DOI: 10.5061/dryad.xwdbrv1ff
title: Admixture in Africanized honey bees (Apis mellifera) from Panamá to San Diego, California (U.S.A.) honey bee dataset

description: The Africanized honey bee (AHB) is a New World amalgamation of several
 subspecies of the western honey bee (Apis mellifera), a diverse taxon
 historically grouped into four major biogeographic lineages: A (African),
 M (Western European), C (Eastern European), and O (Middle Eastern). In
 1956, accidental release of experimentally bred “Africanized” hybrids from
 a research apiary in Sao Paulo, Brazil, initiated a hybrid species
 expansion that now extends from northern Argentina to northern California
 (U.S.A.). Here, we assess nuclear admixture and mitochondrial ancestry in
 60 bees from four countries (Panamá; Costa Rica, Mexico; U.S.A) across
 this expansive range to assess ancestry of AHB several decades following
 initial introduction and test the prediction that African ancestry
 decreases with increasing latitude. We find that AHB nuclear genomes from
 Central America and Mexico have predominately African genomes (76–89%)
 with smaller contributions from Western and Eastern European lineages.
 Similarly, nearly all honey bees from Central America and Mexico possess
 mitochondrial ancestry from the African lineage with few individuals
 having European mitochondria. In contrast, AHB from San Diego (CA) show
 markedly lower African ancestry (38%) with substantial genomic
 contributions from all four major honey bee lineages and mitochondrial
 ancestry from all four clades as well. Genetic diversity measures from all
 New World populations equal or exceed those of ancestral populations.
 Interestingly, the feral honey bee population of San Diego emerges as a
 reservoir of diverse admixture and high genetic diversity, making it a
 potentially rich source of genetic material for honey bee breeding.
description: We collected 60 Western honey
 bees (n = 15/country) from sites in each of four countries: the isthmus of
 Panamá; Guanacaste National Park, Costa Rica; Chiapas, Mexico; San Diego
 County, California, U.S.A. (Table 1). All samples were collected in June
 2015 – August 2016 by hand-netting. Honey bees in Panamá were collected
 with an insect net while they foraged either on natural vegetation in
 rural areas, or on street vendor syrup dispensers in urban areas. Honey
 bees were collected across the isthmus of Panamá from five sites, each
 separated by &gt; 5 km: Panamá City, Gamboa, Barro Colorado Island
 (BCI), Santa Rita Arriba, and Cólon. Individuals from Costa Rica were
 collected from the Santa Rosa sector of Guanacaste National Park in
 northwestern Costa Rica. These bees were collected from a localized region
 and likely originate from a small number of feral colonies. Honey bees
 from Mexico were collected from an apiary in the southern state of
 Chiapas, with each bee collected from a different hive. Honey bees from
 San Diego County, California, U.S.A. were workers collected while foraging
 on flowers. San Diego bees were collected across 15 sites each separated
 by &gt; 5 km so that each likely represents a worker from a different
 colony. The furthest collection sites were separated by 65 km. Collection
 sites ranged from urban to rural settings. Due to the presence of hobbyist
 and agricultural beekeeping we do not rule out the possibility that the
 captured honey bees were from managed rather than feral hives. However,
 most honey bee foragers in San Diego are from feral hives. We extracted
 DNA from crushed heads of the 60 sampled honey bees using the standard
 protocol of the Qiagen DNAeasy Blood & Tissue extraction kit. DNA
 purity and appropriate concentration for sequencing were validated with a
 Qubit fluorometer prior to submission for library preparation. The DNA was
 submitted for DNA KAPA library construction and whole-genome sequencing at
 the Institute for Genomic Medicine (IGM), UC San Diego. All 60 individuals
 were multiplexed and sequenced across three lanes of an Illumina HiSeq4000
 platform to produce 100-bp paired end reads. Average genomic coverage per
 individual was 29±1.2X.