201
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Heng LM, Zheng YL, Zhao YB, Wang YJ. Radiation of members of the Soroserishookeriana complex (Asteraceae) on the Qinghai-Tibetan Plateau and their proposed taxonomic treatment. PHYTOKEYS 2018; 114:11-25. [PMID: 30613179 PMCID: PMC6308221 DOI: 10.3897/phytokeys.114.29914] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/20/2018] [Accepted: 11/27/2018] [Indexed: 06/09/2023]
Abstract
The existence of intermediate types is a major obstacle that can hinder the circumscription of species. Elucidating the mechanism responsible for intermediate types is essential for achieving a reasonable taxonomical treatment. In this study, we explored the evolutionary history and taxonomic treatment of the Soroserishookeriana (C.B.Clarke) Stebbins complex, which comprises six named taxa that may be taxonomically distinct and are all native to the Qingha-Tibetan Plateau (QTP). We made an investigation across the distribution range of Soroseris Stebbins and sampled 27 populations, mostly from the complex. Internal transcribed spacer (ITS) and two chloroplast loci were sequenced and analysed using the neighbour-joining and Bayesian inference methods. The resulting phylogenies show no well supported inconsistence in topologies, in line with the lack of incongruence detected by the length difference test. However, all the trees were largely unresolved within S.hookeriana complex, irrespective of the optimality criterion employed. We interpret these results as an experience of radiation, which is a common process for native genera on the QTP. Thus, we suggest that all of the morphotypes might be different forms, generated by incipient speciation due to recent explosive differentiation, possibly triggered by the drastic environmental changes of the QTP. Given their evolutionary history, we propose a pragmatic method for treating all of these species as subspecies with a total of four new combinations.
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Affiliation(s)
- La-Mei Heng
- State Key Laboratory of Grassland Agro-Ecosystem, School of Life Sciences, Lanzhou University, Lanzhou 730000, PR ChinaLanzhou UniversityLanzhouChina
| | - Yu-Lin Zheng
- State Key Laboratory of Grassland Agro-Ecosystem, School of Life Sciences, Lanzhou University, Lanzhou 730000, PR ChinaLanzhou UniversityLanzhouChina
| | - Yong-Bao Zhao
- State Key Laboratory of Grassland Agro-Ecosystem, School of Life Sciences, Lanzhou University, Lanzhou 730000, PR ChinaLanzhou UniversityLanzhouChina
| | - Yu-Jin Wang
- State Key Laboratory of Grassland Agro-Ecosystem, School of Life Sciences, Lanzhou University, Lanzhou 730000, PR ChinaLanzhou UniversityLanzhouChina
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202
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Beck RMD, Baillie C. Improvements in the fossil record may largely resolve current conflicts between morphological and molecular estimates of mammal phylogeny. Proc Biol Sci 2018; 285:20181632. [PMID: 30963896 PMCID: PMC6304057 DOI: 10.1098/rspb.2018.1632] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2018] [Accepted: 11/23/2018] [Indexed: 01/16/2023] Open
Abstract
Phylogenies of mammals based on morphological data continue to show several major areas of conflict with the current consensus view of their relationships, which is based largely on molecular data. This raises doubts as to whether current morphological character sets are able to accurately resolve mammal relationships. We tested this under a hypothetical 'best case scenario' by using ancestral state reconstruction (under both maximum parsimony and maximum likelihood) to infer the morphologies of fossil ancestors for all clades present in a recent comprehensive DNA sequence-based phylogeny of mammals, and then seeing what effect the subsequent inclusion of these predicted ancestors had on unconstrained phylogenetic analyses of morphological data. We found that this resulted in topologies that are highly congruent with the current consensus phylogeny, at least when the predicted ancestors are assumed to be well preserved and densely sampled. Most strikingly, several analyses recovered the monophyly of clades that have never been found in previous morphology-only studies, such as Afrotheria and Laurasiatheria. Our results suggest that, at least in principle, improvements in the fossil record-specifically the discovery of fossil taxa that preserve the ancestral or near-ancestral morphologies of the nodes in the current consensus-may be sufficient to largely reconcile morphological and molecular estimates of mammal phylogeny, even using current morphological character sets.
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Affiliation(s)
- Robin M. D. Beck
- School of Environment and Life Sciences, University of Salford, Manchester M5 4WT, UK
| | - Charles Baillie
- School of Environment and Life Sciences, University of Salford, Manchester M5 4WT, UK
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203
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Silvestro D, Warnock RCM, Gavryushkina A, Stadler T. Closing the gap between palaeontological and neontological speciation and extinction rate estimates. Nat Commun 2018; 9:5237. [PMID: 30532040 PMCID: PMC6286320 DOI: 10.1038/s41467-018-07622-y] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2017] [Accepted: 11/13/2018] [Indexed: 11/09/2022] Open
Abstract
Measuring the pace at which speciation and extinction occur is fundamental to understanding the origin and evolution of biodiversity. Both the fossil record and molecular phylogenies of living species can provide independent estimates of speciation and extinction rates, but often produce strikingly divergent results. Despite its implications, the theoretical reasons for this discrepancy remain unknown. Here, we reveal a conceptual and methodological basis able to reconcile palaeontological and molecular evidence: discrepancies are driven by different implicit assumptions about the processes of speciation and species evolution in palaeontological and neontological analyses. We present the "birth-death chronospecies" model that clarifies the definition of speciation and extinction processes allowing for a coherent joint analysis of fossil and phylogenetic data. Using simulations and empirical analyses we demonstrate not only that this model explains much of the apparent incongruence between fossils and phylogenies, but that differences in rate estimates are actually informative about the prevalence of different speciation modes.
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Affiliation(s)
- Daniele Silvestro
- Department of Biological and Environmental Sciences, University of Gothenburg, 41319, Gothenburg, Sweden.
- Global Gothenburg Biodiversity Centre, 41319, Gothenburg, Sweden.
- Department of Computational Biology, University of Lausanne, Lausanne, 1015, Switzerland.
- Swiss Institute of Bioinformatics (SIB), 1015, Lausanne, Switzerland.
| | - Rachel C M Warnock
- Swiss Institute of Bioinformatics (SIB), 1015, Lausanne, Switzerland
- Department of Biosystems Science & Engineering, Eidgenössische Technische Hochschule Zürich, 4058, Basel, Switzerland
| | | | - Tanja Stadler
- Swiss Institute of Bioinformatics (SIB), 1015, Lausanne, Switzerland
- Department of Biosystems Science & Engineering, Eidgenössische Technische Hochschule Zürich, 4058, Basel, Switzerland
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204
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Strullu-Derrien C, Selosse MA, Kenrick P, Martin FM. The origin and evolution of mycorrhizal symbioses: from palaeomycology to phylogenomics. THE NEW PHYTOLOGIST 2018; 220:1012-1030. [PMID: 29573278 DOI: 10.1111/nph.15076] [Citation(s) in RCA: 124] [Impact Index Per Article: 20.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2017] [Accepted: 01/14/2018] [Indexed: 05/05/2023]
Abstract
Contents Summary 1012 I. Introduction 1013 II. The mycorrhizal symbiosis at the dawn and rise of the land flora 1014 III. From early land plants to early trees: the origin of roots and true mycorrhizas 1016 IV. The diversification of the AM symbiosis 1019 V. The ECM symbiosis 1021 VI. The recently evolved ericoid and orchid mycorrhizas 1023 VII. Limits of paleontological vs genetic approaches and perspectives 1023 Acknowledgements 1025 References 1025 SUMMARY: The ability of fungi to form mycorrhizas with plants is one of the most remarkable and enduring adaptations to life on land. The occurrence of mycorrhizas is now well established in c. 85% of extant plants, yet the geological record of these associations is sparse. Fossils preserved under exceptional conditions provide tantalizing glimpses into the evolutionary history of mycorrhizas, showing the extent of their occurrence and aspects of their evolution in extinct plants. The fossil record has important roles to play in establishing a chronology of when key fungal associations evolved and in understanding their importance in ecosystems through time. Together with calibrated phylogenetic trees, these approaches extend our understanding of when and how groups evolved in the context of major environmental change on a global scale. Phylogenomics furthers this understanding into the evolution of different types of mycorrhizal associations, and genomic studies of both plants and fungi are shedding light on how the complex set of symbiotic traits evolved. Here we present a review of the main phases of the evolution of mycorrhizal interactions from palaeontological, phylogenetic and genomic perspectives, with the aim of highlighting the potential of fossil material and a geological perspective in a cross-disciplinary approach.
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Affiliation(s)
- Christine Strullu-Derrien
- Department of Earth Sciences, The Natural History Museum, Cromwell Road, London, SW7 5BD, UK
- Interactions Arbres/Microorganismes, Laboratoire d'excellence ARBRE, Centre INRA-Lorraine, Institut national de la recherche agronomique (INRA), Unité Mixte de Recherche 1136 INRA-Université de Lorraine, 54280, Champenoux, France
| | - Marc-André Selosse
- Institut Systématique Evolution Biodiversité (ISYEB), Muséum national d'Histoire naturelle, CNRS, Sorbonne Université, EPHE, 57 rue Cuvier, CP39, 75005, Paris, France
- Department of Plant Taxonomy and Nature Conservation, Faculty of Biology, University of Gdańsk, Wita Stwosza 59, 80-308, Gdansk, Poland
| | - Paul Kenrick
- Department of Earth Sciences, The Natural History Museum, Cromwell Road, London, SW7 5BD, UK
| | - Francis M Martin
- Interactions Arbres/Microorganismes, Laboratoire d'excellence ARBRE, Centre INRA-Lorraine, Institut national de la recherche agronomique (INRA), Unité Mixte de Recherche 1136 INRA-Université de Lorraine, 54280, Champenoux, France
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205
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Niu G, Korkmaz EM, Doğan Ö, Zhang Y, Aydemir MN, Budak M, Du S, Başıbüyük HH, Wei M. The first mitogenomes of the superfamily Pamphilioidea (Hymenoptera: Symphyta): Mitogenome architecture and phylogenetic inference. Int J Biol Macromol 2018; 124:185-199. [PMID: 30448489 DOI: 10.1016/j.ijbiomac.2018.11.129] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2018] [Revised: 10/30/2018] [Accepted: 11/14/2018] [Indexed: 10/27/2022]
Abstract
The Pamphilioidea represents a small superfamily of the phytophagous suborder Symphyta (Hymenoptera). Here, nearly complete mitochondrial genomes (mitogenomes) of three pamphilioid species: Chinolyda flagellicornis (Pamphiliidae), Megalodontes spiraeae and M. cephalotes (Megalodontesidae) were newly sequenced using next generation sequencing and comparatively analysed with the previously reported symphytan mitogenomes. A positive AT skew (0.013) and a negative GC skew (-0.194) were found in pamphilioid mitogenome, and a deviation from strand asymmetry was also observed in the PCGs encoded on both strands. Several gene rearrangement events were observed in four tRNA gene clusters (WCY, IQM, ARNS1EF and TP clusters), which have not been reported from symphytan mitogenomes to date. As the most parsimonious explanation, compared with the inferred insect ancestral mitogenome architecture, the occurrence of gene rearrangements in pamphilioid mitogenomes requires totally five evolutionary steps, including four transpositions and one inversion. The predicted secondary structures of tRNAs, rrnS and rrnL genes are mostly consistent with reported hymenopteran species. Phylogenetic analyses recovered the monophyly of superfamily Pamphilioidea and indicated the relationship Tenthredinoidea + (Pamphilioidea + (Cephoidea + (Orussoidea + Apocrita))) with strong nodal supports.
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Affiliation(s)
- Gengyun Niu
- College of Life Sciences, Jiangxi Normal University, 99 Ziyang Road, Nanchang 330022, PR China
| | - Ertan Mahir Korkmaz
- Department of Molecular Biology and Genetics, Faculty of Science, Sivas Cumhuriyet University, Sivas, Turkey.
| | - Özgül Doğan
- Department of Molecular Biology and Genetics, Faculty of Science, Sivas Cumhuriyet University, Sivas, Turkey
| | - Yaoyao Zhang
- Key Laboratory of Cultivation and Protection for Non-Wood Forest Trees (Central South University of Forestry and Technology), Ministry of Education, Central South University of Forestry and Technology, 498 South Shaoshan Road, Changsha 410004, PR China
| | - Merve Nur Aydemir
- Department of Molecular Biology and Genetics, Faculty of Science, Sivas Cumhuriyet University, Sivas, Turkey
| | - Mahir Budak
- Department of Molecular Biology and Genetics, Faculty of Science, Sivas Cumhuriyet University, Sivas, Turkey
| | - Shiyu Du
- Key Laboratory of Cultivation and Protection for Non-Wood Forest Trees (Central South University of Forestry and Technology), Ministry of Education, Central South University of Forestry and Technology, 498 South Shaoshan Road, Changsha 410004, PR China
| | | | - Meicai Wei
- College of Life Sciences, Jiangxi Normal University, 99 Ziyang Road, Nanchang 330022, PR China
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206
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Boudinot BE. A general theory of genital homologies for the Hexapoda (Pancrustacea) derived from skeletomuscular correspondences, with emphasis on the Endopterygota. ARTHROPOD STRUCTURE & DEVELOPMENT 2018; 47:563-613. [PMID: 30419291 DOI: 10.1016/j.asd.2018.11.001] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2017] [Revised: 10/16/2018] [Accepted: 11/03/2018] [Indexed: 06/09/2023]
Abstract
No consensus exists for the homology and terminology of the male genitalia of the Hexapoda despite over a century of debate. Based on dissections and the literature, genital skeletomusculature was compared across the Hexapoda and contrasted with the Remipedia, the closest pancrustacean outgroup. The pattern of origin and insertion for extrinsic and intrinsic genitalic musculature was found to be consistent among the Ectognatha, Protura, and the Remipedia, allowing for the inference of homologies given recent phylogenomic studies. The penis of the Hexapoda is inferred to be derived from medially-fused primary gonopods (gonopore-bearing limbs), while the genitalia of the Ectognatha are inferred to include both the tenth-segmental penis and the ninth-segmental secondary gonopods, similar to the genitalia of female insects which comprise gonopods of the eighth and ninth segments. A new nomenclatural system for hexapodan genitalic musculature is presented and applied, and a general list of anatomical concepts is provided. Novel and refined homologies are proposed for all hexapodan orders, and a series of groundplans are postulated. Emphasis is placed on the Endopterygota, for which fine-grained transition series are hypothesized given observed skeletomuscular correspondences.
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Affiliation(s)
- Brendon E Boudinot
- Department of Entomology & Nematology, University of California, Davis, One Shields Ave., Davis, CA 95616, USA.
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207
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Guindon S. Accounting for Calibration Uncertainty: Bayesian Molecular Dating as a "Doubly Intractable" Problem. Syst Biol 2018; 67:651-661. [PMID: 29385558 DOI: 10.1093/sysbio/syy003] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2017] [Accepted: 01/23/2018] [Indexed: 11/13/2022] Open
Abstract
This study introduces a new Bayesian technique for molecular dating that explicitly accommodates for uncertainty in the phylogenetic position of calibrated nodes derived from the analysis of fossil data. The proposed approach thus defines an adequate framework for incorporating expert knowledge and/or prior information about the way fossils were collected in the inference of node ages. Although it belongs to the class of "node-dating" approaches, this method shares interesting properties with "tip-dating" techniques. Yet, it alleviates some of the computational and modeling difficulties that hamper tip-dating approaches. The influence of fossil data on the probabilistic distribution of trees is the crux of the matter considered here. More specifically, among all the phylogenies that a tree model (e.g., the birth-death process) generates, only a fraction of them "agree" with the fossil data. Bayesian inference under the new model requires taking this fraction into account. However, evaluating this quantity is difficult in practice. A generic solution to this issue is presented here. The proposed approach relies on a recent statistical technique, the so-called exchange algorithm, dedicated to drawing samples from "doubly intractable" distributions. A small example illustrates the problem of interest and the impact of uncertainty in the placement of calibration constraints in the phylogeny given fossil data. An analysis of land plant sequences and multiple fossils further highlights the pertinence of the proposed approach.
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Affiliation(s)
- Stéphane Guindon
- Laboratoire d'Informatique, de Robotique et de Microélectronique de Montpellier, UMR 5506, CNRS, Université de Montpellier, Montpellier, France
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208
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Stange M, Sánchez-Villagra MR, Salzburger W, Matschiner M. Bayesian Divergence-Time Estimation with Genome-Wide Single-Nucleotide Polymorphism Data of Sea Catfishes (Ariidae) Supports Miocene Closure of the Panamanian Isthmus. Syst Biol 2018; 67:681-699. [PMID: 29385552 PMCID: PMC6005153 DOI: 10.1093/sysbio/syy006] [Citation(s) in RCA: 90] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2017] [Accepted: 01/23/2018] [Indexed: 02/03/2023] Open
Abstract
The closure of the Isthmus of Panama has long been considered to be one of the best defined biogeographic calibration points for molecular divergence-time estimation. However, geological and biological evidence has recently cast doubt on the presumed timing of the initial isthmus closure around 3 Ma but has instead suggested the existence of temporary land bridges as early as the Middle or Late Miocene. The biological evidence supporting these earlier land bridges was based either on only few molecular markers or on concatenation of genome-wide sequence data, an approach that is known to result in potentially misleading branch lengths and divergence times, which could compromise the reliability of this evidence. To allow divergence-time estimation with genomic data using the more appropriate multispecies coalescent (MSC) model, we here develop a new method combining the single-nucleotide polymorphism-based Bayesian species-tree inference of the software SNAPP with a molecular clock model that can be calibrated with fossil or biogeographic constraints. We validate our approach with simulations and use our method to reanalyze genomic data of Neotropical army ants (Dorylinae) that previously supported divergence times of Central and South American populations before the isthmus closure around 3 Ma. Our reanalysis with the MSC model shifts all of these divergence times to ages younger than 3 Ma, suggesting that the older estimates supporting the earlier existence of temporary land bridges were artifacts resulting at least partially from the use of concatenation. We then apply our method to a new restriction-site associated DNA-sequencing data set of Neotropical sea catfishes (Ariidae) and calibrate their species tree with extensive information from the fossil record. We identify a series of divergences between groups of Caribbean and Pacific sea catfishes around 10 Ma, indicating that processes related to the emergence of the isthmus led to vicariant speciation already in the Late Miocene, millions of years before the final isthmus closure.
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Affiliation(s)
- Madlen Stange
- Department of Palaeontology and Museum, University of Zurich, Karl-Schmid-Strasse 4, 8006 Zurich, Switzerland.,Zoological Institute, University of Basel, Vesalgasse 1, 4051 Basel, Switzerland
| | - Marcelo R Sánchez-Villagra
- Department of Palaeontology and Museum, University of Zurich, Karl-Schmid-Strasse 4, 8006 Zurich, Switzerland
| | - Walter Salzburger
- Zoological Institute, University of Basel, Vesalgasse 1, 4051 Basel, Switzerland.,Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, 0316 Oslo, Norway
| | - Michael Matschiner
- Zoological Institute, University of Basel, Vesalgasse 1, 4051 Basel, Switzerland.,Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, 0316 Oslo, Norway
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209
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Crouch NMA, Ramanauskas K, Igić B. Tip-dating and the origin of Telluraves. Mol Phylogenet Evol 2018; 131:55-63. [PMID: 30385308 DOI: 10.1016/j.ympev.2018.10.006] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2017] [Revised: 09/05/2018] [Accepted: 10/09/2018] [Indexed: 10/28/2022]
Abstract
Despite a relatively vast accumulation of molecular data, the timing of diversification of modern bird lineages remains elusive. Accurate dating of the origination of Telluraves-a clade of birds defined by their arboreality-is of particular interest, as it contains the most species-rich avian group, the passerines. Historically, neontological studies have estimated a Cretaceous origin for the group, but more recent studies have recovered Cenozoic dates, closer to the oldest known fossils for the group. We employ total-evidence dating to estimate divergence times that are expected to be both less sensitive to prior assumptions and more accurate. Specifically, we use a large collection of morphological character data from arboreal bird fossils, along with combined molecular sequence and morphological character data from extant taxa. Our analyses recover a Late Cretaceous origin for crown Telluraves, with a few lineages crossing the K-Pg boundary. Following the K-Pg boundary, our results show the group underwent rapid diversification, likely benefiting from increased ecological opportunities in the aftermath of the extinction event. We find very little confidence for the precise topological placement of many extinct taxa, possibly due to rapid diversification, paucity of character data, and rapid morphological differentiation during the early history of the group.
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Affiliation(s)
- Nicholas M A Crouch
- Dept. of Biological Sciences, University of Illinois at Chicago, 840 West Taylor St. MC067, Chicago, IL 60607, USA; Department of Zoology, The Field Museum, 1400 S. Lake Shore Drive, Chicago, IL 60605, USA.
| | - Karolis Ramanauskas
- Dept. of Biological Sciences, University of Illinois at Chicago, 840 West Taylor St. MC067, Chicago, IL 60607, USA; Department of Zoology, The Field Museum, 1400 S. Lake Shore Drive, Chicago, IL 60605, USA.
| | - Boris Igić
- Dept. of Biological Sciences, University of Illinois at Chicago, 840 West Taylor St. MC067, Chicago, IL 60607, USA; Department of Zoology, The Field Museum, 1400 S. Lake Shore Drive, Chicago, IL 60605, USA.
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210
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Billet G, Bardin J. Serial Homology and Correlated Characters in Morphological Phylogenetics: Modeling the Evolution of Dental Crests in Placentals. Syst Biol 2018; 68:267-280. [DOI: 10.1093/sysbio/syy071] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2018] [Accepted: 10/22/2018] [Indexed: 01/24/2023] Open
Affiliation(s)
- Guillaume Billet
- CR2P, UMR 7207, Muséum national d’Histoire naturelle, CNRS, Sorbonne Université, 8 rue Buffon 75005 Paris, France
| | - Jérémie Bardin
- CR2P, UMR 7207, Sorbonne Université, MNHN, CNRS, T.46-56, E.5, case 104, 4 place Jussieu, 75252 Paris cedex 05, France
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211
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Garbin RC, Ascarrunz E, Joyce WG. Polymorphic characters in the reconstruction of the phylogeny of geoemydid turtles. Zool J Linn Soc 2018. [DOI: 10.1093/zoolinnean/zlx106] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Affiliation(s)
- Rafaella C Garbin
- Department of Geosciences, University of Fribourg, Fribourg, Switzerland
| | - Eduardo Ascarrunz
- Department of Geosciences, University of Fribourg, Fribourg, Switzerland
| | - Walter G Joyce
- Department of Geosciences, University of Fribourg, Fribourg, Switzerland
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212
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Casanovas-Vilar I, Garcia-Porta J, Fortuny J, Sanisidro Ó, Prieto J, Querejeta M, Llácer S, Robles JM, Bernardini F, Alba DM. Oldest skeleton of a fossil flying squirrel casts new light on the phylogeny of the group. eLife 2018; 7:39270. [PMID: 30296996 PMCID: PMC6177260 DOI: 10.7554/elife.39270] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2018] [Accepted: 09/10/2018] [Indexed: 11/29/2022] Open
Abstract
Flying squirrels are the only group of gliding mammals with a remarkable diversity and wide geographical range. However, their evolutionary story is not well known. Thus far, identification of extinct flying squirrels has been exclusively based on dental features, which, contrary to certain postcranial characters, are not unique to them. Therefore, fossils attributed to this clade may indeed belong to other squirrel groups. Here we report the oldest fossil skeleton of a flying squirrel (11.6 Ma) that displays the gliding-related diagnostic features shared by extant forms and allows for a recalibration of the divergence time between tree and flying squirrels. Our phylogenetic analyses combining morphological and molecular data generally support older dates than previous molecular estimates (~23 Ma), being congruent with the inclusion of some of the earliest fossils (~36 Ma) into this clade. They also show that flying squirrels experienced little morphological change for almost 12 million years. Mammals can walk, hop, swim and fly; a few, like marsupial sugar gliders or colugos, can even glide. With 52 species scattered across the Northern hemisphere, flying squirrels are by far the most successful group that adopted this way of going airborne. To drift from tree to tree, these small animals pack their own ‘parachute’: a membrane draping between their lower limbs and the long cartilage rods that extend from their wrists. Tiny specialized wrist bones, which are unique to flying squirrels, help to support the cartilaginous extensions. The origin of flying squirrels is a point of contention: while most genetic studies point towards the group splitting from tree squirrels about 23 million years ago, the oldest remains – mostly cheek teeth – suggest the animals were already soaring through forests 36 million years ago. However, recent studies show that the dental features used to distinguish between gliding and non-gliding squirrels may actually be shared by the two groups. In 2002, the digging of a dump site in Barcelona unearthed a peculiar skeleton: first a tail and two thigh bones, big enough that the researchers thought it could be the fossil of a small primate. In fact, and much to the disappointment of paleoprimatologists, further excavating revealed that it was a rodent. As the specimen – nearly an entire skeleton – was being prepared, paleontologists insisted that all the ‘dirt’ attached to the bones had to be carefully screen-washed. From the mud emerged the minuscule specialized wrist bones: the primate-turned-rodent was in fact Miopetaurista neogrivensis, an extinct flying squirrel. Here, Casanovas-Vilar et al. describe the 11.6 million years old fossil, the oldest ever found. The wrist bones reveal that the animal belongs to the group of flying squirrels that have large sizes. Evolutionary analyses that combined molecular and paleontological data demonstrated that flying squirrels evolved from tree squirrels as far back as 31 to 25 million years ago, and possibly even earlier. In addition, the results show that Miopetaurista is closely related to Petaurista, a modern group of giant flying squirrels. In fact, their skeletons are so similar that the large species that currently inhabit the tropical and subtropical forests of Asia could be considered living fossils. Molecular and paleontological data are often at odds, but this fossil shows that they can be reconciled and combined to retrace history. Discovering older fossils, or even transitional forms, could help to retrace how flying squirrels took a leap from the rest of their evolutionary tree.
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Affiliation(s)
- Isaac Casanovas-Vilar
- Institut Català de Paleontologia Miquel Crusafont, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Joan Garcia-Porta
- Centre de Recerca Ecològica i Aplicacions Forestals, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Josep Fortuny
- Institut Català de Paleontologia Miquel Crusafont, Universitat Autònoma de Barcelona, Barcelona, Spain.,Centre de Recherches sur les Paléoenvironnements et la Paléobiodiversité, Muséum national d'Histoire naturelle, Paris, France
| | - Óscar Sanisidro
- Biodiversity Institute, University of Kansas, Lawrence, United States
| | - Jérôme Prieto
- Department für Geo- und Umweltwissenschaften, Paläontologie, Ludwig-Maximilians-Universität München, Munich, Germany.,Bayerische Staatssammlung für Paläontologie und Geologie, Munich, Germany
| | | | - Sergio Llácer
- Institut Català de Paleontologia Miquel Crusafont, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Josep M Robles
- Institut Català de Paleontologia Miquel Crusafont, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Federico Bernardini
- Centro Fermi, Museo Storico della Fisica e Centro Studi e Ricerche Enrico Fermi, Roma, Italy.,Multidisciplinary Laboratory, The 'Abdus Salam' International Centre for Theoretical Physics, Trieste, Italy
| | - David M Alba
- Institut Català de Paleontologia Miquel Crusafont, Universitat Autònoma de Barcelona, Barcelona, Spain
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213
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Antonelli A, Ariza M, Albert J, Andermann T, Azevedo J, Bacon C, Faurby S, Guedes T, Hoorn C, Lohmann LG, Matos-Maraví P, Ritter CD, Sanmartín I, Silvestro D, Tejedor M, ter Steege H, Tuomisto H, Werneck FP, Zizka A, Edwards SV. Conceptual and empirical advances in Neotropical biodiversity research. PeerJ 2018; 6:e5644. [PMID: 30310740 PMCID: PMC6174874 DOI: 10.7717/peerj.5644] [Citation(s) in RCA: 83] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2017] [Accepted: 08/27/2018] [Indexed: 01/23/2023] Open
Abstract
The unparalleled biodiversity found in the American tropics (the Neotropics) has attracted the attention of naturalists for centuries. Despite major advances in recent years in our understanding of the origin and diversification of many Neotropical taxa and biotic regions, many questions remain to be answered. Additional biological and geological data are still needed, as well as methodological advances that are capable of bridging these research fields. In this review, aimed primarily at advanced students and early-career scientists, we introduce the concept of "trans-disciplinary biogeography," which refers to the integration of data from multiple areas of research in biology (e.g., community ecology, phylogeography, systematics, historical biogeography) and Earth and the physical sciences (e.g., geology, climatology, palaeontology), as a means to reconstruct the giant puzzle of Neotropical biodiversity and evolution in space and time. We caution against extrapolating results derived from the study of one or a few taxa to convey general scenarios of Neotropical evolution and landscape formation. We urge more coordination and integration of data and ideas among disciplines, transcending their traditional boundaries, as a basis for advancing tomorrow's ground-breaking research. Our review highlights the great opportunities for studying the Neotropical biota to understand the evolution of life.
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Affiliation(s)
- Alexandre Antonelli
- Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden
- Gothenburg Global Biodiversity Centre, Gothenburg, Sweden
- Gothenburg Botanical Garden, Gothenburg, Sweden
- Department of Organismic Biology and Evolutionary Biology, Museum of Comparative Zoology, Harvard University, Cambridge, MA, USA
| | - María Ariza
- Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden
- Gothenburg Global Biodiversity Centre, Gothenburg, Sweden
- Laboratory Ecologie et Biologie des Interactions, Team “Ecologie, Evolution, Symbiose”, Université de Poitiers, Poitiers, France
| | - James Albert
- Department of Biology, University of Louisiana at Lafayette, Lafayette, LA, USA
| | - Tobias Andermann
- Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden
- Gothenburg Global Biodiversity Centre, Gothenburg, Sweden
| | - Josué Azevedo
- Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden
- Gothenburg Global Biodiversity Centre, Gothenburg, Sweden
| | - Christine Bacon
- Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden
- Gothenburg Global Biodiversity Centre, Gothenburg, Sweden
| | - Søren Faurby
- Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden
- Gothenburg Global Biodiversity Centre, Gothenburg, Sweden
| | - Thais Guedes
- Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden
- Gothenburg Global Biodiversity Centre, Gothenburg, Sweden
- Federal University of São Paulo, Diadema, Brazil
- Museum of Zoology, University of São Paulo, São Paulo, Brazil
| | - Carina Hoorn
- Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, Netherlands
- Universidad Regional Amazonica IKIAM, Napo, Ecuador
| | - Lúcia G. Lohmann
- Instituto de Biociências, Departamento de Botânica, Universidade de São Paulo, São Paulo, Brazil
- Integrative Biology, University of California, Berkeley, CA, USA
| | - Pável Matos-Maraví
- Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden
- Gothenburg Global Biodiversity Centre, Gothenburg, Sweden
| | - Camila D. Ritter
- Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden
- Gothenburg Global Biodiversity Centre, Gothenburg, Sweden
| | | | - Daniele Silvestro
- Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden
- Gothenburg Global Biodiversity Centre, Gothenburg, Sweden
- Department of Computational Biology, University of Lausanne, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Marcelo Tejedor
- Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden
- Gothenburg Global Biodiversity Centre, Gothenburg, Sweden
- Instituto Patagónico de Geología y Paleontología, Puerto Madryn, Guatemala
| | - Hans ter Steege
- Naturalis Biodiversity Center, Leiden, Netherlands
- Systems Ecology, Free University, Amsterdam, Netherlands
| | - Hanna Tuomisto
- Department of Biology, University of Turku, Turku, Finland
| | | | - Alexander Zizka
- Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden
- Gothenburg Global Biodiversity Centre, Gothenburg, Sweden
| | - Scott V. Edwards
- Gothenburg Global Biodiversity Centre, Gothenburg, Sweden
- Department of Organismic Biology and Evolutionary Biology, Museum of Comparative Zoology, Harvard University, Cambridge, MA, USA
- Gothenburg Centre for Advanced Studies in Science and Technology, Chalmers University of Technology and University of Gothenburg, Gothenburg, Sweden
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214
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Varela L, Tambusso PS, McDonald HG, Fariña RA. Phylogeny, Macroevolutionary Trends and Historical Biogeography of Sloths: Insights From a Bayesian Morphological Clock Analysis. Syst Biol 2018; 68:204-218. [DOI: 10.1093/sysbio/syy058] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2017] [Accepted: 09/10/2018] [Indexed: 11/14/2022] Open
Affiliation(s)
- Luciano Varela
- Departamento de Paleontología, Facultad de Ciencias, Universidad de la República, Iguá 4225, 11400 Montevideo, Uruguay
| | - P Sebastián Tambusso
- Departamento de Paleontología, Facultad de Ciencias, Universidad de la República, Iguá 4225, 11400 Montevideo, Uruguay
| | - H Gregory McDonald
- Bureau of Land Management, Utah State Office, 440 West 200 South, Salt Lake City, UT 84101 USA
| | - Richard A Fariña
- Departamento de Paleontología, Facultad de Ciencias, Universidad de la República, Iguá 4225, 11400 Montevideo, Uruguay
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215
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Leslie AB, Beaulieu J, Holman G, Campbell CS, Mei W, Raubeson LR, Mathews S. An overview of extant conifer evolution from the perspective of the fossil record. AMERICAN JOURNAL OF BOTANY 2018; 105:1531-1544. [PMID: 30157290 DOI: 10.1002/ajb2.1143] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/02/2017] [Accepted: 05/29/2018] [Indexed: 05/07/2023]
Abstract
PREMISE OF THE STUDY Conifers are an important living seed plant lineage with an extensive fossil record spanning more than 300 million years. The group therefore provides an excellent opportunity to explore congruence and conflict between dated molecular phylogenies and the fossil record. METHODS We surveyed the current state of knowledge in conifer phylogenetics to present a new time-calibrated molecular tree that samples ~90% of extant species diversity. We compared phylogenetic relationships and estimated divergence ages in this new phylogeny with the paleobotanical record, focusing on clades that are species-rich and well known from fossils. KEY RESULTS Molecular topologies and estimated divergence ages largely agree with the fossil record in Cupressaceae, conflict with it in Araucariaceae, and are ambiguous in Pinaceae and Podocarpaceae. Molecular phylogenies provide insights into some fundamental questions in conifer evolution, such as the origin of their seed cones, but using them to reconstruct the evolutionary history of specific traits can be challenging. CONCLUSIONS Molecular phylogenies are useful for answering deep questions in conifer evolution if they depend on understanding relationships among extant lineages. Because of extinction, however, molecular datasets poorly sample diversity from periods much earlier than the Late Cretaceous. This fundamentally limits their utility for understanding deep patterns of character evolution and resolving the overall pattern of conifer phylogeny.
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Affiliation(s)
- Andrew B Leslie
- Department of Ecology and Evolutionary Biology, Brown University, Box G-W, 80 Waterman Street, Providence, Rhode Island, 02912, USA
| | - Jeremy Beaulieu
- Department of Biological Sciences, University of Arkansas, Fayetteville, Arkansas, 72701, USA
| | - Garth Holman
- School of Biology and Ecology, University of Maine, Orono, Maine, 04469, USA
| | | | - Wenbin Mei
- Department of Plant Sciences, University of California, Davis, 1 Shields Avenue, Davis, California, 95616, USA
| | - Linda R Raubeson
- Department of Biological Sciences, Central Washington University, 400 E. University Way, Ellensburg, Washington, 98926, USA
| | - Sarah Mathews
- CSIRO National Research Collections Australia, Australian National Herbarium, Canberra, ACT, 2601, Australia
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216
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Sauquet H, Magallón S. Key questions and challenges in angiosperm macroevolution. THE NEW PHYTOLOGIST 2018; 219:1170-1187. [PMID: 29577323 DOI: 10.1111/nph.15104] [Citation(s) in RCA: 62] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/26/2017] [Accepted: 02/05/2018] [Indexed: 05/26/2023]
Abstract
Contents Summary 1170 I. Introduction 1170 II. Six key questions 1172 III. Three key challenges 1177 IV. Conclusions 1181 Acknowledgements 1182 References 1183 SUMMARY: The origin and rapid diversification of angiosperms (flowering plants) represent one of the most intriguing topics in evolutionary biology. Despite considerable progress made in complementary fields over the last two decades (paleobotany, phylogenetics, ecology, evo-devo, genomics), many important questions remain. For instance, what has been the impact of mass extinctions on angiosperm diversification? Are the angiosperms an adaptive radiation? Has morphological evolution in angiosperms been gradual or pulsed? We propose that the recent and ongoing revolution in macroevolutionary methods provides an unprecedented opportunity to explore long-standing questions that probably hold important clues to understand present-day biodiversity. We present six key questions that explore the origin and diversification of angiosperms. We also identify three key challenges to address these questions: (1) the development of new integrative models that include diversification, multiple intrinsic and environmental traits, biogeography and the fossil record all at once, whilst accounting for sampling bias and heterogeneity of macroevolutionary processes through time and among lineages; (2) the need for large and standardized synthetic databases of morphological variation; and (3) continuous effort on sampling the fossil record, but with a revolution in current paleobotanical practice.
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Affiliation(s)
- Hervé Sauquet
- National Herbarium of New South Wales (NSW), Royal Botanic Gardens and Domain Trust, Sydney, NSW, 2000, Australia
- Laboratoire Écologie, Systématique, Évolution, Université Paris-Sud, CNRS, UMR 8079, Orsay, 91405, France
| | - Susana Magallón
- Instituto de Biología, Universidad Nacional Autónoma de México, Circuito Exterior, Ciudad Universitaria, Coyoacán, México City, 04510, México
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217
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Gillung JP, Winterton SL, Bayless KM, Khouri Z, Borowiec ML, Yeates D, Kimsey LS, Misof B, Shin S, Zhou X, Mayer C, Petersen M, Wiegmann BM. Anchored phylogenomics unravels the evolution of spider flies (Diptera, Acroceridae) and reveals discordance between nucleotides and amino acids. Mol Phylogenet Evol 2018; 128:233-245. [PMID: 30110663 DOI: 10.1016/j.ympev.2018.08.007] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2018] [Revised: 08/03/2018] [Accepted: 08/07/2018] [Indexed: 11/17/2022]
Abstract
The onset of phylogenomics has contributed to the resolution of numerous challenging evolutionary questions while offering new perspectives regarding biodiversity. However, in some instances, analyses of large genomic datasets can also result in conflicting estimates of phylogeny. Here, we present the first phylogenomic scale study of a dipteran parasitoid family, built upon anchored hybrid enrichment and transcriptomic data of 240 loci of 43 ingroup acrocerid taxa. A new hypothesis for the timing of spider fly evolution is proposed, wielding recent advances in divergence time dating, including the fossilized birth-death process to show that the origin of Acroceridae is younger than previously proposed. To test the robustness of our phylogenetic inferences, we analyzed our datasets using different phylogenetic estimation criteria, including supermatrix and coalescent-based approaches, maximum-likelihood and Bayesian methods, combined with other approaches such as permutations of the data, homogeneous versus heterogeneous models, and alternative data and taxon sets. Resulting topologies based on amino acids and nucleotides are both strongly supported but critically discordant, primarily in terms of the monophyly of Panopinae. Conflict was not resolved by controlling for compositional heterogeneity and saturation in third codon positions, which highlights the need for a better understanding of how different biases affect different data sources. In our study, results based on nucleotides were both more robust to alterations of the data and different analytical methods and more compatible with our current understanding of acrocerid morphology and patterns of host usage.
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Affiliation(s)
- Jessica P Gillung
- Bohart Museum of Entomology, University of California, One Shields Ave, Davis, CA 95616, USA; California State Collection of Arthropods, 3294 Meadowview Rd, Sacramento, CA 95832, USA.
| | - Shaun L Winterton
- California State Collection of Arthropods, 3294 Meadowview Rd, Sacramento, CA 95832, USA
| | - Keith M Bayless
- California Academy of Sciences, 55 Music Concourse Drive, San Francisco, CA 94118, USA
| | - Ziad Khouri
- Bohart Museum of Entomology, University of California, One Shields Ave, Davis, CA 95616, USA
| | - Marek L Borowiec
- School of Life Sciences, Social Insect Research Group, Arizona State University, Tempe, AZ, 85287, USA
| | - David Yeates
- National Research Collections Australia, Clunies Ross Street, Acton, ACT 2601, GPO Box 1700, Canberra, ACT 2601, Australia
| | - Lynn S Kimsey
- Bohart Museum of Entomology, University of California, One Shields Ave, Davis, CA 95616, USA
| | - Bernhard Misof
- Center for Molecular Biodiversity Research, Zoological Research Museum Alexander Koenig, 53113 Bonn, Germany
| | - Seunggwan Shin
- Department of Biological Sciences, University of Memphis, 3700 Walker Avenue, Memphis, TN 38152, USA
| | - Xin Zhou
- Department of Entomology, China Agricultural University, Beijing 100193, China
| | - Christoph Mayer
- Center for Molecular Biodiversity Research, Zoological Research Museum Alexander Koenig, 53113 Bonn, Germany
| | - Malte Petersen
- Center for Molecular Biodiversity Research, Zoological Research Museum Alexander Koenig, 53113 Bonn, Germany
| | - Brian M Wiegmann
- Department of Entomology & Plant Pathology, North Carolina State University, 3114 Gardner Hall, Raleigh, NC 27695-7613, USA
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218
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Flammensbeck CK, Pollerspöck J, Schedel FDB, Matzke NJ, Straube N. Of teeth and trees: A fossil tip‐dating approach to infer divergence times of extinct and extant squaliform sharks. ZOOL SCR 2018. [DOI: 10.1111/zsc.12299] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
| | | | | | - Nicholas J. Matzke
- Division of Ecology, Evolution, and Genetics Research School of Biology The Australian National University Canberra Australia
- School of Biological Sciences University of Auckland Auckland New Zealand
| | - Nicolas Straube
- SNSB – Bavarian State Collection of Zoology (ZSM) Munich Germany
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219
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Smith SY, Iles WJD, Benedict JC, Specht CD. Building the monocot tree of death: Progress and challenges emerging from the macrofossil-rich Zingiberales. AMERICAN JOURNAL OF BOTANY 2018; 105:1389-1400. [PMID: 30071130 DOI: 10.1002/ajb2.1123] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2017] [Accepted: 05/02/2018] [Indexed: 06/08/2023]
Abstract
PREMISE OF THE STUDY Inclusion of fossils in phylogenetic analyses is necessary in order to construct a comprehensive "tree of death" and elucidate evolutionary history of taxa; however, such incorporation of fossils in phylogenetic reconstruction is dependent on the availability and interpretation of extensive morphological data. Here, the Zingiberales, whose familial relationships have been difficult to resolve with high support, are used as a case study to illustrate the importance of including fossil taxa in systematic studies. METHODS Eight fossil taxa and 43 extant Zingiberales were coded for 39 morphological seed characters, and these data were concatenated with previously published molecular sequence data for analysis in the program MrBayes. KEY RESULTS Ensete oregonense is confirmed to be part of Musaceae, and the other seven fossils group with Zingiberaceae. There is strong support for Spirematospermum friedrichii, Spirematospermum sp. 'Goth', S. wetzleri, and Striatornata sanantoniensis in crown Zingiberaceae while "Musa" cardiosperma, Spirematospermum chandlerae, and Tricostatocarpon silvapinedae are best considered stem Zingiberaceae. Inclusion of fossils explains how different topologies from morphological and molecular data sets is due to shared plesiomorphic characters shared by Musaceae, Zingiberaceae, and Costaceae, and most of the fossils. CONCLUSIONS Inclusion of eight fossil taxa expands the Zingiberales tree and helps explain the difficulty in resolving relationships. Inclusion of fossils was possible in part due to a large morphological data set built using nondestructive microcomputed tomography data. Collaboration between paleo- and neobotanists and technology such as microcomputed tomography will help to build the tree of death and ultimately improve our understanding of the evolutionary history of monocots.
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Affiliation(s)
- Selena Y Smith
- Department of Earth & Environmental Sciences, University of Michigan, Ann Arbor, MI 48109, USA
- Museum of Paleontology, University of Michigan, Ann Arbor, MI, 48109, USA
- Program in the Environment, University of Michigan, Ann Arbor, MI, 48109, USA
| | - William J D Iles
- Department of Earth & Environmental Sciences, University of Michigan, Ann Arbor, MI 48109, USA
- Department of Integrative Biology and the University and Jepson Herbaria, University of California, Berkeley, CA, 94720, USA
| | - John C Benedict
- Department of Earth & Environmental Sciences, University of Michigan, Ann Arbor, MI 48109, USA
- Program in the Environment, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Chelsea D Specht
- School of Integrative Plant Sciences, Section of Plant Biology and the Bailey Hortorium, Cornell University, Ithaca, NY, 14853, USA
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220
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Wright AM. Editor's note on 'Putting fossils in trees' special issue. Biol Lett 2018; 13:rsbl.2017.0103. [PMID: 28330978 DOI: 10.1098/rsbl.2017.0103] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2017] [Accepted: 03/02/2017] [Indexed: 11/12/2022] Open
Affiliation(s)
- April M Wright
- Ecology, Evolution and Organismal Biology, Iowa State University, Ames, IA 50010, USA .,The Field Museum, Chicago, IL 60605, USA
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221
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Parins-Fukuchi C. Bayesian placement of fossils on phylogenies using quantitative morphometric data. Evolution 2018; 72:1801-1814. [PMID: 29998561 DOI: 10.1111/evo.13516] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2018] [Accepted: 05/25/2018] [Indexed: 11/29/2022]
Abstract
Jointly developing a comprehensive tree of life from living and fossil taxa has long been a fundamental goal in evolutionary biology. One major challenge has stemmed from difficulties in merging evidence from extant and extinct organisms. While these efforts have resulted in varying stages of synthesis, they have been hindered by their dependence on qualitative descriptions of morphology. Though rarely applied to phylogenetic inference, traditional and geometric morphometric data can improve these issues by generating more rigorous ways to quantify variation in morphological structures. They may also facilitate the rapid and objective aggregation of large morphological datasets. I describe a new Bayesian method that leverages quantitative trait data to reconstruct the positions of fossil taxa on fixed reference trees composed of extant taxa. Unlike most formulations of phylogenetic Brownian motion models, this method expresses branch lengths in units of morphological disparity, suggesting a new framework through which to construct Bayesian node calibration priors for molecular dating and explore comparative patterns in morphological disparity. I am hopeful that the approach described here will help to facilitate a deeper integration of neo- and paleontological data to move morphological phylogenetics further into the genomic era.
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Affiliation(s)
- Caroline Parins-Fukuchi
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, Michigan 48109
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222
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Schrago CG, Aguiar BO, Mello B. Comparative evaluation of maximum parsimony and Bayesian phylogenetic reconstruction using empirical morphological data. J Evol Biol 2018; 31:1477-1484. [DOI: 10.1111/jeb.13344] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2018] [Revised: 06/13/2018] [Accepted: 06/27/2018] [Indexed: 11/27/2022]
Affiliation(s)
- Carlos G. Schrago
- Department of Genetics; Federal University of Rio de Janeiro; Rio de Janeiro Brazil
| | - Barbara O. Aguiar
- Department of Genetics; Federal University of Rio de Janeiro; Rio de Janeiro Brazil
| | - Beatriz Mello
- Department of Genetics; Federal University of Rio de Janeiro; Rio de Janeiro Brazil
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223
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Reis MD, Gunnell GF, Barba-Montoya J, Wilkins A, Yang Z, Yoder AD. Using Phylogenomic Data to Explore the Effects of Relaxed Clocks and Calibration Strategies on Divergence Time Estimation: Primates as a Test Case. Syst Biol 2018; 67:594-615. [PMID: 29342307 PMCID: PMC6005039 DOI: 10.1093/sysbio/syy001] [Citation(s) in RCA: 94] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2017] [Revised: 12/26/2017] [Accepted: 01/05/2018] [Indexed: 11/13/2022] Open
Abstract
Primates have long been a test case for the development of phylogenetic methods for divergence time estimation. Despite a large number of studies, however, the timing of origination of crown Primates relative to the Cretaceous-Paleogene (K-Pg) boundary and the timing of diversification of the main crown groups remain controversial. Here, we analysed a data set of 372 taxa (367 Primates and 5 outgroups, 3.4 million aligned base pairs) that includes nine primate genomes. We systematically explore the effect of different interpretations of fossil calibrations and molecular clock models on primate divergence time estimates. We find that even small differences in the construction of fossil calibrations can have a noticeable impact on estimated divergence times, especially for the oldest nodes in the tree. Notably, choice of molecular rate model (autocorrelated or independently distributed rates) has an especially strong effect on estimated times, with the independent rates model producing considerably more ancient age estimates for the deeper nodes in the phylogeny. We implement thermodynamic integration, combined with Gaussian quadrature, in the program MCMCTree, and use it to calculate Bayes factors for clock models. Bayesian model selection indicates that the autocorrelated rates model fits the primate data substantially better, and we conclude that time estimates under this model should be preferred. We show that for eight core nodes in the phylogeny, uncertainty in time estimates is close to the theoretical limit imposed by fossil uncertainties. Thus, these estimates are unlikely to be improved by collecting additional molecular sequence data. All analyses place the origin of Primates close to the K-Pg boundary, either in the Cretaceous or straddling the boundary into the Palaeogene.
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Affiliation(s)
- Mario Dos Reis
- School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, UK
- Department of Genetics, Evolution and Environment, University College London, Gower Street, London WC1E 6BT, UK
| | - Gregg F Gunnell
- Division of Fossil Primates, Duke University Lemur Center, Durham, 1013 Broad Street, NC 27705, USA
| | - Jose Barba-Montoya
- Department of Genetics, Evolution and Environment, University College London, Gower Street, London WC1E 6BT, UK
| | - Alex Wilkins
- Division of Fossil Primates, Duke University Lemur Center, Durham, 1013 Broad Street, NC 27705, USA
- Department of Anthropology, The Ohio State University, Columbus, OH 43210, USA
| | - Ziheng Yang
- Department of Genetics, Evolution and Environment, University College London, Gower Street, London WC1E 6BT, UK
| | - Anne D Yoder
- Department of Biology, Duke University, Durham, NC 27708, USA
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224
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Seminal Simian Immunodeficiency Virus in Chronically Infected Cynomolgus Macaques Is Dominated by Virus Originating from Multiple Genital Organs. J Virol 2018; 92:JVI.00133-18. [PMID: 29720516 PMCID: PMC6026730 DOI: 10.1128/jvi.00133-18] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2018] [Accepted: 04/16/2018] [Indexed: 11/20/2022] Open
Abstract
The sexual transmission of viruses is responsible for the spread of multiple infectious diseases. Although the human immunodeficiency virus (HIV)/AIDS pandemic remains fueled by sexual contacts with infected semen, the origin of virus in semen is still unknown. In a substantial number of HIV-infected men, viral strains present in semen differ from the ones in blood, suggesting that HIV is locally produced within the genital tract. Such local production may be responsible for the persistence of HIV in semen despite effective antiretroviral therapy. In this study, we used single-genome amplification, amplicon sequencing (env gene), and phylogenetic analyses to compare the genetic structures of simian immunodeficiency virus (SIV) populations across all the male genital organs and blood in intravenously inoculated cynomolgus macaques in the chronic stage of infection. Examination of the virus populations present in the male genital tissues of the macaques revealed compartmentalized SIV populations in testis, epididymis, vas deferens, seminal vesicles, and urethra. We found genetic similarities between the viral strains present in semen and those in epididymis, vas deferens, and seminal vesicles. The contribution of male genital organs to virus shedding in semen varied among individuals and could not be predicted based on their infection or proinflammatory cytokine mRNA levels. These data indicate that rather than a single source, multiple genital organs are involved in the release of free virus and infected cells into semen. These findings have important implications for our understanding of systemic virus shedding and persistence in semen and for the design of eradication strategies to access viral reservoirs. IMPORTANCE Semen is instrumental for the dissemination of viruses through sexual contacts. Worryingly, a number of systemic viruses, such as HIV, can persist in this body fluid in the absence of viremia. The local source(s) of virus in semen, however, remains unknown. To elucidate the anatomic origin(s) of the virus released in semen, we compared viral populations present in semen with those in the male genital organs and blood of the Asian macaque model, using single-genome amplification, amplicon sequencing (env gene), and phylogenetic analysis. Our results show that multiple genital tissues harbor compartmentalized strains, some of them (i.e., from epididymis, vas deferens, and seminal vesicles) displaying genetic similarities with the viral populations present in semen. This study is the first to uncover local genital sources of viral populations in semen, providing a new basis for innovative targeted strategies to prevent and eradicate HIV in the male genital tract.
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225
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Lee MSY, Yates AM. Tip-dating and homoplasy: reconciling the shallow molecular divergences of modern gharials with their long fossil record. Proc Biol Sci 2018; 285:20181071. [PMID: 30051855 PMCID: PMC6030529 DOI: 10.1098/rspb.2018.1071] [Citation(s) in RCA: 57] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2018] [Accepted: 05/30/2018] [Indexed: 01/12/2023] Open
Abstract
Simultaneously analysing morphological, molecular and stratigraphic data suggests a potential resolution to a major remaining inconsistency in crocodylian evolution. The ancient, long-snouted thoracosaurs have always been placed near the Indian gharial Gavialis, but their antiquity (ca 72 Ma) is highly incongruous with genomic evidence for the young age of the Gavialis lineage (ca 40 Ma). We reconcile this contradiction with an updated morphological dataset and novel analysis, and demonstrate that thoracosaurs are an ancient iteration of long-snouted stem crocodylians unrelated to modern gharials. The extensive similarities between thoracosaurs and Gavialis are shown to be an almost 'perfect storm' of homoplasy, combining convergent adaptions to fish-eating, as well resemblances between genuinely primitive traits (thoracosaurs) and atavisms (Gavialis). Phylogenetic methods that ignore stratigraphy (parsimony and undated Bayesian methods) are unable to tease apart these similarities and invariably unite thoracosaurs and Gavialis. However, tip-dated Bayesian approaches additionally consider the large temporal gap separating ancient (thoracosaurs) and modern (Gavialis) iterations of similar long-snouted crocodyliforms. These analyses robustly favour a phylogeny which places thoracosaurs basal to crocodylians, far removed from modern gharials, which accordingly are a very young radiation. This phylogenetic uncoupling of ancient and modern gharial-like crocs is more consistent with molecular clock divergence estimates, and also the bulk of the crocodylian fossil record (e.g. all unequivocal gharial fossils are very young). Provided that the priors and models attribute appropriate relative weights to the morphological and stratigraphic signals-an issue that requires investigation-tip-dating approaches are potentially better able to detect homoplasy and improve inferences about phylogenetic relationships, character evolution and divergence dates.
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Affiliation(s)
- Michael S Y Lee
- School of Biological Sciences, Flinders University, GPO Box 2100, South Australia 5001, Australia
- South Australian Museum, North Terrace, Adelaide South Australia 5000, Australia
| | - Adam M Yates
- Museum of Central Australia, Museum and Art Gallery of the Northern Territory, 4 Memorial Avenue, Alice Springs, Northern Territory 0870, Australia
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226
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Field DJ, Hsiang AY. A North American stem turaco, and the complex biogeographic history of modern birds. BMC Evol Biol 2018; 18:102. [PMID: 29936914 PMCID: PMC6016133 DOI: 10.1186/s12862-018-1212-3] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2017] [Accepted: 06/06/2018] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Earth's lower latitudes boast the majority of extant avian species-level and higher-order diversity, with many deeply diverging clades restricted to vestiges of Gondwana. However, palaeontological analyses reveal that many avian crown clades with restricted extant distributions had stem group relatives in very different parts of the world. RESULTS Our phylogenetic analyses support the enigmatic fossil bird Foro panarium Olson 1992 from the early Eocene (Wasatchian) of Wyoming as a stem turaco (Neornithes: Pan-Musophagidae), a clade that is presently endemic to sub-Saharan Africa. Our analyses offer the first well-supported evidence for a stem musophagid (and therefore a useful fossil calibration for avian molecular divergence analyses), and reveal surprising new information on the early morphology and biogeography of this clade. Total-clade Musophagidae is identified as a potential participant in dispersal via the recently proposed 'North American Gateway' during the Palaeogene, and new biogeographic analyses illustrate the importance of the fossil record in revealing the complex historical biogeography of crown birds across geological timescales. CONCLUSIONS In the Palaeogene, total-clade Musophagidae was distributed well outside the range of crown Musophagidae in the present day. This observation is consistent with similar biogeographic observations for numerous other modern bird clades, illustrating shortcomings of historical biogeographic analyses that do not incorporate information from the avian fossil record.
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Affiliation(s)
- Daniel J. Field
- Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, Claverton Down, Bath, BA2 7AY UK
- Department of Geology and Geophysics, Yale University, 210 Whitney Avenue, New Haven, CT 06511 USA
| | - Allison Y. Hsiang
- Department of Geology and Geophysics, Yale University, 210 Whitney Avenue, New Haven, CT 06511 USA
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, 10405 Stockholm, Sweden
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227
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Fabre PH, Tilak MK, Denys C, Gaubert P, Nicolas V, Douzery EJP, Marivaux L. Flightless scaly-tailed squirrels never learned how to fly: A reappraisal of Anomaluridae phylogeny. ZOOL SCR 2018. [DOI: 10.1111/zsc.12286] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- Pierre-Henri Fabre
- Institut des Sciences de l’Évolution de Montpellier (ISE-M, UMR 5554, CNRS/UM/IRD/EPHE); c.c. 064; Université de Montpellier; Montpellier France
- National Museum of Natural History; Smithsonian Institution; Washington DC USA
| | - Marie-Ka Tilak
- Institut des Sciences de l’Évolution de Montpellier (ISE-M, UMR 5554, CNRS/UM/IRD/EPHE); c.c. 064; Université de Montpellier; Montpellier France
| | - Christiane Denys
- Institut de Systématique, Évolution, Biodiversité; ISYEB - UMR 7205, CNRS, MNHN, UPMC, EPHE; Muséum National d’Histoire Naturelle; Sorbonne Universités; Paris France
| | - Philippe Gaubert
- Institut des Sciences de l’Évolution de Montpellier (ISE-M, UMR 5554, CNRS/UM/IRD/EPHE); c.c. 064; Université de Montpellier; Montpellier France
- Laboratoire Evolution et Diversité Biologique (EDB) - UPS-CNRS- IRD; Université Paul Sabatier; Toulouse France
| | - Violaine Nicolas
- Institut de Systématique, Évolution, Biodiversité; ISYEB - UMR 7205, CNRS, MNHN, UPMC, EPHE; Muséum National d’Histoire Naturelle; Sorbonne Universités; Paris France
| | - Emmanuel J. P. Douzery
- Institut des Sciences de l’Évolution de Montpellier (ISE-M, UMR 5554, CNRS/UM/IRD/EPHE); c.c. 064; Université de Montpellier; Montpellier France
| | - Laurent Marivaux
- Institut des Sciences de l’Évolution de Montpellier (ISE-M, UMR 5554, CNRS/UM/IRD/EPHE); c.c. 064; Université de Montpellier; Montpellier France
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228
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Arcila D, Tyler JC. Mass extinction in tetraodontiform fishes linked to the Palaeocene-Eocene thermal maximum. Proc Biol Sci 2018; 284:rspb.2017.1771. [PMID: 29118135 DOI: 10.1098/rspb.2017.1771] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2017] [Accepted: 10/09/2017] [Indexed: 12/18/2022] Open
Abstract
Integrative evolutionary analyses based upon fossil and extant species provide a powerful approach for understanding past diversification events and for assessing the tempo of evolution across the Tree of Life. Herein, we demonstrate the importance of integrating fossil and extant species for inferring patterns of lineage diversification that would otherwise be masked in analyses that examine only one source of evidence. We infer the phylogeny and macroevolutionary history of the Tetraodontiformes (triggerfishes, pufferfishes and allies), a group with one of the most extensive fossil records among fishes. Our analyses combine molecular and morphological data, based on an expanded matrix that adds newly coded fossil species and character states. Beyond confidently resolving the relationships and divergence times of tetraodontiforms, our diversification analyses detect a major mass-extinction event during the Palaeocene-Eocene Thermal Maximum (PETM), followed by a marked increase in speciation rates. This pattern is consistently obtained when fossil and extant species are integrated, whereas examination of the fossil occurrences alone failed to detect major diversification changes during the PETM. When taking into account non-homogeneous models, our analyses also detect a rapid lineage diversification increase in one of the groups (tetraodontoids) during the middle Miocene, which is considered a key period in the evolution of reef fishes associated with trophic changes and ecological opportunity. In summary, our analyses show distinct diversification dynamics estimated from phylogenies and the fossil record, suggesting that different episodes shaped the evolution of tetraodontiforms during the Cenozoic.
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Affiliation(s)
- Dahiana Arcila
- Department of Biological Sciences, The George Washington University, 2023 G Street NW, Washington, DC 20052, USA
| | - James C Tyler
- Department of Paleobiology, National Museum of Natural History, Smithsonian Institution, PO Box 37012, MRC 121, Washington, DC 20013, USA
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229
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The origin of squamates revealed by a Middle Triassic lizard from the Italian Alps. Nature 2018; 557:706-709. [PMID: 29849156 DOI: 10.1038/s41586-018-0093-3] [Citation(s) in RCA: 86] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2017] [Accepted: 02/28/2018] [Indexed: 11/08/2022]
Abstract
Modern squamates (lizards, snakes and amphisbaenians) are the world's most diverse group of tetrapods along with birds 1 and have a long evolutionary history, with the oldest known fossils dating from the Middle Jurassic period-168 million years ago2-4. The evolutionary origin of squamates is contentious because of several issues: (1) a fossil gap of approximately 70 million years exists between the oldest known fossils and their estimated origin5-7; (2) limited sampling of squamates in reptile phylogenies; and (3) conflicts between morphological and molecular hypotheses regarding the origin of crown squamates6,8,9. Here we shed light on these problems by using high-resolution microfocus X-ray computed tomography data from the articulated fossil reptile Megachirella wachtleri (Middle Triassic period, Italian Alps 10 ). We also present a phylogenetic dataset, combining fossils and extant taxa, and morphological and molecular data. We analysed this dataset under different optimality criteria to assess diapsid reptile relationships and the origins of squamates. Our results re-shape the diapsid phylogeny and present evidence that M. wachtleri is the oldest known stem squamate. Megachirella is 75 million years older than the previously known oldest squamate fossils, partially filling the fossil gap in the origin of lizards, and indicates a more gradual acquisition of squamatan features in diapsid evolution than previously thought. For the first time, to our knowledge, morphological and molecular data are in agreement regarding early squamate evolution, with geckoes-and not iguanians-as the earliest crown clade squamates. Divergence time estimates using relaxed combined morphological and molecular clocks show that lepidosaurs and most other diapsids originated before the Permian/Triassic extinction event, indicating that the Triassic was a period of radiation, not origin, for several diapsid lineages.
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230
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Gokhman VE, Kuznetsova VG. Presence of the canonical TTAGG insect telomeric repeat in the Tenthredinidae (Symphyta) suggests its ancestral nature in the order Hymenoptera. Genetica 2018; 146:341-344. [PMID: 29730744 DOI: 10.1007/s10709-018-0019-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2018] [Accepted: 04/23/2018] [Indexed: 11/29/2022]
Abstract
Telomeric repeats in two members of the sawfly family Tenthredinidae (Hymenoptera), namely, Tenthredo omissa (Förster, 1844) and Taxonus agrorum (Fallén, 1808) (both have n = 10), were studied using fluorescence in situ hybridization (FISH). Chromosomes of both species were demonstrated to contain the canonical TTAGG insect telomeric repeat, which constitutes the first report of the (TTAGG)n telomeric motif for the Tenthredinidae as well as for the clade Eusymphyta and the suborder Symphyta in general. Taken together with the presence of this repeat in many other Holometabola as well as in the hymenopteran families Formicidae and Apidae from the suborder Apocrita, these results collectively suggest the ancestral nature of the (TTAGG)n telomeric motif in the Hymenoptera as well as its subsequent loss within the clade Unicalcarida and independent reappearance in ants and bees. If this is true, the loss of the TTAGG repeat can be considered as a synapomorphy of the corresponding clade.
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231
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Hagen O, Andermann T, Quental TB, Antonelli A, Silvestro D. Estimating Age-Dependent Extinction: Contrasting Evidence from Fossils and Phylogenies. Syst Biol 2018; 67:458-474. [PMID: 29069434 PMCID: PMC5920349 DOI: 10.1093/sysbio/syx082] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2016] [Revised: 03/03/2017] [Accepted: 10/15/2017] [Indexed: 01/12/2023] Open
Abstract
The estimation of diversification rates is one of the most vividly debated topics in modern systematics, with considerable controversy surrounding the power of phylogenetic and fossil-based approaches in estimating extinction. Van Valen's seminal work from 1973 proposed the "Law of constant extinction," which states that the probability of extinction of taxa is not dependent on their age. This assumption of age-independent extinction has prevailed for decades with its assessment based on survivorship curves, which, however, do not directly account for the incompleteness of the fossil record, and have rarely been applied at the species level. Here, we present a Bayesian framework to estimate extinction rates from the fossil record accounting for age-dependent extinction (ADE). Our approach, unlike previous implementations, explicitly models unobserved species and accounts for the effects of fossil preservation on the observed longevity of sampled lineages. We assess the performance and robustness of our method through extensive simulations and apply it to a fossil data set of terrestrial Carnivora spanning the past 40 myr. We find strong evidence of ADE, as we detect the extinction rate to be highest in young species and declining with increasing species age. For comparison, we apply a recently developed analogous ADE model to a dated phylogeny of extant Carnivora. Although the phylogeny-based analysis also infers ADE, it indicates that the extinction rate, instead, increases with increasing taxon age. The estimated mean species longevity also differs substantially, with the fossil-based analyses estimating 2.0 myr, in contrast to 9.8 myr derived from the phylogeny-based inference. Scrutinizing these discrepancies, we find that both fossil and phylogeny-based ADE models are prone to high error rates when speciation and extinction rates increase or decrease through time. However, analyses of simulated and empirical data show that fossil-based inferences are more robust. This study shows that an accurate estimation of ADE from incomplete fossil data is possible when the effects of preservation are jointly modeled, thus allowing for a reassessment of Van Valen's model as a general rule in macroevolution.
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Affiliation(s)
- Oskar Hagen
- Swiss Federal Research Institute WSL, 8903 Birmensdorf, Switzerland
- Landscape Ecology, Institute of Terrestrial Ecosystems, ETH Zurich, 8092 Zurich, Switzerland
- Department of Biological and Environmental Sciences, University of Gothenburg, SE-405 30 Göteborg, Sweden
| | - Tobias Andermann
- Department of Biological and Environmental Sciences, University of Gothenburg, SE-405 30 Göteborg, Sweden
- Gothenburg Global Biodiversity Centre, Box 461, SE-405 30 Göteborg, Sweden
| | - Tiago B Quental
- Departamento de Ecologia, Universidade de São Paulo, 05508-900 São Paulo, Brazil
| | - Alexandre Antonelli
- Department of Biological and Environmental Sciences, University of Gothenburg, SE-405 30 Göteborg, Sweden
- Gothenburg Global Biodiversity Centre, Box 461, SE-405 30 Göteborg, Sweden
- Gothenburg Botanical Garden, Carl Skottsbergs gata 22A, SE-413 19 Göteborg, Sweden
| | - Daniele Silvestro
- Department of Biological and Environmental Sciences, University of Gothenburg, SE-405 30 Göteborg, Sweden
- Gothenburg Global Biodiversity Centre, Box 461, SE-405 30 Göteborg, Sweden
- Department of Computational Biology, University of Lausanne, 1015 Lausanne, Switzerland
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232
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Matzke NJ, Irmis RB. Including autapomorphies is important for paleontological tip-dating with clocklike data, but not with non-clock data. PeerJ 2018; 6:e4553. [PMID: 29637019 PMCID: PMC5890724 DOI: 10.7717/peerj.4553] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2016] [Accepted: 03/08/2018] [Indexed: 12/01/2022] Open
Abstract
Tip-dating, where fossils are included as dated terminal taxa in Bayesian dating inference, is an increasingly popular method. Data for these studies often come from morphological character matrices originally developed for non-dated, and usually parsimony, analyses. In parsimony, only shared derived characters (synapomorphies) provide grouping information, so many character matrices have an ascertainment bias: they omit autapomorphies (unique derived character states), which are considered uninformative. There has been no study of the effect of this ascertainment bias in tip-dating, but autapomorphies can be informative in model-based inference. We expected that excluding autapomorphies would shorten the morphological branchlengths of terminal branches, and thus bias downwards the time branchlengths inferred in tip-dating. We tested for this effect using a matrix for Carboniferous-Permian eureptiles where all autapomorphies had been deliberately coded. Surprisingly, date estimates are virtually unchanged when autapomorphies are excluded, although we find large changes in morphological rate estimates and small effects on topological and dating confidence. We hypothesized that the puzzling lack of effect on dating was caused by the non-clock nature of the eureptile data. We confirm this explanation by simulating strict clock and non-clock datasets, showing that autapomorphy exclusion biases dating only for the clocklike case. A theoretical solution to ascertainment bias is computing the ascertainment bias correction (Mkparsinf), but we explore this correction in detail, and show that it is computationally impractical for typical datasets with many character states and taxa. Therefore we recommend that palaeontologists collect autapomorphies whenever possible when assembling character matrices.
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Affiliation(s)
- Nicholas J Matzke
- Division of Ecology and Evolution, Research School of Biology, The Australian National University, Canberra, Australian Capital Territory, Australia.,School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - Randall B Irmis
- Department of Geology & Geophysics, University of Utah, Salt Lake City, UT, United States of America.,Natural History Museum of Utah, Salt Lake City, UT, United States of America
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Barba‐Montoya J, dos Reis M, Schneider H, Donoghue PCJ, Yang Z. Constraining uncertainty in the timescale of angiosperm evolution and the veracity of a Cretaceous Terrestrial Revolution. THE NEW PHYTOLOGIST 2018; 218:819-834. [PMID: 29399804 PMCID: PMC6055841 DOI: 10.1111/nph.15011] [Citation(s) in RCA: 96] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2017] [Accepted: 12/20/2017] [Indexed: 05/02/2023]
Abstract
Through the lens of the fossil record, angiosperm diversification precipitated a Cretaceous Terrestrial Revolution (KTR) in which pollinators, herbivores and predators underwent explosive co-diversification. Molecular dating studies imply that early angiosperm evolution is not documented in the fossil record. This mismatch remains controversial. We used a Bayesian molecular dating method to analyse a dataset of 83 genes from 644 taxa and 52 fossil calibrations to explore the effect of different interpretations of the fossil record, molecular clock models, data partitioning, among other factors, on angiosperm divergence time estimation. Controlling for different sources of uncertainty indicates that the timescale of angiosperm diversification is much less certain than previous molecular dating studies have suggested. Discord between molecular clock and purely fossil-based interpretations of angiosperm diversification may be a consequence of false precision on both sides. We reject a post-Jurassic origin of angiosperms, supporting the notion of a cryptic early history of angiosperms, but this history may be as much as 121 Myr, or as little as 23 Myr. These conclusions remain compatible with palaeobotanical evidence and a more general KTR in which major groups of angiosperms diverged later within the Cretaceous, alongside the diversification of pollinators, herbivores and their predators.
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Affiliation(s)
- Jose Barba‐Montoya
- Department of Genetics, Evolution and EnvironmentUniversity College LondonDarwin BuildingGower StreetLondonWC1E 6BTUK
| | - Mario dos Reis
- School of Biological and Chemical SciencesQueen Mary University of LondonMile End RoadLondonE1 4NSUK
| | - Harald Schneider
- Center of Integrative ConservationXishuangbanna Tropical Botanical GardenChinese Academy of SciencesMenglunYunnanChina
- Department of BotanyNatural History MuseumCromwell RoadLondonSW7 5BDUK
| | - Philip C. J. Donoghue
- School of Earth SciencesUniversity of BristolLife Sciences BuildingTyndall AvenueBristolBS8 1TQUK
| | - Ziheng Yang
- Department of Genetics, Evolution and EnvironmentUniversity College LondonDarwin BuildingGower StreetLondonWC1E 6BTUK
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234
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Parins-Fukuchi C. Use of Continuous Traits Can Improve Morphological Phylogenetics. Syst Biol 2018; 67:328-339. [PMID: 28945906 DOI: 10.1093/sysbio/syx072] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2017] [Accepted: 08/30/2017] [Indexed: 12/21/2022] Open
Abstract
The recent surge in enthusiasm for simultaneously inferring relationships from extinct and extant species has reinvigorated interest in statistical approaches for modeling morphological evolution. Current statistical methods use the Mk model to describe substitutions between discrete character states. Although representing a significant step forward, the Mk model presents challenges in biological interpretation, and its adequacy in modeling morphological evolution has not been well explored. Another major hurdle in morphological phylogenetics concerns the process of character coding of discrete characters. The often subjective nature of discrete character coding can generate discordant results that are rooted in individual researchers' subjective interpretations. Employing continuous measurements to infer phylogenies may alleviate some of these issues. Although not widely used in the inference of topology, models describing the evolution of continuous characters have been well examined, and their statistical behavior is well understood. Also, continuous measurements avoid the substantial ambiguity often associated with the assignment of discrete characters to states. I present a set of simulations to determine whether use of continuous characters is a feasible alternative or supplement to discrete characters for inferring phylogeny. I compare relative reconstruction accuracy by inferring phylogenies from simulated continuous and discrete characters. These tests demonstrate significant promise for continuous traits by demonstrating their higher overall accuracy as compared to reconstruction from discrete characters under Mk when simulated under unbounded Brownian motion, and equal performance when simulated under an Ornstein-Uhlenbeck model. Continuous characters also perform reasonably well in the presence of covariance between sites. I argue that inferring phylogenies directly from continuous traits may be benefit efforts to maximize phylogenetic information in morphological data sets by preserving larger variation in state space compared to many discretization schemes. I also suggest that the use of continuous trait models in phylogenetic reconstruction may alleviate potential concerns of discrete character model adequacy, while identifying areas that require further study in this area. This study provides an initial controlled demonstration of the efficacy of continuous characters in phylogenetic inference.
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Affiliation(s)
- Caroline Parins-Fukuchi
- Department of Ecology and Evolutionary Biology, University of Michigan, 830 N. University, Ann Arbor, MI 48109, USA
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235
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Brown JW, Smith SA. The Past Sure is Tense: On Interpreting Phylogenetic Divergence Time Estimates. Syst Biol 2018; 67:340-353. [PMID: 28945912 DOI: 10.1093/sysbio/syx074] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2017] [Accepted: 09/04/2017] [Indexed: 11/12/2022] Open
Abstract
Divergence time estimation-the calibration of a phylogeny to geological time-is an integral first step in modeling the tempo of biological evolution (traits and lineages). However, despite increasingly sophisticated methods to infer divergence times from molecular genetic sequences, the estimated age of many nodes across the tree of life contrast significantly and consistently with timeframes conveyed by the fossil record. This is perhaps best exemplified by crown angiosperms, where molecular clock (Triassic) estimates predate the oldest (Early Cretaceous) undisputed angiosperm fossils by tens of millions of years or more. While the incompleteness of the fossil record is a common concern, issues of data limitation and model inadequacy are viable (if underexplored) alternative explanations. In this vein, Beaulieu et al. (2015) convincingly demonstrated how methods of divergence time inference can be misled by both (i) extreme state-dependent molecular substitution rate heterogeneity and (ii) biased sampling of representative major lineages. These results demonstrate the impact of (potentially common) model violations. Here, we suggest another potential challenge: that the configuration of the statistical inference problem (i.e., the parameters, their relationships, and associated priors) alone may preclude the reconstruction of the paleontological timeframe for the crown age of angiosperms. We demonstrate, through sampling from the joint prior (formed by combining the tree (diversification) prior with the calibration densities specified for fossil-calibrated nodes) that with no data present at all, that an Early Cretaceous crown angiosperms is rejected (i.e., has essentially zero probability). More worrisome, however, is that for the 24 nodes calibrated by fossils, almost all have indistinguishable marginal prior and posterior age distributions when employing routine lognormal fossil calibration priors. These results indicate that there is inadequate information in the data to over-rule the joint prior. Given that these calibrated nodes are strategically placed in disparate regions of the tree, they act to anchor the tree scaffold, and so the posterior inference for the tree as a whole is largely determined by the pseudodata present in the (often arbitrary) calibration densities. We recommend, as for any Bayesian analysis, that marginal prior and posterior distributions be carefully compared to determine whether signal is coming from the data or prior belief, especially for parameters of direct interest. This recommendation is not novel. However, given how rarely such checks are carried out in evolutionary biology, it bears repeating. Our results demonstrate the fundamental importance of prior/posterior comparisons in any Bayesian analysis, and we hope that they further encourage both researchers and journals to consistently adopt this crucial step as standard practice. Finally, we note that the results presented here do not refute the biological modeling concerns identified by Beaulieu et al. (2015). Both sets of issues remain apposite to the goals of accurate divergence time estimation, and only by considering them in tandem can we move forward more confidently.
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Affiliation(s)
- Joseph W Brown
- Department of Ecology & Evolutionary Biology, University of Michigan, 830 North University Avenue, Ann Arbor, MI 48109, USA
| | - Stephen A Smith
- Department of Ecology & Evolutionary Biology, University of Michigan, 830 North University Avenue, Ann Arbor, MI 48109, USA
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236
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O'Reilly JE, Donoghue PCJ. The Efficacy of Consensus Tree Methods for Summarizing Phylogenetic Relationships from a Posterior Sample of Trees Estimated from Morphological Data. Syst Biol 2018; 67:354-362. [PMID: 29106675 PMCID: PMC5837340 DOI: 10.1093/sysbio/syx086] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2017] [Accepted: 10/24/2017] [Indexed: 01/16/2023] Open
Abstract
Consensus trees are required to summarize trees obtained through MCMC sampling of a posterior distribution, providing an overview of the distribution of estimated parameters such as topology, branch lengths, and divergence times. Numerous consensus tree construction methods are available, each presenting a different interpretation of the tree sample. The rise of morphological clock and sampled-ancestor methods of divergence time estimation, in which times and topology are coestimated, has increased the popularity of the maximum clade credibility (MCC) consensus tree method. The MCC method assumes that the sampled, fully resolved topology with the highest clade credibility is an adequate summary of the most probable clades, with parameter estimates from compatible sampled trees used to obtain the marginal distributions of parameters such as clade ages and branch lengths. Using both simulated and empirical data, we demonstrate that MCC trees, and trees constructed using the similar maximum a posteriori (MAP) method, often include poorly supported and incorrect clades when summarizing diffuse posterior samples of trees. We demonstrate that the paucity of information in morphological data sets contributes to the inability of MCC and MAP trees to accurately summarise of the posterior distribution. Conversely, majority-rule consensus (MRC) trees represent a lower proportion of incorrect nodes when summarizing the same posterior samples of trees. Thus, we advocate the use of MRC trees, in place of MCC or MAP trees, in attempts to summarize the results of Bayesian phylogenetic analyses of morphological data.
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Affiliation(s)
- Joseph E O'Reilly
- School of Earth Sciences, University of Bristol, Life Sciences Building, Tyndall Avenue, Bristol BS8 1TQ, UK
| | - Philip C J Donoghue
- School of Earth Sciences, University of Bristol, Life Sciences Building, Tyndall Avenue, Bristol BS8 1TQ, UK
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237
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Stadler T, Gavryushkina A, Warnock RCM, Drummond AJ, Heath TA. The fossilized birth-death model for the analysis of stratigraphic range data under different speciation modes. J Theor Biol 2018; 447:41-55. [PMID: 29550451 PMCID: PMC5931795 DOI: 10.1016/j.jtbi.2018.03.005] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2017] [Revised: 09/15/2017] [Accepted: 03/05/2018] [Indexed: 10/26/2022]
Abstract
A birth-death-sampling model gives rise to phylogenetic trees with samples from the past and the present. Interpreting "birth" as branching speciation, "death" as extinction, and "sampling" as fossil preservation and recovery, this model - also referred to as the fossilized birth-death (FBD) model - gives rise to phylogenetic trees on extant and fossil samples. The model has been mathematically analyzed and successfully applied to a range of datasets on different taxonomic levels, such as penguins, plants, and insects. However, the current mathematical treatment of this model does not allow for a group of temporally distinct fossil specimens to be assigned to the same species. In this paper, we provide a general mathematical FBD modeling framework that explicitly takes "stratigraphic ranges" into account, with a stratigraphic range being defined as the lineage interval associated with a single species, ranging through time from the first to the last fossil appearance of the species. To assign a sequence of fossil samples in the phylogenetic tree to the same species, i.e., to specify a stratigraphic range, we need to define the mode of speciation. We provide expressions to account for three common speciation modes: budding (or asymmetric) speciation, bifurcating (or symmetric) speciation, and anagenetic speciation. Our equations allow for flexible joint Bayesian analysis of paleontological and neontological data. Furthermore, our framework is directly applicable to epidemiology, where a stratigraphic range is the observed duration of infection of a single patient, "birth" via budding is transmission, "death" is recovery, and "sampling" is sequencing the pathogen of a patient. Thus, we present a model that allows for incorporation of multiple observations through time from a single patient.
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Affiliation(s)
- Tanja Stadler
- Department of Biosystems Science & Engineering, Eidgenössische Technische Hochschule Zürich, Basel 4058, Switzerland; Swiss Institute of Bioinformatics (SIB), Switzerland.
| | - Alexandra Gavryushkina
- Department of Biosystems Science & Engineering, Eidgenössische Technische Hochschule Zürich, Basel 4058, Switzerland; Swiss Institute of Bioinformatics (SIB), Switzerland
| | - Rachel C M Warnock
- Department of Biosystems Science & Engineering, Eidgenössische Technische Hochschule Zürich, Basel 4058, Switzerland; Swiss Institute of Bioinformatics (SIB), Switzerland
| | - Alexei J Drummond
- Department of Computer Science, Centre for Computational Evolution, University of Auckland, Auckland 1010, New Zealand
| | - Tracy A Heath
- Department of Ecology, Evolution, & Organismal Biology, Iowa State University, Ames, Iowa 50011, USA
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238
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Morris JL, Puttick MN, Clark JW, Edwards D, Kenrick P, Pressel S, Wellman CH, Yang Z, Schneider H, Donoghue PCJ. The timescale of early land plant evolution. Proc Natl Acad Sci U S A 2018; 115:E2274-E2283. [PMID: 29463716 PMCID: PMC5877938 DOI: 10.1073/pnas.1719588115] [Citation(s) in RCA: 400] [Impact Index Per Article: 66.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Establishing the timescale of early land plant evolution is essential for testing hypotheses on the coevolution of land plants and Earth's System. The sparseness of early land plant megafossils and stratigraphic controls on their distribution make the fossil record an unreliable guide, leaving only the molecular clock. However, the application of molecular clock methodology is challenged by the current impasse in attempts to resolve the evolutionary relationships among the living bryophytes and tracheophytes. Here, we establish a timescale for early land plant evolution that integrates over topological uncertainty by exploring the impact of competing hypotheses on bryophyte-tracheophyte relationships, among other variables, on divergence time estimation. We codify 37 fossil calibrations for Viridiplantae following best practice. We apply these calibrations in a Bayesian relaxed molecular clock analysis of a phylogenomic dataset encompassing the diversity of Embryophyta and their relatives within Viridiplantae. Topology and dataset sizes have little impact on age estimates, with greater differences among alternative clock models and calibration strategies. For all analyses, a Cambrian origin of Embryophyta is recovered with highest probability. The estimated ages for crown tracheophytes range from Late Ordovician to late Silurian. This timescale implies an early establishment of terrestrial ecosystems by land plants that is in close accord with recent estimates for the origin of terrestrial animal lineages. Biogeochemical models that are constrained by the fossil record of early land plants, or attempt to explain their impact, must consider the implications of a much earlier, middle Cambrian-Early Ordovician, origin.
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Affiliation(s)
- Jennifer L Morris
- School of Earth Sciences, University of Bristol, Bristol BS8 1TQ, United Kingdom
| | - Mark N Puttick
- School of Earth Sciences, University of Bristol, Bristol BS8 1TQ, United Kingdom
- Department of Earth Sciences, Natural History Museum, London SW7 5BD, United Kingdom
| | - James W Clark
- School of Earth Sciences, University of Bristol, Bristol BS8 1TQ, United Kingdom
| | - Dianne Edwards
- School of Earth and Ocean Sciences, Cardiff University, Cardiff CF10, United Kingdom
| | - Paul Kenrick
- Department of Earth Sciences, Natural History Museum, London SW7 5BD, United Kingdom
| | - Silvia Pressel
- Department of Life Sciences, Natural History Museum, London SW7 5BD, United Kingdom
| | - Charles H Wellman
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield S10 2TN, United Kingdom
| | - Ziheng Yang
- Department of Genetics, Evolution and Environment, University College London, London WC1E 6BT, United Kingdom
- Radclie Institute for Advanced Studies, Harvard University, Cambridge, MA 02138
| | - Harald Schneider
- School of Earth Sciences, University of Bristol, Bristol BS8 1TQ, United Kingdom;
- Department of Life Sciences, Natural History Museum, London SW7 5BD, United Kingdom
- Center of Integrative Conservation, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Yunnan 666303, China
| | - Philip C J Donoghue
- School of Earth Sciences, University of Bristol, Bristol BS8 1TQ, United Kingdom;
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239
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Pyron RA. Novel Approaches for Phylogenetic Inference from Morphological Data and Total-Evidence Dating in Squamate Reptiles (Lizards, Snakes, and Amphisbaenians). Syst Biol 2018; 66:38-56. [PMID: 28173602 DOI: 10.1093/sysbio/syw068] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2015] [Revised: 07/12/2016] [Accepted: 07/20/2016] [Indexed: 02/04/2023] Open
Abstract
Here, I combine previously underutilized models and priors to perform more biologically realistic phylogenetic inference from morphological data, with an example from squamate reptiles. When coding morphological characters, it is often possible to denote ordered states with explicit reference to observed or hypothetical ancestral conditions. Using this logic, we can integrate across character-state labels and estimate meaningful rates of forward and backward transitions from plesiomorphy to apomorphy. I refer to this approach as MkA, for “asymmetric.” The MkA model incorporates the biological reality of limited reversal for many phylogenetically informative characters, and significantly increases likelihoods in the empirical data sets. Despite this, the phylogeny of Squamata remains contentious. Total-evidence analyses using combined morphological and molecular data and the MkA approach tend toward recent consensus estimates supporting a nested Iguania. However, support for this topology is not unambiguous across data sets or analyses, and no mechanism has been proposed to explain the widespread incongruence between partitions, or the hidden support for various topologies in those partitions. Furthermore, different morphological data sets produced by different authors contain both different characters and different states for the same or similar characters, resulting in drastically different placements for many important fossil lineages. Effort is needed to standardize ontology for morphology, resolve incongruence, and estimate a robust phylogeny. The MkA approach provides a preliminary avenue for investigating morphological evolution while accounting for temporal evidence and asymmetry in character-state changes.
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Affiliation(s)
- R Alexander Pyron
- Department of Biological Sciences, The George Washington University, 2023 G St. NW, Washington, DC, USA
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240
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Matschiner M, Musilová Z, Barth JMI, Starostová Z, Salzburger W, Steel M, Bouckaert R. Bayesian Phylogenetic Estimation of Clade Ages Supports Trans-Atlantic Dispersal of Cichlid Fishes. Syst Biol 2018; 66:3-22. [PMID: 28173588 DOI: 10.1093/sysbio/syw076] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2016] [Revised: 06/21/2016] [Accepted: 08/23/2016] [Indexed: 11/13/2022] Open
Abstract
Divergence-time estimation based on molecular phylogenies and the fossil record has provided insights into fundamental questions of evolutionary biology. In Bayesian node dating, phylogenies are commonly time calibrated through the specification of calibration densities on nodes representing clades with known fossil occurrences. Unfortunately, the optimal shape of these calibration densities is usually unknown and they are therefore often chosen arbitrarily, which directly impacts the reliability of the resulting age estimates. As possible solutions to this problem, two nonexclusive alternative approaches have recently been developed, the “fossilized birth–death” (FBD) model and “total-evidence dating.” While these approaches have been shown to perform well under certain conditions, they require including all (or a random subset) of the fossils of each clade in the analysis, rather than just relying on the oldest fossils of clades. In addition, both approaches assume that fossil records of different clades in the phylogeny are all the product of the same underlying fossil sampling rate, even though this rate has been shown to differ strongly between higher level taxa. We here develop a flexible new approach to Bayesian age estimation that combines advantages of node dating and the FBD model. In our new approach, calibration densities are defined on the basis of first fossil occurrences and sampling rate estimates that can be specified separately for all clades. We verify our approach with a large number of simulated data sets, and compare its performance to that of the FBD model. We find that our approach produces reliable age estimates that are robust to model violation, on par with the FBD model. By applying our approach to a large data set including sequence data from over 1000 species of teleost fishes as well as 147 carefully selected fossil constraints, we recover a timeline of teleost diversification that is incompatible with previously assumed vicariant divergences of freshwater fishes. Our results instead provide strong evidence for transoceanic dispersal of cichlids and other groups of teleost fishes.
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Affiliation(s)
- Michael Matschiner
- Department of Biosciences, Centre for Ecological and Evolutionary Synthesis (CEES), University of Oslo, Oslo, Norway.,Zoological Institute, University of Basel, Basel, Switzerland
| | - Zuzana Musilová
- Department of Zoology, Faculty of Science, Charles University in Prague, Prague, Czech Republic.,Zoological Institute, University of Basel, Basel, Switzerland
| | - Julia M I Barth
- Department of Biosciences, Centre for Ecological and Evolutionary Synthesis (CEES), University of Oslo, Oslo, Norway
| | - Zuzana Starostová
- Department of Zoology, Faculty of Science, Charles University in Prague, Prague, Czech Republic
| | - Walter Salzburger
- Department of Biosciences, Centre for Ecological and Evolutionary Synthesis (CEES), University of Oslo, Oslo, Norway.,Zoological Institute, University of Basel, Basel, Switzerland
| | - Mike Steel
- Department of Mathematics and Statistics, University of Canterbury, Christchurch, New Zealand
| | - Remco Bouckaert
- Department of Computer Science, University of Auckland, Auckland, New Zealand.,Computational Evolution Group, University of Auckland, Auckland, New Zealand
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241
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Condamine FL, Rolland J, Höhna S, Sperling FAH, Sanmartín I. Testing the Role of the Red Queen and Court Jester as Drivers of the Macroevolution of Apollo Butterflies. Syst Biol 2018; 67:940-964. [DOI: 10.1093/sysbio/syy009] [Citation(s) in RCA: 60] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2016] [Accepted: 02/06/2018] [Indexed: 11/13/2022] Open
Affiliation(s)
- Fabien L Condamine
- CNRS, UMR 5554 Institut des Sciences de l’Evolution (Université de Montpellier
- CNRS IRD
- EPHE), Place Eugène Bataillon, 34095 Montpellier, France
- Department of Biodiversity and Conservation, Real Jardín Botánico, CSIC, Plaza de Murillo, 2, 28014 Madrid, Spain
- Department of Biological Sciences, University of Alberta, Edmonton T6G 2E9, Alberta, Canada
| | - Jonathan Rolland
- Department of Ecology and Evolution, University of Lausanne, 1015 Lausanne, Switzerland
| | - Sebastian Höhna
- Division of Evolutionary Biology, Ludwig-Maximilian-Universität München, Grosshaderner Strasse 2, Planegg-Martinsried 82152, Germany
| | - Felix A H Sperling
- Department of Biological Sciences, University of Alberta, Edmonton T6G 2E9, Alberta, Canada
| | - Isabel Sanmartín
- Department of Biodiversity and Conservation, Real Jardín Botánico, CSIC, Plaza de Murillo, 2, 28014 Madrid, Spain
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242
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Heustis A, Moise ERD, Johns R, Pureswaran DS, Heard SB. Impact of an Invasive Longhorned Beetle, Tetropium fuscum (Coleoptera: Cerambycidae), on Community Structure of Subcortical and Wood-Associated Insects in Eastern Canada. ENVIRONMENTAL ENTOMOLOGY 2018; 47:39-47. [PMID: 29300848 DOI: 10.1093/ee/nvx190] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2017] [Indexed: 06/07/2023]
Abstract
Tetropium fuscum (Fabricius) (Coleoptera: Cerambycidae), a phloem-feeding and wood-boring beetle introduced from Eurasia, attacks spruce in eastern Canada alongside its native congener Tetropium cinnamopterum Kirby. We reared phloem- and wood-feeding insects (and their predators) from bolts of red and Norway spruce (Picea rubens and Picea abies) in Nova Scotia, comparing insect communities between bolts with added eggs of T. fuscum or T. cinnamopterum and bolts without added Tetropium (controls). We tested for impacts of each Tetropium on insect community structure (Simpson's diversity, richness, and evenness). We also asked whether, consistent with Darwin's Naturalization Hypothesis, Tetropium spp. would have greater impacts on emergence of its closer relatives (which might be most likely to compete and/or share natural enemies). Addition of Tetropium eggs (either species) to bolts lowered insect diversity in both host trees. Both richness and evenness components of diversity were always lower in +Tetropium treatments, although different components reached statistical significance in different Tetropium species × host combinations. Addition of Tetropium spp. significantly reduced emergence of some species: Evodinus monticola (Randall) (Coleoptera: Cerambycidae) was reduced by T. fuscum on both hosts and by T. cinnamopterum on Norway spruce; Hylobius congener Dalla Torre, Schenkling, and Marshall was reduced by T. fuscum on red spruce; and Xylophagus sp. (Diptera: Xylophagidae) was reduced by T. cinnamopterum on Norway spruce. However, there was no relationship between Tetropium's impact on a community member and their phylogenetic relatedness, and the overall impacts of Tetropium presence were not very different between T. fuscum and T. cinnamopterum.
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Affiliation(s)
- Allyson Heustis
- Department of Biology, University of New Brunswick, Fredericton, Canada
| | - Eric R D Moise
- Natural Resources Canada, Canadian Forest Service-Atlantic Forestry Centre, Corner Brook, Canada
| | - Rob Johns
- Natural Resources Canada, Canadian Forest Service-Atlantic Forestry Centre, Fredericton, Canada
| | - Deepa S Pureswaran
- Natural Resources Canada, Canadian Forest Service-Laurentian Forestry Centre, Québec, Canada
| | - Stephen B Heard
- Department of Biology, University of New Brunswick, Fredericton, Canada
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243
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Title PO, Rabosky DL. Do Macrophylogenies Yield Stable Macroevolutionary Inferences? An Example from Squamate Reptiles. Syst Biol 2018; 66:843-856. [PMID: 27821703 DOI: 10.1093/sysbio/syw102] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2015] [Accepted: 10/27/2016] [Indexed: 01/03/2023] Open
Abstract
Advances in the generation, retrieval, and analysis of phylogenetic data have enabled researchers to create phylogenies that contain many thousands of taxa. These "macrophylogenies"-large trees that typically derive from megaphylogeny, supermatrix, or supertree approaches-provide researchers with an unprecedented ability to conduct evolutionary analyses across broad phylogenetic scales. Many studies have now used these phylogenies to explore the dynamics of speciation, extinction, and phenotypic evolution across large swaths of the tree of life. These trees are characterized by substantial phylogenetic uncertainty on multiple levels, and the stability of macroevolutionary inferences from these data sets has not been rigorously explored. As a case study, we tested whether five recently published phylogenies for squamate reptiles-each consisting of more than 4000 species-yield congruent inferences about the processes that underlie variation in species richness across replicate evolutionary radiations of Australian snakes and lizards. We find discordance across the five focal phylogenies with respect to clade age and several diversification rate metrics, and in the effects of clade age on species richness. We also find that crown clade ages reported in the literature on these Australian groups are in conflict with all of the large phylogenies examined. Macrophylogenies offer an unprecedented opportunity to address evolutionary and ecological questions at broad phylogenetic scales, but accurately representing the uncertainty that is inherent to such analyses remains a critical challenge to our field. [Australia; macroevolution; macrophylogeny; squamates; time calibration.].
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Affiliation(s)
- Pascal O Title
- Department of Ecology and Evolutionary Biology and Museum of Zoology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Daniel L Rabosky
- Department of Ecology and Evolutionary Biology and Museum of Zoology, University of Michigan, Ann Arbor, MI 48109, USA
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244
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Foster CSP, Sauquet H, van der Merwe M, McPherson H, Rossetto M, Ho SYW. Evaluating the Impact of Genomic Data and Priors on Bayesian Estimates of the Angiosperm Evolutionary Timescale. Syst Biol 2018; 66:338-351. [PMID: 27650175 DOI: 10.1093/sysbio/syw086] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2015] [Accepted: 09/10/2016] [Indexed: 11/14/2022] Open
Abstract
The evolutionary timescale of angiosperms has long been a key question in biology. Molecular estimates of this timescale have shown considerable variation, being influenced by differences in taxon sampling, gene sampling, fossil calibrations, evolutionary models, and choices of priors. Here, we analyze a data set comprising 76 protein-coding genes from the chloroplast genomes of 195 taxa spanning 86 families, including novel genome sequences for 11 taxa, to evaluate the impact of models, priors, and gene sampling on Bayesian estimates of the angiosperm evolutionary timescale. Using a Bayesian relaxed molecular-clock method, with a core set of 35 minimum and two maximum fossil constraints, we estimated that crown angiosperms arose 221 (251-192) Ma during the Triassic. Based on a range of additional sensitivity and subsampling analyses, we found that our date estimates were generally robust to large changes in the parameters of the birth-death tree prior and of the model of rate variation across branches. We found an exception to this when we implemented fossil calibrations in the form of highly informative gamma priors rather than as uniform priors on node ages. Under all other calibration schemes, including trials of seven maximum age constraints, we consistently found that the earliest divergences of angiosperm clades substantially predate the oldest fossils that can be assigned unequivocally to their crown group. Overall, our results and experiments with genome-scale data suggest that reliable estimates of the angiosperm crown age will require increased taxon sampling, significant methodological changes, and new information from the fossil record. [Angiospermae, chloroplast, genome, molecular dating, Triassic.].
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Affiliation(s)
- Charles S P Foster
- School of Life and Environmental Sciences, Edgeworth David Building A11, University of Sydney, Sydney, New South Wales 2006, Australia
| | - Hervê Sauquet
- Laboratoire écologie, Systématique, évolution, Université Paris-Sud, CNRS UMR 8079, bat. 360, Orsay 91405, France
| | - Marlien van der Merwe
- National Herbarium of New South Wales, Royal Botanic Gardens & Domain Trust, Mrs Macquaries Road, Sydney, New South Wales 2000, Australia
| | - Hannah McPherson
- National Herbarium of New South Wales, Royal Botanic Gardens & Domain Trust, Mrs Macquaries Road, Sydney, New South Wales 2000, Australia
| | - Maurizio Rossetto
- National Herbarium of New South Wales, Royal Botanic Gardens & Domain Trust, Mrs Macquaries Road, Sydney, New South Wales 2000, Australia
| | - Simon Y W Ho
- School of Life and Environmental Sciences, Edgeworth David Building A11, University of Sydney, Sydney, New South Wales 2006, Australia
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245
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Lozano-Fernandez J, Dos Reis M, Donoghue PCJ, Pisani D. RelTime Rates Collapse to a Strict Clock When Estimating the Timeline of Animal Diversification. Genome Biol Evol 2018; 9:1320-1328. [PMID: 28449025 PMCID: PMC5447329 DOI: 10.1093/gbe/evx079] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/24/2017] [Indexed: 12/16/2022] Open
Abstract
Establishing an accurate timescale for the history of life is crucial to understand evolutionary processes. For this purpose, relaxed molecular clock models implemented in a Bayesian MCMC framework are generally used. However, these methods are time consuming. RelTime, a non-Bayesian method implementing a fast, ad hoc, algorithm for relative dating, was developed to overcome the computational inefficiencies of Bayesian software. RelTime was recently used to investigate the timing of origin of animals, yielding results consistent with early strict clock studies from the 1980s and 1990s, estimating metazoans to have a Mesoproterozoic origin—over a billion years ago. RelTime results are unexpected and disagree with the largest majority of modern, relaxed, Bayesian molecular clock analyses, which suggest animals originated in the Tonian-Cryogenian (less that 850 million years ago). Here, we demonstrate that RelTime-inferred divergence times for the origin of animals are spurious, a consequence of the inability of RelTime to relax the clock along the internal branches of the animal phylogeny. RelTime-inferred divergence times are comparable to strict-clock estimates because they are essentially inferred under a strict clock. Our results warn us of the danger of using ad hoc algorithms making implicit assumptions about rate changes along a tree. Our study roundly rejects a Mesoproterozoic origin of animals; metazoans emerged in the Tonian-Cryogenian, and diversified in the Ediacaran, in the immediate prelude to the routine fossilization of animals in the Cambrian associated with the emergence of readily preserved skeletons.
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Affiliation(s)
- Jesus Lozano-Fernandez
- School of Earth Sciences, Life Sciences Building, University of Bristol, United Kingdom.,School of Biological Sciences, Life Sciences Building, University of Bristol, United Kingdom
| | - Mario Dos Reis
- School of Biological and Chemical Sciences, Queen Mary University of London, United Kingdom
| | - Philip C J Donoghue
- School of Earth Sciences, Life Sciences Building, University of Bristol, United Kingdom
| | - Davide Pisani
- School of Earth Sciences, Life Sciences Building, University of Bristol, United Kingdom.,School of Biological Sciences, Life Sciences Building, University of Bristol, United Kingdom
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246
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Ilves KL, Torti D, López-Fernández H. Exon-based phylogenomics strengthens the phylogeny of Neotropical cichlids and identifies remaining conflicting clades (Cichliformes: Cichlidae: Cichlinae). Mol Phylogenet Evol 2018; 118:232-243. [DOI: 10.1016/j.ympev.2017.10.008] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2017] [Revised: 10/05/2017] [Accepted: 10/06/2017] [Indexed: 01/13/2023]
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247
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Kealy S, Beck R. Total evidence phylogeny and evolutionary timescale for Australian faunivorous marsupials (Dasyuromorphia). BMC Evol Biol 2017; 17:240. [PMID: 29202687 PMCID: PMC5715987 DOI: 10.1186/s12862-017-1090-0] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2017] [Accepted: 11/22/2017] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND The order Dasyuromorphia is a diverse radiation of faunivorous marsupials, comprising >80 modern species in Australia and New Guinea. It includes dasyurids, the numbat (the myrmecobiid Myrmecobius fasciatus) and the recently extinct thylacine (the thylacinid Thylacinus cyncocephalus). There is also a diverse fossil record of dasyuromorphians and "dasyuromorphian-like" taxa known from Australia. We present the first total evidence phylogenetic analyses of the order, based on combined morphological and molecular data (including a novel set of 115 postcranial characters), to resolve relationships and calculate divergence dates. We use this information to analyse the diversification dynamics of modern dasyuromorphians. RESULTS Our morphology-only analyses are poorly resolved, but our molecular and total evidence analyses confidently resolve most relationships within the order, and are strongly congruent with recent molecular studies. Thylacinidae is the first family to diverge within the order, and there is strong support for four tribes within Dasyuridae (Dasyurini, Phascogalini, Planigalini and Sminthopsini). Among fossil taxa, Ankotarinja and Keeuna do not appear to be members of Dasyuromorphia, whilst Barinya and Mutpuracinus are of uncertain relationships within the order. Divergence dates calculated using total evidence tip-and-node dating are younger than both molecular node-dating and total evidence tip-dating, but appear more congruent with the fossil record and are relatively insensitive to calibration strategy. The tip-and-node divergence dates indicate that Dasyurini, Phascogalini and Sminthopsini began to radiate almost simultaneously during the middle-to-late Miocene (11.5-13.1 MYA; composite 95% HPD: 9.5-15.9 MYA); the median estimates for these divergences are shortly after a drop in global temperatures (the middle Miocene Climatic Transition), and coincide with a faunal turnover event in the mammalian fossil record of Australia. Planigalini radiated much later, during the latest Miocene to earliest Pliocene (6.5 MYA; composite 95% HPD: 4.4-8.9 MYA); the median estimates for these divergences coincide with an increase in grass pollen in the Australian palynological record that suggests the development of more open habitats, which are preferred by modern planigale species. CONCLUSIONS Our results provide a phylogenetic and temporal framework for interpreting the evolution of modern and fossil dasyuromorphians, but future progress will require a much improved fossil record.
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Affiliation(s)
- Shimona Kealy
- Archaeology and Natural History, School of Culture, History and Language, College of Asia and the Pacific, Australian National University, Acton, ACT Australia
| | - Robin Beck
- School of Environment and Life Sciences, University of Salford, Salford, M5 4WT UK
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248
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Lee MSY. Multiple morphological clocks and total-evidence tip-dating in mammals. Biol Lett 2017; 12:rsbl.2016.0033. [PMID: 27381882 DOI: 10.1098/rsbl.2016.0033] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2016] [Accepted: 06/14/2016] [Indexed: 11/12/2022] Open
Abstract
Morphological integration predicts that correlated characters will coevolve; thus, each distinct suite of correlated characters might be expected to evolve according to a separate clock or 'pacemaker'. Characters in a large morphological dataset for mammals were found to be evolving according to seven separate clocks, each distinct from the molecular clock. Total-evidence tip-dating using these multiple clocks inflated divergence time estimates, but potentially improved topological inference. In particular, single-clock analyses placed several meridiungulates and condylarths in a heterodox position as stem placentals, but multi-clock analyses retrieved a more plausible and orthodox position within crown placentals. Several shortcomings (including uneven character sampling) currently impact upon the accuracy of total-evidence dating, but this study suggests that when sufficiently large and appropriately constructed phenotypic datasets become more commonplace, multi-clock approaches are feasible and can affect both divergence dates and phylogenetic relationships.
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Affiliation(s)
- Michael S Y Lee
- Earth Sciences Section, South Australian Museum, North Terrace, Adelaide, South Australia 5000, Australia School of Biological Sciences, Flinders University, GPO Box 2100, Adelaide, South Australia 5001, Australia
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249
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Matzke NJ, Wright A. Inferring node dates from tip dates in fossil Canidae: the importance of tree priors. Biol Lett 2017; 12:rsbl.2016.0328. [PMID: 27512133 DOI: 10.1098/rsbl.2016.0328] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2016] [Accepted: 07/19/2016] [Indexed: 11/12/2022] Open
Abstract
Tip-dating methods are becoming popular alternatives to traditional node calibration approaches for building time-scaled phylogenetic trees, but questions remain about their application to empirical datasets. We compared the performance of the most popular methods against a dated tree of fossil Canidae derived from previously published monographs. Using a canid morphology dataset, we performed tip-dating using BEAST v. 2.1.3 and MrBayes v. 3.2.5. We find that for key nodes (Canis, approx. 3.2 Ma, Caninae approx. 11.7 Ma) a non-mechanistic model using a uniform tree prior produces estimates that are unrealistically old (27.5, 38.9 Ma). Mechanistic models (incorporating lineage birth, death and sampling rates) estimate ages that are closely in line with prior research. We provide a discussion of these two families of models (mechanistic versus non-mechanistic) and their applicability to fossil datasets.
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Affiliation(s)
- Nicholas J Matzke
- Moritz Laboratory, Division of Ecology, Evolution, and Genetics, The Australian National University, Canberra, Australian Capital Territory 2601, Australia
| | - April Wright
- Department of Ecology, Evolution and Organismal Biology, Iowa State University, Ames, IA 50011-4009, USA Department of Ecology, Evolution and Behavior, University of Kansas, Lawrence, KS 66045, USA
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