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Genome adaptations to high altitude in the Eastern honeybee
- 1. Santiago Montero-Mendieta Genome adaptations to high altitude in the Eastern Honey bee 2018 SEVINOMICS Spring Meeting 9 April 2018
- 2. What is adaptation? • A feature of an organism that has been favored by natural selection because of that feature’s positive effect on relative fitness
- 3. What is local adaptation? • Evolution, through divergent natural selection, of traits that have high fitness in the environmental conditions specific to a population These adaptations are local because they are NOT found throughout the whole species, only in certain populations E.g. Local adaptation to high altitude habitats
- 4. Local adaptation to altitude Human populations in Tibet have adapted to survive at extremely high altitudes (>2500m) Yi et al. (2010). Science Genes involved in decreased hemoglobin levels: EPAS1, EGLN1, PPARA
- 5. Local adaptation to altitude Wallberg et al. (2017) PLOS Genetics Kenyan honeybees inhabiting mountain forests differ in behavior and morphology from those found in the surrounding lowland savannahs Octopamine receptor genes: learning and foraging behavior in honeybees
- 6. Social behavior in bees can change with altitude Social Sweat Bee (Halictus rubicundus) has solitary behavior in high-altitude habitats
- 7. Bees are crucial as pollinators
- 8. Distribution of Apis mellifera
- 9. Distribution of Apis cerana
- 10. Deqin (2714 m) Lijiang (2485 m) Kunming (1800 m) Tianshui (1100 m) Hekou (67 m) Xishuangbanna (570 m) Thai A (1377 m) Thai B (299 m) Sampling
- 11. Aims of the study • Understanding the genetic structure of these populations • Identifying regions of the genome associated with adaptation to high altitude habitats
- 12. Experimental procedure DNA extraction & library prep Whole-genome sequencing Bioinformatics analysis • Reads were mapped against the Apis cerana reference genome • 5.8 million biallelic SNPs were detected using FreeBayes • We did a series of population genomic analyses: ADXMITURE, FST scans, genetic diversity, environmental association, haplotype homozygosity
- 13. Results
- 14. xtbg_cn_570 ca_th_200 da_th_1400 ynhk_cn_67 yndqg_cn_2714 ynlj_cn_2485 gsts_cn_1100 sol_jp_100 ynkm_cn_1890 0.01 Deqin Lijiang Tianshui Kunming Thai A Thai B Xishuangbanna Hekou Japan Highland (> 2000 m.a.s.l.) Intermediate (1000-2000 m.a.s.l.) Lowland (< 1000 m.a.s.l.) Outgroup Genetic distance across eight populations of Apis cerana 0.01 Reynolds-FST
- 15. Xishuangbanna Hekou Lijiang Kunming Tianshui Deqin Thai A Thai B Reynolds-FST Genetic differentiation
- 16. Population structure ADMIXTURE sNMF Alexander et al. (2009) Genome Research Frichot et al. (2014) Genetics
- 18. Deqin (2714 m) Lijiang (2485 m) Hekou (67 m) Xishuangbanna (570 m)
- 19. (2714 m) (2485 m) (570 m) (67 m) Highland vs Lowland
- 20. Highly differentiated SNPs are not common between highland and lowland bees (Log) Number of SNPs 412 SNPs (0.01% out of the total)
- 21. Highly differentiated SNPs are more frequently located in UTRs and CDS ProportionofSNPs
- 22. Highly differentiated SNPs found in CDS often cause non- synonymous mutations SNPs that are non-synonymous mutations
- 23. XP-EHH scores increase at high FST regions, implying haplotype homozygosity on highland bees 0,00 0,50 1,00 1,50 2,00 2,50 3,00 3,50 4,00 4,50 0,0 0,1 0,2 0,3 0,4 0,5 0,6 0,7 0,8 0,9 1,0 XP-EHH FST
- 24. Selective sweeps in highland bees occur on a restricted set of genes
- 25. Genes involved on high altitude adaptation in Apis cerana Sweep # SNPs Scaffold Gene annotation B 27 0015 esterase FE4-like F 17 0041 leucokinin receptor J 22 1417 NMDA receptor … … … … • Development • Reproduction • Courtship behavior • Olfactory learning • Memory formation • Feeding and sucrose responses • Affect blood pressure • Enhance memory retention • Disturb circadian rhythmicity
- 26. SUMMARY 1. Several extremely differentiated genomic regions between highland and lowland bees 2. These regions are biased towards coding sequences and contain a higher proportion of non-synonymous mutations 3. These regions show high haplotype homozygosity in the highland bees, indicating selective sweeps in them 4. Genes associated with these regions have diverse functionality – further investigation is required !
- 27. Thank you!
Editor's Notes
- Coloration for reproduction, spikes for defense
- Traits that only some populations have
- Chronic mountain sickness (CMS)
- These genes have a role in learning / foraging behavior in honey bees and are strong candidates for adaptation to highland habitats
- Bees play a major role in nature / Bees are vital to the human food supply
- Worldwide
- In asia, that’s why they are called Eastern honeybee
- Explain the colors
- Read the text
- You can address any lab questions to Anna
- No extreme genetic distance, colors cluster together
- No extreme genetic distance, colors cluster together
- Deqin is very different from the rest – not so much structure in the others
- Same as the other admixture plot
- Weir and Cockerham 1984
- SNPs located in gene bodies, hint for selection (because they are adaptive)
- CHANGE the amino acid sequence of a protein, evidence for adaptive mutations (functional consequence)
- implying that high FST SNPs are associated with long haplotypes in highland bees
- Seems to be involved in feeding (meal size) and sucrose response in flies and mosquitoes. These are very similar functions to what we see in octopamine that we think is important in the Kenyan mountain bees.