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Xiao L, Labandeira CC, Wu Y, Shih C, Ren D, Wang Y. Middle Jurassic insect mines on gymnosperms provide missing links to early mining evolution. THE NEW PHYTOLOGIST 2024; 242:2803-2816. [PMID: 38184785 DOI: 10.1111/nph.19517] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/23/2023] [Accepted: 12/14/2023] [Indexed: 01/08/2024]
Abstract
We investigated the mining mode of insect feeding, involving larval consumption of a plant's internal tissues, from the Middle Jurassic (165 million years ago) Daohugou locality of Northeastern China. Documentation of mining from the Jurassic Period is virtually unknown, and results from this time interval would address mining evolution during the temporal gap of mine-seed plant diversifications from the previous Late Triassic to the subsequent Early Cretaceous. Plant fossils were examined with standard microscopic procedures for herbivory and used the standard functional feeding group-damage-type system of categorizing damage. All fossil mines were photographed and databased. We examined 2014 plant specimens, of which 27 occurrences on 14 specimens resulted in eight, new, mine damage types (DTs) present on six genera of bennettitalean, ginkgoalean, and pinalean gymnosperms. Three conclusions emerge from this study. First, these mid-Mesozoic mines are morphologically conservative and track plant host anatomical structure rather than plant phylogeny. Second, likely insect fabricators of these mines were three basal lineages of polyphagan beetles, four basal lineages of monotrysian moths, and a basal lineage tenthredinoid sawflies. Third, the nutrition hypothesis, indicating that miners had greater access to nutritious, inner tissues of new plant lineages, best explains mine evolution during the mid-Mesozoic.
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Affiliation(s)
- Lifang Xiao
- Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Guangdong Public Laboratory of Wild Animal Conservation and Utilization, Institute of Zoology, Guangdong Academy of Sciences, Guangzhou, 510260, China
- College of Life Science and Academy for Multidisciplinary Studies, Capital Normal University, Beijing, 100048, China
- Department of Paleobiology, National Museum of Natural History, Smithsonian Institution, Tenth St. and Constitution Ave, Washington, DC, 20013, USA
| | - Conrad C Labandeira
- College of Life Science and Academy for Multidisciplinary Studies, Capital Normal University, Beijing, 100048, China
- Department of Paleobiology, National Museum of Natural History, Smithsonian Institution, Tenth St. and Constitution Ave, Washington, DC, 20013, USA
- Department of Entomology and BEES Program, University of Maryland, College Park, MD, 20742, USA
| | - Yuekun Wu
- College of Life Science and Academy for Multidisciplinary Studies, Capital Normal University, Beijing, 100048, China
| | - ChungKun Shih
- College of Life Science and Academy for Multidisciplinary Studies, Capital Normal University, Beijing, 100048, China
- Department of Paleobiology, National Museum of Natural History, Smithsonian Institution, Tenth St. and Constitution Ave, Washington, DC, 20013, USA
| | - Dong Ren
- College of Life Science and Academy for Multidisciplinary Studies, Capital Normal University, Beijing, 100048, China
| | - Yongjie Wang
- Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Guangdong Public Laboratory of Wild Animal Conservation and Utilization, Institute of Zoology, Guangdong Academy of Sciences, Guangzhou, 510260, China
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2
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Pol D, Baiano MA, Černý D, Novas FE, Cerda IA, Pittman M. A new abelisaurid dinosaur from the end Cretaceous of Patagonia and evolutionary rates among the Ceratosauria. Cladistics 2024; 40:307-356. [PMID: 38771085 DOI: 10.1111/cla.12583] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2024] [Revised: 04/24/2024] [Accepted: 04/24/2024] [Indexed: 05/22/2024] Open
Abstract
Gondwanan dinosaur faunae during the 20 Myr preceding the Cretaceous-Palaeogene (K/Pg) extinction included several lineages that were absent or poorly represented in Laurasian landmasses. Among these, the South American fossil record contains diverse abelisaurids, arguably the most successful groups of carnivorous dinosaurs from Gondwana in the Cretaceous, reaching their highest diversity towards the end of this period. Here we describe Koleken inakayali gen. et sp. n., a new abelisaurid from the La Colonia Formation (Maastrichtian, Upper Cretaceous) of Patagonia. Koleken inakayali is known from several skull bones, an almost complete dorsal series, complete sacrum, several caudal vertebrae, pelvic girdle and almost complete hind limbs. The new abelisaurid shows a unique set of features in the skull and several anatomical differences from Carnotaurus sastrei (the only other abelisaurid known from the La Colonia Formation). Koleken inakayali is retrieved as a brachyrostran abelisaurid, clustered with other South American abelisaurids from the latest Cretaceous (Campanian-Maastrichtian), such as Aucasaurus, Niebla and Carnotaurus. Leveraging our phylogeny estimates, we explore rates of morphological evolution across ceratosaurian lineages, finding them to be particularly high for elaphrosaurine noasaurids and around the base of Abelisauridae, before the Early Cretaceous radiation of the latter clade. The Noasauridae and their sister clade show contrasting patterns of morphological evolution, with noasaurids undergoing an early phase of accelerated evolution of the axial and hind limb skeleton in the Jurassic, and the abelisaurids exhibiting sustained high rates of cranial evolution during the Early Cretaceous. These results provide much needed context for the evolutionary dynamics of ceratosaurian theropods, contributing to broader understanding of macroevolutionary patterns across dinosaurs.
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Affiliation(s)
- Diego Pol
- Museo Argentino de Ciencias Naturales Bernardino Rivadavia, Buenos Aires, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - Mattia Antonio Baiano
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
- School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
- Área Laboratorio e Investigación, Museo Municipal Ernesto Bachmann, Villa El Chocón, Neuquén, Argentina
- Universidad Nacional de Río Negro (UNRN), General Roca, Río Negro, Argentina
| | - David Černý
- Department of the Geophysical Sciences, University of Chicago, Chicago, IL, USA
| | - Fernando E Novas
- Museo Argentino de Ciencias Naturales Bernardino Rivadavia, Buenos Aires, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - Ignacio A Cerda
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
- Universidad Nacional de Río Negro (UNRN), General Roca, Río Negro, Argentina
- Instituto de Investigación en Paleobiología y Geología (IIPG), General Roca, Río Negro, Argentina
- Museo Provincial Carlos Ameghino, Cipolletti, Río Negro, Argentina
| | - Michael Pittman
- School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
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Tejada JV, Antoine PO, Münch P, Billet G, Hautier L, Delsuc F, Condamine FL. Bayesian Total-Evidence Dating Revisits Sloth Phylogeny and Biogeography: A Cautionary Tale on Morphological Clock Analyses. Syst Biol 2024; 73:125-139. [PMID: 38041854 PMCID: PMC11129595 DOI: 10.1093/sysbio/syad069] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Revised: 11/06/2023] [Accepted: 11/14/2023] [Indexed: 12/04/2023] Open
Abstract
Combining morphological and molecular characters through Bayesian total-evidence dating allows inferring the phylogenetic and timescale framework of both extant and fossil taxa, while accounting for the stochasticity and incompleteness of the fossil record. Such an integrative approach is particularly needed when dealing with clades such as sloths (Mammalia: Folivora), for which developmental and biomechanical studies have shown high levels of morphological convergence whereas molecular data can only account for a limited percentage of their total species richness. Here, we propose an alternative hypothesis of sloth evolution that emphasizes the pervasiveness of morphological convergence and the importance of considering the fossil record and an adequate taxon sampling in both phylogenetic and biogeographic inferences. Regardless of different clock models and morphological datasets, the extant sloth Bradypus is consistently recovered as a megatherioid, and Choloepus as a mylodontoid, in agreement with molecular-only analyses. The recently extinct Caribbean sloths (Megalocnoidea) are found to be a monophyletic sister-clade of Megatherioidea, in contrast to previous phylogenetic hypotheses. Our results contradict previous morphological analyses and further support the polyphyly of "Megalonychidae," whose members were found in five different clades. Regardless of taxon sampling and clock models, the Caribbean colonization of sloths is compatible with the exhumation of islands along Aves Ridge and its geological time frame. Overall, our total-evidence analysis illustrates the difficulty of positioning highly incomplete fossils, although a robust phylogenetic framework was recovered by an a posteriori removal of taxa with high percentages of missing characters. Elimination of these taxa improved topological resolution by reducing polytomies and increasing node support. However, it introduced a systematic and geographic bias because most of these incomplete specimens are from northern South America. This is evident in biogeographic reconstructions, which suggest Patagonia as the area of origin of many clades when taxa are underrepresented, but Amazonia and/or Central and Southern Andes when all taxa are included. More generally, our analyses demonstrate the instability of topology and divergence time estimates when using different morphological datasets and clock models and thus caution against making macroevolutionary inferences when node support is weak or when uncertainties in the fossil record are not considered.
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Affiliation(s)
- Julia V Tejada
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, CA 91125, USA
- Institut des Sciences de l’Évolution de Montpellier, UMR 5554, Université de Montpellier, CNRS, IRD, Place Eugène Bataillon, 34095 Montpellier Cedex 5, France
| | - Pierre-Olivier Antoine
- Institut des Sciences de l’Évolution de Montpellier, UMR 5554, Université de Montpellier, CNRS, IRD, Place Eugène Bataillon, 34095 Montpellier Cedex 5, France
| | - Philippe Münch
- Géosciences Montpellier, UMR 5243, Université de Montpellier, CNRS, Université des Antilles, Place Eugène Bataillon, 34095 Montpellier, France
| | - Guillaume Billet
- Centre de Recherche en Paléontologie—Paris, CR2P—UMR 7207, Muséum National d’Histoire Naturelle, CNRS, Sorbonne Université, 8 rue Buffon 75005, Paris
| | - Lionel Hautier
- Institut des Sciences de l’Évolution de Montpellier, UMR 5554, Université de Montpellier, CNRS, IRD, Place Eugène Bataillon, 34095 Montpellier Cedex 5, France
| | - Frédéric Delsuc
- Institut des Sciences de l’Évolution de Montpellier, UMR 5554, Université de Montpellier, CNRS, IRD, Place Eugène Bataillon, 34095 Montpellier Cedex 5, France
| | - Fabien L Condamine
- Institut des Sciences de l’Évolution de Montpellier, UMR 5554, Université de Montpellier, CNRS, IRD, Place Eugène Bataillon, 34095 Montpellier Cedex 5, France
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4
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Zhang R, Drummond AJ, Mendes FK. Fast Bayesian Inference of Phylogenies from Multiple Continuous Characters. Syst Biol 2024; 73:102-124. [PMID: 38085256 PMCID: PMC11129596 DOI: 10.1093/sysbio/syad067] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Revised: 03/23/2023] [Accepted: 11/07/2023] [Indexed: 05/28/2024] Open
Abstract
Time-scaled phylogenetic trees are an ultimate goal of evolutionary biology and a necessary ingredient in comparative studies. The accumulation of genomic data has resolved the tree of life to a great extent, yet timing evolutionary events remain challenging if not impossible without external information such as fossil ages and morphological characters. Methods for incorporating morphology in tree estimation have lagged behind their molecular counterparts, especially in the case of continuous characters. Despite recent advances, such tools are still direly needed as we approach the limits of what molecules can teach us. Here, we implement a suite of state-of-the-art methods for leveraging continuous morphology in phylogenetics, and by conducting extensive simulation studies we thoroughly validate and explore our methods' properties. While retaining model generality and scalability, we make it possible to estimate absolute and relative divergence times from multiple continuous characters while accounting for uncertainty. We compile and analyze one of the most data-type diverse data sets to date, comprised of contemporaneous and ancient molecular sequences, and discrete and continuous morphological characters from living and extinct Carnivora taxa. We conclude by synthesizing lessons about our method's behavior, and suggest future research venues.
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Affiliation(s)
- Rong Zhang
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School 169857, Singapore
| | - Alexei J Drummond
- Centre for Computational Evolution, The University of Auckland, Auckland 1010, New Zealand
- School of Biological Sciences, The University of Auckland, Auckland 1010, New Zealand
| | - Fábio K Mendes
- Department of Biology, Washington University in St. Louis, St. Louis, MO 63130, USA
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5
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Mao F, Li Z, Wang Z, Zhang C, Rich T, Vickers-Rich P, Meng J. Jurassic shuotheriids show earliest dental diversification of mammaliaforms. Nature 2024; 628:569-575. [PMID: 38570681 DOI: 10.1038/s41586-024-07258-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Accepted: 02/29/2024] [Indexed: 04/05/2024]
Abstract
Shuotheriids are Jurassic mammaliaforms that possess pseudotribosphenic teeth in which a pseudotalonid is anterior to the trigonid in the lower molar, contrasting with the tribosphenic pattern of therian mammals (placentals, marsupials and kin) in which the talonid is posterior to the trigonid1-4. The origin of the pseudotribosphenic teeth remains unclear, obscuring our perception of shuotheriid affinities and the early evolution of mammaliaforms1,5-9. Here we report a new Jurassic shuotheriid represented by two skeletal specimens. Their complete pseudotribosphenic dentitions allow reidentification of dental structures using serial homology and the tooth occlusal relationship. Contrary to the conventional view1,2,6,10,11, our findings show that dental structures of shuotheriids can be homologized to those of docodontans and partly support homologous statements for some dental structures between docodontans and other mammaliaforms6,12. The phylogenetic analysis based on new evidence removes shuotheriids from the tribosphenic ausktribosphenids (including monotremes) and clusters them with docodontans to form a new clade, Docodontiformes, that is characterized by pseudotribosphenic features. In the phylogeny, docodontiforms and 'holotherians' (Kuehneotherium, monotremes and therians)13 evolve independently from a Morganucodon-like ancestor with triconodont molars by labio-lingual widening their posterior teeth for more efficient food processing. The pseudotribosphenic pattern passed a cusp semitriangulation stage9, whereas the tribosphenic pattern and its precursor went through a stage of cusp triangulation. The two different processes resulted in complex tooth structures and occlusal patterns that elucidate the earliest diversification of mammaliaforms.
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Affiliation(s)
- Fangyuan Mao
- Key Laboratory of Evolutionary Systematics of Vertebrates, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing, China.
- Division of Paleontology, American Museum of Natural History, New York, NY, USA.
| | - Zhiyu Li
- Inner Mongolia Museum of Natural History, Hohhot, China
| | - Zhili Wang
- Inner Mongolia Museum of Natural History, Hohhot, China
| | - Chi Zhang
- Key Laboratory of Evolutionary Systematics of Vertebrates, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing, China
| | - Thomas Rich
- Museums Victoria, Melbourne, Victoria, Australia
- School of Earth, Atmosphere and Environment, Monash University, Melbourne, Victoria, Australia
| | - Patricia Vickers-Rich
- Museums Victoria, Melbourne, Victoria, Australia
- School of Earth, Atmosphere and Environment, Monash University, Melbourne, Victoria, Australia
- School of Earth and Planetary Sciences, Curtin University, Perth, Western Australia, Australia
| | - Jin Meng
- Division of Paleontology, American Museum of Natural History, New York, NY, USA.
- Earth and Environmental Sciences, City University of New York, New York, NY, USA.
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6
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Ulrich S, Vieira M, Coiro M, Bouchal JM, Geier C, Jacobs BF, Currano ED, Lenz OK, Wilde V, Zetter R, Grímsson F. Origin and Early Evolution of Hydrocharitaceae and the Ancestral Role of Stratiotes. PLANTS (BASEL, SWITZERLAND) 2024; 13:1008. [PMID: 38611537 PMCID: PMC11013807 DOI: 10.3390/plants13071008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2024] [Revised: 03/27/2024] [Accepted: 03/29/2024] [Indexed: 04/14/2024]
Abstract
The combined morphological features of Stratiotes (Hydrocharitaceae) pollen, observed with light and electron microscopy, make it unique among all angiosperm pollen types and easy to identify. Unfortunately, the plant is (and most likely was) insect-pollinated and produces relatively few pollen grains per flower, contributing to its apparent absence in the paleopalynological record. Here, we present fossil Stratiotes pollen from the Eocene of Germany (Europe) and Kenya (Africa), representing the first reliable pre-Pleistocene pollen records of this genus worldwide and the only fossils of this family discovered so far in Africa. The fossil Stratiotes pollen grains are described and compared to pollen from a single modern species, Stratiotes aloides L. The paleophytogeographic significance and paleoecological aspects of these findings are discussed in relation to the Hydrocharitaceae fossil records and molecular phylogeny, as well as the present-day distribution patterns of its modern genera.
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Affiliation(s)
- Silvia Ulrich
- Department of Botany and Biodiversity Research, University of Vienna, 1030 Vienna, Austria; (S.U.); (J.M.B.); (C.G.); (R.Z.)
- Department of Historical Archaeology, Austrian Archaeological Institute (OeAI), Austrian Academy of Sciences (OeAW), 1010 Vienna, Austria
| | - Manuel Vieira
- Department of Earth Sciences, GeoBioTec, NOVA School of Science and Technology, Campus de Caparica, 2829-516 Caparica, Portugal;
| | - Mario Coiro
- Department of Palaeontology, University of Vienna, 1090 Vienna, Austria
| | - Johannes M. Bouchal
- Department of Botany and Biodiversity Research, University of Vienna, 1030 Vienna, Austria; (S.U.); (J.M.B.); (C.G.); (R.Z.)
| | - Christian Geier
- Department of Botany and Biodiversity Research, University of Vienna, 1030 Vienna, Austria; (S.U.); (J.M.B.); (C.G.); (R.Z.)
| | - Bonnie F. Jacobs
- Roy M. Huffington Department of Earth Sciences, Southern Methodist University, Dallas, TX 75275, USA;
| | - Ellen D. Currano
- Departments of Botany and Geology & Geophysics, University of Wyoming, Laramie, WY 82071, USA;
| | - Olaf K. Lenz
- Institute of Applied Geosciences, Technical University Darmstadt, 64287 Darmstadt, Germany;
| | - Volker Wilde
- Section Palaeobotany, Division Palaeontology and Historical Geology, Senckenberg Research Institute and Natural History Museum Frankfurt, 60325 Frankfurt am Main, Germany;
| | - Reinhard Zetter
- Department of Botany and Biodiversity Research, University of Vienna, 1030 Vienna, Austria; (S.U.); (J.M.B.); (C.G.); (R.Z.)
| | - Friðgeir Grímsson
- Department of Botany and Biodiversity Research, University of Vienna, 1030 Vienna, Austria; (S.U.); (J.M.B.); (C.G.); (R.Z.)
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7
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Li W, Wang R, Liu MF, Folk RA, Xue B, Saunders RMK. Climatic and biogeographic processes underlying the diversification of the pantropical flowering plant family Annonaceae. FRONTIERS IN PLANT SCIENCE 2024; 15:1287171. [PMID: 38525154 PMCID: PMC10957689 DOI: 10.3389/fpls.2024.1287171] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Accepted: 02/20/2024] [Indexed: 03/26/2024]
Abstract
Tropical forests harbor the richest biodiversity among terrestrial ecosystems, but few studies have addressed the underlying processes of species diversification in these ecosystems. We use the pantropical flowering plant family Annonaceae as a study system to investigate how climate and biogeographic events contribute to diversification. A super-matrix phylogeny comprising 835 taxa (34% of Annonaceae species) based on eight chloroplast regions was used in this study. We show that global temperature may better explain the recent rapid diversification in Annonaceae than time and constant models. Accelerated accumulation of niche divergence (around 15 Ma) lags behind the increase of diversification rate (around 25 Ma), reflecting a heterogeneous transition to recent diversity increases. Biogeographic events are related to only two of the five diversification rate shifts detected. Shifts in niche evolution nevertheless appear to be associated with increasingly seasonal environments. Our results do not support the direct correlation of any particular climatic niche shifts or historical biogeographical event with shifts in diversification rate. Instead, we suggest that Annonaceae diversification can lead to later niche divergence as a result of increasing interspecific competition arising from species accumulation. Shifts in niche evolution appear to be associated with increasingly seasonal environments. Our results highlight the complexity of diversification in taxa with long evolutionary histories.
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Affiliation(s)
- Weixi Li
- Division of Ecology & Biodiversity, School of Biological Sciences, The University of Hong Kong, Hong Kong, Hong Kong SAR, China
| | - Runxi Wang
- Division of Ecology & Biodiversity, School of Biological Sciences, The University of Hong Kong, Hong Kong, Hong Kong SAR, China
| | - Ming-Fai Liu
- Division of Ecology & Biodiversity, School of Biological Sciences, The University of Hong Kong, Hong Kong, Hong Kong SAR, China
| | - Ryan A. Folk
- Department of Biological Sciences, Mississippi State University, Starkville, MS, United States
| | - Bine Xue
- College of Horticulture and Landscape Architecture, Zhongkai University of Agriculture and Engineering, Guangzhou, China
| | - Richard M. K. Saunders
- Division of Ecology & Biodiversity, School of Biological Sciences, The University of Hong Kong, Hong Kong, Hong Kong SAR, China
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Brocklehurst N, Field DJ. Tip dating and Bayes factors provide insight into the divergences of crown bird clades across the end-Cretaceous mass extinction. Proc Biol Sci 2024; 291:20232618. [PMID: 38351798 PMCID: PMC10865003 DOI: 10.1098/rspb.2023.2618] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Accepted: 01/05/2024] [Indexed: 02/16/2024] Open
Abstract
The origin of crown birds (Neornithes) remains contentious owing to conflicting divergence time hypotheses obtained from alternative sources of data. The fossil record suggests limited diversification of Neornithes in the Late Mesozoic and a substantial radiation in the aftermath of the Cretaceous-Palaeogene (K-Pg) mass extinction, approximately 66 Ma. Molecular clock studies, however, have yielded estimates for neornithine origins ranging from the Early Cretaceous (130 Ma) to less than 10 Myr before the K-Pg. We use Bayes factors to compare the fit of node ages from different molecular clock studies to an independent morphological dataset. Our results allow us to reject scenarios of crown bird origins deep in the Early Cretaceous, as well as an origin of crown birds within the last 10 Myr of the Cretaceous. The scenario best supported by our analyses is one where Neornithes originated between the Early and Late Cretaceous (ca 100 Ma), while numerous divergences within major neoavian clades either span or postdate the K-Pg. This study affirms the importance of the K-Pg on the diversification of modern birds, and the potential of combined-evidence tip-dating analyses to illuminate recalcitrant 'rocks versus clocks' debates.
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Affiliation(s)
- Neil Brocklehurst
- Department of Earth Sciences, University of Cambridge, Cambridge, UK
| | - Daniel J. Field
- Department of Earth Sciences, University of Cambridge, Cambridge, UK
- Museum of Zoology, University of Cambridge, Cambridge, UK
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9
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Coiro M. Embracing uncertainty: The way forward in plant fossil phylogenetics. AMERICAN JOURNAL OF BOTANY 2024; 111:e16282. [PMID: 38334302 DOI: 10.1002/ajb2.16282] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2023] [Revised: 12/12/2023] [Accepted: 12/13/2023] [Indexed: 02/10/2024]
Abstract
Although molecular phylogenetics remains the most widely used method of inferring the evolutionary history of living groups, the last decade has seen a renewed interest in morphological phylogenetics, mostly driven by the promises that integrating the fossil record in phylogenetic trees offers to our understanding of macroevolutionary processes and dynamics and the possibility that the inclusion of fossil taxa could lead to more accurate phylogenetic hypotheses. The plant fossil record presents some challenges to its integration in a phylogenetic framework. Phylogenies including plant fossils often retrieve uncertain relationships with low support, or lack of resolution. This low support is due to the pervasiveness of morphological convergence among plant organs and the fragmentary nature of many plant fossils, and it is often perceived as a fundamental weakness reducing the utility of plant fossils in phylogenetics. Here I discuss the importance of uncertainty in morphological phylogenetics and how we can identify important information from different patterns and types of uncertainty. I also review a set of methodologies that can allow us to understand the causes underpinning uncertainty and how these practices can help us to further our knowledge of plant fossils. I also propose that a new visual language, including the use of networks instead of trees, represents an improvement on the old visualization based on consensus trees and more adequately serves phylogeneticists working with plant fossils. This set of methods and visualization tools represents an important way forward in a fundamental field for our understanding of the evolutionary history of plants.
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Affiliation(s)
- Mario Coiro
- Department of Palaeontology, University of Vienna, Vienna, Austria
- Ronin Institute for Independent Scholarship, Montclair, NJ, USA
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10
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Scarpetta SG. A Palaeogene stem crotaphytid ( Aciprion formosum) and the phylogenetic affinities of early fossil pleurodontan iguanians. ROYAL SOCIETY OPEN SCIENCE 2024; 11:221139. [PMID: 38204790 PMCID: PMC10776235 DOI: 10.1098/rsos.221139] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/02/2023] [Accepted: 12/13/2023] [Indexed: 01/12/2024]
Abstract
Pleurodonta is an ancient, diverse clade of iguanian lizard distributed primarily in the Western Hemisphere. Although the clade is a frequent subject of systematic research, phylogenetic resolution among the major pleurodontan clades is elusive. That uncertainty has complicated the interpretations of many fossil pleurodontans. I describe a fossil skull of a pleurodontan lizard from the Palaeogene of Wyoming that was previously allocated to the puzzling taxon Aciprion formosum, and provide an updated morphological matrix for iguanian lizards. Phylogenetic analyses using Bayesian inference demonstrate that the fossil skull is the oldest and first definitive stem member of Crotaphytidae (collared and leopard lizards), establishing the presence of that clade in North America during the Palaeogene. I also discuss new or revised hypotheses for the relationships of several early pleurodontans. In particular, I examine potential evidence for crown-Pleurodonta in the Cretaceous of Mongolia (Polrussia), stem Pleurodonta in the Cretaceous of North America (Magnuviator) and a stem anole in the Eocene of North America (Afairiguana). I suggest that the placement of the fossil crotaphytid is stable to the uncertain phylogeny of Pleurodonta, but recognize the dynamic nature of fossil diagnosis and the potential for updated systematic hypotheses for the other fossils analysed here.
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Affiliation(s)
- Simon G. Scarpetta
- Museum of Vertebrate Zoology, University of California Berkeley, 3101 UC Berkeley Road, Berkeley, CA 94720, USA
- Department of Environmental Science, University of San Francisco, San Francisco, CA 94117, USA
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11
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Zhang C, Ronquist F, Stadler T. Skyline Fossilized Birth-Death Model is Robust to Violations of Sampling Assumptions in Total-Evidence Dating. Syst Biol 2023; 72:1316-1336. [PMID: 37605524 DOI: 10.1093/sysbio/syad054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Revised: 08/07/2023] [Accepted: 08/15/2023] [Indexed: 08/23/2023] Open
Abstract
Several total-evidence dating studies under the fossilized birth-death (FBD) model have produced very old age estimates, which are not supported by the fossil record. This phenomenon has been termed "deep root attraction (DRA)." For two specific data sets, involving divergence time estimation for the early radiations of ants, bees, and wasps (Hymenoptera) and of placental mammals (Eutheria), it has been shown that the DRA effect can be greatly reduced by accommodating the fact that extant species in these trees have been sampled to maximize diversity, so-called diversified sampling. Unfortunately, current methods to accommodate diversified sampling only consider the extreme case where it is possible to identify a cut-off time such that all splits occurring before this time are represented in the sampled tree but none of the younger splits. In reality, the sampling bias is rarely this extreme and may be difficult to model properly. Similar modeling challenges apply to the sampling of the fossil record. This raises the question of whether it is possible to find dating methods that are more robust to sampling biases. Here, we show that the skyline FBD (SFBD) process, where the diversification and fossil-sampling rates can vary over time in a piecewise fashion, provides age estimates that are more robust to inadequacies in the modeling of the sampling process and less sensitive to DRA effects. In the SFBD model we consider, rates in different time intervals are either considered to be independent and identically distributed or assumed to be autocorrelated following an Ornstein-Uhlenbeck (OU) process. Through simulations and reanalyses of Hymenoptera and Eutheria data, we show that both variants of the SFBD model unify age estimates under random and diversified sampling assumptions. The SFBD model can resolve DRA by absorbing the deviations from the sampling assumptions into the inferred dynamics of the diversification process over time. Although this means that the inferred diversification dynamics must be interpreted with caution, taking sampling biases into account, we conclude that the SFBD model represents the most robust approach currently available for addressing DRA in total-evidence dating.
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Affiliation(s)
- Chi Zhang
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing 100044, China
| | - Fredrik Ronquist
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, SE.10405 Stockholm, Sweden
| | - Tanja Stadler
- Department of Biosystems Science and Engineering, Eidgenössische Technische Hochschule Zürich, 4058 Basel, Switzerland
- Swiss Institute of Bioinformatics (SIB), 1015 Lausanne, Switzerland
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12
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Voje KL, Saulsbury JG, Starrfelt J, Latorre DV, Rojas A, Kinneberg VB, Liow LH, Wilson CJ, Saupe EE, Grabowski M. Measurement theory and paleobiology. Trends Ecol Evol 2023; 38:1165-1176. [PMID: 37696719 DOI: 10.1016/j.tree.2023.08.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Revised: 08/07/2023] [Accepted: 08/08/2023] [Indexed: 09/13/2023]
Abstract
Measurement theory, a branch of applied mathematics, offers guiding principles for extracting meaning from empirical observations and is applicable to any science involving measurements. Measurement theory is highly relevant in paleobiology because statistical approaches assuming ratio-scaled variables are commonly used on data belonging to nominal and ordinal scale types. We provide an informal introduction to representational measurement theory and argue for its importance in robust scientific inquiry. Although measurement theory is widely applicable in paleobiology research, we use the study of disparity to illustrate measurement theoretical challenges in the quantitative study of the fossil record. Respecting the inherent properties of different measurements enables meaningful inferences about evolutionary and ecological processes from paleontological data.
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Affiliation(s)
| | | | | | | | - Alexis Rojas
- Department of Computer Science, University of Helsinki, Helsinki, Finland
| | | | | | - Connor J Wilson
- Natural History Museum, University of Oslo, Oslo, Norway; School of Geography and the Environment, University of Oxford, Oxford, UK
| | - Erin E Saupe
- Department of Earth Sciences, University of Oxford, Oxford, UK
| | - Mark Grabowski
- Research Centre in Evolutionary Anthropology and Paleoecology, Liverpool John Moores University, Liverpool, UK
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13
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Rust K, Ni X, Tietjen K, Beard KC. Phylogeny and paleobiogeography of the enigmatic North American primate Ekgmowechashala illuminated by new fossils from Nebraska (USA) and Guangxi Zhuang Autonomous Region (China). J Hum Evol 2023; 185:103452. [PMID: 37935595 DOI: 10.1016/j.jhevol.2023.103452] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Revised: 09/25/2023] [Accepted: 09/27/2023] [Indexed: 11/09/2023]
Abstract
Ekgmowechashala is a poorly documented but very distinctive primate known only from the late early Oligocene (early Arikareean) of western North America. Because of its highly autapomorphous dentition and spatiotemporal isolation, the phylogenetic and biogeographic affinities of Ekgmowechashala have long been debated. Here, we describe the oldest known fossils of Ekgmowechashala from the Brown Siltstone Beds of the Brule Formation, White River Group of western Nebraska. We also describe a new ekgmowechashaline taxon from the Nadu Formation (late Eocene) in the Baise Basin of Guangxi Zhuang Autonomous Region in southern China. Phylogenetic analysis suggests that North American Ekgmowechashala and the new Chinese taxon are sister taxa that are nested within a radiation of southern Asian adapiforms that also includes Gatanthropus, Muangthanhinius, and Bugtilemur. The new Chinese ekgmowechashaline helps fill the considerable disparity in dental morphology between Ekgmowechashala and more primitive ekgmowechashalids known from southern Asia. Our study underscores the fundamental role of southern Asia as a refugium for multiple primate clades during the cooler and drier climatic regime that prevailed after the Eocene-Oligocene transition. The colonization of North America by Ekgmowechashala helps define the beginning of the Arikareean Land Mammal Age and corresponds to an example of the Lazarus effect, whereby a taxon (in this case, the order Primates) reappears suddenly in the fossil record after a lengthy hiatus.
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Affiliation(s)
- Kathleen Rust
- Biodiversity Institute, University of Kansas, 1345 Jayhawk Boulevard, Lawrence, KS, 66045-7561, USA; Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, KS, 66045-7561, USA
| | - Xijun Ni
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate, Paleontology and Paleoanthropology (IVPP), Chinese Academy of Sciences, 142 Xi Zhi Men Wai Street, Beijing, 100044, China; College of Earth and Planetary Sciences, University of Chinese Academy of Sciences, 19A Yuquan Road, 100049, Beijing, China
| | - Kristen Tietjen
- Biodiversity Institute, University of Kansas, 1345 Jayhawk Boulevard, Lawrence, KS, 66045-7561, USA
| | - K Christopher Beard
- Biodiversity Institute, University of Kansas, 1345 Jayhawk Boulevard, Lawrence, KS, 66045-7561, USA; Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, KS, 66045-7561, USA.
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14
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Osozawa S. Geologically calibrated mammalian tree and its correlation with global events, including the emergence of humans. Ecol Evol 2023; 13:e10827. [PMID: 38116126 PMCID: PMC10728886 DOI: 10.1002/ece3.10827] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Revised: 10/09/2023] [Accepted: 11/28/2023] [Indexed: 12/21/2023] Open
Abstract
A robust timetree for Mammalia was constructed using the time calibration function of BEAST v1.10.4 and MEGA 11. The analysis involved the application of times of the most recent common ancestors, including a total of 19 mammalian fossil calibration ages following Benton et al. (Palaeontologia Electronica, 2015, 1-106) for their minimum ages. Additionally, fossil calibration ages for Gorilla, Pan, and a geologic event calibration age for otters were incorporated. Using these calibration ages, I constructed a geologically calibrated tree that estimates the age of the Homo and Pan splitting to be 5.69 Ma. The tree carries several significant implications. First, after the initial rifting at 120 Ma, the Atlantic Ocean expanded by over 500 km around Chron 34 (84 Ma), and vicariant speciation between Afrotheria (Africa) and Xenarthra (South America) appears to have commenced around 70 Ma. Additionally, ordinal level differentiations began immediately following the K-Pg boundary (66.0 Ma), supporting previous hypothesis that mammalian radiation rapidly filled ecological niches left vacant by non-avian dinosaurs. I constructed a diagram depicting the relationship between base substitution rate and age using an additional function in BEAST v1.10.4. The diagram reveals an exponential increase in the base substitution rate approaching recent times. This increased base substitution rate during the Neogene period may have contributed to the expansion of biodiversity, including the extensive adaptive radiation that led to the evolution of Homo sapiens. One significant driving factor behind this radiation could be attributed to the emergence and proliferation of C4 grasses since 20 Ma. These grasses have played a role in increasing carbon fixation, reducing atmospheric CO2 concentration, inducing global cooling, and initiating Quaternary glacial-interglacial cycles, thereby causing significant climatic changes.
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Affiliation(s)
- Soichi Osozawa
- Faculty of Science, Institute of Geology and PaleontologyTohoku UniversitySendaiJapan
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15
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Flores JR, Bippus AC, de Ullivarri CF, Suárez GM, Hyvönen J, Tomescu AMF. Dating the evolution of the complex thalloid liverworts (Marchantiopsida): total-evidence dating analysis supports a Late Silurian-Early Devonian origin and post-Mesozoic morphological stasis. THE NEW PHYTOLOGIST 2023; 240:2137-2150. [PMID: 37697646 DOI: 10.1111/nph.19254] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Accepted: 08/19/2023] [Indexed: 09/13/2023]
Abstract
Divergence times based on molecular clock analyses often differ from those derived from total-evidence dating (TED) approaches. For bryophytes, fossils have been excluded from previous assessments of divergence times, and thus, their utility in dating analyses remains unexplored. Here, we conduct the first TED analyses of the complex thalloid liverworts (Marchantiopsida) that include fossils and evaluate macroevolutionary trends in morphological 'diversity' (disparity) and rates. Phylogenetic analyses were performed on a combined dataset of 130 discrete characters and 11 molecular markers (sampled from nuclear, plastid and mitochondrial genomes). Taxon sampling spanned 56 extant species - representing all the orders within Marchantiophyta and extant genera within Marchantiales - and eight fossil taxa. Total-evidence dating analyses support the radiation of Marchantiopsida during Late Silurian-Early Devonian (or Middle Ordovician when the outgroup is excluded) and that of Ricciaceae in the Middle Jurassic. Morphological change rate was high early in the history of the group, but it barely increased after Late Cretaceous. Disparity-through-time analyses support a fast increase in diversity until the Middle Triassic (c. 250 Ma), after which phenotypic evolution slows down considerably. Incorporating fossils in analyses challenges previous assumptions on the affinities of extinct taxa and indicates that complex thalloid liverworts radiated c. 125 Ma earlier than previously inferred.
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Affiliation(s)
- Jorge R Flores
- Unidad Ejecutora Lillo (UEL), CONICET-Fundación Miguel Lillo, Miguel Lillo 251, San Miguel del Tucumán, CP 4000, Tucumán, Argentina
- Instituto de Paleontología y Sedimentología, Sección Paleobotánica, Fundación Miguel Lillo, Miguel Lillo 251, San Miguel del Tucumán, CP 4000, Tucumán, Argentina
| | - Alexander C Bippus
- Indian Natural Resource Science and Engineering Program + Diversity in STEM, 1 Harpst St, Arcata, CA, 95521, USA
| | - Carmen Fernández de Ullivarri
- Unidad Ejecutora Lillo (UEL), CONICET-Fundación Miguel Lillo, Miguel Lillo 251, San Miguel del Tucumán, CP 4000, Tucumán, Argentina
| | - Guillermo M Suárez
- Unidad Ejecutora Lillo (UEL), CONICET-Fundación Miguel Lillo, Miguel Lillo 251, San Miguel del Tucumán, CP 4000, Tucumán, Argentina
- Facultad de Ciencias Naturales e Instituto Miguel Lillo, Universidad Nacional de Tucumán, Miguel Lillo 251, T4000JFE, San Miguel de Tucumán, Argentina
| | - Jaakko Hyvönen
- Finnish Museum of Natural History (Botany) & Organismal and Evolutionary Biology & Viikki Plant Science Centre, University of Helsinki, PO Box 7, FI-00014, Helsinki, Finland
| | - Alexandru M F Tomescu
- Department of Biological Sciences, California State Polytechnic University Humboldt, Arcata, CA, 95521, USA
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16
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Bolik S, Schlaich A, Mukhina T, Amato A, Bastien O, Schneck E, Demé B, Jouhet J. Lipid bilayer properties potentially contributed to the evolutionary disappearance of betaine lipids in seed plants. BMC Biol 2023; 21:275. [PMID: 38017456 PMCID: PMC10685587 DOI: 10.1186/s12915-023-01775-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Accepted: 11/21/2023] [Indexed: 11/30/2023] Open
Abstract
BACKGROUND Many organisms rely on mineral nutrients taken directly from the soil or aquatic environment, and therefore, developed mechanisms to cope with the limitation of a given essential nutrient. For example, photosynthetic cells have well-defined responses to phosphate limitation, including the replacement of cellular membrane phospholipids with non-phosphorous lipids. Under phosphate starvation, phospholipids in extraplastidial membranes are replaced by betaine lipids in microalgae. In higher plants, the synthesis of betaine lipid is lost, driving plants to other strategies to cope with phosphate starvation where they replace their phospholipids by glycolipids. RESULTS The aim of this work was to evaluate to what extent betaine lipids and PC lipids share physicochemical properties and could substitute for each other. By neutron diffraction experiments and dynamic molecular simulation of two synthetic lipids, the dipalmitoylphosphatidylcholine (DPPC) and the dipalmitoyl-diacylglyceryl-N,N,N-trimethylhomoserine (DP-DGTS), we found that DP-DGTS bilayers are thicker than DPPC bilayers and therefore are more rigid. Furthermore, DP-DGTS bilayers are more repulsive, especially at long range, maybe due to unexpected unscreened electrostatic contribution. Finally, DP-DGTS bilayers could coexist in the gel and fluid phases. CONCLUSION The different properties and hydration responses of PC and DGTS provide an explanation for the diversity of betaine lipids observed in marine organisms and for their disappearance in seed plants.
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Affiliation(s)
- Stéphanie Bolik
- Laboratoire Physiologie Cellulaire Et Végétale, Univ. Grenoble Alpes, CNRS, CEA, INRAE, IRIG, Grenoble, France
- Large Scale Structures Group, Institut Laue-Langevin, 38000, Grenoble, France
| | - Alexander Schlaich
- Institute for Computational Physics, Universität Stuttgart, Stuttgart, Germany
- Stuttgart Center for Simulation Science (SimTech), Universität Stuttgart, Stuttgart, Germany
| | - Tetiana Mukhina
- Institute for Condensed Matter Physics, Darmstadt, Darmstadt, TU, Germany
| | - Alberto Amato
- Laboratoire Physiologie Cellulaire Et Végétale, Univ. Grenoble Alpes, CNRS, CEA, INRAE, IRIG, Grenoble, France
| | - Olivier Bastien
- Laboratoire Physiologie Cellulaire Et Végétale, Univ. Grenoble Alpes, CNRS, CEA, INRAE, IRIG, Grenoble, France
| | - Emanuel Schneck
- Institute for Condensed Matter Physics, Darmstadt, Darmstadt, TU, Germany
| | - Bruno Demé
- Large Scale Structures Group, Institut Laue-Langevin, 38000, Grenoble, France.
| | - Juliette Jouhet
- Laboratoire Physiologie Cellulaire Et Végétale, Univ. Grenoble Alpes, CNRS, CEA, INRAE, IRIG, Grenoble, France.
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17
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Barido-Sottani J, Schwery O, Warnock RCM, Zhang C, Wright AM. Practical guidelines for Bayesian phylogenetic inference using Markov Chain Monte Carlo (MCMC). OPEN RESEARCH EUROPE 2023; 3:204. [PMID: 38481771 PMCID: PMC10933576 DOI: 10.12688/openreseurope.16679.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Accepted: 11/03/2023] [Indexed: 06/06/2024]
Abstract
Phylogenetic estimation is, and has always been, a complex endeavor. Estimating a phylogenetic tree involves evaluating many possible solutions and possible evolutionary histories that could explain a set of observed data, typically by using a model of evolution. Modern statistical methods involve not just the estimation of a tree, but also solutions to more complex models involving fossil record information and other data sources. Markov Chain Monte Carlo (MCMC) is a leading method for approximating the posterior distribution of parameters in a mathematical model. It is deployed in all Bayesian phylogenetic tree estimation software. While many researchers use MCMC in phylogenetic analyses, interpreting results and diagnosing problems with MCMC remain vexing issues to many biologists. In this manuscript, we will offer an overview of how MCMC is used in Bayesian phylogenetic inference, with a particular emphasis on complex hierarchical models, such as the fossilized birth-death (FBD) model. We will discuss strategies to diagnose common MCMC problems and troubleshoot difficult analyses, in particular convergence issues. We will show how the study design, the choice of models and priors, but also technical features of the inference tools themselves can all be adjusted to obtain the best results. Finally, we will also discuss the unique challenges created by the incorporation of fossil information in phylogenetic inference, and present tips to address them.
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Affiliation(s)
- Joëlle Barido-Sottani
- Institut de Biologie de l’ENS (IBENS), École normale supérieure, CNRS, INSERM, Université PSL, Paris, Île-de-France, 75005, France
| | - Orlando Schwery
- Department of Biological Sciences, Southeastern Louisiana University, Hammond, Louisiana, 70402, USA
- Department of Biological Sciences, Virginia Polytechnic Institute and State University, Blacksburg, Virginia, 24061, USA
- Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana, 70803, USA
| | - Rachel C. M. Warnock
- GeoZentrum Nordbayern, Department of Geography and Geosciences, Friedrich-Alexander Universität Erlangen-Nürnberg, Erlangen, Bavaria, 91054, Germany
| | - Chi Zhang
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing, 100044, China
| | - April Marie Wright
- Department of Biological Sciences, Southeastern Louisiana University, Hammond, Louisiana, 70402, USA
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18
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Hand SJ, Maugoust J, Beck RMD, Orliac MJ. A 50-million-year-old, three-dimensionally preserved bat skull supports an early origin for modern echolocation. Curr Biol 2023; 33:4624-4640.e21. [PMID: 37858341 DOI: 10.1016/j.cub.2023.09.043] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Revised: 07/24/2023] [Accepted: 09/18/2023] [Indexed: 10/21/2023]
Abstract
Bats are among the most recognizable, numerous, and widespread of all mammals. But much of their fossil record is missing, and bat origins remain poorly understood, as do the relationships of early to modern bats. Here, we describe a new early Eocene bat that helps bridge the gap between archaic stem bats and the hyperdiverse modern bat radiation of more than 1,460 living species. Recovered from ∼50 million-year-old cave sediments in the Quercy Phosphorites of southwestern France, Vielasia sigei's remains include a near-complete, three-dimensionally preserved skull-the oldest uncrushed bat cranium yet found. Phylogenetic analyses of a 2,665 craniodental character matrix, with and without 36.8 kb of DNA sequence data, place Vielasia outside modern bats, with total evidence tip-dating placing it sister to the crown clade. Vielasia retains the archaic dentition and skeletal features typical of early Eocene bats, but its inner ear shows specializations found in modern echolocating bats. These features, which include a petrosal only loosely attached to the basicranium, an expanded cochlea representing ∼25% basicranial width, and a long basilar membrane, collectively suggest that the kind of laryngeal echolocation used by most modern bats predates the crown radiation. At least 23 individuals of V. sigei are preserved together in a limestone cave deposit, indicating that cave roosting behavior had evolved in bats by the end of the early Eocene; this period saw the beginning of significant global climate cooling that may have been an evolutionary driver for bats to first congregate in caves.
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Affiliation(s)
- Suzanne J Hand
- ESSRC, School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, NSW 2052, Australia
| | - Jacob Maugoust
- Institut des Sciences de l'Evolution, UMR 5554 CNRS, IRD, EPHE, Université de Montpellier, Place Eugène Bataillon, 34095 Montpellier Cedex 5, France
| | - Robin M D Beck
- School of Science, Engineering and Environment, University of Salford, Manchester M5 4WT, UK.
| | - Maeva J Orliac
- Institut des Sciences de l'Evolution, UMR 5554 CNRS, IRD, EPHE, Université de Montpellier, Place Eugène Bataillon, 34095 Montpellier Cedex 5, France
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19
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Coiro M, Allio R, Mazet N, Seyfullah LJ, Condamine FL. Reconciling fossils with phylogenies reveals the origin and macroevolutionary processes explaining the global cycad biodiversity. THE NEW PHYTOLOGIST 2023; 240:1616-1635. [PMID: 37302411 PMCID: PMC10953041 DOI: 10.1111/nph.19010] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Accepted: 05/01/2023] [Indexed: 06/13/2023]
Abstract
The determinants of biodiversity patterns can be understood using macroevolutionary analyses. The integration of fossils into phylogenies offers a deeper understanding of processes underlying biodiversity patterns in deep time. Cycadales are considered a relict of a once more diverse and globally distributed group but are restricted to low latitudes today. We still know little about their origin and geographic range evolution. Combining molecular data for extant species and leaf morphological data for extant and fossil species, we study the origin of cycad global biodiversity patterns through Bayesian total-evidence dating analyses. We assess the ancestral geographic origin and trace the historical biogeography of cycads with a time-stratified process-based model. Cycads originated in the Carboniferous on the Laurasian landmass and expanded in Gondwana in the Jurassic. Through now-vanished continental connections, Antarctica and Greenland were crucial biogeographic crossroads for cycad biogeography. Vicariance is an essential speciation mode in the deep and recent past. Their latitudinal span increased in the Jurassic and restrained toward subtropical latitudes in the Neogene in line with biogeographic inferences of high-latitude extirpations. We show the benefits of integrating fossils into phylogenies to estimate ancestral areas of origin and to study evolutionary processes explaining the global distribution of present-day relict groups.
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Affiliation(s)
- Mario Coiro
- Department of PalaeontologyUniversity of Vienna1090ViennaAustria
- Ronin Institute for Independent ScholarshipMontclairNJ07043USA
| | - Rémi Allio
- Centre de Biologie pour la Gestion des Populations, INRAE, CIRAD, IRD, Montpellier SupAgroUniversité de Montpellier34988MontpellierFrance
| | - Nathan Mazet
- CNRS, Institut des Sciences de l'Evolution de Montpellier, Université de MontpellierPlace Eugène Bataillon34095MontpellierFrance
| | | | - Fabien L. Condamine
- CNRS, Institut des Sciences de l'Evolution de Montpellier, Université de MontpellierPlace Eugène Bataillon34095MontpellierFrance
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Almeida EAB, Bossert S, Danforth BN, Porto DS, Freitas FV, Davis CC, Murray EA, Blaimer BB, Spasojevic T, Ströher PR, Orr MC, Packer L, Brady SG, Kuhlmann M, Branstetter MG, Pie MR. The evolutionary history of bees in time and space. Curr Biol 2023; 33:3409-3422.e6. [PMID: 37506702 DOI: 10.1016/j.cub.2023.07.005] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Revised: 07/04/2023] [Accepted: 07/04/2023] [Indexed: 07/30/2023]
Abstract
Bees are the most significant pollinators of flowering plants. This partnership began ca. 120 million years ago, but the uncertainty of how and when bees spread across the planet has greatly obscured investigations of this key mutualism. We present a novel analysis of bee biogeography using extensive new genomic and fossil data to demonstrate that bees originated in Western Gondwana (Africa and South America). Bees likely originated in the Early Cretaceous, shortly before the breakup of Western Gondwana, and the early evolution of any major bee lineage is associated with either the South American or African land masses. Subsequently, bees colonized northern continents via a complex history of vicariance and dispersal. The notable early absences from large landmasses, particularly in Australia and India, have important implications for understanding the assembly of local floras and diverse modes of pollination. How bees spread around the world from their hypothesized Southern Hemisphere origin parallels the histories of numerous flowering plant clades, providing an essential step to studying the evolution of angiosperm pollination syndromes in space and time.
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Affiliation(s)
- Eduardo A B Almeida
- Departamento de Biologia, Faculdade de Filosofia, Ciências e Letras, Universidade de São Paulo, Ribeirão Preto, São Paulo 14040-901, Brazil.
| | - Silas Bossert
- Department of Entomology, Washington State University, Pullman, WA 99164, USA; Department of Entomology, National Museum of Natural History, Smithsonian Institution, Washington, DC 20560, USA.
| | - Bryan N Danforth
- Department of Entomology, Cornell University, Comstock Hall, Ithaca, NY 14853, USA
| | - Diego S Porto
- Departamento de Biologia, Faculdade de Filosofia, Ciências e Letras, Universidade de São Paulo, Ribeirão Preto, São Paulo 14040-901, Brazil; Finnish Museum of Natural History - LUOMUS, University of Helsinki, Helsinki 00014, Finland
| | - Felipe V Freitas
- Departamento de Biologia, Faculdade de Filosofia, Ciências e Letras, Universidade de São Paulo, Ribeirão Preto, São Paulo 14040-901, Brazil; Department of Entomology, Washington State University, Pullman, WA 99164, USA
| | - Charles C Davis
- Department of Organismic and Evolutionary Biology, Harvard University Herbaria, 22 Divinity Avenue, Cambridge, MA 02138, USA
| | - Elizabeth A Murray
- Department of Entomology, Washington State University, Pullman, WA 99164, USA; Department of Entomology, National Museum of Natural History, Smithsonian Institution, Washington, DC 20560, USA
| | - Bonnie B Blaimer
- Department of Entomology, National Museum of Natural History, Smithsonian Institution, Washington, DC 20560, USA; Center for Integrative Biodiversity Discovery, Museum für Naturkunde, Leibniz-Institute for Evolution and Biodiversity Science, 10115 Berlin, Germany
| | - Tamara Spasojevic
- Department of Entomology, National Museum of Natural History, Smithsonian Institution, Washington, DC 20560, USA; Life Sciences, Natural History Museum Basel, 4051 Basel, Switzerland; Institute of Ecology and Evolution, University of Bern, 3012 Bern, Switzerland
| | - Patrícia R Ströher
- Departamento de Zoologia, Universidade Federal do Paraná, Curitiba, Paraná 81531-990, Brazil; Department of Anthropology and Archaeology, University of Calgary, Calgary, AB T2N 1N4, Canada
| | - Michael C Orr
- Entomologie, Staatliches Museum für Naturkunde Stuttgart, 70191 Stuttgart, Germany; Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Laurence Packer
- Department of Biology, York University, Toronto, ON M3J 1P3, Canada
| | - Seán G Brady
- Department of Entomology, National Museum of Natural History, Smithsonian Institution, Washington, DC 20560, USA
| | - Michael Kuhlmann
- Zoological Museum, University of Kiel, Hegewischstr. 3, 24105 Kiel, Germany
| | - Michael G Branstetter
- U.S. Department of Agriculture, Agricultural Research Service, Pollinating Insects Research Unit, Utah State University, Logan, UT 84322, USA
| | - Marcio R Pie
- Departamento de Zoologia, Universidade Federal do Paraná, Curitiba, Paraná 81531-990, Brazil; Department of Biology, Edge Hill University, St Helens Rd, Ormskirk, Lancashire L39 4QP, UK
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21
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López-Martínez AM, Schönenberger J, von Balthazar M, González-Martínez CA, Ramírez-Barahona S, Sauquet H, Magallón S. Integrating Fossil Flowers into the Angiosperm Phylogeny Using Molecular and Morphological Evidence. Syst Biol 2023; 72:837-855. [PMID: 36995161 DOI: 10.1093/sysbio/syad017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Revised: 03/23/2023] [Accepted: 03/28/2023] [Indexed: 03/31/2023] Open
Abstract
Fossils are essential to infer past evolutionary processes. The assignment of fossils to extant clades has traditionally relied on morphological similarity and on apomorphies shared with extant taxa. The use of explicit phylogenetic analyses to establish fossil affinities has so far remained limited. In this study, we built a comprehensive framework to investigate the phylogenetic placement of 24 exceptionally preserved fossil flowers. For this, we assembled a new species-level data set of 30 floral traits for 1201 extant species that were sampled to capture the stem and crown nodes of all angiosperm families. We explored multiple analytical approaches to integrate the fossils into the phylogeny, including different phylogenetic estimation methods, topological-constrained analyses, and combining molecular and morphological data of extant and fossil species. Our results were widely consistent across approaches and showed minor differences in the support of fossils at different phylogenetic positions. The placement of some fossils agrees with previously suggested relationships, but for others, a new placement is inferred. We also identified fossils that are well supported within particular extant families, whereas others showed high phylogenetic uncertainty. Finally, we present recommendations for future analyses combining molecular and morphological evidence, regarding the selection of fossils and appropriate methodologies, and provide some perspectives on how to integrate fossils into the investigation of divergence times and the temporal evolution of morphological traits. [Angiosperms; fossil flowers; phylogenetic uncertainty; RoguePlots.].
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Affiliation(s)
- Andrea M López-Martínez
- Posgrado en Ciencias Biológicas, Universidad Nacional Autónoma de México, Edificio D, 1° Piso, Circuito de Posgrados, Ciudad Universitaria, Coyoacán, Ciudad de México 04510, Mexico
- Departamento de Botánica, Instituto de Biología, Universidad Nacional Autónoma de México, 3er Circuito de Ciudad Universitaria, Coyoacán, Ciudad de México 04510, Mexico
| | - Jürg Schönenberger
- Department of Botany and Biodiversity Research, University of Vienna, Rennweg 14, Vienna 1030, Austria
| | - Maria von Balthazar
- Department of Botany and Biodiversity Research, University of Vienna, Rennweg 14, Vienna 1030, Austria
| | - César A González-Martínez
- Departamento de Botánica, Instituto de Biología, Universidad Nacional Autónoma de México, 3er Circuito de Ciudad Universitaria, Coyoacán, Ciudad de México 04510, Mexico
| | - Santiago Ramírez-Barahona
- Departamento de Botánica, Instituto de Biología, Universidad Nacional Autónoma de México, 3er Circuito de Ciudad Universitaria, Coyoacán, Ciudad de México 04510, Mexico
| | - Hervé Sauquet
- National Herbarium of New South Wales (NSW), Royal Botanic Gardens and Domain Trust, Sydney, NSW 2000, Australia
- Evolution and Ecology Research Centre, School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, NSW 2052, Australia
| | - Susana Magallón
- Departamento de Botánica, Instituto de Biología, Universidad Nacional Autónoma de México, 3er Circuito de Ciudad Universitaria, Coyoacán, Ciudad de México 04510, Mexico
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22
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Luo A, Zhang C, Zhou QS, Ho SYW, Zhu CD. Impacts of Taxon-Sampling Schemes on Bayesian Tip Dating Under the Fossilized Birth-Death Process. Syst Biol 2023; 72:781-801. [PMID: 36919368 PMCID: PMC10405359 DOI: 10.1093/sysbio/syad011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2021] [Revised: 01/18/2023] [Accepted: 03/14/2023] [Indexed: 03/16/2023] Open
Abstract
Evolutionary timescales can be inferred by molecular-clock analyses of genetic data and fossil evidence. Bayesian phylogenetic methods such as tip dating provide a powerful framework for inferring evolutionary timescales, but the most widely used priors for tree topologies and node times often assume that present-day taxa have been sampled randomly or exhaustively. In practice, taxon sampling is often carried out so as to include representatives of major lineages, such as orders or families. We examined the impacts of different densities of diversified sampling on Bayesian tip dating on unresolved fossilized birth-death (FBD) trees, in which fossil taxa are topologically constrained but their exact placements are averaged out. We used synthetic data generated by simulations of nucleotide sequence evolution, fossil occurrences, and diversified taxon sampling. Our analyses under the diversified-sampling FBD process show that increasing taxon-sampling density does not necessarily improve divergence-time estimates. However, when informative priors were specified for the root age or when tree topologies were fixed to those used for simulation, the performance of tip dating on unresolved FBD trees maintains its accuracy and precision or improves with taxon-sampling density. By exploring three situations in which models are mismatched, we find that including all relevant fossils, without pruning off those that are incompatible with the diversified-sampling FBD process, can lead to underestimation of divergence times. Our reanalysis of a eutherian mammal data set confirms some of the findings from our simulation study, and reveals the complexity of diversified taxon sampling in phylogenomic data sets. In highlighting the interplay of taxon-sampling density and other factors, the results of our study have practical implications for using Bayesian tip dating to infer evolutionary timescales across the Tree of Life. [Bayesian tip dating; eutherian mammals; fossilized birth-death process; phylogenomics; taxon sampling.].
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Affiliation(s)
- Arong Luo
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Chi Zhang
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing 100044, China
- Center for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Beijing 100044, China
| | - Qing-Song Zhou
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Simon Y W Ho
- School of Life and Environmental Sciences, University of Sydney, Sydney, New South Wales 2006, Australia
| | - Chao-Dong Zhu
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- State Key Laboratory of Integrated Pest Management, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
- International College, University of Chinese Academy of Sciences, Beijing, 100049, China
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23
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Barba-Montoya J, Sharma S, Kumar S. Molecular timetrees using relaxed clocks and uncertain phylogenies. FRONTIERS IN BIOINFORMATICS 2023; 3:1225807. [PMID: 37600967 PMCID: PMC10435864 DOI: 10.3389/fbinf.2023.1225807] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Accepted: 07/21/2023] [Indexed: 08/22/2023] Open
Abstract
A common practice in molecular systematics is to infer phylogeny and then scale it to time by using a relaxed clock method and calibrations. This sequential analysis practice ignores the effect of phylogenetic uncertainty on divergence time estimates and their confidence/credibility intervals. An alternative is to infer phylogeny and times jointly to incorporate phylogenetic errors into molecular dating. We compared the performance of these two alternatives in reconstructing evolutionary timetrees using computer-simulated and empirical datasets. We found sequential and joint analyses to produce similar divergence times and phylogenetic relationships, except for some nodes in particular cases. The joint inference performed better when the phylogeny was not well resolved, situations in which the joint inference should be preferred. However, joint inference can be infeasible for large datasets because available Bayesian methods are computationally burdensome. We present an alternative approach for joint inference that combines the bag of little bootstraps, maximum likelihood, and RelTime approaches for simultaneously inferring evolutionary relationships, divergence times, and confidence intervals, incorporating phylogeny uncertainty. The new method alleviates the high computational burden imposed by Bayesian methods while achieving a similar result.
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Affiliation(s)
- Jose Barba-Montoya
- Institute for Genomics and Evolutionary Medicine, Temple University, Philadelphia, PA, United States
- Department of Biology, Temple University, Philadelphia, PA, United States
| | - Sudip Sharma
- Institute for Genomics and Evolutionary Medicine, Temple University, Philadelphia, PA, United States
- Department of Biology, Temple University, Philadelphia, PA, United States
| | - Sudhir Kumar
- Institute for Genomics and Evolutionary Medicine, Temple University, Philadelphia, PA, United States
- Department of Biology, Temple University, Philadelphia, PA, United States
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24
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Herting J, Schönenberger J, Sauquet H. Profile of a flower: How rates of morphological evolution drive floral diversification in Ericales and angiosperms. AMERICAN JOURNAL OF BOTANY 2023; 110:e16213. [PMID: 37459475 DOI: 10.1002/ajb2.16213] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Revised: 05/26/2023] [Accepted: 05/26/2023] [Indexed: 08/12/2023]
Abstract
PREMISE Recent studies of floral disparity in the asterid order Ericales have shown that flowers vary strongly among families and that disparity is unequally distributed between the three flower modules (perianth, androecium, gynoecium). However, it remains unknown whether these patterns are driven by heterogeneous rates of morphological evolution or other factors. METHODS Here, we compiled a data set of 33 floral characters scored for 414 species of Ericales sampled from 346 genera and all 22 families. We conducted ancestral state reconstructions using an equal-rates Markov model for each character. We estimated rates of morphological evolution for Ericales and for a separate angiosperm-wide data set of 19 characters and 792 species, creating "rate profiles" for Ericales, angiosperms, and major angiosperm subclades. We compared morphological rates among flower modules within each data set separately and between data sets, and we compared rates among angiosperm subclades using the angiosperm data set. RESULTS The androecium exhibits the highest evolutionary rates across most characters, whereas most perianth and gynoecium characters evolve more slowly in both Ericales and angiosperms. Both high and low rates of morphological evolution can result in high floral disparity in Ericales. Analyses of an angiosperm-wide floral data set reveal that this pattern appears to be conserved across most major angiosperm clades. CONCLUSIONS Elevated rates of morphological evolution in the androecium of Ericales may explain the higher disparity reported for this floral module. Comparing rates of morphological evolution through rate profiles proves to be a powerful tool in understanding floral evolution.
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Affiliation(s)
- Julian Herting
- National Herbarium of New South Wales, Botanic Gardens Sydney, Locked Bag 6002, Mount Annan, NSW 2567, Australia
| | - Jürg Schönenberger
- Department of Botany and Biodiversity Research, University of Vienna, Rennweg 14, Vienna, A-1030, Austria
| | - Hervé Sauquet
- National Herbarium of New South Wales, Botanic Gardens Sydney, Locked Bag 6002, Mount Annan, NSW 2567, Australia
- Evolution and Ecology Research Centre, School of Biological, Earth and Environmental Sciences, University of New South Wales Sydney, NSW 2052, Australia
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25
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Marivaux L, Negri FR, Antoine PO, Stutz NS, Condamine FL, Kerber L, Pujos F, Ventura Santos R, Alvim AMV, Hsiou AS, Bissaro MC, Adami-Rodrigues K, Ribeiro AM. An eosimiid primate of South Asian affinities in the Paleogene of Western Amazonia and the origin of New World monkeys. Proc Natl Acad Sci U S A 2023; 120:e2301338120. [PMID: 37399374 PMCID: PMC10334725 DOI: 10.1073/pnas.2301338120] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Accepted: 05/22/2023] [Indexed: 07/05/2023] Open
Abstract
Recent fossil discoveries in Western Amazonia revealed that two distinct anthropoid primate clades of African origin colonized South America near the Eocene/Oligocene transition (ca. 34 Ma). Here, we describe a diminutive fossil primate from Brazilian Amazonia and suggest that, surprisingly, a third clade of anthropoids was involved in the Paleogene colonization of South America by primates. This new taxon, Ashaninkacebus simpsoni gen. et sp. nov., has strong dental affinities with Asian African stem anthropoids: the Eosimiiformes. Morphology-based phylogenetic analyses of early Old World anthropoids and extinct and extant New World monkeys (platyrrhines) support relationships of both Ashaninkacebus and Amamria (late middle Eocene, North Africa) to the South Asian Eosimiidae. Afro-Arabia, then a mega island, played the role of a biogeographic stopover between South Asia and South America for anthropoid primates and hystricognathous rodents. The earliest primates from South America bear little adaptive resemblance to later Oligocene-early Miocene platyrrhine monkeys, and the scarcity of available paleontological data precludes elucidating firmly their affinities with or within Platyrrhini. Nonetheless, these data shed light on some of their life history traits, revealing a particularly small body size and a diet consisting primarily of insects and possibly fruit, which would have increased their chances of survival on a natural floating island during this extraordinary over-water trip to South America from Africa. Divergence-time estimates between Old and New World taxa indicate that the transatlantic dispersal(s) could source in the intense flooding events associated with the late middle Eocene climatic optimum (ca. 40.5 Ma) in Western Africa.
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Affiliation(s)
- Laurent Marivaux
- Laboratoire de Paléontologie, Institut des Sciences de l’Évolution de Montpellier (UMR 5554, CNRS/Université de Montpellier/Institut de Recherche pour le Développement), Université de Montpellier, 34095Montpellier, France
| | - Francisco R. Negri
- Laboratório de Paleontologia, Universidade Federal do Acre, 69980-000Cruzeiro do Sul, Brazil
| | - Pierre-Olivier Antoine
- Laboratoire de Paléontologie, Institut des Sciences de l’Évolution de Montpellier (UMR 5554, CNRS/Université de Montpellier/Institut de Recherche pour le Développement), Université de Montpellier, 34095Montpellier, France
| | - Narla S. Stutz
- Laboratoire de Paléontologie, Institut des Sciences de l’Évolution de Montpellier (UMR 5554, CNRS/Université de Montpellier/Institut de Recherche pour le Développement), Université de Montpellier, 34095Montpellier, France
- Programa de Pós-Graduação em Geociências, Universidade Federal do Rio Grande do Sul, 91501-970Porto Alegre, Brazil
| | - Fabien L. Condamine
- Laboratoire de Paléontologie, Institut des Sciences de l’Évolution de Montpellier (UMR 5554, CNRS/Université de Montpellier/Institut de Recherche pour le Développement), Université de Montpellier, 34095Montpellier, France
| | - Leonardo Kerber
- Centro de Apoio à Pesquisa Paleontológica da Quarta Colônia, Universidade Federal de Santa Maria, 97230-000São João do Polêsine, Brazil
| | - François Pujos
- Instituto Argentino de Nivología, Glaciología y Ciencias Ambientales, CONICET–Universidad Nacional de Cuyo-Mendoza, 5500Mendoza, Argentina
| | - Roberto Ventura Santos
- Laboratório de Geocronologia, Instituto de Geociências, Universidade de Brasília, 70910-000Brasília, Brazil
| | - André M. V. Alvim
- Laboratório de Geocronologia, Instituto de Geociências, Universidade de Brasília, 70910-000Brasília, Brazil
| | - Annie S. Hsiou
- Laboratório de Paleontologia, Universidade de São Paulo, 14040-901Ribeirão Preto, Brazil
| | - Marcos C. Bissaro
- Laboratório de Paleontologia, Universidade de São Paulo, 14040-901Ribeirão Preto, Brazil
| | - Karen Adami-Rodrigues
- Núcleo de Estudos em Paleontologia e Estratigrafia, Centro das Engenharias, Universidade Federal de Pelotas, 96010-020Pelotas, Brazil
| | - Ana Maria Ribeiro
- Programa de Pós-Graduação em Geociências, Universidade Federal do Rio Grande do Sul, 91501-970Porto Alegre, Brazil
- Seção de Paleontologia, Museu de Ciências Naturais, Secretaria do Meio Ambiente e Infraestrutura, 90690-000Porto Alegre, Brazil
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26
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Keating JN, Garwood RJ, Sansom RS. Phylogenetic congruence, conflict and consilience between molecular and morphological data. BMC Ecol Evol 2023; 23:30. [PMID: 37403037 DOI: 10.1186/s12862-023-02131-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Accepted: 06/08/2023] [Indexed: 07/06/2023] Open
Abstract
Morphology and molecules are important data sources for estimating evolutionary relationships. Modern studies often utilise morphological and molecular partitions alongside each other in combined analyses. However, the effect of combining phenomic and genomic partitions is unclear. This is exacerbated by their size imbalance, and conflict over the efficacy of different inference methods when using morphological characters. To systematically address the effect of topological incongruence, size imbalance, and tree inference methods, we conduct a meta-analysis of 32 combined (molecular + morphology) datasets across metazoa. Our results reveal that morphological-molecular topological incongruence is pervasive: these data partitions yield very different trees, irrespective of which method is used for morphology inference. Analysis of the combined data often yields unique trees that are not sampled by either partition individually, even with the inclusion of relatively small quantities of morphological characters. Differences between morphology inference methods in terms of resolution and congruence largely relate to consensus methods. Furthermore, stepping stone Bayes factor analyses reveal that morphological and molecular partitions are not consistently combinable, i.e. data partitions are not always best explained under a single evolutionary process. In light of these results, we advise that the congruence between morphological and molecular data partitions needs to be considered in combined analyses. Nonetheless, our results reveal that, for most datasets, morphology and molecules can, and should, be combined in order to best estimate evolutionary history and reveal hidden support for novel relationships. Studies that analyse only phenomic or genomic data in isolation are unlikely to provide the full evolutionary picture.
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Affiliation(s)
- Joseph N Keating
- Department of Earth and Environmental Sciences, University of Manchester, Manchester, M13 9PL, UK
- School of Earth Sciences, University of Bristol, Life Sciences Building, Tyndall Avenue, Bristol, BS8 1TQ, UK
| | - Russell J Garwood
- Department of Earth and Environmental Sciences, University of Manchester, Manchester, M13 9PL, UK
- Natural History Museum, London, SW7 5BD, UK
| | - Robert S Sansom
- Department of Earth and Environmental Sciences, University of Manchester, Manchester, M13 9PL, UK.
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27
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Barido-Sottani J, Żyła D, Heath TA. Estimating the Age of Poorly Dated Fossil Specimens and Deposits Using a Total-Evidence Approach and the Fossilized Birth-Death Process. Syst Biol 2023; 72:466-475. [PMID: 36382797 PMCID: PMC10275547 DOI: 10.1093/sysbio/syac073] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Accepted: 11/04/2022] [Indexed: 02/02/2024] Open
Abstract
Bayesian total-evidence approaches under the fossilized birth-death model enable biologists to combine fossil and extant data while accounting for uncertainty in the ages of fossil specimens, in an integrative phylogenetic analysis. Fossil age uncertainty is a key feature of the fossil record as many empirical data sets may contain a mix of precisely dated and poorly dated fossil specimens or deposits. In this study, we explore whether reliable age estimates for fossil specimens can be obtained from Bayesian total-evidence phylogenetic analyses under the fossilized birth-death model. Through simulations based on the example of the Baltic amber deposit, we show that estimates of fossil ages obtained through such an analysis are accurate, particularly when the proportion of poorly dated specimens remains low and the majority of fossil specimens have precise dates. We confirm our results using an empirical data set of living and fossil penguins by artificially increasing the age uncertainty around some fossil specimens and showing that the resulting age estimates overlap with the recorded age ranges. Our results are applicable to many empirical data sets where classical methods of establishing fossil ages have failed, such as the Baltic amber and the Gobi Desert deposits. [Bayesian phylogenetic inference; fossil age estimates; fossilized birth-death; Lagerstätte; total-evidence.].
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Affiliation(s)
- Joëlle Barido-Sottani
- Department of Ecology, Evolution and Organismal Biology, Iowa State University, 251 Bessey Hall, 2200 Osborne Drive, Ames, IA 50011, USA
- Institut de Biologie de l’ENS (IBENS), École normale supérieure, CNRS, INSERM, Université PSL, 46 rue d’Ulm, 75005 Paris, France
| | - Dagmara Żyła
- Department of Ecology, Evolution and Organismal Biology, Iowa State University, 251 Bessey Hall, 2200 Osborne Drive, Ames, IA 50011, USA
- Department of Invertebrate Zoology and Parasitology, University of Gdańsk, Wita Stwosza 59, 80-308 Gdańsk, Poland
- Museum of Nature Hamburg, Leibniz Institute for the Analysis of Biodiversity Change, Martin-Luther-King Platz 3, 20146 Hamburg, Germany
| | - Tracy A Heath
- Department of Ecology, Evolution and Organismal Biology, Iowa State University, 251 Bessey Hall, 2200 Osborne Drive, Ames, IA 50011, USA
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28
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Jiangzuo Q, Werdelin L, Sanisidro O, Yang R, Fu J, Li S, Wang S, Deng T. Origin of adaptations to open environments and social behaviour in sabretoothed cats from the northeastern border of the Tibetan Plateau. Proc Biol Sci 2023; 290:20230019. [PMID: 37072045 PMCID: PMC10113030 DOI: 10.1098/rspb.2023.0019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/20/2023] Open
Abstract
The iconic sabretooth Homotherium is thought to have hunted cooperatively, but the origin of this behaviour and correlated morphological adaptations are largely unexplored. Here we report the most primitive species of Amphimachairodus (Amphimachairodus hezhengensis sp. nov.), a member of Machairodontini basal to Homotherium, from the Linxia Basin, northeastern border of the Tibetan Plateau (9.8-8.7 Ma). The long snout, laterally oriented and posteriorly located orbit of Amphimachairodus suggest a better ability to observe the surrounding environment, rather than targeting single prey, pointing to an adaptation to the open environment or social behaviour. A pathological forepaw of Amphimachairodus provides direct evidence of partner care. Our analyses of trait evolutionary rates support that traits correlated with killing behaviour and open environment adaptation evolved prior to other traits, suggesting that changes in hunting behaviour may be the major evolutionary driver in the early evolution of the lineage. A. hezhengensis represents one of the most important transitions in the evolution of Machairodontini, leading to adaptation in open environments and contributing to their further dispersal and radiation worldwide. This rapid morphological change is likely to be correlated with increasingly arid environments caused by the rise of the Tibetan Plateau, and competition from abundant large carnivores in this area.
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Affiliation(s)
- Qigao Jiangzuo
- Key Laboratory of Orogenic Belts and Crustal Evolution, School of Earth and Space Sciences, Peking University, 5 Yiheyuan Road, Beijing 100871, People's Republic of China
- Key Laboratory of Vertebrate Evolution and Human Origins of Chinese Academy of Sciences, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing 100871, People's Republic of China
- CAS Center for Excellence in Life and Paleoenvironment, Beijing 100044, People's Republic of China
- Division of Paleontology, American Museum of Natural History, New York, NY 10024-5102, USA
| | - Lars Werdelin
- Department of Palaeobiology, Swedish Museum of Natural History, Box 50007, S-104 05 Stockholm, Sweden
| | - Oscar Sanisidro
- Departamento de Ciencias de la Vida, Universidad de Alcalá, GloCEE -Global Change Ecology and Evolution Research Group, Alcalá de Henares 28801, Spain
| | - Rong Yang
- Hezheng Paleozoological Museum, Hezheng 731200, People's Republic of China
| | - Jiao Fu
- Key Laboratory of Vertebrate Evolution and Human Origins of Chinese Academy of Sciences, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing 100871, People's Republic of China
- CAS Center for Excellence in Life and Paleoenvironment, Beijing 100044, People's Republic of China
- University of Chinese Academy of Sciences, Beijing 100049, People's Republic of China
| | - Shijie Li
- Key Laboratory of Vertebrate Evolution and Human Origins of Chinese Academy of Sciences, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing 100871, People's Republic of China
- CAS Center for Excellence in Life and Paleoenvironment, Beijing 100044, People's Republic of China
- University of Chinese Academy of Sciences, Beijing 100049, People's Republic of China
| | - Shiqi Wang
- Key Laboratory of Vertebrate Evolution and Human Origins of Chinese Academy of Sciences, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing 100871, People's Republic of China
- CAS Center for Excellence in Life and Paleoenvironment, Beijing 100044, People's Republic of China
| | - Tao Deng
- Key Laboratory of Vertebrate Evolution and Human Origins of Chinese Academy of Sciences, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing 100871, People's Republic of China
- CAS Center for Excellence in Life and Paleoenvironment, Beijing 100044, People's Republic of China
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29
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Blaimer BB, Santos BF, Cruaud A, Gates MW, Kula RR, Mikó I, Rasplus JY, Smith DR, Talamas EJ, Brady SG, Buffington ML. Key innovations and the diversification of Hymenoptera. Nat Commun 2023; 14:1212. [PMID: 36869077 PMCID: PMC9984522 DOI: 10.1038/s41467-023-36868-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Accepted: 02/21/2023] [Indexed: 03/05/2023] Open
Abstract
The order Hymenoptera (wasps, ants, sawflies, and bees) represents one of the most diverse animal lineages, but whether specific key innovations have contributed to its diversification is still unknown. We assembled the largest time-calibrated phylogeny of Hymenoptera to date and investigated the origin and possible correlation of particular morphological and behavioral innovations with diversification in the order: the wasp waist of Apocrita; the stinger of Aculeata; parasitoidism, a specialized form of carnivory; and secondary phytophagy, a reversal to plant-feeding. Here, we show that parasitoidism has been the dominant strategy since the Late Triassic in Hymenoptera, but was not an immediate driver of diversification. Instead, transitions to secondary phytophagy (from parasitoidism) had a major influence on diversification rate in Hymenoptera. Support for the stinger and the wasp waist as key innovations remains equivocal, but these traits may have laid the anatomical and behavioral foundations for adaptations more directly associated with diversification.
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Affiliation(s)
- Bonnie B Blaimer
- Museum für Naturkunde, Leibniz Institute for Evolution and Biodiversity Science, Center for Integrative Biodiversity Discovery, Invalidenstraße 43, Berlin, 10115, Germany.
- National Museum of Natural History, Smithsonian Institution, 10th & Constitution Ave. NW, Washington, DC, USA.
| | - Bernardo F Santos
- Museum für Naturkunde, Leibniz Institute for Evolution and Biodiversity Science, Center for Integrative Biodiversity Discovery, Invalidenstraße 43, Berlin, 10115, Germany
- National Museum of Natural History, Smithsonian Institution, 10th & Constitution Ave. NW, Washington, DC, USA
| | - Astrid Cruaud
- CBGP, INRAe, CIRAD, IRD, Montpellier SupAgro, Université de Montpellier, Montpellier, France
| | - Michael W Gates
- Systematic Entomology Laboratory, USDA-ARS, c/o NMNH, Smithsonian Institution, 10th & Constitution Ave. NW, Washington, DC, USA
| | - Robert R Kula
- Systematic Entomology Laboratory, USDA-ARS, c/o NMNH, Smithsonian Institution, 10th & Constitution Ave. NW, Washington, DC, USA
| | - István Mikó
- Department of Biological Sciences, University of New Hampshire, Durham, NH, USA
| | - Jean-Yves Rasplus
- CBGP, INRAe, CIRAD, IRD, Montpellier SupAgro, Université de Montpellier, Montpellier, France
| | - David R Smith
- Systematic Entomology Laboratory, USDA-ARS, c/o NMNH, Smithsonian Institution, 10th & Constitution Ave. NW, Washington, DC, USA
| | - Elijah J Talamas
- Florida State Collection of Arthropods, Division of Plant Industry, Florida Department of Agriculture and Consumer Services, 1911 SW 34th St, Gainesville, FL, 32608, USA
| | - Seán G Brady
- National Museum of Natural History, Smithsonian Institution, 10th & Constitution Ave. NW, Washington, DC, USA
| | - Matthew L Buffington
- Systematic Entomology Laboratory, USDA-ARS, c/o NMNH, Smithsonian Institution, 10th & Constitution Ave. NW, Washington, DC, USA
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Prokop J, Nel A, Engel MS. Diversity, Form, and Postembryonic Development of Paleozoic Insects. ANNUAL REVIEW OF ENTOMOLOGY 2023; 68:401-429. [PMID: 36689304 DOI: 10.1146/annurev-ento-120220-022637] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
While Mesozoic, Paleogene, and Neogene insect faunas greatly resemble the modern one, the Paleozoic fauna provides unique insights into key innovations in insect evolution, such as the origin of wings and modifications of postembryonic development including holometaboly. Deep-divergence estimates suggest that the majority of contemporary insect orders originated in the Late Paleozoic, but these estimates reflect divergences between stem groups of each lineage rather than the later appearance of the crown groups. The fossil record shows the initial radiations of the extant hyperdiverse clades during the Early Permian, as well as the specialized fauna present before the End Permian mass extinction. This review summarizes the recent discoveries related to the documented diversity of Paleozoic hexapods, as well as current knowledge about what has actually been verified from fossil evidence as it relates to postembryonic development and the morphology of different body parts.
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Affiliation(s)
- Jakub Prokop
- Department of Zoology, Faculty of Science, Charles University, Prague, Czech Republic;
| | - André Nel
- Institut de Systématique, Évolution, Biodiversité (ISYEB), Muséum national d'Histoire naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, Paris, France;
| | - Michael S Engel
- Division of Entomology, University of Kansas Natural History Museum, Lawrence, Kansas, USA;
- Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, Kansas, USA
- Division of Invertebrate Zoology, American Museum of Natural History, New York, New York, USA
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31
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Beck RMD, de Vries D, Janiak MC, Goodhead IB, Boubli JP. Total evidence phylogeny of platyrrhine primates and a comparison of undated and tip-dating approaches. J Hum Evol 2023; 174:103293. [PMID: 36493598 DOI: 10.1016/j.jhevol.2022.103293] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Revised: 10/21/2022] [Accepted: 10/21/2022] [Indexed: 12/12/2022]
Abstract
There have been multiple published phylogenetic analyses of platyrrhine primates (New World monkeys) using both morphological and molecular data, but relatively few that have integrated both types of data into a total evidence approach. Here, we present phylogenetic analyses of recent and fossil platyrrhines, based on a total evidence data set of 418 morphological characters and 10.2 kilobases of DNA sequence data from 17 nuclear genes taken from previous studies, using undated and tip-dating approaches in a Bayesian framework. We compare the results of these analyses with molecular scaffold analyses using maximum parsimony and Bayesian approaches, and we use a formal information theoretic approach to identify unstable taxa. After a posteriori pruning of unstable taxa, the undated and tip-dating topologies appear congruent with recent molecular analyses and support largely similar relationships, with strong support for Stirtonia as a stem alouattine, Neosaimiri as a stem saimirine, Cebupithecia as a stem pitheciine, and Lagonimico as a stem callitrichid. Both analyses find three Greater Antillean subfossil platyrrhines (Xenothrix, Antillothrix, and Paralouatta) to form a clade that is related to Callicebus, congruent with a single dispersal event by the ancestor of this clade to the Greater Antilles. They also suggest that the fossil Proteropithecia may not be closely related to pitheciines, and that all known platyrrhines older than the Middle Miocene are stem taxa. Notably, the undated analysis found the Early Miocene Panamacebus (currently recognized as the oldest known cebid) to be unstable, and the tip-dating analysis placed it outside crown Platyrrhini. Our tip-dating analysis supports a late Oligocene or earliest Miocene (20.8-27.0 Ma) age for crown Platyrrhini, congruent with recent molecular clock analyses.
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Affiliation(s)
- Robin M D Beck
- Ecosystems and Environment Research Centre, School of Science, Engineering and Environment, University of Salford, Manchester, UK.
| | - Dorien de Vries
- Ecosystems and Environment Research Centre, School of Science, Engineering and Environment, University of Salford, Manchester, UK
| | - Mareike C Janiak
- Ecosystems and Environment Research Centre, School of Science, Engineering and Environment, University of Salford, Manchester, UK
| | - Ian B Goodhead
- Ecosystems and Environment Research Centre, School of Science, Engineering and Environment, University of Salford, Manchester, UK
| | - Jean P Boubli
- Ecosystems and Environment Research Centre, School of Science, Engineering and Environment, University of Salford, Manchester, UK
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Brée B, Condamine FL, Guinot G. Combining palaeontological and neontological data shows a delayed diversification burst of carcharhiniform sharks likely mediated by environmental change. Sci Rep 2022; 12:21906. [PMID: 36535995 PMCID: PMC9763247 DOI: 10.1038/s41598-022-26010-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Accepted: 12/07/2022] [Indexed: 12/23/2022] Open
Abstract
Estimating deep-time species-level diversification processes remains challenging. Both the fossil record and molecular phylogenies allow the estimation of speciation and extinction rates, but each type of data may still provide an incomplete picture of diversification dynamics. Here, we combine species-level palaeontological (fossil occurrences) and neontological (molecular phylogenies) data to estimate deep-time diversity dynamics through process-based birth-death models for Carcharhiniformes, the most speciose shark order today. Despite their abundant fossil record dating back to the Middle Jurassic, only a small fraction of extant carcharhiniform species is recorded as fossils, which impedes relying only on the fossil record to study their recent diversification. Combining fossil and phylogenetic data, we recover a complex evolutionary history for carcharhiniforms, exemplified by several variations in diversification rates with an early low diversity period followed by a Cenozoic radiation. We further reveal a burst of diversification in the last 30 million years, which is partially recorded with fossil data only. We also find that reef expansion and temperature change can explain variations in speciation and extinction through time. These results pinpoint the primordial importance of these environmental variables in the evolution of marine clades. Our study also highlights the benefit of combining the fossil record with phylogenetic data to address macroevolutionary questions.
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Affiliation(s)
- Baptiste Brée
- grid.462058.d0000 0001 2188 7059Institut des Sciences de l’Evolution de Montpellier, CNRS, IRD, EPHE, Université de Montpellier, 34095 Montpellier, France
| | - Fabien L. Condamine
- grid.462058.d0000 0001 2188 7059Institut des Sciences de l’Evolution de Montpellier, CNRS, IRD, EPHE, Université de Montpellier, 34095 Montpellier, France
| | - Guillaume Guinot
- grid.462058.d0000 0001 2188 7059Institut des Sciences de l’Evolution de Montpellier, CNRS, IRD, EPHE, Université de Montpellier, 34095 Montpellier, France
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Bacon CD, Silvestro D, Hoorn C, Bogotá-Ángel G, Antonelli A, Chazot N. The origin of modern patterns of continental diversity in Mauritiinae palms: the Neotropical museum and the Afrotropical graveyard. Biol Lett 2022; 18:20220214. [PMID: 36382374 PMCID: PMC9667138 DOI: 10.1098/rsbl.2022.0214] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2022] [Accepted: 10/25/2022] [Indexed: 11/18/2023] Open
Abstract
While the latitudinal diversity gradient has received much attention, biodiversity and species richness also vary between continents across similar latitudes. Fossil information can be used to understand the evolutionary mechanisms that generated such variation between continents of similar latitudes. We integrated fossil data into a phylogenetic analysis of the Mauritiinae palms, whose extant diversity is restricted to the Neotropics, but extended across Africa and India during most of the Cenozoic. Mauritiinae diverged from its sister lineage Raphiinae ca 106 Ma. Using ancestral state estimation and a lineage through time analysis, we found that diversity arose globally during the late Cretaceous and Palaeocene across South America, Africa and India. The Palaeocene-Eocene transition (ca 56 Ma) marked the end of global Mauritiinae expansion, and the beginning of their decline in both Africa and India. Mauritiinae disappeared from the Indian subcontinent and Africa at the end of the Eocene and the Miocene, respectively. By contrast, Neotropical diversity steadily increased over the last 80 Myr. Taken together, our results suggest that the Neotropics functioned as a continental-scale refuge for Mauritiinae palms, where lineages survived and diversified while global climatic changes that drastically reduced rainforests led to their demise on other continents.
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Affiliation(s)
- Christine D. Bacon
- Gothenburg Global Biodiversity Centre, SE-405 30 Gothenburg, Sweden
- Department of Biological and Environmental Sciences, University of Gothenburg, SE-405 30 Gothenburg, Sweden
| | - Daniele Silvestro
- Gothenburg Global Biodiversity Centre, SE-405 30 Gothenburg, Sweden
- Department of Biological and Environmental Sciences, University of Gothenburg, SE-405 30 Gothenburg, Sweden
- Department of Biology, University of Fribourg, 1700 Fribourg, Switzerland
- Swiss Institute of Bioinformatics, Quartier Sorge, 1700 Fribourg, Switzerland
| | - Carina Hoorn
- Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, 1098 XH Amsterdam, The Netherlands
| | - Giovanni Bogotá-Ángel
- Universidad Distrital Francisco José Caldas, Facultad del Medio Ambiente y Recursos Naturales, Bogotá DC, Colombia
| | - Alexandre Antonelli
- Gothenburg Global Biodiversity Centre, SE-405 30 Gothenburg, Sweden
- Department of Biological and Environmental Sciences, University of Gothenburg, SE-405 30 Gothenburg, Sweden
- Royal Botanical Gardens Kew, Richmond TW9 3AE, UK
- Department of Biology, University of Oxford, Oxford OX1 3RB, UK
| | - Nicolas Chazot
- Gothenburg Global Biodiversity Centre, SE-405 30 Gothenburg, Sweden
- Department of Biological and Environmental Sciences, University of Gothenburg, SE-405 30 Gothenburg, Sweden
- Department of Ecology, Swedish University of Agricultural Sciences, SE-750 Uppsala, Sweden
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The complete mitochondrial genome of the woodwasp Euxiphydria potanini (Hymenoptera, Xiphydrioidea) and phylogenetic implications for symphytans. Sci Rep 2022; 12:17677. [PMID: 36271278 PMCID: PMC9587024 DOI: 10.1038/s41598-022-21457-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Accepted: 09/27/2022] [Indexed: 01/18/2023] Open
Abstract
The long-necked woodwasp superfamily Xiphydrioidea belongs to the suborder Symphyta (Hymenoptera). Here we newly characterize the complete mitochondrial genome of the South Korean Euxiphydria potanini (Xiphydriidae) using next-generation sequencing: 16,500 bp long with 84.27% A + T content and 37 typical mitochondrial genes including those encoding 13 PCGs, 2 rRNAs, 22 tRNAs, and one A + T rich region. We compare the patterns of symphytan mitochondrial gene arrangement with those of an ancestral insect form and found some synapomorphic rearrangements in phylogenetic context. We use a variety of nucleotide and amino acid sequence alignments (thirteen mtPCGs and/or eight nDNAs) alongside step-by-step exclusions of long-branched taxa to elucidate the phylogenetic position of Xiphydrioidea and phylogenetic relationships among the seven symphytan superfamilies, except for Anaxyeloidea of which no mtgenome was available. The monophyly of symphytan superfamilies (with weak support for Pamphilioidea), sister-group relationship of Xiphydrioidea and Cephoidea, and Symphyta being paraphyletic to Apocrita, etc. are consistently supported by maximum likelihood and Bayesian inference trees. We also discuss the problematic phylogenetic positions of Orussoidea and Siricoidea and propose a hypothetical scenario of morphological character transition during hymenopteran evolution based on morphological key characteristics, such as the cenchrus and the wasp-waist.
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35
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Zhuang J, Rasnitsyn AP, Shih C, Ren D, Wang M. New Pamphiliids with Varying Venations from Lower Cretaceous Yixian Formation of Northeast China (Hymenoptera, Pamphiliidae). INSECTS 2022; 13:947. [PMID: 36292895 PMCID: PMC9604111 DOI: 10.3390/insects13100947] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Revised: 10/13/2022] [Accepted: 10/16/2022] [Indexed: 06/16/2023]
Abstract
One new genus and three new species of Pamphiliidae, Dolicholyda obtusata gen. et sp. nov., Dolicholyda confluens sp. nov., and Dolicholyda angusta sp. nov. are described and illustrated. All of them were collected from the Lower Cretaceous Yixian Formation in Duolun County, Inner Mongolia, China. The new genus is established based on the following characters: body surface without punctations; forewing with pterostigma lanceolate and sclerotized around the margins; angle between 1-M and 1-Cu nearly 90°; cell 1mcu long and obviously longer than length of pterostigma. In most cases, the ap-Cu is present, and its length varied. Additionally, we revise the diagnostic characteristics of Juralydinae based on the new specimens. New findings enhance our understanding of the wing venation characteristics of fossil pamphiliids and expand the diversity of Pamphiliidae in the Mesozoic.
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Affiliation(s)
- Jialiang Zhuang
- Key Laboratory of Forest Protection of National Forestry and Grassland Administration, Ecology and Nature Conservation Institute, Chinese Academy of Forestry, Beijing 100091, China
- College of Life Sciences, Capital Normal University, 105 Xisanhuanbeilu, Haidian District, Beijing 100048, China
| | - Alexandr P. Rasnitsyn
- Paleontological Institute, Russian Academy of Sciences, 123, Profsoyuznaya ul., 117647 Moscow, Russia
- Department of Palaeontology, Natural History Museum, Cromwell Road, London SW7 5BD, UK
| | - Chungkun Shih
- College of Life Sciences, Capital Normal University, 105 Xisanhuanbeilu, Haidian District, Beijing 100048, China
- Department of Paleobiology, National Museum of Natural History, Smithsonian Institution, Washington, DC 20013, USA
| | - Dong Ren
- College of Life Sciences, Capital Normal University, 105 Xisanhuanbeilu, Haidian District, Beijing 100048, China
| | - Mei Wang
- Key Laboratory of Forest Protection of National Forestry and Grassland Administration, Ecology and Nature Conservation Institute, Chinese Academy of Forestry, Beijing 100091, China
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36
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Tihelka E, Howard RJ, Cai C, Lozano-Fernandez J. Was There a Cambrian Explosion on Land? The Case of Arthropod Terrestrialization. BIOLOGY 2022; 11:biology11101516. [PMID: 36290419 PMCID: PMC9598930 DOI: 10.3390/biology11101516] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Revised: 10/06/2022] [Accepted: 10/14/2022] [Indexed: 01/24/2023]
Abstract
Arthropods, the most diverse form of macroscopic life in the history of the Earth, originated in the sea. Since the early Cambrian, at least ~518 million years ago, these animals have dominated the oceans of the world. By the Silurian-Devonian, the fossil record attests to arthropods becoming the first animals to colonize land, However, a growing body of molecular dating and palaeontological evidence suggests that the three major terrestrial arthropod groups (myriapods, hexapods, and arachnids), as well as vascular plants, may have invaded land as early as the Cambrian-Ordovician. These dates precede the oldest fossil evidence of those groups and suggest an unrecorded continental "Cambrian explosion" a hundred million years prior to the formation of early complex terrestrial ecosystems in the Silurian-Devonian. We review the palaeontological, phylogenomic, and molecular clock evidence pertaining to the proposed Cambrian terrestrialization of the arthropods. We argue that despite the challenges posed by incomplete preservation and the scarcity of early Palaeozoic terrestrial deposits, the discrepancy between molecular clock estimates and the fossil record is narrower than is often claimed. We discuss strategies for closing the gap between molecular clock estimates and fossil data in the evolution of early ecosystems on land.
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Affiliation(s)
- Erik Tihelka
- School of Earth and Biological Sciences, University of Bristol, Bristol BS8 1TQ, UK
| | - Richard J. Howard
- Department of Earth Sciences, The Natural History Museum, London SW7 5BD, UK
| | - Chenyang Cai
- School of Earth and Biological Sciences, University of Bristol, Bristol BS8 1TQ, UK
- State Key Laboratory of Palaeobiology and Stratigraphy, Nanjing Institute of Geology and Palaeontology, and Center for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Nanjing 210008, China
| | - Jesus Lozano-Fernandez
- School of Earth and Biological Sciences, University of Bristol, Bristol BS8 1TQ, UK
- Department of Genetics, Microbiology and Statistics & Biodiversity Research Institute (IRBio), University of Barcelona, 08028 Barcelona, Spain
- Correspondence:
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37
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Jiangzuo Q, Niu K, Li S, Fu J, Wang S. A Diverse Metailurine Guild from the Latest Miocene Xingjiawan Fauna, Yongdeng, Northwestern China, and Generic Differentiation of Metailurine Felids. J MAMM EVOL 2022. [DOI: 10.1007/s10914-022-09622-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
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38
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Divergence Dating and Biogeography of Xenosauridae Including Fossils as Terminal Taxa. J HERPETOL 2022. [DOI: 10.1670/21-068] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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39
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Niu G, Budak M, Korkmaz EM, Doğan Ö, Nel A, Wan S, Cai C, Jouault C, Li M, Wei M. Phylogenomic Analyses of the Tenthredinoidea Support the Familial Rank of Athaliidae (Insecta, Tenthredinoidea). INSECTS 2022; 13:858. [PMID: 36292806 PMCID: PMC9604231 DOI: 10.3390/insects13100858] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/11/2022] [Revised: 09/07/2022] [Accepted: 09/14/2022] [Indexed: 06/16/2023]
Abstract
The systematic status of the genus Athalia and related genera is a perennial controversy in sawfly taxonomy. Several authors have hypothesized that the placement of Athalia within the Tenthredinidae is artificial, but no studies have focused on this topic. If the hypothesis that Athalia does not belong to Tenthredinidae can be supported, the taxonomic framework of Tenthredinoidea needs revision. We present a comprehensive phylogenomic study of Tenthredinoidae, focusing on the positions of Athalia and related genera by sampling 80 representatives mainly of the Tenthredinoidea, including Heptamelinae and Blasticotomidae. Our phylogenetic reconstructions based on nuclear genes and mitochondrial (mt) sequences support Athalia and related genera as a distinct clade sister to Tenthredinidae + (Cimbicidae + Diprionidae). A comparison of symphytan mitochondrial genomes reveals an innovative gene rearrangement pattern in Athaliidae, in which Dentathalia demonstrates a more ancestral pattern than Athalia and Hypsathalia. The lineage specificity of mt rRNA secondary structures also provides sufficient support to consider Athaliidae as a separate family. In summary, the phylogeny and genomic structural changes unanimously support the taxonomic treatment of Athaliidae as a family and the re-establishment of Dentathalia as a valid genus.
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Affiliation(s)
- Gengyun Niu
- Laboratory of Insect Systematics and Evolutionary Biology, College of Life Sciences, Jiangxi Normal University, Nanchang 330022, China
| | - Mahir Budak
- Department of Molecular Biology and Genetics, Faculty of Science, Sivas Cumhuriyet University, Sivas 58140, Turkey
| | - Ertan Mahir Korkmaz
- Department of Molecular Biology and Genetics, Faculty of Science, Sivas Cumhuriyet University, Sivas 58140, Turkey
| | - Özgül Doğan
- Department of Molecular Biology and Genetics, Faculty of Science, Sivas Cumhuriyet University, Sivas 58140, Turkey
| | - André Nel
- Institut de Systématique, Évolution, Biodiversité (ISYEB) Muséum National d’Histoire Naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, CP50, 57 rue Cuvier, 75005 Paris, France
| | - Siying Wan
- Laboratory of Insect Systematics and Evolutionary Biology, College of Life Sciences, Jiangxi Normal University, Nanchang 330022, China
| | - Chenyang Cai
- State Key Laboratory of Palaeobiology and Stratigraphy, Nanjing Institute of Geology and Palaeontology, Centre for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Nanjing 210008, China
| | - Corentin Jouault
- Institut de Systématique, Évolution, Biodiversité (ISYEB) Muséum National d’Histoire Naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, CP50, 57 rue Cuvier, 75005 Paris, France
- Univ. Rennes, CNRS, Géosciences Rennes, UMR 6118, F-35000 Rennes, France
- CNRS, Institut des Sciences de l’Évolution de Montpellier, UMR 5554, 34090 Montpellier, France
| | - Min Li
- Laboratory of Insect Systematics and Evolutionary Biology, College of Life Sciences, Jiangxi Normal University, Nanchang 330022, China
| | - Meicai Wei
- Laboratory of Insect Systematics and Evolutionary Biology, College of Life Sciences, Jiangxi Normal University, Nanchang 330022, China
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Claramunt S. CladeDate
: Calibration information generator for divergence time estimation. Methods Ecol Evol 2022. [DOI: 10.1111/2041-210x.13977] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Santiago Claramunt
- Department of Natural History Royal Ontario Museum Toronto Ontario Canada
- Department of Ecology and Evolutionary Biology University of Toronto Toronto Ontario Canada
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41
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Asar Y, Ho SYW, Sauquet H. Early diversifications of angiosperms and their insect pollinators: were they unlinked? TRENDS IN PLANT SCIENCE 2022; 27:858-869. [PMID: 35568622 DOI: 10.1016/j.tplants.2022.04.004] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Revised: 03/24/2022] [Accepted: 04/05/2022] [Indexed: 06/15/2023]
Abstract
The present-day ubiquity of angiosperm-insect pollination has led to the hypothesis that these two groups coevolved early in their evolutionary history. However, recent fossil discoveries and fossil-calibrated molecular dating analyses challenge the notion that early diversifications of angiosperms and insects were inextricably linked. In this article, we examine (i) the discrepancies between dates of emergence for angiosperms and major clades of insects; (ii) the long history of gymnosperm-insect pollination modes, which likely shaped early angiosperm-insect pollination mutualisms; and (iii) how the K-Pg (Cretaceous-Paleogene) mass extinction event was vital in propelling modern angiosperm-insect mutualisms. We posit that the early diversifications of angiosperms and their insect pollinators were largely decoupled until the end of the Cretaceous.
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Affiliation(s)
- Yasmin Asar
- School of Life and Environmental Sciences, University of Sydney, Sydney, NSW 2006, Australia.
| | - Simon Y W Ho
- School of Life and Environmental Sciences, University of Sydney, Sydney, NSW 2006, Australia
| | - Hervé Sauquet
- National Herbarium of New South Wales (NSW), Royal Botanic Gardens and Domain Trust, Sydney, NSW 2000, Australia; Evolution and Ecology Research Centre, School of Biological, Earth, and Environmental Sciences, University of New South Wales, Sydney, NSW 2052, Australia
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42
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Heritage S, Seiffert ER. Total evidence time-scaled phylogenetic and biogeographic models for the evolution of sea cows (Sirenia, Afrotheria). PeerJ 2022; 10:e13886. [PMID: 36042864 PMCID: PMC9420408 DOI: 10.7717/peerj.13886] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Accepted: 07/21/2022] [Indexed: 01/18/2023] Open
Abstract
Molecular phylogenetic studies that have included sirenians from the genera Trichechus, Dugong, and Hydrodamalis have resolved their interrelationships but have yielded divergence age estimates that are problematically discordant. The ages of these lineage splits have profound implications for how to interpret the sirenian fossil record-including clade membership, biogeographic patterns, and correlations with Earth history events. In an effort to address these issues, here we present a total evidence phylogenetic analysis of Sirenia that includes living and fossil species and applies Bayesian tip-dating methods to estimate their interrelationships and divergence times. In addition to extant sirenians, our dataset includes 56 fossil species from 106 dated localities and numerous afrotherian outgroup taxa. Genetic, morphological, temporal, and biogeographic data are assessed simultaneously to bring all available evidence to bear on sirenian phylogeny. The resulting time-tree is then used for Bayesian geocoordinates reconstruction analysis, which models ancestral geographic areas at splits throughout the phylogeny, thereby allowing us to infer the direction and timing of dispersals. Our results suggest that Pan-Sirenia arose in North Africa during the latest Paleocene and that the Eocene evolution of stem sirenians was primarily situated in the Tethyan realm. In the late Eocene, some lineages moved into more northern European latitudes, an area that became the source region for a key trans-Atlantic dispersal towards the Caribbean and northern-adjacent west Atlantic. This event led to the phylogenetic and biogeographic founding of crown Sirenia with the Dugongidae-Trichechidae split occurring at the Eocene-Oligocene boundary (~33.9 Ma), temporally coincident with the onset of dropping global sea levels and temperatures. This region became the nexus of sirenian diversification and supported taxonomically-rich dugongid communities until the earliest Pliocene. The Dugonginae-Hydrodamalinae split occurred near Florida during the early Miocene (~21.2 Ma) and was followed by a west-bound dispersal that gave rise to the Pacific hydrodamalines. The late middle Miocene (~12.2 Ma) split of Dugong from all other dugongines also occurred near Florida and our analyses suggest that the Indo-Pacific distribution of modern dugongs is the result of a trans-Pacific dispersal. From at least the early Miocene, trichechid evolution was based entirely in South America, presumably within the Pebas Wetlands System. We infer that the eventual establishment of Amazon drainage into the South Atlantic allowed the dispersal of Trichechus out of South America no earlier than the mid-Pliocene. Our analyses provide a new temporal and biogeographic framework for understanding major events in sirenian evolution and their possible relationships to oceanographic and climatic changes. These hypotheses can be further tested with the recovery and integration of new fossil evidence.
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Affiliation(s)
- Steven Heritage
- Duke Lemur Center Museum of Natural History, Duke University, Durham, NC, USA
| | - Erik R. Seiffert
- Duke Lemur Center Museum of Natural History, Duke University, Durham, NC, USA,Department of Integrative Anatomical Sciences, Keck School of Medicine of USC, University of Southern California, Los Angeles, CA, USA,Department of Mammalogy, Natural History Museum of Los Angeles County, Los Angeles, CA, USA
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43
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Simões TR, Kammerer CF, Caldwell MW, Pierce SE. Successive climate crises in the deep past drove the early evolution and radiation of reptiles. SCIENCE ADVANCES 2022; 8:eabq1898. [PMID: 35984885 PMCID: PMC9390993 DOI: 10.1126/sciadv.abq1898] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
Climate change-induced mass extinctions provide unique opportunities to explore the impacts of global environmental disturbances on organismal evolution. However, their influence on terrestrial ecosystems remains poorly understood. Here, we provide a new time tree for the early evolution of reptiles and their closest relatives to reconstruct how the Permian-Triassic climatic crises shaped their long-term evolutionary trajectory. By combining rates of phenotypic evolution, mode of selection, body size, and global temperature data, we reveal an intimate association between reptile evolutionary dynamics and climate change in the deep past. We show that the origin and phenotypic radiation of reptiles was not solely driven by ecological opportunity following the end-Permian extinction as previously thought but also the result of multiple adaptive responses to climatic shifts spanning 57 million years.
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Affiliation(s)
- Tiago R. Simões
- Museum of Comparative Zoology and Department of Organismic and Evolutionary Biology, Harvard University, 26 Oxford St., Cambridge, MA 02138, USA
- Corresponding author.
| | - Christian F. Kammerer
- North Carolina Museum of Natural Sciences, 11 W. Jones Street, Raleigh, NC 27601, USA
- Department of Biological Sciences, North Carolina State University, Campus Box 7617, Raleigh, NC 27695, USA
| | - Michael W. Caldwell
- Department of Biological Sciences, University of Alberta, 11645 Saskatchewan Drive, Edmonton, Alberta T6G 2E9, Canada
- Department of Earth and Atmospheric Sciences, University of Alberta, 11645 Saskatchewan Drive, Edmonton, Alberta T6G 2E9, Canada
| | - Stephanie E. Pierce
- Museum of Comparative Zoology and Department of Organismic and Evolutionary Biology, Harvard University, 26 Oxford St., Cambridge, MA 02138, USA
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Zhou W, Jenny Xiang QY. Phylogenomics and Biogeography of Castanea (Chestnut) and Hamamelis (Witch-hazel) - Choosing between RAD-seq and Hyb-Seq Approaches. Mol Phylogenet Evol 2022; 176:107592. [DOI: 10.1016/j.ympev.2022.107592] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Revised: 06/18/2022] [Accepted: 07/20/2022] [Indexed: 10/31/2022]
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45
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Flouri T, Huang J, Jiao X, Kapli P, Rannala B, Yang Z. Bayesian phylogenetic inference using relaxed-clocks and the multispecies coalescent. Mol Biol Evol 2022; 39:6652437. [PMID: 35907248 PMCID: PMC9366188 DOI: 10.1093/molbev/msac161] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
The multispecies coalescent (MSC) model accommodates both species divergences and within-species coalescent and provides a natural framework for phylogenetic analysis of genomic data when the gene trees vary across the genome. The MSC model implemented in the program bpp assumes a molecular clock and the Jukes–Cantor model, and is suitable for analyzing genomic data from closely related species. Here we extend our implementation to more general substitution models and relaxed clocks to allow the rate to vary among species. The MSC-with-relaxed-clock model allows the estimation of species divergence times and ancestral population sizes using genomic sequences sampled from contemporary species when the strict clock assumption is violated, and provides a simulation framework for evaluating species tree estimation methods. We conducted simulations and analyzed two real datasets to evaluate the utility of the new models. We confirm that the clock-JC model is adequate for inference of shallow trees with closely related species, but it is important to account for clock violation for distant species. Our simulation suggests that there is valuable phylogenetic information in the gene-tree branch lengths even if the molecular clock assumption is seriously violated, and the relaxed-clock models implemented in bpp are able to extract such information. Our Markov chain Monte Carlo algorithms suffer from mixing problems when used for species tree estimation under the relaxed clock and we discuss possible improvements. We conclude that the new models are currently most effective for estimating population parameters such as species divergence times when the species tree is fixed.
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Affiliation(s)
- Tomáš Flouri
- Department of Genetics, Evolution, and Environment, University College London, Gower Street, London WC1E 6BT, UK
| | - Jun Huang
- Department of Genetics, Evolution, and Environment, University College London, Gower Street, London WC1E 6BT, UK.,School of Biomedical Engineering, Capital Medical University, Beijing, 100069, China
| | - Xiyun Jiao
- Department of Genetics, Evolution, and Environment, University College London, Gower Street, London WC1E 6BT, UK.,Department of Statistics and Data Science, China Southern University of Science and Technology, Shenzhen, Guangdong 518055, China
| | - Paschalia Kapli
- Department of Genetics, Evolution, and Environment, University College London, Gower Street, London WC1E 6BT, UK
| | - Bruce Rannala
- Department of Evolution and Ecology, University of California, Davis, CA 95616, USA
| | - Ziheng Yang
- Department of Genetics, Evolution, and Environment, University College London, Gower Street, London WC1E 6BT, UK
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46
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Püschel HP, Bertrand OC, Reilly JEO, Bobe R, Püschel TA. Reply to: Modelling hominin evolution requires accurate hominin data. Nat Ecol Evol 2022; 6:1092-1094. [PMID: 35788711 DOI: 10.1038/s41559-022-01792-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Accepted: 05/17/2022] [Indexed: 11/09/2022]
Affiliation(s)
- Hans P Püschel
- School of GeoSciences, University of Edinburgh, Grant Institute, Edinburgh, UK.
| | - Ornella C Bertrand
- School of GeoSciences, University of Edinburgh, Grant Institute, Edinburgh, UK
| | - Joseph E O' Reilly
- MRC Human Genetics Unit, MRC Institute of Genetics & Molecular Medicine, University of Edinburgh, Western General Hospital, Edinburgh, UK
| | - René Bobe
- Primate Models for Behavioural Evolution Lab, Institute of Human Sciences, School of Anthropology, University of Oxford, Oxford, UK.,Gorongosa National Park, Sofala, Mozambique
| | - Thomas A Püschel
- Primate Models for Behavioural Evolution Lab, Institute of Human Sciences, School of Anthropology, University of Oxford, Oxford, UK. .,School of Biological Sciences, University of Reading, Reading, UK.
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47
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Beck RM, Voss RS, Jansa SA. Craniodental Morphology and Phylogeny of Marsupials. BULLETIN OF THE AMERICAN MUSEUM OF NATURAL HISTORY 2022. [DOI: 10.1206/0003-0090.457.1.1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Affiliation(s)
- Robin M.D. Beck
- School of Science, Engineering and Environment University of Salford, U.K. School of Biological, Earth & Environmental Sciences University of New South Wales, Australia Division of Vertebrate Zoology (Mammalogy) American Museum of Natural History
| | - Robert S. Voss
- Division of Vertebrate Zoology (Mammalogy) American Museum of Natural History
| | - Sharon A. Jansa
- Bell Museum and Department of Ecology, Evolution, and Behavior University of Minnesota
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48
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Sauquet H, Ramírez-Barahona S, Magallón S. What is the age of flowering plants? JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:3840-3853. [PMID: 35438718 DOI: 10.1093/jxb/erac130] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Accepted: 03/31/2022] [Indexed: 06/14/2023]
Abstract
The origin of flowering plants (angiosperms) was one of the most transformative events in the history of our planet. Despite considerable interest from multiple research fields, numerous questions remain, including the age of the group as a whole. Recent studies have reported a perplexing range of estimates for the crown-group age of angiosperms, from ~140 million years (Ma; Early Cretaceous) to 270 Ma (Permian). Both ends of the spectrum are now supported by both macroevolutionary analyses of the fossil record and fossil-calibrated molecular dating analyses. Here, we first clarify and distinguish among the three ages of angiosperms: the age of their divergence with acrogymnosperms (stem age); the age(s) of emergence of their unique, distinctive features including flowers (morphological age); and the age of the most recent common ancestor of all their living species (crown age). We then demonstrate, based on recent studies, that fossil-calibrated molecular dating estimates of the crown-group age of angiosperms have little to do with either the amount of molecular data or the number of internal fossil calibrations included. Instead, we argue that this age is almost entirely conditioned by its own prior distribution (typically a calibration density set by the user in Bayesian analyses). Lastly, we discuss which future discoveries or novel types of analyses are most likely to bring more definitive answers. In the meantime, we propose that the age of angiosperms is best described as largely unknown (140-270 Ma) and that contrasting age estimates in the literature mostly reflect conflicting prior distributions. We also suggest that future work that depends on the time scale of flowering plant diversification be designed to integrate over this vexing uncertainty.
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Affiliation(s)
- Hervé Sauquet
- National Herbarium of New South Wales (NSW), Royal Botanic Gardens and Domain Trust, Sydney, Australia
- Evolution and Ecology Research Centre, School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, Australia
| | | | - Susana Magallón
- Instituto de Biología, Universidad Nacional Autónoma de México, Ciudad de México, México
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49
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Wang SQ, Ye J, Meng J, Li C, Costeur L, Mennecart B, Zhang C, Zhang J, Aiglstorfer M, Wang Y, Wu Y, Wu WY, Deng T. Sexual selection promotes giraffoid head-neck evolution and ecological adaptation. Science 2022; 376:eabl8316. [PMID: 35653459 DOI: 10.1126/science.abl8316] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The long neck of the giraffe has been held as a classic example of adaptive evolution since Darwin's time. Here we report on an unusual fossil giraffoid, Discokeryx xiezhi, from the early Miocene, which has an unusual disk-shaped headgear and the most complicated head-neck joints in known mammals. The distinctive morphology and our finite element analyses indicate an adaptation for fierce head-butting behavior. Tooth enamel isotope data suggest that D. xiezhi occupied a niche different from that of other herbivores, comparable to the characteristic high-level browsing niche of modern giraffes. The study shows that giraffoids exhibit a higher headgear diversity than other ruminants and that living in specific ecological niches may have fostered various intraspecific combat behaviors that resulted in extreme head-neck morphologies in different giraffoid lineages.
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Affiliation(s)
- Shi-Qi Wang
- Key Laboratory of Vertebrate Evolution and Human Origins of Chinese Academy of Sciences, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences (CAS), Beijing 100044, China.,CAS Center for Excellence in Life and Paleoenvironment, Beijing 100101, China
| | - Jie Ye
- Key Laboratory of Vertebrate Evolution and Human Origins of Chinese Academy of Sciences, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences (CAS), Beijing 100044, China.,CAS Center for Excellence in Life and Paleoenvironment, Beijing 100101, China
| | - Jin Meng
- American Museum of Natural History, New York, NY 10024, USA
| | - Chunxiao Li
- Key Laboratory of Vertebrate Evolution and Human Origins of Chinese Academy of Sciences, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences (CAS), Beijing 100044, China.,CAS Center for Excellence in Life and Paleoenvironment, Beijing 100101, China.,College of Earth and Planetary Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Loïc Costeur
- Naturhistorisches Museum Basel, 4001 Basel, Switzerland
| | - Bastien Mennecart
- Naturhistorisches Museum Basel, 4001 Basel, Switzerland.,Naturhistorisches Museum Wien, Vienna 1010, Austria
| | - Chi Zhang
- Key Laboratory of Vertebrate Evolution and Human Origins of Chinese Academy of Sciences, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences (CAS), Beijing 100044, China.,CAS Center for Excellence in Life and Paleoenvironment, Beijing 100101, China
| | - Ji Zhang
- School of Civil and Hydraulic Engineering, Huazhong University of Science and Technology, Wuhan 430047, China.,Department of Civil and Environmental Engineering, University of California, Berkeley, CA 94720, USA
| | - Manuela Aiglstorfer
- Naturhistorisches Museum Mainz/Landessammlung für Naturkunde Rheinland-Pfalz, 55116 Mainz, Germany
| | - Yang Wang
- Department of Earth, Ocean, and Atmospheric Science, Florida State University, Tallahassee, FL 32306, USA.,National High Magnetic Field Laboratory, Tallahassee, FL 32310, USA
| | - Yan Wu
- Key Laboratory of Vertebrate Evolution and Human Origins of Chinese Academy of Sciences, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences (CAS), Beijing 100044, China.,CAS Center for Excellence in Life and Paleoenvironment, Beijing 100101, China
| | - Wen-Yu Wu
- Key Laboratory of Vertebrate Evolution and Human Origins of Chinese Academy of Sciences, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences (CAS), Beijing 100044, China.,CAS Center for Excellence in Life and Paleoenvironment, Beijing 100101, China
| | - Tao Deng
- Key Laboratory of Vertebrate Evolution and Human Origins of Chinese Academy of Sciences, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences (CAS), Beijing 100044, China.,CAS Center for Excellence in Life and Paleoenvironment, Beijing 100101, China.,College of Earth and Planetary Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
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50
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Ecological radiations of insects in the Mesozoic. Trends Ecol Evol 2022; 37:529-540. [PMID: 35287981 DOI: 10.1016/j.tree.2022.02.007] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2022] [Revised: 02/18/2022] [Accepted: 02/22/2022] [Indexed: 01/02/2023]
Abstract
The Mesozoic is a key era for the rise of the modern insect fauna. Among the most important evolutionary events in Mesozoic insects are the radiation of holometabolous insects, the origin of eusocial and parasitoid insects, diversification of pollinating insects, and development of advanced mimicry and camouflage. These events are closely associated with the diversification of insect ecological behaviors and colonization of new ecospaces. At the same time, insects had evolved more complex and closer ecological associations with various plants and animals. Mesozoic insects played a key and underappreciated ecological role in reconstructing and maintaining terrestrial ecosystems. A greater understanding of the history of insects may help to mitigate future changes in insect diversity and abundance.
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