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Mennecart B, Dziomber I, Aiglstorfer M, Bibi F, DeMiguel D, Fujita M, Kubo MO, Laurens F, Meng J, Métais G, Müller B, Ríos M, Rössner GE, Sánchez IM, Schulz G, Wang S, Costeur L. Ruminant inner ear shape records 35 million years of neutral evolution. Nat Commun 2022; 13:7222. [PMID: 36473836 PMCID: PMC9726890 DOI: 10.1038/s41467-022-34656-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2021] [Accepted: 11/02/2022] [Indexed: 12/12/2022] Open
Abstract
Extrinsic and intrinsic factors impact diversity. On deep-time scales, the extrinsic impact of climate and geology are crucial, but poorly understood. Here, we use the inner ear morphology of ruminant artiodactyls to test for a deep-time correlation between a low adaptive anatomical structure and both extrinsic and intrinsic variables. We apply geometric morphometric analyses in a phylogenetic frame to X-ray computed tomographic data from 191 ruminant species. Contrasting results across ruminant clades show that neutral evolutionary processes over time may strongly influence the evolution of inner ear morphology. Extant, ecologically diversified clades increase their evolutionary rate with decreasing Cenozoic global temperatures. Evolutionary rate peaks with the colonization of new continents. Simultaneously, ecologically restricted clades show declining or unchanged rates. These results suggest that both climate and paleogeography produced heterogeneous environments, which likely facilitated Cervidae and Bovidae diversification and exemplifies the effect of extrinsic and intrinsic factors on evolution in ruminants.
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Affiliation(s)
- Bastien Mennecart
- Naturhistorisches Museum Basel, Augustinergasse 2, 4001, Basel, Switzerland.
| | - Ilya Dziomber
- Institute of Plant Sciences, University of Bern, 3013, Bern, Switzerland
- Oeschger Centre for Climate Change Research, University of Bern, 3012, Bern, Switzerland
| | - Manuela Aiglstorfer
- Naturhistorisches Museum Mainz / Landessammlung für Naturkunde Rheinland-Pfalz, Reichklarastraße 10, 55116, Mainz, Germany
| | - Faysal Bibi
- Museum für Naturkunde, Leibniz Institute for Evolution and Biodiversity Science, Berlin, 10115, Germany
| | - Daniel DeMiguel
- Fundación ARAID, Zaragoza, Spain
- Departamento de Ciencias de la Tierra, Área de Paleontología / Instituto Universitario de Investigación en Ciencias Ambientales de Aragón (IUCA). Universidad de Zaragoza, Pedro Cerbuna 12, 50009, Zaragoza, Spain
- Institut Català de Palaeontologia Miquel Crusafont (ICP), Edifici Z, c/de les columnes s/n, Universitat Autònoma de Barcelona, 08193, Cerdanyola del Vallès, Barcelona, Spain
| | - Masaki Fujita
- National Museum of Nature and Science, Tsukuba, Japan
| | - Mugino O Kubo
- Department of Natural Environmental Studies, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, Japan
| | - Flavie Laurens
- Swiss National Data and Service Center for the Humanities, 4123, Allschwil, Switzerland
| | - Jin Meng
- American Museum of Natural History, 10024 New York; Earth and Environmental Sciences, Graduate Center, City University of New York, New York, NY, 10016, USA
| | - Grégoire Métais
- CR2P - Centre de Recherche en Paléontologie - Paris, UMR 7207, CNRS, MNHN, Sorbonne Université. Muséum national d'Histoire naturelle, CP38, 8 rue Buffon, 75005, Paris, France
| | - Bert Müller
- Biomaterials Science Center, Department of Biomedical Engineering, University of Basel, Gewerbestrasse 14, 4123, Allschwil, Switzerland
| | - María Ríos
- Department of Earth Sciences, GeoBioTec, Nova School of Science and Technology, Universidade NOVA de Lisboa, Campus de Caparica, 2829-516, Caparica, Portugal
| | - Gertrud E Rössner
- Staatliche Naturwissenschaftliche Sammlungen Bayerns - Bayerische Staatssammlung für Paläontologie und Geologie, Richard-Wagner-Strasse 10, 80333, Munich, Germany
- Department für Geo- und Umweltwissenschaften, Paläontologie & Geobiologie, Ludwig-Maximilians-Universität München, Richard-Wagner-Strasse 10, 80333, Munich, Germany
| | - Israel M Sánchez
- Institut Català de Palaeontologia Miquel Crusafont (ICP), Edifici Z, c/de les columnes s/n, Universitat Autònoma de Barcelona, 08193, Cerdanyola del Vallès, Barcelona, Spain
| | - Georg Schulz
- Biomaterials Science Center, Department of Biomedical Engineering, University of Basel, Gewerbestrasse 14, 4123, Allschwil, Switzerland
- Micro- and Nanotomography Core Facility, Department of Biomedical Engineering, University of Basel Gewerbestrasse 14, 4123, Allschwil, Switzerland
| | - Shiqi Wang
- Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, 142 Xizhimenwai Street, Beijing, 100044, China
| | - Loïc Costeur
- Naturhistorisches Museum Basel, Augustinergasse 2, 4001, Basel, Switzerland
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Thioulouse J, Renaud S, Dufour AB, Dray S. Overcoming the Spurious Groups Problem in Between-Group PCA. Evol Biol 2021. [DOI: 10.1007/s11692-021-09550-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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Renaud S, Girard C, Dufour AB. Morphometric variance, evolutionary constraints and their change through time in Late Devonian Palmatolepis conodonts. Evolution 2021; 75:2911-2929. [PMID: 34396530 DOI: 10.1111/evo.14330] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2019] [Revised: 07/08/2021] [Accepted: 07/29/2021] [Indexed: 11/28/2022]
Abstract
Phenotypic variation is the raw material of evolution. Standing variation can facilitate response to selection along "lines of least evolutionary resistance", but selection itself might alter the structure of the variance. Shape was quantified using 2D geometric morphometrics in Palmatolepis conodonts through the Late Devonian period. Patterns of variance were characterized along the record by the variance-covariance matrix (P-matrix) and its first axis (Pmax). The Late Frasnian was marked by environmental oscillations culminating with the Frasnian/Famennian mass extinction. A shape response was associated with these fluctuations, together with a deflection of the Pmax and the P-matrix. Thereafter, along the Famennian, Palmatolepis mean shape shifted from broad elements with a large platform to slender elements devoid of platform. This shift in shape was associated with a reorientation of Pmax and the P-matrix, due to profound changes in the functioning of the elements selecting for new types of variants. Both cases provide empirical evidences that moving adaptive optimum can reorient phenotypic variation, boosting response to environmental changes. On such time scales, the question seems thus not to be whether the P-matrix is stable, but how it is varying in response to changes in selection regimes and shifts in adaptive optimum. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Sabrina Renaud
- Laboratoire de Biométrie et Biologie Evolutive, UMR 5558, CNRS, Université Claude Bernard Lyon 1, Université de Lyon, Villeurbanne, 69622, France
| | - Catherine Girard
- Institut des Sciences de l'Evolution de Montpellier (ISEM), Université de Montpellier, CNRS, EPHE, IRD, Montpellier, France
| | - Anne-Béatrice Dufour
- Laboratoire de Biométrie et Biologie Evolutive, UMR 5558, CNRS, Université Claude Bernard Lyon 1, Université de Lyon, Villeurbanne, 69622, France
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Del Bove A, Profico A, Riga A, Bucchi A, Lorenzo C. A geometric morphometric approach to the study of sexual dimorphism in the modern human frontal bone. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2020; 173:643-654. [PMID: 33025582 DOI: 10.1002/ajpa.24154] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2019] [Revised: 08/28/2020] [Accepted: 09/13/2020] [Indexed: 01/15/2023]
Abstract
OBJECTIVES We analyzed the main anatomical traits found in the human frontal bone by using a geometric morphometric approach. The objectives of this study are to explore how the frontal bone morphology varies between the sexes and to detect which part of the frontal bone are sexually dimorphic. MATERIALS AND METHODS The sample is composed of 161 skulls of European and North American individuals of known sex. For each cranium, we collected 3D landmarks and semilandmarks on the frontal bone, to examine the entire morphology and separate modules (frontal squama, supraorbital ridges, glabellar region, temporal lines, and mid-sagittal profile). We used Procrustes ANOVAs and LDAs (linear discriminant analyses) to evaluate the relation between frontal bone morphology and sexual dimorphism and to calculate precision and accuracy in the classification of sex. RESULTS All the frontal bone traits are influenced by sexual dimorphism, though each in a different manner. Variation in shape and size differs between the sexes, and this study confirmed that the supraorbital ridges and glabella are the most important regions for sex determination, although there is no covariation between them. The variable size does not contribute significantly to the discrimination between sexes. Thanks to a geometric morphometric analysis, it was found that the size variable is not an important element for the determination of sex in the frontal bone. CONCLUSION The usage of geometric morphometrics in analyzing the frontal bone has led to new knowledge on the morphological variations due to sexual dimorphism. The proposed protocol permits to quantify morphological covariation between modules, to calculate the shape variations related to sexual dimorphism including or omitting the variable size.
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Affiliation(s)
- Antonietta Del Bove
- Àrea de Prehistòria, Facultat de Lletres, Universitat Rovira i Virgili, Tarragona, Spain.,Catalan Institute of Human Paleoecology and Social Evolution IPHES, Tarragona, Spain
| | - Antonio Profico
- PalaeoHub-Department of Archaeology, University of York, York, UK
| | - Alessandro Riga
- Department of Biology, University of Florence, Florence, Italy.,Laboratory of Archaeoanthropology, SABAP-FI, Scandicci, Italy
| | - Ana Bucchi
- Àrea de Prehistòria, Facultat de Lletres, Universitat Rovira i Virgili, Tarragona, Spain.,Catalan Institute of Human Paleoecology and Social Evolution IPHES, Tarragona, Spain
| | - Carlos Lorenzo
- Àrea de Prehistòria, Facultat de Lletres, Universitat Rovira i Virgili, Tarragona, Spain.,Catalan Institute of Human Paleoecology and Social Evolution IPHES, Tarragona, Spain
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Galeta P, Lázničková-Galetová M, Sablin M, Germonpré M. Morphological evidence for early dog domestication in the European Pleistocene: New evidence from a randomization approach to group differences. Anat Rec (Hoboken) 2020; 304:42-62. [PMID: 32869467 DOI: 10.1002/ar.24500] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2019] [Revised: 05/25/2020] [Accepted: 05/26/2020] [Indexed: 12/26/2022]
Abstract
The antiquity of the wolf/dog domestication has been recently pushed back in time from the Late Upper Paleolithic (~14,000 years ago) to the Early Upper Paleolithic (EUP; ~36,000 years ago). Some authors questioned this early dog domestication claiming that the putative (EUP) Paleolithic dogs fall within the morphological range of recent wolves. In this study, we reanalyzed a data set of large canid skulls using unbalanced- and balanced-randomized discriminant analyses to assess whether the putative Paleolithic dogs are morphologically unique or whether they represent a subsample of the wolf morpho-population. We evaluated morphological differences between 96 specimens of the 4 a priori reference groups (8 putative Paleolithic dogs, 41 recent northern dogs, 7 Pleistocene wolves, and 40 recent northern wolves) using discriminant analysis based on 5 ln-transformed raw and allometrically size-adjusted cranial measurements. Putative Paleolithic dogs are classified with high accuracies (87.5 and 100.0%, cross-validated) and randomization experiment suggests that these classification rates cannot be exclusively explained by the small and uneven sample sizes of reference groups. It indicates that putative Upper Paleolithic dogs may represent a discrete canid group with morphological signs of domestication (a relatively shorter skull and wider palate and braincase) that distinguish them from sympatric Pleistocene wolves. The present results add evidence to the view that these specimens could represent incipient Paleolithic dogs that were involved in daily activities of European Upper Paleolithic forager groups.
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Affiliation(s)
- Patrik Galeta
- Department of Anthropology, University of West Bohemia, Pilsen, Czech Republic
| | - Martina Lázničková-Galetová
- Department of Anthropology, University of West Bohemia, Pilsen, Czech Republic.,The Moravian Museum, Brno, Czech Republic
| | - Mikhail Sablin
- Zoological Institute, Russian Academy of Sciences, Saint-Petersburg, Russia
| | - Mietje Germonpré
- Operational Direction "Earth and History of Life", Royal Belgian Institute of Natural Sciences, Brussels, Belgium
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Zhang X, Ritchie SR, Chang H, Arnold DL, Jackson RW, Rainey PB. Genotypic and phenotypic analyses reveal distinct population structures and ecotypes for sugar beet-associated Pseudomonas in Oxford and Auckland. Ecol Evol 2020; 10:5963-5975. [PMID: 32607204 PMCID: PMC7319117 DOI: 10.1002/ece3.6334] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Revised: 04/09/2020] [Accepted: 04/14/2020] [Indexed: 01/02/2023] Open
Abstract
Fluorescent pseudomonads represent one of the largest groups of bacteria inhabiting the surfaces of plants, but their genetic composition in planta is poorly understood. Here, we examined the population structure and diversity of fluorescent pseudomonads isolated from sugar beet grown at two geographic locations (Oxford, United Kingdom and Auckland, New Zealand). To seek evidence for niche adaptation, bacteria were sampled from three types of leaves (immature, mature, and senescent) and then characterized using a combination of genotypic and phenotypic analysis. We first performed multilocus sequence analysis (MLSA) of three housekeeping genes (gapA, gltA, and acnB) in a total of 152 isolates (96 from Oxford, 56 from Auckland). The concatenated sequences were grouped into 81 sequence types and 22 distinct operational taxonomic units (OTUs). Significant levels of recombination were detected, particularly for the Oxford isolates (rate of recombination to mutation (r/m) = 5.23 for the whole population). Subsequent ancestral analysis performed in STRUCTURE found evidence of six ancestral populations, and their distributions significantly differed between Oxford and Auckland. Next, their ability to grow on 95 carbon sources was assessed using the Biolog™ GN2 microtiter plates. A distance matrix was generated from the raw growth data (A 660) and subjected to multidimensional scaling (MDS) analysis. There was a significant correlation between substrate utilization profiles and MLSA genotypes. Both phenotypic and genotypic analyses indicated presence of a geographic structure for strains from Oxford and Auckland. Significant differences were also detected for MLSA genotypes between strains isolated from immature versus mature/senescent leaves. The fluorescent pseudomonads thus showed an ecotypic population structure, suggestive of adaptation to both geographic conditions and local plant niches.
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Affiliation(s)
- Xue‐Xian Zhang
- New Zealand Institute for Advanced StudyMassey UniversityAucklandNew Zealand
- School of Natural and Computational SciencesMassey UniversityAucklandNew Zealand
| | - Stephen R. Ritchie
- New Zealand Institute for Advanced StudyMassey UniversityAucklandNew Zealand
- Faculty of Medical and Health SciencesUniversity of AucklandAucklandNew Zealand
| | - Hao Chang
- New Zealand Institute for Advanced StudyMassey UniversityAucklandNew Zealand
| | - Dawn L. Arnold
- Centre for Research in BioscienceUniversity of the West of EnglandBristolUK
| | - Robert W. Jackson
- School of Biosciences and Birmingham Institute of Forest ResearchUniversity of BirminghamBirminghamUK
| | - Paul B. Rainey
- New Zealand Institute for Advanced StudyMassey UniversityAucklandNew Zealand
- Department of Microbial Population BiologyMax Planck Institute for Evolutionary BiologyPlönGermany
- Laboratoire de Génétique de l'Evolution, Chemistry, Biology and Innovation (CBI)UMR8231ESPCI ParisCNRSPSL Research UniversityParisFrance
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7
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Chevret P, Renaud S, Helvaci Z, Ulrich RG, Quéré J, Michaux JR. Genetic structure, ecological versatility, and skull shape differentiation in
Arvicola
water voles (Rodentia, Cricetidae). J ZOOL SYST EVOL RES 2020. [DOI: 10.1111/jzs.12384] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Pascale Chevret
- Laboratoire de Biométrie et Biologie Evolutive UMR 5558 CNRS Université Claude Bernard Lyon 1Université de Lyon Villeurbanne France
| | - Sabrina Renaud
- Laboratoire de Biométrie et Biologie Evolutive UMR 5558 CNRS Université Claude Bernard Lyon 1Université de Lyon Villeurbanne France
| | - Zeycan Helvaci
- Conservation Genetics Laboratory Institut de Botanique Liège Belgium
| | - Rainer G. Ulrich
- Institute of Novel and Emerging Infectious Diseases Friedrich‐Loeffler‐Institut Federal Research Institute for Animal Health Greifswald ‐ Insel Riems Germany
| | - Jean‐Pierre Quéré
- Centre de Biologie et Gestion des Populations (INRA/IRD/Cirad/Montpellier SupAgro)Campus International de Baillarguet Montferrier‐sur‐Lez Cedex France
| | - Johan R. Michaux
- Conservation Genetics Laboratory Institut de Botanique Liège Belgium
- CIRAD/INRA UMR117 ASTRECampus International de Baillarguet Montpellier Cedex France
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Renaud S, Delépine C, Ledevin R, Pisanu B, Quéré J, Hardouin EA. A sharp incisor tool for predator house mice back to the wild. J ZOOL SYST EVOL RES 2019. [DOI: 10.1111/jzs.12292] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Sabrina Renaud
- Laboratoire de Biométrie et Biologie Evolutive UMR5558 CNRS Université Lyon 1 Villeurbanne France
| | - Claire Delépine
- Laboratoire de Biométrie et Biologie Evolutive UMR5558 CNRS Université Lyon 1 Villeurbanne France
| | | | - Benoît Pisanu
- Centre d’Ecologie et des Sciences de la Conservation, UMR 7204, Sorbonne Universités Muséum National d’Histoire Naturelle, CNRS, Université Pierre et Marie Curie Paris France
| | - Jean‐Pierre Quéré
- Centre de Biologie et Gestion des Populations (INRA/IRD/Cirad/Montpellier SupAgro) Montferrier‐sur‐Lez Cedex France
| | - Emilie A. Hardouin
- Department of Life and Environmental Sciences, Faculty of Sciences and Technology Bournemouth University Poole UK
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Patterns and Constraints of Craniofacial Variation in Colobine Monkeys: Disentangling the Effects of Phylogeny, Allometry and Diet. Evol Biol 2019. [DOI: 10.1007/s11692-019-09469-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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Three-Dimensional Geometric Morphometrics in Paleoecology. VERTEBRATE PALEOBIOLOGY AND PALEOANTHROPOLOGY 2018. [DOI: 10.1007/978-3-319-94265-0_14] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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Renaud S, Hardouin EA, Quéré JP, Chevret P. Morphometric variations at an ecological scale: Seasonal and local variations in feral and commensal house mice. Mamm Biol 2017. [DOI: 10.1016/j.mambio.2017.04.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
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Renaud S, Alibert P, Auffray JC. Impact of Hybridization on Shape, Variation and Covariation of the Mouse Molar. Evol Biol 2016. [DOI: 10.1007/s11692-016-9391-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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