Eur. J. Entomol. 119: 309-317, 2022 | DOI: 10.14411/eje.2022.032

DNA barcoding reveals long-term speciation processes in subspecies of the Melipona (Michmelia) seminigra complex (Hymenoptera: Apidae)Original article

Izaura Bezerra FRANCINI ORCID...1, 6, João Marcos Guimarães CAPURUCHO ORCID...2, Antônio Saulo Cunha MACHADO ORCID...3, Carlos Gustavo NUNES-SILVA ORCID...4, Jacqueline Da Silva BATISTA ORCID...1, 3, Luciano COSTA ORCID...5, Gislene Almeida CARVALHO-ZILSE ORCID...1, 6, *
1 Programa de Pós-Graduação em Genética, Conservação e Biologia Evolutiva (PPG-GCBEv), Instituto Nacional de Pesquisas da Amazônia (INPA), Av. André Araújo 2936, 69060-001 Manaus, AM, Brazil; e-mails: izaurabfrancini@gmail.com, dourada@gmail.com, gislenezilse@gmail.com
2 Life Sciences Section, Negaunee Integrative Research Center, The Field Museum of Natural History, 1400 S. Lake Shore Drive, Chicago, IL 60605, USA; e-mail: jcapurucho@fieldmuseum.org
3 Laboratório de Biologia Molecular, Centro de Biotecnologia da Amazônia - CBA, Manaus, AM, Brazil; e-mail: ascmbio@gmail.com
4 Instituto de Ciências Biológicas (ICB), Universidade Federal do Amazonas (UFAM), Avenida Gal. Rodrigo Otávio 3000, 69077-000 Manaus, AM, Brazil; e-mail: cgmanaus@gmail.com
5 Instituto Tecnológico Vale, Desenvolvimento Sustentável, Rua Boaventura da Silva, 955, Belém, PA 66055-090, Brazil; e-mail: costa.luciano@itv.org
6 Grupo de Pesquisas em Abelhas (GPA), Coordenação de Biodiversidade (COBIO), Instituto Nacional de Pesquisas da Amazônia (INPA), Av. André Araújo 2936, 69060-001 Manaus, AM, Brazil

The stingless bee Melipona (Michmelia) seminigra Friese is a polytypic species widely distributed in Brazilian Amazon and Bolivia. Seven subspecies are recognized, four are described, which inhabit mutually exclusive areas in the Amazon basin, although zones of hybridization are recorded. The three other subspecies, despite being recognized by taxonomists are undescribed. Melipona seminigra is a good honey-producer and an important pollinator of native flora and crops. Partial DNA sequence of cytochrome c oxidase subunit 1 (COI) mitochondrial gene (526 bp) was used to identify the four described subspecies of M. seminigra (M. s. abunensis, M. s. merrillae, M. s. pernigra, M. s. seminigra) and two other possible subspecies (M. s. ssp1 and M. s. ssp2). We added public data (sequences of ten other Melipona species) of the same subgenera and carried out phylogenetic analyses. The aim was to evaluate if subspecies in the M. seminigra complex could be delimited using COI and measure the genetic distances between them. Our results revealed that the genetic distances between subspecies of M. seminigra ranged from 0.4 to 2.7% (average 1.80 ± 0.47) and among Melipona species from 0.2 to 2.9% (average 2.13 ± 0.5). The average haplotype diversity was 0.8770 ± 0.0140 and average nucleotide diversity 0.0166 ± 0.0004. Phylogenetic and clustering analysis revealed well delimited clusters for subspecies of M. seminigra and that the inter subspecies divergences are similar to inter species divergence. Our findings indicate that the COI gene can be used for delimiting subspecies of M. seminigra.

Keywords: mtDNA, COI diversity, genetic distance, barcoding delimitation, bees, Meliponini

Received: April 1, 2022; Revised: June 24, 2022; Accepted: June 24, 2022; Published online: August 12, 2022  Show citation

ACS AIP APA ASA Harvard Chicago Chicago Notes IEEE ISO690 MLA NLM Turabian Vancouver
FRANCINI, I.B., CAPURUCHO, J.M.G., MACHADO, A.S.C., NUNES-SILVA, C.G., BATISTA, J.D.S., COSTA, L., & CARVALHO-ZILSE, G.A. (2022). DNA barcoding reveals long-term speciation processes in subspecies of the Melipona (Michmelia) seminigra complex (Hymenoptera: Apidae). EJE, 119, Article 309-317. https://doi.org/10.14411/eje.2022.032
Share...
Download citation
  • BibTeX (.bib)
  • Bookends (.ris)
  • EasyBib (.ris)
  • EndNote (.enw)
  • EndNote 8 (.xml)
  • ISI WoS (.isi)
  • Medlars (.medlars)
  • Mendeley (.ris)
  • MODS (.xml)
  • Papers (.ris)
  • RefWorks (.txt)
  • RefManager (.ris)
  • RIS (.ris)
  • MS Word (.xml)
  • Zotero (.ris)
    • Open full article

    References

    1. Absy M.L. & Kerr W.E. 1977: Some plants visited by workers of Melipona seminigra merrillae to obtain pollen, at Manaus. - Acta Amazon. 7: 309-315 [in Portuguese]. Go to original source...
    2. Alattal Y., Alsharhi M., Alghamdi A., Alfaify S., Migdadi H. & Ansari M. 2014: Characterization of the native honeybee subspecies in Saudi Arabia using the mtDNA COI-COII intergenic region and morphometric characteristics. - Bull. Insectol. 67: 31-37.
    3. Alghamdi A. & Alattal Y. 2021: Assessment of genetic variation in Apis mellifera jemenitica (Hymenoptera: Apidae) using Cytochrome Oxidase I gene sequences. - Saudi J. Biol. Sci. 28: 6586-6591. Go to original source...
    4. Avise J.C. & Aquadro C.F. 1982: A comparative summary of genetic distances in the vertebrates: patterns and correlations. - Evol. Biol. 15: 151-185. Go to original source...
    5. Bacelar-Lima C.G., Freire D.C.B., Coletto-Silva A., Costa K.B., Laray J.P.B., Vilas-Boas H.C. & Carvalho-Zilse G.A. 2006: Melitocoria from Zygia racemosa (Ducke) Barneby & Grimes by Melipona seminigra merrillae Cockerell, 1919 and Melipona compressipes manaosensis Schwarz, 1932 (Hymenoptera, Meliponina) in Central Amazon, Brazil. - Acta Amaz. 36: 343-348. Go to original source...
    6. Camargo J.M.F. & Pedro S.R.M. 2013: Meliponini Lepeletier, 1836. In Moure J.S., Urban D. & Melo G.A.R. (eds): Catalogue of Bees (Hymenoptera, Apoidea) in the Neotropical Region. URL: http://www.moure.cria.org.br/catalogue (last accessed 24 Nov. 2021).
    7. Carvalho-Zilse G.A. & Nunes-Silva C.G. 2012: Threats to the stingless bees in the Brazilian Amazon: How to deal with scarce biological data and an increasing rate of destruction. In Florio R.M. (ed.): Bees: Biology, Threats and Colonies. Nova Science Publishers, Hauppauge, NY, pp. 147-168.
    8. Corander J. & Tang J. 2007: Bayesian analysis of population structure based on linked molecular information. - Math. Bio­sci. 205: 19-31. Go to original source...
    9. Corander J., Marttinen P., Sirén J. & Tang J. 2008: Enhanced Bayesian modelling in BAPS software for learning genetic structures of populations. - BMC Bioinformatics 9: 539, 14 pp. Go to original source...
    10. Francini I.B., Gross M.C., Nunes-Silva C.G. & Carvalho-Zilse G.A. 2011: Cytogenetic analysis of the Amazon stingless bee Melipona seminigra merrillae reveals different chromosome number for the genus. - Sci. Agric. 68: 592-593. Go to original source...
    11. Francini I.B., Nunes-Silva C.G. & Carvalho-Zilse G.A. 2012: Diploid male production of two Amazonian Melipona bees (Hymenoptera: Apidae). - Psyche 2012: 484618, 7 pp. Go to original source...
    12. Franck P., Garnery L., Loiseau A., Oldroyd B.P., Hepburn H.R., Solignac M. & Cornuet J.M. 2001: Genetic diversity of the honeybee in Africa: microsatellite and mitochondrial data. - Heredity 86: 420-430. Go to original source...
    13. Garnery L., Cornuet J.M. & Solignac M. 1992: Evolutionary history of the honeybee Apis mellifera inferred from mitochondrial DNA analysis. - Mol. Ecol. 1: 145-154. Go to original source...
    14. Hajibabaei M., Janzen D.H., Burns J.M., Hallwachs W. & Herbert P.D.N. 2006: DNA barcodes distinguish species of tropical Lepidoptera. - Proc. Natl. Acad. Sci. U.S.A. 103: 968-971. Go to original source...
    15. Hajibabaei M., Singer G.A.C., Hebert P.D.N. & Hickey D.A. 2007: DNA barcoding: how it complements taxonomy, molecular phylogenetics and population genetics. - Trends Genet. 23: 167-172. Go to original source...
    16. Hall T.A. 1999: BioEdit: a user-Friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. - Nucl. Acids Symp. Ser. 41: 95-98.
    17. Hawlitschek O., Nagy Z.T. & Glaw F. 2012: Island evolution and systematic revision of Comoran snakes: Why and when subspecies still make sense. - PloS ONE 7(8): e42970, 19 pp. Go to original source...
    18. Heard A. 1999: The role of stingless bees in crop pollination. - Annu. Rev. Entomol. 44: 183-206. Go to original source...
    19. Hebert P.D.N., Cywinska A., Ball S.L. & Dewaard J.R. 2003a: Biological identification through DNA barcodes. - Proc. R. Soc. Lond. (B) 270: 313-322. Go to original source...
    20. Hebert P.D.N., Ratnasingham S. & de Waard J.R. 2003b: Barcoding animal life: cytochrome c oxidase subunit 1 divergences among closely related species. - Proc. R. Soc. Lond. (B) 270: S96-S99. Go to original source...
    21. Hebert P.D.N., Stoeckle M.Y., Zemlak T.S. & Francis C.M. 2004: Identification of birds through DNA barcodes. - PLoS Biol. 2(10): e312, 7 pp. Go to original source...
    22. Hurtado-Burillo M., Ruiz C., May-Itzá W., Quezada-Eúan J.J.G. & De La Rúa P. 2013: Barcoding stingless bees: genetic diversity of the economically important genus Scaptotrigona in Mesoamerica. - Apidologie 44: 1-10. Go to original source...
    23. ICZN 1999: International Code of Zoological Nomenclature. URL: https://www.iczn.org/the-code/the-code-online/ (last accessed 6 June 2022).
    24. Ilyasov R., Nikolenko A., Tuktarov V., Goto K., Takahashi J.-I. & Kwon H.W. 2019: Comparative analysis of mitochondrial genomes of the honey bee subspecies A. m. caucasica and A. m. carpathica and refinement of their evolutionary lineages. - J. Apic. Res. 58: 567-579. Go to original source...
    25. Kambhampati S. & Smith P.T. 1995: PCR primers for the amplification of four insect mitochondrial gene fragments. - Insect Mol. Biol. 4: 233-236. Go to original source...
    26. Kimura M. 1980: A simple method for estimating evolutionary rates of base substitutions through the comparative studies of sequence evolution. - J. Mol. Evol. 16: 111-120. Go to original source...
    27. Librado P. & Rozas J. 2009: DnaSP v5: A software for comprehensive analysis of DNA polymorphism data. - Bioinformatics 25: 1451-1452. Go to original source...
    28. Mayr E. 1942: Systematics and the Origin of Species. Columbia Univ. Press, New York, 334 pp.
    29. Mayr E. 1963: Animal Species and Evolution. Harvard University Press, Cambridge, 797 pp. Go to original source...
    30. Mayr E. & Ashlock P.D. 1991: Principles of Systematic Zoology. 2nd ed. McGrawHill, New York, 475 pp.
    31. Michener C.D. 2007: The Bees of the World. 2nd ed. Johns Hopkins University Press, Baltimore, 953 pp.
    32. Moure J.S. & Kerr W.E. 1950: Suggestions for modifying the systematics of the genus Melipona (Hymenoptera, Apoidea). - Dusenia 1: 105-131 [in Portuguese].
    33. Paithankar K.R. & Prasad K.S.N. 1991: Precipitation of DNA by polyethylene glycol and ethanol. - Nucleic Acids Res. 19: 1346. Go to original source...
    34. Patten M.A. 2015: Subspecies and the philosophy of science. - The Auk: Ornithol. Adv. 132: 481-485. Go to original source...
    35. Patten M.A. & Remsen Jr J.V. 2017: Complementary roles of phenotype and genotype in subspecies delimitation. - J. Hered. 108: 462-464. Go to original source...
    36. Pedro S.R.M. 2014: The stingless bee fauna in Brazil (Hymeno­ptera: Apidae). - Sociobiology 61: 348-354. Go to original source...
    37. Platt A.R., Woodhall R.W. & George Jr. A.L. 2007: Improved DNA sequencing quality and efficiency using an optimized fast cycle sequencing protocol. - Biotechniques 43: 58-62. Go to original source...
    38. Posada D. & Crandall K.A. 1998: MODELTEST: Testing the model of DNA substitution. - Bioinformatics 14: 817-818. Go to original source...
    39. Ramírez S.R., Nieh J.C., Quental T.B., Roubik D.W., Imperatriz-Fonseca V.L. & Pierce N.E. 2010: A molecular phylogeny of the stingless bee genus Melipona (Hymenoptera: Apidae). - Mol. Phylogenet. Evol. 56: 519-525. Go to original source...
    40. Roubik D.W. 1989: Ecology and Natural History of Tropical Bees. Cambridge University Press, New York, 514 pp. Go to original source...
    41. Silveira F.A., Melo G.A.R. & Almeida E.A. 2002: Abelhas Brasileiras: Sistemática e Identificação. 1st ed. Araucaria Foundation, Belo Horizonte, MG, 253 pp.
    42. Simon C., Frati F., Beckenbach A., Crespi B., Liu H. & Flook P. 1994: Evolution, weighting and phylogenetic utility of mitochondrial gene sequences and a compilation of conserved polymerase chain reaction primers. - Ann. Entomol. Soc. Am. 87: 651-701. Go to original source...
    43. Slaa E.J., Chaves L.A.S., Malgodi-Braga K.S. & Hofstede F.E. 2006: Stingless bees in applied pollination: practice and perspectives. - Apidologie 37: 293-315. Go to original source...
    44. Stamatakis A., Hoover P. & Rougemont J. 2008: A rapid bootstrap algorithm for the RAxML web servers. - Syst. Biol. 57: 758-771. Go to original source...
    45. Swofford D.L. 2002: PAUP* Phylogenetic Analysis Using Parsimony and Other Methods. Sinauer Associates, Sunderland, MA.
    46. Syromyatnikov M.Y., Borodachev A.V., Kokina A.V. & Popov V.N. 2018: A molecular method for the identification of honey bee subspecies used by beekeepers in Russia. - Insects 9: 10, 12 pp. Go to original source...
    47. Tamura K., Peterson D., Peterson N., Stecher G., Nei M. & Kumar S. 2011: MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. - Mol. Biol. Evol. 28: 2731-2739. Go to original source...
    48. Thompson J.D., Higgins D.G. & Gibson T.J. 1994: ClustalW: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. - Nucleic Acids Res. 22: 4673-4680. Go to original source...
    49. Torstrom S.M., Pangle K.L., Bradley J. & Swanson B.J. 2014: Shedding subspecies: The influence of genetics on reptile subspecies taxonomy - Mol. Phylogenet. Evol. 76: 134-143. Go to original source...
    50. Waugh J. 2007: DNA barcoding in animal species, progress, potential and pitfalls. - Bioessays 29: 188-197. Go to original source...
    51. Winker K. 2010: Subspecies represent geographically partitioned variation, a gold mine of evolutionary biology, and a challenge for conservation. - Ornithol. Monogr. 67: 6-23. Go to original source...
    52. Winker K. 2021: An overview of speciation and species limits in birds. - Ornithology 138: 1-27. Go to original source...

    This is an open access article distributed under the terms of the Creative Commons Attribution 4.0 International License (CC BY 4.0), which permits use, distribution, and reproduction in any medium, provided the original publication is properly cited. No use, distribution or reproduction is permitted which does not comply with these terms.


    Return to the content