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Donthu R, Marcelino JAP, Giordano R, Tao Y, Weber E, Avalos A, Band M, Akraiko T, Chen SC, Reyes MP, Hao H, Ortiz-Alvarado Y, Cuff CA, Claudio EP, Soto-Adames F, Smith-Pardo AH, Meikle WG, Evans JD, Giray T, Abdelkader FB, Allsopp M, Ball D, Morgado SB, Barjadze S, Correa-Benitez A, Chakir A, Báez DR, Chavez NHM, Dalmon A, Douglas AB, Fraccica C, Fernández-Marín H, Galindo-Cardona A, Guzman-Novoa E, Horsburgh R, Kence M, Kilonzo J, Kükrer M, Le Conte Y, Mazzeo G, Mota F, Muli E, Oskay D, Ruiz-Martínez JA, Oliveri E, Pichkhaia I, Romane A, Sanchez CG, Sikombwa E, Satta A, Scannapieco AA, Stanford B, Soroker V, Velarde RA, Vercelli M, Huang Z. HBeeID: a molecular tool that identifies honey bee subspecies from different geographic populations. BMC Bioinformatics 2024; 25:278. [PMID: 39192185 DOI: 10.1186/s12859-024-05776-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Accepted: 04/10/2024] [Indexed: 08/29/2024] Open
Abstract
BACKGROUND Honey bees are the principal commercial pollinators. Along with other arthropods, they are increasingly under threat from anthropogenic factors such as the incursion of invasive honey bee subspecies, pathogens and parasites. Better tools are needed to identify bee subspecies. Genomic data for economic and ecologically important organisms is increasing, but in its basic form its practical application to address ecological problems is limited. RESULTS We introduce HBeeID a means to identify honey bees. The tool utilizes a knowledge-based network and diagnostic SNPs identified by discriminant analysis of principle components and hierarchical agglomerative clustering. Tests of HBeeID showed that it identifies African, Americas-Africanized, Asian, and European honey bees with a high degree of certainty even when samples lack the full 272 SNPs of HBeeID. Its prediction capacity decreases with highly admixed samples. CONCLUSION HBeeID is a high-resolution genomic, SNP based tool, that can be used to identify honey bees and screen species that are invasive. Its flexible design allows for future improvements via sample data additions from other localities.
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Affiliation(s)
- Ravikiran Donthu
- Puerto Rico Science, Technology and Research Trust, San Juan, PR, 00927, USA
- Centre for Life Sciences, Mahindra University, Bahadurpally, Hyderabad, 500043, India
| | - Jose A P Marcelino
- Puerto Rico Science, Technology and Research Trust, San Juan, PR, 00927, USA
- Florida Department of Agriculture and Consumer Services, Division of Plant Industry, Gainesville, FL, 32608, USA
| | - Rosanna Giordano
- Puerto Rico Science, Technology and Research Trust, San Juan, PR, 00927, USA.
- Institute of Environment, Florida International University, Miami, FL, 33199, USA.
| | - Yudong Tao
- Department of Electrical and Computer Engineering, University of Miami, Coral Gables, FL, 33146, USA
| | - Everett Weber
- Office of Institutional Research, Dartmouth College, Hanover, NH, 03755, USA
| | - Arian Avalos
- USDA-ARS, Honey Bee Breeding, Genetics and Physiology Research, Baton Rouge, LA, 70820, USA
| | - Mark Band
- Roy J. Carver Biotechnology Center, University of Illinois, Urbana-Champaign, IL, 61801, USA
| | - Tatsiana Akraiko
- Roy J. Carver Biotechnology Center, University of Illinois, Urbana-Champaign, IL, 61801, USA
| | - Shu-Ching Chen
- Data Science and Analytics Innovation Center (dSAIC), University of Missouri-Kansas City, Kansas City, MO, 64110, USA
| | - Maria P Reyes
- Knight Foundation School of Computing and Information Sciences, Florida International University, Miami, FL, 33199, USA
| | - Haiping Hao
- Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | | | - Charles A Cuff
- Department of Biology, University of Puerto Rico, San Juan, PR, 00931, USA
| | - Eddie Pérez Claudio
- Department of Biomedical Informatics, School of Medicine, University of Pittsburgh, Pittsburgh, PA, 15206, USA
| | - Felipe Soto-Adames
- Florida Department of Agriculture and Consumer Services, Division of Plant Industry, Gainesville, FL, 32608, USA
| | | | - William G Meikle
- USDA-ARS, Carl Hayden Bee Research Center, Tucson, AZ, 85719, USA
| | - Jay D Evans
- USDA-ARS, Bee Research Laboratory, Beltsville, MD, 20705, USA.
| | - Tugrul Giray
- Department of Biology, University of Puerto Rico, San Juan, PR, 00931, USA.
| | - Faten B Abdelkader
- University of Carthage, National Agronomic Institute of Tunisia, 1082, Tunis, Tunisia
| | - Mike Allsopp
- Honey Bee Research Section, ARC-Plant Protection & Health, P/Bag X5017, Stellenbosch, 7599, South Africa
| | | | - Susana B Morgado
- Meltagus, Associação de Apicultores do Parque Natural do Tejo Internacional, 6000-790, Castelo Branco, Portugal
| | - Shalva Barjadze
- Institute of Zoology, Ilia State University, 3 Giorgi Tsereteli Street, 0162, Tbilisi, Georgia
| | - Adriana Correa-Benitez
- Facultad de MedicinaVeterinaria y Zootecnia, Departamento de Medicina y Zootecnia de Abejas, Conejos y Organismos Aquáticos (DMZ:ACyOA), Universidad Nacional Autónoma de México, 04510, Ciudad de Mexico, CP, Mexico
| | - Amina Chakir
- Applied Chemistry Laboratory, Semlalia Faculty of Sciences, University Cadi Ayyad, Marrakech, Morocco
| | | | - Nabor H M Chavez
- Cochabamba Beekeepers Federation (FEDAC), Aniceto Padilla, 493, Cochabamba, Bolivia
| | - Anne Dalmon
- INRAE, French National Research Institute for Agriculture, Food and Environment. UR Abeilles et Environment, 84914, Avignon, France
| | - Adrian B Douglas
- Institute of Earth Systems, Rural Sciences Farmhouse, University of Malta, Msida, 2080, MSD, Malta
| | - Carmen Fraccica
- Florida Department of Agriculture and Consumer Services, Division of Plant Industry, Gainesville, FL, 32608, USA
| | - Hermógenes Fernández-Marín
- Centro de Biodiversidad y Descubrimiento de Drogas, Instituto de Investigaciones Científicas y Servicios de Alta Tecnología (INDICASAT AIP), Clayton Panama, 0843-01103, Panama
| | - Alberto Galindo-Cardona
- Instituto de Ecología Regional (IER), Universidad Nacional de Tucumán (UNT) - Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET). Yerba Buena, CC 34, CP 4107, Tucumán, Argentina
| | - Ernesto Guzman-Novoa
- School of Environmental Sciences, University of Guelph, 50 Stone Road East, Guelph, ON, N1G 2W1, Canada
| | - Robert Horsburgh
- Florida Department of Agriculture and Consumer Services, Division of Plant Industry, Gainesville, FL, 32608, USA
| | - Meral Kence
- Biology Department, Middle East Technical University, 06530, Ankara, Turkey
| | - Joseph Kilonzo
- International Centre of Insect Physiology and Ecology, Nairobi, Kenya
| | - Mert Kükrer
- Biology Department, Middle East Technical University, 06530, Ankara, Turkey
- Molecular Biology and Genetics Department, Kilis 7 Aralık University, Kilis, Turkey
| | - Yves Le Conte
- INRAE, French National Research Institute for Agriculture, Food and Environment. UR Abeilles et Environment, 84914, Avignon, France
| | - Gaetana Mazzeo
- Dipartimento di Agricoltura, Alimentazione e Ambiente (Di3A), Università Degli Studi Di Catania, Catania, Italy
| | - Fernando Mota
- Independent Beekeeper, 6000, Castelo Branco, Portugal
| | - Elliud Muli
- International Centre of Insect Physiology and Ecology, Nairobi, Kenya
- South Eastern Kenya University (SEKU), JXFW+X3C, Kitui, Kenya
| | - Devrim Oskay
- Department of Agricultural Biotechnology, Tekirdağ Namık Kemal University, 59030, Tekirdağ, Turkey
| | - José A Ruiz-Martínez
- Professional Training in Livestock and Animal Health, High School Lope de Vega, Fuente Obejuna, Córdoba, Spain
| | - Eugenia Oliveri
- Istituto Zooprofilattico Sperimentale della Sicilia, 90129, Palermo, Italy
| | - Igor Pichkhaia
- Chkhorotsku Local Historical Museum, David Aghmashenebeli St., 5000, Chkhorotsku, Georgia
| | - Abderrahmane Romane
- Applied Chemistry Laboratory, Semlalia Faculty of Sciences, University Cadi Ayyad, Marrakech, Morocco
| | - Cesar Guillen Sanchez
- Escuela de Agronomía, Sede del Atlántico, University of Costa Rica, Turrialba, 30501, Costa Rica
| | | | - Alberto Satta
- Department of Agricultural Sciences, University of Sassari, Viale Italia 39A, 07100, Sassari, Italy
| | | | - Brandi Stanford
- Florida Department of Agriculture and Consumer Services, Division of Plant Industry, Gainesville, FL, 32608, USA
| | - Victoria Soroker
- Agricultural Research Organization, The Volcani Center, Institute of Plant Protection, Department of Entomology, Bet-Dagan, Israel
| | - Rodrigo A Velarde
- Bolivian Apiculture Institute (IAB), PROMIEL-SEDEM, Jaimes Freyre No 2344, La Paz, Bolivia
| | | | - Zachary Huang
- Department of Entomology, MSU Apiculture Lab, Michigan State University, East Lansing, MI, 48824, USA
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Teixeira-Cruz JM, Strauch MA, Monteiro-Machado M, Tavares-Henriques MS, de Moraes JA, Ribeiro da Cunha LE, Ferreira, Jr. RS, Barraviera B, Quintas LEM, Melo PA. A Novel Apilic Antivenom to Treat Massive, Africanized Honeybee Attacks: A Preclinical Study from the Lethality to Some Biochemical and Pharmacological Activities Neutralization. Toxins (Basel) 2021; 13:toxins13010030. [PMID: 33466223 PMCID: PMC7824798 DOI: 10.3390/toxins13010030] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Revised: 12/22/2020] [Accepted: 12/24/2020] [Indexed: 12/25/2022] Open
Abstract
Massive, Africanized honeybee attacks have increased in Brazil over the years. Humans and animals present local and systemic effects after envenomation, and there is no specific treatment for this potentially lethal event. This study evaluated the ability of a new Apilic antivenom, which is composed of F(ab’)2 fraction of specific immunoglobulins in heterologous and hyperimmune equine serum, to neutralize A. mellifera venom and melittin, in vitro and in vivo, in mice. Animal experiments were performed in according with local ethics committee license (UFRJ protocol no. DFBCICB072-04/16). Venom dose-dependent lethality was diminished with 0.25–0.5 μL of intravenous Apilic antivenom/μg honeybee venom. In vivo injection of 0.1–1 μg/g bee venom induced myotoxicity, hemoconcentration, paw edema, and increase of vascular permeability which were antagonized by Apilic antivenom. Cytotoxicity, assessed in renal LLC-PK1 cells and challenged with 10 μg/mL honeybee venom or melittin, was neutralized by preincubation with Apilic antivenom, as well the hemolytic activity. Apilic antivenom inhibited phospholipase and hyaluronidase enzymatic activities. In flow cytometry experiments, Apilic antivenom neutralized reduction of cell viability due to necrosis by honeybee venom or melittin. These results showed that this antivenom is effective inhibitor of honeybee venom actions. Thus, this next generation of Apilic antivenom emerges as a new promising immunobiological product for the treatment of massive, Africanized honeybee attacks.
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Affiliation(s)
- Jhonatha Mota Teixeira-Cruz
- Graduate Program in Pharmacology and Medicinal Chemistry, Institute of Biomedical Sciences, Federal University of Rio de Janeiro, Rio de Janeiro 21941-902, Brazil; (J.M.T.-C.); (M.M.-M.); (M.S.T.-H.); (J.A.d.M.)
| | - Marcelo Abrahão Strauch
- Graduate Program in Pharmacology and Medicinal Chemistry, Institute of Biomedical Sciences, Federal University of Rio de Janeiro, Rio de Janeiro 21941-902, Brazil; (J.M.T.-C.); (M.M.-M.); (M.S.T.-H.); (J.A.d.M.)
- Scientific Board, Vital Brazil Institute (IVB), Niterói, Rio de Janeiro 24230-410, Brazil;
- Correspondence: (M.A.S.); (L.E.M.Q.); (P.A.M.)
| | - Marcos Monteiro-Machado
- Graduate Program in Pharmacology and Medicinal Chemistry, Institute of Biomedical Sciences, Federal University of Rio de Janeiro, Rio de Janeiro 21941-902, Brazil; (J.M.T.-C.); (M.M.-M.); (M.S.T.-H.); (J.A.d.M.)
| | - Matheus Silva Tavares-Henriques
- Graduate Program in Pharmacology and Medicinal Chemistry, Institute of Biomedical Sciences, Federal University of Rio de Janeiro, Rio de Janeiro 21941-902, Brazil; (J.M.T.-C.); (M.M.-M.); (M.S.T.-H.); (J.A.d.M.)
| | - João Alfredo de Moraes
- Graduate Program in Pharmacology and Medicinal Chemistry, Institute of Biomedical Sciences, Federal University of Rio de Janeiro, Rio de Janeiro 21941-902, Brazil; (J.M.T.-C.); (M.M.-M.); (M.S.T.-H.); (J.A.d.M.)
| | | | - Rui Seabra Ferreira, Jr.
- Center for the Study of Venoms and Venomous Animals (CEVAP), São Paulo State University (UNESP), Botucatu, São Paulo 18610-307, Brazil; (R.S.F.J.); (B.B.)
| | - Benedito Barraviera
- Center for the Study of Venoms and Venomous Animals (CEVAP), São Paulo State University (UNESP), Botucatu, São Paulo 18610-307, Brazil; (R.S.F.J.); (B.B.)
| | - Luis Eduardo M. Quintas
- Graduate Program in Pharmacology and Medicinal Chemistry, Institute of Biomedical Sciences, Federal University of Rio de Janeiro, Rio de Janeiro 21941-902, Brazil; (J.M.T.-C.); (M.M.-M.); (M.S.T.-H.); (J.A.d.M.)
- Correspondence: (M.A.S.); (L.E.M.Q.); (P.A.M.)
| | - Paulo A. Melo
- Graduate Program in Pharmacology and Medicinal Chemistry, Institute of Biomedical Sciences, Federal University of Rio de Janeiro, Rio de Janeiro 21941-902, Brazil; (J.M.T.-C.); (M.M.-M.); (M.S.T.-H.); (J.A.d.M.)
- Correspondence: (M.A.S.); (L.E.M.Q.); (P.A.M.)
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Calfee E, Agra MN, Palacio MA, Ramírez SR, Coop G. Selection and hybridization shaped the rapid spread of African honey bee ancestry in the Americas. PLoS Genet 2020; 16:e1009038. [PMID: 33075065 PMCID: PMC7595643 DOI: 10.1371/journal.pgen.1009038] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Revised: 10/29/2020] [Accepted: 08/09/2020] [Indexed: 02/07/2023] Open
Abstract
Recent biological invasions offer 'natural' laboratories to understand the genetics and ecology of adaptation, hybridization, and range limits. One of the most impressive and well-documented biological invasions of the 20th century began in 1957 when Apis mellifera scutellata honey bees swarmed out of managed experimental colonies in Brazil. This newly-imported subspecies, native to southern and eastern Africa, both hybridized with and out-competed previously-introduced European honey bee subspecies. Populations of scutellata-European hybrid honey bees rapidly expanded and spread across much of the Americas in less than 50 years. We use broad geographic sampling and whole genome sequencing of over 300 bees to map the distribution of scutellata ancestry where the northern and southern invasions have presently stalled, forming replicated hybrid zones with European bee populations in California and Argentina. California is much farther from Brazil, yet these hybrid zones occur at very similar latitudes, consistent with the invasion having reached a climate barrier. At these range limits, we observe genome-wide clines for scutellata ancestry, and parallel clines for wing length that span hundreds of kilometers, supporting a smooth transition from climates favoring scutellata-European hybrid bees to climates where they cannot survive winter. We find no large effect loci maintaining exceptionally steep ancestry transitions. Instead, we find most individual loci have concordant ancestry clines across South America, with a build-up of somewhat steeper clines in regions of the genome with low recombination rates, consistent with many loci of small effect contributing to climate-associated fitness trade-offs. Additionally, we find no substantial reductions in genetic diversity associated with rapid expansions nor complete dropout of scutellata ancestry at any individual loci on either continent, which suggests that the competitive fitness advantage of scutellata ancestry at lower latitudes has a polygenic basis and that scutellata-European hybrid bees maintained large population sizes during their invasion. To test for parallel selection across continents, we develop a null model that accounts for drift in ancestry frequencies during the rapid expansion. We identify several peaks within a larger genomic region where selection has pushed scutellata ancestry to high frequency hundreds of kilometers past the present cline centers in both North and South America and that may underlie high-fitness traits driving the invasion.
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Affiliation(s)
- Erin Calfee
- Center for Population Biology, University of California, Davis, California, United States of America
- Department of Evolution and Ecology, University of California, Davis, California, United States of America
| | | | - María Alejandra Palacio
- Instituto Nacional de Tecnología Agropecuaria (INTA), Balcarce, Argentina
- Facultad de Ciencias Agrarias, Universidad de Mar del Plata, Balcarce, Argentina
| | - Santiago R. Ramírez
- Center for Population Biology, University of California, Davis, California, United States of America
- Department of Evolution and Ecology, University of California, Davis, California, United States of America
| | - Graham Coop
- Center for Population Biology, University of California, Davis, California, United States of America
- Department of Evolution and Ecology, University of California, Davis, California, United States of America
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