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.

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