38701cd58d3f1a35e7adf09948951fa6 genes-14-00743-v3.pdf a2f178ffafac5bc15f1ab9e303d56afa9a8e95bb genes-14-00743-v3.pdf 0081ff37673e7d2db2c5eb6bc2569fdf8e61e45b045e51b27ec2065ab5f12294 genes-14-00743-v3.pdf Title: Past Connectivity but Recent Inbreeding in Cross River Gorillas Determined Using Whole Genomes from Single Hairs Subject: The critically endangered western gorillas (Gorilla gorilla) are divided into two subspecies: the western lowland (G. g. gorilla) and the Cross River (G. g. diehli) gorilla. Given the difficulty in sampling wild great ape populations and the small estimated size of the Cross River gorilla population, only one whole genome of a Cross River gorilla has been sequenced to date, hindering the study of this subspecies at the population level. In this study, we expand the number of whole genomes available for wild western gorillas, generating 41 new genomes (25 belonging to Cross River gorillas) using single shed hairs collected from gorilla nests. By combining these genomes with publicly available wild gorilla genomes, we confirm that Cross River gorillas form three population clusters. We also found little variation in genome-wide heterozygosity among them. Our analyses reveal long runs of homozygosity (>10 Mb), indicating recent inbreeding in Cross River gorillas. This is similar to that seen in mountain gorillas but with a much more recent bottleneck. We also detect past gene flow between two Cross River sites, Afi Mountain Wildlife Sanctuary and the Mbe Mountains. Furthermore, we observe past allele sharing between Cross River gorillas and the northern western lowland gorilla sites, as well as with the eastern gorilla species. This is the first study using single shed hairs from a wild species for whole genome sequencing to date. Taken together, our results highlight the importance of implementing conservation measures to increase connectivity among Cross River gorilla sites. Keywords: non-invasive; hairs; inbreeding; bottleneck; gene flow; wild gorillas; NGS; Cross River gorilla Author: Marina Alvarez-Estape, Harvinder Pawar, Claudia Fontsere, Amber E. Trujillo, Jessica L. Gunson, Richard A. Bergl, Magdalena Bermejo, Joshua M. Linder, Kelley McFarland, John F. Oates, Jacqueline L. Sunderland-Groves, Joseph Orkin, James P. Higham, Karine A. Viaud-Martinez, Esther Lizano and Tomas Marques-Bonet Creator: LaTeX with hyperref Producer: pdfTeX-1.40.21 CreationDate: Tue Mar 21 04:08:55 2023 CET ModDate: Wed Mar 22 07:45:18 2023 CET Tagged: no UserProperties: no Suspects: no Form: none JavaScript: no Pages: 15 Encrypted: no Page size: 595.276 x 841.89 pts (A4) Page rot: 0 File size: 1860756 bytes Optimized: no PDF version: 1.7 name type encoding emb sub uni object ID ------------------------------------ ----------------- ---------------- --- --- --- --------- IYDCBB+VnURWPalladioL Type 1 Custom yes yes no 10 0 IGSRFE+URWPalladioL-Bold Type 1 Custom yes yes no 15 0 IYNPSW+URWPalladioL-Roma Type 1 Custom yes yes no 20 0 DFJGFL+URWPalladioL-Ital Type 1 Custom yes yes no 24 0 KONDUX+EuphemiaUCAS-Bold Type 1C WinAnsi yes yes no 42 0 HIZBRM+TimesNewRomanPS-BoldItalicMT Type 1C WinAnsi yes yes no 45 0 VBAQIR+CMSY10 Type 1 Builtin yes yes no 70 0 OVNEXW+EURM10 Type 1 Builtin yes yes no 74 0 BCDEEE+PalatinoLinotype-Bold TrueType WinAnsi 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TrueType Identity-H yes yes yes 191 0 BCDJEE+PalatinoLinotype-Roman CID TrueType Identity-H yes yes yes 198 0 Jhove (Rel. 1.22.1, 2019-04-17) Date: 2023-04-21 02:26:37 CEST RepresentationInformation: genes-14-00743-v3.pdf ReportingModule: PDF-hul, Rel. 1.12.1 (2019-04-17) LastModified: 2023-04-17 14:22:19 CEST Size: 1860756 Format: PDF Version: 1.7 Status: Well-Formed and valid SignatureMatches: PDF-hul MIMEtype: application/pdf PDFMetadata: Objects: 495 FreeObjects: 1 IncrementalUpdates: 0 DocumentCatalog: PageLayout: SinglePage PageMode: UseNone Outlines: Item: Title: Introduction Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@44c8afef Item: Title: Materials and Methods Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@7b69c6ba Children: Item: Title: Samples, DNA Extraction, and Library Preparation Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@46daef40 Item: Title: Sequencing Data Processing (FASTQ to Genotypes/Likelihoods) Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@12f41634 Item: Title: Quality Control (Depth of Coverage and Contamination) Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@13c27452 Item: Title: Genotype Likelihoods and SNP Calling Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@262b2c86 Item: Title: Genetic Sexing from Coverage Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@371a67ec Item: Title: Relatedness Test Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@5ed828d Item: Title: Population Structure Assessment Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@50d0686 Item: Title: Heterozygosity Estimates Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@7a3d45bd Item: Title: Estimation of Runs of Homozygosity and Inbreeding Coefficients Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@1e7c7811 Item: Title: Past and Present Demographic History Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@77ec78b9 Item: Title: Assessment of Gene Flow and Connectivity Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@1a3869f4 Item: Title: Results Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@a38d7a3 Children: Item: Title: Single Hairs as a Source for Genomic DNA Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@77f99a05 Item: Title: Increased Resolution of Western Gorilla Population Structure Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@63440df3 Item: Title: Genetic Diversity among Gorilla Species Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@3aeaafa6 Item: Title: Strong Bottleneck in Cross River Gorillas Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@76a3e297 Item: Title: Past Gene Flow among Gorilla Subspecies Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@4d3167f4 Item: Title: Discussion Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@ed9d034 Item: Title: References Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@6121c9d6 Info: Title: Past Connectivity but Recent Inbreeding in Cross River Gorillas Determined Using Whole Genomes from Single Hairs Author: Marina Alvarez-Estape, Harvinder Pawar, Claudia Fontsere, Amber E. Trujillo, Jessica L. Gunson, Richard A. Bergl, Magdalena Bermejo, Joshua M. Linder, Kelley McFarland, John F. Oates, Jacqueline L. Sunderland-Groves, Joseph Orkin, James P. Higham, Karine A. Viaud-Martinez, Esther Lizano and Tomas Marques-Bonet Subject: The critically endangered western gorillas (Gorilla gorilla) are divided into two subspecies: the western lowland (G. g. gorilla) and the Cross River (G. g. diehli) gorilla. Given the difficulty in sampling wild great ape populations and the small estimated size of the Cross River gorilla population, only one whole genome of a Cross River gorilla has been sequenced to date, hindering the study of this subspecies at the population level. In this study, we expand the number of whole genomes available for wild western gorillas, generating 41 new genomes (25 belonging to Cross River gorillas) using single shed hairs collected from gorilla nests. By combining these genomes with publicly available wild gorilla genomes, we confirm that Cross River gorillas form three population clusters. We also found little variation in genome-wide heterozygosity among them. Our analyses reveal long runs of homozygosity (>10 Mb), indicating recent inbreeding in Cross River gorillas. This is similar to that seen in mountain gorillas but with a much more recent bottleneck. We also detect past gene flow between two Cross River sites, Afi Mountain Wildlife Sanctuary and the Mbe Mountains. Furthermore, we observe past allele sharing between Cross River gorillas and the northern western lowland gorilla sites, as well as with the eastern gorilla species. This is the first study using single shed hairs from a wild species for whole genome sequencing to date. Taken together, our results highlight the importance of implementing conservation measures to increase connectivity among Cross River gorilla sites. Keywords: non-invasive; hairs; inbreeding; bottleneck; gene flow; wild gorillas; NGS; Cross River gorilla Creator: LaTeX with hyperref Producer: pdfTeX-1.40.21 CreationDate: Tue Mar 21 04:08:55 CET 2023 ModDate: Wed Mar 22 07:45:18 CET 2023 ID: 0xa1e85a0229bfd859b27d2f71df44b241, 0xa1e85a0229bfd859b27d2f71df44b241 Filters: FilterPipeline: FlateDecode Fonts: Type1: Font: BaseFont: IYNPSW+URWPalladioL-Roma FontSubset: true FirstChar: 2 LastChar: 252 FontDescriptor: FontName: IYNPSW+URWPalladioL-Roma Flags: Symbolic FontBBox: -166, -283, 1021, 943 FontFile: true EncodingDictionary: Differences: true Font: BaseFont: VBAQIR+CMSY10 FontSubset: true FirstChar: 0 LastChar: 21 FontDescriptor: FontName: VBAQIR+CMSY10 Flags: Symbolic FontBBox: -29, -960, 1116, 775 FontFile: true Font: BaseFont: DFJGFL+URWPalladioL-Ital FontSubset: true FirstChar: 2 LastChar: 150 FontDescriptor: FontName: DFJGFL+URWPalladioL-Ital Flags: Symbolic FontBBox: -170, -305, 1010, 941 FontFile: true EncodingDictionary: 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