Presented at Evolution 2014 in Raleigh, NC (http://evolution2014.org) Jumping genes and life history: De novo transposable element insertions respond to selection for accelerated and delayed development times Kate L Hertweck, NESCent, k8hertweck@gmail.com Mira Han, UNLV, mira.han@unlv.edu Lee F Greer, University of California, Irvine, lgreer@uci.edu Mark A Phillips, UC Irvine, mphillips6789@gmail.com Michael R Rose, University of California, Irvine, mrrose@uci.edu Joseph L Graves, JSNN, North Carolina A&T State University, gravesjl@ncat.edu A wealth of scientific literature has speculated on the response of both the genome and organism to proliferation of transposable elements (TEs, or jumping genes). In particular, the relationship between TEs and aging has been addressed by both theory and empirical studies. Theory suggests TEs may contribute to life history features such as aging, by introducing detrimental somatic mutation. However, a comparison TEs between organisms indicate the number of copies may increase, decrease, or have no effect on lifespan, depending on the model system and type of TE investigated. Long-term studies in experimental evolution allow explicit testing of such hypothesis using replicated populations. Our data represent pooled population genome-wide resequencing from Drosophila selected for both delayed and accelerated reproduction times and development. Our previous results indicate that insertion frequencies of ancestral TEs (i.e., annotated in the fully sequenced reference genome) respond fairly consistently to selection. For the present study, we use two independent approaches (PoPoolation TE and RelocaTE) to identify de novo TE insertions. We find that the magnitude of TE proliferation varies among multiple families of LTRs, LINEs, and DNA transposons. We present methodological considerations for interpreting such results.

1. Jumping genes and aging: de novo
transposable element insertions respond
to selection for time to development
Kate L. Hertweck
Mira Han (NESCent)
Lee F. Greer (UC Irvine)
Mark A. Phillips (UC Irvine)
Joseph L. Graves, Jr. (NC A&T, UNC Greensboro)
Michael R. Rose (UC Irvine)
Twitter @k8hert
Google+ k8hertweck@gmail.com
Blog: k8hert.blogspot.com
www.slideshare.net/katehertweck
Wikicommons

2. Transposable elements as a model system
K. Hertweck (@k8hert), NESCent, de novo TEs and time to development
●
TEs, mobile genetic elements, or jumping genes
●
Parasitic, self-replicating
●
Similar to or derived from viruses
●
Move independently in a genome
Class I: Retrotransposons
(copy and paste)
LTR
LINE
SINE
ERV
SVA
Class II: DNA transposons
(cut and paste)
TIR (P elements)
MITE
Crypton
Helitron
Maverick

3. Genome-wide TE insertions and lifespan
Kate Hertweck, Genomic effects of repetitive DNAKate Hertweck, NESCent, Genomic effects of junk DNAK. Hertweck (@k8hert), NESCent, de novo TEs and time to development
Empirical data: it depends!
●
TIR DNA transposons: decrease or have no effect on lifespan
(Drosophila: Nikitin and Woodruff 1995; C. elegans: Egilmez and Reis 1994)
●
LTR retrotransposons decrease lifespan (Drosophila: Driver and McKechnie 1992)
●
Alu SINEs reverse senescence (human cell lines: Wang et al. 2011)
●
TEs linked with epigenetic changes (Wilkins 2010, Baillie et al. 2011)
Theory: TE proliferation will decrease lifespan, accumulation of
mutations (Kirkwood 1986, Murrey 1990)
What is the relationship between TE insertions and lifespan?

4. K. Hertweck (@k8hert), NESCent, de novo TEs and time to development
Rose laboratory Drosophila stocks
Long term experimental evolution system
Established 1980
A 9-day life cycle
B 14-day life cycle (baseline)
C 28-day life cycle
ACO
CO
BO
NCO AO
B
O
Original
population
A, B, C derived twice each
Reversal of selection
Testing for convergence
All populations replicated five times
Joe Graves, “Genome-wide convergence with repeated evolution in Drosophila
melanogaster, Monday 10:30 305B (Experimental Evolution)

5. Experimental data
K. Hertweck (@k8hert), NESCent, de novo TEs and time to development
●
Whole-genome resequencing (Illumina Hi-Seq)
120 females x six treatments x five replicates
●
Are there areas of significant differentiation in the genome?
Where? Hard vs. soft sweeps (Burke et al., 2010)?
SNP analysis: Popoolation2 (Kofler et al., 2011)
Known (ancestral) TE detection: Tlex (Fiston-Lavier et al. 2010)
Structural variant analysis: Delly (Rausch et al., 2012)
How do frequencies of known TE insertions respond to
selective pressures?
How does total TE load respond to selective pressures?

6. Bioinformatics approach
K. Hertweck (@k8hert), NESCent, de novo TEs and time to development
●
RelocaTE 1.0.4 (Robb et al. 2013)
●
Uses TSD sequence motifs (LTR and TIR) and reference genome
●
82 canonical sequences (Bergman, v.9.43) and Dmel v5
●
Filtered for read count >10 (custom)
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PoPoolationTE 1.02 (Kofler et al. 2012)
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Uses known insertions, reference genome, TE hierarchy
●
5200 insertions from annotation 5.55
●
Filtered for read count >10
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Summarizing data
●
Total TE insertions identified (by order)
●
Total TE families (by order)

7. RelocaTE: total TE insertions
K. Hertweck (@k8hert), NESCent, de novo TEs and time to development
CO NCOACO AO BO B
*
*
Populations of flies with
short v long lifespan
have significantly
different numbers of total
TEs (all C v all A:
p=0.028*)
This difference appears
to be driven by
retrotransposons
(shorter lifespan, more
LTRs)

8. RelocaTE: total TE families
K. Hertweck (@k8hert), NESCent, de novo TEs and time to development
CO NCOACO AO BO B
No significant
differences
between
treatments for
number of TE
families
What about other
types of TEs?

9. PoPoolationTE: total TE insertions
K. Hertweck (@k8hert), NESCent, de novo TEs and time to development
CO NCOACO AO BO B
No significant
differences
between groups
What's the deal
with replicate 5?

10. PoPoolationTE: total TE families
K. Hertweck (@k8hert), NESCent, de novo TEs and time to development
CO NCOACO AO BO B
PoPoolationTE more
consistently IDs TE
families
ACO
CO
BO
NCO AO
B
O
Original
population

11. Conclusions
●
RelocaTE is more conservative than PoPoolationTE in estimates of
de novo TE insertions, but appears to miss some families
●
Some evidence for more TEs associated with shorter lifespan, most
variation in LTRs
●
One population replicate presents a much different profile in overall
TE load:
●
Not apparent with all algorithms
●
Multiple types of genomic responses to same selection?
K. Hertweck (@k8hert), NESCent, de novo TEs and time to development

12. Continuing work
K. Hertweck (@k8hert), NESCent, de novo TEs and time to development
●
Additional filtering and screening to determine exact
specificity of de novo TE calls between algorithms
●
Overlap between TE calls from different programs
●
Genome-wide tests for significance of different genomic
events (SNPs, structural variation, TEs)
●
Testing for repeatability of evolution? What is up with replicate
5?

13. Acknowledgements
●
Fellow NESCent scientists (for abiding my gluttonous shared computer
cluster appetite)
●
Casey Bergman and Michael Nelson (U Manchester)
●
Joe Graves, “Genome-wide convergence with repeated evolution in
Drosophila melanogaster, Monday 10:30 305B (Experimental Evolution)
Blog:
k8hert.blogspot.com
www.slideshare.net/katehertweck
Twitter @k8hert
Google+ k8hertweck@gmail.com

14. Variation in replicate 5 from sequencing coverage?
K. Hertweck (@k8hert), NESCent, de novo TEs and time to development