Flanagan Evolution2017 talk
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Genome-wide selection components analysis was performed on a fish species, Syngnathus scovelli, that exhibits male pregnancy to understand patterns of sexual and viability selection. RAD-seq was used to genotype over 300,000 SNPs in adult males, females and embryos. Both pairwise FST comparisons and maximum likelihood approaches identified genomic regions under sexual and sex-biased viability selection, though few regions overlapped between the analyses. Functional analysis found the selected regions were involved in similar biological processes despite targeting different loci, showing genome-wide patterns of selection. Selection components analysis provides a detailed view of how sexual and viability selection have shaped the genome in this unique fish.
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Donald Kendall has studied biology at Widener University and Hillsborough Community College, earning a BSc and ASc respectively. His research has focused on topics in evolutionary biology, ecology, and biodiversity. He has authored research on the phylogeography of Lepidoptera and co-authored work on the taxonomy of Latin American moths and effects of urbanization on stream macroinvertebrates. Kendall has skills in areas like DNA analysis, chromatography, and spectroscopy. He currently works as a biology and chemistry tutor at Widener University.
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2:同时对留学生所学专业登记给予评定
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Flanagan Evolution2017 talk
- 1. Genome-wide selection components analysis in a fish with male pregnancy Sarah P. Flanagan, PhD @sarahpf19
- 2. Selection requires a genetic basis Understanding Evolution. 2016. University of California Museum of Paleontology. 22 August 2008 <http://evolution.berkeley.edu/>
- 3. Selection leaves a signature on the genome Hohenlohe et al. 2010, Int J Plant Sci Hard Sweep Linked to Sweep Neutral NeutralBalancing selection Soft Sweep Genomic signatures of selection
- 4. Sexual Selection Viability Selection What type of selection? ©Michael L. Baird ©Jebulon ©Tim Cronin ©Matt Kieffer
- 5. Modified from Christiansen & Frydenberg 1973, Theor. Pop. Biol. compare allele frequencies Selection components analysis (SCA)
- 6. Two SCA approaches Pairwise FST comparisons • Successfully detects strong selection, even when the trait has environmental component • Sample sizes should be large (>250 individuals) and many loci (across multiple chromosomes) should be sampled Maximum likelihoods • Sequential testing of models allows model comparisons • Original approach has been modified to incorporate sequencing error – Identified genome-wide viability selection in Mimulus guttatus Flanagan & Jones 2015, Ecol. Evol.Monnahan et al 2015, Evolution Christiansen & Frydenberg 1973, Theor. Pop. Biol.
- 7. Syngnathus scovelli are ideal for SCA Dad: CT Embryo: TT Mom: T Photo credits: Sarah Flanagan
- 8. Sexual selection favors band area or band number, primarily during mate choice Flanagan et al. 2014, JEB
- 9. Poor swimmers, rely on camouflage Photo credit: Sarah Flanagan Photo credit: Sarah Flanagan ©Michael L. Baird
- 10. Adult Females Pregnant Males Non- Pregnant Males Adults Embryos Viability Selection Sexual Selection 57 159 8 130 225 Selection components analysis in pipefish Group 1 Group 2 Type of selection Mode of Comparison Parent-offspring combination (Inferred pipefish female allele) Adult females (collected from the field) Sexual selection FST Adults (males and females) Adult females Sexual selection Likelihood Ratio Test Adult Males Adult Females Sex-biased viability FST, Likelihood Ratio Test
- 11. The approach: ddRAD-seq with reference genome RAD-sequencing Photo credits: Sarah Flanagan Reference genome: Small et al. 2016 Genome Biology
- 12. 34086 SNPs 48126 SNPs Flanagan & Jones 2017, Evolution 18 loci shared between these two 55 sig. SNPs (47 RAD loci) 611 sig. SNPs (473 RAD loci)
- 13. Flanagan & Jones 2017, Evolution 15 Shared Male-Female Viability SNPs Nuclear transport factor 2-like Provirus ancestral envelope polyprotein, partial 55 sig. SNPs
- 14. Flanagan & Jones 2017, Evolution Only few loci overlapped, but GO categories were mostly shared
- 15. • Both sexual and viability selection are genome-wide – Different genomic regions but not different functions • FST and likelihood approaches have similar results SCA reveals genome-wide patterns of sexual selection Genome-wide selection components analysis can provide more detailed understanding of selection
- 16. Acknowledgements Adam Jones John Kelly Jones lab Questions? Gulf pipefish genome: William Cresko Susie Bassham Clay Small
Editor's Notes
- I = hard selective sweep Ii = region linked to hard sweep Iii=neutral Iv = balancing selection V = neutral Vi = soft sweep