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Using genotype-by-sequencing to uncover the population history of fungus farming ambrosia beetles. Entomological Society of America Annual Meeting, November 9-14, Austin, TX
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Population structure in a haplo-diploid fungus farming beetle New insights from genotype-by-sequencing
female
male
Caroline Storer & Jiri Hulcr University of Florida
Ambrosia beetles build galleries in the xylem of dying trees for farming their symbiotic fungus
The Xyleborini are a hyper-diverse (~1,200 species) tribe of Ambrosia beetles
The Xyleborini have bizarre genetics
The Xyleborini have bizarre genetics
diploid mother
haploid son
Haplo-diploid: Females produce many diploid
daughters and one haploid son
The Xyleborini have bizarre genetics
diploid mother
haploid son
Haplo-diploid: Females produce many diploid
daughters and one haploid son
Inbreed: The haploid son mates with its sisters
1) What is the effect of haplo-diploid inbreeding on genetic diversity and population structure?
1) What is the effect of haplo-diploid inbreeding on genetic diversity and population structure?
2) Are new high-throughput genotype-by-sequencing methods suitable for these near-clonal organisms?
Why genotype-by-sequencing?
Why genotype-by-sequencing?
o Fast - No marker development - Sample prep takes days
Why genotype-by-sequencing?
o Fast - No marker development - Sample prep takes days
o High-throughput
- 100s of individuals - 100s of genotypes
Why genotype-by-sequencing?
o Fast - No marker development - Sample prep takes days
o High-throughput
- 100s of individuals - 100s of genotypes
o Robust - High-quality sequence data - Biological signals are recoverable (Buerkle & Gompert 2013)
Why genotype-by-sequencing?
o Fast - No marker development - Sample prep takes days
o High-throughput
- 100s of individuals - 100s of genotypes
o Robust - High-quality sequence data - Biological signals are recoverable (Buerkle & Gompert 2013)
Xylosandrus crassiusculus
1 mm
Xylosandrus crassiusculus
1 mm
o Abundant
Xylosandrus crassiusculus
1 mm
o Abundant
o Exotic (in the US)
Xylosandrus crassiusculus
1 mm
o Abundant
o Exotic (in the US)
o Sometimes pest
Xylosandrus crassiusculus
1 mm
o Abundant
o Exotic (in the US)
o Sometimes pest
Maryland
Northern NC
Southern NC
North Florida
South Carolina
Central Florida
2-3 beetles sequenced from 6 locations
restriction-site associated sequencing (RADseq)
restriction-site associated sequencing (RADseq)
Petterson et al. 2012
restriction-site associated sequencing (RADseq)
Petterson et al. 2012
ddRADseq enables the sequencing of the same genomic region in many taxonomically related individuals
Sequences are sorted by an individual’s unique barcode... 1
Sequences are sorted by an individual’s unique barcode...
Stack 1 Stack 2
then assembled into locus stacks based on sequence similarity
Stack X
1
2
89,429 stacks in catalog
89,429 stacks in catalog
89,429 stacks in catalog
21,860 stacks shared across
individuals
89,429 stacks in catalog
2,984 SNP loci
genotyped
21,860 stacks shared across
individuals
-‐1
-‐0.8
-‐0.6
-‐0.4
-‐0.2
0
0.2
0.4
0.6
0.8
1
FIS
locus
FIS > 0 inbreeding
FIS < 0 outbreeding
Inbreeding detected at most loci
No population structure associated with geographic location
Central Florida North Florida South Carolina Southern North Carolina Northern North Carolina Maryland
Principal coordinate 1 (35.34%)
Principal coordinate 2
(14.54%)
In summary...
In summary...
o Genotype-by-sequencing is possible
In summary...
o Genotype-by-sequencing is possible o High inbreeding (>0.8) at most loci, but
some outbreeding may occur
In summary...
o Genotype-by-sequencing is possible o High inbreeding (>0.8) at most loci, but
some outbreeding may occur o No genetic structure associated with
geographic location
In summary...
o Genotype-by-sequencing is possible o High inbreeding (>0.8) at most loci, but
some outbreeding may occur o No genetic structure associated with
geographic location o High genetic similarity between some
individuals, but not clonal
o What is the global population structure ambrosia beetles?
o What is the global population structure ambrosia beetles?
o How does population structure differ between outbreeding and inbreeding ambrosia beetles?
o What is the global population structure ambrosia beetles?
o How does population structure differ between outbreeding and inbreeding ambrosia beetles? Native and exotic?
o What is the global population structure ambrosia beetles?
o How does population structure differ between outbreeding and inbreeding ambrosia beetles? Native and exotic?
o Is population structure correlated with fungal symbiont biodiversity?
o What is the global population structure ambrosia beetles?
o How does population structure differ between outbreeding and inbreeding ambrosia beetles? Native and exotic?
o Is population structure correlated with fungal symbiont biodiversity?
o Are species complexes a phenotypically plastic single species or distinct cryptic species?
The Forest Entomology Lab at University of
Florida
Dr. Jiri Hulcr
Martin Kostovcik
Craig Bateman
Andrew Johnson
Polly Harding (not shown)
UF Graduate Student Council
quality filtered
sequences
sequences per library
total sequences
used sequences
total_seqs filtered_seqs used_seqs unique_seqs
2e+05
4e+05
6e+05
8e+05
1e+06
1,000,000
800,000
600,000
400,000
200,000
> 40,000 sequence targets for marker discovery
stacks
stacks per library
60,000
50,000
20,000
30,000
40,000
20000
30000
40000
50000
60000
o 58% of stacks identical between individuals o 9,054 stacks contain putative SNPs o Calling genotypes: – Present in > 80% of individuals – 5 sequences (RAD-tags) required to confirm each
genotype within an individual – Minimum minor allele frequency of 0.1
o 2,948 loci genotyped in 16 individuals
