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      Testing Species Assignments in Extant Terebratulide Brachiopods: A Three-dimensional Geometric Morphometric Analysis of Long-Looped Brachidia

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          Abstract

          Species of terebratulide brachiopods have been largely characterized qualitatively on the basis of morphology. Furthermore, species-level morphological variability has rarely been analyzed within a quantitative framework. The objective of our research is to quantify morphological variation to test the validity of extant named species of terebratulide brachiopods, focusing on the lophophore-supporting structures—the “long loops.” Long loops are the most distinctive and complex morphological feature in terebratellidine brachiopods and are considered to be phylogenetically and taxonomically informative. We studied eight species with problematic species identities in three genera distributed in the North Pacific: Laqueus, Terebratalia, and Dallinella. Given how geometrically complex long loops are, we generated 3D models from computed tomography (CT) scans of specimens of these eight species and analyzed them using 3D geometric morphometrics. Our goal was to determine ranges of variation and to test whether species are clearly distinguishable from one another in morphospace and statistically. Previous studies have suggested that some species might be overly split and are indistinguishable. Our results show that these extant species of terebratellidines can be reliably distinguished on the basis of quantitative loop morphometrics. Using 3D geometric morphometric methods, we demonstrate the utility of CT beyond purely descriptive imaging purposes in testing the morphometric validity of named species. It is crucial to treat species described and named from qualitative morphology as working hypotheses to be tested; many macroevolutionary studies depend upon the accurate assessment of species in order to identify and seek to explain macroevolutionary patterns. Our results provide quantitative documentation of the distinction of these species and thus engender greater confidence in their use to characterize macroevolutionary patterns among extant terebratellidine brachiopods. These methods, however, require further testing in extinct terebratellidines, which only rarely preserve the delicate long loop in three dimensions. In addition, molecular analyses of extant terebratellidines will test the species delimitations supported by the morphometric analyses presented in this study. [Species determination; morphological variability; 3D geometric morphometrics; terebratulide brachiopods; long loops.]

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          Geometric Morphometrics

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            Revisiting metazoan phylogeny with genomic sampling of all phyla

            Proper biological interpretation of a phylogeny can sometimes hinge on the placement of key taxa—or fail when such key taxa are not sampled. In this light, we here present the first attempt to investigate (though not conclusively resolve) animal relationships using genome-scale data from all phyla. Results from the site-heterogeneous CAT + GTR model recapitulate many established major clades, and strongly confirm some recent discoveries, such as a monophyletic Lophophorata, and a sister group relationship between Gnathifera and Chaetognatha, raising continued questions on the nature of the spiralian ancestor. We also explore matrix construction with an eye towards testing specific relationships; this approach uniquely recovers support for Panarthropoda, and shows that Lophotrochozoa (a subclade of Spiralia) can be constructed in strongly conflicting ways using different taxon- and/or orthologue sets. Dayhoff-6 recoding sacrifices information, but can also reveal surprising outcomes, e.g. full support for a clade of Lophophorata and Entoprocta + Cycliophora, a clade of Placozoa + Cnidaria, and raising support for Ctenophora as sister group to the remaining Metazoa, in a manner dependent on the gene and/or taxon sampling of the matrix in question. Future work should test the hypothesis that the few remaining uncertainties in animal phylogeny might reflect violations of the various stationarity assumptions used in contemporary inference methods.
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              Distances and directions in multidimensional shape spaces: implications for morphometric applications.

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                Author and article information

                Contributors
                Role: ConceptualizationRole: Data curationRole: Formal analysisRole: Funding acquisitionRole: InvestigationRole: MethodologyRole: Project administrationRole: ResourcesRole: SoftwareRole: ValidationRole: VisualizationRole: Writing – original draftRole: Writing – review & editing
                Role: ConceptualizationRole: Funding acquisitionRole: SupervisionRole: Writing – review & editing
                Role: Editor
                Journal
                PLoS One
                PLoS ONE
                plos
                plosone
                PLoS ONE
                Public Library of Science (San Francisco, CA USA )
                1932-6203
                27 November 2019
                2019
                : 14
                : 11
                : e0225528
                Affiliations
                [001]Department of Earth and Planetary Sciences, University of California, Davis, CA, United States of America
                Laboratoire de Biologie du Développement de Villefranche-sur-Mer, FRANCE
                Author notes

                Competing Interests: The authors have declared that no competing interests exist.

                Author information
                http://orcid.org/0000-0002-1393-2902
                Article
                PONE-D-19-18706
                10.1371/journal.pone.0225528
                6881017
                31774831
                3c4b9e34-c77a-4df6-a64e-387998f5c85b
                © 2019 López Carranza, Carlson

                This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

                History
                : 3 July 2019
                : 6 November 2019
                Page count
                Figures: 7, Tables: 5, Pages: 20
                Funding
                Funded by: funder-id http://dx.doi.org/10.13039/100000076, Directorate for Biological Sciences;
                Award ID: EAR 1147537
                Award Recipient : Sandra J. Carlson
                Funded by: NSF Division of Environmental Biology
                Award ID: DEB 1747704
                Award Recipient : Sandra J. Carlson
                Funded by: Consejo Nacional de Ciencia y Tecnología
                Award Recipient :
                Funded by: University of California Institute for Mexico and the United States (UCMEXUS)
                Award Recipient :
                Funded by: Secretaría de Educación Pública (SEP)
                Award Recipient :
                This work was partially supported by grants from the National Science Foundation (EAR 1147537 and DEB 1747704) to S.J. Carlson and the University of California, Davis Department of Earth and Planetary Sciences and Cordell Durrell Funds to N. López Carranza. N. López Carranza gratefully acknowledges support from Consejo Nacional de Ciencia y Tecnología (CONACYT), the University of California Institute for Mexico and the United States (UCMEXUS), and Secretaría de Educación Pública (SEP, México). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
                Categories
                Research Article
                Research and Analysis Methods
                Imaging Techniques
                Morphometry
                Research and Analysis Methods
                Mathematical and Statistical Techniques
                Statistical Methods
                Multivariate Analysis
                Principal Component Analysis
                Physical Sciences
                Mathematics
                Statistics
                Statistical Methods
                Multivariate Analysis
                Principal Component Analysis
                Biology and Life Sciences
                Paleontology
                Biostratigraphy
                Index Fossils
                Brachiopods
                Earth Sciences
                Paleontology
                Biostratigraphy
                Index Fossils
                Brachiopods
                Earth Sciences
                Geology
                Stratigraphy
                Biostratigraphy
                Index Fossils
                Brachiopods
                Biology and Life Sciences
                Paleontology
                Fossils
                Index Fossils
                Brachiopods
                Earth Sciences
                Paleontology
                Fossils
                Index Fossils
                Brachiopods
                Biology and Life Sciences
                Evolutionary Biology
                Evolutionary Systematics
                Phylogenetics
                Biology and Life Sciences
                Taxonomy
                Evolutionary Systematics
                Phylogenetics
                Computer and Information Sciences
                Data Management
                Taxonomy
                Evolutionary Systematics
                Phylogenetics
                Biology and Life Sciences
                Taxonomy
                Computer and Information Sciences
                Data Management
                Taxonomy
                Biology and Life Sciences
                Paleontology
                Fossils
                Fossil Record
                Earth Sciences
                Paleontology
                Fossils
                Fossil Record
                Biology and Life Sciences
                Paleontology
                Fossils
                Earth Sciences
                Paleontology
                Fossils
                Research and Analysis Methods
                Imaging Techniques
                Neuroimaging
                Computed Axial Tomography
                Biology and Life Sciences
                Neuroscience
                Neuroimaging
                Computed Axial Tomography
                Medicine and Health Sciences
                Diagnostic Medicine
                Diagnostic Radiology
                Tomography
                Computed Axial Tomography
                Research and Analysis Methods
                Imaging Techniques
                Diagnostic Radiology
                Tomography
                Computed Axial Tomography
                Medicine and Health Sciences
                Radiology and Imaging
                Diagnostic Radiology
                Tomography
                Computed Axial Tomography
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