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Genome-wide analysis of signatures of selection in populations of African honey bees (Apis mellifera) using new web-based tools.

Fuller ZL, Niño EL, Patch HM, Bedoya-Reina OC, Baumgarten T, Muli E, Mumoki F, Ratan A, McGraw J, Frazier M, Masiga D, Schuster S, Grozinger CM, Miller W - BMC Genomics (2015)

Bottom Line: The dense coverage allowed us to apply several computational procedures to study population structure and the evolutionary relationships among the populations, and to detect signs of adaptive evolution across the genome.While there is considerable gene flow among the sampled populations, there are clear distinctions between populations from the northern desert region and those from the temperate, savannah region.We identified several genes showing population genetic patterns consistent with positive selection within African bee populations, and between these populations and European A. mellifera or Asian Apis florea.

View Article: PubMed Central - PubMed

Affiliation: Department of Biology, Pennsylvania State University, University Park, PA, USA. zlf105@psu.edu.

ABSTRACT

Background: With the development of inexpensive, high-throughput sequencing technologies, it has become feasible to examine questions related to population genetics and molecular evolution of non-model species in their ecological contexts on a genome-wide scale. Here, we employed a newly developed suite of integrated, web-based programs to examine population dynamics and signatures of selection across the genome using several well-established tests, including F ST, pN/pS, and McDonald-Kreitman. We applied these techniques to study populations of honey bees (Apis mellifera) in East Africa. In Kenya, there are several described A. mellifera subspecies, which are thought to be localized to distinct ecological regions.

Results: We performed whole genome sequencing of 11 worker honey bees from apiaries distributed throughout Kenya and identified 3.6 million putative single-nucleotide polymorphisms. The dense coverage allowed us to apply several computational procedures to study population structure and the evolutionary relationships among the populations, and to detect signs of adaptive evolution across the genome. While there is considerable gene flow among the sampled populations, there are clear distinctions between populations from the northern desert region and those from the temperate, savannah region. We identified several genes showing population genetic patterns consistent with positive selection within African bee populations, and between these populations and European A. mellifera or Asian Apis florea.

Conclusions: These results lay the groundwork for future studies of adaptive ecological evolution in honey bees, and demonstrate the use of new, freely available web-based tools and workflows ( http://usegalaxy.org/r/kenyanbee ) that can be applied to any model system with genomic information.

No MeSH data available.


Evidence for a selective sweep near Forkhead Box Protein O (Foxo) in Desert population. The average heterozygosity is shown for all individuals sequenced in the Savannah and Desert populations across a 1.5 Mb region on chromosome 7. The shaded area indicates the location of Foxo. A marked reduction in heterozygosity for the region surrounding Foxo is observed in the Desert population
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Fig4: Evidence for a selective sweep near Forkhead Box Protein O (Foxo) in Desert population. The average heterozygosity is shown for all individuals sequenced in the Savannah and Desert populations across a 1.5 Mb region on chromosome 7. The shaded area indicates the location of Foxo. A marked reduction in heterozygosity for the region surrounding Foxo is observed in the Desert population

Mentions: We observed one such region surrounding the Forkhead Box Protein O (Foxo, GB48301) gene in the Desert population (Fig. 4). Heterozygosity levels in the Desert population are consistent with the Savannah bees around 500 kb upstream and downstream of the region. However, heterozygosity levels are strongly reduced in a 500 kb stretch containing Foxo within the Desert population relative to the Savannah population. The protein expressed by Foxo is a transcription factor that is thought to play a major role in caste differentiation and division of labor by regulating insulin signaling [78, 79]. Foxo was also found in a QTL that suppressed reproduction of Varroa destructor, a major parasite of honey bees [80]. Interestingly, a recent survey of honey bee populations in Kenya revealed that Varroa destructor is present throughout the southern and central honey bee populations but absent from the northern desert regions [12]. However, Varroa was likely introduced relatively recently (ie, with the last 10 years) into Kenya [81] and thus likely does not account for this population difference.Fig. 4


Genome-wide analysis of signatures of selection in populations of African honey bees (Apis mellifera) using new web-based tools.

Fuller ZL, Niño EL, Patch HM, Bedoya-Reina OC, Baumgarten T, Muli E, Mumoki F, Ratan A, McGraw J, Frazier M, Masiga D, Schuster S, Grozinger CM, Miller W - BMC Genomics (2015)

Evidence for a selective sweep near Forkhead Box Protein O (Foxo) in Desert population. The average heterozygosity is shown for all individuals sequenced in the Savannah and Desert populations across a 1.5 Mb region on chromosome 7. The shaded area indicates the location of Foxo. A marked reduction in heterozygosity for the region surrounding Foxo is observed in the Desert population
© Copyright Policy - open-access
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC4496815&req=5

Fig4: Evidence for a selective sweep near Forkhead Box Protein O (Foxo) in Desert population. The average heterozygosity is shown for all individuals sequenced in the Savannah and Desert populations across a 1.5 Mb region on chromosome 7. The shaded area indicates the location of Foxo. A marked reduction in heterozygosity for the region surrounding Foxo is observed in the Desert population
Mentions: We observed one such region surrounding the Forkhead Box Protein O (Foxo, GB48301) gene in the Desert population (Fig. 4). Heterozygosity levels in the Desert population are consistent with the Savannah bees around 500 kb upstream and downstream of the region. However, heterozygosity levels are strongly reduced in a 500 kb stretch containing Foxo within the Desert population relative to the Savannah population. The protein expressed by Foxo is a transcription factor that is thought to play a major role in caste differentiation and division of labor by regulating insulin signaling [78, 79]. Foxo was also found in a QTL that suppressed reproduction of Varroa destructor, a major parasite of honey bees [80]. Interestingly, a recent survey of honey bee populations in Kenya revealed that Varroa destructor is present throughout the southern and central honey bee populations but absent from the northern desert regions [12]. However, Varroa was likely introduced relatively recently (ie, with the last 10 years) into Kenya [81] and thus likely does not account for this population difference.Fig. 4

Bottom Line: The dense coverage allowed us to apply several computational procedures to study population structure and the evolutionary relationships among the populations, and to detect signs of adaptive evolution across the genome.While there is considerable gene flow among the sampled populations, there are clear distinctions between populations from the northern desert region and those from the temperate, savannah region.We identified several genes showing population genetic patterns consistent with positive selection within African bee populations, and between these populations and European A. mellifera or Asian Apis florea.

View Article: PubMed Central - PubMed

Affiliation: Department of Biology, Pennsylvania State University, University Park, PA, USA. zlf105@psu.edu.

ABSTRACT

Background: With the development of inexpensive, high-throughput sequencing technologies, it has become feasible to examine questions related to population genetics and molecular evolution of non-model species in their ecological contexts on a genome-wide scale. Here, we employed a newly developed suite of integrated, web-based programs to examine population dynamics and signatures of selection across the genome using several well-established tests, including F ST, pN/pS, and McDonald-Kreitman. We applied these techniques to study populations of honey bees (Apis mellifera) in East Africa. In Kenya, there are several described A. mellifera subspecies, which are thought to be localized to distinct ecological regions.

Results: We performed whole genome sequencing of 11 worker honey bees from apiaries distributed throughout Kenya and identified 3.6 million putative single-nucleotide polymorphisms. The dense coverage allowed us to apply several computational procedures to study population structure and the evolutionary relationships among the populations, and to detect signs of adaptive evolution across the genome. While there is considerable gene flow among the sampled populations, there are clear distinctions between populations from the northern desert region and those from the temperate, savannah region. We identified several genes showing population genetic patterns consistent with positive selection within African bee populations, and between these populations and European A. mellifera or Asian Apis florea.

Conclusions: These results lay the groundwork for future studies of adaptive ecological evolution in honey bees, and demonstrate the use of new, freely available web-based tools and workflows ( http://usegalaxy.org/r/kenyanbee ) that can be applied to any model system with genomic information.

No MeSH data available.