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Suárez Menéndez M, Rivera-León VE, Robbins J, Berube M, Palsbøll PJ. PHFinder: assisted detection of point heteroplasmy in Sanger sequencing chromatograms. PeerJ 2023; 11:e16028. [PMID: 37744223 PMCID: PMC10516101 DOI: 10.7717/peerj.16028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Accepted: 08/13/2023] [Indexed: 09/26/2023] Open
Abstract
Heteroplasmy is the presence of two or more organellar genomes (mitochondrial or plastid DNA) in an organism, tissue, cell or organelle. Heteroplasmy can be detected by visual inspection of Sanger sequencing chromatograms, where it appears as multiple peaks of fluorescence at a single nucleotide position. Visual inspection of chromatograms is both consuming and highly subjective, as heteroplasmy is difficult to differentiate from background noise. Few software solutions are available to automate the detection of point heteroplasmies, and those that are available are typically proprietary, lack customization or are unsuitable for automated heteroplasmy assessment in large datasets. Here, we present PHFinder, a Python-based, open-source tool to assist in the detection of point heteroplasmies in large numbers of Sanger chromatograms. PHFinder automatically identifies point heteroplasmies directly from the chromatogram trace data. The program was tested with Sanger sequencing data from 100 humpback whales (Megaptera novaeangliae) tissue samples with known heteroplasmies. PHFinder detected most (90%) of the known heteroplasmies thereby greatly reducing the amount of visual inspection required. PHFinder is flexible and enables explicit specification of key parameters to infer double peaks (i.e., heteroplasmies).
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Affiliation(s)
- Marcos Suárez Menéndez
- Marine Evolution and Conservation, Groningen Institute for Evolutionary Life Sciences, University of Groningen, Groningen, The Netherlands
| | - Vania E. Rivera-León
- Marine Evolution and Conservation, Groningen Institute for Evolutionary Life Sciences, University of Groningen, Groningen, The Netherlands
| | - Jooke Robbins
- Center for Coastal Studies, Provincetown, MA, United States of America
| | - Martine Berube
- Marine Evolution and Conservation, Groningen Institute for Evolutionary Life Sciences, University of Groningen, Groningen, The Netherlands
- Center for Coastal Studies, Provincetown, MA, United States of America
| | - Per J. Palsbøll
- Marine Evolution and Conservation, Groningen Institute for Evolutionary Life Sciences, University of Groningen, Groningen, The Netherlands
- Center for Coastal Studies, Provincetown, MA, United States of America
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Suárez-Menéndez M, Bérubé M, Furni F, Rivera-León VE, Heide-Jørgensen MP, Larsen F, Sears R, Ramp C, Eriksson BK, Etienne RS, Robbins J, Palsbøll PJ. Wild pedigrees inform mutation rates and historic abundance in baleen whales. Science 2023; 381:990-995. [PMID: 37651509 DOI: 10.1126/science.adf2160] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Accepted: 07/25/2023] [Indexed: 09/02/2023]
Abstract
Phylogeny-based estimates suggesting a low germline mutation rate (μ) in baleen whales have influenced research ranging from assessments of whaling impacts to evolutionary cancer biology. We estimated μ directly from pedigrees in four baleen whale species for both the mitochondrial control region and nuclear genome. The results suggest values higher than those obtained through phylogeny-based estimates and similar to pedigree-based values for primates and toothed whales. Applying our estimate of μ reduces previous genetic-based estimates of preexploitation whale abundance by 86% and suggests that μ cannot explain low cancer rates in gigantic mammals. Our study shows that it is feasible to estimate μ directly from pedigrees in natural populations, with wide-ranging implications for ecological and evolutionary research.
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Affiliation(s)
- Marcos Suárez-Menéndez
- Groningen Institute for Evolutionary Life Sciences, University of Groningen, Groningen, Netherlands
| | - Martine Bérubé
- Groningen Institute for Evolutionary Life Sciences, University of Groningen, Groningen, Netherlands
- Center for Coastal Studies, Provincetown, MA, USA
| | - Fabrício Furni
- Groningen Institute for Evolutionary Life Sciences, University of Groningen, Groningen, Netherlands
| | - Vania E Rivera-León
- Groningen Institute for Evolutionary Life Sciences, University of Groningen, Groningen, Netherlands
| | | | - Finn Larsen
- National Institute of Aquatic Resources, Kongens Lyngby, Denmark
| | - Richard Sears
- Mingan Island Cetacean Study Inc., St. Lambert, Quebec, Canada
| | - Christian Ramp
- Mingan Island Cetacean Study Inc., St. Lambert, Quebec, Canada
- Scottish Oceans Institute, University of St. Andrews, St. Andrews, UK
| | - Britas Klemens Eriksson
- Groningen Institute for Evolutionary Life Sciences, University of Groningen, Groningen, Netherlands
| | - Rampal S Etienne
- Groningen Institute for Evolutionary Life Sciences, University of Groningen, Groningen, Netherlands
| | | | - Per J Palsbøll
- Groningen Institute for Evolutionary Life Sciences, University of Groningen, Groningen, Netherlands
- Center for Coastal Studies, Provincetown, MA, USA
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Rivera-León VE, Urbán J, Mizroch S, Brownell RL, Oosting T, Hao W, Palsbøll PJ, Bérubé M. Long-term isolation at a low effective population size greatly reduced genetic diversity in Gulf of California fin whales. Sci Rep 2019; 9:12391. [PMID: 31455830 PMCID: PMC6712047 DOI: 10.1038/s41598-019-48700-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2018] [Accepted: 08/06/2019] [Indexed: 11/09/2022] Open
Abstract
The Gulf of California, Mexico is home to many cetacean species, including a presumed resident population of fin whales, Balaenoptera physalus. Past studies reported very low levels of genetic diversity among Gulf of California fin whales and a significant level of genetic differentiation from con-specifics in the eastern North Pacific. The aim of the present study was to assess the degree and timing of the isolation of Gulf of California fin whales in a population genetic analysis of 18 nuclear microsatellite genotypes from 402 samples and 565 mitochondrial control region DNA sequences (including mitochondrial sequences retrieved from NCBI). The analyses revealed that the Gulf of California fin whale population was founded ~2.3 thousand years ago and has since remained at a low effective population size (~360) and isolated from the eastern North Pacific (Nem between 0.89-1.4). The low effective population size and high degree of isolation implied that Gulf of California fin whales are vulnerable to the negative effects of genetic drift, human-caused mortality and habitat change.
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Affiliation(s)
- Vania E Rivera-León
- Marine Evolution and Conservation, Groningen Institute of Evolutionary Life Sciences, University of Groningen, Nijenborgh 7, 9747 AG, Groningen, The Netherlands.
| | - Jorge Urbán
- Departamento de Ciencias Marinas y Costeras, Universidad Autónoma de Baja California Sur, Km 5.5 Carretera al Sur, 23081, La Paz, Baja California Sur, Mexico
| | - Sally Mizroch
- Blue Sea Research PO Box 15805, Seattle, WA, 98115, United States of America
| | - Robert L Brownell
- Southwest Fisheries Science Center, NOAA Fisheries, 34500 Highway 1, Monterey, CA, 93940, United States of America
| | - Tom Oosting
- Marine Evolution and Conservation, Groningen Institute of Evolutionary Life Sciences, University of Groningen, Nijenborgh 7, 9747 AG, Groningen, The Netherlands
| | - Wensi Hao
- Marine Evolution and Conservation, Groningen Institute of Evolutionary Life Sciences, University of Groningen, Nijenborgh 7, 9747 AG, Groningen, The Netherlands
| | - Per J Palsbøll
- Marine Evolution and Conservation, Groningen Institute of Evolutionary Life Sciences, University of Groningen, Nijenborgh 7, 9747 AG, Groningen, The Netherlands. .,Centre for Coastal Studies, 5 Holway Avenue, Provincetown, Massachusetts, 02657, United States of America.
| | - Martine Bérubé
- Marine Evolution and Conservation, Groningen Institute of Evolutionary Life Sciences, University of Groningen, Nijenborgh 7, 9747 AG, Groningen, The Netherlands. .,Centre for Coastal Studies, 5 Holway Avenue, Provincetown, Massachusetts, 02657, United States of America.
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