is unlikely that ancestors of the crown group common ancestor would have fulfilled a character-based definition of (and thereby required expansion of the concept of) an angiosperm; they would instead form a new element of the non-angiosperm members of the 'anthophyte' grade, competing with Caytonia to be viewed as morphologically determined sister group for angiosperms. Conclusions drawn from molecular phylogenetics should not be allowed to routinely constrain palaeobotanical inferences; reciprocal illumination between different categories of data offers greater explanatory power than immediately resorting to Grand Syntheses. The Jurassic angiosperm-essentially a product of molecular phylogenetics-may have become the holy grail of palaeobotany but it appears equally mythical.
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35
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Friis EM, Crane PR, Pedersen KR. The endothelium in seeds of early angiosperms. THE NEW PHYTOLOGIST 2019; 224:1419-1424. [PMID: 31240716 DOI: 10.1111/nph.16024] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Accepted: 06/20/2019] [Indexed: 06/09/2023]
Affiliation(s)
- Else Marie Friis
- Department of Palaeobiology, Swedish Museum of Natural History, PO Box 50007, SE-104 05, Stockholm, Sweden
| | - Peter R Crane
- Oak Spring Garden Foundation, 1776 Loughborough Lane, Upperville, VA, 20184, USA
- School of Forestry and Environmental Studies, Yale University, New Haven, CT, 06511, USA
| | - Kaj Raunsgaard Pedersen
- Department of Geoscience, University of Aarhus, Høegh-Guldbergs Gade 2, DK-8000, Aarhus C, Denmark
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36
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Abstract
Lepidoptera play key roles in many biological systems. Butterflies are hypothesized to have evolved contemporaneously with flowering plants, and moths are thought to have gained anti-bat defenses in response to echolocating predatory bats, but these hypotheses have largely gone untested. Using a transcriptomic, dated evolutionary tree of Lepidoptera, we demonstrate that the most recent common ancestor of Lepidoptera is considerably older than previously hypothesized. The oldest moths in crown Lepidoptera were present in the Carboniferous, some 300 million years ago, and began to diversify largely in synchrony with angiosperms. We show that multiple lineages of moths independently evolved hearing organs well before the origin of bats, rejecting the hypothesis that lepidopteran hearing organs arose in response to these predators. Butterflies and moths (Lepidoptera) are one of the major superradiations of insects, comprising nearly 160,000 described extant species. As herbivores, pollinators, and prey, Lepidoptera play a fundamental role in almost every terrestrial ecosystem. Lepidoptera are also indicators of environmental change and serve as models for research on mimicry and genetics. They have been central to the development of coevolutionary hypotheses, such as butterflies with flowering plants and moths’ evolutionary arms race with echolocating bats. However, these hypotheses have not been rigorously tested, because a robust lepidopteran phylogeny and timing of evolutionary novelties are lacking. To address these issues, we inferred a comprehensive phylogeny of Lepidoptera, using the largest dataset assembled for the order (2,098 orthologous protein-coding genes from transcriptomes of 186 species, representing nearly all superfamilies), and dated it with carefully evaluated synapomorphy-based fossils. The oldest members of the Lepidoptera crown group appeared in the Late Carboniferous (∼300 Ma) and fed on nonvascular land plants. Lepidoptera evolved the tube-like proboscis in the Middle Triassic (∼241 Ma), which allowed them to acquire nectar from flowering plants. This morphological innovation, along with other traits, likely promoted the extraordinary diversification of superfamily-level lepidopteran crown groups. The ancestor of butterflies was likely nocturnal, and our results indicate that butterflies became day-flying in the Late Cretaceous (∼98 Ma). Moth hearing organs arose multiple times before the evolutionary arms race between moths and bats, perhaps initially detecting a wide range of sound frequencies before being co-opted to specifically detect bat sonar. Our study provides an essential framework for future comparative studies on butterfly and moth evolution.
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Bromham L. Six Impossible Things before Breakfast: Assumptions, Models, and Belief in Molecular Dating. Trends Ecol Evol 2019; 34:962. [DOI: 10.1016/j.tree.2019.07.015] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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38
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A Nearly Complete Juvenile Skull of the Marsupial Sparassocynus derivatus from the Pliocene of Argentina, the Affinities of “Sparassocynids”, and the Diversification of Opossums (Marsupialia; Didelphimorphia; Didelphidae). J MAMM EVOL 2019. [DOI: 10.1007/s10914-019-09471-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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39
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Coiro M, Doyle JA, Hilton J. How deep is the conflict between molecular and fossil evidence on the age of angiosperms? THE NEW PHYTOLOGIST 2019; 223:83-99. [PMID: 30681148 DOI: 10.1111/nph.15708] [Citation(s) in RCA: 65] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Accepted: 01/04/2019] [Indexed: 05/06/2023]
Abstract
The timing of the origin of angiosperms is a hotly debated topic in plant evolution. Molecular dating analyses that consistently retrieve pre-Cretaceous ages for crown-group angiosperms have eroded confidence in the fossil record, which indicates a radiation and possibly also origin in the Early Cretaceous. Here, we evaluate paleobotanical evidence on the age of the angiosperms, showing how fossils provide crucial data for clarifying the situation. Pollen floras document a Northern Gondwanan appearance of monosulcate angiosperms in the Valanginian and subsequent poleward spread of monosulcates and tricolpate eudicots, accelerating in the Albian. The sequence of pollen types agrees with molecular phylogenetic inferences on the course of pollen evolution, but it conflicts strongly with Triassic and early Jurassic molecular ages, and the discrepancy is difficult to explain by geographic or taphonomic biases. Critical scrutiny shows that supposed pre-Cretaceous angiosperms either represent other plant groups or lack features that might confidently assign them to the angiosperms. However, the record may allow the Late Jurassic existence of ecologically restricted angiosperms, like those seen in the basal ANITA grade. Finally, we examine recently recognized biases in molecular dating and argue that a thoughtful integration of fossil and molecular evidence could help resolve these conflicts.
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Affiliation(s)
- Mario Coiro
- Department of Systematic and Evolutionary Botany, University of Zurich, 8008, Zurich, Switzerland
| | - James A Doyle
- Department of Evolution and Ecology, University of California, Davis, CA, 95616, USA
| | - Jason Hilton
- School of Geography, Earth and Environmental Sciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
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40
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Tao Q, Tamura K, U. Battistuzzi F, Kumar S. A Machine Learning Method for Detecting Autocorrelation of Evolutionary Rates in Large Phylogenies. Mol Biol Evol 2019; 36:811-824. [PMID: 30689923 PMCID: PMC6804408 DOI: 10.1093/molbev/msz014] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
New species arise from pre-existing species and inherit similar genomes and environments. This predicts greater similarity of the tempo of molecular evolution between direct ancestors and descendants, resulting in autocorrelation of evolutionary rates in the tree of life. Surprisingly, molecular sequence data have not confirmed this expectation, possibly because available methods lack the power to detect autocorrelated rates. Here, we present a machine learning method, CorrTest, to detect the presence of rate autocorrelation in large phylogenies. CorrTest is computationally efficient and performs better than the available state-of-the-art method. Application of CorrTest reveals extensive rate autocorrelation in DNA and amino acid sequence evolution of mammals, birds, insects, metazoans, plants, fungi, parasitic protozoans, and prokaryotes. Therefore, rate autocorrelation is a common phenomenon throughout the tree of life. These findings suggest concordance between molecular and nonmolecular evolutionary patterns, and they will foster unbiased and precise dating of the tree of life.
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Affiliation(s)
- Qiqing Tao
- Institute for Genomics and Evolutionary Medicine, Temple University, Philadelphia, PA
- Department of Biology, Temple University, Philadelphia, PA
| | - Koichiro Tamura
- Department of Biological Sciences, Tokyo Metropolitan University, Tokyo, Japan
- Research Center for Genomics and Bioinformatics, Tokyo Metropolitan University, Tokyo, Japan
| | | | - Sudhir Kumar
- Institute for Genomics and Evolutionary Medicine, Temple University, Philadelphia, PA
- Department of Biology, Temple University, Philadelphia, PA
- Center for Excellence in Genome Medicine and Research, King Abdulaziz University, Jeddah, Saudi Arabia
- Corresponding author: E-mail:
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41
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Widhelm TJ, Grewe F, Huang JP, Mercado-Díaz JA, Goffinet B, Lücking R, Moncada B, Mason-Gamer R, Lumbsch HT. Multiple historical processes obscure phylogenetic relationships in a taxonomically difficult group (Lobariaceae, Ascomycota). Sci Rep 2019; 9:8968. [PMID: 31222061 PMCID: PMC6586878 DOI: 10.1038/s41598-019-45455-x] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2018] [Accepted: 06/03/2019] [Indexed: 12/19/2022] Open
Abstract
In the age of next-generation sequencing, the number of loci available for phylogenetic analyses has increased by orders of magnitude. But despite this dramatic increase in the amount of data, some phylogenomic studies have revealed rampant gene-tree discordance that can be caused by many historical processes, such as rapid diversification, gene duplication, or reticulate evolution. We used a target enrichment approach to sample 400 single-copy nuclear genes and estimate the phylogenetic relationships of 13 genera in the lichen-forming family Lobariaceae to address the effect of data type (nucleotides and amino acids) and phylogenetic reconstruction method (concatenation and species tree approaches). Furthermore, we examined datasets for evidence of historical processes, such as rapid diversification and reticulate evolution. We found incongruence associated with sequence data types (nucleotide vs. amino acid sequences) and with different methods of phylogenetic reconstruction (species tree vs. concatenation). The resulting phylogenetic trees provided evidence for rapid and reticulate evolution based on extremely short branches in the backbone of the phylogenies. The observed rapid and reticulate diversifications may explain conflicts among gene trees and the challenges to resolving evolutionary relationships. Based on divergence times, the diversification at the backbone occurred near the Cretaceous-Paleogene (K-Pg) boundary (65 Mya) which is consistent with other rapid diversifications in the tree of life. Although some phylogenetic relationships within the Lobariaceae family remain with low support, even with our powerful phylogenomic dataset of up to 376 genes, our use of target-capturing data allowed for the novel exploration of the mechanisms underlying phylogenetic and systematic incongruence.
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Affiliation(s)
- Todd J Widhelm
- Field Museum, Science and Education, Chicago, 60605, USA.
- University of Illinois at Chicago, Biological Sciences, Chicago, 60607, USA.
| | - Felix Grewe
- Field Museum, Grainger Bioinformatics Center, Chicago, 60605, USA
| | - Jen-Pan Huang
- Field Museum, Science and Education, Chicago, 60605, USA
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
| | | | - Bernard Goffinet
- University of Connecticut, Ecology and Evolutionary Biology, Storrs, 06268, USA
| | - Robert Lücking
- Botanischer Garten und Botanisches Museum, Herbarium, Berlin, 14195, Germany
| | - Bibiana Moncada
- Universidad Distrital Francisco José de Caldas, Torre de Laboratorios, Herbario, Bogotá, 11021, Colombia
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Tamura K, Tao Q, Kumar S. Theoretical Foundation of the RelTime Method for Estimating Divergence Times from Variable Evolutionary Rates. Mol Biol Evol 2019; 35:1770-1782. [PMID: 29893954 PMCID: PMC5995221 DOI: 10.1093/molbev/msy044] [Citation(s) in RCA: 118] [Impact Index Per Article: 23.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
RelTime estimates divergence times by relaxing the assumption of a strict molecular clock in a phylogeny. It shows excellent performance in estimating divergence times for both simulated and empirical molecular sequence data sets in which evolutionary rates varied extensively throughout the tree. RelTime is computationally efficient and scales well with increasing size of data sets. Until now, however, RelTime has not had a formal mathematical foundation. Here, we show that the basis of the RelTime approach is a relative rate framework (RRF) that combines comparisons of evolutionary rates in sister lineages with the principle of minimum rate change between evolutionary lineages and their respective descendants. We present analytical solutions for estimating relative lineage rates and divergence times under RRF. We also discuss the relationship of RRF with other approaches, including the Bayesian framework. We conclude that RelTime will be useful for phylogenies with branch lengths derived not only from molecular data, but also morphological and biochemical traits.
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Affiliation(s)
- Koichiro Tamura
- Department of Biological Sciences, Tokyo Metropolitan University, Hachioji, Tokyo, Japan.,Research Center for Genomics and Bioinformatics, Tokyo Metropolitan University, Hachioji, Tokyo, Japan
| | - Qiqing Tao
- Institute for Genomics and Evolutionary Medicine, Temple University, Philadelphia, PA.,Department of Biology, Temple University, Philadelphia, PA
| | - Sudhir Kumar
- Institute for Genomics and Evolutionary Medicine, Temple University, Philadelphia, PA.,Department of Biology, Temple University, Philadelphia, PA.,Center for Excellence in Genome Medicine and Research, King Abdulaziz University, Jeddah, Saudi Arabia
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43
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Cusimano N, Renner SS. Sequential horizontal gene transfers from different hosts in a widespread Eurasian parasitic plant, Cynomorium coccineum. AMERICAN JOURNAL OF BOTANY 2019; 106:679-689. [PMID: 31081928 DOI: 10.1002/ajb2.1286] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2018] [Accepted: 03/19/2019] [Indexed: 06/09/2023]
Abstract
PREMISE Parasitic plants with large geographic ranges, and different hosts in parts of their range, may acquire horizontally transferred genes (HGTs), which might sometimes leave a footprint of gradual host and range expansion. Cynomorium coccineum, the only member of the Saxifragales family Cynomoriaceae, is a root holoparasite that occurs in water-stressed habitats from western China to the Canary Islands. It parasitizes at least 10 angiosperm families from different orders, some of them only in parts of its range. This parasite therefore offers an opportunity to trace HGTs as long as parasite-host pairs can be obtained and sequenced. METHODS By sequencing mitochondrial, plastid, and nuclear loci from parasite-host pairs from throughout the parasite's range and with prior information from completely assembled mitochondrial and plastid genomes, we detected 10 HGTs of five mitochondrial genes. RESULTS The 10 HGTs appear to have occurred sequentially as C. coccineum expanded from East to West. Molecular-clock models yield Cynomorium stem ages between 66 and 156 Myr, with relaxed clocks converging on 66-67 Myr. Chinese Sapindales, probably Nitraria, were the first source of transferred genes, followed by Iranian and Mediterranean Caryophyllales. The most recently acquired gene appears to come from a Tamarix host in the Iberian Peninsula. CONCLUSIONS Data on HGTs that have accumulated over the past 15 years, along with this discovery of multiple HGTs within a single widespread species, underline the need for more whole-genome data from parasite-host pairs to investigate whether and how transferred copies coexist with, or replace, native functional genes.
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Affiliation(s)
- Natalie Cusimano
- Systematic Botany and Mycology, Faculty of Biology, University of Munich (LMU), Munich, Germany
| | - Susanne S Renner
- Systematic Botany and Mycology, Faculty of Biology, University of Munich (LMU), Munich, Germany
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44
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Li HT, Yi TS, Gao LM, Ma PF, Zhang T, Yang JB, Gitzendanner MA, Fritsch PW, Cai J, Luo Y, Wang H, van der Bank M, Zhang SD, Wang QF, Wang J, Zhang ZR, Fu CN, Yang J, Hollingsworth PM, Chase MW, Soltis DE, Soltis PS, Li DZ. Origin of angiosperms and the puzzle of the Jurassic gap. NATURE PLANTS 2019; 5:461-470. [PMID: 31061536 DOI: 10.1038/s41477-019-0421-0] [Citation(s) in RCA: 360] [Impact Index Per Article: 72.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2018] [Accepted: 04/02/2019] [Indexed: 05/19/2023]
Abstract
Angiosperms are by far the most species-rich clade of land plants, but their origin and early evolutionary history remain poorly understood. We reconstructed angiosperm phylogeny based on 80 genes from 2,881 plastid genomes representing 85% of extant families and all orders. With a well-resolved plastid tree and 62 fossil calibrations, we dated the origin of the crown angiosperms to the Upper Triassic, with major angiosperm radiations occurring in the Jurassic and Lower Cretaceous. This estimated crown age is substantially earlier than that of unequivocal angiosperm fossils, and the difference is here termed the 'Jurassic angiosperm gap'. Our time-calibrated plastid phylogenomic tree provides a highly relevant framework for future comparative studies of flowering plant evolution.
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Affiliation(s)
- Hong-Tao Li
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
| | - Ting-Shuang Yi
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
| | - Lian-Ming Gao
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
| | - Peng-Fei Ma
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
| | - Ting Zhang
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
| | - Jun-Bo Yang
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
| | - Matthew A Gitzendanner
- Florida Museum of Natural History, University of Florida, Gainesville, FL, USA
- Department of Biology, University of Florida, Gainesville, FL, USA
| | | | - Jie Cai
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
| | - Yang Luo
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
| | - Hong Wang
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
| | - Michelle van der Bank
- Department of Botany & Plant Biotechnology, University of Johannesburg, Johannesburg, South Africa
| | - Shu-Dong Zhang
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
| | - Qing-Feng Wang
- Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China
| | - Jian Wang
- Queensland Herbarium, Department of Environment and Science, Brisbane Botanic Gardens, Toowong, Queensland, Australia
| | - Zhi-Rong Zhang
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
| | - Chao-Nan Fu
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
- Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, China
| | - Jing Yang
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
| | | | - Mark W Chase
- Royal Botanic Gardens, Kew, UK
- Department of Environment and Agriculture, Curtin University, Bentley, Western Australia, Australia
| | - Douglas E Soltis
- Florida Museum of Natural History, University of Florida, Gainesville, FL, USA
- Department of Biology, University of Florida, Gainesville, FL, USA
- Genetics Institute, University of Florida, Gainesville, FL, USA
- Biodiversity Institute, University of Florida, Gainesville, FL, USA
| | - Pamela S Soltis
- Florida Museum of Natural History, University of Florida, Gainesville, FL, USA.
- Genetics Institute, University of Florida, Gainesville, FL, USA.
- Biodiversity Institute, University of Florida, Gainesville, FL, USA.
| | - De-Zhu Li
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China.
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China.
- Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, China.
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45
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Borowiec ML, Rabeling C, Brady SG, Fisher BL, Schultz TR, Ward PS. Compositional heterogeneity and outgroup choice influence the internal phylogeny of the ants. Mol Phylogenet Evol 2019; 134:111-121. [DOI: 10.1016/j.ympev.2019.01.024] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2017] [Revised: 01/25/2019] [Accepted: 01/29/2019] [Indexed: 10/27/2022]
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46
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Affiliation(s)
- Jennifer R Mandel
- Department of Biological Sciences, The University of Memphis, Memphis, TN, USA.
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47
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Anderson BM, Thiele KR, Grierson PF, Krauss SL, Nevill PG, Small ID, Zhong X, Barrett MD. Recent range expansion in Australian hummock grasses ( Triodia) inferred using genotyping-by-sequencing. AOB PLANTS 2019; 11:plz017. [PMID: 31037212 PMCID: PMC6481909 DOI: 10.1093/aobpla/plz017] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2018] [Accepted: 03/20/2019] [Indexed: 05/30/2023]
Abstract
The Australian arid zone (AAZ) has undergone aridification and the formation of vast sandy deserts since the mid-Miocene. Studies on AAZ organisms, particularly animals, have shown patterns of mesic ancestry, persistence in rocky refugia and range expansions in arid lineages. There has been limited molecular investigation of plants in the AAZ, particularly of taxa that arrived in Australia after the onset of aridification. Here we investigate populations of the widespread AAZ grass Triodia basedowii to determine whether there is evidence for a recent range expansion, and if so, its source and direction. We also undertake a dating analysis for the species complex to which T. basedowii belongs, in order to place its diversification in relation to changes in AAZ climate and landscapes. We analyse a genomic single nucleotide polymorphism data set from 17 populations of T. basedowii in a recently developed approach for detecting the signal and likely origin of a range expansion. We also use alignments from existing and newly sequenced plastomes from across Poaceae for analysis in BEAST to construct fossil-calibrated phylogenies. Across a range of sampling parameters and outgroups, we detected a consistent signal of westward expansion for T. basedowii, originating in central or eastern Australia. Divergence time estimation indicates that Triodia began to diversify in the late Miocene (crown 7.0-8.8 million years (Ma)), and the T. basedowii complex began to radiate during the Pleistocene (crown 1.4-2.0 Ma). This evidence for range expansion in an arid-adapted plant is consistent with similar patterns in AAZ animals and likely reflects a general response to the opening of new habitat during aridification. Radiation of the T. basedowii complex through the Pleistocene has been associated with preferences for different substrates, providing an explanation why only one lineage is widespread across sandy deserts.
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Affiliation(s)
- Benjamin M Anderson
- School of Biological Sciences, The University of Western Australia, Crawley, Western Australia, Australia
- Kings Park and Botanic Garden, Botanic Gardens and Parks Authority, Kings Park, Western Australia, Australia
| | - Kevin R Thiele
- School of Biological Sciences, The University of Western Australia, Crawley, Western Australia, Australia
| | - Pauline F Grierson
- School of Biological Sciences, The University of Western Australia, Crawley, Western Australia, Australia
| | - Siegfried L Krauss
- School of Biological Sciences, The University of Western Australia, Crawley, Western Australia, Australia
- Kings Park and Botanic Garden, Botanic Gardens and Parks Authority, Kings Park, Western Australia, Australia
| | - Paul G Nevill
- School of Biological Sciences, The University of Western Australia, Crawley, Western Australia, Australia
- Australian Research Council Centre for Mine Site Restoration, Curtin University, Bentley, Western Australia, Australia
| | - Ian D Small
- Australian Research Council Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, Crawley, Western Australia, Australia
| | - Xiao Zhong
- Australian Research Council Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, Crawley, Western Australia, Australia
| | - Matthew D Barrett
- School of Biological Sciences, The University of Western Australia, Crawley, Western Australia, Australia
- Kings Park and Botanic Garden, Botanic Gardens and Parks Authority, Kings Park, Western Australia, Australia
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48
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Gamboa M, Muranyi D, Kanmori S, Watanabe K. Molecular phylogeny and diversification timing of the Nemouridae family (Insecta, Plecoptera) in the Japanese Archipelago. PLoS One 2019; 14:e0210269. [PMID: 30633758 PMCID: PMC6329508 DOI: 10.1371/journal.pone.0210269] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2018] [Accepted: 12/19/2018] [Indexed: 11/30/2022] Open
Abstract
The generation of the high species diversity of insects in Japan was profoundly influenced by the formation of the Japanese Archipelago. We explored the species diversification and biogeographical history of the Nemouridae Billberg, 1820 family in the Japanese Archipelago using mitochondrial DNA and nuclear DNA markers. We collected 49 species among four genera: Indonemoura Baumann, 1975; Protonemura Kempny, 1898; Amphinemura, Ris 1902 and Nemoura Latreille, 1796 in Japan, China, South Korea and North America. We estimated their divergence times-based on three molecular clock node calibrations-using Bayesian phylogeography approaches. Our results suggested that Japanese Archipelago formation events resulted in diversification events in the middle of the Cretaceous (<120 Ma), speciation in the Paleogene (<50 Ma) and intra-species diversification segregated into eastern and western Japan of the Fossa Magna region at late Neogene (20 Ma). The Indonemoura samples were genetically separated into two clades-that of Mainland China and that of Japan. The Japanese clade clustered with the Nemouridae species from North America, suggesting the possibility of a colonisation event prior to the formation of the Japanese Archipelago. We believe that our results enhanced the understanding both of the origin of the species and of local species distribution in the Japanese Archipelago.
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Affiliation(s)
- Maribet Gamboa
- Department of Civil and Environmental Engineering, Ehime University, Matsuyama, Japan
| | - David Muranyi
- Department of Civil and Environmental Engineering, Ehime University, Matsuyama, Japan
- Deparment of Zoology, Plant Protection Institute Centre for Agricultural Research, Hungarian Academy of Sciences, Budapest, Hungary
| | - Shota Kanmori
- Department of Civil and Environmental Engineering, Ehime University, Matsuyama, Japan
| | - Kozo Watanabe
- Department of Civil and Environmental Engineering, Ehime University, Matsuyama, Japan
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49
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Phylogenomics recovers monophyly and early Tertiary diversification of Dipteronia (Sapindaceae). Mol Phylogenet Evol 2019; 130:9-17. [DOI: 10.1016/j.ympev.2018.09.012] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2018] [Revised: 09/16/2018] [Accepted: 09/19/2018] [Indexed: 11/23/2022]
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50
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Abstract
This study investigated long-term substitution rate differences using three calibration points, divergences between lobe-finned vertebrates and ray-finned fish, between mammals and sauropsids, and between holosteans (gar and bowfin) and teleost fish with amino acid sequence data of 625 genes for 25 bony vertebrates. The result showed that the substitution rate was two to three times higher in the stem branches of lobe-finned vertebrates before the mammal-sauropsid divergence than in amniotes. The rate in the stem branch of ray-finned fish before the holostean-teleost fish divergence was also a few times higher than the holostean rate, whereas it was similar to or somewhat slower than the teleost fish rate. The phylogenetic relationship of coelacanth and lungfish with tetrapod was difficult to determine because of the short interval of the divergences. Considering the high rate in the stem branches, the divergences of coelacanth and lungfish from the stem branch were estimated as 408–427 Ma and 399–414 Ma, respectively, with the interval of 9–13 Myr. With the external calibration of the mammal-sauropsid split, the estimated times for ordinal divergences within eutherian mammals tend to be smaller than those in previous studies that used the calibration points within the lineage, with deeper divergences before the Cretaceous–Paleogene boundary and shallower ones after the boundary. In contrast the estimated times within birds were larger than those of previous studies, with the divergence between Galliformes and Anseriformes ∼80 Ma and that between Galloanserae and Neoaves 110 Ma.
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Affiliation(s)
- Naoko Takezaki
- Life Science Research Center, Kagawa University, Kitagun, Kagawa, Japan
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