Elevational Melanism in East African Honey Bees Involves a Major-Effect Locus
Abstract
Thermal melanism, whereby darker pigmentation occurs in colder environments, is a widespread pattern; yet, its genetic and physiological basis in eusocial insects remains poorly understood. East African honey bees (Apis mellifera) occupy elevational gradients in which highland populations are darker, larger, and more cold-tolerant than lowland conspecifics. Here, we integrated population genomics, structural variations, and functional genomics to investigate elevational melanism. We sampled, phenotyped, and resequenced 139 workers from five East African mountain systems. A genome-wide association study identified 977 single-nucleotide polymorphisms (SNPs) significantly associated with abdominal pigmentation, with a single peak at the ebony ortholog AmEbony on chromosome 1. Allelic variation at AmEbony formed three genetic clusters tracking a continuous pigmentation gradient, and 77 divergent SNPs (DXY = 1) almost perfectly discriminated dark from light bees. Two inversions (r7, r9), previously linked to high-elevation adaptation, were detected across additional mountain systems and enriched in dark, highland genomic backgrounds but did not replace AmEbony as the primary pigmentation locus. CRISPR/Cas9 disruption of AmEbony in A. mellifera carnica produced darker adults in a qualitative comparison, supporting a conserved role in pigmentation. Head RNA-seq and GENIE3 analysis identified recurrent genotype-associated modules involving oxidoreductase activity and odorant binding. Because population structure covaries with elevation and pigmentation, the GWAS supports AmEbony as a major-effect locus but cannot identify causal variants. Similarly, head-expression data identify molecular changes associated with AmEbony disruption but cannot establish whether they contribute to pigmentation or whether naturally segregating East African alleles act through the same pathways.
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BibTeX
@article{mazzoni2026elevational,
title = {{Elevational Melanism in East African Honey Bees Involves a Major-Effect Locus}},
author = {Marco Mazzoni and Florian Loidolt and Sonja Kersten and Mark Otieno and Henry Njovu and Julius Vincent Lasway and Ricarda Scheiner and Martin Hasselmann},
journal = {Genome Biology and Evolution},
year = {2026},
month = oct,
doi = {10.1093/gbe/evag260},
url = {https://doi.org/10.1093/gbe/evag260},
note = {CC BY 4.0},
}
RIS
TY - JOUR
TI - Elevational Melanism in East African Honey Bees Involves a Major-Effect Locus
AU - Marco Mazzoni
AU - Florian Loidolt
AU - Sonja Kersten
AU - Mark Otieno
AU - Henry Njovu
AU - Julius Vincent Lasway
AU - Ricarda Scheiner
AU - Martin Hasselmann
PY - 2026
DA - 2026/10/14
JO - Genome Biology and Evolution
DO - 10.1093/gbe/evag260
UR - https://doi.org/10.1093/gbe/evag260
AB - Thermal melanism, whereby darker pigmentation occurs in colder environments, is a widespread pattern; yet, its genetic and physiological basis in eusocial insects remains poorly understood. East African honey bees (Apis mellifera) occupy elevational gradients in which highland populations are darker, larger, and more cold-tolerant than lowland conspecifics. Here, we integrated population genomics, structural variations, and functional genomics to investigate elevational melanism. We sampled, phenotyped, and resequenced 139 workers from five East African mountain systems. A genome-wide association study identified 977 single-nucleotide polymorphisms (SNPs) significantly associated with abdominal pigmentation, with a single peak at the ebony ortholog AmEbony on chromosome 1. Allelic variation at AmEbony formed three genetic clusters tracking a continuous pigmentation gradient, and 77 divergent SNPs (DXY = 1) almost perfectly discriminated dark from light bees. Two inversions (r7, r9), previously linked to high-elevation adaptation, were detected across additional mountain systems and enriched in dark, highland genomic backgrounds but did not replace AmEbony as the primary pigmentation locus. CRISPR/Cas9 disruption of AmEbony in A. mellifera carnica produced darker adults in a qualitative comparison, supporting a conserved role in pigmentation. Head RNA-seq and GENIE3 analysis identified recurrent genotype-associated modules involving oxidoreductase activity and odorant binding. Because population structure covaries with elevation and pigmentation, the GWAS supports AmEbony as a major-effect locus but cannot identify causal variants. Similarly, head-expression data identify molecular changes associated with AmEbony disruption but cannot establish whether they contribute to pigmentation or whether naturally segregating East African alleles act through the same pathways.
SN - 1759-6653
ER -