Inversions and nucleotide diversity in Drosophila yakubaPatrick F. Reilly*, Julie Z. Peng^, Peter Andolfatto^

*QCB Graduate Program, ^Department of Ecology and Evolutionary Biology, Princeton University

Background

Future Plans• ABC for better estimate of inversion

age (in progress)• Deeper sampling of D. santomea to

check for 2R inversion polymorphism• Modeling to estimate effects of double

crossovers and gene conversion on diversity within the 2R inversion

Results

Acknowledgments• Discussions with J.J. Emerson, Mahul

Chakraborty, Alisa Sedghifar, Jim Baldwin-Brown, and Tony Long

• Work funded by NIH R01-GM114093 (PI: Peter Andolfatto)

• PFR supported by NHGRI award T32HG003284• Partly supported by UC-Irvine GHTF Support

Grant CA-62203 and NIH shared instrumentation grants 1S10RR025496-01 and 1S10OD010794-01

QCB Graduate Program

Figure 2. Windowed polymorphism within arrangements and divergence between arrangements and species for the major chromosome arms of D. yakuba.Vertical lines indicate inversion breakpoints. A=NY73PB, B=Taï18E2

Figure 1. Dot plot of D. yakuba Taï18E2 (y-axis) against NY73PB (x-axis).Note the large inversions on 2L and 2R.

3R3L2LX 2R 4

References[MA] M Ashburner et al. (1976) Proc R Soc Lond B[RC-D] R Corbett-Detig et al. (2012) PLoS Genetics[AL] A Llopart et al. (2002) Evolution[BSC] BS Cooper et al. (2017) BiorXiv[FL] F Lemeunier et al. (1976) Proc R Soc Lond B[EH] E Hasson et al. (1996) Genetics[EAB] EA Beck et al. (2015) Evolution

D. yakuba is of evolutionary interest• Hybridizes with closely related sister species D.

santomea[AL] and D. teissieri[BSC] (diverged ~400-500 and 800-1000 KYA)

• Many inversions between D. teissieri and D. yakuba, plus polymorphic inversions within species[FL]

Conclusions• 2R inversion is older than species

split (551-585 KYA vs. 430 KYA)

• 2R arrangement A (NY73PB) is ancestral

• 2L inversion younger

Left and Middle figures.Linkage LOD plots of the Taï18E2 and NY73PB 2R chromosomes (left and right, resp.).Note the off-diagonal signature of nested inversions.

Right figure.Dotplot of D. santomea against D. yakuba NY73PB showing NY73PB is collinear on 2R, but not 2L.

To download this poster:

Inversions• Reduce local recombination rate (especially at breakpoints)• Polymorphic in some species (e.g. D. melanogaster), but

absent/fixed in others (e.g. D. simulans)[MA]• D. melanogaster polymorphic inversions all young (< ~300k years),

ancestor may not have had polymorphic inversions[RC-D]

3R

3L

2L

X

2R

4

Taï1

8E2

NY73PB

4 X

3L 3R

2L 2R

0e+00 5e+05 1e+06 0.0e+005.0e+06

1.0e+071.5e+07

2.0e+07

0.0e+005.0e+06

1.0e+071.5e+07

2.0e+072.5e+07 0e+00 1e+07 2e+07 3e+07

0.0e+005.0e+06

1.0e+071.5e+07

2.0e+072.5e+07

0.0e+005.0e+06

1.0e+071.5e+07

2.0e+07

0.00

0.01

0.02

0.03

0.00

0.01

0.02

0.03

0.00

0.01

0.02

0.03

Position

Value

StatisticDxy_cross_inv

Pi_A

Pi_B

Dxy_cross_species

Dxy and Pi in 100kb windows across the genome for Dyak_2Rinv

2R:9200001

2R:18900001

8.5e+069.0e+06

9.5e+061.0e+07

1800000018500000

1900000019500000

20000000

0.00

0.01

0.02

0.03

0.04

0.05

0.00

0.01

0.02

0.03

0.04

0.05

Position

Value

StatisticDxy_cross_inv

Dxy_yakA_san

Dxy_yakB_san

Dxy_cross_species

Dxy amongst Dyak arrangements and Dsan in 10kb windows around inversion breakpoints for Dyak_2Rinv_outerOnly

Figure 3. Windowed divergence between each arrangement and D. santomeasurrounding the breakpoints of the 2R inversion.

2LX 2R 3L 3R

D.

sant

omea

Distal breakpoint

Proximal breakpoint

Methods: De novo assemblies with 80-120x PacBio data (FALCON+Canu->Quickmerge->FinisherSC->Quiver)Polymorphism and divergence from ≥30x Illumina for 6 synthetic diploids of each species, variants called with GATK

T_species

T_inversion

𝑇"#$%&'"(#= 𝑇'*%+"%'

∗ 𝐷𝑥𝑦+&(''_"#$ − 𝜋4

𝐷𝑥𝑦+&(''_'*%+"%' − 𝜋4[EH]

𝑇'*%+"%' ≈ 430𝐾𝑌𝐴[EAB]

Question: How do inversions of various ages structure nucleotide diversity in D. yakuba?

Arm NY73PB Taï18E2 FlyBase NY73PB Diff.

Taï18E2 Diff.

# NY73PB contigs

# Taï18E2 contigs

X 23,707,472 23,451,772 21,770,863 +1,936,609 +1,680,909 4 52L 24,234,981 29,953,808 22,324,452 +1,910,529 +7,629,356 2 22R 21,728,136 20,761,686 21,139,217 +588,919 -377,531 3 13L 24,690,472 26,806,978 24,197,627 +492,845 +2,609,351 1 23R 30,661,805 30,741,958 28,832,112 +1,829,693 +1,909,846 1 24 1,410,457 1,430,623 1,374,474 +35,983 +56,149 1 1

Total 169,716,061 147,994,109 165,693,946 +4,022,115 -17,699,837 428 66

Table 1. Comparison of the two new D. yakuba assemblies and the FlyBase genome.

Join me on Twitter:

@LePatoptera