Genetic Characterization of Honeybee (Apis mellifera) in Comoros Islands using Mitochondrial and Microsatellite Markers

Abstract

Honeybees, Apis mellifera, are key contributors to the global economy, nutrition, food security and ecological biodiversity. Despite their robust benefits, declines in honeybee populations have been reported owing to a number of factors. Such include pests and diseases, climate change, poor management practices, change in land usage and low ge-netic diversity. High intra-colonial genetic diversity is associated with resilience and re-sistance to pest and diseases as well as increased colony level fitness. The use of morpho-logical characters to characterize honeybees is limited by the fact that they are subject to manipulation by environmental selection pressures and introgression resulting from hy-bridization between sub-species. Hence, mitochondrial and microsatellite markers which are more powerful and neutral have been used. Honeybees native to the Comoros islands have not been characterized despite the fact that islands often possess endemic species which serve as distinct genetic reservoirs with unusual adaptations. This study aimed at generating extensive knowledge on the genetic diversity and population structure of hon-eybees in Comoros islands using mitochondrial and microsatellite markers. In the study, 160 wild and managed colonies were sampled across the Comoros archipelagos and char-acterized. Mitochondrial analyses involved PCR amplification and sequencing of the in-tergenic region spanning between COI- COII genes followed by phylogenetic analyses. In addition, 16 colonies distributed across the three islands were analyzed using 19 mi-crosatellite markers. The mtDNA sequences analyses revealed the existence of three hap-lotypes in Comoros Islands where A1 haplotype, with a distribution of 51%, 80% and 91% in Anjouan, Moheli and Ngazidja respectively was predominant. Two other haplo-types (L1 and L2) were newly described in this study. They had a cumulative distribution of 48% in Anjouan, 20% in Moheli and 9% in Ngazidja. L1 and L2 showed high levels of variability as compared to A1 lineage. L2 arose from rare mtDNA recombination be-tween L1 and A1 lineages. Discriminant Analysis of Principal Components, Provesti‘s neighbor joining tree and Bayesian clustering in STRUCTURE clustered the samples according to geography suggesting a restricted gene flow between islands. The popula-tion is strongly differentiated (GST=0.41(±0.068)) with a much stronger differentiation between Ngazidja and Moheli (GST = 0.53) than Anjouan and Moheli (GST = 0.37) or Anjouan and Ngazidja (GST =0.38)). High levels of genetic diversity evidenced by high number of alleles per locus (5.92 (±0.05)), and the high expected heterozygosity (0.66 (±0.03)). Private alleles (216 and 218) were detected at A113 locus. In conclusion, mtDNA haplotypes can coexist and undergo rare mtDNA recombination as well as hy-bridization at the nuclear genome. There is need to investigate mechanisms that enable mtDNA recombination in honeybees.