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Some hybridization events resulted in mitochondrial introgression between distant lineages, likely facilitated by cointrogression of coadapted nuclear variants. Although the genomic landscapes of introgression were largely lineage specific, we found that genes with immune functions were overrepresented in introgressing regions, in line with adaptive introgression, whereas genes involved in pigmentation and morphology may contribute to reproductive isolation. In line with reports from other systems that hybridization might facilitate diversification, we find that some of the most species-rich guenon clades are of admixed origin. This study provides important insights into the prevalence, role, and outcomes of ancestral hybridization in a large mammalian radiation. Keywords: phylogenomics; speciation; ancient hybridization; evolutionary genomics; mammalian radiation; guenon Author: Axel Jensen Creator: Servigistics Arbortext Advanced Print Publisher 11.1.4546/W-x64 Producer: PDFlib+PDI 9.0.7p3 (C++/Win64); modified using iTextSharp 4.1.6 by 1T3XT CreationDate: Thu Nov 30 02:25:30 2023 CET ModDate: Wed Dec 20 14:07:45 2023 CET Tagged: yes UserProperties: no Suspects: no Form: AcroForm JavaScript: no Pages: 19 Encrypted: no Page size: 595.276 x 782.362 pts Page rot: 0 File size: 9101903 bytes Optimized: no PDF version: 1.6 name type encoding emb sub uni object ID ------------------------------------ ----------------- ---------------- --- --- --- --------- RFENSN+CronosPro-Italic Type 1C Custom yes yes yes 50 0 KJXUDN+CronosPro-BoldIt Type 1C Custom yes yes yes 2197 0 GZWBWR+CronosPro-Bold Type 1C Custom yes yes yes 51 0 KKRQJX+CronosPro-Regular Type 1C Custom yes yes yes 52 0 UMDSOZ+CronosPro-Semibold Type 1C Custom yes yes yes 2198 0 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Destination: secmsad247-s1.2 Item: Title: Mitonuclear Discordances Suggest Ancient Hybridization Destination: secmsad247-s1.3 Item: Title: Ancient Gene Flow is Prevalent Among Guenons Destination: secmsad247-s1.4 Item: Title: A Combination of Introgression and ILS Best Explains Mitonuclear Discordances Destination: secmsad247-s1.5 Item: Title: Mitochondrial Introgression Across Deeply Divergent Lineages was Facilitated by the Co-sorting of Alleles in Nuclear Genes With Mitonuclear Interacting Functions Destination: secmsad247-s1.6 Item: Title: Admixed Genomes are a Mosaic of Different Ancestries With Elevated Heterozygosity in Introgressed Regions Destination: secmsad247-s1.7 Item: Title: Introgressed Regions Show Low Repeatability Across Independent Gene Flow Events and are Enriched for Immune Genes Destination: secmsad247-s1.8 Item: Title: Introgression Deserts Contain Genes Encoding Morphological Traits Destination: secmsad247-s1.9 Item: Title: Discussion Destination: secmsad247-s2 Item: Title: Materials and Methods Destination: secmsad247-s3 Children: Item: Title: Mapping and Variant Calling Destination: secmsad247-s3.1 Item: Title: Phylogenetic Inferences Destination: secmsad247-s3.2 Children: Item: Title: Autosomal and X-chromosomal Trees Destination: secmsad247-s3.2.1 Item: Title: Mitochondrial Genome Assembly and mtDNA Phylogenic Tree Destination: secmsad247-s3.2.2 Item: Title: Phylogenetic Simulations to Explore the Role of ILS Destination: secmsad247-s3.2.3 Item: Title: Y-chromosome Phylogenetic Tree Destination: secmsad247-s3.2.4 Item: Title: Gene Flow Destination: secmsad247-s3.3 Children: Item: Title: D-statistics Destination: secmsad247-s3.3.1 Item: Title: Phylogenetic Networks Destination: secmsad247-s3.3.2 Item: Title: Reconstructing Ancestral Chromosome Numbers Destination: secmsad247-s3.4 Item: Title: Characterizing and Comparing the Introgression Landscapes Destination: secmsad247-s3.5 Item: Title: The Effect of Introgression on Species Divergence Time Estimates Destination: secmsad247-s3.6 Item: Title: Coevolution/introgression of Mitonuclear Genes Destination: secmsad247-s3.7 Item: Title: Supplementary Material Destination: secmsad247-s4 Item: Title: Acknowledgments Destination: acknow Item: Title: Author Contributions Destination: secmsad247-s5 Item: Title: Data Availability Destination: secmsad247-s6 Item: Title: References Destination: reflist Info: Title: Complex Evolutionary History With Extensive Ancestral Gene Flow in an African Primate Radiation Author: Axel Jensen Subject: DOI: 10.1093/molbev/msad247; Molecular Biology and Evolution, 40, 12, 2023-11-21.; Abstract: Understanding the drivers of speciation is fundamental in evolutionary biology, and recent studies highlight hybridization as an important evolutionary force. Using whole-genome sequencing data from 22 species of guenons (tribe Cercopithecini), one of the world's largest primate radiations, we show that rampant gene flow characterizes their evolutionary history and identify ancient hybridization across deeply divergent lineages that differ in ecology, morphology, and karyotypes. Some hybridization events resulted in mitochondrial introgression between distant lineages, likely facilitated by cointrogression of coadapted nuclear variants. Although the genomic landscapes of introgression were largely lineage specific, we found that genes with immune functions were overrepresented in introgressing regions, in line with adaptive introgression, whereas genes involved in pigmentation and morphology may contribute to reproductive isolation. In line with reports from other systems that hybridization might facilitate diversification, we find that some of the most species-rich guenon clades are of admixed origin. This study provides important insights into the prevalence, role, and outcomes of ancestral hybridization in a large mammalian radiation. Keywords: phylogenomics; speciation; ancient hybridization; evolutionary genomics; mammalian radiation; guenon Creator: Servigistics Arbortext Advanced Print Publisher 11.1.4546/W-x64 Producer: PDFlib+PDI 9.0.7p3 (C++/Win64); modified using iTextSharp 4.1.6 by 1T3XT CreationDate: Thu Nov 30 02:55:30 CET 2023 ModDate: Wed Dec 20 14:07:45 CET 2023 ID: 0x89f174ae1e44902288357441acb581cd, 0xebab2b69d9ea7b862f9805c2901ff4f1 Filters: FilterPipeline: FlateDecode Fonts: Type0: Font: BaseFont: UHESJH+Cronos-Light Encoding: Identity-H ToUnicode: true Font: BaseFont: GVRWFB+TimesNewRomanPSMT Encoding: Identity-H ToUnicode: true Type1: Font: BaseFont: MBOWUI+STIXGeneral-Regular FontSubset: true FirstChar: 1 LastChar: 10 FontDescriptor: FontName: MBOWUI+STIXGeneral-Regular Flags: Nonsymbolic FontBBox: -995, -455, 2000, 1055 FontFile3: true EncodingDictionary: BaseEncoding: WinAnsiEncoding Differences: true ToUnicode: true Font: BaseFont: RFENSN+CronosPro-Italic FontSubset: true FirstChar: 1 LastChar: 62 FontDescriptor: FontName: RFENSN+CronosPro-Italic Flags: Nonsymbolic, Italic FontBBox: -191, -281, 1129, 880 FontFile3: true EncodingDictionary: BaseEncoding: WinAnsiEncoding Differences: true ToUnicode: true Font: BaseFont: GZWBWR+CronosPro-Bold FontSubset: true FirstChar: 1 LastChar: 57 FontDescriptor: FontName: GZWBWR+CronosPro-Bold Flags: Nonsymbolic, ForceBold FontBBox: -187, -295, 1137, 885 FontFile3: true EncodingDictionary: BaseEncoding: WinAnsiEncoding Differences: true ToUnicode: true Font: BaseFont: KKRQJX+CronosPro-Regular FontSubset: true FirstChar: 1 LastChar: 99 FontDescriptor: FontName: KKRQJX+CronosPro-Regular Flags: Nonsymbolic FontBBox: -179, -270, 1129, 886 FontFile3: true EncodingDictionary: BaseEncoding: WinAnsiEncoding Differences: true ToUnicode: true Font: BaseFont: KJXUDN+CronosPro-BoldIt FontSubset: true FirstChar: 1 LastChar: 10 FontDescriptor: FontName: KJXUDN+CronosPro-BoldIt Flags: Nonsymbolic, Italic, ForceBold FontBBox: -189, -312, 1137, 886 FontFile3: true EncodingDictionary: BaseEncoding: WinAnsiEncoding Differences: true ToUnicode: true Font: BaseFont: UMDSOZ+CronosPro-Semibold FontSubset: true FirstChar: 1 LastChar: 30 FontDescriptor: FontName: UMDSOZ+CronosPro-Semibold Flags: Nonsymbolic FontBBox: -185, -287, 1135, 885 FontFile3: true EncodingDictionary: BaseEncoding: WinAnsiEncoding Differences: true ToUnicode: true Font: BaseFont: Times_rm FirstChar: 33 LastChar: 251 FontDescriptor: FontName: Times_rm Flags: Symbolic FontBBox: -50, -180, 1000, 720 FontFile: true ToUnicode: true TrueType: Font: BaseFont: ATRTAZ+ArialMT FontSubset: true FirstChar: 32 LastChar: 121 FontDescriptor: FontName: ATRTAZ+ArialMT Flags: Nonsymbolic FontBBox: -664, -324, 2000, 1039 FontFile2: true Encoding: WinAnsiEncoding CIDFontType2: Font: BaseFont: GVRWFB+TimesNewRomanPSMT CIDSystemInfo: Registry: Adobe Registry: Identity Supplement: 0 FontDescriptor: FontName: GVRWFB+TimesNewRomanPSMT Flags: Nonsymbolic FontBBox: -568, -307, 2046, 1040 FontFile2: true Font: BaseFont: UHESJH+Cronos-Light CIDSystemInfo: Registry: Adobe Registry: Identity Supplement: 0 FontDescriptor: FontName: UHESJH+Cronos-Light Flags: Nonsymbolic FontBBox: -175, -250, 914, 822 FontFile2: true XMP: uuid:fbe7c5af-4979-40c5-acaf-854f64d45a0e uuid:1E490DAB-8151-D837-9725-EEA9D522C12E True phylogenomics; speciation; ancient hybridization; evolutionary genomics; mammalian radiation; guenon PDFlib+PDI 9.0.7p3 (C++/Win64); modified using iTextSharp 4.1.6 by 1T3XT application/pdf 10.1093/molbev/msad247 en Oxford University Press Complex Evolutionary History With Extensive Ancestral Gene Flow in an African Primate Radiation Axel Jensen Frances Swift Dorien de Vries Robin M.D. Beck Lukas F.K. Kuderna Sascha Knauf Idrissa S. Chuma Julius D. Keyyu Andrew C. Kitchener Kyle Farh Jeffrey Rogers Tomas Marques-Bonet Kate M. Detwiler Christian Roos Katerina Guschanski DOI: 10.1093/molbev/msad247; Molecular Biology and Evolution, 40, 12, 2023-11-21.; Abstract: Understanding the drivers of speciation is fundamental in evolutionary biology, and recent studies highlight hybridization as an important evolutionary force. Using whole-genome sequencing data from 22 species of guenons (tribe Cercopithecini), one of the world's largest primate radiations, we show that rampant gene flow characterizes their evolutionary history and identify ancient hybridization across deeply divergent lineages that differ in ecology, morphology, and karyotypes. Some hybridization events resulted in mitochondrial introgression between distant lineages, likely facilitated by cointrogression of coadapted nuclear variants. Although the genomic landscapes of introgression were largely lineage specific, we found that genes with immune functions were overrepresented in introgressing regions, in line with adaptive introgression, whereas genes involved in pigmentation and morphology may contribute to reproductive isolation. In line with reports from other systems that hybridization might facilitate diversification, we find that some of the most species-rich guenon clades are of admixed origin. This study provides important insights into the prevalence, role, and outcomes of ancestral hybridization in a large mammalian radiation. © The Author(s) 2023. Published by Oxford University Press on behalf of Society for Molecular Biology and Evolution. phylogenomics speciation ancient hybridization evolutionary genomics mammalian radiation guenon Journal Molecular Biology and Evolution © The Author(s) 2023. 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