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Momeni J, Parejo M, Nielsen RO, Langa J, Montes I, Papoutsis L, Farajzadeh L, Bendixen C, Căuia E, Charrière JD, Coffey MF, Costa C, Dall'Olio R, De la Rúa P, Drazic MM, Filipi J, Galea T, Golubovski M, Gregorc A, Grigoryan K, Hatjina F, Ilyasov R, Ivanova E, Janashia I, Kandemir I, Karatasou A, Kekecoglu M, Kezic N, Matray ES, Mifsud D, Moosbeckhofer R, Nikolenko AG, Papachristoforou A, Petrov P, Pinto MA, Poskryakov AV, Sharipov AY, Siceanu A, Soysal MI, Uzunov A, Zammit-Mangion M, Vingborg R, Bouga M, Kryger P, Meixner MD, Estonba A. Authoritative subspecies diagnosis tool for European honey bees based on ancestry informative SNPs. BMC Genomics 2021; 22:101. [PMID: 33535965 PMCID: PMC7860026 DOI: 10.1186/s12864-021-07379-7] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Accepted: 01/08/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND With numerous endemic subspecies representing four of its five evolutionary lineages, Europe holds a large fraction of Apis mellifera genetic diversity. This diversity and the natural distribution range have been altered by anthropogenic factors. The conservation of this natural heritage relies on the availability of accurate tools for subspecies diagnosis. Based on pool-sequence data from 2145 worker bees representing 22 populations sampled across Europe, we employed two highly discriminative approaches (PCA and FST) to select the most informative SNPs for ancestry inference. RESULTS Using a supervised machine learning (ML) approach and a set of 3896 genotyped individuals, we could show that the 4094 selected single nucleotide polymorphisms (SNPs) provide an accurate prediction of ancestry inference in European honey bees. The best ML model was Linear Support Vector Classifier (Linear SVC) which correctly assigned most individuals to one of the 14 subspecies or different genetic origins with a mean accuracy of 96.2% ± 0.8 SD. A total of 3.8% of test individuals were misclassified, most probably due to limited differentiation between the subspecies caused by close geographical proximity, or human interference of genetic integrity of reference subspecies, or a combination thereof. CONCLUSIONS The diagnostic tool presented here will contribute to a sustainable conservation and support breeding activities in order to preserve the genetic heritage of European honey bees.
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Affiliation(s)
- Jamal Momeni
- Eurofins Genomics Europe Genotyping A/S (EFEG), (Former GenoSkan A/S), Aarhus, Denmark.
| | - Melanie Parejo
- Laboratory Genetics, University of the Basque Country (UPV/EHU), Leioa, Bilbao, Spain.,Swiss Bee Research Center, Agroscope, Bern, Switzerland
| | - Rasmus O Nielsen
- Eurofins Genomics Europe Genotyping A/S (EFEG), (Former GenoSkan A/S), Aarhus, Denmark
| | - Jorge Langa
- Laboratory Genetics, University of the Basque Country (UPV/EHU), Leioa, Bilbao, Spain
| | - Iratxe Montes
- Laboratory Genetics, University of the Basque Country (UPV/EHU), Leioa, Bilbao, Spain
| | - Laetitia Papoutsis
- Laboratory of Agricultural Zoology and Entomology, Agricultural University of Athens, Athens, Greece
| | - Leila Farajzadeh
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
| | - Christian Bendixen
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
| | - Eliza Căuia
- Institutul de Cercetare Dezvoltare pentru Apicultura SA, Bucharest, Romania
| | | | | | - Cecilia Costa
- CREA Research Centre for Agriculture and Environment, Bologna, Italy
| | | | | | | | - Janja Filipi
- Department of Ecology, Agronomy and Aquaculture, University of Zadar, Zadar, Croatia
| | | | | | - Ales Gregorc
- Faculty of Agriculture and Life Sciences, University of Maribor, Maribor, Slovenia
| | | | - Fani Hatjina
- Department of Apiculture, Agricultural Organization 'DEMETER', Thessaloniki, Greece
| | - Rustem Ilyasov
- Division of Life Sciences, Major of Biological Sciences, and Convergence Research Center for Insect Vectors, Incheon National University, Incheon, Korea.,Institute of Biochemistry and Genetics, Ufa Federal Research Centre of the Russian Academy of Sciences, Ufa, Russia
| | | | | | | | | | | | | | | | - David Mifsud
- Division of Rural Sciences and Food Systems, Institute of Earth Systems, University of Malta, Msida, Malta
| | - Rudolf Moosbeckhofer
- Österreichische Agentur für Gesundheit und Ernährungssicherheit GmbH, Wien, Austria
| | - Alexei G Nikolenko
- Institute of Biochemistry and Genetics, Ufa Federal Research Centre of the Russian Academy of Sciences, Ufa, Russia
| | | | - Plamen Petrov
- Agricultural University of Plovdiv, Plovdiv, Bulgaria
| | - M Alice Pinto
- Centro de Investigação de Montanha (CIMO), Instituto Politécnico de Bragança, Bragança, Portugal
| | - Aleksandr V Poskryakov
- Institute of Biochemistry and Genetics, Ufa Federal Research Centre of the Russian Academy of Sciences, Ufa, Russia
| | | | - Adrian Siceanu
- Institutul de Cercetare Dezvoltare pentru Apicultura SA, Bucharest, Romania
| | | | - Aleksandar Uzunov
- Landesbetrieb Landwirtschaft Hessen, Bee Institute Kirchhain, Kirchhain, Germany.,Faculty of Agricultural Sciences and Food, University Ss. Cyril and Methodius, Skopje, Republic of Macedonia
| | | | - Rikke Vingborg
- Eurofins Genomics Europe Genotyping A/S (EFEG), (Former GenoSkan A/S), Aarhus, Denmark
| | - Maria Bouga
- Laboratory of Agricultural Zoology and Entomology, Agricultural University of Athens, Athens, Greece
| | - Per Kryger
- Department of Agroecology, Aarhus University, Slagelse, Denmark
| | - Marina D Meixner
- Landesbetrieb Landwirtschaft Hessen, Bee Institute Kirchhain, Kirchhain, Germany
| | - Andone Estonba
- Laboratory Genetics, University of the Basque Country (UPV/EHU), Leioa, Bilbao, Spain.
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Hemmer‐Hansen J, Hüssy K, Baktoft H, Huwer B, Bekkevold D, Haslob H, Herrmann J, Hinrichsen H, Krumme U, Mosegaard H, Nielsen EE, Reusch TBH, Storr‐Paulsen M, Velasco A, von Dewitz B, Dierking J, Eero M. Genetic analyses reveal complex dynamics within a marine fish management area. Evol Appl 2019; 12:830-844. [PMID: 30976313 PMCID: PMC6439499 DOI: 10.1111/eva.12760] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2018] [Revised: 11/20/2018] [Accepted: 11/29/2018] [Indexed: 01/01/2023] Open
Abstract
Genetic data have great potential for improving fisheries management by identifying the fundamental management units-that is, the biological populations-and their mixing. However, so far, the number of practical cases of marine fisheries management using genetics has been limited. Here, we used Atlantic cod in the Baltic Sea to demonstrate the applicability of genetics to a complex management scenario involving mixing of two genetically divergent populations. Specifically, we addressed several assumptions used in the current assessment of the two populations. Through analysis of 483 single nucleotide polymorphisms (SNPs) distributed across the Atlantic cod genome, we confirmed that a model of mechanical mixing, rather than hybridization and introgression, best explained the pattern of genetic differentiation. Thus, the fishery is best monitored as a mixed-stock fishery. Next, we developed a targeted panel of 39 SNPs with high statistical power for identifying population of origin and analyzed more than 2,000 tissue samples collected between 2011 and 2015 as well as 260 otoliths collected in 2003/2004. These data provided high spatial resolution and allowed us to investigate geographical trends in mixing, to compare patterns for different life stages and to investigate temporal trends in mixing. We found similar geographical trends for the two time points represented by tissue and otolith samples and that a recently implemented geographical management separation of the two populations provided a relatively close match to their distributions. In contrast to the current assumption, we found that patterns of mixing differed between juveniles and adults, a signal likely linked to the different reproductive dynamics of the two populations. Collectively, our data confirm that genetics is an operational tool for complex fisheries management applications. We recommend focussing on developing population assessment models and fisheries management frameworks to capitalize fully on the additional information offered by genetically assisted fisheries monitoring.
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Affiliation(s)
- Jakob Hemmer‐Hansen
- National Institute of Aquatic ResourcesTechnical University of DenmarkSilkeborgDenmark
| | - Karin Hüssy
- National Institute of Aquatic ResourcesTechnical University of DenmarkKgs. LyngbyDenmark
| | - Henrik Baktoft
- National Institute of Aquatic ResourcesTechnical University of DenmarkSilkeborgDenmark
| | - Bastian Huwer
- National Institute of Aquatic ResourcesTechnical University of DenmarkKgs. LyngbyDenmark
| | - Dorte Bekkevold
- National Institute of Aquatic ResourcesTechnical University of DenmarkSilkeborgDenmark
| | | | - Jens‐Peter Herrmann
- Institute of Marine Ecosystem and Fishery ScienceUniversity of HamburgHamburgGermany
| | - Hans‐Harald Hinrichsen
- Evolutionary Ecology of Marine FishesGEOMAR Helmholtz Center for Ocean Research KielKielGermany
| | - Uwe Krumme
- Thünen Institute of Baltic Sea FisheriesRostockGermany
| | - Henrik Mosegaard
- National Institute of Aquatic ResourcesTechnical University of DenmarkKgs. LyngbyDenmark
| | - Einar Eg Nielsen
- National Institute of Aquatic ResourcesTechnical University of DenmarkSilkeborgDenmark
| | - Thorsten B. H. Reusch
- Evolutionary Ecology of Marine FishesGEOMAR Helmholtz Center for Ocean Research KielKielGermany
| | - Marie Storr‐Paulsen
- National Institute of Aquatic ResourcesTechnical University of DenmarkKgs. LyngbyDenmark
| | | | - Burkhard von Dewitz
- Evolutionary Ecology of Marine FishesGEOMAR Helmholtz Center for Ocean Research KielKielGermany
| | - Jan Dierking
- Evolutionary Ecology of Marine FishesGEOMAR Helmholtz Center for Ocean Research KielKielGermany
| | - Margit Eero
- National Institute of Aquatic ResourcesTechnical University of DenmarkKgs. LyngbyDenmark
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