2014 11-28-lyon

Genomic architecture
underlying a major transition in
social evolution
2014-11-30-Lyon
y.wurm@qmul.ac.uk http://wurmlab.github.io

Atta leaf-cutter ants
© National Geographic

Oecophylla Weaver ants
© ameisenforum.de

© ameisenforum.de
Fourmis tisserandes

© ameisenforum.de
Oecophylla Weaver ants

Tofilski et al 2008
Forelius pusillus

Forelius pusillus hides the nest entrance at night
Tofilski et al 2008

Forelius pusillus hides the nest entrance at night
Avant
Workers staying outside die
« preventive self-sacrifice »
Tofilski et al 2008

Dorylus driver ants: ants with no home
© BBC

Animal biomass (Brazilian rainforest)
Mammals
Birds
Reptiles
Other insects Amphibians
from Fittkau & Klinge 1973
Earthworms
Spiders
Soil fauna excluding
earthworms,
ants & termites
Ants & termites

Well-studied:
• behavior
• morphology
• evolutionary context
• ecology
Genetic basis?

Downloaded from www.sciencemag.org on March 12, 2013 Solenopsis invicta fire ants are
REPORTS
a big problem!
very well studied!
Ascunce et al 2011

Solenopsis invicta fire ant:
two social forms
Single-queen form: Multiple-queen form:
•1 large queen
•Independent founding
•Highly territorial
•Many sizes of workers
•2-100 smaller queens
•Dependent founding
•No inter-colony aggression
•All workers similar size

L. Keller
Population genetics: Allozyme screen
Fire ants
+
Ken Ross
+ “starch gel”
1 2 3

Allozyme screen Social form associated to Gp-9 locus
Frequency of
the most
common allele
Ddh-1!
Pro-5!
Locus!
1.0!
0.9!
0.8!
0.7!
0.6!
0.5!
0.4!
0.3!
Single queen!
Multiple queen!
Est-4!
G3pdh-1! Ca-4!
Est-6!
Pgm-4!
Acy-1!
Pgm-1!
acoh-1!
Pgm-3!
Acoh-5!
Aat-2!
Gp-9!
Ken Ross and colleagues
Laurent Keller and colleagues

Social form completely associated to Gp-9 locus
Single queen form Multiple queen form

BB BB Bb bb

x
BB BB Bb bb
Gp-9 bb females rare

BB BB Bb

BB BB Bb
x

BB BB Bb
x x

(< 5% ) (>15% )
BB BB Bb
x x x

• Is this gene the single überregulator?

• Is this gene the single überregulator?
•Only 14 allozyme markers were used
maybe 1/14th of the genome?
Ddh-1!
Pro-5!
Locus!
1.0!
0.9!
0.8!
0.7!
0.6!
0.5!
0.4!
0.3!
Single queen!
Multiple queen!
Est-4!
G3pdh-1! Ca-4!
Est-6!
Pgm-4!
Acy-1!
Pgm-1!
acoh-1!
Pgm-3!
Acoh-5!
Aat-2!
Gp-9!

This changes
454 everything.
Illumina
Solid...
Any lab can
sequence
anything!

Are other genes linked to Gp-9?
Sequenced:
•Genome
of a Gp-9 B ♂
Sequencing from haploid males (for easier assembly):
45× (330bp-insert paired reads) + (normal single-Single ♂:
His brothers:
B 20x
11×
4×
(8,000 & 20,000bp-insert paired reads)

Genome of a Gp-9 B ♂ fire ant
★ Expansion of lipid-processing gene families (for Cuticular Hydrocarbons?)
★ 420 putative olfactory receptors (more than any other insect!)
SiOR06843+3
SiOR06723+1 SiOR02694+4
12
SiOR04648+SiOR04171+17
SiOR00899+6 SiOR04171+29
SiOR04171+14
SiOR04609+1
SiOR04510+16 SiOR04171+12 SiOR04510+13
SiOR04171+25 SiOR06577
SiOR04171+24
SiOR01629+3 SiOR01968+26
SiOR04171+21 SiOR06792+6
SiOR02883+2
SiOR05431+SiOR01858+1 1
SiOR05431+4
SiOR04510+7 SiOR04609+5
SiOR01321
SiOR04609+19
SiOR00899+8 SiOR04648+7
SiOR01968+21
SiOR05431+3 SiOR04510+6
SiOR01629+1
SiOR01968+7 SiOR01629+6
SiOR05285+2
SiOR03663
0.05
SiOR04648+10
SiOR03038
SiOR04648+6
SiOR00899+12 SiOR05901+1
SiOR01224+3
SiOR01968+4
SiOR00899+7
SiOR02814+3
SiOR04171+6
SiOR04609+4
SiOR00330+28
SiOR02694+25
SiOR04609+20
SiOR05285+6
25
SiOR04510+15
SiOR00330+18 SiOR04609+23
SiOR01968+23
SiOR03952+4
SiOR04648+16
SiOR05901+2
SiOR02944+4
SiOR01968+5
SiOR04171+19
SiOR04648+5
SiOR10535+3
SiOR06723+2
SiOR01968+9 SiOR02883+1
SiOR00899+3
SiOR04171+1
SiOR01629+11
SiOR04171+10
SiOR04171+13
SiOR02694+3
SiOR04171+20
SiOR02694+35
SiOR04171+15
SiOR04609+7
SiOR00899+13
SiOR05118+2
SiOR07837+2
SiOR02694+27
SiOR01968+10
SiOR04648+17
SiOR01968+19
SiOR02694+17
13
SiOR01968+6
SiOR00330+20
SiOR02648+2
SiOR02659+2
SiOR01968+16
SiOR00899+11
SiOR02974
SiOR04171+2
SiOR03952+2
SiOR06792+2
SiOR04510+4
SiOR04171+28
SiOR05285+5
SiOR05285+9 SiOR00899+15 SiOR04648+3
SiOR02694+36
SiOR10535+1
SiOR02694+19
SiOR02694+23
SiOR02694+1
SiOR04609+14
SiOR01122
9
SiOR02694+34
SiOR01629+8
SiOR04648+8
SiOR04510+8
SiOR06573
SiOR02944+1
26
SiOR00330+1
SiOR02694+15
SiOR05285+7
SiOR00899+5
SiOR04609+10
SiOR04609+3 SiOR04339
SiOR08068
SiOR04510+2
SiOR05285+8
SiOR01573+4
SiOR04171+8
SiOR01858+2 SiOR01968+2
SiOR01968+1
SiOR02694+5
SiOR 01968+3
SiOR06723+3
SiOR01968+15
SiOR 05285+1
SiOR00899+4
SiOR04609+22
SiOR04171+9
SiOR02694+9 SiOR02648+1
SiOR06792+3
SiOR01573+2
SiOR02694+20
SiOR10542
SiOR04609+15
SiOR02694+8
SiOR00330+16
SiOR00899+2
SiOR02694+10
SiOR04510+9
SiOR05285+3
SiOR04609+2
SiOR05285+11 SiOR02694+14
SiOR01573+1
SiOR00613
SiOR01968+22
SiOR00899+9
SiOR06843+2
SiOR02694+37
SiOR00899+1
SiOR04609+9
SiOR05431+2 SiOR10535+2
SiOR00330+15
SiOR02694+18
SiOR01224+2
SiOR04510+11
SiOR00330+23
SiOR02694+29
SiOR05416
SiOR05285+10 SiOR02694+2
SiOR01629+9
SiOR08341 SiOR02694+22
SiOR01224+1
SiOR01968+12
SiOR02694+7
SiOR02944+2
SiOR03952+3
SiOR01968+8
SiOR04609+24
SiOR02694+30
SiOR01629+10
SiOR04510+14
SiOR00565 SiOR05118+3
SiOR00330+14
SiOR02694+38 SiOR04609+8
SiOR04171+16
SiOR10455
SiOR04609+16
SiOR04609+21
SiOR02694+28 SiOR02659+1
SiOR04171+5 SiOR00330+29
SiOR01968+14
SiOR03983
SiOR00330+27
SiOR05285+4
SiOR04510+1
SiOR04609+17 SiOR00330+5
SiOR02694+21
SiOR02814+4
SiOR00330+7
SiOR02694+31
SiOR04648+2
SiOR02694+39
SiOR01968+25
SiOR04609+11
SiOR02694+11
SiOR06792+1
SiOR04171+4
SiOR01629+5
SiOR00330+21
SiOR04648+15
SiOR00330+6
SiOR02694+16
11
SiOR04648+4
SiOR00330+3
SiOR06535
SiOR04171+7
SiOR10493
SiOR02694+32
SiOR06792+4
SiOR04510+3
SiOR06890
SiOR01968+20
SiOR04609+12
SiOR04171+3
SiOR01968+18
SiOR01968+11
SiOR04609+13
SiOR01629+12
SiOR00330+22
SiOR02694+33
SiOR00330+13
SiOR01573+3
SiOR05118+1
SiOR02944+3
SiOR04171+26
SiOR00899+14
SiOR02694+13
SiOR00330+24
SiOR00330+19
SiOR04171+27
SiOR02694+24
SiOR04510+5
SiOR07090
SiOR03952+1
SiOR04510+10
SiOR00330+17
SiOR02694+26
SiOR02814+2
SiOR00330+11
SiOR04171+18
SiOR01968+17
SiOR00330+10
SiOR00330+9
SiOR01629+2
SiOR04171+11
SiOR04510+12
SiOR00330+8
SiOR02694+6
SiOR01968+13
SiOR00330+4 SiOR04609+18
SiOR00899+10
SiOR00330+12
SiOR00330+31
SiOR06843+1
SiOR07837+1
SiOR00330+2
SiOR01629+4
SiOR04648+1
SiOR01968+24
SiOR04171+23
SiOR01629+7 SiOR04648+14
SiOR06792+5
SiOR02883+3
SiOR02694+12
SiOR05118+4
SiOR04171+22
SiOR01080 SiOR04609+6
SiOR02814+1
SiOR00330+30
SiOR05285+12
Wurm et al 2011
> 400
Nasonia wasp 225
honey bee 165
65
10

★ Expansion of lipid-processing gene families (for Cuticular Hydrocarbons)
420 putative olfactory receptors 1
2
SiOR04609+SiOR04609+SiOR01321
SiOR03038
SiOR04609+SiOR04609+SiOR04609+SiOR04609+SiOR04609+SiOR04609+SiOR04609+SiOR04609+SiOR04609+SiOR04609+SiOR04609+SiOR04609+SiOR04609+3
SiOR04609+SiOR06843+SiOR05416
SiOR06843+SiOR06843+3
2
SiOR04609+SiOR02944+1
SiOR02944+SiOR02944+1
SiOR02648+SiOR04609+SiOR08341 1
3
1
3
SiOR04609+SiOR04609+1 11
12
21
13
14
15
16
17 18
19
SiOR02659+SiOR06890
SiOR03952+12
1
SiOR03952+SiOR06723+SiOR06723+SiOR01122
SiOR05285+11 SiOR04171+3 10 SiOR04171+10
24
2
7
8
8
9
SiOR05285+22
5
6
SiOR05285+SiOR05285+SiOR05285+★ 23
(more than any other insect!)
8
4
★ Functional DNA-methylation system
SiOR02694+SiOR02694+2
SiOR02694+9 14
SiOR02694+22
28 SiOR02694+SiOR01080 SiOR00330+SiOR00330+SiOR04339
SiOR02694+SiOR02694+4 5
38 SiOR04171+9 7
SiOR04648+3
SiOR00899+15 SiOR00565 SiOR05118+3
SiOR04171+5 SiOR00330+29
SiOR04171+SiOR04171+SiOR04171+SiOR04171+12
SiOR04171+SiOR04648+3
4
2
11
16
SiOR00899+6 11
SiOR04648+4
SiOR00899+8 SiOR04648+7
SiOR04171+17
SiOR04171+18
SiOR04171+20
SiOR04171+22
SiOR04171+9
SiOR04171+15
SiOR02648+2
SiOR02659+2
SiOR02974
SiOR03952+2
SiOR04171+28
9
SiOR04648+8
SiOR04648+6
SiOR04648+2
SiOR04648+1
SiOR04648+15
SiOR04648+14
SiOR08068
SiOR01629+7 SiOR04171+29
SiOR04171+26
SiOR04171+14
SiOR00899+12 SiOR05901+1
SiOR04171+13
SiOR04510+16 SiOR04171+12 SiOR04510+13
SiOR04171+25 SiOR06577
SiOR04171+24
SiOR02883+1
SiOR10542
SiOR01224+2
SiOR01224+1
SiOR01629+3 SiOR01968+26
SiOR04171+SiOR02883+SiOR01968+25
24
21 3
SiOR01968+SiOR01968+22
SiOR06792+6
SiOR02883+2
SiOR04171+27
SiOR05431+SiOR01858+1 1
SiOR05431+4
SiOR04510+7 SiOR01968+21
SiOR01968+20
SiOR01858+2 SiOR01968+2
SiOR05431+2 SiOR10535+2
SiOR01968+18
SiOR05431+3 SiOR04510+6
SiOR01629+1
SiOR02814+1
SiOR02814+2
SiOR02814+3
SiOR07090
SiOR02814+4
SiOR01968+7 SiOR01629+6
SiOR01629+4
SiOR01629+5
SiOR05285+1
SiOR10493
SiOR05285+3
SiOR05285+4
SiOR05285+5
SiOR05285+6
SiOR05285+2
SiOR01629+10
SiOR06573
SiOR01629+11
SiOR01629+12
SiOR01629+8
SiOR01629+9
SiOR10455
SiOR03663
SiOR01629+2
SiOR07837+1
SiOR07837+2
SiOR01573+4
SiOR01573+1
SiOR01573+3
SiOR01573+2
0.05
SiOR03952+4
SiOR05901+2
SiOR02944+4
SiOR06723+2
SiOR04609+7
SiOR00330+18 SiOR04609+23
SiOR04648+17
13
SiOR04648+10
SiOR04648+5
SiOR04648+16
SiOR01224+3
SiOR01968+23
SiOR01968+19
SiOR01968+17
SiOR01968+16
SiOR01968+15
SiOR01968+14
SiOR01968+13
SiOR01968+12
SiOR01968+11
SiOR01968+6
SiOR01968+5
SiOR01968+4
SiOR04171+1
SiOR04171+10
SiOR04171+19
SiOR00899+3
SiOR00899+2
SiOR00899+1
SiOR00899+4
SiOR00899+5
SiOR00899+7
SiOR04171+6
SiOR04609+4
SiOR01968+3
SiOR01968+1
SiOR01968+8
SiOR06792+3
SiOR06792+1
SiOR03983
SiOR06792+5
SiOR06792+4
SiOR10535+1
SiOR04510+14
SiOR04510+12
SiOR04510+11
SiOR04510+10
SiOR04510+9
SiOR04510+8
SiOR04510+5
SiOR04510+4
SiOR04510+3
SiOR04510+2
SiOR04510+1
SiOR00330+31
SiOR00330+30
SiOR00330+28
SiOR02694+12
SiOR02694+13
SiOR00330+12
SiOR00330+9
SiOR00330+8
SiOR00330+6SiOR02694+16
SiOR02694+21
SiOR02694+26
SiOR02694+25
SiOR04609+20
SiOR00330+27
SiOR00330+22
26
SiOR00330+24
SiOR00330+19
25
SiOR01968+10
SiOR01968+9
SiOR06792+2
SiOR10535+3
SiOR04510+15
SiOR00899+10
SiOR00899+13
SiOR00899+14
SiOR00899+9
SiOR05118+1
SiOR05118+4
SiOR00613
SiOR02694+1
SiOR02694+3
SiOR00330+2
SiOR02694+39
SiOR02694+37
SiOR02694+36
SiOR02694+35
SiOR05118+2
SiOR02694+27
SiOR02694+6
SiOR02694+11
SiOR02694+15
SiOR02694+17
SiOR00330+21
SiOR00330+20
SiOR00899+11
SiOR02694+18
SiOR02694+19
SiOR02694+24
SiOR02694+23
SiOR02694+34
SiOR00330+3
SiOR00330+1
SiOR02694+5
SiOR02694+20
SiOR02694+7
SiOR02694+8
SiOR00330+17
SiOR00330+16
SiOR02694+10
SiOR00330+15
23
SiOR02694+29
SiOR02694+33
SiOR02694+32
SiOR02694+31
SiOR02694+30
SiOR00330+14
SiOR00330+11
SiOR00330+10
SiOR00330+7
SiOR06535
SiOR00330+13
Wurm et al 2011

Deuterostomia 173
Nematoda 25
Cnidaria 100
Not assigned 274
★ Expansion of lipid-processing gene families (for Cuticular Hydrocarbons)
420 putative olfactory receptors 3
SiOR03038
SiOR04609+SiOR06843+1 1
SiOR06723+12
★ (more than any other insect!)
SiOR04648+★ Functional DNA-methylation system
SiOR00899+6 SiOR02694+4
★Ant-specific duplication and subfunctionalization
of vitellogenin (in bees: involved in reproduction & division of labor)
SiOR00899+8 SiOR04648+7
SiOR04648+6
SiOR04171+17
SiOR04171+29
SiOR04171+14
SiOR04609+5
SiOR01321
SiOR04609+19
SiOR00899+12 SiOR05901+1
SiOR04171+3
12 SiOR01224+SiOR04510+SiOR04510+16 13
SiOR04171+25 SiOR06577
SiOR04171+24
SiOR01629+3 SiOR01968+26
SiOR04171+21 SiOR06792+6
SiOR02883+2
SiOR05431+SiOR01858+1 1
SiOR05431+4
SiOR04510+7 SiOR01968+21
SiOR05431+3 SiOR04510+6
SiOR01629+1
SiOR01968+7 SiOR01629+6
SiOR05285+2
SiOR03663
SiOR00899+13
Wurm et al 2011
significance of these duplication events in vitellogenins, odor
perception genes, and a family of lipid-processing genes. We also
discuss additional features of interest in the fire ant genome rel-evant
to the complex social biology of this species, including sex
determination genes, DNA methylation genes, telomerase, and
the insulin and juvenile hormone pathways.
Vitellogenins. In contrast to other insects that mainly have only one
or two vitellogenins, the fire ant genome harbors four adjacent
after duplication to acquire caste-specific functions.
Odor Perception. Consistent with studies in other insects, we find
a single S. invicta ortholog to DmOr83b, a broadly expressed ol-factory
receptor (OR) required to interact with other ORs for
Drosophila and Tribolium castaneum olfaction (30–32). Beyond
OR83b, OR number varies greatly between insect species. Blast
searches and GeneWise searches using an HMM profile con-structed
with aligned ORs from N. vitripennis (33) and Pogono-myrmex
barbatus identified more than 400 loci in the S. invicta
genome with significant sequence similarity to ORs. Preliminary
work on gene model reconstruction identified 297 intact full-length
proteins. Many S. invicta ORs are in tandem arrays (Fig.
S2A) and derive from recent expansions. S. invicta may thus har-bor
the largest identified insect OR repertoire because there are
10 ORs in Pediculus humanus (34), 60 in Drosophila, 165 in
A. mellifera, 225 in N. vitripennis (33), and 259 in T. castaneum
(32). The large numbers of N. vitripennis and T. castaneum ORs
are thought to be due to current or past difficulties in host and
food finding. As has been suggested for A. mellifera (35), the large
number of S. invicta ORs may result from the importance of
chemical communication in ants. The odorant-binding proteins
(OBPs) are another family of genes also known to play roles in
chemosensation in Drosophila (36). Intriguingly, the social orga-nization
of S. invicta colonies is completely associated with se-
No hits 3424
Fig. 2. Taxonomic distribution of best blastp hits of S. invicta proteins to the
nonredundant (nr) protein database (E < 10−5). Results were first plotted
using MEGAN software (22) and then branches with fewer than 20 hits were
removed, branch lengths were reduced for compactness, and tree topology
was adjusted to reflect consensus phylogenies (23, 24).
2,330,000 bp 2,360,000 bp A
Vg4 Vg1 Vg3 Vg2
B Solenopsis Vg1 C
Solenopsis Vg4
Solenopsis Vg2
Solenopsis Vg3
Apis Vg
Bombus Vg
Nasonia Vg1
Pteromalus Vg
Nasonia Vg2
Encarsia Vg
Pimpla Vg
Athalia Vg
Apocrita
Tenthedinoidea
Vespoidea
Apoidea
Aculeata
Chalcidoidea
25000 Vg2 Vg3
20000
15000
10000
5000
Vg1 Vg4
* ***
600
500
400
300
200
100
Ichneumonoidea 0
*** ***
Q W Q W Q W Q W
142 389 1 40 17820 1.4 9269 0.6
0
Fig. 3. S. invicta vitellogenins. (A) Four vitellogenins are located within a single 40,000-bp region of the S. invicta genome. (B) Parsimony tree of known hy-menopteran
EVOLUTION
0.05
SiOR04648+10
SiOR01968+4
SiOR00899+7
SiOR02814+3
SiOR04171+6
SiOR04609+4
SiOR00330+28
SiOR02694+25
SiOR04609+20
SiOR05285+6
25
SiOR04510+15
SiOR00330+18 SiOR04609+23
SiOR01968+23
SiOR03952+4
SiOR04648+16
SiOR05901+2
SiOR02944+4
SiOR01968+5
SiOR04171+19
SiOR04648+5
SiOR10535+3
SiOR06723+2
SiOR01968+9
SiOR02883+1
SiOR00899+3
SiOR04171+1
SiOR01629+11
SiOR04171+10
SiOR04171+13
SiOR02694+3
SiOR04171+20
SiOR02694+35
SiOR04171+15
SiOR04609+7
SiOR05118+2
SiOR07837+2
SiOR02694+27
SiOR01968+10
SiOR04648+17
SiOR01968+19
SiOR02694+17
13
SiOR01968+6
SiOR00330+20
SiOR02648+2
SiOR02659+2
SiOR01968+16
SiOR00899+11
SiOR02974
SiOR04171+2
SiOR03952+2
SiOR06792+2
SiOR04510+4
SiOR04171+28
SiOR05285+5
9 SiOR00899+15 SiOR04648+3
SiOR02694+36
SiOR10535+1
SiOR02694+19
SiOR02694+23
SiOR02694+1
SiOR04609+14
SiOR01122
9
SiOR02694+34
SiOR01629+8
SiOR04648+8
SiOR04510+8
SiOR06573
SiOR02944+1
26
SiOR00330+1
SiOR02694+15
SiOR05285+7
SiOR00899+5
SiOR04609+10
SiOR04609+3 SiOR04339
SiOR08068
SiOR04510+2
SiOR05285+8
SiOR01573+4
SiOR04171+8
SiOR01858+2 SiOR01968+2
SiOR01968+1
SiOR02694+5
SiOR01968+3
SiOR06723+3
SiOR01968+15
SiOR05285+1
SiOR00899+4
SiOR04609+22
SiOR04171+9
SiOR02694+9 SiOR02648+1
SiOR06792+3
SiOR01573+2
SiOR02694+20
SiOR10542
SiOR04609+15
SiOR02694+8
SiOR00330+16
SiOR00899+2
SiOR02694+10
SiOR04510+9
SiOR05285+3
SiOR04609+2
SiOR05285+11 SiOR02694+14
SiOR01573+1
SiOR00613
SiOR01968+22
SiOR00899+9
SiOR06843+2
SiOR02694+37
SiOR00899+1
SiOR04609+9
SiOR05431+2 SiOR10535+2
SiOR00330+15
SiOR02694+18
SiOR01224+2
SiOR04510+11
23
SiOR02694+29
SiOR05416
SiOR05285+10 SiOR02694+2
SiOR01629+9
SiOR08341 SiOR02694+22
SiOR01224+1
SiOR01968+12
SiOR02694+7
SiOR02944+2
SiOR03952+3
SiOR01968+8
SiOR04609+24
SiOR02694+30
SiOR01629+10
SiOR04510+14
SiOR00565 SiOR05118+3
SiOR00330+14
SiOR02694+38 SiOR04609+8
SiOR04171+16
SiOR10455
SiOR04609+16
SiOR04609+21
SiOR02694+28 SiOR02659+1
SiOR04171+5 SiOR00330+29
SiOR01968+14
SiOR03983
SiOR00330+27
SiOR05285+4
SiOR04510+1
SiOR04609+17 SiOR00330+5
SiOR02694+21
SiOR02814+4
SiOR00330+7
SiOR02694+31
SiOR04648+2
SiOR02694+39
SiOR01968+25
SiOR04609+11
SiOR02694+11
SiOR06792+1
SiOR04171+4
SiOR01629+5
SiOR00330+21
SiOR04648+15
SiOR00330+6SiOR02694+16
11
SiOR04648+4
SiOR00330+3
SiOR06535
SiOR04171+7
SiOR10493
SiOR02694+32
SiOR06792+4
SiOR04510+3
SiOR06890
SiOR01968+20
SiOR04609+12
SiOR04171+3
SiOR01968+18
SiOR01968+11
SiOR04609+13
SiOR01629+12
SiOR00330+22
SiOR02694+33
SiOR00330+13
SiOR01573+3
SiOR05118+1
SiOR02944+3
SiOR04171+26
SiOR00899+14
SiOR02694+13
SiOR00330+24
SiOR00330+19
SiOR04171+27
SiOR02694+24
SiOR04510+5
SiOR07090
SiOR03952+1
SiOR04510+10
SiOR00330+17
SiOR02694+26
SiOR02814+2
SiOR00330+11
SiOR04171+18
SiOR01968+17
SiOR00330+10
SiOR00330+9
SiOR01629+2
SiOR04171+11
SiOR04510+12
SiOR00330+8
SiOR02694+6
SiOR01968+13
SiOR00330+4 SiOR04609+18
SiOR00899+10
SiOR00330+12
SiOR00330+31
SiOR06843+1
SiOR07837+1
SiOR00330+2
SiOR01629+4
SiOR04648+1
SiOR01968+24
SiOR04171+23
SiOR01629+7 SiOR04648+14
SiOR06792+5
SiOR02883+3
SiOR02694+12
SiOR05118+4
SiOR04171+22
SiOR01080 SiOR04609+6
SiOR02814+1
SiOR00330+30
SiOR05285+12
Wurm et al 2011

(< 5% ) (>15% )
BB BB Bb
x x x

Sequenced:
•Genome of a Gp-9 B ♂
•Genome of a Gp-9 b ♂
RAD sequencing
“Next Generation Genotyping.”

RAD sequencing
“Next Generation Genotyping.”
Bb
unfertilised eggs
haploid ♂
Gp-9 B Gp-9 b Gp-9 B Gp-9 b Gp-9 b Gp-9 B
38 B♂ & 38 b♂

RAD sequencing of haploid ♂ for SNP
EcoR1 EcoR1 EcoR1
Gp-9 B
discovery & genotyping

EcoR1 EcoR1 EcoR1
AACTG
AACTG
AACTG
AACTG
Gp-9 B
Gp-9 B

Gp-9 B
AACTG
Gp-9 B
Gp-9 B
GGCCT
Gp-9 B
Gp-9 B
AAGGT
Gp-9 B
Gp-9 b
CCAGT
Gp-9 b
Gp-9 b
TAAAT
Gp-9 b
Gp-9 b
GGAAT
Gp-9 b
38 Gp-9 B
males
38 Gp-9 b
males

RADseq: sequencing the same 0.01% of the
genome in many individuals
Identify polymorphism
individual x locus
genotype table
A B C D E F
L1 A C A A C C
L2 G G T - T G
L3 - A G A - G
L4 C - - G G C
L5 T T C T C -
L6 G A A - - G
2419 loci
38 B 38 b
PCA: Principal Component Analysis
Amount of variance explained per principal component
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20+
% Variance Explained
0 5 10 15 20 25 30
12.7%
6.1% 5.4% 4.8% 4.7% 3.9% 3.5% 3.2% 3.1% 2.9% 2.8% 2.6% 2.4% 2.3% 2.2% 2.0% 1.9% 1.7% 1.6%
30.2%

Principal Components: PC2 vs PC3
pc: 2 % variance: 6.073
0.2
0.1
0.0
-0.1
-0.2
-0.2 -0.1 0.0 0.1 0.2
Gp-9 B
Gp-9 b

Principal Components: PC1 vs PC2
0.2
0.1
0.0
-0.1
-0.2
-0.10 -0.05 0.00 0.05 0.10 0.15
Gp-9 B ♂
Gp-9 b ♂

brc_m013_0280
brc_m013_0281..brc_m013_0294
brc_m013_0295..brc_m013_0303
brc_m013_0304
brc_m013_0305..brc_m013_0307
brc_m013_0308
brc_m013_0309..brc_m013_0314
brc_m013_0315..brc_m013_0317
brc_m013_0318..brc_m013_0320
brc_m013_0321..brc_m013_0326
brc_m013_0327
brc_m013_0328
brc_m013_0329..brc_m013_0330
brc_m013_0331..brc_m013_0333
brc_m013_0334..brc_m013_0339
brc_m013_0340
brc_m013_0341..brc_m013_0343
brc_m013_0344
brc_m013_0345..brc_m013_0349
brc_m013_0350
4% of genome linked 140
160
brc_m013_0351..brc_m013_0354
brc_m013_0355
to Gp-9
brc_m013_0356
brc_m013_0357..brc_m013_0361
brc_m013_0362..brc_m013_0376
brc_m013_0377..brc_m013_0390
brc_m013_0391..brc_m013_0393
180
brc_m013_0394..brc_m013_0400
brc_m013_0401..brc_m013_0439
brc_m013_0440..brc_m013_0478
brc_m013_0479..brc_m013_0480
brc_m013_0802..brc_m013_0805
brc_m013_0806..brc_m013_0809
brc_m013_0810..brc_m013_0811
brc_m013_0812..brc_m013_0824
brc_m013_0825..brc_m013_0826
brc_m013_0827..brc_m013_0829
brc_m013_0830..brc_m013_0831
brc_m013_0832..brc_m013_0842
brc_m013_0843..brc_m013_0854
brc_m013_0855..brc_m013_0861
brc_m013_0862
brc_m013_0863..brc_m013_0864
brc_m013_0865..brc_m013_0867
brc_m013_0868..brc_m013_0883
brc_m013_0884..brc_m013_0893
brc_m013_0894
brc_m013_0895..brc_m013_0897
brc_m013_0898..brc_m013_0906
brc_m013_0907..brc_m013_0910
brc_m013_0911..brc_m013_0925
brc_m013_0926..brc_m013_0928
brc_m013_0929..brc_m013_0931
140
brc_m013_1275..brc_m013_1280
brc_m013_1281
brc_m013_1282..brc_m013_1286
brc_m013_1287..brc_m013_1298
brc_m013_1299..brc_m013_1307
brc_m013_1308
brc_m013_1309..brc_m013_1313
brc_m013_1314..brc_m013_1317
brc_m013_1318..brc_m013_1319
brc_m013_1320..brc_m013_1326
brc_m013_1327..brc_m013_1340
brc_m013_1341..brc_m013_1362
brc_m013_1363..brc_m013_1385
140
brc_m013_1683
brc_m013_1684
brc_m013_1685..brc_m013_1686
brc_m013_1687..brc_m013_1700
brc_m013_1701..brc_m013_1702
brc_m013_1703
brc_m013_1704..brc_m013_1707
brc_m013_1708..brc_m013_1709
brc_m013_1710..brc_m013_1714
brc_m013_1715..brc_m013_1728
brc_m013_1729..brc_m013_1742
140
brc_m013_1967..brc_m013_1968
brc_m013_1969..brc_m013_1970
brc_m013_1971
brc_m013_1972
brc_m013_1973..brc_m013_1980
brc_m013_1981..brc_m013_1983
brc_m013_1984..brc_m013_1990
brc_m013_1991..brc_m013_1993
brc_m013_1994..brc_m013_1996
brc_m013_1997..brc_m013_2009
brc_m013_2302..brc_m013_2305
brc_m013_2306..brc_m013_2307
brc_m013_2308..brc_m013_2330
brc_m013_2331..brc_m013_2337
brc_m013_2338..brc_m013_2352
Figure 1
a b
LG9
brc_m013_2897..brc_m013_2920
brc_m013_2921..brc_m013_2928
brc_m013_2929..brc_m013_2931
brc_m013_2932
brc_m013_2933
brc_m013_2934..brc_m013_2935
brc_m013_2936
brc_m013_2937..brc_m013_2943
brc_m013_2944
brc_m013_2945..brc_m013_2946
brc_m013_2947
brc_m013_2948
brc_m013_2949..brc_m013_2950
brc_m013_2951..brc_m013_2957
brc_m013_2958..brc_m013_2961
brc_m013_2962..brc_m013_2970
brc_m013_2971..brc_m013_2980
brc_m013_2981..brc_m013_2992
brc_m013_2993..brc_m013_2996
brc_m013_2997..brc_m013_2998
brc_m013_2999..brc_m013_3000
brc_m013_3001
brc_m013_3002..brc_m013_3003
brc_m013_3004
brc_m013_3005
brc_m013_3006..brc_m013_3010
brc_m013_3011..brc_m013_3014
brc_m013_3015
brc_m013_3016..brc_m013_3019
brc_m013_3020
brc_m013_3021..brc_m013_3030
brc_m013_3031..brc_m013_3032
brc_m013_3033..brc_m013_3034
brc_m013_3035..brc_m013_3036
brc_m013_3037..brc_m013_3045
brc_m013_3046..brc_m013_3052
brc_m013_3053
brc_m013_3054..brc_m013_3061
brc_m013_3062..brc_m013_3066
brc_m013_3067..brc_m013_3068
brc_m013_3069..brc_m013_3076
brc_m013_3077..brc_m013_3084
brc_m013_3085..brc_m013_3087
brc_m013_3088..brc_m013_3089
brc_m013_3090..brc_m013_3096
brc_m013_3097..brc_m013_3100
brc_m013_3101..brc_m013_3104
brc_m013_3105
brc_m013_3106..brc_m013_3112
brc_m013_3113..brc_m013_3122
brc_m013_3123..brc_m013_3124
brc_m013_3125..brc_m013_3127
brc_m013_3128..brc_m013_3145
brc_m013_3146..brc_m013_3159
brc_m013_3160..brc_m013_3172
0
20
40
60
80
100
LG10
LGS B
from M013
brc_m013_3173..brc_m013_3175
brc_m013_3176..brc_m013_3180
brc_m013_3181..brc_m013_3189
brc_m013_3190..brc_m013_3198
brc_m013_3199
brc_m013_3200..brc_m013_3201
brc_m013_3202..brc_m013_3203
brc_m013_3204
brc_m013_3205..brc_m013_3206
brc_m013_3207..brc_m013_3211
brc_m013_3212..brc_m013_3214
brc_m013_3215..brc_m013_3227
brc_m013_3228..brc_m013_3230
brc_m013_3231..brc_m013_3235
brc_m013_3236..brc_m013_3238
brc_m013_3239..brc_m013_3242
brc_m013_3243..brc_m013_3244
brc_m013_3245
brc_m013_3246..brc_m013_3247
brc_m013_3248..brc_m013_3249
brc_m013_3250..brc_m013_3252
brc_m013_3253..brc_m013_3257
brc_m013_3258
brc_m013_3259
brc_m013_3260..brc_m013_3261
brc_m013_3262..brc_m013_3263
brc_m013_3264
brc_m013_3265..brc_m013_3269
brc_m013_3270..brc_m013_3274
brc_m013_3275..brc_m013_3276
brc_m013_3277..brc_m013_3281
brc_m013_3282..brc_m013_3284
brc_m013_3285
brc_m013_3286..brc_m013_3289
brc_m013_3290..brc_m013_3296
brc_m013_3297
brc_m013_3298..brc_m013_3300
brc_m013_3301..brc_m013_3302
brc_m013_3303..brc_m013_3305
brc_m013_3306..brc_m013_3308
brc_m013_3309..brc_m013_3314
brc_m013_3315..brc_m013_3317
brc_m013_3318..brc_m013_3329
brc_m013_3330..brc_m013_3331
brc_m013_3332..brc_m013_3338
brc_m013_3339..brc_m013_3340
brc_m013_3341..brc_m013_3344
brc_m013_3345..brc_m013_3349
brc_m013_3350..brc_m013_3357
brc_m013_3358..brc_m013_3359
brc_m013_3360
brc_m013_3361..brc_m013_3368
brc_m013_3369..brc_m013_3372
brc_m013_3373..brc_m013_3376
brc_m013_3377
brc_m013_3378..brc_m013_3386
brc_m013_3387..brc_m013_3388
brc_m013_3389..brc_m013_3395
brc_m013_3396..brc_m013_3399
0
20
40
60
80
LGS B/b
from P034
LG11
brc_m013_3400..brc_m013_3411
brc_m013_3412
brc_m013_3413..brc_m013_3424
brc_m013_3425
brc_m013_3426
brc_m013_3427..brc_m013_3429
brc_m013_3430
brc_m013_3431..brc_m013_3432
brc_m013_3433..brc_m013_3435
brc_m013_3436
brc_m013_3437..brc_m013_3439
brc_m013_3440..brc_m013_3441
brc_m013_3442
brc_m013_3443..brc_m013_3445
brc_m013_3446..brc_m013_3447
brc_m013_3448..brc_m013_3449
brc_m013_3450..brc_m013_3454
brc_m013_3455
brc_m013_3456..brc_m013_3462
brc_m013_3463..brc_m013_3464
brc_m013_3465
brc_m013_3466..brc_m013_3467
brc_m013_3468..brc_m013_3472
brc_m013_3473
brc_m013_3474..brc_m013_3476
brc_m013_3477..brc_m013_3487
brc_m013_3488
brc_m013_3489..brc_m013_3491
brc_m013_3492..brc_m013_3500
brc_m013_3501..brc_m013_3512
brc_m013_3513..brc_m013_3514
brc_m013_3515..brc_m013_3524
brc_m013_3525..brc_m013_3527
brc_m013_3528..brc_m013_3531
brc_m013_3532..brc_m013_3547
brc_m013_3548..brc_m013_3557
brc_m013_3558..brc_m013_3566
brc_m013_3567..brc_m013_3568
brc_m013_3569..brc_m013_3570
brc_m013_3571..brc_m013_3574
brc_m013_3575..brc_m013_3582
brc_m013_3583..brc_m013_3592
brc_m013_3593..brc_m013_3605
brc_m013_3606..brc_m013_3616
brc_m013_3617..brc_m013_3618
brc_m013_3619..brc_m013_3622
brc_m013_3623..brc_m013_3624
brc_m013_3625..brc_m013_3628
brc_m013_3629..brc_m013_3635
0
20
40
60
80
LG12
brc_m013_3636..brc_m013_3661
brc_m013_3662..brc_m013_3665
brc_m013_3666..brc_m013_3667
brc_m013_3668
brc_m013_3669..brc_m013_3671
brc_m013_3672
brc_m013_3673..brc_m013_3674
brc_m013_3675..brc_m013_3682
brc_m013_3683..brc_m013_3685
brc_m013_3686..brc_m013_3688
brc_m013_3689..brc_m013_3693
brc_m013_3694..brc_m013_3698
brc_m013_3699
brc_m013_3700
brc_m013_3701..brc_m013_3702
brc_m013_3703..brc_m013_3704
brc_m013_3705..brc_m013_3712
brc_m013_3713
brc_m013_3714..brc_m013_3716
brc_m013_3717..brc_m013_3724
brc_m013_3725..brc_m013_3730
brc_m013_3731..brc_m013_3752
brc_m013_3753..brc_m013_3758
brc_m013_3759..brc_m013_3789
brc_m013_3790..brc_m013_3801
brc_m013_3802..brc_m013_3814
brc_m013_3815..brc_m013_3818
brc_m013_3819..brc_m013_3822
brc_m013_3823..brc_m013_3826
brc_m013_3827..brc_m013_3832
brc_m013_3833..brc_m013_3837
brc_m013_3838
brc_m013_3839..brc_m013_3841
brc_m013_3842..brc_m013_3847
brc_m013_3848..brc_m013_3853
brc_m013_3854..brc_m013_3858
brc_m013_3859..brc_m013_3868
brc_m013_3869..brc_m013_3871
brc_m013_3872..brc_m013_3901
brc_m013_3902
brc_m013_3903..brc_m013_3909
brc_m013_3910
brc_m013_3911..brc_m013_3926
brc_m013_3927..brc_m013_3931
brc_m013_3932..brc_m013_3948
0
20
40
60
80
LG13
brc_m013_3949..brc_m013_3952
brc_m013_3953..brc_m013_3958
brc_m013_3959..brc_m013_3970
brc_m013_3971
brc_m013_3972..brc_m013_3975
brc_m013_3976
brc_m013_3977..brc_m013_3985
brc_m013_3986
brc_m013_3987..brc_m013_3994
brc_m013_3995..brc_m013_3997
brc_m013_3998..brc_m013_4004
brc_m013_4005..brc_m013_4006
brc_m013_4007..brc_m013_4008
brc_m013_4009..brc_m013_4010
brc_m013_4011..brc_m013_4013
brc_m013_4014
brc_m013_4015
brc_m013_4016..brc_m013_4019
brc_m013_4020..brc_m013_4021
brc_m013_4022..brc_m013_4025
brc_m013_4026..brc_m013_4032
brc_m013_4033..brc_m013_4036
brc_m013_4037..brc_m013_4041
brc_m013_4042..brc_m013_4043
brc_m013_4044..brc_m013_4046
brc_m013_4047..brc_m013_4056
brc_m013_4057
brc_m013_4058..brc_m013_4063
brc_m013_4064..brc_m013_4071
brc_m013_4072..brc_m013_4075
brc_m013_4076
brc_m013_4077
brc_m013_4078..brc_m013_4085
brc_m013_4086..brc_m013_4089
brc_m013_4090..brc_m013_4091
brc_m013_4092..brc_m013_4093
brc_m013_4094..brc_m013_4095
brc_m013_4096..brc_m013_4114
brc_m013_4115..brc_m013_4117
brc_m013_4118..brc_m013_4131
brc_m013_4132..brc_m013_4133
brc_m013_4134..brc_m013_4146
0
20
40
60
80
LG14
brc_m013_4147..brc_m013_4150
brc_m013_4151..brc_m013_4167
brc_m013_4168
brc_m013_4169
brc_m013_4170
brc_m013_4171..brc_m013_4172
brc_m013_4173..brc_m013_4175
brc_m013_4176
brc_m013_4177..brc_m013_4178
brc_m013_4179..brc_m013_4183
brc_m013_4184..brc_m013_4185
brc_m013_4186..brc_m013_4187
brc_m013_4188..brc_m013_4191
brc_m013_4192
brc_m013_4193..brc_m013_4194
brc_m013_4195..brc_m013_4206
brc_m013_4207..brc_m013_4210
brc_m013_4211..brc_m013_4213
brc_m013_4214
brc_m013_4215..brc_m013_4217
brc_m013_4218..brc_m013_4221
brc_m013_4222..brc_m013_4223
brc_m013_4224..brc_m013_4231
brc_m013_4232..brc_m013_4234
brc_m013_4235..brc_m013_4239
brc_m013_4240..brc_m013_4246
brc_m013_4247..brc_m013_4248
brc_m013_4249..brc_m013_4258
brc_m013_4259..brc_m013_4260
brc_m013_4261..brc_m013_4269
brc_m013_4270..brc_m013_4271
brc_m013_4272..brc_m013_4278
brc_m013_4279..brc_m013_4280
brc_m013_4281..brc_m013_4284
brc_m013_4285
brc_m013_4286..brc_m013_4288
brc_m013_4289..brc_m013_4294
brc_m013_4295..brc_m013_4296
brc_m013_4297..brc_m013_4301
brc_m013_4302..brc_m013_4313
brc_m013_4314..brc_m013_4320
brc_m013_4321..brc_m013_4322
brc_m013_4323..brc_m013_4345
brc_m013_4346..brc_m013_4351
0
20
40
60
LG15
brc_m013_4352..brc_m013_4366
brc_m013_4367
brc_m013_4368
brc_m013_4369..brc_m013_4373
brc_m013_4374..brc_m013_4381
brc_m013_4382..brc_m013_4383
brc_m013_4384..brc_m013_4385
brc_m013_4386
brc_m013_4387..brc_m013_4388
brc_m013_4389
brc_m013_4390..brc_m013_4404
brc_m013_4405
brc_m013_4406..brc_m013_4409
brc_m013_4410..brc_m013_4411
brc_m013_4412..brc_m013_4418
brc_m013_4419..brc_m013_4434
brc_m013_4435..brc_m013_4442
brc_m013_4443..brc_m013_4448
brc_m013_4449..brc_m013_4451
brc_m013_4452..brc_m013_4461
brc_m013_4462..brc_m013_4471
brc_m013_4472..brc_m013_4475
brc_m013_4476..brc_m013_4477
brc_m013_4478
brc_m013_4479
brc_m013_4480..brc_m013_4485
brc_m013_4486
brc_m013_4487..brc_m013_4491
brc_m013_4492
brc_m013_4493
brc_m013_4494..brc_m013_4495
brc_m013_4496..brc_m013_4501
brc_m013_4502..brc_m013_4510
brc_m013_4511..brc_m013_4531
brc_m013_4532
brc_m013_4533..brc_m013_4534
brc_m013_4535..brc_m013_4541
brc_m013_4542..brc_m013_4543
brc_m013_4544..brc_m013_4545
brc_m013_4546..brc_m013_4548
brc_m013_4549..brc_m013_4551
brc_m013_4552..brc_m013_4555
brc_m013_4556..brc_m013_4561
0
20
40
60
LGSB
brc_m013_4562..brc_m013_4577
brc_m013_4578..brc_m013_4594
brc_m013_4595..brc_m013_4599
brc_m013_4600..brc_m013_4625
brc_m013_4626..brc_m013_4638
brc_m013_4639..brc_m013_4642
brc_m013_4643..brc_m013_4644
brc_m013_4645..brc_m013_4650
brc_m013_4651..brc_m013_4663
brc_m013_4664..brc_m013_4668
brc_m013_4669..brc_m013_4670
brc_m013_4671..brc_m013_4674
brc_m013_4675..brc_m013_4679
brc_m013_4680..brc_m013_4681
brc_m013_4682
brc_m013_4683..brc_m013_4688
brc_m013_4689..brc_m013_4692
brc_m013_4693..brc_m013_4695
brc_m013_4696..brc_m013_4701
brc_m013_4702
brc_m013_4703..brc_m013_4712
brc_m013_4713..brc_m013_4717
brc_m013_4718..brc_m013_4720
brc_m013_4721
brc_m013_4722..brc_m013_4726
brc_m013_4727..brc_m013_4728
brc_m013_4729..brc_m013_4742
brc_m013_4743
brc_m013_4744..brc_m013_4746
brc_m013_4747
brc_m013_4748..brc_m013_4749
brc_m013_4750..brc_m013_4752
brc_m013_4753..brc_m013_4756
brc_m013_4757..brc_m013_4759
brc_m013_4760..brc_m013_4762
brc_m013_4763
brc_m013_4764..brc_m013_4766
brc_m013_4767..brc_m013_4769
brc_m013_4770
brc_m013_4771..brc_m013_4774
brc_m013_4775..brc_m013_4776
brc_m013_4777..brc_m013_4778
brc_m013_4779..brc_m013_4780
brc_m013_4781..brc_m013_4793
brc_m013_4794
brc_m013_4795..brc_m013_4798
brc_m013_4799..brc_m013_4802
brc_m013_4803..brc_m013_4806
brc_m013_4807
brc_m013_4808..brc_m013_4814
brc_m013_4815..brc_m013_4819
brc_m013_4820
brc_m013_4821
brc_m013_4822..brc_m013_4823
brc_m013_4824
brc_m013_4825..brc_m013_4855
brc_m013_4856..brc_m013_4858
brc_m013_4859..brc_m013_4863
brc_m013_4864..brc_m013_4865
brc_m013_4866..brc_m013_4875
brc_m013_4876..brc_m013_4881
brc_m013_4882..brc_m013_4891
brc_m013_4892..brc_m013_4895
brc_m013_4896..brc_m013_4911
brc_m013_4912..brc_m013_4938
brc_m013_4939
brc_m013_4940..brc_m013_4957
brc_m013_4958..brc_m013_4959
brc_m013_4960..brc_m013_4972
brc_m013_4973..brc_m013_4981
brc_m013_4982..brc_m013_4983
0
20
40
60
80
100
120
Gp-9
Gp-9
LG1
brc_m013_0001..brc_m013_0005 brc_m013_0006..brc_m013_0014
brc_m013_0015..brc_m013_0017
brc_m013_0018
brc_m013_0019..brc_m013_0020
brc_m013_0021..brc_m013_0029
brc_m013_0030..brc_m013_0031
brc_m013_0032..brc_m013_0034
brc_m013_0035..brc_m013_0036
brc_m013_0037..brc_m013_0038
brc_m013_0039..brc_m013_0043
brc_m013_0044
brc_m013_0045
brc_m013_0046..brc_m013_0048
brc_m013_0049
brc_m013_0050..brc_m013_0051
brc_m013_0052..brc_m013_0056
brc_m013_0057..brc_m013_0061
brc_m013_0062..brc_m013_0075
brc_m013_0076..brc_m013_0078
brc_m013_0079..brc_m013_0081
brc_m013_0082..brc_m013_0088
brc_m013_0089..brc_m013_0092
brc_m013_0093..brc_m013_0096
brc_m013_0097
brc_m013_0098..brc_m013_0113
brc_m013_0114..brc_m013_0119
brc_m013_0120..brc_m013_0130
brc_m013_0131
brc_m013_0132..brc_m013_0134
brc_m013_0135..brc_m013_0136
brc_m013_0137..brc_m013_0139
brc_m013_0140..brc_m013_0142
brc_m013_0143
brc_m013_0144..brc_m013_0146
brc_m013_0147..brc_m013_0154
brc_m013_0155
brc_m013_0156
brc_m013_0157..brc_m013_0180
brc_m013_0181
brc_m013_0182
brc_m013_0183..brc_m013_0188
brc_m013_0189..brc_m013_0208
brc_m013_0209
brc_m013_0210..brc_m013_0211
brc_m013_0212..brc_m013_0215
brc_m013_0216
brc_m013_0217
brc_m013_0218..brc_m013_0224
brc_m013_0225..brc_m013_0228
brc_m013_0229..brc_m013_0237
brc_m013_0238..brc_m013_0245
brc_m013_0246..brc_m013_0270
brc_m013_0271..brc_m013_0274
brc_m013_0275
brc_m013_0276..brc_m013_0278
brc_m013_0279
brc_m013_0280
brc_m013_0281..brc_m013_0294
brc_m013_0295..brc_m013_0303
brc_m013_0304
brc_m013_0305..brc_m013_0307
brc_m013_0308
brc_m013_0309..brc_m013_0314
brc_m013_0315..brc_m013_0317
brc_m013_0318..brc_m013_0320
brc_m013_0321..brc_m013_0326
brc_m013_0327
brc_m013_0328
brc_m013_0329..brc_m013_0330
brc_m013_0331..brc_m013_0333
brc_m013_0334..brc_m013_0339
brc_m013_0340
brc_m013_0341..brc_m013_0343
brc_m013_0344
brc_m013_0345..brc_m013_0349
brc_m013_0350
brc_m013_0351..brc_m013_0354
brc_m013_0355
brc_m013_0356
brc_m013_0357..brc_m013_0361
brc_m013_0362..brc_m013_0376
brc_m013_0377..brc_m013_0390
brc_m013_0391..brc_m013_0393
brc_m013_0394..brc_m013_0400
brc_m013_0401..brc_m013_0439
brc_m013_0440..brc_m013_0478
brc_m013_0479..brc_m013_0480
0
20
40
60
80
100
120
140
160
180
LG2
brc_m013_0481
brc_m013_0482..brc_m013_0484
brc_m013_0485..brc_m013_0488
brc_m013_0489..brc_m013_0502
brc_m013_0503
brc_m013_0504..brc_m013_0519
brc_m013_0520..brc_m013_0532
brc_m013_0533..brc_m013_0534
brc_m013_0535..brc_m013_0537
brc_m013_0538..brc_m013_0540
brc_m013_0541..brc_m013_0543
brc_m013_0544..brc_m013_0545
brc_m013_0546..brc_m013_0549
brc_m013_0550..brc_m013_0554
brc_m013_0555..brc_m013_0560
brc_m013_0561..brc_m013_0562
brc_m013_0563..brc_m013_0565
brc_m013_0566
brc_m013_0567
brc_m013_0568..brc_m013_0570
brc_m013_0571..brc_m013_0573
brc_m013_0574..brc_m013_0575
brc_m013_0576..brc_m013_0578
brc_m013_0579..brc_m013_0580
brc_m013_0581
brc_m013_0582..brc_m013_0584
brc_m013_0585
brc_m013_0586
brc_m013_0587
brc_m013_0588..brc_m013_0591
brc_m013_0592
brc_m013_0593
brc_m013_0594..brc_m013_0612
brc_m013_0613..brc_m013_0614
brc_m013_0615..brc_m013_0632
brc_m013_0633
brc_m013_0634..brc_m013_0648
brc_m013_0649..brc_m013_0655
brc_m013_0656
brc_m013_0657..brc_m013_0694
brc_m013_0695..brc_m013_0703
brc_m013_0704
brc_m013_0705
brc_m013_0706..brc_m013_0707
brc_m013_0708
brc_m013_0709..brc_m013_0711
brc_m013_0712..brc_m013_0715
brc_m013_0716..brc_m013_0721
brc_m013_0722
brc_m013_0723
brc_m013_0724..brc_m013_0728
brc_m013_0729
brc_m013_0730
brc_m013_0731
brc_m013_0732..brc_m013_0735
brc_m013_0736..brc_m013_0769
brc_m013_0770..brc_m013_0771
brc_m013_0772..brc_m013_0773
brc_m013_0774..brc_m013_0775
brc_m013_0776..brc_m013_0782
brc_m013_0783
brc_m013_0784..brc_m013_0795
brc_m013_0796..brc_m013_0798
brc_m013_0799..brc_m013_0801
brc_m013_0802..brc_m013_0805
brc_m013_0806..brc_m013_0809
brc_m013_0810..brc_m013_0811
brc_m013_0812..brc_m013_0824
brc_m013_0825..brc_m013_0826
brc_m013_0827..brc_m013_0829
brc_m013_0830..brc_m013_0831
brc_m013_0832..brc_m013_0842
brc_m013_0843..brc_m013_0854
brc_m013_0855..brc_m013_0861
brc_m013_0862
brc_m013_0863..brc_m013_0864
brc_m013_0865..brc_m013_0867
brc_m013_0868..brc_m013_0883
brc_m013_0884..brc_m013_0893
brc_m013_0894
brc_m013_0895..brc_m013_0897
brc_m013_0898..brc_m013_0906
brc_m013_0907..brc_m013_0910
brc_m013_0911..brc_m013_0925
brc_m013_0926..brc_m013_0928
brc_m013_0929..brc_m013_0931
0
20
40
60
80
100
120
140
LG3
brc_m013_0932..brc_m013_0941
brc_m013_0942..brc_m013_0943
brc_m013_0944..brc_m013_0945
brc_m013_0946..brc_m013_0949
brc_m013_0950..brc_m013_0952
brc_m013_0953..brc_m013_0975
brc_m013_0976..brc_m013_1019
brc_m013_1020
brc_m013_1021
brc_m013_1022..brc_m013_1061
brc_m013_1062
brc_m013_1063
brc_m013_1064..brc_m013_1065
brc_m013_1066..brc_m013_1068
brc_m013_1069
brc_m013_1070
brc_m013_1071..brc_m013_1074
brc_m013_1075
brc_m013_1076..brc_m013_1081
brc_m013_1082..brc_m013_1086
brc_m013_1087..brc_m013_1088
brc_m013_1089..brc_m013_1098
brc_m013_1099..brc_m013_1106
brc_m013_1107..brc_m013_1116
brc_m013_1117
brc_m013_1118..brc_m013_1121
brc_m013_1122..brc_m013_1127
brc_m013_1128
brc_m013_1129..brc_m013_1136
brc_m013_1137..brc_m013_1138
brc_m013_1139..brc_m013_1141
brc_m013_1142..brc_m013_1144
brc_m013_1145..brc_m013_1156
brc_m013_1157
brc_m013_1158..brc_m013_1170
brc_m013_1171..brc_m013_1181
brc_m013_1182..brc_m013_1185
brc_m013_1186
brc_m013_1187..brc_m013_1205
brc_m013_1206..brc_m013_1218
brc_m013_1219..brc_m013_1220
brc_m013_1221..brc_m013_1224
brc_m013_1225..brc_m013_1228
brc_m013_1229
brc_m013_1230..brc_m013_1236
brc_m013_1237
brc_m013_1238..brc_m013_1247
brc_m013_1248..brc_m013_1251
brc_m013_1252
brc_m013_1253..brc_m013_1268
brc_m013_1269..brc_m013_1270
brc_m013_1271..brc_m013_1273
brc_m013_1274
brc_m013_1275..brc_m013_1280
brc_m013_1281
brc_m013_1282..brc_m013_1286
brc_m013_1287..brc_m013_1298
brc_m013_1299..brc_m013_1307
brc_m013_1308
brc_m013_1309..brc_m013_1313
brc_m013_1314..brc_m013_1317
brc_m013_1318..brc_m013_1319
brc_m013_1320..brc_m013_1326
brc_m013_1327..brc_m013_1340
brc_m013_1341..brc_m013_1362
brc_m013_1363..brc_m013_1385
0
20
40
60
80
100
120
140
LG4
brc_m013_1386..brc_m013_1388
brc_m013_1389..brc_m013_1398
brc_m013_1399..brc_m013_1406
brc_m013_1407..brc_m013_1411
brc_m013_1412..brc_m013_1413
brc_m013_1414..brc_m013_1416
brc_m013_1417
brc_m013_1418..brc_m013_1420
brc_m013_1421..brc_m013_1424
brc_m013_1425..brc_m013_1432
brc_m013_1433..brc_m013_1442
brc_m013_1443
brc_m013_1444..brc_m013_1450
brc_m013_1451
brc_m013_1452
brc_m013_1453..brc_m013_1455
brc_m013_1456..brc_m013_1467
brc_m013_1468..brc_m013_1469
brc_m013_1470
brc_m013_1471..brc_m013_1474
brc_m013_1475
brc_m013_1476
brc_m013_1477
brc_m013_1478..brc_m013_1482
brc_m013_1483
brc_m013_1484
brc_m013_1485..brc_m013_1487
brc_m013_1488..brc_m013_1490
brc_m013_1491
brc_m013_1492..brc_m013_1494
brc_m013_1495..brc_m013_1496
brc_m013_1497..brc_m013_1500
brc_m013_1501
brc_m013_1502..brc_m013_1513
brc_m013_1514..brc_m013_1562
brc_m013_1563..brc_m013_1565
brc_m013_1566..brc_m013_1567
brc_m013_1568..brc_m013_1580
brc_m013_1581..brc_m013_1587
brc_m013_1588..brc_m013_1591
brc_m013_1592..brc_m013_1593
brc_m013_1594..brc_m013_1604
brc_m013_1605..brc_m013_1607
brc_m013_1608..brc_m013_1609
brc_m013_1610..brc_m013_1611
brc_m013_1612..brc_m013_1616
brc_m013_1617..brc_m013_1618
brc_m013_1619..brc_m013_1620
brc_m013_1621..brc_m013_1629
brc_m013_1630..brc_m013_1633
brc_m013_1634..brc_m013_1638
brc_m013_1639..brc_m013_1647
brc_m013_1648..brc_m013_1649
brc_m013_1650..brc_m013_1656
brc_m013_1657..brc_m013_1665
brc_m013_1666..brc_m013_1672
brc_m013_1673..brc_m013_1674
brc_m013_1675..brc_m013_1678
brc_m013_1679..brc_m013_1682
brc_m013_1683
brc_m013_1684
brc_m013_1685..brc_m013_1686
brc_m013_1687..brc_m013_1700
brc_m013_1701..brc_m013_1702
brc_m013_1703
brc_m013_1704..brc_m013_1707
brc_m013_1708..brc_m013_1709
brc_m013_1710..brc_m013_1714
brc_m013_1715..brc_m013_1728
brc_m013_1729..brc_m013_1742
0
20
40
60
80
100
120
140
LG5
brc_m013_1743..brc_m013_1750
brc_m013_1751..brc_m013_1766
brc_m013_1767
brc_m013_1768
brc_m013_1769..brc_m013_1772
brc_m013_1773..brc_m013_1779
brc_m013_1780
brc_m013_1781
brc_m013_1782..brc_m013_1783
brc_m013_1784
brc_m013_1785..brc_m013_1786
brc_m013_1787
brc_m013_1788
brc_m013_1789..brc_m013_1790
brc_m013_1791..brc_m013_1793
brc_m013_1794..brc_m013_1797
brc_m013_1798..brc_m013_1800
brc_m013_1801..brc_m013_1804
brc_m013_1805
brc_m013_1806..brc_m013_1808
brc_m013_1809
brc_m013_1810..brc_m013_1813
brc_m013_1814..brc_m013_1818
brc_m013_1819..brc_m013_1820
brc_m013_1821..brc_m013_1822
brc_m013_1823..brc_m013_1824
brc_m013_1825
brc_m013_1826..brc_m013_1840
brc_m013_1841..brc_m013_1842
brc_m013_1843
brc_m013_1844..brc_m013_1848
brc_m013_1849
brc_m013_1850
brc_m013_1851..brc_m013_1853
brc_m013_1854..brc_m013_1858
brc_m013_1859..brc_m013_1866
brc_m013_1867..brc_m013_1868
brc_m013_1869
brc_m013_1870..brc_m013_1874
brc_m013_1875..brc_m013_1876
brc_m013_1877..brc_m013_1878
brc_m013_1879..brc_m013_1883
brc_m013_1884
brc_m013_1885
brc_m013_1886..brc_m013_1888
brc_m013_1889..brc_m013_1895
brc_m013_1896..brc_m013_1899
brc_m013_1900..brc_m013_1913
brc_m013_1914
brc_m013_1915..brc_m013_1922
brc_m013_1923
brc_m013_1924..brc_m013_1928
brc_m013_1929..brc_m013_1942
brc_m013_1943..brc_m013_1946
brc_m013_1947..brc_m013_1948
brc_m013_1949
brc_m013_1950..brc_m013_1953
brc_m013_1954..brc_m013_1955
brc_m013_1956
brc_m013_1957..brc_m013_1963
brc_m013_1964..brc_m013_1966
brc_m013_1967..brc_m013_1968
brc_m013_1969..brc_m013_1970
brc_m013_1971
brc_m013_1972
brc_m013_1973..brc_m013_1980
brc_m013_1981..brc_m013_1983
brc_m013_1984..brc_m013_1990
brc_m013_1991..brc_m013_1993
brc_m013_1994..brc_m013_1996
brc_m013_1997..brc_m013_2009
0
20
40
60
80
100
120
LG6
brc_m013_2010..brc_m013_2028
brc_m013_2029..brc_m013_2038
brc_m013_2039
brc_m013_2040..brc_m013_2041
brc_m013_2042..brc_m013_2047
brc_m013_2048..brc_m013_2050
brc_m013_2051..brc_m013_2053
brc_m013_2054..brc_m013_2062
brc_m013_2063
brc_m013_2064..brc_m013_2065
brc_m013_2066..brc_m013_2067
brc_m013_2068
brc_m013_2069..brc_m013_2071
brc_m013_2072..brc_m013_2081
brc_m013_2082
brc_m013_2083
brc_m013_2084
brc_m013_2085..brc_m013_2099
brc_m013_2100
brc_m013_2101..brc_m013_2102
brc_m013_2103..brc_m013_2107
brc_m013_2108
brc_m013_2109..brc_m013_2112
brc_m013_2113..brc_m013_2114
brc_m013_2115..brc_m013_2123
brc_m013_2124..brc_m013_2131
brc_m013_2132
brc_m013_2133
brc_m013_2134..brc_m013_2136
brc_m013_2137
brc_m013_2138..brc_m013_2139
brc_m013_2140..brc_m013_2142
brc_m013_2143..brc_m013_2150
brc_m013_2151..brc_m013_2152
brc_m013_2153..brc_m013_2161
brc_m013_2162..brc_m013_2163
brc_m013_2164..brc_m013_2165
brc_m013_2166..brc_m013_2170
brc_m013_2171..brc_m013_2172
brc_m013_2173
brc_m013_2174..brc_m013_2182
brc_m013_2183..brc_m013_2186
brc_m013_2187..brc_m013_2190
brc_m013_2191..brc_m013_2193
brc_m013_2194
brc_m013_2195..brc_m013_2201
brc_m013_2202..brc_m013_2203
brc_m013_2204..brc_m013_2220
brc_m013_2221..brc_m013_2232
brc_m013_2233..brc_m013_2239
brc_m013_2240..brc_m013_2261
brc_m013_2262..brc_m013_2267
brc_m013_2268..brc_m013_2269
brc_m013_2270..brc_m013_2271
brc_m013_2272..brc_m013_2282
brc_m013_2283..brc_m013_2284
brc_m013_2285..brc_m013_2299
brc_m013_2300..brc_m013_2301
brc_m013_2302..brc_m013_2305
brc_m013_2306..brc_m013_2307
brc_m013_2308..brc_m013_2330
brc_m013_2331..brc_m013_2337
brc_m013_2338..brc_m013_2352
0
20
40
60
80
100
120
LG7
brc_m013_2353..brc_m013_2365
brc_m013_2366..brc_m013_2369
brc_m013_2370..brc_m013_2372
brc_m013_2373..brc_m013_2378
brc_m013_2379..brc_m013_2386
brc_m013_2387
brc_m013_2388..brc_m013_2394
brc_m013_2395..brc_m013_2397
brc_m013_2398
brc_m013_2399
brc_m013_2400
brc_m013_2401
brc_m013_2402..brc_m013_2407
brc_m013_2408..brc_m013_2411
brc_m013_2412..brc_m013_2416
brc_m013_2417
brc_m013_2418
brc_m013_2419..brc_m013_2436
brc_m013_2437..brc_m013_2441
brc_m013_2442
brc_m013_2443..brc_m013_2444
brc_m013_2445
brc_m013_2446..brc_m013_2453
brc_m013_2454
brc_m013_2455..brc_m013_2460
brc_m013_2461
brc_m013_2462..brc_m013_2470
brc_m013_2471..brc_m013_2474
brc_m013_2475..brc_m013_2482
brc_m013_2483
brc_m013_2484..brc_m013_2487
brc_m013_2488
brc_m013_2489..brc_m013_2492
brc_m013_2493..brc_m013_2496
brc_m013_2497
brc_m013_2498..brc_m013_2504
brc_m013_2505
brc_m013_2506..brc_m013_2510
brc_m013_2511..brc_m013_2523
brc_m013_2524..brc_m013_2531
brc_m013_2532..brc_m013_2536
brc_m013_2537..brc_m013_2555
brc_m013_2556..brc_m013_2571
brc_m013_2572..brc_m013_2573
brc_m013_2574..brc_m013_2579
brc_m013_2580..brc_m013_2581
brc_m013_2582..brc_m013_2587
brc_m013_2588
brc_m013_2589..brc_m013_2594
brc_m013_2595
brc_m013_2596..brc_m013_2597
brc_m013_2598..brc_m013_2604
brc_m013_2605
brc_m013_2606..brc_m013_2616
brc_m013_2617..brc_m013_2619
brc_m013_2620..brc_m013_2623
brc_m013_2624
brc_m013_2625..brc_m013_2626
brc_m013_2627..brc_m013_2628
brc_m013_2629..brc_m013_2630
0
20
40
60
80
100
LG8
brc_m013_2631..brc_m013_2632
brc_m013_2633
brc_m013_2634..brc_m013_2635
brc_m013_2636..brc_m013_2642
brc_m013_2643..brc_m013_2657
brc_m013_2658..brc_m013_2659
brc_m013_2660..brc_m013_2661
brc_m013_2662
brc_m013_2663
brc_m013_2664
brc_m013_2665..brc_m013_2666
brc_m013_2667..brc_m013_2668
brc_m013_2669..brc_m013_2670
brc_m013_2671..brc_m013_2680
brc_m013_2681..brc_m013_2682
brc_m013_2683
brc_m013_2684..brc_m013_2685
brc_m013_2686..brc_m013_2694
brc_m013_2695..brc_m013_2698
brc_m013_2699..brc_m013_2713
brc_m013_2714..brc_m013_2725
brc_m013_2726..brc_m013_2727
brc_m013_2728..brc_m013_2731
brc_m013_2732
brc_m013_2733..brc_m013_2753
brc_m013_2754..brc_m013_2758
brc_m013_2759..brc_m013_2763
brc_m013_2764..brc_m013_2779
brc_m013_2780
brc_m013_2781
brc_m013_2782..brc_m013_2784
brc_m013_2785..brc_m013_2787
brc_m013_2788..brc_m013_2791
brc_m013_2792..brc_m013_2797
brc_m013_2798..brc_m013_2799
brc_m013_2800
brc_m013_2801..brc_m013_2804
brc_m013_2805..brc_m013_2809
brc_m013_2810..brc_m013_2811
brc_m013_2812..brc_m013_2813
brc_m013_2814..brc_m013_2817
brc_m013_2818..brc_m013_2827
brc_m013_2828
brc_m013_2829..brc_m013_2832
brc_m013_2833
brc_m013_2834..brc_m013_2840
brc_m013_2841..brc_m013_2846
brc_m013_2847
brc_m013_2848..brc_m013_2852
brc_m013_2853
brc_m013_2854..brc_m013_2856
brc_m013_2857..brc_m013_2862
brc_m013_2863..brc_m013_2868
brc_m013_2869..brc_m013_2874
brc_m013_2875..brc_m013_2896
0
20
40
60
80
100
brc_m013_2897..brc_m013_2920
brc_m013_2921..brc_m013_2928
brc_m013_2929..brc_m013_2931
brc_m013_2932
brc_m013_2933
brc_m013_2934..brc_m013_2935
brc_m013_2936
brc_m013_2937..brc_m013_2943
brc_m013_2944
brc_m013_2945..brc_m013_2946
brc_m013_2947
brc_m013_2948
brc_m013_2949..brc_m013_2950
brc_m013_2951..brc_m013_2957
brc_m013_2958..brc_m013_2961
brc_m013_2962..brc_m013_2970
brc_m013_2971..brc_m013_2980
brc_m013_2981..brc_m013_2992
brc_m013_2993..brc_m013_2996
brc_m013_2997..brc_m013_2998
brc_m013_2999..brc_m013_3000
brc_m013_3001
brc_m013_3002..brc_m013_3003
brc_m013_3004
brc_m013_3005
brc_m013_3006..brc_m013_3010
brc_m013_3011..brc_m013_3014
brc_m013_3015
brc_m013_3016..brc_m013_3019
brc_m013_3020
brc_m013_3021..brc_m013_3030
brc_m013_3031..brc_m013_3032
brc_m013_3033..brc_m013_3034
brc_m013_3035..brc_m013_3036
brc_m013_3037..brc_m013_3045
brc_m013_3046..brc_m013_3052
brc_m013_3053
brc_m013_3054..brc_m013_3061
brc_m013_3062..brc_m013_3066
brc_m013_3067..brc_m013_3068
brc_m013_3069..brc_m013_3076
brc_m013_3077..brc_m013_3084
brc_m013_3085..brc_m013_3087
brc_m013_3088..brc_m013_3089
brc_m013_3090..brc_m013_3096
brc_m013_3097..brc_m013_3100
brc_m013_3101..brc_m013_3104
brc_m013_3105
brc_m013_3106..brc_m013_3112
brc_m013_3113..brc_m013_3122
brc_m013_3123..brc_m013_3124
brc_m013_3125..brc_m013_3127
brc_m013_3128..brc_m013_3145
brc_m013_3146..brc_m013_3159
brc_m013_3160..brc_m013_3172
0
20
40
60
80
Total
285 non-recombining
markers No recombination between B and b
over ⅔ of a chromosme!
Confirmed 100
in 8 additional families (sons of Bb queens)
with RAD (3 families) and PCR (5 families).
BBqueens: normal recombination throughout (RAD 3 families)
⟹ Gp-9 is not a “recombination cold-spot”
LG9
brc_m013_3173..brc_m013_3175
brc_m013_3176..brc_m013_3180
brc_m013_3181..brc_m013_3189
brc_m013_3190..brc_m013_3198
brc_m013_3199
brc_m013_3200..brc_m013_3201
brc_m013_3202..brc_m013_3203
brc_m013_3204
brc_m013_3205..brc_m013_3206
brc_m013_3207..brc_m013_3211
brc_m013_3212..brc_m013_3214
brc_m013_3215..brc_m013_3227
brc_m013_3228..brc_m013_3230
brc_m013_3231..brc_m013_3235
brc_m013_3236..brc_m013_3238
brc_m013_3239..brc_m013_3242
brc_m013_3243..brc_m013_3244
brc_m013_3245
brc_m013_3246..brc_m013_3247
brc_m013_3248..brc_m013_3249
brc_m013_3250..brc_m013_3252
brc_m013_3253..brc_m013_3257
brc_m013_3258
brc_m013_3259
brc_m013_3260..brc_m013_3261
brc_m013_3262..brc_m013_3263
brc_m013_3264
brc_m013_3265..brc_m013_3269
brc_m013_3270..brc_m013_3274
brc_m013_3275..brc_m013_3276
brc_m013_3277..brc_m013_3281
brc_m013_3282..brc_m013_3284
brc_m013_3285
brc_m013_3286..brc_m013_3289
brc_m013_3290..brc_m013_3296
brc_m013_3297
brc_m013_3298..brc_m013_3300
brc_m013_3301..brc_m013_3302
brc_m013_3303..brc_m013_3305
brc_m013_3306..brc_m013_3308
brc_m013_3309..brc_m013_3314
brc_m013_3315..brc_m013_3317
brc_m013_3318..brc_m013_3329
brc_m013_3330..brc_m013_3331
brc_m013_3332..brc_m013_3338
brc_m013_3339..brc_m013_3340
brc_m013_3341..brc_m013_3344
brc_m013_3345..brc_m013_3349
brc_m013_3350..brc_m013_3357
brc_m013_3358..brc_m013_3359
brc_m013_3360
brc_m013_3361..brc_m013_3368
brc_m013_3369..brc_m013_3372
brc_m013_3373..brc_m013_3376
brc_m013_3377
brc_m013_3378..brc_m013_3386
brc_m013_3387..brc_m013_3388
brc_m013_3389..brc_m013_3395
brc_m013_3396..brc_m013_3399
0
20
40
60
80
LG10
brc_m013_3400..brc_m013_3411
brc_m013_3412
brc_m013_3413..brc_m013_3424
brc_m013_3425
brc_m013_3426
brc_m013_3427..brc_m013_3429
brc_m013_3430
brc_m013_3431..brc_m013_3432
brc_m013_3433..brc_m013_3435
brc_m013_3436
brc_m013_3437..brc_m013_3439
brc_m013_3440..brc_m013_3441
brc_m013_3442
brc_m013_3443..brc_m013_3445
brc_m013_3446..brc_m013_3447
brc_m013_3448..brc_m013_3449
brc_m013_3450..brc_m013_3454
brc_m013_3455
brc_m013_3456..brc_m013_3462
brc_m013_3463..brc_m013_3464
brc_m013_3465
brc_m013_3466..brc_m013_3467
brc_m013_3468..brc_m013_3472
brc_m013_3473
brc_m013_3474..brc_m013_3476
brc_m013_3477..brc_m013_3487
brc_m013_3488
brc_m013_3489..brc_m013_3491
brc_m013_3492..brc_m013_3500
brc_m013_3501..brc_m013_3512
brc_m013_3513..brc_m013_3514
brc_m013_3515..brc_m013_3524
brc_m013_3525..brc_m013_3527
brc_m013_3528..brc_m013_3531
brc_m013_3532..brc_m013_3547
brc_m013_3548..brc_m013_3557
brc_m013_3558..brc_m013_3566
brc_m013_3567..brc_m013_3568
brc_m013_3569..brc_m013_3570
brc_m013_3571..brc_m013_3574
brc_m013_3575..brc_m013_3582
brc_m013_3583..brc_m013_3592
brc_m013_3593..brc_m013_3605
brc_m013_3606..brc_m013_3616
brc_m013_3617..brc_m013_3618
brc_m013_3619..brc_m013_3622
brc_m013_3623..brc_m013_3624
brc_m013_3625..brc_m013_3628
brc_m013_3629..brc_m013_3635
0
20
40
60
80
LG11
brc_m013_3636..brc_m013_3661
brc_m013_3662..brc_m013_3665
brc_m013_3666..brc_m013_3667
brc_m013_3668
brc_m013_3669..brc_m013_3671
brc_m013_3672
brc_m013_3673..brc_m013_3674
brc_m013_3675..brc_m013_3682
brc_m013_3683..brc_m013_3685
brc_m013_3686..brc_m013_3688
brc_m013_3689..brc_m013_3693
brc_m013_3694..brc_m013_3698
brc_m013_3699
brc_m013_3700
brc_m013_3701..brc_m013_3702
brc_m013_3703..brc_m013_3704
brc_m013_3705..brc_m013_3712
brc_m013_3713
brc_m013_3714..brc_m013_3716
brc_m013_3717..brc_m013_3724
brc_m013_3725..brc_m013_3730
brc_m013_3731..brc_m013_3752
brc_m013_3753..brc_m013_3758
brc_m013_3759..brc_m013_3789
brc_m013_3790..brc_m013_3801
brc_m013_3802..brc_m013_3814
brc_m013_3815..brc_m013_3818
brc_m013_3819..brc_m013_3822
brc_m013_3823..brc_m013_3826
brc_m013_3827..brc_m013_3832
brc_m013_3833..brc_m013_3837
brc_m013_3838
brc_m013_3839..brc_m013_3841
brc_m013_3842..brc_m013_3847
brc_m013_3848..brc_m013_3853
brc_m013_3854..brc_m013_3858
brc_m013_3859..brc_m013_3868
brc_m013_3869..brc_m013_3871
brc_m013_3872..brc_m013_3901
brc_m013_3902
brc_m013_3903..brc_m013_3909
brc_m013_3910
brc_m013_3911..brc_m013_3926
brc_m013_3927..brc_m013_3931
brc_m013_3932..brc_m013_3948
0
20
40
60
80
LG12
brc_m013_3949..brc_m013_3952
brc_m013_3953..brc_m013_3958
brc_m013_3959..brc_m013_3970
brc_m013_3971
brc_m013_3972..brc_m013_3975
brc_m013_3976
brc_m013_3977..brc_m013_3985
brc_m013_3986
brc_m013_3987..brc_m013_3994
brc_m013_3995..brc_m013_3997
brc_m013_3998..brc_m013_4004
brc_m013_4005..brc_m013_4006
brc_m013_4007..brc_m013_4008
brc_m013_4009..brc_m013_4010
brc_m013_4011..brc_m013_4013
brc_m013_4014
brc_m013_4015
brc_m013_4016..brc_m013_4019
brc_m013_4020..brc_m013_4021
brc_m013_4022..brc_m013_4025
brc_m013_4026..brc_m013_4032
brc_m013_4033..brc_m013_4036
brc_m013_4037..brc_m013_4041
brc_m013_4042..brc_m013_4043
brc_m013_4044..brc_m013_4046
brc_m013_4047..brc_m013_4056
brc_m013_4057
brc_m013_4058..brc_m013_4063
brc_m013_4064..brc_m013_4071
brc_m013_4072..brc_m013_4075
brc_m013_4076
brc_m013_4077
brc_m013_4078..brc_m013_4085
brc_m013_4086..brc_m013_4089
brc_m013_4090..brc_m013_4091
brc_m013_4092..brc_m013_4093
brc_m013_4094..brc_m013_4095
brc_m013_4096..brc_m013_4114
brc_m013_4115..brc_m013_4117
brc_m013_4118..brc_m013_4131
brc_m013_4132..brc_m013_4133
brc_m013_4134..brc_m013_4146
0
20
40
60
80
LG13
brc_m013_4147..brc_m013_4150
brc_m013_4151..brc_m013_4167
brc_m013_4168
brc_m013_4169
brc_m013_4170
brc_m013_4171..brc_m013_4172
brc_m013_4173..brc_m013_4175
brc_m013_4176
brc_m013_4177..brc_m013_4178
brc_m013_4179..brc_m013_4183
brc_m013_4184..brc_m013_4185
brc_m013_4186..brc_m013_4187
brc_m013_4188..brc_m013_4191
brc_m013_4192
brc_m013_4193..brc_m013_4194
brc_m013_4195..brc_m013_4206
brc_m013_4207..brc_m013_4210
brc_m013_4211..brc_m013_4213
brc_m013_4214
brc_m013_4215..brc_m013_4217
brc_m013_4218..brc_m013_4221
brc_m013_4222..brc_m013_4223
brc_m013_4224..brc_m013_4231
brc_m013_4232..brc_m013_4234
brc_m013_4235..brc_m013_4239
brc_m013_4240..brc_m013_4246
brc_m013_4247..brc_m013_4248
brc_m013_4249..brc_m013_4258
brc_m013_4259..brc_m013_4260
brc_m013_4261..brc_m013_4269
brc_m013_4270..brc_m013_4271
brc_m013_4272..brc_m013_4278
brc_m013_4279..brc_m013_4280
brc_m013_4281..brc_m013_4284
brc_m013_4285
brc_m013_4286..brc_m013_4288
brc_m013_4289..brc_m013_4294
brc_m013_4295..brc_m013_4296
brc_m013_4297..brc_m013_4301
brc_m013_4302..brc_m013_4313
brc_m013_4314..brc_m013_4320
brc_m013_4321..brc_m013_4322
brc_m013_4323..brc_m013_4345
brc_m013_4346..brc_m013_4351
0
20
40
60
LG14
brc_m013_4352..brc_m013_4366
brc_m013_4367
brc_m013_4368
brc_m013_4369..brc_m013_4373
brc_m013_4374..brc_m013_4381
brc_m013_4382..brc_m013_4383
brc_m013_4384..brc_m013_4385
brc_m013_4386
brc_m013_4387..brc_m013_4388
brc_m013_4389
brc_m013_4390..brc_m013_4404
brc_m013_4405
brc_m013_4406..brc_m013_4409
brc_m013_4410..brc_m013_4411
brc_m013_4412..brc_m013_4418
brc_m013_4419..brc_m013_4434
brc_m013_4435..brc_m013_4442
brc_m013_4443..brc_m013_4448
brc_m013_4449..brc_m013_4451
brc_m013_4452..brc_m013_4461
brc_m013_4462..brc_m013_4471
brc_m013_4472..brc_m013_4475
brc_m013_4476..brc_m013_4477
brc_m013_4478
brc_m013_4479
brc_m013_4480..brc_m013_4485
brc_m013_4486
brc_m013_4487..brc_m013_4491
brc_m013_4492
brc_m013_4493
brc_m013_4494..brc_m013_4495
brc_m013_4496..brc_m013_4501
brc_m013_4502..brc_m013_4510
brc_m013_4511..brc_m013_4531
brc_m013_4532
brc_m013_4533..brc_m013_4534
brc_m013_4535..brc_m013_4541
brc_m013_4542..brc_m013_4543
brc_m013_4544..brc_m013_4545
brc_m013_4546..brc_m013_4548
brc_m013_4549..brc_m013_4551
brc_m013_4552..brc_m013_4555
brc_m013_4556..brc_m013_4561
0
20
40
60
LG15
brc_m013_4562..brc_m013_4577
brc_m013_4578..brc_m013_4594
brc_m013_4595..brc_m013_4599
brc_m013_4600..brc_m013_4625
brc_m013_4626..brc_m013_4638
brc_m013_4639..brc_m013_4642
brc_m013_4643..brc_m013_4644
brc_m013_4645..brc_m013_4650
brc_m013_4651..brc_m013_4663
brc_m013_4664..brc_m013_4668
brc_m013_4669..brc_m013_4670
brc_m013_4671..brc_m013_4674
brc_m013_4675..brc_m013_4679
brc_m013_4680..brc_m013_4681
brc_m013_4682
brc_m013_4683..brc_m013_4688
brc_m013_4689..brc_m013_4692
brc_m013_4693..brc_m013_4695
brc_m013_4696..brc_m013_4701
brc_m013_4702
brc_m013_4703..brc_m013_4712
brc_m013_4713..brc_m013_4717
brc_m013_4718..brc_m013_4720
brc_m013_4721
brc_m013_4722..brc_m013_4726
brc_m013_4727..brc_m013_4728
brc_m013_4729..brc_m013_4742
brc_m013_4743
brc_m013_4744..brc_m013_4746
brc_m013_4747
brc_m013_4748..brc_m013_4749
brc_m013_4750..brc_m013_4752
brc_m013_4753..brc_m013_4756
brc_m013_4757..brc_m013_4759
brc_m013_4760..brc_m013_4762
brc_m013_4763
brc_m013_4764..brc_m013_4766
brc_m013_4767..brc_m013_4769
brc_m013_4770
brc_m013_4771..brc_m013_4774
brc_m013_4775..brc_m013_4776
brc_m013_4777..brc_m013_4778
brc_m013_4779..brc_m013_4780
brc_m013_4781..brc_m013_4793
brc_m013_4794
brc_m013_4795..brc_m013_4798
brc_m013_4799..brc_m013_4802
brc_m013_4803..brc_m013_4806
brc_m013_4807
brc_m013_4808..brc_m013_4814
brc_m013_4815..brc_m013_4819
brc_m013_4820
brc_m013_4821
brc_m013_4822..brc_m013_4823
brc_m013_4824
brc_m013_4825..brc_m013_4855
brc_m013_4856..brc_m013_4858
brc_m013_4859..brc_m013_4863
brc_m013_4864..brc_m013_4865
brc_m013_4866..brc_m013_4875
brc_m013_4876..brc_m013_4881
brc_m013_4882..brc_m013_4891
brc_m013_4892..brc_m013_4895
brc_m013_4896..brc_m013_4911
brc_m013_4912..brc_m013_4938
brc_m013_4939
brc_m013_4940..brc_m013_4957
brc_m013_4958..brc_m013_4959
brc_m013_4960..brc_m013_4972
brc_m013_4973..brc_m013_4981
brc_m013_4982..brc_m013_4983
0
20
40
60
80
100
120
LGSB
Gp-9
1.7 Si_gnF.scaffold00779_nt277843
Si_gnF.scaffold00779_nt1255229
104.4
115.8
22.2
81.8
Gp-9

Sex chromosomes
X Y
“Social chromosomes”
Gp-9 B
Gp-9 b
?
SB Sb
Why non-recombining?

Structural differences between B and b
likely inhibit recombination
Small portion (200,000bp) of social chromosome
SB
Sb

Structural differences between B and b
likely inhibit recombination
Gp-9B
genetic map
SB Sb
a Gp-9 B male A22
A22
Gp-9 b male
male Gp-9 b male
E17
E3
Gp-9 B male SB Sb
Gp-9B
genetic map
A22
A22
E17
E17
E3
SB Sb
Gp-9B
genetic map
E3
b SB Sb
Gp-9B
genetic map
E17
E3
Gp-9 b male
Flourescence in situ
Hybridization
John Wang @ Taipei

“Social chromosomes”
Gp-9 B
Gp-9 b
SB Sb
Likely several rearrangments

X
♀
♂
X X Y
Single queen colony Multiple queen colony
Likely several
rearrangements
•Prediction:
SB SB SB Sb
Differences between SB and Sb?
•genes?
Region contains 800 genes! only small differences
⟹ Prediction: directional (antagonistic?) selection?
Sb is degenerating?

• More, larger repetitive DNA in Sb compared to SB
• larger introns in Sb
• larger intergenic regions in Sb
• assembly worse (smaller scaffolds) in Sb
• increased dN/dS
SB
Sb
[a] vs. [c]: p 10-7
[b] vs. [c]: p 10-4
Gp-9B male Gp-9b male
6,000,000
5,000,000
4,000,000
3,000,000
2,000,000
1,000,000
Region:
Genome assembly:
Normally recombining
regions from all 16
linkage groups
Normally recombining
regions from all 16
linkage groups
Sb region without
recombination
in Gp-9 Bb queens
SB region without
recombination
in Gp-9 Bb queens
Scaffold length (bp)
0
[a] [a], [b] [a] [c]
SB Sb
Sb is degenerating?

X
♀
♂
X X Y
Single queen colony Multiple queen colony
Likely several
rearrangements
•Prediction:
SB SB SB Sb
Differences between SB and Sb?
•genes?
Region contains 800 genes! only small differences
⟹ Prediction: directional (antagonistic?) selection?
Sb is degenerating?
•Probably ♂ haploidy: strong purifying selection
⟹ slower degeneration

Formica selysi
Alpine silver ant
Common ancestor with fire ant: 130 MYA
Purcell et al 2014 Convergent social chromosome architecture
J Meunier

≠ social chromosomes
Purcell et al 2014
Solenopsis
invicta social
chromosome
Formica selysi
social
chromosome

Social chromosomes also for
other major social transitions?

Summary
Ants are cool.
Fire ant Solenopsis invicta queen number determined by Gp-9 genotypes:
•only BB workers ➔ single BB queen
•with Bb workers ➔ multiple Bb queens
Genome sequencing + RAD Genotyping 500 individuals
•Gp-9 marks ~4% of genome ➔ social chromosomes:
SB is like X; Sb is like Y
Structural differences between SB and Sb ➔ no recombination
Formica selysi: Convergent evolution of social chromosomes

Generally
genome evolution social evolution
Single- vs. Multiple queenness
in fire ants
in similar independent species
•one or many loci?
•one or many genes?
•convergence?
Social parasitism
Strengths of selection in
social evolution
concepts mechanisms
Candidate gene studies
Vitellogenin
Sex determination genes
Molecular response to
social upheaval
Caste differentiation (Medically
relevant)
Tools for genomics work on emerging model organisms

Four tools that
Four tools
suck less.
(hopefully)

“Can you BLAST this for me?”

“Can you BLAST this for me?”
Antgenomes.org SequenceServer
BLAST made easy
(well, we’re trying...)

http://www.sequenceserver.com/
(requires a BLAST+ install)
Do you have BLAST-formatted databases? If not:
sequenceserver format-databases /path/to/fastas
1. Installing
gem install sequenceserver
2. Configure.
# ~/.sequenceserver.conf
bin: ~/ncbi-blast-2.2.25+/bin/
database: /Users/me/blast_databases/
3. Launch.
sequenceserver
### Launched SequenceServer at: http://0.0.0.0:4567

bionode.io (online shell)
Examples
BASH
bionode-ncbi urls assembly Solenopsis invicta | grep genomic.fna
http://ftp.ncbi.nlm.nih.gov/genomes/all/GCA_000188075.1_Si_gnG/
GCA_000188075.1_Si_gnG_genomic.fna.gz
bionode-ncbi download sra arthropoda | bionode-sra
bionode-ncbi download gff bacteria
JavaScript
#GetdescriptionsforpapersrelatedtoSRAsearch!
bionode!ncbi!search!sra!Solenopsis!invicta!|!!
!!!!!!!!tool3stream!extractProperty!uid!|!!
!!!!!!!!bionode!ncbi!link!sra!pubmed!|!!
!!!!!!!!tool3stream!extractProperty!destUID!|!
!!!!!!!!bionode!ncbi!search!pubmed!
var ncbi = require('bionode-ncbi')
ncbi.urls('assembly', 'Solenopsis invicta'), gotData)
function gotData(urls) {
var genome = urls[0].genomic.fna
download(genome)
})

Difficulty writing scalable, reproducible and
complex bioinformatic pipelines.
Solution: Node.js Streams everywhere
var ncbi = require('bionode-ncbi')
var tool = require('tool-stream')
var through = require('through2')
var fork1 = through.obj()
var fork2 = through.obj()
ncbi
.search('sra', 'Solenopsis invicta')
.pipe(fork1)
.pipe(dat.reads)
fork1
.pipe(tool.extractProperty('expxml.Biosample.id'))
.pipe(ncbi.search('biosample'))
.pipe(dat.samples)
fork1
.pipe(tool.extractProperty('uid'))
.pipe(ncbi.link('sra', 'pubmed'))

Gene prediction
Dozens of software algorithms: dozens of predictions
TTCAATAATAATATCAAATTCACATTCAAAGCTTTCAAGTTAGACAAAAGTTTTAATGCCGTTTTtACCTGTTTTtGAAAAGGTAATTTTCTTTAGATATATTATGTTGAATaTTAGGGTTTTTATAAAGAATGTGTATATTGUTTACAATATAAAAGACACAATTGCAAACTAGCATGATTGTAAACAATTGCTAAACGGATCAATATAAATTAAAATTGTAATATTAAGTATCAAACCGATAATTTTTATTTEvidence
20% failure rate:
•missing pieces
•extra pieces
•incorrect merging
•incorrect splitting
Visual inspection... and
manual fixing required.
1 gene = 5 minutes to 3 days
Yandell Ence 2013 NRG
Consensus:

Ismail Moghul
Monica Dragan
https://github.com/monicadragan/GeneValidator
https://github.com/IsmailM/GeneValidatorApp

Monica Dragan
https://github.com/monicadragan/GeneValidator
https://github.com/IsmailM/GeneValidatorApp
Ismail Moghul

GeneValidator
Run on:
whole geneset: identify most problematic predictions
alternative models for a gene (choose best)
individual genes (while manually curating)

4. Afra: Crowdsourcing
gene model curation

Gene prediction
Dozens of software algorithms: dozens of predictions
TTCAATAATAATATCAAATTCACATTCAAAGCTTTCAAGTTAGACAAAAGTTTTAATGCCGTTTTtACCTGTTTTtGAAAAGGTAATTTTCTTTAGATATATACAGTTTGTAATaTTAGGTATTTTATAAACAGTGTGTATATTTCTTACAATATAAAAGACACAATTGCAAACTAGCATGATTGTAAACAATTGCTAAACGGATCAATATAAATTAAAATTGTAATATTAAGTATCAAACCGATAATTTTTATEvidence
20% failure rate:
•missing pieces
•extra pieces
•incorrect merging
•incorrect splitting
Visual inspection... and
manual fixing required.
1 gene = 20 minutes to 3 days
15,000 genes * 20 species =
impossible.
Yandell Ence 2013 NRG
Consensus:

Afra: Crowdsourcing gene model curation
Challenges
• Recruiting retaining contributors
Begin
• Ensuring quality
Create initial tasks
Needs curation
Curate
Being curated
Curate
Being curated
Curate
Being curated
Submit Submit Submit
Auto-check
Done
Inconsistent: create
“review” task
Consistent:
create next required task

Timelines
• Rolled out to:
• 8 MSc students
• 20 3rd year students
• Need to improve tutorials/guidance/documentation
• Roll out to 200 first years (few months)
• Expand

Summary
Ants are cool.
Fire ant Solenopsis invicta queen number determined by Gp-9 genotypes:
•only BB workers ➔ single BB queen
•with Bb workers ➔ multiple Bb queens
Genome sequencing + RAD Genotyping 500 individuals
•Gp-9 marks ~4% of genome ➔ social chromosomes:
SB is like X; Sb is like Y
Structural differences between SB and Sb ➔ no recombination
Formica selysi: Convergent evolution of social chromosomes
A few tools for genomics:
• http://sequenceserver.com (easy custom BLAST server)
• http://bionode.io (Agile data analysis workflows)
• http://afra.sbcs.qmul.ac.uk (Crowdsourcing gene feature curation)
• http://genevalidator.sbcs.qmul.ac.uk Identifying gene prediction
problems

QMUL lab (R Pracana, B Vieira, E
Stolle, A Priyam, I Moghul et al)
Laurent Keller lab (J WANG, D
SHOEMAKER,O RIBA-GROGNUZ,
M Nipitwattanaphon)
Michel Chapuisat, Jess Purcell,
Alan Breslford, Nicolas Perrin
Ecology Evolution Vital-IT
@ Lausanne
Organismal Biology Psych
@ Queen Mary
http://wurmlab.github.io
M Corona, S Nygaard, BG Hunt, KK Ingram, L
Falquet, M Nipitwattanaphon, D Gotzek, MB Dijkstra,
J Oettler, F Comtesse, CJ Shih, WJ Wu, CC Yang, J
Thomas, E Beaudoing, S Pradervand, V Flegel, ED
Cook, R Fabbretti, H Stockinger, L Long, WG
Farmerie, J Oakey, JJ Boomsma, P Pamilo, SV Yi, J
Heinze, MAD Goodisman, L Farinelli, K Harshman, N
Hulo, L Cerutti, Ioannis Xenarios

2014 11-28-lyon

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2014 11-28-lyon