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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.


Related in: MedlinePlus

Selected chromosomal regions with signatures of positive selection according to Tajima’s D analysis. The top panel shows a section of chromosome 5. Tajima’s D was calculated in 5 kb windows and scores are represented by vertical bars. Any bar colored red represents a window where Tajima’s D is significantly negative. Conversely, bars colored light blue represent windows where Tajima’s D is not significantly different from values expected under a site evolving neutrally. The bottom panel is a magnification of the area containing a ~20 kb stretch of significant Tajima’s D scores. Green blocks represent locations of genes contained within the interval
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Fig6: Selected chromosomal regions with signatures of positive selection according to Tajima’s D analysis. The top panel shows a section of chromosome 5. Tajima’s D was calculated in 5 kb windows and scores are represented by vertical bars. Any bar colored red represents a window where Tajima’s D is significantly negative. Conversely, bars colored light blue represent windows where Tajima’s D is not significantly different from values expected under a site evolving neutrally. The bottom panel is a magnification of the area containing a ~20 kb stretch of significant Tajima’s D scores. Green blocks represent locations of genes contained within the interval

Mentions: When tests against a neutral hypothesis, such as D and H, are performed repeatedly across a genome in a sliding window analysis, an issue of multiple comparisons arises. Although several strategies have been proposed to account for multiple testing, such as controlling the false discovery rate or Bonferroni procedures, here we use the experiment-wide simulation approach suggested by Nielsen et al. (2005) [43]. Several genes were found in intervals testing significantly negative for both Tajima’s D and Fay and Wu’s H (see Additional file 1: Table S9A for a complete list and Additional file 1: S9B for the results of a GO analysis), including Derlin-1 (GB46979). Derlins are rhomboid pseudoproteases involved with endoplasmic reticulum associated degredation and play a role in the dislocation of misfolded proteins [101]. A ~20 kb region of chromosome 5 harbors several genes that intersect significantly negative windows of Tajima’s D (Fig. 6). Furthermore, Fay and Wu’s H values in the region are also detected as significantly negative (Additional file 1: Table S9A), providing additional evidence of a true departure from neutrality. Genes located in this region include replication-protein- A 70 kDa subunit (RpA70; GB44421), zinc finger FYVE domain containing protein 26 (ZFYVE26; GB44416) and alpha-mannosidase II (GB44414).Fig. 6


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)

Selected chromosomal regions with signatures of positive selection according to Tajima’s D analysis. The top panel shows a section of chromosome 5. Tajima’s D was calculated in 5 kb windows and scores are represented by vertical bars. Any bar colored red represents a window where Tajima’s D is significantly negative. Conversely, bars colored light blue represent windows where Tajima’s D is not significantly different from values expected under a site evolving neutrally. The bottom panel is a magnification of the area containing a ~20 kb stretch of significant Tajima’s D scores. Green blocks represent locations of genes contained within the interval
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Fig6: Selected chromosomal regions with signatures of positive selection according to Tajima’s D analysis. The top panel shows a section of chromosome 5. Tajima’s D was calculated in 5 kb windows and scores are represented by vertical bars. Any bar colored red represents a window where Tajima’s D is significantly negative. Conversely, bars colored light blue represent windows where Tajima’s D is not significantly different from values expected under a site evolving neutrally. The bottom panel is a magnification of the area containing a ~20 kb stretch of significant Tajima’s D scores. Green blocks represent locations of genes contained within the interval
Mentions: When tests against a neutral hypothesis, such as D and H, are performed repeatedly across a genome in a sliding window analysis, an issue of multiple comparisons arises. Although several strategies have been proposed to account for multiple testing, such as controlling the false discovery rate or Bonferroni procedures, here we use the experiment-wide simulation approach suggested by Nielsen et al. (2005) [43]. Several genes were found in intervals testing significantly negative for both Tajima’s D and Fay and Wu’s H (see Additional file 1: Table S9A for a complete list and Additional file 1: S9B for the results of a GO analysis), including Derlin-1 (GB46979). Derlins are rhomboid pseudoproteases involved with endoplasmic reticulum associated degredation and play a role in the dislocation of misfolded proteins [101]. A ~20 kb region of chromosome 5 harbors several genes that intersect significantly negative windows of Tajima’s D (Fig. 6). Furthermore, Fay and Wu’s H values in the region are also detected as significantly negative (Additional file 1: Table S9A), providing additional evidence of a true departure from neutrality. Genes located in this region include replication-protein- A 70 kDa subunit (RpA70; GB44421), zinc finger FYVE domain containing protein 26 (ZFYVE26; GB44416) and alpha-mannosidase II (GB44414).Fig. 6

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.


Related in: MedlinePlus