b7158d0e459c823a9ae0ab8d2fcb35b8 pmc_10489743.pdf 6a1849dd904e9b6cd2e3bfd3026c76bfa7af17cb pmc_10489743.pdf 6aec4ff14b1f891a838419a124bc4557bc5609e3f0c1fd1e8967e52e4ec32662 pmc_10489743.pdf Title: African Mountain Thistles: Three New Genera in the Carduus-Cirsium Group Subject: The floras on the highest mountains in tropical eastern Africa are among the most unique floras in the world. Despite the exceptionally high concentration of endemic species, these floras remain understudied from an evolutionary point of view. In this study, we focus on the Carduus-Cirsium group (subtribe Carduinae) to unravel the evolutionary relationships of the species endemic to the tropical Afromontane and Afroalpine floras, aiming to improve the systematics of the group. We applied the Hyb-Seq approach using the Compositae1061 probe set on 190 samples (159 species), encompassing representatives of all genera of Carduinae. We used two recently developed pipelines that enabled the processing of raw sequence reads, identification of paralogous sequences and segregation into orthologous alignments. After the implementation of a missing data filter, we retained sequences from 986 nuclear loci and 177 plastid regions. Phylogenomic analyses were conducted using both concatenated and summary-coalescence methods. The resulting phylogenies were highly resolved and revealed three distinct evolutionary lineages consisting of the African species traditionally referred to as Carduus and Cirsium. Consequently, we propose the three new genera Afrocarduus, Afrocirsium and Nuriaea; the latter did notably not belong to the Carduus-Cirsium group. We detected some incongruences between the phylogenies based on concatenation vs. coalescence and on nuclear vs. plastid datasets, likely attributable to incomplete lineage sorting and/or hybridization. Keywords: Afroalpine; Afromontane; Carduinae; Carduus-Cirsium group; Hyb-Seq; systematics Author: Lucía D. Moreyra, Núria Garcia-Jacas, Cristina Roquet, Jennifer R. Ackerfield, Turan Arabacı, Carme Blanco-Gavaldà, Christian Brochmann, Juan Antonio Calleja, Tuncay Dirmenci, Kazumi Fujikawa, Mercè Galbany-Casals, Tiangang Gao, Abel Gizaw, Javier López-Alvarado, Iraj Mehregan, Roser Vilatersana, Bayram Yıldız, Frederik Leliaert, Alexey P. Seregin and Alfonso Susanna Creator: LaTeX with hyperref Producer: pdfTeX-1.40.21 CreationDate: Wed Aug 30 03:08:31 2023 CEST ModDate: Wed Aug 30 03:24:04 2023 CEST Tagged: no UserProperties: no Suspects: no Form: none JavaScript: no Pages: 22 Encrypted: no Page size: 595.276 x 841.89 pts (A4) Page rot: 0 File size: 4828175 bytes Optimized: no PDF version: 1.7 name type encoding emb sub uni object ID ------------------------------------ ----------------- ---------------- --- --- --- --------- JNOYHB+VnURWPalladioL Type 1 Custom yes yes no 10 0 IZQPWK+URWPalladioL-Bold Type 1 Custom yes yes no 15 0 SPPNKZ+URWPalladioL-Roma Type 1 Custom yes yes no 20 0 QAZYPL+URWPalladioL-Ital Type 1 Custom yes yes no 24 0 HALRXV+URWPalladioL-BoldItal Type 1 Custom yes yes no 28 0 STVZQP+VnURWPalladioL-Bold Type 1 Custom yes yes no 32 0 VTLKDP+TimesNewRomanPS-BoldItalicMT Type 1C WinAnsi yes yes no 51 0 HBERVQ+CMSY10 Type 1 Builtin yes yes no 84 0 BDHPEM+PalatinoLinotype,Bold TrueType WinAnsi yes yes no 101 0 BDHPEO+PalatinoLinotype TrueType WinAnsi yes yes no 104 0 BDHPFA+PalatinoLinotype,Italic TrueType WinAnsi yes yes no 107 0 BDHPEM+PalatinoLinotype,Bold TrueType WinAnsi yes yes no 126 0 BDHPEO+PalatinoLinotype TrueType WinAnsi yes yes no 129 0 BDHPFA+PalatinoLinotype,Italic TrueType WinAnsi yes yes no 132 0 BDHPEM+PalatinoLinotype,Bold TrueType WinAnsi yes yes no 148 0 BDHPEO+PalatinoLinotype TrueType WinAnsi yes yes no 151 0 BDHPFA+PalatinoLinotype,Italic TrueType WinAnsi yes yes no 154 0 BDHPEM+PalatinoLinotype,Bold TrueType WinAnsi yes yes no 169 0 BDHPEO+PalatinoLinotype TrueType WinAnsi yes yes no 172 0 BDHPFA+PalatinoLinotype,Italic TrueType WinAnsi yes yes no 175 0 OVNEXW+EURM10 Type 1 Builtin yes yes no 183 0 BDIABA+PalatinoLinotype TrueType MacRoman yes yes no 194 0 BDHPEM+PalatinoLinotype,Bold TrueType WinAnsi yes yes no 197 0 BDHPEN+PalatinoLinotype CID TrueType Identity-H yes yes yes 200 0 BDHPEO+PalatinoLinotype TrueType WinAnsi yes yes no 206 0 BDHPFA+PalatinoLinotype,Italic TrueType WinAnsi yes yes no 209 0 RLWFJE+VnURWPalladioL-Italic Type 1 Custom yes yes no 238 0 Jhove (Rel. 1.28.0, 2023-05-18) Date: 2024-02-02 02:32:59 CET RepresentationInformation: pmc_10489743.pdf ReportingModule: PDF-hul, Rel. 1.12.4 (2023-03-16) LastModified: 2023-09-27 02:18:00 CEST Size: 4828175 Format: PDF Version: 1.7 Status: Well-Formed and valid SignatureMatches: PDF-hul MIMEtype: application/pdf PDFMetadata: Objects: 543 FreeObjects: 1 IncrementalUpdates: 0 DocumentCatalog: PageLayout: SinglePage PageMode: UseNone Outlines: Item: Title: Introduction Destination: section.1 Item: Title: Results Destination: section.2 Children: Item: Title: Target Loci Recovery Destination: subsection.2.1 Item: Title: Phylogenetic Relationships Destination: subsection.2.2 Children: Item: Title: Nuclear Dataset Destination: subsubsection.2.2.1 Item: Title: Plastid Dataset Destination: subsubsection.2.2.2 Item: Title: Materials and Methods Destination: section.3 Children: Item: Title: Taxon Sampling Destination: subsection.3.1 Item: Title: DNA Extraction, Library, Capture and Sequencing Destination: subsection.3.2 Item: Title: Molecular Data Processing Destination: subsection.3.3 Item: Title: Phylogenetic Analyses Destination: subsection.3.4 Item: Title: Morphological Examination Destination: subsection.3.5 Item: Title: Discussion Destination: section.4 Children: Item: Title: Utility of Hyb-Seq and Incongruence between the Phylogenies Destination: subsection.4.1 Item: Title: The African Carduus and Cirsium Destination: subsection.4.2 Item: Title: The Carduus-Cirsium Group Destination: subsection.4.3 Item: Title: Taxonomic Proposal Destination: section.5 Item: Title: References Destination: section.A. Info: Title: African Mountain Thistles: Three New Genera in the Carduus-Cirsium Group Author: Lucía D. Moreyra, Núria Garcia-Jacas, Cristina Roquet, Jennifer R. Ackerfield, Turan Arabacı, Carme Blanco-Gavaldà, Christian Brochmann, Juan Antonio Calleja, Tuncay Dirmenci, Kazumi Fujikawa, Mercè Galbany-Casals, Tiangang Gao, Abel Gizaw, Javier López-Alvarado, Iraj Mehregan, Roser Vilatersana, Bayram Yıldız, Frederik Leliaert, Alexey P. Seregin and Alfonso Susanna Subject: The floras on the highest mountains in tropical eastern Africa are among the most unique floras in the world. Despite the exceptionally high concentration of endemic species, these floras remain understudied from an evolutionary point of view. In this study, we focus on the Carduus-Cirsium group (subtribe Carduinae) to unravel the evolutionary relationships of the species endemic to the tropical Afromontane and Afroalpine floras, aiming to improve the systematics of the group. We applied the Hyb-Seq approach using the Compositae1061 probe set on 190 samples (159 species), encompassing representatives of all genera of Carduinae. We used two recently developed pipelines that enabled the processing of raw sequence reads, identification of paralogous sequences and segregation into orthologous alignments. After the implementation of a missing data filter, we retained sequences from 986 nuclear loci and 177 plastid regions. Phylogenomic analyses were conducted using both concatenated and summary-coalescence methods. The resulting phylogenies were highly resolved and revealed three distinct evolutionary lineages consisting of the African species traditionally referred to as Carduus and Cirsium. Consequently, we propose the three new genera Afrocarduus, Afrocirsium and Nuriaea; the latter did notably not belong to the Carduus-Cirsium group. We detected some incongruences between the phylogenies based on concatenation vs. coalescence and on nuclear vs. plastid datasets, likely attributable to incomplete lineage sorting and/or hybridization. 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