700086cf579a50f2dbfcf7bae08e1442 sysbio_a2025m7v74n4p672.pdf ac8cda4e4a2899c7bd871ac459593982fbb1557c sysbio_a2025m7v74n4p672.pdf f9007e04f61f6041d6e3d67f1ac9c966853b986d8e9fefaa6b3a4972c73a2309 sysbio_a2025m7v74n4p672.pdf Title: PlaceMyFossils: An Integrative Approach to Analyze and Visualize the Phylogenetic Placement of Fossils Using Backbone Trees Subject: DOI: 10.1093/sysbio/syaf025 Systematic Biology, Volume. XX, Issue. XX, 17 April 2025 Associate Editor: Seraina Klopfstein Abstract.—In recent years, there has been a growing interest in using morphology to establish the placement of species on phylogenetic trees derived from molecular data. This is relevant in the case of recently extinct or fossil species, which are usually represented only by fragmentary morphology. In the latter case, constrained analyses using backbone trees have also proven helpful in evaluating the placement of fragmentary specimens on phylogenetic trees derived from morphological data. Consequently, several available phylogenetic programs now include functions to run constrained searches. However, a comprehensive evaluation of the obtained results is not readily available within existing analytical tools. Here, we present an integrated approach—PlaceMyFossils—specifically designed to (i) thoroughly evaluate the phylogenetic placement of given query species (especially fossils) on a reference tree, (ii) determine which characters and character partitions are most relevant in defining the phylogenetic placement, (iii) assess the confidence of the results, and (iv) define the optimal analytical conditions to place the query species. PlaceMyFossils combines several analyses implemented as an interactive script for TNT (Tree Analysis Using New Technologies software), a popular—and free—phylogenetic software that is widely used in paleontological studies. Finally, we demonstrate the utility and investigate the performance of PlaceMyFossils compared to other available tools using two disparate empirical datasets drawn from conifers and dinosaurs. While primarily designed for working with fossils, this tool also holds great potential for advancing morphological and molecular systematics. It offers a powerful resource for empirical systematists aiming to integrate molecular and morphological data. This is particularly relevant given the growing interest in morphological evolution as a complementary perspective on evolutionary processes and the drivers of diversification. [Keywords: backbone topology; error in placement; fossils; maximum likelihood; maximum parsimony; molecular scaffolds.] Author: Santiago A. 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HideMenubar: false HideWindowUI: false FitWindow: false CenterWindow: false DisplayDocTitle: false NonFullScreenPageMode: UseNone Direction: L2R ViewArea: CropBox ViewClip: CropBox PrintArea: CropBox PageClip: CropBox PageLayout: SinglePage PageMode: UseNone Language: en-US Outlines: Item: Title: PlaceMyFossils: An Integrative Approach to Analyze and Visualize the Phylogenetic Placement of Fossils Using Backbone Trees Children: Item: Title: PlaceMyFossils Description Children: Item: Title: Assessing and Visualizing the Placement of Fossil Species Item: Title: Multiple Optimality Criteria Analysis Item: Title: Sensitivity Analysis Item: Title: Characters and Character Partitions Analysis Item: Title: LOOV Analysis Item: Title: EP and Subtree Error Analyses Item: Title: Handling Multiple Reference Trees Item: Title: Effect of Query Species on Reference Topology Item: Title: Empirical Examples Children: Item: Title: Araucariaceae Example Item: Title: Dinosaurs Example Item: Title: Discussion and Final Remarks Item: Title: SUPPLEMENTARY MATERIAL Item: Title: Acknowledgments Item: Title: References Info: Title: PlaceMyFossils: An Integrative Approach to Analyze and Visualize the Phylogenetic Placement of Fossils Using Backbone Trees Author: Santiago A. Catalano Subject: DOI: 10.1093/sysbio/syaf025 Systematic Biology, Volume. XX, Issue. XX, 17 April 2025 Associate Editor: Seraina Klopfstein Abstract. In recent years, there has been a growing interest in using morphology to establish the placement of species on phylogenetic trees derived from molecular data. This is relevant in the case of recently extinct or fossil species, which are usually represented only by fragmentary morphology. In the latter case, constrained analyses using backbone trees have also proven helpful in evaluating the placement of fragmentary specimens on phylogenetic trees derived from morphological data. Consequently, several available phylogenetic programs now include functions to run constrained searches. However, a comprehensive evaluation of the obtained results is not readily available within existing analytical tools. Here, we present an integrated approach PlaceMyFossils specifically designed to (i) thoroughly evaluate the phylogenetic placement of given query species (especially fossils) on a reference tree, (ii) determine which characters and character partitions are most relevant in defining the phylogenetic placement, (iii) assess the confidence of the results, and (iv) define the optimal analytical conditions to place the query species. PlaceMyFossils combines several analyses implemented as an interactive script for TNT (Tree Analysis Using New Technologies software), a popular and free phylogenetic software that is widely used in paleontological studies. Finally, we demonstrate the utility and investigate the performance of PlaceMyFossils compared to other available tools using two disparate empirical datasets drawn from conifers and dinosaurs. While primarily designed for working with fossils, this tool also holds great potential for advancing morphological and molecular systematics. It offers a powerful resource for empirical systematists aiming to integrate molecular and morphological data. This is particularly relevant given the growing interest in morphological evolution as a complementary perspective on evolutionary processes and the drivers of diversification. [Keywords: backbone topology; error in placement; fossils; maximum likelihood; maximum parsimony; molecular scaffolds.] Creator: Adobe InDesign 15.1 (Windows) Producer: Adobe PDF Library 15.0; modified using iTextSharp.LGPLv2.Core 3.7.4.0 CreationDate: Fri Jul 25 08:58:46 CEST 2025 ModDate: Thu Jan 08 10:45:05 CET 2026 Trapped: False ID: 0xb2ff23d895b09eabe8f7fddfbebfd9c7, 0xaa63c6f575493ce49cd7758f6495dcd8 Filters: FilterPipeline: FlateDecode FilterPipeline: DCTDecode Images: Image: NisoImageMetadata: FormatName: image/jpg CompressionScheme: JPEG ImageWidth: 1384 ImageHeight: 761 ColorSpace: CMYK BitsPerSample: 8 BitsPerSampleUnit: integer Intent: RelativeColorimetric Name: X Image: NisoImageMetadata: FormatName: image/png ImageWidth: 1127 ImageHeight: 1633 ColorSpace: CMYK BitsPerSample: 8 BitsPerSampleUnit: integer Filter: FlateDecode Intent: RelativeColorimetric Name: X Image: NisoImageMetadata: FormatName: image/png ImageWidth: 275 ImageHeight: 83 BitsPerSample: 8 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FontDescriptor: FontName: EKMZHF+PalatinoLTStd-Roman Flags: Serif, Symbolic FontBBox: -166, -283, 1021, 927 FontFile3: true XMP: application/pdf PlaceMyFossils: An Integrative Approach to Analyze and Visualize the Phylogenetic Placement of Fossils Using Backbone Trees DOI: 10.1093/sysbio/syaf025 Systematic Biology, Volume. XX, Issue. XX, 17 April 2025 Associate Editor: Seraina Klopfstein Abstract.—In recent years, there has been a growing interest in using morphology to establish the placement of species on phylogenetic trees derived from molecular data. This is relevant in the case of recently extinct or fossil species, which are usually represented only by fragmentary morphology. In the latter case, constrained analyses using backbone trees have also proven helpful in evaluating the placement of fragmentary specimens on phylogenetic trees derived from morphological data. Consequently, several available phylogenetic programs now include functions to run constrained searches. However, a comprehensive evaluation of the obtained results is not readily available within existing analytical tools. Here, we present an integrated approach—PlaceMyFossils—specifically designed to (i) thoroughly evaluate the phylogenetic placement of given query species (especially fossils) on a reference tree, (ii) determine which characters and character partitions are most relevant in defining the phylogenetic placement, (iii) assess the confidence of the results, and (iv) define the optimal analytical conditions to place the query species. PlaceMyFossils combines several analyses implemented as an interactive script for TNT (Tree Analysis Using New Technologies software), a popular—and free—phylogenetic software that is widely used in paleontological studies. Finally, we demonstrate the utility and investigate the performance of PlaceMyFossils compared to other available tools using two disparate empirical datasets drawn from conifers and dinosaurs. While primarily designed for working with fossils, this tool also holds great potential for advancing morphological and molecular systematics. It offers a powerful resource for empirical systematists aiming to integrate molecular and morphological data. This is particularly relevant given the growing interest in morphological evolution as a complementary perspective on evolutionary processes and the drivers of diversification. [Keywords: backbone topology; error in placement; fossils; maximum likelihood; maximum parsimony; molecular scaffolds.] © The Author(s) 2025. Published by Oxford University Press on behalf of the Society of Systematic Biologists. Santiago A. Catalano Ignacio Escapa Kelsey D. Pugh Ashley S. Hammond Pablo Goloboff Sergio Almécija Seraina Klopfstein backbone topology error in placement fossils maximum likelihood maximum parsimony molecular scaffolds. 2025-07-25T11:58:46+05:30 Adobe InDesign 15.1 (Windows) 2026-01-08T09:45:05+00:00 2026-01-08T09:45:05+00:00 uuid:e62ffd6a-03cf-4cb8-acc6-1d2fdcb05bcb xmp.did:6dd139a7-58da-1a4b-ab7b-5c391ae5c64f xmp.id:e8179c4e-3cce-7f43-928e-95c958b7452d proof:pdf 1 xmp.iid:d95f794c-1089-c644-a9fc-73b77de57555 xmp.did:4094c89a-2f11-0247-b068-d97723e16257 default converted from application/x-indesign to application/pdf Adobe InDesign 15.1 (Windows) 2025-07-25T11:58:46+05:30 converted uuid:9fbeb439-6375-4dcb-a3ff-927edb13e113 converted to PDF/A-3a Preflight 2025-07-25T13:11:24+05:30 converted uuid:4cbb23e0-9bc4-4eed-bc62-f8589477f14b PDF/A conversion failed; Version and conformance level identification removed Preflight 2025-07-25T13:11:28+05:30 True Adobe PDF Library 15.0; modified using iTextSharp.LGPLv2.Core 3.7.4.0 False 1 http://ns.adobe.com/pdf/1.3/ pdf Adobe PDF Schema internal A name object indicating whether the document has been modified to include trapping information Trapped Text http://ns.adobe.com/xap/1.0/mm/ xmpMM XMP Media Management Schema internal UUID based identifier for specific incarnation of a document InstanceID URI internal The common identifier for all versions and renditions of a document. 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