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Bianchi EM, Ferrari C, Aguirre NC, Filippi CV, Vera PA, Puebla AF, Gennari GP, Rodríguez GA, Scannapieco AC, Acuña CV, Lanzavecchia SB. Phenotypic and genetic characterization of Africanized Apis mellifera colonies with natural tolerance to Varroa destructor and contrasting defensive behavior. FRONTIERS IN INSECT SCIENCE 2023; 3:1175760. [PMID: 38469487 PMCID: PMC10926445 DOI: 10.3389/finsc.2023.1175760] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Accepted: 07/27/2023] [Indexed: 03/13/2024]
Abstract
Africanized Apis mellifera colonies with promising characteristics for beekeeping have been detected in northern Argentina (subtropical climate) and are considered of interest for breeding programs. Integral evaluation of this feral material revealed high colony strength and resistance/tolerance to brood diseases. However, these Africanized honeybees (AHB) also showed variable negative behavioral traits for beekeeping, such as defensiveness, tendency to swarm and avoidance behavior. We developed a protocol for the selection of AHB stocks based on defensive behavior and characterized contrasting colonies for this trait using NGS technologies. For this purpose, population and behavioral parameters were surveyed throughout a beekeeping season in nine daughter colonies obtained from a mother colony (A1 mitochondrial haplotype) with valuable characteristics (tolerance to the mite Varroa destructor, high colony strength and low defensiveness). A Defensive Behavior Index was developed and tested in the colonies under study. Mother and two daughter colonies displaying contrasting defensive behavior were analyzed by ddRADseq. High-quality DNA samples were obtained from 16 workers of each colony. Six pooled samples, including two replicates of each of the three colonies, were processed. A total of 12,971 SNPs were detected against the reference genome of A. mellifera, 142 of which showed significant differences between colonies. We detected SNPs in coding regions, lncRNA, miRNA, rRNA, tRNA, among others. From the original data set, we also identified 647 SNPs located in protein-coding regions, 128 of which are related to 21 genes previously associated with defensive behavior, such as dop3 and dopR2, CaMKII and ADAR, obp9 and obp10, and members of the 5-HT family. We discuss the obtained results by considering the influence of polyandry and paternal lineages on the defensive behavior in AHB and provide baseline information to use this innovative molecular approach, ddRADseq, to assist in the selection and evaluation of honey bee stocks showing low defensive behavior for commercial uses.
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Affiliation(s)
- Eliana Mariel Bianchi
- Área Animal, Instituto de Investigación Animal del Chaco-Semiárido (IIACS) - Instituto Nacional de Tecnología Agropecuaria (INTA), Santa Rosa de Leales, Tucumán, Argentina
| | - Carolina Ferrari
- Escuela de Ciencias Agrarias, Naturales y Ambientales (ECANA), Universidad Nacional del Noroeste de Buenos Aires (UNNOBA), Pergamino, Buenos Aires, Argentina
| | - Natalia C. Aguirre
- Instituto de Agrobiotecnología y Biología Molecular (IABIMO), Instituto Nacional de Tecnología Agropecuaria (INTA) - Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Hurlingham, Buenos Aires, Argentina
| | - Carla V. Filippi
- Instituto de Agrobiotecnología y Biología Molecular (IABIMO), Instituto Nacional de Tecnología Agropecuaria (INTA) - Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Hurlingham, Buenos Aires, Argentina
- Laboratorio de Bioquímica, Departamento de Biología Vegetal, Facultad de Agronomía, Universidad de la República, Montevideo, Uruguay
| | - Pablo A. Vera
- Unidad de Genómica, Instituto de Biotecnología-Instituto de Agrobiotecnología y Biología Molecular (IABIMO), Centro de Investigación en Ciencias Veterinarias y Agronómicas (CICVyA), Instituto Nacional de Tecnología Agropecuaria (INTA)-Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Hurlingham, Buenos Aires, Argentina
| | - Andrea Fabiana Puebla
- Unidad de Genómica, Instituto de Biotecnología-Instituto de Agrobiotecnología y Biología Molecular (IABIMO), Centro de Investigación en Ciencias Veterinarias y Agronómicas (CICVyA), Instituto Nacional de Tecnología Agropecuaria (INTA)-Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Hurlingham, Buenos Aires, Argentina
| | - Gerardo P. Gennari
- Estación Experimental Agropecuaria (EEA) Famaillá, Instituto Nacional de Tecnología Agropecuaria (INTA), Famaillá, Tucumán, Argentina
| | - Graciela A. Rodríguez
- Estación Experimental Agropecuaria (EEA) Ascasubi, Instituto Nacional de Tecnología Agropecuaria (INTA), Hilario Ascasubi, Buenos Aires, Argentina
| | - Alejandra Carla Scannapieco
- Instituto de Genética, Instituto Nacional de Tecnología Agropecuaria (INTA), Instituto de Agrobiotecnología y Biología Molecular (IABIMO) Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Hurlingham, Buenos Aires, Argentina
| | - Cintia V. Acuña
- Instituto de Agrobiotecnología y Biología Molecular (IABIMO), Instituto Nacional de Tecnología Agropecuaria (INTA) - Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Hurlingham, Buenos Aires, Argentina
| | - Silvia B. Lanzavecchia
- Instituto de Genética, Instituto Nacional de Tecnología Agropecuaria (INTA), Instituto de Agrobiotecnología y Biología Molecular (IABIMO) Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Hurlingham, Buenos Aires, Argentina
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Carr SM. Multiple mitogenomes indicate Things Fall Apart with Out of Africa or Asia hypotheses for the phylogeographic evolution of Honey Bees (Apis mellifera). Sci Rep 2023; 13:9386. [PMID: 37296293 PMCID: PMC10256785 DOI: 10.1038/s41598-023-35937-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Accepted: 05/26/2023] [Indexed: 06/12/2023] Open
Abstract
Previous morpho-molecular studies of evolutionary relationships within the economically important genus of honey bees (Apis), including the Western Honey Bee (A. mellifera L.), have suggested Out of Africa or Asia origins and subsequent spread to Europe. I test these hypotheses by a meta-analysis of complete mitochondrial DNA coding regions (11.0 kbp) from 22 nominal subspecies represented by 78 individual sequences in A. mellifera. Parsimony, distance, and likelihood analyses identify six nested clades: Things Fall Apart with Out of Africa or Asia hypotheses. Molecular clock-calibrated phylogeographic analysis shows instead a basal origin of A. m. mellifera in Europe ~ 780 Kya, and expansion to Southeast Europe and Asia Minor ~ 720 Kya. Eurasian bees spread southward via a Levantine/Nilotic/Arabian corridor into Africa ~ 540 Kya. An African clade re-established in Iberia ~ 100 Kya spread thereafter to westerly Mediterranean islands and back into North Africa. Nominal subspecies within the Asia Minor and Mediterranean clades are less differentiated than are individuals within other subspecies. Names matter: paraphyletic anomalies are artefacts of mis-referral in GenBank of sequences to the wrong subspecies, or use of faulty sequences, which are clarified by inclusion of multiple sequences from available subspecies.
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Affiliation(s)
- Steven M Carr
- Genetics, Evolution, and Molecular Systematics Laboratory, Department of Biology, Memorial University of Newfoundland, St John's, NL, A1C 5S9, Canada.
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Mohamed WMA, Moustafa MAM, Thu MJ, Kakisaka K, Chatanga E, Ogata S, Hayashi N, Taya Y, Ohari Y, Naguib D, Qiu Y, Matsuno K, Bawm S, Htun LL, Barker SC, Katakura K, Ito K, Nonaka N, Nakao R. Comparative mitogenomics elucidates the population genetic structure of
Amblyomma testudinarium
in Japan and a closely related
Amblyomma
species in Myanmar. Evol Appl 2022; 15:1062-1078. [PMID: 35899249 PMCID: PMC9309438 DOI: 10.1111/eva.13426] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2022] [Revised: 04/27/2022] [Accepted: 05/29/2022] [Indexed: 12/05/2022] Open
Abstract
Ticks are the second most important vector capable of transmitting diseases affecting the health of both humans and animals. Amblyomma testudinarium Koch 1844 (Acari: Ixodidae), is a hard tick species having a wide geographic distribution in Asia. In this study, we analyzed the composition of A. testudinarium whole mitogenomes from various geographical regions in Japan and investigated the population structure, demographic patterns, and phylogeographic relationship with other ixodid species. In addition, we characterized a potentially novel tick species closely related to A. testudinarium from Myanmar. Phylogeographic inference and evolutionary dynamics based on the 15 mitochondrial coding genes supported that A. testudinarium population in Japan is resolved into a star‐like haplogroup and suggested a distinct population structure of A. testudinarium from Amami island in Kyushu region. Correlation analysis using Mantel test statistics showed that no significant correlation was observed between the genetic and geographic distances calculated between the A. testudinarium population from different localities in Japan. Finally, demographic analyses, including mismatch analysis and Tajima’s D test, suggested a possibility of recent population expansion occurred within Japanese haplogroup after a bottleneck event. Although A. testudinarium has been considered widespread and common in East and Southeast Asia, the current study suggested that potentially several cryptic Amblyomma spp. closely related to A. testudinarium are present in Asia.
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Affiliation(s)
- Wessam Mohamed Ahmed Mohamed
- Laboratory of Parasitology, Department of Disease Control, Faculty of Veterinary Medicine Hokkaido University Sapporo Hokkaido Japan
- Division of Bioinformatics, International Institute for Zoonosis Control Hokkaido University Sapporo Hokkaido Japan
| | - Mohamed Abdallah Mohamed Moustafa
- Laboratory of Parasitology, Department of Disease Control, Faculty of Veterinary Medicine Hokkaido University Sapporo Hokkaido Japan
- Department of Animal Medicine, Faculty of Veterinary Medicine South Valley University Qena Egypt
| | - May June Thu
- Laboratory of Parasitology, Department of Disease Control, Faculty of Veterinary Medicine Hokkaido University Sapporo Hokkaido Japan
- Department of Food and Drug Administration, Ministry of Health, Zabu Thiri, Nay Pyi Taw 15011 Myanmar
| | - Keita Kakisaka
- Laboratory of Parasitology, Department of Disease Control, Faculty of Veterinary Medicine Hokkaido University Sapporo Hokkaido Japan
| | - Elisha Chatanga
- Laboratory of Parasitology, Department of Disease Control, Faculty of Veterinary Medicine Hokkaido University Sapporo Hokkaido Japan
- Department of Veterinary Pathobiology, Faculty of Veterinary Medicine Lilongwe University of Agriculture and Natural Resources Lilongwe Malawi
| | - Shohei Ogata
- Laboratory of Parasitology, Department of Disease Control, Faculty of Veterinary Medicine Hokkaido University Sapporo Hokkaido Japan
| | - Naoki Hayashi
- Laboratory of Parasitology, Department of Disease Control, Faculty of Veterinary Medicine Hokkaido University Sapporo Hokkaido Japan
| | - Yurie Taya
- Laboratory of Parasitology, Department of Disease Control, Faculty of Veterinary Medicine Hokkaido University Sapporo Hokkaido Japan
| | - Yuma Ohari
- Laboratory of Parasitology, Department of Disease Control, Faculty of Veterinary Medicine Hokkaido University Sapporo Hokkaido Japan
| | - Doaa Naguib
- Laboratory of Parasitology, Department of Disease Control, Faculty of Veterinary Medicine Hokkaido University Sapporo Hokkaido Japan
- Department of Hygiene and Zoonoses, Faculty of Veterinary Medicine Mansoura University Mansoura Egypt
| | - Yongjin Qiu
- Division of International Research Promotion, International Institute for Zoonosis Control Hokkaido University Sapporo Hokkaido Japan
| | - Keita Matsuno
- Division of Risk Analysis and Management, International Institute for Zoonosis Control Hokkaido University Sapporo Hokkaido Japan
- International Collaboration Unit, International Institute for Zoonosis Control Hokkaido University Sapporo Hokkaido Japan
- One Health Research Center Hokkaido University Sapporo Hokkaido Japan
| | - Saw Bawm
- Department of International Relations and Information Technology University of Veterinary Science Yezin, Nay Pyi Taw Myanmar
- Department of Pharmacology and Parasitology University of Veterinary Science Yezin, Nay Pyi Taw Myanmar
| | - Lat Lat Htun
- Department of Pharmacology and Parasitology University of Veterinary Science Yezin, Nay Pyi Taw Myanmar
| | - Stephen C. Barker
- Department of Parasitology, School of Chemistry and Molecular Biosciences The University of Queensland Brisbane QLD Australia
| | - Ken Katakura
- Laboratory of Parasitology, Department of Disease Control, Faculty of Veterinary Medicine Hokkaido University Sapporo Hokkaido Japan
| | - Kimihito Ito
- Division of Bioinformatics, International Institute for Zoonosis Control Hokkaido University Sapporo Hokkaido Japan
| | - Nariaki Nonaka
- Laboratory of Parasitology, Department of Disease Control, Faculty of Veterinary Medicine Hokkaido University Sapporo Hokkaido Japan
| | - Ryo Nakao
- Laboratory of Parasitology, Department of Disease Control, Faculty of Veterinary Medicine Hokkaido University Sapporo Hokkaido Japan
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Moškrič A, Marinč A, Ferk P, Leskošek B, Mosbech MB, Bunikis I, Pettersson OV, Soler L, Prešern J. The Carniolan Honeybee from Slovenia—A Complete and Annotated Mitochondrial Genome with Comparisons to Closely Related Apis mellifera Subspecies. INSECTS 2022; 13:insects13050403. [PMID: 35621738 PMCID: PMC9146700 DOI: 10.3390/insects13050403] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Revised: 04/18/2022] [Accepted: 04/20/2022] [Indexed: 02/01/2023]
Abstract
Simple Summary The western honeybee, Apis mellifera, is a globally distributed bee species with many recognised subspecies, one of which is Apis mellifera carnica, the Carniolan honeybee. Apis m. carnica is native to southern Central Europe and parts of the Balkans, with the locus classicus in Slovenia. It is also widely popular with beekeepers in parts of Central and Northern Europe and other parts of the world, including the USA, Canada, and even New Zealand. In Slovenia, A. m. carnica is protected, with measures to conserve the subspecies’ autochthonous domestic population in place. Such efforts depend heavily upon genomic and phylogenetic information. In this study, we sequenced and annotated the mitochondrial genome of a specimen from Slovenia and compared the obtained data with a previously published sample of the A. m. carnica from Austria and the closely related Italian honeybee A. m. ligustica. We found several features unique to the new mitochondrial genome. We also phylogenetically analyzed the relationship between our sequence and the selected available A. mellifera mitochondrial sequences. The acquired position of the sequenced A. m. carnica from Slovenia on the phylogenetic tree brings new evidence for close relationships among C and O lineages and reflects their recent historical matrilinear ancestry. Abstract The complete mitochondrial genome of the Carniolan honeybee (Apis mellifera carnica) from Slovenia, a homeland of this subspecies, was acquired in two contigs from WGS data and annotated. The newly obtained mitochondrial genome is a circular closed loop of 16,447 bp. It comprises 37 genes (13 protein coding genes, 22 tRNA genes, and 2 rRNA genes) and an AT-rich control region. The order of the tRNA genes resembles the order characteristic of A. mellifera. The mitogenomic sequence of A. m. carnica from Slovenia contains 44 uniquely coded sites in comparison to the closely related subspecies A. m. ligustica and to A. m. carnica from Austria. Furthermore, 24 differences were recognised in comparison between A. m. carnica and A. m. ligustica subspecies. Among them, there are three SNPs that affect translation in the nd2, nd4, and cox2 genes, respectively. The phylogenetic placement of A. m. carnica from Slovenia within C lineage deviates from the expected position and changes the perspective on relationship between C and O lineages. The results of this study represent a valuable addition to the information available in the phylogenomic studies of A. mellifera—a pollinator species of worldwide importance. Such genomic information is essential for this local subspecies’ conservation and preservation as well as its breeding and selection.
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Affiliation(s)
- Ajda Moškrič
- Animal Production Department, Agricultural Institute of Slovenia, Hacquetova ulica 17, SI-1000 Ljubljana, Slovenia; (A.M.); (J.P.)
- Correspondence:
| | - Andraž Marinč
- Animal Production Department, Agricultural Institute of Slovenia, Hacquetova ulica 17, SI-1000 Ljubljana, Slovenia; (A.M.); (J.P.)
| | - Polonca Ferk
- Faculty of Medicine, Institute for Biostatistics and Medical Informatics/Centre ELIXIR-SI, University of Ljubljana, Vrazov trg 2, SI-1000 Ljubljana, Slovenia; (P.F.); (B.L.)
| | - Brane Leskošek
- Faculty of Medicine, Institute for Biostatistics and Medical Informatics/Centre ELIXIR-SI, University of Ljubljana, Vrazov trg 2, SI-1000 Ljubljana, Slovenia; (P.F.); (B.L.)
| | - Mai-Britt Mosbech
- Uppsala Genome Center, Science for Life Laboratory, Department of Immunology, Genetics and Pathology, Uppsala University, BMC, Box 815, 752 37 Uppsala, Sweden; (M.-B.M.); (I.B.); (O.V.P.)
| | - Ignas Bunikis
- Uppsala Genome Center, Science for Life Laboratory, Department of Immunology, Genetics and Pathology, Uppsala University, BMC, Box 815, 752 37 Uppsala, Sweden; (M.-B.M.); (I.B.); (O.V.P.)
| | - Olga Vinnere Pettersson
- Uppsala Genome Center, Science for Life Laboratory, Department of Immunology, Genetics and Pathology, Uppsala University, BMC, Box 815, 752 37 Uppsala, Sweden; (M.-B.M.); (I.B.); (O.V.P.)
| | - Lucile Soler
- Department of Medical Biochemistry and Microbiology (IMBIM), Uppsala University, National Bioinformatics Infrastructure Sweden (NBIS), Science for Life Laboratory, 751 24 Uppsala, Sweden;
| | - Janez Prešern
- Animal Production Department, Agricultural Institute of Slovenia, Hacquetova ulica 17, SI-1000 Ljubljana, Slovenia; (A.M.); (J.P.)
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Mohamadzade Namin S, Yeasmin F, Choi HW, Jung C. DNA-Based Method for Traceability and Authentication of Apis cerana and A. dorsata Honey (Hymenoptera: Apidae), Using the NADH dehydrogenase 2 Gene. Foods 2022; 11:foods11070928. [PMID: 35407015 PMCID: PMC8997381 DOI: 10.3390/foods11070928] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 03/21/2022] [Accepted: 03/22/2022] [Indexed: 02/01/2023] Open
Abstract
Honey is a widely used natural product and the price of honey from Apis cerana (ACH) and A. dorsata (ADH) is several times more expensive than the one from A. mellifera (AMH), thus there are increasing fraud issues reported in the market by mislabeling or mixing honeys with different entomological origins. In this study, three species-specific primers, targeting the NADH dehydrogenase 2 (ND2) region of honeybee mitochondrial DNA, were designed and tested to distinguish the entomological origin of ACH, ADH, and AMH. Molecular analysis showed that each primer set can specifically detect the ND2 region from the targeted honeybee DNA, but not from the others. The amplicon size for A. cerana, A. dorsata and A. mellifera were 224, 302, and 377 bp, respectively. Importantly, each primer set also specifically produced amplicons with expected size from the DNA prepared from honey samples with different entomological origins. The PCR adulteration test allowed detection of 1% of AMH in the mixture with either ACH or ADH. Furthermore, real-time PCR and melting curve analysis indicated the possible discrimination of origin of honey samples. Therefore, we provide the newly developed PCR-based method that can be used to determine the entomological origin of the three kinds of honey.
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Affiliation(s)
- Saeed Mohamadzade Namin
- Agricultural Science and Technology Institute, Andong National University, Andong 36729, Korea;
- Department of Plant Protection, Faculty of Agriculture, Varamin-Pishva Branch, Islamic Azad University, Varamin 3381774895, Iran
| | - Fatema Yeasmin
- Department of Plant Medicals, Andong National University, Andong 36729, Korea; (F.Y.); (H.W.C.)
| | - Hyong Woo Choi
- Department of Plant Medicals, Andong National University, Andong 36729, Korea; (F.Y.); (H.W.C.)
| | - Chuleui Jung
- Agricultural Science and Technology Institute, Andong National University, Andong 36729, Korea;
- Department of Plant Medicals, Andong National University, Andong 36729, Korea; (F.Y.); (H.W.C.)
- Correspondence:
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6
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Patterson Rosa L, Eimanifar A, Kimes AG, Brooks SA, Ellis JD. Attack of the dark clones the genetics of reproductive and color traits of South African honey bees (Apis mellifera spp.). PLoS One 2021; 16:e0260833. [PMID: 34905583 PMCID: PMC8670704 DOI: 10.1371/journal.pone.0260833] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Accepted: 11/17/2021] [Indexed: 12/29/2022] Open
Abstract
The traits of two subspecies of western honey bees, Apis mellifera scutellata and A.m. capensis, endemic to the Republic of South Africa (RSA), are of biological and commercial relevance. Nevertheless, the genetic basis of important phenotypes found in these subspecies remains poorly understood. We performed a genome wide association study on three traits of biological relevance in 234 A.m. capensis, 73 A.m. scutellata and 158 hybrid individuals. Thirteen markers were significantly associated to at least one trait (P ≤ 4.28 × 10−6): one for ovariole number, four for scutellar plate and eight for tergite color. We discovered two possible causative variants associated to the respective phenotypes: a deletion in GB46429 or Ebony (NC_007070.3:g.14101325G>del) (R69Efs*85) and a nonsense on GB54634 (NC_007076.3:g.4492792A>G;p.Tyr128*) causing a premature stop, substantially shortening the predicted protein. The mutant genotypes are significantly associated to phenotypes in A.m. capensis. Loss-of-function of Ebony can cause accumulation of circulating dopamine, and increased dopamine levels correlate to ovary development in queenless workers and pheromone production. Allelic association (P = 1.824 x 10−5) of NC_007076.3:g.4492792A>G;p.Tyr128* to ovariole number warrants further investigation into function and expression of the GB54634 gene. Our results highlight genetic components of relevant production/conservation behavioral phenotypes in honey bees.
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Affiliation(s)
- Laura Patterson Rosa
- Honey Bee Research and Extension Laboratory, Entomology and Nematology Department, University of Florida, Gainesville, Florida, United States of America
- * E-mail:
| | - Amin Eimanifar
- Independent Senior Research Scientist, Industrial District, Easton, Maryland, United States of America
| | - Abigail G. Kimes
- Department of Animal Sciences, University of Florida, Gainesville, Florida, United States of America
| | - Samantha A. Brooks
- Department of Animal Sciences, University of Florida, Gainesville, Florida, United States of America
- UF Genetics Institute, University of Florida, Gainesville, Florida, United States of America
| | - James D. Ellis
- Honey Bee Research and Extension Laboratory, Entomology and Nematology Department, University of Florida, Gainesville, Florida, United States of America
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7
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Alghamdi A, Alattal Y. Assessment of genetic variation in Apis mellifera jemenitica (Hymenoptera: Apidae) using Cytochrome Oxidase I gene sequences. Saudi J Biol Sci 2021; 28:6586-6591. [PMID: 34764774 PMCID: PMC8568832 DOI: 10.1016/j.sjbs.2021.07.033] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Revised: 07/04/2021] [Accepted: 07/08/2021] [Indexed: 11/23/2022] Open
Abstract
The Arabian Honeybee Apis mellifera jemenitica is endemic to the Arabian Peninsula. It is highly adapted to temperature extremes and drought dominating the region. In this study, the mitochondrial Cytochrome Oxidase I (COI) was analyzed in 133 specimens of A. m. jemenitica from eight localities along the Red Sea cost of Saudi Arabia. Results revealed 33 synonymous, and 6 non-synonymous mutations within the COI sequences, resulting in change of 4 amino acids. Phylogenetic analysis based on either type of mutations revealed two main haplogroups accounting for 94% of the samples. In total Eighteen new haplotypes were identified and uploaded in the genebank, Fourteen of them are restricted to one/both haplogroups. All haplotypes identified in this study clustered with reference COI sequences of the sub-lineag Z (African Lineage). However one Haplotype (MW428270) represents high COI variability compared to other haplotypes and may resemble different evolutionary sub-lineage. Tajima's Neutrality Test (Ps = 0.025; D = -1.5) indicated population size expansion that took place after selective sweep and/or purifying selection.
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Affiliation(s)
- A Alghamdi
- Abdullah Bagshan Chair for Bee Research, Department of Plant Protection, College of Food and Agricultural Sciences, King Saud University, P.O. Box 2460, Riyadh 11451, Saudi Arabia
| | - Yehya Alattal
- Abdullah Bagshan Chair for Bee Research, Department of Plant Protection, College of Food and Agricultural Sciences, King Saud University, P.O. Box 2460, Riyadh 11451, Saudi Arabia
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8
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Genetic diversity and population structure of the native Western African honeybee (Apis mellifera adansonii Latreille, 1804) in Nigeria based on mitochondrial COI sequences. ZOOL ANZ 2021. [DOI: 10.1016/j.jcz.2021.05.007] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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9
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Abou-Shaara HF, Al-Ghamdi AA, Khan KA, Al-Kahtani SN. Genetic network analysis between Apis mellifera subspecies based on mtDNA argues the purity of specimens from North Africa, the Levant and Saudi Arabia. Saudi J Biol Sci 2021; 28:2718-2725. [PMID: 34025158 PMCID: PMC8117108 DOI: 10.1016/j.sjbs.2021.03.032] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Revised: 03/07/2021] [Accepted: 03/08/2021] [Indexed: 11/27/2022] Open
Abstract
Objectives This study aimed to analyze the genetic relationships between honey bee subspecies using reference specimens and recently collected specimens from different parts of the world. The purity of these specimens was discussed in light of the obtained results. Methods The genetic networks were constructed between 21 subspecies of honey bees, Apis mellifera L.: 9 in Africa, 7 in Europe and 5 in Asia. The analysis was performed using the mtDNA of these subspecies and the Population Analysis with Reticulate Trees software. Some subspecies were represented by more than two specimens based on the available online sequences. Results and conclusions The subspecies A. m. sahariensis from Africa showed unique characteristics and is genetically isolated than all other studied bee subspecies. Specimens collected from Saudi Arabia showed genetic relatedness to A. m. jemenitica, A. m. lamarckii, and some European subspecies, suggesting high degree of hybridization. The close genetic relationship between the Egyptian bees, A. m. lamarckii, and the Syrian bees, A. m. syriaca, were emphasized. The overall genetic network showed the presence of three distinct branches in relation to geographical locations. The high accurateness of the used analysis was confirmed by previous phylogenetic studies as well as the genetic relationships between hybrid bees of A. m. capensis and A. m. scutellata. The genetic networks showed the presence of bee subspecies from Africa in all branches including Europe and Asia. The study suggests the impurity of some specimens mostly due to the hybridization between subspecies. Specific recommendations for future conservation efforts of bees were presented in light of this study.
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Affiliation(s)
- Hossam F Abou-Shaara
- Department of Plant Protection, Faculty of Agriculture, Damanhour University, Damanhour 22516, Egypt
| | - Ahmad A Al-Ghamdi
- Chair of Engineer Abdullah Ahmad Buqshan for Bee Research, Department of Plant Protection, College of Food and Agriculture Sciences, King Saud University, Riyadh 11451, Saudi Arabia
| | - Khalid Ali Khan
- Unit of Bee Research and Honey Production, Faculty of Science, King Khalid University, P.O. Box 9004, Abha 61413, Saudi Arabia.,Department of Biology, Faculty of Science, King Khalid University, P.O. Box 9004, Abha 61413, Saudi Arabia
| | - Saad N Al-Kahtani
- Arid Land Agriculture Department, College of Agricultural Sciences & Foods, King Faisal University, P.O. Box 400, Al-Ahsa 31982, Saudi Arabia
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Mitochondrial DNA Suggests the Introduction of Honeybees of African Ancestry to East-Central Europe. INSECTS 2021; 12:insects12050410. [PMID: 34063321 PMCID: PMC8147603 DOI: 10.3390/insects12050410] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Revised: 04/28/2021] [Accepted: 04/30/2021] [Indexed: 11/17/2022]
Abstract
Simple Summary In Europe, a well-known threat to the conservation of honeybee diversity is the loss of genetic uniqueness of local populations due to beekeepers’ preference for a few genetic lineages. However, due to climate change and large-scale ongoing movement of breeding individuals, the expansion of bees of African origin could represent another threat. This issue has not yet been recognised in detail, although bees bearing African mitochondrial DNA occur in South-West and South Europe due to natural gene flow. Here, we determine the diversity of mitochondrial DNA in honey bees from East-Central Europe. We sequenced the COI-COII region in 427 bees sampled along two 900 km transects (17.5° N and 23° E). We found that 1.64% of bees (95% CI: 0.66–3.35%) had African mitochondrial DNA. It is unlikely that their presence in the area resulted from natural migration but instead human-driven introductions of hybrids of African ancestry. This expansion deserves more attention, as it may contribute to the dissemination of undesirable traits, parasites and diseases. Abstract In Europe, protecting the genetic diversity of Apis mellifera is usually perceived in the context of limiting the spread of the evolutionary C-lineage within the original range of the M-lineage. However, due to climate change and large-scale ongoing movement of breeding individuals, the expansion of bees from the African A-lineage could represent another threat. This issue has not yet been investigated in detail, although A-mitotypes occur in South-West and South Europe due to natural gene flow. Here, we determine the diversity of mtDNA in honey bees from East-Central Europe. We sequenced the COI-COII region in 427 bees sampled along two 900 km transects (17.5° N and 23° E). We found that 1.64% of bees (95% CI: 0.66–3.35 %) had A-mitotypes. It is unlikely that their presence in the area resulted from natural migration but instead human driven introductions of hybrids of African ancestry. This expansion deserves more attention, as it may contribute to the dissemination of undesirable traits, parasites and diseases.
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Tassone EE, Miles LS, Dyer RJ, Rosenberg MS, Cowling RM, Verrelli BC. Evolutionary stability, landscape heterogeneity, and human land-usage shape population genetic connectivity in the Cape Floristic Region biodiversity hotspot. Evol Appl 2021; 14:1109-1123. [PMID: 33897824 PMCID: PMC8061270 DOI: 10.1111/eva.13185] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Revised: 12/03/2020] [Accepted: 12/08/2020] [Indexed: 01/06/2023] Open
Abstract
As human-induced change eliminates natural habitats, it impacts genetic diversity and population connectivity for local biodiversity. The South African Cape Floristic Region (CFR) is the most diverse extratropical area for plant biodiversity, and much of its habitat is protected as a UNESCO World Heritage site. There has long been great interest in explaining the underlying factors driving this unique diversity, especially as much of the CFR is endangered by urbanization and other anthropogenic activity. Here, we use a population and landscape genetic analysis of SNP data from the CFR endemic plant Leucadendron salignum or "common sunshine conebush" as a model to address the evolutionary and environmental factors shaping the vast CFR diversity. We found that high population structure, along with relatively deeper and older genealogies, is characteristic of the southwestern CFR, whereas low population structure and more recent lineage coalescence depict the eastern CFR. Population network analyses show genetic connectivity is facilitated in areas of lower elevation and higher seasonal precipitation. These population genetic signatures corroborate CFR species-level patterns consistent with high Pleistocene biome stability and landscape heterogeneity in the southwest, but with coincident instability in the east. Finally, we also find evidence of human land-usage as a significant gene flow barrier, especially in severely threatened lowlands where genetic connectivity has been historically the highest. These results help identify areas where conservation plans can prioritize protecting high genetic diversity threatened by contemporary human activities within this unique cultural UNESCO site.
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Affiliation(s)
| | - Lindsay S. Miles
- Center for the Study of Biological ComplexityVirginia Commonwealth UniversityRichmondVirginiaUSA
| | - Rodney J. Dyer
- Center for Environmental StudiesVirginia Commonwealth UniversityRichmondVirginiaUSA
| | - Michael S. Rosenberg
- School of Life SciencesArizona State UniversityTempeArizonaUSA
- Center for the Study of Biological ComplexityVirginia Commonwealth UniversityRichmondVirginiaUSA
| | - Richard M. Cowling
- African Centre for Coastal PalaeoscienceBotany DepartmentNelson Mandela UniversityPort ElizabethSouth Africa
| | - Brian C. Verrelli
- School of Life SciencesArizona State UniversityTempeArizonaUSA
- Center for the Study of Biological ComplexityVirginia Commonwealth UniversityRichmondVirginiaUSA
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12
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Reanalysis and Revision of the Complete Mitochondrial Genome of Artemia urmiana Günther, 1899 (Crustacea: Anostraca). DIVERSITY 2021. [DOI: 10.3390/d13010014] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
In the previously published mitochondrial genome sequence of Artemia urmiana (NC_021382 [JQ975176]), the taxonomic status of the examined Artemia had not been determined, due to parthenogenetic populations coexisting with A. urmiana in Urmia Lake. Additionally, NC_021382 [JQ975176] has been obtained with pooled cysts of Artemia (0.25 g cysts consists of 20,000–25,000 cysts), not a single specimen. With regard to coexisting populations in Urmia Lake, and intra- and inter-specific variations in the pooled samples, NC_021382 [JQ975176] cannot be recommended as a valid sequence and any attempt to attribute it to A. urmiana or a parthenogenetic population is unreasonable. With the aid of next-generation sequencing methods, we characterized and assembled a complete mitochondrial genome of A. urmiana with defined taxonomic status. Our results reveal that in the previously published mitogenome (NC_021382 [JQ975176]), tRNA-Phe has been erroneously attributed to the heavy strand but it is encoded in the light strand. There was a major problem in the position of the ND5. It was extended over the tRNA-Phe, which is biologically incorrect. We have also identified a partial nucleotide sequence of 311 bp that was probably erroneously duplicated in the assembly of the control region of NC_021382 [JQ975176], which enlarges the control region length by 16%. This partial sequence could not be recognized in our assembled mitogenome as well as in 48 further examined specimens of A. urmiana. Although, only COX1 and 16S genes have been widely used for phylogenetic studies in Artemia, our findings reveal substantial differences in the nucleotide composition of some other genes (including ATP8, ATP6, ND3, ND6, ND1 and COX3) among Artemia species. It is suggested that these markers should be included in future phylogenetic studies.
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13
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Abou-Shaara HF, Syed Abbas A, AL-Kahtani SN, Taha EKA, Ali Khan K, Jamal ZA, Alhumaidi Alotaibi M, Ahmad B, Ahmad Khan N, Qamer S, Ishtiaq Anjum S, Khan S, Hossam Mahmoud A, Mohammed OB, Gamal El Den Nasser M. Exploring the non-coding regions in the mtDNA of some honey bee species and subspecies. Saudi J Biol Sci 2021; 28:204-209. [PMID: 33424298 PMCID: PMC7783669 DOI: 10.1016/j.sjbs.2020.09.047] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2020] [Revised: 09/20/2020] [Accepted: 09/22/2020] [Indexed: 11/22/2022] Open
Abstract
The sequence of the DNA contains coding and non-coding regions. The role of the non-coding regions is not known and is hypothesized to maintain the structure of the DNA. This study aimed to investigate the structure of the non-coding sequences in honey bees utilizing bioinformatics. The non-coding sequences of the mtDNA of three honey bee species Apis dorosata, Apis florea, Apis cerana, and ten subspecies of Apis mellifera were investigated. Different techniques were utilized to explore the non-coding regions of these bees including sequence analysis, phylogenetic relationships, enzymatic digestion, and statistical tests. Variations in size and sequences of nucleotides were detected in the studied species and subspecies, but with the same nucleotide abundance (i.e. nucleotides A were more than T and nucleotides G were less than C). The phylogenetic tree based on the non-coding regions was partially similar to the known phylogenetic relationships between these bees. The enzymatic digestion using four restriction enzymes confirmed the results of the phylogenetic relationships. The statistical analysis based on numerical codes for nucleotides showed the absence of significant variations between the studied bees in their sequences in a similar way to results of neutrality tests. This study suggests that the non-coding regions have the same functional role in all the studied bees regardless of the number of nucleotides, and not just to maintain the structure of the DNA. This is approximately the first study to shade lights on the non-coding regions of the mtDNA of honey bees.
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Affiliation(s)
- Hossam F. Abou-Shaara
- Department of Plant Protection, Faculty of Agriculture, Damanhour University, Damanhour, 22516, Egypt
| | - Afshan Syed Abbas
- Department of Zoology, University of Education, Lower Mall Campus, Lahore, Pakistan
| | - Saad N. AL-Kahtani
- Arid Land Agriculture Department, Faculty of Agriculture & Food Sciences, King Faisal University, Al-Ahsa, Saudi Arabia
| | - El-Kazafy A. Taha
- Economic Entomology Department, Faculty of Agriculture, Kafrelsheikh University, Kafrelsheikh, Egypt
| | - Khalid Ali Khan
- Unit of Bee Research and Honey Production, Faculty of Science, King Khalid University, P.O. Box 9004, Abha 61413, Saudi Arabia
- Research Center for Advanced Materials Science (RCAMS), King Khalid University, P.O. Box 9004, Abha 61413, Saudi Arabia
- Biology Department, Faculty of Science, King Khalid University, P.O. Box 9004, Abha 61413, Saudi Arabia
| | - Zakia A. Jamal
- Biology Department, Faculty of Science, Taibah University, Al-Sharm, Yanbu El-Bahr 46429, Saudi Arabia
| | | | - Bilal Ahmad
- Department of Zoology, Government College University, Faisalabad 38000, Pakistan
| | - Naveed Ahmad Khan
- Institute of Pure and Applied Biology, Zoology Division, Bahauddin Zakariya University, Multan 60800, Pakistan
| | - Samina Qamer
- Department of Zoology, Government College University, Faisalabad, Pakistan
| | - Syed Ishtiaq Anjum
- Department of Zoology, Kohat University of Science and Technology, Kohat 26000, Khyber Pakhtunkhwa, Pakistan
| | - Sanaullah Khan
- Department of Zoology, University of Peshawar, Khyber Pakhtunkhwa, Pakistan
| | - Ahmed Hossam Mahmoud
- Department Zoology, College of Science, King Saud University, P.O Box 2455, Riyadh 11451, Saudi Arabia
| | - Osama B. Mohammed
- Department Zoology, College of Science, King Saud University, P.O Box 2455, Riyadh 11451, Saudi Arabia
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14
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Fisher KE, Bradbury SP, Coates BS. Prediction of mitochondrial genome-wide variation through sequencing of mitochondrion-enriched extracts. Sci Rep 2020; 10:19123. [PMID: 33154458 PMCID: PMC7645498 DOI: 10.1038/s41598-020-76088-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Accepted: 10/19/2020] [Indexed: 11/08/2022] Open
Abstract
Although mitochondrial DNA (mtDNA) haplotype variation is often applied for estimating population dynamics and phylogenetic relationships, economical and generalized methods for entire mtDNA genome enrichment prior to high-throughput sequencing are not readily available. This study demonstrates the utility of differential centrifugation to enrich for mitochondrion within cell extracts prior to DNA extraction, short-read sequencing, and assembly using exemplars from eight maternal lineages of the insect species, Ostrinia nubilalis. Compared to controls, enriched extracts showed a significant mean increase of 48.2- and 86.1-fold in mtDNA based on quantitative PCR, and proportion of subsequent short sequence reads that aligned to the O. nubilalis reference mitochondrial genome, respectively. Compared to the reference genome, our de novo assembled O. nubilalis mitochondrial genomes contained 82 intraspecific substitution and insertion/deletion mutations, and provided evidence for correction of mis-annotated 28 C-terminal residues within the NADH dehydrogenase subunit 4. Comparison to a more recent O. nubilalis mtDNA assembly from unenriched short-read data analogously showed 77 variant sites. Twenty-eight variant positions, and a triplet ATT codon (Ile) insertion within ATP synthase subunit 8, were unique within our assemblies. This study provides a generalizable pipeline for whole mitochondrial genome sequence acquisition adaptable to applications across a range of taxa.
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Affiliation(s)
- Kelsey E Fisher
- Department of Entomology, Iowa State University, Ames, IA, 50011, USA.
| | - Steven P Bradbury
- Department of Entomology, Iowa State University, Ames, IA, 50011, USA
- Department of Natural Resource Ecology and Management, Iowa State University, Ames, IA, 50011, USA
| | - Brad S Coates
- Department of Agriculture, Agriculture Research Station, Corn Insects and Crop Genetics Research Unit, Ames, IA, 50011, USA
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15
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Tang Y, Zheng X, Liu H, Sunxie F. Population genetics and comparative mitogenomic analyses reveal cryptic diversity of Amphioctopus neglectus (Cephalopoda: Octopodidae). Genomics 2020; 112:3893-3902. [PMID: 32603760 DOI: 10.1016/j.ygeno.2020.06.036] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Revised: 06/14/2020] [Accepted: 06/22/2020] [Indexed: 12/28/2022]
Abstract
This study presented 96 cox1 and 76 cox3 genes of Amphioctopus neglectus populations. Three distinct lineages were formed from phylogenetic trees and networks constructed using haplotypes. Mitogenomes of A. neglectus-a and A. neglectus-b as the representatives of two lineages separated from population genetics were sequenced to compare with A. neglectus at the genome-level. Amphioctopus neglectus-a showed significant differences with A. neglectus, mainly reflected in gene length, intergenic regions and the secondary structure of tandem repeat motifs. Notably, two sequence deletions in mitogenomes of the two representative species were detected in different positions of major non-coding regions, which were the most distinct differences with A. neglectus. Pairwise genetic distances and the phylogenetic analysis supported the relationship of (A. neglectus-a + (A. neglectus + A. neglectus-b)). This study suggested that A. neglectus-a should be considered as a potential cryptic species of this complex, while A. neglectus-b needed further verification to be defined.
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Affiliation(s)
- Yan Tang
- Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao 266003, China; Key Laboratory of Mariculture, Ocean University of China, Qingdao 266003, China
| | - Xiaodong Zheng
- Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao 266003, China; Key Laboratory of Mariculture, Ocean University of China, Qingdao 266003, China.
| | - Haijuan Liu
- Guangxi Key Laboratory of Marine Biotechnology, Guangxi Institute of Oceanology, Beihai 536000, China
| | - Feige Sunxie
- Dongshan Boguangtianxing Foods Co., Ltd., Zhangzhou 363000, China
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16
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Bluher SE, Miller SE, Sheehan MJ. Fine-Scale Population Structure but Limited Genetic Differentiation in a Cooperatively Breeding Paper Wasp. Genome Biol Evol 2020; 12:701-714. [PMID: 32271866 PMCID: PMC7259676 DOI: 10.1093/gbe/evaa070] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/03/2020] [Indexed: 12/16/2022] Open
Abstract
Relatively little is known about the processes shaping population structure in cooperatively breeding insect species, despite the long-hypothesized importance of population structure in shaping patterns of cooperative breeding. Polistes paper wasps are primitively eusocial insects, with a cooperative breeding system in which females often found nests in cooperative associations. Prior mark-recapture studies of Polistes have documented extreme female philopatry, although genetic studies frequently fail to detect the strong population structure expected for highly philopatric species. Together these findings have led to lack of consensus on the degree of dispersal and population structure in these species. This study assessed population structure of female Polistes fuscatus wasps at three scales: within a single site, throughout Central New York, and across the Northeastern United States. Patterns of spatial genetic clustering and isolation by distance were observed in nuclear and mitochondrial genomes at the continental scale. Remarkably, population structure was evident even at fine spatial scales within a single collection site. However, P. fuscatus had low levels of genetic differentiation across long distances. These results suggest that P. fuscatus wasps may employ multiple dispersal strategies, including extreme natal philopatry as well as longer-distance dispersal. We observed greater genetic differentiation in mitochondrial genes than in the nuclear genome, indicative of increased dispersal distances in males. Our findings support the hypothesis that limited female dispersal contributes toward population structure in paper wasps.
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Affiliation(s)
- Sarah E Bluher
- Department of Neurobiology and Behavior, Cornell University
| | - Sara E Miller
- Department of Neurobiology and Behavior, Cornell University
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17
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Eimanifar A, Pieplow JT, Asem A, Ellis JD. Genetic diversity and population structure of two subspecies of western honey bees ( Apis mellifera L.) in the Republic of South Africa as revealed by microsatellite genotyping. PeerJ 2020; 8:e8280. [PMID: 31915579 PMCID: PMC6944124 DOI: 10.7717/peerj.8280] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2019] [Accepted: 11/22/2019] [Indexed: 12/14/2022] Open
Abstract
Apis mellifera scutellata and Apis mellifera capensis, two native subspecies of western honey bees in the Republic of South Africa (RSA), are important to beekeepers in their native region because beekeepers use these bees for honey production and pollination purposes. Additionally, both bees are important invasive pests outside of their native ranges. Recently, whole mitogenome sequencing and single nucleotide polymorphisms were used to study their genetic diversity. To add to our knowledge of the molecular ecology of both bees, we tested the ability of microsatellites to be used as a tool to discriminate between A.m. capensis and A.m. scutellata. We analyzed the genetic variability and overall population structure of both bee subspecies and hybrids of the two by genotyping individuals collected from RSA (N = 813 bees from 75 apiaries) at 19 microsatellite DNA loci. Overall, populations averaged between 9.2 and 11.3 alleles per locus, with unbiased heterozygosity values ranging from 0.81 to 0.86 per population. Bayesian clustering analyses revealed two distinct evolutionary units, though the results did not match those of earlier morphometric and molecular analyses. This suggests that the microsatellites we tested were not sufficient for subspecies identification purposes, especially for Cape and hybrid bees. Nevertheless, the microsatellite data highlight the considerable genetic diversity within both populations and a larger-than-expected hybridization zone between the natural distributions of A.m. capensis and A.m. scutellata.
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Affiliation(s)
- Amin Eimanifar
- Entomology and Nematology Department, Honey Bee Research and Extension Laboratory, Gainesville, FL, USA.,Independent Senior Scientist, Industrial District, Easton, MD, USA
| | - Johanna T Pieplow
- Molekulare Ökologie, Institut Für Biologie, Molekulare Ökologie, Martin-Luther-Universität Halle-Wittenberg, Halle, Germany
| | - Alireza Asem
- College of Fisheries and Life Science, Hainan Tropical Ocean University, Yucai Road, Sanya, China
| | - James D Ellis
- Entomology and Nematology Department, Honey Bee Research and Extension Laboratory, Gainesville, FL, USA
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18
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Cejas D, López‐López A, Muñoz I, Ornosa C, De la Rúa P. Unveiling introgression in bumblebee (
Bombus terrestris
) populations through mitogenome‐based markers. Anim Genet 2019; 51:70-77. [DOI: 10.1111/age.12874] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2019] [Revised: 07/09/2019] [Accepted: 10/04/2019] [Indexed: 01/05/2023]
Affiliation(s)
- D. Cejas
- Área de Biología Animal Departamento de Zoología y Antropología Física Facultad de Veterinaria Universidad de Murcia Murcia 30100 Spain
| | - A. López‐López
- Área de Biología Animal Departamento de Zoología y Antropología Física Facultad de Veterinaria Universidad de Murcia Murcia 30100 Spain
- Área de Zoología Departamento de Agroquímica y Medio Ambiente Campus de Elche Universidad Miguel Hernández Elche 03202 Spain
| | - I. Muñoz
- Área de Biología Animal Departamento de Zoología y Antropología Física Facultad de Veterinaria Universidad de Murcia Murcia 30100 Spain
| | - C. Ornosa
- Departamento de Biodiversidad Ecología y Evolución Facultad de Ciencias Biológicas Universidad Complutense Madrid 28040 Spain
| | - P. De la Rúa
- Área de Biología Animal Departamento de Zoología y Antropología Física Facultad de Veterinaria Universidad de Murcia Murcia 30100 Spain
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Eimanifar A, Brooks SA, Bustamante T, Ellis JD. Population genomics and morphometric assignment of western honey bees (Apis mellifera L.) in the Republic of South Africa. BMC Genomics 2018; 19:615. [PMID: 30111292 PMCID: PMC6094452 DOI: 10.1186/s12864-018-4998-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2018] [Accepted: 08/07/2018] [Indexed: 12/27/2022] Open
Abstract
BACKGROUNDS Apis mellifera scutellata and A.m. capensis (the Cape honey bee) are western honey bee subspecies indigenous to the Republic of South Africa (RSA). Both bees are important for biological and economic reasons. First, A.m. scutellata is the invasive "African honey bee" of the Americas and exhibits a number of traits that beekeepers consider undesirable. They swarm excessively, are prone to absconding (vacating the nest entirely), usurp other honey bee colonies, and exhibit heightened defensiveness. Second, Cape honey bees are socially parasitic bees; the workers can reproduce thelytokously. Both bees are indistinguishable visually. Therefore, we employed Genotyping-by-Sequencing (GBS), wing geometry and standard morphometric approaches to assess the genetic diversity and population structure of these bees to search for diagnostic markers that can be employed to distinguish between the two subspecies. RESULTS Apis mellifera scutellata possessed the highest mean number of polymorphic SNPs (among 2449 informative SNPs) with minor allele frequencies > 0.05 (Np = 88%). The RSA honey bees generated a high level of expected heterozygosity (Hexp = 0.24). The mean genetic differentiation (FST; 6.5%) among the RSA honey bees revealed that approximately 93% of the genetic variation was accounted for within individuals of these subspecies. Two genetically distinct clusters (K = 2) corresponding to both subspecies were detected by Model-based Bayesian clustering and supported by Principal Coordinates Analysis (PCoA) inferences. Selected highly divergent loci (n = 83) further reinforced a distinctive clustering of two subspecies across geographical origins, accounting for approximately 83% of the total variation in the PCoA plot. The significant correlation of allele frequencies at divergent loci with environmental variables suggested that these populations are adapted to local conditions. Only 17 of 48 wing geometry and standard morphometric parameters were useful for clustering A.m. capensis, A.m. scutellata, and hybrid individuals. CONCLUSIONS We produced a minimal set of 83 SNP loci and 17 wing geometry and standard morphometric parameters useful for identifying the two RSA honey bee subspecies by genotype and phenotype. We found that genes involved in neurology/behavior and development/growth are the most prominent heritable traits evolved in the functional evolution of honey bee populations in RSA. These findings provide a starting point for understanding the functional basis of morphological differentiations and ecological adaptations of the two honey bee subspecies in RSA.
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Affiliation(s)
- Amin Eimanifar
- Honey Bee Research and Extension Laboratory, Entomology and Nematology Department, University of Florida, Gainesville, Florida, 32611-0620 USA
| | - Samantha A. Brooks
- Department of Animal Sciences, University of Florida, Gainesville, FL 32611 USA
| | - Tomas Bustamante
- Honey Bee Research and Extension Laboratory, Entomology and Nematology Department, University of Florida, Gainesville, Florida, 32611-0620 USA
| | - James D. Ellis
- Honey Bee Research and Extension Laboratory, Entomology and Nematology Department, University of Florida, Gainesville, Florida, 32611-0620 USA
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