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Transcript of 2013 11-25-sheffield
A social chromosome in the red fire ant.
[email protected] Sheffield 2013-11-25
© Alex Wild & others
© National Geographic
Atta leaf-cutter ants
© National Geographic
Atta leaf-cutter ants
© National Geographic
Atta leaf-cutter ants
Oecophylla Weaver ants
© ameisenforum.de
© ameisenforum.de
Fourmis tisserandes
© ameisenforum.de
Oecophylla Weaver ants
© forestryimages.org© wynnie@flickr
Tofilski et al 2008
Forelius pusillus
Tofilski et al 2008
Forelius pusillus hides the nest entrance at night
Tofilski et al 2008
Forelius pusillus hides the nest entrance at night
Tofilski et al 2008
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
Forelius pusillus hides the nest entrance at night
Dorylus driver ants: ants with no home
© BBC
Animal biomass (Brazilian rainforest)
from Fittkau & Klinge 1973
Other insects 49.6
Amphibians 2.8
Reptiles 3.7
Birds 5.3
Mammals 14.5
!Earthworms
17.3
!!
Spiders 4.7
Soil fauna excluding earthworms,
ants & termites 148
Ants & termites 114
www.sciencemag.org SCIENCE VOL 331 25 FEBRUARY 2011 1067
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Solenopsis invicta fire ants are a big problem!very well studied!
Ascunce et al 2011
Solenopsis invicta fire ant: two social forms
!
•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
Single-queen form: Multiple-queen form:
Fire ants+
Population genetics: Allozyme screen
Ken Ross L. Keller
“starch gel”+
1 2 3
Allozyme screen Social form associated to Gp-9 locus
Frequency of the most
common allele!
Locus!
0.3!0.4!0.5!0.6!0.7!0.8!0.9!1.0!
Single queen!Multiple queen!
Est-6!Est-4!G3pdh-1!Ca-4!Pgm-4!Ddh-1!Pro-5!
Pgm-3!
Acoh-5!
acoh-1!
Acy-1!
Pgm-1!
Aat-2!
Gp-9!
Ken Ross and colleagues"Laurent Keller and colleagues
Single queen form Multiple queen form
Ken Ross and colleagues"Laurent Keller and colleagues
Social form completely associated to Gp-9 locus
bbbbBB BB Bb bb
Ken Ross and colleagues"Laurent Keller and colleagues
Single queen form Multiple queen form
Social form completely associated to Gp-9 locus
bbBB BB Bb
x
Gp-9 bb females rareKen Ross and colleagues"
Laurent Keller and colleagues
Single queen form Multiple queen form
Social form completely associated to Gp-9 locus
BB BB Bb
Ken Ross and colleagues"Laurent Keller and colleagues
Single queen form Multiple queen form
Social form completely associated to Gp-9 locus
BB BB Bb
xKen Ross and colleagues"
Laurent Keller and colleagues
Single queen form Multiple queen form
Social form completely associated to Gp-9 locus
BB BB Bb
x xKen Ross and colleagues"
Laurent Keller and colleagues
Social form completely associated to Gp-9 locus
Single queen form Multiple queen form
BB BB Bb
x x xKen Ross and colleagues"
Laurent Keller and colleagues
Single queen form Multiple queen form(>15% ) (< 5% )
Social form completely associated to Gp-9 locus
•Is this gene the single überregulator?
Social form completely associated to Gp-9 locus
Hypothesis: influences queen odor & how workers « smell » queens"
Gp-9 is an odorant binding protein
Krieger & Ross
dN/dS = infinityKrieger & Ross
•Is this gene the single überregulator?
Social form completely associated to Gp-9 locus
maybe 1/14th of the genome?•Only 14 allozyme markers were used
Locus!
0.3!0.4!0.5!0.6!0.7!0.8!0.9!1.0!
Single queen!Multiple queen!
Est-6!Est-4!G3pdh-1!Ca-4!Pgm-4!Ddh-1!Pro-5!
Pgm-3!
Acoh-5!
acoh-1!
Acy-1!
Pgm-1!
Aat-2!
Gp-9!
This changes everything.454"
Illumina"Solid...
Any lab can sequence anything!
Are other genes linked to Gp-9?
Sequenced:"•a Gp-9 B � genome"
!
!
Single ♂:His brothers:
11×4×
(330bp-insert paired reads) (normal single-end reads)45× +Sequencing from haploid males (for easier assembly):
(8,000 & 20,000bp-insert paired reads)
B 20x
The genome of a Gp-9 B � fire ant
Single ♂:His brothers:
11×4×
(330bp-insert paired reads) (normal single-end reads)45× +Sequencing from haploid males (for easier assembly):
(8,000 & 20,000bp-insert paired reads)
B 20x
The genome of a Gp-9 B � fire ant
Assembly approach:1. Assemble short Illumina reads with SOAPdenovo→N50: 3600 bp"2. Chop assembly into “fake 454 reads” (300bp)"3. Assemble fake + real 454 reads with Newbler→N50: 720,000 bp
10,000 scaffolds (100 biggest scaffolds: 50% of genome)
Total: 350,000,000 bp assembled. The rest: repeats→Wurm et al 2011
★ Expansion of lipid-processing gene families (for Cuticular Hydrocarbons?)"
★ 420 putative olfactory receptors (more than any other insect!)
The genome of the fire antSome findings:
0.05
SiOR
04648+10
SiOR01968+4
SiOR0
0899+7
SiOR02814+3
SiOR04171+6
SiO
R04609+4
SiOR00330+28
SiO
R02
694+25
SiO
R04609+20
SiOR05285+6
SiOR00330+25
SiOR04510+15
SiOR00330+18
SiOR04609+23
SiOR01
968+23
SiO
R03
952+4
SiOR0
4648+16
SiO
R05
901+2
SiO
R02
944+4
SiOR01968+5
SiOR04171+19 SiOR
04648+5
SiOR10535+3
SiOR0
1224+3
SiOR06723+2
SiOR01968+9
SiOR02883+1
SiOR0
0899+3
SiOR01629+1
SiOR04171+1
SiOR01629+11
SiOR04171+10
SiOR04171+13
SiOR02694+3
SiOR04171+20
SiO
R02694+35
SiOR04171+15
SiOR04609+7
SiOR05118+2
SiOR07
837+2
SiO
R02
694+27
SiOR01968+10
SiOR04648+17
SiOR0196
8+19
SiO
R02
694+17
SiOR04648+13
SiOR01968+6
SiOR
00899+1
2
SiOR0
5901+1
SiOR00330+20
SiO
R02
648+2
SiO
R02
659+2
SiOR01968+1
6
SiOR0
0899+11
SiO
R02974
SiOR04171+2
SiOR03952+2
SiOR06792+2
SiOR04510+4
SiOR04171+28
SiOR05285+5
SiOR05285+9
SiOR
00899+1
5
SiOR
04648+3
SiO
R02694+36
SiOR10535+1
SiO
R02
694+19
SiO
R02
694+23
SiOR02694+1
SiO
R04609+14
SiOR01122
SiOR
04648+9
SiO
R02694+34
SiOR01629+8
SiOR
04648+8
SiOR04510+8
SiOR06573
SiO
R02
944+1
SiOR00330+26
SiO
R00330+1S
iOR02
694+15
SiO
R03038
SiOR05285+7
SiOR0
0899+5
SiOR04609+10
SiO
R04609+3
SiOR04339
SiOR0
8068
SiOR
04648+6
SiOR04510+2
SiOR05285+8
SiOR01
573+4
SiOR0366
3
SiOR04171+8
SiOR01858+2
SiOR01968+2SiOR01968+1
SiOR02694+5
SiOR01968+3
SiOR06723+3
SiOR01968+15
SiOR05285+1
SiOR0
0899+4
SiOR04609+22
SiOR04171+9
SiOR02694+9
SiO
R02
648+1
SiOR06792+3
SiOR0
1573+2
SiO
R02
694+20
SiOR1
0542
SiO
R04609+15
SiOR02694+8
SiOR00330+16
SiOR0
0899+2
SiOR02694+10
SiOR04510+9
SiOR05285+3
SiOR04171+24
SiO
R04609+2
SiOR05285+11
SiOR02
694+14
SiOR01
573+1
SiOR05285+2
SiOR00613
SiOR0196
8+22
SiOR
00899+9
SiO
R06
843+2
SiO
R02694+37
SiOR0
0899+1
SiOR04609+9
SiOR05431+2
SiOR10535+2
SiOR00330+15
SiO
R02
694+18
SiOR0
1224+2
SiOR04510+11
SiOR00330+23
SiO
R02
694+29
SiOR05416
SiOR05285+10
SiOR02694+2
SiOR01629+9
SiOR05431+1
SiOR02883+2
SiOR04171+14
SiO
R08
341
SiO
R02
694+22
SiOR01
224+1
SiOR01968+12
SiOR05431+3
SiOR04510+6
SiOR02694+7
SiOR04609+5
SiO
R02
944+2
SiOR03
952+3
SiOR01968+8
SiOR04609+24
SiO
R02
694+30
SiOR01629+10
SiOR04510+14
SiOR00565
SiOR05118+3
SiO
R01321
SiO
R04609+19
SiOR00330+14
SiO
R02694+38
SiOR04609+8
SiOR04171+16
SiOR10455
SiO
R04609+16
SiO
R04609+21
SiO
R02
694+28
SiO
R02
659+1
SiOR04171+5
SiOR00330+29
SiOR01968+14
SiOR03983
SiOR00330+27
SiOR05285+4
SiOR04510+1
SiOR
00899+8
SiOR
04648+7
SiO
R04609+17
SiO
R00330+5
SiO
R02
694+21
SiOR02814+4
SiOR00330+7
SiOR01
629+3
SiOR01
968+26
SiO
R02694+31
SiOR0
4648+2
SiO
R02694+39
SiOR04171+25
SiOR06577
SiOR01
968+25
SiOR04171+21
SiOR06792+6
SiO
R04609+11
SiOR02694+11
SiOR06792+1
SiOR04171+4
SiOR01629+5
SiOR00330+21
SiOR0
4648+15
SiO
R00330+6
SiO
R02
694+16
SiOR
04648+11
SiOR
04648+4
SiO
R00330+3
SiO
R06
535
SiOR04171+7
SiOR10493
SiO
R02694+32
SiOR06792+4
SiOR04510+3
SiO
R06
890
SiOR0196
8+20
SiO
R04609+12
SiOR04171+3
SiOR01968
+18
SiOR01968+11
SiO
R04609+13
SiOR01629+12
SiOR00330+22
SiO
R02694+33
SiOR00330+13
SiOR01
573+3
SiOR04510+16
SiOR04171+12
SiOR04510+13
SiOR
05118+1
SiO
R02
944+3
SiOR04171+26
SiOR04171+17
SiOR
00899+14
SiOR04171+29
SiOR
00899+1
3
SiOR02694+13
SiOR00330+24
SiOR00330+19
SiOR04171+27
SiO
R02
694+24
SiOR04510+5
SiOR07090
SiOR03952+1
SiOR04510+10
SiOR00330+17
SiO
R02
694+26
SiO
R04609+1
SiOR0
0899+6
SiOR04648+12
SiOR02814+2
SiOR00330+11
SiOR04171+18
SiOR01968+1
7
SiOR00330+10
SiOR00330+9
SiOR0162
9+2
SiOR04171+11
SiOR04510+12
SiOR0196
8+21
SiOR00330+8
SiOR01858+1
SiOR04510+7
SiOR05431+4
SiOR02694+6
SiOR01968+13
SiO
R00330+4
SiO
R04609+18
SiOR0
0899+10
SiOR00330+12
SiOR00330+31
SiO
R06
843+1
SiOR07
837+1
SiO
R00330+2
SiOR01629+4
SiOR0
4648+1
SiOR01
968+24
SiOR04171+23
SiOR0162
9+7
SiOR0
4648+14
SiO
R06
843+3
SiOR06792+5
SiOR01968+7
SiOR01629
+6
SiOR02883+3
SiOR02694+12
SiOR
05118+4
SiOR04171+22
SiO
R01080
SiOR04609+6
SiOR02814+1
SiOR00330+30
SiOR05285+12
SiOR06723+1
SiOR02694+4
Wurm et al 2011
> 400Harvester ant 399 344Nasonia wasp 225honey bee 165
6510
★ Expansion of lipid-processing gene families (for Cuticular Hydrocarbons)"
★ 420 putative olfactory receptors (more than any other insect!)"
★ Functional DNA-methylation system
The genome of the fire antSome findings:
Wurm et al 2011
0.05
SiOR
04648+10
SiOR01968+4
SiOR0
0899+7
SiOR02814+3
SiOR04171+6
SiO
R04609+4
SiOR00330+28
SiO
R02
694+25
SiO
R04609+20
SiOR05285+6
SiOR00330+25
SiOR04510+15
SiOR00330+18
SiOR04609+23
SiOR01
968+23
SiO
R03
952+4
SiOR0
4648+16
SiO
R05
901+2
SiO
R02
944+4
SiOR01968+5
SiOR04171+19 SiOR
04648+5
SiOR10535+3
SiOR0
1224+3
SiOR06723+2
SiOR01968+9
SiOR02883+1
SiOR0
0899+3
SiOR01629+1
SiOR04171+1
SiOR01629+11
SiOR04171+10
SiOR04171+13
SiOR02694+3
SiOR04171+20
SiO
R02694+35
SiOR04171+15
SiOR04609+7
SiOR05118+2
SiOR07
837+2
SiO
R02
694+27
SiOR01968+10
SiOR04648+17
SiOR0196
8+19
SiO
R02
694+17
SiOR04648+13
SiOR01968+6
SiOR
00899+1
2
SiOR0
5901+1
SiOR00330+20
SiO
R02
648+2
SiO
R02
659+2
SiOR01968+1
6
SiOR0
0899+11
SiO
R02974
SiOR04171+2
SiOR03952+2
SiOR06792+2
SiOR04510+4
SiOR04171+28
SiOR05285+5
SiOR05285+9
SiOR
00899+1
5
SiOR
04648+3
SiO
R02694+36
SiOR10535+1
SiO
R02
694+19
SiO
R02
694+23
SiOR02694+1
SiO
R04609+14
SiOR01122
SiOR
04648+9
SiO
R02694+34
SiOR01629+8
SiOR
04648+8
SiOR04510+8
SiOR06573
SiO
R02
944+1
SiOR00330+26
SiO
R00330+1S
iOR02
694+15
SiO
R03038
SiOR05285+7
SiOR0
0899+5
SiOR04609+10
SiO
R04609+3
SiOR04339
SiOR0
8068
SiOR
04648+6
SiOR04510+2
SiOR05285+8
SiOR01
573+4
SiOR0366
3
SiOR04171+8
SiOR01858+2
SiOR01968+2SiOR01968+1
SiOR02694+5
SiOR01968+3
SiOR06723+3
SiOR01968+15
SiOR05285+1
SiOR0
0899+4
SiOR04609+22
SiOR04171+9
SiOR02694+9
SiO
R02
648+1
SiOR06792+3
SiOR0
1573+2
SiO
R02
694+20
SiOR1
0542
SiO
R04609+15
SiOR02694+8
SiOR00330+16
SiOR0
0899+2
SiOR02694+10
SiOR04510+9
SiOR05285+3
SiOR04171+24
SiO
R04609+2
SiOR05285+11
SiOR02
694+14
SiOR01
573+1
SiOR05285+2
SiOR00613
SiOR0196
8+22
SiOR
00899+9
SiO
R06
843+2
SiO
R02694+37
SiOR0
0899+1
SiOR04609+9
SiOR05431+2
SiOR10535+2
SiOR00330+15
SiO
R02
694+18
SiOR0
1224+2
SiOR04510+11
SiOR00330+23
SiO
R02
694+29
SiOR05416
SiOR05285+10
SiOR02694+2
SiOR01629+9
SiOR05431+1
SiOR02883+2
SiOR04171+14
SiO
R08
341
SiO
R02
694+22
SiOR01
224+1
SiOR01968+12
SiOR05431+3
SiOR04510+6
SiOR02694+7
SiOR04609+5
SiO
R02
944+2
SiOR03
952+3
SiOR01968+8
SiOR04609+24
SiO
R02
694+30
SiOR01629+10
SiOR04510+14
SiOR00565
SiOR05118+3
SiO
R01321
SiO
R04609+19
SiOR00330+14
SiO
R02694+38
SiOR04609+8
SiOR04171+16
SiOR10455
SiO
R04609+16
SiO
R04609+21
SiO
R02
694+28
SiO
R02
659+1
SiOR04171+5
SiOR00330+29
SiOR01968+14
SiOR03983
SiOR00330+27
SiOR05285+4
SiOR04510+1
SiOR
00899+8
SiOR
04648+7
SiO
R04609+17
SiO
R00330+5
SiO
R02
694+21
SiOR02814+4
SiOR00330+7
SiOR01
629+3
SiOR01
968+26
SiO
R02694+31
SiOR0
4648+2
SiO
R02694+39
SiOR04171+25
SiOR06577
SiOR01
968+25
SiOR04171+21
SiOR06792+6
SiO
R04609+11
SiOR02694+11
SiOR06792+1
SiOR04171+4
SiOR01629+5
SiOR00330+21
SiOR0
4648+15
SiO
R00330+6
SiO
R02
694+16
SiOR
04648+11
SiOR
04648+4
SiO
R00330+3
SiO
R06
535
SiOR04171+7
SiOR10493
SiO
R02694+32
SiOR06792+4
SiOR04510+3
SiO
R06
890
SiOR0196
8+20
SiO
R04609+12
SiOR04171+3
SiOR01968
+18
SiOR01968+11
SiO
R04609+13
SiOR01629+12
SiOR00330+22
SiO
R02694+33
SiOR00330+13
SiOR01
573+3
SiOR04510+16
SiOR04171+12
SiOR04510+13
SiOR
05118+1
SiO
R02
944+3
SiOR04171+26
SiOR04171+17
SiOR
00899+14
SiOR04171+29
SiOR
00899+1
3
SiOR02694+13
SiOR00330+24
SiOR00330+19
SiOR04171+27
SiO
R02
694+24
SiOR04510+5
SiOR07090
SiOR03952+1
SiOR04510+10
SiOR00330+17
SiO
R02
694+26
SiO
R04609+1
SiOR0
0899+6
SiOR04648+12
SiOR02814+2
SiOR00330+11
SiOR04171+18
SiOR01968+1
7
SiOR00330+10
SiOR00330+9
SiOR0162
9+2
SiOR04171+11
SiOR04510+12
SiOR0196
8+21
SiOR00330+8
SiOR01858+1
SiOR04510+7
SiOR05431+4
SiOR02694+6
SiOR01968+13
SiO
R00330+4
SiO
R04609+18
SiOR0
0899+10
SiOR00330+12
SiOR00330+31
SiO
R06
843+1
SiOR07
837+1
SiO
R00330+2
SiOR01629+4
SiOR0
4648+1
SiOR01
968+24
SiOR04171+23
SiOR0162
9+7
SiOR0
4648+14
SiO
R06
843+3
SiOR06792+5
SiOR01968+7
SiOR01629
+6
SiOR02883+3
SiOR02694+12
SiOR
05118+4
SiOR04171+22
SiO
R01080
SiOR04609+6
SiOR02814+1
SiOR00330+30
SiOR05285+12
SiOR06723+1
SiOR02694+4
★ Expansion of lipid-processing gene families (for Cuticular Hydrocarbons)"
★ 420 putative olfactory receptors (more than any other insect!)"
★ Functional DNA-methylation system "★Ant-specific duplication and subfunctionalization
of vitellogenin (in bees: involved in reproduction & division of labor)
The genome of the fire antSome findings:
Wurm et al 2011
significance of these duplication events in vitellogenins, odorperception genes, and a family of lipid-processing genes. We alsodiscuss additional features of interest in the fire ant genome rel-evant to the complex social biology of this species, including sexdetermination genes, DNA methylation genes, telomerase, andthe insulin and juvenile hormone pathways.
Vitellogenins. In contrast to other insects that mainly have only oneor two vitellogenins, the fire ant genome harbors four adjacent
copies of vitellogenin (Vg1-4) (Fig. 3A), all of which are at leastpartially supported by EST reads. A phylogenetic analysis revealsthat an ancestral vitellogenin gene first underwent duplication,followed by possibly independent duplications of each of thedaughter vitellogenins, thus giving rise to Vg1 and Vg4 and to Vg2andVg3. All of these duplications occurred after the ancestor offireants split from wasps and bees (Fig. 3B). The single vitellogeninfound inA.mellifera is amultifunctional protein (26) involved in theregulation of life span (27, 28) and division of labor (29). Quanti-tative RT-PCR shows thatVg1 andVg4 are preferentially expressedin workers and Vg2 and Vg3 in queens (Fig. 3C, SI Materials andMethods, and Table S1G). Vitellogenin expression in S. invictaworkers is surprising because they lack ovaries. Given the super-organism properties of ant societies, the expression patterns sug-gest that vitellogenins underwent neo- or subfunctionalizationafter duplication to acquire caste-specific functions.
Odor Perception. Consistent with studies in other insects, we finda single S. invicta ortholog to DmOr83b, a broadly expressed ol-factory receptor (OR) required to interact with other ORs forDrosophila and Tribolium castaneum olfaction (30–32). BeyondOR83b, OR number varies greatly between insect species. Blastsearches 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. invictagenome with significant sequence similarity to ORs. Preliminarywork 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 are10 ORs in Pediculus humanus (34), 60 in Drosophila, 165 inA. mellifera, 225 in N. vitripennis (33), and 259 in T. castaneum(32). The large numbers of N. vitripennis and T. castaneum ORsare thought to be due to current or past difficulties in host andfood finding. As has been suggested for A. mellifera (35), the largenumber of S. invicta ORs may result from the importance ofchemical communication in ants. The odorant-binding proteins(OBPs) are another family of genes also known to play roles inchemosensation in Drosophila (36). Intriguingly, the social orga-nization of S. invicta colonies is completely associated with se-
Eum
etaz
oa
No hits 3424
Not assigned 274
Cnidaria 100
Art
hro
po
da
Ne
op
tera
Coe
lom
ata
Bila
teri
a
Nematoda 25
Deuterostomia 173
Arachnida 50
Paraneoptera 577
End
opte
rygo
ta
Hym
en
op
tera
Apoidea 7398
Chalcidoidea 3271
Ichneumonoidea 94
Diptera 404
Lepidoptera 29
Coleoptera 713
Fig. 2. Taxonomic distribution of best blastp hits of S. invicta proteins to thenonredundant (nr) protein database (E < 10−5). Results were first plottedusing MEGAN software (22) and then branches with fewer than 20 hits wereremoved, branch lengths were reduced for compactness, and tree topologywas adjusted to reflect consensus phylogenies (23, 24).
Vg1Vg4 Vg3 Vg2
2,330,000 bp 2,360,000 bpA
B CSolenopsis Vg1Solenopsis Vg4Solenopsis Vg2Solenopsis Vg3
Apis VgBombus Vg
Nasonia Vg1
Nasonia Vg2Pteromalus Vg
Encarsia VgPimpla Vg
Athalia Vg
Apocrita
Tenthedinoidea
Vespoidea
Apoidea
Aculeata
Chalcidoidea
Ichneumonoidea 0
5000
10000
15000
20000
25000 Vg3Vg2
142 389 17820 1.4 9269 0.61 40WQ WQW Q WQ
*** ***Vg1 Vg4* ***
0
100
200
300
400
500
600
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 vitellogenin protein sequences suggests that two rounds of vitellogenin duplication occurred after the split between ants and other hyme-nopterans including bees and wasps. (C) Quantitative RT-PCR of the four putative S. invicta vitellogenins on whole bodies of major workers (W) and matedqueens (Q) (n = 10). The y axis indicates mRNA concentrations for the different vitellogenins. Values depicted by each bar are shown below the x-axis labels.Error bars represent SEs. Expression differences between queens and workers were significant (Bonferroni-corrected two-tailed t tests: *P < 0.05, ***P < 10−10).
Wurm et al. PNAS Early Edition | 3 of 6
EVOLU
TION
0.05
SiOR
04648+10
SiOR01968+4
SiOR0
0899+7
SiOR02814+3
SiOR04171+6
SiO
R04609+4
SiOR00330+28
SiO
R02
694+25
SiO
R04609+20
SiOR05285+6
SiOR00330+25
SiOR04510+15
SiOR00330+18
SiOR04609+23
SiOR01
968+23
SiO
R03
952+4
SiOR0
4648+16
SiO
R05
901+2
SiO
R02
944+4
SiOR01968+5
SiOR04171+19 SiOR
04648+5
SiOR10535+3
SiOR0
1224+3
SiOR06723+2
SiOR01968+9
SiOR02883+1
SiOR0
0899+3
SiOR01629+1
SiOR04171+1
SiOR01629+11
SiOR04171+10
SiOR04171+13
SiOR02694+3
SiOR04171+20
SiO
R02694+35
SiOR04171+15
SiOR04609+7
SiOR05118+2
SiOR07
837+2
SiO
R02
694+27
SiOR01968+10
SiOR04648+17
SiOR0196
8+19
SiO
R02
694+17
SiOR04648+13
SiOR01968+6
SiOR
00899+1
2
SiOR0
5901+1
SiOR00330+20
SiO
R02
648+2
SiO
R02
659+2
SiOR01968+1
6
SiOR0
0899+11
SiO
R02974
SiOR04171+2
SiOR03952+2
SiOR06792+2
SiOR04510+4
SiOR04171+28
SiOR05285+5
SiOR05285+9
SiOR
00899+1
5
SiOR
04648+3
SiO
R02694+36
SiOR10535+1
SiO
R02
694+19
SiO
R02
694+23
SiOR02694+1
SiO
R04609+14
SiOR01122
SiOR
04648+9
SiO
R02694+34
SiOR01629+8
SiOR
04648+8
SiOR04510+8
SiOR06573
SiO
R02
944+1
SiOR00330+26
SiO
R00330+1S
iOR02
694+15
SiO
R03038
SiOR05285+7
SiOR0
0899+5
SiOR04609+10
SiO
R04609+3
SiOR04339
SiOR0
8068
SiOR
04648+6
SiOR04510+2
SiOR05285+8
SiOR01
573+4
SiOR0366
3
SiOR04171+8
SiOR01858+2
SiOR01968+2SiOR01968+1
SiOR02694+5
SiOR01968+3
SiOR06723+3
SiOR01968+15
SiOR05285+1
SiOR0
0899+4
SiOR04609+22
SiOR04171+9
SiOR02694+9
SiO
R02
648+1
SiOR06792+3
SiOR0
1573+2
SiO
R02
694+20
SiOR1
0542
SiO
R04609+15
SiOR02694+8
SiOR00330+16
SiOR0
0899+2
SiOR02694+10
SiOR04510+9
SiOR05285+3
SiOR04171+24
SiO
R04609+2
SiOR05285+11
SiOR02
694+14
SiOR01
573+1
SiOR05285+2
SiOR00613
SiOR0196
8+22
SiOR
00899+9
SiO
R06
843+2
SiO
R02694+37
SiOR0
0899+1
SiOR04609+9
SiOR05431+2
SiOR10535+2
SiOR00330+15
SiO
R02
694+18
SiOR0
1224+2
SiOR04510+11
SiOR00330+23
SiO
R02
694+29
SiOR05416
SiOR05285+10
SiOR02694+2
SiOR01629+9
SiOR05431+1
SiOR02883+2
SiOR04171+14
SiO
R08
341
SiO
R02
694+22
SiOR01
224+1
SiOR01968+12
SiOR05431+3
SiOR04510+6
SiOR02694+7
SiOR04609+5
SiO
R02
944+2
SiOR03
952+3
SiOR01968+8
SiOR04609+24
SiO
R02
694+30
SiOR01629+10
SiOR04510+14
SiOR00565
SiOR05118+3
SiO
R01321
SiO
R04609+19
SiOR00330+14
SiO
R02694+38
SiOR04609+8
SiOR04171+16
SiOR10455
SiO
R04609+16
SiO
R04609+21
SiO
R02
694+28
SiO
R02
659+1
SiOR04171+5
SiOR00330+29
SiOR01968+14
SiOR03983
SiOR00330+27
SiOR05285+4
SiOR04510+1
SiOR
00899+8
SiOR
04648+7
SiO
R04609+17
SiO
R00330+5
SiO
R02
694+21
SiOR02814+4
SiOR00330+7
SiOR01
629+3
SiOR01
968+26
SiO
R02694+31
SiOR0
4648+2
SiO
R02694+39
SiOR04171+25
SiOR06577
SiOR01
968+25
SiOR04171+21
SiOR06792+6
SiO
R04609+11
SiOR02694+11
SiOR06792+1
SiOR04171+4
SiOR01629+5
SiOR00330+21
SiOR0
4648+15
SiO
R00330+6
SiO
R02
694+16
SiOR
04648+11
SiOR
04648+4
SiO
R00330+3
SiO
R06
535
SiOR04171+7
SiOR10493
SiO
R02694+32
SiOR06792+4
SiOR04510+3
SiO
R06
890
SiOR0196
8+20
SiO
R04609+12
SiOR04171+3
SiOR01968
+18
SiOR01968+11
SiO
R04609+13
SiOR01629+12
SiOR00330+22
SiO
R02694+33
SiOR00330+13
SiOR01
573+3
SiOR04510+16
SiOR04171+12
SiOR04510+13
SiOR
05118+1
SiO
R02
944+3
SiOR04171+26
SiOR04171+17
SiOR
00899+14
SiOR04171+29
SiOR
00899+1
3
SiOR02694+13
SiOR00330+24
SiOR00330+19
SiOR04171+27
SiO
R02
694+24
SiOR04510+5
SiOR07090
SiOR03952+1
SiOR04510+10
SiOR00330+17
SiO
R02
694+26
SiO
R04609+1
SiOR0
0899+6
SiOR04648+12
SiOR02814+2
SiOR00330+11
SiOR04171+18
SiOR01968+1
7
SiOR00330+10
SiOR00330+9
SiOR0162
9+2
SiOR04171+11
SiOR04510+12
SiOR0196
8+21
SiOR00330+8
SiOR01858+1
SiOR04510+7
SiOR05431+4
SiOR02694+6
SiOR01968+13
SiO
R00330+4
SiO
R04609+18
SiOR0
0899+10
SiOR00330+12
SiOR00330+31
SiO
R06
843+1
SiOR07
837+1
SiO
R00330+2
SiOR01629+4
SiOR0
4648+1
SiOR01
968+24
SiOR04171+23
SiOR0162
9+7
SiOR0
4648+14
SiO
R06
843+3
SiOR06792+5
SiOR01968+7
SiOR01629
+6
SiOR02883+3
SiOR02694+12
SiOR
05118+4
SiOR04171+22
SiO
R01080
SiOR04609+6
SiOR02814+1
SiOR00330+30
SiOR05285+12
SiOR06723+1
SiOR02694+4
Social form completely associated to Gp-9 locus
BB BB Bb
x x x
Single queen form Multiple queen form(>15% ) (< 5% )
Are other genes linked to Gp-9?
Are other genes linked to Gp-9?
Sequenced:"•a Gp-9 B � genome"
!
!•a Gp-9 b � genome
“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
RAD sequencing
38 B� & 38 b�
EcoR1 EcoR1 EcoR1
RAD sequencing of haploid � for SNP discovery & genotypingGp-9 B
EcoR1 EcoR1 EcoR1
AACTG
AACTG
AACTG
AACTG
Gp-9 B
RAD sequencing of haploid � for SNP discovery & genotypingGp-9 B
AACTGGp-9 B
Gp-9 B
GGCCT
Gp-9 B
Gp-9 B
AAGGTGp-9 B
Gp-9 B
CCAGTGp-9 b
Gp-9 b
TAAATGp-9 b
Gp-9 b
GGAATGp-9 b
Gp-9 b
38 Gp-9 B "males
38 Gp-9 b "males
RAD sequencing of haploid � for SNP discovery & genotyping
Identify polymorphismindividual x locus
genotype table
RADseq: sequencing the same 0.01% of the genome in many individuals
A B C D E FL1 A C A A C CL2 G G T - T GL3 - A G A - GL4 C - - G G CL5 T T C T C -L6 G A A - - G
2419
loci
38 B� & 38 b�
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20+
Amount of variance explained per principal component
Principal Component
% V
aria
nce
Exp
lain
ed
05
1015
2025
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%
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20+
Amount of variance explained per principal component
Principal Component
% V
aria
nce
Exp
lain
ed
05
1015
2025
30
PCA: Principal Component Analysis
pc: 2 % variance: 6.073
pc: 3
%
var
ianc
e: 5
.441
-0.2
-0.1
0.0
0.1
0.2
-0.2 -0.1 0.0 0.1 0.2pc: 2 % variance: 6.073
pc: 3
%
var
ianc
e: 5
.441
-0.2
-0.1
0.0
0.1
0.2
-0.2 -0.1 0.0 0.1 0.2
Principal Components: PC2 vs PC3
Gp-9 B �Gp-9 b �
pc: 1 % variance: 12.666
pc: 2
%
var
ianc
e: 6
.073
-0.2
-0.1
0.0
0.1
0.2
-0.10 -0.05 0.00 0.05 0.10 0.15
Principal Components: PC1 vs PC2
pc: 1 % variance: 12.666
pc: 2
%
var
ianc
e: 6
.073
-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 �
Amount of sequence linked to Gp-9
Confirmed 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”
brc_m013_0001..brc_m013_0005brc_m013_0006..brc_m013_0014brc_m013_0015..brc_m013_0017brc_m013_0018brc_m013_0019..brc_m013_0020brc_m013_0021..brc_m013_0029brc_m013_0030..brc_m013_0031brc_m013_0032..brc_m013_0034brc_m013_0035..brc_m013_0036brc_m013_0037..brc_m013_0038brc_m013_0039..brc_m013_0043brc_m013_0044brc_m013_0045brc_m013_0046..brc_m013_0048brc_m013_0049brc_m013_0050..brc_m013_0051brc_m013_0052..brc_m013_0056brc_m013_0057..brc_m013_0061
brc_m013_0062..brc_m013_0075brc_m013_0076..brc_m013_0078brc_m013_0079..brc_m013_0081
brc_m013_0082..brc_m013_0088
brc_m013_0089..brc_m013_0092
brc_m013_0093..brc_m013_0096brc_m013_0097brc_m013_0098..brc_m013_0113brc_m013_0114..brc_m013_0119brc_m013_0120..brc_m013_0130brc_m013_0131brc_m013_0132..brc_m013_0134brc_m013_0135..brc_m013_0136brc_m013_0137..brc_m013_0139brc_m013_0140..brc_m013_0142brc_m013_0143brc_m013_0144..brc_m013_0146brc_m013_0147..brc_m013_0154brc_m013_0155
brc_m013_0156brc_m013_0157..brc_m013_0180brc_m013_0181brc_m013_0182brc_m013_0183..brc_m013_0188brc_m013_0189..brc_m013_0208brc_m013_0209brc_m013_0210..brc_m013_0211brc_m013_0212..brc_m013_0215brc_m013_0216brc_m013_0217brc_m013_0218..brc_m013_0224brc_m013_0225..brc_m013_0228brc_m013_0229..brc_m013_0237brc_m013_0238..brc_m013_0245
brc_m013_0246..brc_m013_0270
brc_m013_0271..brc_m013_0274brc_m013_0275brc_m013_0276..brc_m013_0278
brc_m013_0279
brc_m013_0280
brc_m013_0281..brc_m013_0294
brc_m013_0295..brc_m013_0303brc_m013_0304brc_m013_0305..brc_m013_0307brc_m013_0308brc_m013_0309..brc_m013_0314brc_m013_0315..brc_m013_0317brc_m013_0318..brc_m013_0320brc_m013_0321..brc_m013_0326brc_m013_0327brc_m013_0328brc_m013_0329..brc_m013_0330brc_m013_0331..brc_m013_0333brc_m013_0334..brc_m013_0339brc_m013_0340brc_m013_0341..brc_m013_0343brc_m013_0344brc_m013_0345..brc_m013_0349brc_m013_0350
brc_m013_0351..brc_m013_0354brc_m013_0355brc_m013_0356brc_m013_0357..brc_m013_0361brc_m013_0362..brc_m013_0376brc_m013_0377..brc_m013_0390brc_m013_0391..brc_m013_0393brc_m013_0394..brc_m013_0400brc_m013_0401..brc_m013_0439brc_m013_0440..brc_m013_0478brc_m013_0479..brc_m013_0480
0
20
40
60
80
100
120
140
160
180
LG1brc_m013_0481brc_m013_0482..brc_m013_0484brc_m013_0485..brc_m013_0488brc_m013_0489..brc_m013_0502brc_m013_0503brc_m013_0504..brc_m013_0519brc_m013_0520..brc_m013_0532brc_m013_0533..brc_m013_0534brc_m013_0535..brc_m013_0537brc_m013_0538..brc_m013_0540brc_m013_0541..brc_m013_0543brc_m013_0544..brc_m013_0545brc_m013_0546..brc_m013_0549
brc_m013_0550..brc_m013_0554
brc_m013_0555..brc_m013_0560
brc_m013_0561..brc_m013_0562brc_m013_0563..brc_m013_0565
brc_m013_0566brc_m013_0567brc_m013_0568..brc_m013_0570brc_m013_0571..brc_m013_0573
brc_m013_0574..brc_m013_0575brc_m013_0576..brc_m013_0578brc_m013_0579..brc_m013_0580brc_m013_0581brc_m013_0582..brc_m013_0584brc_m013_0585brc_m013_0586brc_m013_0587brc_m013_0588..brc_m013_0591brc_m013_0592brc_m013_0593brc_m013_0594..brc_m013_0612brc_m013_0613..brc_m013_0614brc_m013_0615..brc_m013_0632brc_m013_0633brc_m013_0634..brc_m013_0648brc_m013_0649..brc_m013_0655brc_m013_0656brc_m013_0657..brc_m013_0694brc_m013_0695..brc_m013_0703brc_m013_0704brc_m013_0705brc_m013_0706..brc_m013_0707brc_m013_0708brc_m013_0709..brc_m013_0711brc_m013_0712..brc_m013_0715brc_m013_0716..brc_m013_0721brc_m013_0722brc_m013_0723brc_m013_0724..brc_m013_0728brc_m013_0729brc_m013_0730brc_m013_0731brc_m013_0732..brc_m013_0735brc_m013_0736..brc_m013_0769brc_m013_0770..brc_m013_0771brc_m013_0772..brc_m013_0773brc_m013_0774..brc_m013_0775brc_m013_0776..brc_m013_0782brc_m013_0783brc_m013_0784..brc_m013_0795brc_m013_0796..brc_m013_0798brc_m013_0799..brc_m013_0801brc_m013_0802..brc_m013_0805brc_m013_0806..brc_m013_0809brc_m013_0810..brc_m013_0811brc_m013_0812..brc_m013_0824brc_m013_0825..brc_m013_0826brc_m013_0827..brc_m013_0829brc_m013_0830..brc_m013_0831brc_m013_0832..brc_m013_0842brc_m013_0843..brc_m013_0854brc_m013_0855..brc_m013_0861brc_m013_0862brc_m013_0863..brc_m013_0864brc_m013_0865..brc_m013_0867brc_m013_0868..brc_m013_0883brc_m013_0884..brc_m013_0893brc_m013_0894brc_m013_0895..brc_m013_0897brc_m013_0898..brc_m013_0906brc_m013_0907..brc_m013_0910brc_m013_0911..brc_m013_0925brc_m013_0926..brc_m013_0928brc_m013_0929..brc_m013_0931
0
20
40
60
80
100
120
140
LG2brc_m013_0932..brc_m013_0941brc_m013_0942..brc_m013_0943brc_m013_0944..brc_m013_0945brc_m013_0946..brc_m013_0949brc_m013_0950..brc_m013_0952
brc_m013_0953..brc_m013_0975
brc_m013_0976..brc_m013_1019brc_m013_1020brc_m013_1021brc_m013_1022..brc_m013_1061brc_m013_1062brc_m013_1063
brc_m013_1064..brc_m013_1065
brc_m013_1066..brc_m013_1068brc_m013_1069brc_m013_1070
brc_m013_1071..brc_m013_1074
brc_m013_1075
brc_m013_1076..brc_m013_1081
brc_m013_1082..brc_m013_1086brc_m013_1087..brc_m013_1088brc_m013_1089..brc_m013_1098brc_m013_1099..brc_m013_1106brc_m013_1107..brc_m013_1116brc_m013_1117brc_m013_1118..brc_m013_1121brc_m013_1122..brc_m013_1127brc_m013_1128brc_m013_1129..brc_m013_1136brc_m013_1137..brc_m013_1138brc_m013_1139..brc_m013_1141brc_m013_1142..brc_m013_1144brc_m013_1145..brc_m013_1156brc_m013_1157brc_m013_1158..brc_m013_1170brc_m013_1171..brc_m013_1181brc_m013_1182..brc_m013_1185brc_m013_1186brc_m013_1187..brc_m013_1205brc_m013_1206..brc_m013_1218brc_m013_1219..brc_m013_1220brc_m013_1221..brc_m013_1224brc_m013_1225..brc_m013_1228brc_m013_1229brc_m013_1230..brc_m013_1236brc_m013_1237brc_m013_1238..brc_m013_1247brc_m013_1248..brc_m013_1251
brc_m013_1252brc_m013_1253..brc_m013_1268brc_m013_1269..brc_m013_1270brc_m013_1271..brc_m013_1273brc_m013_1274brc_m013_1275..brc_m013_1280brc_m013_1281
brc_m013_1282..brc_m013_1286brc_m013_1287..brc_m013_1298brc_m013_1299..brc_m013_1307brc_m013_1308brc_m013_1309..brc_m013_1313brc_m013_1314..brc_m013_1317brc_m013_1318..brc_m013_1319brc_m013_1320..brc_m013_1326brc_m013_1327..brc_m013_1340brc_m013_1341..brc_m013_1362brc_m013_1363..brc_m013_1385
0
20
40
60
80
100
120
140
LG3brc_m013_1386..brc_m013_1388brc_m013_1389..brc_m013_1398brc_m013_1399..brc_m013_1406brc_m013_1407..brc_m013_1411brc_m013_1412..brc_m013_1413brc_m013_1414..brc_m013_1416
brc_m013_1417brc_m013_1418..brc_m013_1420brc_m013_1421..brc_m013_1424brc_m013_1425..brc_m013_1432brc_m013_1433..brc_m013_1442brc_m013_1443brc_m013_1444..brc_m013_1450brc_m013_1451brc_m013_1452brc_m013_1453..brc_m013_1455brc_m013_1456..brc_m013_1467brc_m013_1468..brc_m013_1469brc_m013_1470brc_m013_1471..brc_m013_1474brc_m013_1475brc_m013_1476brc_m013_1477brc_m013_1478..brc_m013_1482brc_m013_1483
brc_m013_1484brc_m013_1485..brc_m013_1487brc_m013_1488..brc_m013_1490
brc_m013_1491brc_m013_1492..brc_m013_1494brc_m013_1495..brc_m013_1496
brc_m013_1497..brc_m013_1500brc_m013_1501brc_m013_1502..brc_m013_1513brc_m013_1514..brc_m013_1562brc_m013_1563..brc_m013_1565brc_m013_1566..brc_m013_1567
brc_m013_1568..brc_m013_1580brc_m013_1581..brc_m013_1587brc_m013_1588..brc_m013_1591brc_m013_1592..brc_m013_1593brc_m013_1594..brc_m013_1604brc_m013_1605..brc_m013_1607brc_m013_1608..brc_m013_1609brc_m013_1610..brc_m013_1611brc_m013_1612..brc_m013_1616brc_m013_1617..brc_m013_1618brc_m013_1619..brc_m013_1620brc_m013_1621..brc_m013_1629brc_m013_1630..brc_m013_1633brc_m013_1634..brc_m013_1638brc_m013_1639..brc_m013_1647brc_m013_1648..brc_m013_1649brc_m013_1650..brc_m013_1656brc_m013_1657..brc_m013_1665brc_m013_1666..brc_m013_1672brc_m013_1673..brc_m013_1674brc_m013_1675..brc_m013_1678brc_m013_1679..brc_m013_1682brc_m013_1683brc_m013_1684brc_m013_1685..brc_m013_1686brc_m013_1687..brc_m013_1700brc_m013_1701..brc_m013_1702brc_m013_1703brc_m013_1704..brc_m013_1707brc_m013_1708..brc_m013_1709brc_m013_1710..brc_m013_1714brc_m013_1715..brc_m013_1728brc_m013_1729..brc_m013_1742
0
20
40
60
80
100
120
140
LG4brc_m013_1743..brc_m013_1750
brc_m013_1751..brc_m013_1766brc_m013_1767brc_m013_1768
brc_m013_1769..brc_m013_1772
brc_m013_1773..brc_m013_1779brc_m013_1780brc_m013_1781brc_m013_1782..brc_m013_1783brc_m013_1784brc_m013_1785..brc_m013_1786
brc_m013_1787
brc_m013_1788brc_m013_1789..brc_m013_1790brc_m013_1791..brc_m013_1793brc_m013_1794..brc_m013_1797brc_m013_1798..brc_m013_1800brc_m013_1801..brc_m013_1804brc_m013_1805brc_m013_1806..brc_m013_1808brc_m013_1809brc_m013_1810..brc_m013_1813brc_m013_1814..brc_m013_1818brc_m013_1819..brc_m013_1820brc_m013_1821..brc_m013_1822brc_m013_1823..brc_m013_1824brc_m013_1825brc_m013_1826..brc_m013_1840brc_m013_1841..brc_m013_1842brc_m013_1843brc_m013_1844..brc_m013_1848brc_m013_1849brc_m013_1850brc_m013_1851..brc_m013_1853brc_m013_1854..brc_m013_1858brc_m013_1859..brc_m013_1866brc_m013_1867..brc_m013_1868brc_m013_1869brc_m013_1870..brc_m013_1874brc_m013_1875..brc_m013_1876brc_m013_1877..brc_m013_1878brc_m013_1879..brc_m013_1883brc_m013_1884brc_m013_1885brc_m013_1886..brc_m013_1888brc_m013_1889..brc_m013_1895brc_m013_1896..brc_m013_1899brc_m013_1900..brc_m013_1913brc_m013_1914brc_m013_1915..brc_m013_1922brc_m013_1923brc_m013_1924..brc_m013_1928brc_m013_1929..brc_m013_1942brc_m013_1943..brc_m013_1946brc_m013_1947..brc_m013_1948brc_m013_1949brc_m013_1950..brc_m013_1953brc_m013_1954..brc_m013_1955brc_m013_1956brc_m013_1957..brc_m013_1963brc_m013_1964..brc_m013_1966brc_m013_1967..brc_m013_1968brc_m013_1969..brc_m013_1970brc_m013_1971brc_m013_1972brc_m013_1973..brc_m013_1980brc_m013_1981..brc_m013_1983brc_m013_1984..brc_m013_1990brc_m013_1991..brc_m013_1993brc_m013_1994..brc_m013_1996brc_m013_1997..brc_m013_2009
0
20
40
60
80
100
120
LG5brc_m013_2010..brc_m013_2028
brc_m013_2029..brc_m013_2038brc_m013_2039
brc_m013_2040..brc_m013_2041brc_m013_2042..brc_m013_2047brc_m013_2048..brc_m013_2050brc_m013_2051..brc_m013_2053brc_m013_2054..brc_m013_2062brc_m013_2063brc_m013_2064..brc_m013_2065brc_m013_2066..brc_m013_2067brc_m013_2068brc_m013_2069..brc_m013_2071brc_m013_2072..brc_m013_2081brc_m013_2082
brc_m013_2083brc_m013_2084brc_m013_2085..brc_m013_2099brc_m013_2100brc_m013_2101..brc_m013_2102brc_m013_2103..brc_m013_2107brc_m013_2108brc_m013_2109..brc_m013_2112
brc_m013_2113..brc_m013_2114brc_m013_2115..brc_m013_2123brc_m013_2124..brc_m013_2131brc_m013_2132brc_m013_2133brc_m013_2134..brc_m013_2136
brc_m013_2137
brc_m013_2138..brc_m013_2139
brc_m013_2140..brc_m013_2142brc_m013_2143..brc_m013_2150brc_m013_2151..brc_m013_2152brc_m013_2153..brc_m013_2161brc_m013_2162..brc_m013_2163
brc_m013_2164..brc_m013_2165brc_m013_2166..brc_m013_2170brc_m013_2171..brc_m013_2172brc_m013_2173brc_m013_2174..brc_m013_2182brc_m013_2183..brc_m013_2186brc_m013_2187..brc_m013_2190brc_m013_2191..brc_m013_2193brc_m013_2194brc_m013_2195..brc_m013_2201brc_m013_2202..brc_m013_2203brc_m013_2204..brc_m013_2220brc_m013_2221..brc_m013_2232brc_m013_2233..brc_m013_2239brc_m013_2240..brc_m013_2261brc_m013_2262..brc_m013_2267brc_m013_2268..brc_m013_2269brc_m013_2270..brc_m013_2271brc_m013_2272..brc_m013_2282brc_m013_2283..brc_m013_2284brc_m013_2285..brc_m013_2299brc_m013_2300..brc_m013_2301brc_m013_2302..brc_m013_2305brc_m013_2306..brc_m013_2307brc_m013_2308..brc_m013_2330brc_m013_2331..brc_m013_2337brc_m013_2338..brc_m013_2352
0
20
40
60
80
100
120
LG6brc_m013_2353..brc_m013_2365brc_m013_2366..brc_m013_2369
brc_m013_2370..brc_m013_2372brc_m013_2373..brc_m013_2378brc_m013_2379..brc_m013_2386brc_m013_2387brc_m013_2388..brc_m013_2394brc_m013_2395..brc_m013_2397brc_m013_2398brc_m013_2399brc_m013_2400brc_m013_2401brc_m013_2402..brc_m013_2407brc_m013_2408..brc_m013_2411brc_m013_2412..brc_m013_2416brc_m013_2417brc_m013_2418brc_m013_2419..brc_m013_2436brc_m013_2437..brc_m013_2441brc_m013_2442brc_m013_2443..brc_m013_2444brc_m013_2445brc_m013_2446..brc_m013_2453brc_m013_2454brc_m013_2455..brc_m013_2460brc_m013_2461brc_m013_2462..brc_m013_2470brc_m013_2471..brc_m013_2474brc_m013_2475..brc_m013_2482brc_m013_2483brc_m013_2484..brc_m013_2487brc_m013_2488brc_m013_2489..brc_m013_2492brc_m013_2493..brc_m013_2496brc_m013_2497brc_m013_2498..brc_m013_2504brc_m013_2505brc_m013_2506..brc_m013_2510brc_m013_2511..brc_m013_2523brc_m013_2524..brc_m013_2531brc_m013_2532..brc_m013_2536brc_m013_2537..brc_m013_2555brc_m013_2556..brc_m013_2571brc_m013_2572..brc_m013_2573brc_m013_2574..brc_m013_2579brc_m013_2580..brc_m013_2581brc_m013_2582..brc_m013_2587brc_m013_2588brc_m013_2589..brc_m013_2594
brc_m013_2595
brc_m013_2596..brc_m013_2597brc_m013_2598..brc_m013_2604brc_m013_2605brc_m013_2606..brc_m013_2616brc_m013_2617..brc_m013_2619brc_m013_2620..brc_m013_2623
brc_m013_2624brc_m013_2625..brc_m013_2626brc_m013_2627..brc_m013_2628
brc_m013_2629..brc_m013_2630
0
20
40
60
80
100
LG7brc_m013_2631..brc_m013_2632brc_m013_2633brc_m013_2634..brc_m013_2635brc_m013_2636..brc_m013_2642brc_m013_2643..brc_m013_2657brc_m013_2658..brc_m013_2659brc_m013_2660..brc_m013_2661brc_m013_2662
brc_m013_2663
brc_m013_2664brc_m013_2665..brc_m013_2666
brc_m013_2667..brc_m013_2668brc_m013_2669..brc_m013_2670brc_m013_2671..brc_m013_2680brc_m013_2681..brc_m013_2682brc_m013_2683brc_m013_2684..brc_m013_2685brc_m013_2686..brc_m013_2694
brc_m013_2695..brc_m013_2698brc_m013_2699..brc_m013_2713
brc_m013_2714..brc_m013_2725brc_m013_2726..brc_m013_2727brc_m013_2728..brc_m013_2731brc_m013_2732brc_m013_2733..brc_m013_2753brc_m013_2754..brc_m013_2758brc_m013_2759..brc_m013_2763brc_m013_2764..brc_m013_2779brc_m013_2780brc_m013_2781brc_m013_2782..brc_m013_2784brc_m013_2785..brc_m013_2787brc_m013_2788..brc_m013_2791brc_m013_2792..brc_m013_2797brc_m013_2798..brc_m013_2799brc_m013_2800brc_m013_2801..brc_m013_2804brc_m013_2805..brc_m013_2809
brc_m013_2810..brc_m013_2811
brc_m013_2812..brc_m013_2813brc_m013_2814..brc_m013_2817brc_m013_2818..brc_m013_2827brc_m013_2828brc_m013_2829..brc_m013_2832brc_m013_2833brc_m013_2834..brc_m013_2840brc_m013_2841..brc_m013_2846brc_m013_2847brc_m013_2848..brc_m013_2852brc_m013_2853brc_m013_2854..brc_m013_2856brc_m013_2857..brc_m013_2862brc_m013_2863..brc_m013_2868brc_m013_2869..brc_m013_2874brc_m013_2875..brc_m013_2896
0
20
40
60
80
100
LG8
brc_m013_2897..brc_m013_2920brc_m013_2921..brc_m013_2928brc_m013_2929..brc_m013_2931brc_m013_2932
brc_m013_2933
brc_m013_2934..brc_m013_2935brc_m013_2936brc_m013_2937..brc_m013_2943brc_m013_2944brc_m013_2945..brc_m013_2946brc_m013_2947brc_m013_2948brc_m013_2949..brc_m013_2950brc_m013_2951..brc_m013_2957brc_m013_2958..brc_m013_2961brc_m013_2962..brc_m013_2970brc_m013_2971..brc_m013_2980brc_m013_2981..brc_m013_2992brc_m013_2993..brc_m013_2996brc_m013_2997..brc_m013_2998brc_m013_2999..brc_m013_3000brc_m013_3001brc_m013_3002..brc_m013_3003brc_m013_3004brc_m013_3005brc_m013_3006..brc_m013_3010brc_m013_3011..brc_m013_3014brc_m013_3015brc_m013_3016..brc_m013_3019brc_m013_3020brc_m013_3021..brc_m013_3030brc_m013_3031..brc_m013_3032brc_m013_3033..brc_m013_3034brc_m013_3035..brc_m013_3036brc_m013_3037..brc_m013_3045brc_m013_3046..brc_m013_3052brc_m013_3053brc_m013_3054..brc_m013_3061brc_m013_3062..brc_m013_3066brc_m013_3067..brc_m013_3068brc_m013_3069..brc_m013_3076brc_m013_3077..brc_m013_3084brc_m013_3085..brc_m013_3087brc_m013_3088..brc_m013_3089brc_m013_3090..brc_m013_3096brc_m013_3097..brc_m013_3100brc_m013_3101..brc_m013_3104brc_m013_3105brc_m013_3106..brc_m013_3112brc_m013_3113..brc_m013_3122brc_m013_3123..brc_m013_3124brc_m013_3125..brc_m013_3127brc_m013_3128..brc_m013_3145brc_m013_3146..brc_m013_3159brc_m013_3160..brc_m013_3172
0
20
40
60
80
100
LG9brc_m013_3173..brc_m013_3175brc_m013_3176..brc_m013_3180brc_m013_3181..brc_m013_3189brc_m013_3190..brc_m013_3198brc_m013_3199brc_m013_3200..brc_m013_3201brc_m013_3202..brc_m013_3203brc_m013_3204brc_m013_3205..brc_m013_3206brc_m013_3207..brc_m013_3211brc_m013_3212..brc_m013_3214brc_m013_3215..brc_m013_3227brc_m013_3228..brc_m013_3230brc_m013_3231..brc_m013_3235brc_m013_3236..brc_m013_3238brc_m013_3239..brc_m013_3242brc_m013_3243..brc_m013_3244brc_m013_3245brc_m013_3246..brc_m013_3247brc_m013_3248..brc_m013_3249brc_m013_3250..brc_m013_3252brc_m013_3253..brc_m013_3257brc_m013_3258brc_m013_3259brc_m013_3260..brc_m013_3261brc_m013_3262..brc_m013_3263brc_m013_3264brc_m013_3265..brc_m013_3269brc_m013_3270..brc_m013_3274brc_m013_3275..brc_m013_3276brc_m013_3277..brc_m013_3281brc_m013_3282..brc_m013_3284brc_m013_3285brc_m013_3286..brc_m013_3289brc_m013_3290..brc_m013_3296brc_m013_3297brc_m013_3298..brc_m013_3300brc_m013_3301..brc_m013_3302brc_m013_3303..brc_m013_3305brc_m013_3306..brc_m013_3308brc_m013_3309..brc_m013_3314brc_m013_3315..brc_m013_3317brc_m013_3318..brc_m013_3329brc_m013_3330..brc_m013_3331brc_m013_3332..brc_m013_3338brc_m013_3339..brc_m013_3340brc_m013_3341..brc_m013_3344brc_m013_3345..brc_m013_3349brc_m013_3350..brc_m013_3357brc_m013_3358..brc_m013_3359brc_m013_3360brc_m013_3361..brc_m013_3368brc_m013_3369..brc_m013_3372brc_m013_3373..brc_m013_3376brc_m013_3377brc_m013_3378..brc_m013_3386brc_m013_3387..brc_m013_3388brc_m013_3389..brc_m013_3395brc_m013_3396..brc_m013_3399
0
20
40
60
80
LG10brc_m013_3400..brc_m013_3411brc_m013_3412brc_m013_3413..brc_m013_3424brc_m013_3425brc_m013_3426brc_m013_3427..brc_m013_3429
brc_m013_3430
brc_m013_3431..brc_m013_3432brc_m013_3433..brc_m013_3435brc_m013_3436brc_m013_3437..brc_m013_3439
brc_m013_3440..brc_m013_3441brc_m013_3442
brc_m013_3443..brc_m013_3445brc_m013_3446..brc_m013_3447brc_m013_3448..brc_m013_3449brc_m013_3450..brc_m013_3454brc_m013_3455brc_m013_3456..brc_m013_3462brc_m013_3463..brc_m013_3464brc_m013_3465brc_m013_3466..brc_m013_3467brc_m013_3468..brc_m013_3472brc_m013_3473brc_m013_3474..brc_m013_3476brc_m013_3477..brc_m013_3487brc_m013_3488brc_m013_3489..brc_m013_3491brc_m013_3492..brc_m013_3500brc_m013_3501..brc_m013_3512brc_m013_3513..brc_m013_3514brc_m013_3515..brc_m013_3524brc_m013_3525..brc_m013_3527brc_m013_3528..brc_m013_3531brc_m013_3532..brc_m013_3547brc_m013_3548..brc_m013_3557brc_m013_3558..brc_m013_3566brc_m013_3567..brc_m013_3568brc_m013_3569..brc_m013_3570brc_m013_3571..brc_m013_3574brc_m013_3575..brc_m013_3582brc_m013_3583..brc_m013_3592brc_m013_3593..brc_m013_3605brc_m013_3606..brc_m013_3616brc_m013_3617..brc_m013_3618brc_m013_3619..brc_m013_3622brc_m013_3623..brc_m013_3624brc_m013_3625..brc_m013_3628brc_m013_3629..brc_m013_3635
0
20
40
60
80
LG11
brc_m013_3636..brc_m013_3661brc_m013_3662..brc_m013_3665
brc_m013_3666..brc_m013_3667brc_m013_3668brc_m013_3669..brc_m013_3671
brc_m013_3672
brc_m013_3673..brc_m013_3674brc_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_3698brc_m013_3699
brc_m013_3700brc_m013_3701..brc_m013_3702brc_m013_3703..brc_m013_3704brc_m013_3705..brc_m013_3712brc_m013_3713brc_m013_3714..brc_m013_3716brc_m013_3717..brc_m013_3724brc_m013_3725..brc_m013_3730brc_m013_3731..brc_m013_3752brc_m013_3753..brc_m013_3758brc_m013_3759..brc_m013_3789brc_m013_3790..brc_m013_3801brc_m013_3802..brc_m013_3814brc_m013_3815..brc_m013_3818brc_m013_3819..brc_m013_3822brc_m013_3823..brc_m013_3826brc_m013_3827..brc_m013_3832brc_m013_3833..brc_m013_3837brc_m013_3838brc_m013_3839..brc_m013_3841brc_m013_3842..brc_m013_3847
brc_m013_3848..brc_m013_3853brc_m013_3854..brc_m013_3858brc_m013_3859..brc_m013_3868brc_m013_3869..brc_m013_3871brc_m013_3872..brc_m013_3901brc_m013_3902brc_m013_3903..brc_m013_3909brc_m013_3910brc_m013_3911..brc_m013_3926brc_m013_3927..brc_m013_3931brc_m013_3932..brc_m013_3948
0
20
40
60
80
LG12
brc_m013_3949..brc_m013_3952brc_m013_3953..brc_m013_3958brc_m013_3959..brc_m013_3970brc_m013_3971
brc_m013_3972..brc_m013_3975brc_m013_3976
brc_m013_3977..brc_m013_3985
brc_m013_3986brc_m013_3987..brc_m013_3994brc_m013_3995..brc_m013_3997brc_m013_3998..brc_m013_4004
brc_m013_4005..brc_m013_4006brc_m013_4007..brc_m013_4008brc_m013_4009..brc_m013_4010brc_m013_4011..brc_m013_4013brc_m013_4014brc_m013_4015brc_m013_4016..brc_m013_4019brc_m013_4020..brc_m013_4021brc_m013_4022..brc_m013_4025brc_m013_4026..brc_m013_4032brc_m013_4033..brc_m013_4036brc_m013_4037..brc_m013_4041brc_m013_4042..brc_m013_4043
brc_m013_4044..brc_m013_4046brc_m013_4047..brc_m013_4056brc_m013_4057brc_m013_4058..brc_m013_4063brc_m013_4064..brc_m013_4071brc_m013_4072..brc_m013_4075brc_m013_4076brc_m013_4077brc_m013_4078..brc_m013_4085brc_m013_4086..brc_m013_4089brc_m013_4090..brc_m013_4091brc_m013_4092..brc_m013_4093brc_m013_4094..brc_m013_4095brc_m013_4096..brc_m013_4114brc_m013_4115..brc_m013_4117brc_m013_4118..brc_m013_4131brc_m013_4132..brc_m013_4133brc_m013_4134..brc_m013_4146
0
20
40
60
80
LG13
brc_m013_4147..brc_m013_4150brc_m013_4151..brc_m013_4167
brc_m013_4168brc_m013_4169
brc_m013_4170brc_m013_4171..brc_m013_4172brc_m013_4173..brc_m013_4175brc_m013_4176brc_m013_4177..brc_m013_4178brc_m013_4179..brc_m013_4183brc_m013_4184..brc_m013_4185brc_m013_4186..brc_m013_4187brc_m013_4188..brc_m013_4191brc_m013_4192brc_m013_4193..brc_m013_4194brc_m013_4195..brc_m013_4206brc_m013_4207..brc_m013_4210brc_m013_4211..brc_m013_4213brc_m013_4214brc_m013_4215..brc_m013_4217brc_m013_4218..brc_m013_4221brc_m013_4222..brc_m013_4223brc_m013_4224..brc_m013_4231brc_m013_4232..brc_m013_4234brc_m013_4235..brc_m013_4239brc_m013_4240..brc_m013_4246brc_m013_4247..brc_m013_4248brc_m013_4249..brc_m013_4258brc_m013_4259..brc_m013_4260brc_m013_4261..brc_m013_4269brc_m013_4270..brc_m013_4271brc_m013_4272..brc_m013_4278brc_m013_4279..brc_m013_4280brc_m013_4281..brc_m013_4284brc_m013_4285brc_m013_4286..brc_m013_4288brc_m013_4289..brc_m013_4294brc_m013_4295..brc_m013_4296brc_m013_4297..brc_m013_4301brc_m013_4302..brc_m013_4313brc_m013_4314..brc_m013_4320brc_m013_4321..brc_m013_4322brc_m013_4323..brc_m013_4345brc_m013_4346..brc_m013_4351
0
20
40
60
LG14brc_m013_4352..brc_m013_4366brc_m013_4367brc_m013_4368brc_m013_4369..brc_m013_4373brc_m013_4374..brc_m013_4381brc_m013_4382..brc_m013_4383brc_m013_4384..brc_m013_4385brc_m013_4386brc_m013_4387..brc_m013_4388brc_m013_4389brc_m013_4390..brc_m013_4404brc_m013_4405brc_m013_4406..brc_m013_4409brc_m013_4410..brc_m013_4411brc_m013_4412..brc_m013_4418brc_m013_4419..brc_m013_4434brc_m013_4435..brc_m013_4442brc_m013_4443..brc_m013_4448brc_m013_4449..brc_m013_4451brc_m013_4452..brc_m013_4461brc_m013_4462..brc_m013_4471brc_m013_4472..brc_m013_4475brc_m013_4476..brc_m013_4477brc_m013_4478brc_m013_4479brc_m013_4480..brc_m013_4485brc_m013_4486brc_m013_4487..brc_m013_4491brc_m013_4492brc_m013_4493brc_m013_4494..brc_m013_4495brc_m013_4496..brc_m013_4501brc_m013_4502..brc_m013_4510brc_m013_4511..brc_m013_4531brc_m013_4532brc_m013_4533..brc_m013_4534brc_m013_4535..brc_m013_4541brc_m013_4542..brc_m013_4543brc_m013_4544..brc_m013_4545brc_m013_4546..brc_m013_4548brc_m013_4549..brc_m013_4551brc_m013_4552..brc_m013_4555brc_m013_4556..brc_m013_4561
0
20
40
60
LG15
brc_m013_4562..brc_m013_4577brc_m013_4578..brc_m013_4594brc_m013_4595..brc_m013_4599brc_m013_4600..brc_m013_4625brc_m013_4626..brc_m013_4638brc_m013_4639..brc_m013_4642brc_m013_4643..brc_m013_4644brc_m013_4645..brc_m013_4650brc_m013_4651..brc_m013_4663brc_m013_4664..brc_m013_4668brc_m013_4669..brc_m013_4670brc_m013_4671..brc_m013_4674brc_m013_4675..brc_m013_4679brc_m013_4680..brc_m013_4681brc_m013_4682brc_m013_4683..brc_m013_4688brc_m013_4689..brc_m013_4692brc_m013_4693..brc_m013_4695brc_m013_4696..brc_m013_4701brc_m013_4702brc_m013_4703..brc_m013_4712brc_m013_4713..brc_m013_4717brc_m013_4718..brc_m013_4720brc_m013_4721brc_m013_4722..brc_m013_4726brc_m013_4727..brc_m013_4728brc_m013_4729..brc_m013_4742brc_m013_4743brc_m013_4744..brc_m013_4746brc_m013_4747brc_m013_4748..brc_m013_4749brc_m013_4750..brc_m013_4752
brc_m013_4753..brc_m013_4756brc_m013_4757..brc_m013_4759brc_m013_4760..brc_m013_4762brc_m013_4763brc_m013_4764..brc_m013_4766brc_m013_4767..brc_m013_4769brc_m013_4770brc_m013_4771..brc_m013_4774brc_m013_4775..brc_m013_4776brc_m013_4777..brc_m013_4778brc_m013_4779..brc_m013_4780brc_m013_4781..brc_m013_4793brc_m013_4794brc_m013_4795..brc_m013_4798brc_m013_4799..brc_m013_4802brc_m013_4803..brc_m013_4806brc_m013_4807brc_m013_4808..brc_m013_4814brc_m013_4815..brc_m013_4819brc_m013_4820brc_m013_4821brc_m013_4822..brc_m013_4823brc_m013_4824brc_m013_4825..brc_m013_4855brc_m013_4856..brc_m013_4858brc_m013_4859..brc_m013_4863brc_m013_4864..brc_m013_4865brc_m013_4866..brc_m013_4875brc_m013_4876..brc_m013_4881brc_m013_4882..brc_m013_4891brc_m013_4892..brc_m013_4895brc_m013_4896..brc_m013_4911brc_m013_4912..brc_m013_4938brc_m013_4939brc_m013_4940..brc_m013_4957brc_m013_4958..brc_m013_4959brc_m013_4960..brc_m013_4972brc_m013_4973..brc_m013_4981brc_m013_4982..brc_m013_4983
0
20
40
60
80
100
120
LGSB
Gp-9
Figure 1a b
Si_gnF.scaffold00779_nt2778431.7
Si_gnF.scaffold00779_nt1255229Si_gnF.scaffold02684_nt10884.2
Si_gnF.scaffold00779_nt1633919Si_gnF.scaffold00779_nt17842486.5
Si_gnF.scaffold00779_nt3746833Si_gnF.scaffold00779_nt374687927.3Si_gnF.scaffold00779_nt382158728.5
Si_gnF.scaffold00779_nt417489034.2
Si_gnF.scaffold09607_nt698300Si_gnF.scaffold09607_nt69848340.2
Si_gnF.scaffold09758_nt22273252.8
Si_gnF.scaffold05266_nt63430678.4Si_gnF.scaffold05266_nt65952779.7
Si_gnF.scaffold05266_nt733643Si_gnF.scaffold05266_nt75364482.8
Si_gnF.scaffold07090_nt71001087.6
Si_gnF.scaffold07090_nt105177192.7
Si_gnF.scaffold00255_nt314067Si_gnF.scaffold00255_nt40777897.5
Si_gnF.scaffold03404_nt128925Si_gnF.scaffold03404_nt228606Si_gnF.scaffold03404_nt241461
104.4
Si_gnF.scaffold00413_nt676115107.3
Si_gnF.scaffold00413_nt1035856109.6Si_gnF.scaffold01573_nt108462110.8Si_gnF.scaffold01573_nt447618112.1Si_gnF.scaffold00899_nt377419Si_gnF.scaffold00899_nt686574114.4Si_gnF.scaffold00899_nt236146Si_gnF.scaffold00899_nt332715Si_gnF.scaffold00899_nt335756
115.8
Si_gnF.scaffold00469_nt794118.0Si_gnF.scaffold00690_nt229012Si_gnF.scaffold00690_nt415290119.3
Si_gnF.scaffold06914_nt297673125.1
Si_gnF.scaffold01957_nt412242Si_gnF.scaffold02848_nt41846127.6
LGS Bfrom M013
Si_gnF.scaffold00779_nt2778430.0Si_gnF.scaffold00779_nt1255229Si_gnF.scaffold02684_nt10881.2
Si_gnF.scaffold00779_nt1633919Si_gnF.scaffold00779_nt17842486.7
Si_gnF.scaffold00779_nt3746833Si_gnF.scaffold00779_nt3746879Si_gnF.scaffold00779_nt3821587
22.2
Si_gnF.scaffold00779_nt417489029.2
Si_gnF.scaffold09607_nt698300Si_gnF.scaffold09607_nt69848361.9
Si_gnF.scaffold01573_nt10846280.7Si_gnF.scaffold00255_nt314067Si_gnF.scaffold00255_nt407778Si_gnF.scaffold00413_nt1035856Si_gnF.scaffold00413_nt676115Si_gnF.scaffold00469_nt794Si_gnF.scaffold00690_nt229012Si_gnF.scaffold00690_nt415290Si_gnF.scaffold00899_nt236146Si_gnF.scaffold00899_nt332715Si_gnF.scaffold00899_nt335756Si_gnF.scaffold00899_nt377419Si_gnF.scaffold00899_nt686574Si_gnF.scaffold01573_nt447618Si_gnF.scaffold01957_nt412242Si_gnF.scaffold03404_nt128925Si_gnF.scaffold03404_nt228606Si_gnF.scaffold03404_nt241461Si_gnF.scaffold05266_nt634306Si_gnF.scaffold05266_nt659527Si_gnF.scaffold05266_nt733643Si_gnF.scaffold05266_nt753644Si_gnF.scaffold06914_nt297673Si_gnF.scaffold07090_nt1051771Si_gnF.scaffold07090_nt710010Si_gnF.scaffold09758_nt222732
81.8
Si_gnF.scaffold02848_nt4184690.5
LGS B/bfrom P034
Gp-9
Total285 non-recombiningmarkersbrc_m013_0001..brc_m013_0005
brc_m013_0006..brc_m013_0014brc_m013_0015..brc_m013_0017brc_m013_0018brc_m013_0019..brc_m013_0020brc_m013_0021..brc_m013_0029brc_m013_0030..brc_m013_0031brc_m013_0032..brc_m013_0034brc_m013_0035..brc_m013_0036brc_m013_0037..brc_m013_0038brc_m013_0039..brc_m013_0043brc_m013_0044brc_m013_0045brc_m013_0046..brc_m013_0048brc_m013_0049brc_m013_0050..brc_m013_0051brc_m013_0052..brc_m013_0056brc_m013_0057..brc_m013_0061
brc_m013_0062..brc_m013_0075brc_m013_0076..brc_m013_0078brc_m013_0079..brc_m013_0081
brc_m013_0082..brc_m013_0088
brc_m013_0089..brc_m013_0092
brc_m013_0093..brc_m013_0096brc_m013_0097brc_m013_0098..brc_m013_0113brc_m013_0114..brc_m013_0119brc_m013_0120..brc_m013_0130brc_m013_0131brc_m013_0132..brc_m013_0134brc_m013_0135..brc_m013_0136brc_m013_0137..brc_m013_0139brc_m013_0140..brc_m013_0142brc_m013_0143brc_m013_0144..brc_m013_0146brc_m013_0147..brc_m013_0154brc_m013_0155
brc_m013_0156brc_m013_0157..brc_m013_0180brc_m013_0181brc_m013_0182brc_m013_0183..brc_m013_0188brc_m013_0189..brc_m013_0208brc_m013_0209brc_m013_0210..brc_m013_0211brc_m013_0212..brc_m013_0215brc_m013_0216brc_m013_0217brc_m013_0218..brc_m013_0224brc_m013_0225..brc_m013_0228brc_m013_0229..brc_m013_0237brc_m013_0238..brc_m013_0245
brc_m013_0246..brc_m013_0270
brc_m013_0271..brc_m013_0274brc_m013_0275brc_m013_0276..brc_m013_0278
brc_m013_0279
brc_m013_0280
brc_m013_0281..brc_m013_0294
brc_m013_0295..brc_m013_0303brc_m013_0304brc_m013_0305..brc_m013_0307brc_m013_0308brc_m013_0309..brc_m013_0314brc_m013_0315..brc_m013_0317brc_m013_0318..brc_m013_0320brc_m013_0321..brc_m013_0326brc_m013_0327brc_m013_0328brc_m013_0329..brc_m013_0330brc_m013_0331..brc_m013_0333brc_m013_0334..brc_m013_0339brc_m013_0340brc_m013_0341..brc_m013_0343brc_m013_0344brc_m013_0345..brc_m013_0349brc_m013_0350
brc_m013_0351..brc_m013_0354brc_m013_0355brc_m013_0356brc_m013_0357..brc_m013_0361brc_m013_0362..brc_m013_0376brc_m013_0377..brc_m013_0390brc_m013_0391..brc_m013_0393brc_m013_0394..brc_m013_0400brc_m013_0401..brc_m013_0439brc_m013_0440..brc_m013_0478brc_m013_0479..brc_m013_0480
0
20
40
60
80
100
120
140
160
180
LG1brc_m013_0481brc_m013_0482..brc_m013_0484brc_m013_0485..brc_m013_0488brc_m013_0489..brc_m013_0502brc_m013_0503brc_m013_0504..brc_m013_0519brc_m013_0520..brc_m013_0532brc_m013_0533..brc_m013_0534brc_m013_0535..brc_m013_0537brc_m013_0538..brc_m013_0540brc_m013_0541..brc_m013_0543brc_m013_0544..brc_m013_0545brc_m013_0546..brc_m013_0549
brc_m013_0550..brc_m013_0554
brc_m013_0555..brc_m013_0560
brc_m013_0561..brc_m013_0562brc_m013_0563..brc_m013_0565
brc_m013_0566brc_m013_0567brc_m013_0568..brc_m013_0570brc_m013_0571..brc_m013_0573
brc_m013_0574..brc_m013_0575brc_m013_0576..brc_m013_0578brc_m013_0579..brc_m013_0580brc_m013_0581brc_m013_0582..brc_m013_0584brc_m013_0585brc_m013_0586brc_m013_0587brc_m013_0588..brc_m013_0591brc_m013_0592brc_m013_0593brc_m013_0594..brc_m013_0612brc_m013_0613..brc_m013_0614brc_m013_0615..brc_m013_0632brc_m013_0633brc_m013_0634..brc_m013_0648brc_m013_0649..brc_m013_0655brc_m013_0656brc_m013_0657..brc_m013_0694brc_m013_0695..brc_m013_0703brc_m013_0704brc_m013_0705brc_m013_0706..brc_m013_0707brc_m013_0708brc_m013_0709..brc_m013_0711brc_m013_0712..brc_m013_0715brc_m013_0716..brc_m013_0721brc_m013_0722brc_m013_0723brc_m013_0724..brc_m013_0728brc_m013_0729brc_m013_0730brc_m013_0731brc_m013_0732..brc_m013_0735brc_m013_0736..brc_m013_0769brc_m013_0770..brc_m013_0771brc_m013_0772..brc_m013_0773brc_m013_0774..brc_m013_0775brc_m013_0776..brc_m013_0782brc_m013_0783brc_m013_0784..brc_m013_0795brc_m013_0796..brc_m013_0798brc_m013_0799..brc_m013_0801brc_m013_0802..brc_m013_0805brc_m013_0806..brc_m013_0809brc_m013_0810..brc_m013_0811brc_m013_0812..brc_m013_0824brc_m013_0825..brc_m013_0826brc_m013_0827..brc_m013_0829brc_m013_0830..brc_m013_0831brc_m013_0832..brc_m013_0842brc_m013_0843..brc_m013_0854brc_m013_0855..brc_m013_0861brc_m013_0862brc_m013_0863..brc_m013_0864brc_m013_0865..brc_m013_0867brc_m013_0868..brc_m013_0883brc_m013_0884..brc_m013_0893brc_m013_0894brc_m013_0895..brc_m013_0897brc_m013_0898..brc_m013_0906brc_m013_0907..brc_m013_0910brc_m013_0911..brc_m013_0925brc_m013_0926..brc_m013_0928brc_m013_0929..brc_m013_0931
0
20
40
60
80
100
120
140
LG2brc_m013_0932..brc_m013_0941brc_m013_0942..brc_m013_0943brc_m013_0944..brc_m013_0945brc_m013_0946..brc_m013_0949brc_m013_0950..brc_m013_0952
brc_m013_0953..brc_m013_0975
brc_m013_0976..brc_m013_1019brc_m013_1020brc_m013_1021brc_m013_1022..brc_m013_1061brc_m013_1062brc_m013_1063
brc_m013_1064..brc_m013_1065
brc_m013_1066..brc_m013_1068brc_m013_1069brc_m013_1070
brc_m013_1071..brc_m013_1074
brc_m013_1075
brc_m013_1076..brc_m013_1081
brc_m013_1082..brc_m013_1086brc_m013_1087..brc_m013_1088brc_m013_1089..brc_m013_1098brc_m013_1099..brc_m013_1106brc_m013_1107..brc_m013_1116brc_m013_1117brc_m013_1118..brc_m013_1121brc_m013_1122..brc_m013_1127brc_m013_1128brc_m013_1129..brc_m013_1136brc_m013_1137..brc_m013_1138brc_m013_1139..brc_m013_1141brc_m013_1142..brc_m013_1144brc_m013_1145..brc_m013_1156brc_m013_1157brc_m013_1158..brc_m013_1170brc_m013_1171..brc_m013_1181brc_m013_1182..brc_m013_1185brc_m013_1186brc_m013_1187..brc_m013_1205brc_m013_1206..brc_m013_1218brc_m013_1219..brc_m013_1220brc_m013_1221..brc_m013_1224brc_m013_1225..brc_m013_1228brc_m013_1229brc_m013_1230..brc_m013_1236brc_m013_1237brc_m013_1238..brc_m013_1247brc_m013_1248..brc_m013_1251
brc_m013_1252brc_m013_1253..brc_m013_1268brc_m013_1269..brc_m013_1270brc_m013_1271..brc_m013_1273brc_m013_1274brc_m013_1275..brc_m013_1280brc_m013_1281
brc_m013_1282..brc_m013_1286brc_m013_1287..brc_m013_1298brc_m013_1299..brc_m013_1307brc_m013_1308brc_m013_1309..brc_m013_1313brc_m013_1314..brc_m013_1317brc_m013_1318..brc_m013_1319brc_m013_1320..brc_m013_1326brc_m013_1327..brc_m013_1340brc_m013_1341..brc_m013_1362brc_m013_1363..brc_m013_1385
0
20
40
60
80
100
120
140
LG3brc_m013_1386..brc_m013_1388brc_m013_1389..brc_m013_1398brc_m013_1399..brc_m013_1406brc_m013_1407..brc_m013_1411brc_m013_1412..brc_m013_1413brc_m013_1414..brc_m013_1416
brc_m013_1417brc_m013_1418..brc_m013_1420brc_m013_1421..brc_m013_1424brc_m013_1425..brc_m013_1432brc_m013_1433..brc_m013_1442brc_m013_1443brc_m013_1444..brc_m013_1450brc_m013_1451brc_m013_1452brc_m013_1453..brc_m013_1455brc_m013_1456..brc_m013_1467brc_m013_1468..brc_m013_1469brc_m013_1470brc_m013_1471..brc_m013_1474brc_m013_1475brc_m013_1476brc_m013_1477brc_m013_1478..brc_m013_1482brc_m013_1483
brc_m013_1484brc_m013_1485..brc_m013_1487brc_m013_1488..brc_m013_1490
brc_m013_1491brc_m013_1492..brc_m013_1494brc_m013_1495..brc_m013_1496
brc_m013_1497..brc_m013_1500brc_m013_1501brc_m013_1502..brc_m013_1513brc_m013_1514..brc_m013_1562brc_m013_1563..brc_m013_1565brc_m013_1566..brc_m013_1567
brc_m013_1568..brc_m013_1580brc_m013_1581..brc_m013_1587brc_m013_1588..brc_m013_1591brc_m013_1592..brc_m013_1593brc_m013_1594..brc_m013_1604brc_m013_1605..brc_m013_1607brc_m013_1608..brc_m013_1609brc_m013_1610..brc_m013_1611brc_m013_1612..brc_m013_1616brc_m013_1617..brc_m013_1618brc_m013_1619..brc_m013_1620brc_m013_1621..brc_m013_1629brc_m013_1630..brc_m013_1633brc_m013_1634..brc_m013_1638brc_m013_1639..brc_m013_1647brc_m013_1648..brc_m013_1649brc_m013_1650..brc_m013_1656brc_m013_1657..brc_m013_1665brc_m013_1666..brc_m013_1672brc_m013_1673..brc_m013_1674brc_m013_1675..brc_m013_1678brc_m013_1679..brc_m013_1682brc_m013_1683brc_m013_1684brc_m013_1685..brc_m013_1686brc_m013_1687..brc_m013_1700brc_m013_1701..brc_m013_1702brc_m013_1703brc_m013_1704..brc_m013_1707brc_m013_1708..brc_m013_1709brc_m013_1710..brc_m013_1714brc_m013_1715..brc_m013_1728brc_m013_1729..brc_m013_1742
0
20
40
60
80
100
120
140
LG4brc_m013_1743..brc_m013_1750
brc_m013_1751..brc_m013_1766brc_m013_1767brc_m013_1768
brc_m013_1769..brc_m013_1772
brc_m013_1773..brc_m013_1779brc_m013_1780brc_m013_1781brc_m013_1782..brc_m013_1783brc_m013_1784brc_m013_1785..brc_m013_1786
brc_m013_1787
brc_m013_1788brc_m013_1789..brc_m013_1790brc_m013_1791..brc_m013_1793brc_m013_1794..brc_m013_1797brc_m013_1798..brc_m013_1800brc_m013_1801..brc_m013_1804brc_m013_1805brc_m013_1806..brc_m013_1808brc_m013_1809brc_m013_1810..brc_m013_1813brc_m013_1814..brc_m013_1818brc_m013_1819..brc_m013_1820brc_m013_1821..brc_m013_1822brc_m013_1823..brc_m013_1824brc_m013_1825brc_m013_1826..brc_m013_1840brc_m013_1841..brc_m013_1842brc_m013_1843brc_m013_1844..brc_m013_1848brc_m013_1849brc_m013_1850brc_m013_1851..brc_m013_1853brc_m013_1854..brc_m013_1858brc_m013_1859..brc_m013_1866brc_m013_1867..brc_m013_1868brc_m013_1869brc_m013_1870..brc_m013_1874brc_m013_1875..brc_m013_1876brc_m013_1877..brc_m013_1878brc_m013_1879..brc_m013_1883brc_m013_1884brc_m013_1885brc_m013_1886..brc_m013_1888brc_m013_1889..brc_m013_1895brc_m013_1896..brc_m013_1899brc_m013_1900..brc_m013_1913brc_m013_1914brc_m013_1915..brc_m013_1922brc_m013_1923brc_m013_1924..brc_m013_1928brc_m013_1929..brc_m013_1942brc_m013_1943..brc_m013_1946brc_m013_1947..brc_m013_1948brc_m013_1949brc_m013_1950..brc_m013_1953brc_m013_1954..brc_m013_1955brc_m013_1956brc_m013_1957..brc_m013_1963brc_m013_1964..brc_m013_1966brc_m013_1967..brc_m013_1968brc_m013_1969..brc_m013_1970brc_m013_1971brc_m013_1972brc_m013_1973..brc_m013_1980brc_m013_1981..brc_m013_1983brc_m013_1984..brc_m013_1990brc_m013_1991..brc_m013_1993brc_m013_1994..brc_m013_1996brc_m013_1997..brc_m013_2009
0
20
40
60
80
100
120
LG5brc_m013_2010..brc_m013_2028
brc_m013_2029..brc_m013_2038brc_m013_2039
brc_m013_2040..brc_m013_2041brc_m013_2042..brc_m013_2047brc_m013_2048..brc_m013_2050brc_m013_2051..brc_m013_2053brc_m013_2054..brc_m013_2062brc_m013_2063brc_m013_2064..brc_m013_2065brc_m013_2066..brc_m013_2067brc_m013_2068brc_m013_2069..brc_m013_2071brc_m013_2072..brc_m013_2081brc_m013_2082
brc_m013_2083brc_m013_2084brc_m013_2085..brc_m013_2099brc_m013_2100brc_m013_2101..brc_m013_2102brc_m013_2103..brc_m013_2107brc_m013_2108brc_m013_2109..brc_m013_2112
brc_m013_2113..brc_m013_2114brc_m013_2115..brc_m013_2123brc_m013_2124..brc_m013_2131brc_m013_2132brc_m013_2133brc_m013_2134..brc_m013_2136
brc_m013_2137
brc_m013_2138..brc_m013_2139
brc_m013_2140..brc_m013_2142brc_m013_2143..brc_m013_2150brc_m013_2151..brc_m013_2152brc_m013_2153..brc_m013_2161brc_m013_2162..brc_m013_2163
brc_m013_2164..brc_m013_2165brc_m013_2166..brc_m013_2170brc_m013_2171..brc_m013_2172brc_m013_2173brc_m013_2174..brc_m013_2182brc_m013_2183..brc_m013_2186brc_m013_2187..brc_m013_2190brc_m013_2191..brc_m013_2193brc_m013_2194brc_m013_2195..brc_m013_2201brc_m013_2202..brc_m013_2203brc_m013_2204..brc_m013_2220brc_m013_2221..brc_m013_2232brc_m013_2233..brc_m013_2239brc_m013_2240..brc_m013_2261brc_m013_2262..brc_m013_2267brc_m013_2268..brc_m013_2269brc_m013_2270..brc_m013_2271brc_m013_2272..brc_m013_2282brc_m013_2283..brc_m013_2284brc_m013_2285..brc_m013_2299brc_m013_2300..brc_m013_2301brc_m013_2302..brc_m013_2305brc_m013_2306..brc_m013_2307brc_m013_2308..brc_m013_2330brc_m013_2331..brc_m013_2337brc_m013_2338..brc_m013_2352
0
20
40
60
80
100
120
LG6brc_m013_2353..brc_m013_2365brc_m013_2366..brc_m013_2369
brc_m013_2370..brc_m013_2372brc_m013_2373..brc_m013_2378brc_m013_2379..brc_m013_2386brc_m013_2387brc_m013_2388..brc_m013_2394brc_m013_2395..brc_m013_2397brc_m013_2398brc_m013_2399brc_m013_2400brc_m013_2401brc_m013_2402..brc_m013_2407brc_m013_2408..brc_m013_2411brc_m013_2412..brc_m013_2416brc_m013_2417brc_m013_2418brc_m013_2419..brc_m013_2436brc_m013_2437..brc_m013_2441brc_m013_2442brc_m013_2443..brc_m013_2444brc_m013_2445brc_m013_2446..brc_m013_2453brc_m013_2454brc_m013_2455..brc_m013_2460brc_m013_2461brc_m013_2462..brc_m013_2470brc_m013_2471..brc_m013_2474brc_m013_2475..brc_m013_2482brc_m013_2483brc_m013_2484..brc_m013_2487brc_m013_2488brc_m013_2489..brc_m013_2492brc_m013_2493..brc_m013_2496brc_m013_2497brc_m013_2498..brc_m013_2504brc_m013_2505brc_m013_2506..brc_m013_2510brc_m013_2511..brc_m013_2523brc_m013_2524..brc_m013_2531brc_m013_2532..brc_m013_2536brc_m013_2537..brc_m013_2555brc_m013_2556..brc_m013_2571brc_m013_2572..brc_m013_2573brc_m013_2574..brc_m013_2579brc_m013_2580..brc_m013_2581brc_m013_2582..brc_m013_2587brc_m013_2588brc_m013_2589..brc_m013_2594
brc_m013_2595
brc_m013_2596..brc_m013_2597brc_m013_2598..brc_m013_2604brc_m013_2605brc_m013_2606..brc_m013_2616brc_m013_2617..brc_m013_2619brc_m013_2620..brc_m013_2623
brc_m013_2624brc_m013_2625..brc_m013_2626brc_m013_2627..brc_m013_2628
brc_m013_2629..brc_m013_2630
0
20
40
60
80
100
LG7brc_m013_2631..brc_m013_2632brc_m013_2633brc_m013_2634..brc_m013_2635brc_m013_2636..brc_m013_2642brc_m013_2643..brc_m013_2657brc_m013_2658..brc_m013_2659brc_m013_2660..brc_m013_2661brc_m013_2662
brc_m013_2663
brc_m013_2664brc_m013_2665..brc_m013_2666
brc_m013_2667..brc_m013_2668brc_m013_2669..brc_m013_2670brc_m013_2671..brc_m013_2680brc_m013_2681..brc_m013_2682brc_m013_2683brc_m013_2684..brc_m013_2685brc_m013_2686..brc_m013_2694
brc_m013_2695..brc_m013_2698brc_m013_2699..brc_m013_2713
brc_m013_2714..brc_m013_2725brc_m013_2726..brc_m013_2727brc_m013_2728..brc_m013_2731brc_m013_2732brc_m013_2733..brc_m013_2753brc_m013_2754..brc_m013_2758brc_m013_2759..brc_m013_2763brc_m013_2764..brc_m013_2779brc_m013_2780brc_m013_2781brc_m013_2782..brc_m013_2784brc_m013_2785..brc_m013_2787brc_m013_2788..brc_m013_2791brc_m013_2792..brc_m013_2797brc_m013_2798..brc_m013_2799brc_m013_2800brc_m013_2801..brc_m013_2804brc_m013_2805..brc_m013_2809
brc_m013_2810..brc_m013_2811
brc_m013_2812..brc_m013_2813brc_m013_2814..brc_m013_2817brc_m013_2818..brc_m013_2827brc_m013_2828brc_m013_2829..brc_m013_2832brc_m013_2833brc_m013_2834..brc_m013_2840brc_m013_2841..brc_m013_2846brc_m013_2847brc_m013_2848..brc_m013_2852brc_m013_2853brc_m013_2854..brc_m013_2856brc_m013_2857..brc_m013_2862brc_m013_2863..brc_m013_2868brc_m013_2869..brc_m013_2874brc_m013_2875..brc_m013_2896
0
20
40
60
80
100
LG8
brc_m013_2897..brc_m013_2920brc_m013_2921..brc_m013_2928brc_m013_2929..brc_m013_2931brc_m013_2932
brc_m013_2933
brc_m013_2934..brc_m013_2935brc_m013_2936brc_m013_2937..brc_m013_2943brc_m013_2944brc_m013_2945..brc_m013_2946brc_m013_2947brc_m013_2948brc_m013_2949..brc_m013_2950brc_m013_2951..brc_m013_2957brc_m013_2958..brc_m013_2961brc_m013_2962..brc_m013_2970brc_m013_2971..brc_m013_2980brc_m013_2981..brc_m013_2992brc_m013_2993..brc_m013_2996brc_m013_2997..brc_m013_2998brc_m013_2999..brc_m013_3000brc_m013_3001brc_m013_3002..brc_m013_3003brc_m013_3004brc_m013_3005brc_m013_3006..brc_m013_3010brc_m013_3011..brc_m013_3014brc_m013_3015brc_m013_3016..brc_m013_3019brc_m013_3020brc_m013_3021..brc_m013_3030brc_m013_3031..brc_m013_3032brc_m013_3033..brc_m013_3034brc_m013_3035..brc_m013_3036brc_m013_3037..brc_m013_3045brc_m013_3046..brc_m013_3052brc_m013_3053brc_m013_3054..brc_m013_3061brc_m013_3062..brc_m013_3066brc_m013_3067..brc_m013_3068brc_m013_3069..brc_m013_3076brc_m013_3077..brc_m013_3084brc_m013_3085..brc_m013_3087brc_m013_3088..brc_m013_3089brc_m013_3090..brc_m013_3096brc_m013_3097..brc_m013_3100brc_m013_3101..brc_m013_3104brc_m013_3105brc_m013_3106..brc_m013_3112brc_m013_3113..brc_m013_3122brc_m013_3123..brc_m013_3124brc_m013_3125..brc_m013_3127brc_m013_3128..brc_m013_3145brc_m013_3146..brc_m013_3159brc_m013_3160..brc_m013_3172
0
20
40
60
80
100
LG9brc_m013_3173..brc_m013_3175brc_m013_3176..brc_m013_3180brc_m013_3181..brc_m013_3189brc_m013_3190..brc_m013_3198brc_m013_3199brc_m013_3200..brc_m013_3201brc_m013_3202..brc_m013_3203brc_m013_3204brc_m013_3205..brc_m013_3206brc_m013_3207..brc_m013_3211brc_m013_3212..brc_m013_3214brc_m013_3215..brc_m013_3227brc_m013_3228..brc_m013_3230brc_m013_3231..brc_m013_3235brc_m013_3236..brc_m013_3238brc_m013_3239..brc_m013_3242brc_m013_3243..brc_m013_3244brc_m013_3245brc_m013_3246..brc_m013_3247brc_m013_3248..brc_m013_3249brc_m013_3250..brc_m013_3252brc_m013_3253..brc_m013_3257brc_m013_3258brc_m013_3259brc_m013_3260..brc_m013_3261brc_m013_3262..brc_m013_3263brc_m013_3264brc_m013_3265..brc_m013_3269brc_m013_3270..brc_m013_3274brc_m013_3275..brc_m013_3276brc_m013_3277..brc_m013_3281brc_m013_3282..brc_m013_3284brc_m013_3285brc_m013_3286..brc_m013_3289brc_m013_3290..brc_m013_3296brc_m013_3297brc_m013_3298..brc_m013_3300brc_m013_3301..brc_m013_3302brc_m013_3303..brc_m013_3305brc_m013_3306..brc_m013_3308brc_m013_3309..brc_m013_3314brc_m013_3315..brc_m013_3317brc_m013_3318..brc_m013_3329brc_m013_3330..brc_m013_3331brc_m013_3332..brc_m013_3338brc_m013_3339..brc_m013_3340brc_m013_3341..brc_m013_3344brc_m013_3345..brc_m013_3349brc_m013_3350..brc_m013_3357brc_m013_3358..brc_m013_3359brc_m013_3360brc_m013_3361..brc_m013_3368brc_m013_3369..brc_m013_3372brc_m013_3373..brc_m013_3376brc_m013_3377brc_m013_3378..brc_m013_3386brc_m013_3387..brc_m013_3388brc_m013_3389..brc_m013_3395brc_m013_3396..brc_m013_3399
0
20
40
60
80
LG10brc_m013_3400..brc_m013_3411brc_m013_3412brc_m013_3413..brc_m013_3424brc_m013_3425brc_m013_3426brc_m013_3427..brc_m013_3429
brc_m013_3430
brc_m013_3431..brc_m013_3432brc_m013_3433..brc_m013_3435brc_m013_3436brc_m013_3437..brc_m013_3439
brc_m013_3440..brc_m013_3441brc_m013_3442
brc_m013_3443..brc_m013_3445brc_m013_3446..brc_m013_3447brc_m013_3448..brc_m013_3449brc_m013_3450..brc_m013_3454brc_m013_3455brc_m013_3456..brc_m013_3462brc_m013_3463..brc_m013_3464brc_m013_3465brc_m013_3466..brc_m013_3467brc_m013_3468..brc_m013_3472brc_m013_3473brc_m013_3474..brc_m013_3476brc_m013_3477..brc_m013_3487brc_m013_3488brc_m013_3489..brc_m013_3491brc_m013_3492..brc_m013_3500brc_m013_3501..brc_m013_3512brc_m013_3513..brc_m013_3514brc_m013_3515..brc_m013_3524brc_m013_3525..brc_m013_3527brc_m013_3528..brc_m013_3531brc_m013_3532..brc_m013_3547brc_m013_3548..brc_m013_3557brc_m013_3558..brc_m013_3566brc_m013_3567..brc_m013_3568brc_m013_3569..brc_m013_3570brc_m013_3571..brc_m013_3574brc_m013_3575..brc_m013_3582brc_m013_3583..brc_m013_3592brc_m013_3593..brc_m013_3605brc_m013_3606..brc_m013_3616brc_m013_3617..brc_m013_3618brc_m013_3619..brc_m013_3622brc_m013_3623..brc_m013_3624brc_m013_3625..brc_m013_3628brc_m013_3629..brc_m013_3635
0
20
40
60
80
LG11
brc_m013_3636..brc_m013_3661brc_m013_3662..brc_m013_3665
brc_m013_3666..brc_m013_3667brc_m013_3668brc_m013_3669..brc_m013_3671
brc_m013_3672
brc_m013_3673..brc_m013_3674brc_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_3698brc_m013_3699
brc_m013_3700brc_m013_3701..brc_m013_3702brc_m013_3703..brc_m013_3704brc_m013_3705..brc_m013_3712brc_m013_3713brc_m013_3714..brc_m013_3716brc_m013_3717..brc_m013_3724brc_m013_3725..brc_m013_3730brc_m013_3731..brc_m013_3752brc_m013_3753..brc_m013_3758brc_m013_3759..brc_m013_3789brc_m013_3790..brc_m013_3801brc_m013_3802..brc_m013_3814brc_m013_3815..brc_m013_3818brc_m013_3819..brc_m013_3822brc_m013_3823..brc_m013_3826brc_m013_3827..brc_m013_3832brc_m013_3833..brc_m013_3837brc_m013_3838brc_m013_3839..brc_m013_3841brc_m013_3842..brc_m013_3847
brc_m013_3848..brc_m013_3853brc_m013_3854..brc_m013_3858brc_m013_3859..brc_m013_3868brc_m013_3869..brc_m013_3871brc_m013_3872..brc_m013_3901brc_m013_3902brc_m013_3903..brc_m013_3909brc_m013_3910brc_m013_3911..brc_m013_3926brc_m013_3927..brc_m013_3931brc_m013_3932..brc_m013_3948
0
20
40
60
80
LG12
brc_m013_3949..brc_m013_3952brc_m013_3953..brc_m013_3958brc_m013_3959..brc_m013_3970brc_m013_3971
brc_m013_3972..brc_m013_3975brc_m013_3976
brc_m013_3977..brc_m013_3985
brc_m013_3986brc_m013_3987..brc_m013_3994brc_m013_3995..brc_m013_3997brc_m013_3998..brc_m013_4004
brc_m013_4005..brc_m013_4006brc_m013_4007..brc_m013_4008brc_m013_4009..brc_m013_4010brc_m013_4011..brc_m013_4013brc_m013_4014brc_m013_4015brc_m013_4016..brc_m013_4019brc_m013_4020..brc_m013_4021brc_m013_4022..brc_m013_4025brc_m013_4026..brc_m013_4032brc_m013_4033..brc_m013_4036brc_m013_4037..brc_m013_4041brc_m013_4042..brc_m013_4043
brc_m013_4044..brc_m013_4046brc_m013_4047..brc_m013_4056brc_m013_4057brc_m013_4058..brc_m013_4063brc_m013_4064..brc_m013_4071brc_m013_4072..brc_m013_4075brc_m013_4076brc_m013_4077brc_m013_4078..brc_m013_4085brc_m013_4086..brc_m013_4089brc_m013_4090..brc_m013_4091brc_m013_4092..brc_m013_4093brc_m013_4094..brc_m013_4095brc_m013_4096..brc_m013_4114brc_m013_4115..brc_m013_4117brc_m013_4118..brc_m013_4131brc_m013_4132..brc_m013_4133brc_m013_4134..brc_m013_4146
0
20
40
60
80
LG13
brc_m013_4147..brc_m013_4150brc_m013_4151..brc_m013_4167
brc_m013_4168brc_m013_4169
brc_m013_4170brc_m013_4171..brc_m013_4172brc_m013_4173..brc_m013_4175brc_m013_4176brc_m013_4177..brc_m013_4178brc_m013_4179..brc_m013_4183brc_m013_4184..brc_m013_4185brc_m013_4186..brc_m013_4187brc_m013_4188..brc_m013_4191brc_m013_4192brc_m013_4193..brc_m013_4194brc_m013_4195..brc_m013_4206brc_m013_4207..brc_m013_4210brc_m013_4211..brc_m013_4213brc_m013_4214brc_m013_4215..brc_m013_4217brc_m013_4218..brc_m013_4221brc_m013_4222..brc_m013_4223brc_m013_4224..brc_m013_4231brc_m013_4232..brc_m013_4234brc_m013_4235..brc_m013_4239brc_m013_4240..brc_m013_4246brc_m013_4247..brc_m013_4248brc_m013_4249..brc_m013_4258brc_m013_4259..brc_m013_4260brc_m013_4261..brc_m013_4269brc_m013_4270..brc_m013_4271brc_m013_4272..brc_m013_4278brc_m013_4279..brc_m013_4280brc_m013_4281..brc_m013_4284brc_m013_4285brc_m013_4286..brc_m013_4288brc_m013_4289..brc_m013_4294brc_m013_4295..brc_m013_4296brc_m013_4297..brc_m013_4301brc_m013_4302..brc_m013_4313brc_m013_4314..brc_m013_4320brc_m013_4321..brc_m013_4322brc_m013_4323..brc_m013_4345brc_m013_4346..brc_m013_4351
0
20
40
60
LG14brc_m013_4352..brc_m013_4366brc_m013_4367brc_m013_4368brc_m013_4369..brc_m013_4373brc_m013_4374..brc_m013_4381brc_m013_4382..brc_m013_4383brc_m013_4384..brc_m013_4385brc_m013_4386brc_m013_4387..brc_m013_4388brc_m013_4389brc_m013_4390..brc_m013_4404brc_m013_4405brc_m013_4406..brc_m013_4409brc_m013_4410..brc_m013_4411brc_m013_4412..brc_m013_4418brc_m013_4419..brc_m013_4434brc_m013_4435..brc_m013_4442brc_m013_4443..brc_m013_4448brc_m013_4449..brc_m013_4451brc_m013_4452..brc_m013_4461brc_m013_4462..brc_m013_4471brc_m013_4472..brc_m013_4475brc_m013_4476..brc_m013_4477brc_m013_4478brc_m013_4479brc_m013_4480..brc_m013_4485brc_m013_4486brc_m013_4487..brc_m013_4491brc_m013_4492brc_m013_4493brc_m013_4494..brc_m013_4495brc_m013_4496..brc_m013_4501brc_m013_4502..brc_m013_4510brc_m013_4511..brc_m013_4531brc_m013_4532brc_m013_4533..brc_m013_4534brc_m013_4535..brc_m013_4541brc_m013_4542..brc_m013_4543brc_m013_4544..brc_m013_4545brc_m013_4546..brc_m013_4548brc_m013_4549..brc_m013_4551brc_m013_4552..brc_m013_4555brc_m013_4556..brc_m013_4561
0
20
40
60
LG15
brc_m013_4562..brc_m013_4577brc_m013_4578..brc_m013_4594brc_m013_4595..brc_m013_4599brc_m013_4600..brc_m013_4625brc_m013_4626..brc_m013_4638brc_m013_4639..brc_m013_4642brc_m013_4643..brc_m013_4644brc_m013_4645..brc_m013_4650brc_m013_4651..brc_m013_4663brc_m013_4664..brc_m013_4668brc_m013_4669..brc_m013_4670brc_m013_4671..brc_m013_4674brc_m013_4675..brc_m013_4679brc_m013_4680..brc_m013_4681brc_m013_4682brc_m013_4683..brc_m013_4688brc_m013_4689..brc_m013_4692brc_m013_4693..brc_m013_4695brc_m013_4696..brc_m013_4701brc_m013_4702brc_m013_4703..brc_m013_4712brc_m013_4713..brc_m013_4717brc_m013_4718..brc_m013_4720brc_m013_4721brc_m013_4722..brc_m013_4726brc_m013_4727..brc_m013_4728brc_m013_4729..brc_m013_4742brc_m013_4743brc_m013_4744..brc_m013_4746brc_m013_4747brc_m013_4748..brc_m013_4749brc_m013_4750..brc_m013_4752
brc_m013_4753..brc_m013_4756brc_m013_4757..brc_m013_4759brc_m013_4760..brc_m013_4762brc_m013_4763brc_m013_4764..brc_m013_4766brc_m013_4767..brc_m013_4769brc_m013_4770brc_m013_4771..brc_m013_4774brc_m013_4775..brc_m013_4776brc_m013_4777..brc_m013_4778brc_m013_4779..brc_m013_4780brc_m013_4781..brc_m013_4793brc_m013_4794brc_m013_4795..brc_m013_4798brc_m013_4799..brc_m013_4802brc_m013_4803..brc_m013_4806brc_m013_4807brc_m013_4808..brc_m013_4814brc_m013_4815..brc_m013_4819brc_m013_4820brc_m013_4821brc_m013_4822..brc_m013_4823brc_m013_4824brc_m013_4825..brc_m013_4855brc_m013_4856..brc_m013_4858brc_m013_4859..brc_m013_4863brc_m013_4864..brc_m013_4865brc_m013_4866..brc_m013_4875brc_m013_4876..brc_m013_4881brc_m013_4882..brc_m013_4891brc_m013_4892..brc_m013_4895brc_m013_4896..brc_m013_4911brc_m013_4912..brc_m013_4938brc_m013_4939brc_m013_4940..brc_m013_4957brc_m013_4958..brc_m013_4959brc_m013_4960..brc_m013_4972brc_m013_4973..brc_m013_4981brc_m013_4982..brc_m013_4983
0
20
40
60
80
100
120
LGSB
Gp-9
Figure 1a b
Si_gnF.scaffold00779_nt2778431.7
Si_gnF.scaffold00779_nt1255229Si_gnF.scaffold02684_nt10884.2
Si_gnF.scaffold00779_nt1633919Si_gnF.scaffold00779_nt17842486.5
Si_gnF.scaffold00779_nt3746833Si_gnF.scaffold00779_nt374687927.3Si_gnF.scaffold00779_nt382158728.5
Si_gnF.scaffold00779_nt417489034.2
Si_gnF.scaffold09607_nt698300Si_gnF.scaffold09607_nt69848340.2
Si_gnF.scaffold09758_nt22273252.8
Si_gnF.scaffold05266_nt63430678.4Si_gnF.scaffold05266_nt65952779.7
Si_gnF.scaffold05266_nt733643Si_gnF.scaffold05266_nt75364482.8
Si_gnF.scaffold07090_nt71001087.6
Si_gnF.scaffold07090_nt105177192.7
Si_gnF.scaffold00255_nt314067Si_gnF.scaffold00255_nt40777897.5
Si_gnF.scaffold03404_nt128925Si_gnF.scaffold03404_nt228606Si_gnF.scaffold03404_nt241461
104.4
Si_gnF.scaffold00413_nt676115107.3
Si_gnF.scaffold00413_nt1035856109.6Si_gnF.scaffold01573_nt108462110.8Si_gnF.scaffold01573_nt447618112.1Si_gnF.scaffold00899_nt377419Si_gnF.scaffold00899_nt686574114.4Si_gnF.scaffold00899_nt236146Si_gnF.scaffold00899_nt332715Si_gnF.scaffold00899_nt335756
115.8
Si_gnF.scaffold00469_nt794118.0Si_gnF.scaffold00690_nt229012Si_gnF.scaffold00690_nt415290119.3
Si_gnF.scaffold06914_nt297673125.1
Si_gnF.scaffold01957_nt412242Si_gnF.scaffold02848_nt41846127.6
LGS Bfrom M013
Si_gnF.scaffold00779_nt2778430.0Si_gnF.scaffold00779_nt1255229Si_gnF.scaffold02684_nt10881.2
Si_gnF.scaffold00779_nt1633919Si_gnF.scaffold00779_nt17842486.7
Si_gnF.scaffold00779_nt3746833Si_gnF.scaffold00779_nt3746879Si_gnF.scaffold00779_nt3821587
22.2
Si_gnF.scaffold00779_nt417489029.2
Si_gnF.scaffold09607_nt698300Si_gnF.scaffold09607_nt69848361.9
Si_gnF.scaffold01573_nt10846280.7Si_gnF.scaffold00255_nt314067Si_gnF.scaffold00255_nt407778Si_gnF.scaffold00413_nt1035856Si_gnF.scaffold00413_nt676115Si_gnF.scaffold00469_nt794Si_gnF.scaffold00690_nt229012Si_gnF.scaffold00690_nt415290Si_gnF.scaffold00899_nt236146Si_gnF.scaffold00899_nt332715Si_gnF.scaffold00899_nt335756Si_gnF.scaffold00899_nt377419Si_gnF.scaffold00899_nt686574Si_gnF.scaffold01573_nt447618Si_gnF.scaffold01957_nt412242Si_gnF.scaffold03404_nt128925Si_gnF.scaffold03404_nt228606Si_gnF.scaffold03404_nt241461Si_gnF.scaffold05266_nt634306Si_gnF.scaffold05266_nt659527Si_gnF.scaffold05266_nt733643Si_gnF.scaffold05266_nt753644Si_gnF.scaffold06914_nt297673Si_gnF.scaffold07090_nt1051771Si_gnF.scaffold07090_nt710010Si_gnF.scaffold09758_nt222732
81.8
Si_gnF.scaffold02848_nt4184690.5
LGS B/bfrom P034
Gp-9
Total285 non-recombiningmarkers
No recombination between B and b over 4% of genome: ⅔ of a chromosme!
Sex chromosomes
X Y
Gp-9 B
Gp-9 b
SB Sb
“Social chromosomes”
?
Why non-recombining?
SB
Sb
difficult to detect in sequence alignments
Why non-recombining? Structural differences
Sb SB Gp-9B
genetic map
E3
E17
A22
Gp-9 B male Gp-9 b male Figure 2 a
b Diploid Gp-9 Bb
Sb SB Gp-9B
genetic map
E3
E17
A22
Gp-9 B male Gp-9 b male Figure 2 a
b Diploid Gp-9 Bb
Sb SB Gp-9B
genetic map
E3
E17
A22
Gp-9 B male Gp-9 b male Figure 2 a
b Diploid Gp-9 Bb
Sb SB Gp-9B
genetic map
E3
E17
A22
Gp-9 B male Gp-9 b male Figure 2 a
b Diploid Gp-9 Bb
Why non-recombining? Structural differencesusing Flourescence in situ Hybridization
John Wang @ Taipei
X
ʁ
X X Y
ʂ
Maybe several rearrangements
Predictions: •genes in S are responsible for phenotype?
SBSB SB Sb
Single queen colony Multiple queen colony
Most BB vs Bb gene expression differences map to S
Non-recombing region of S contains 800 genes
polygyne colonies (Table 2 and Table S2; all P,0.05). The 11genes encoding mitochondrial and prefoldin complex (molecularchaperone) proteins were all up-regulated in polygyne comparedto monogyne workers. Increased mitochondrial gene expressionmay reflect increased oxidative metabolism, while increasedprefoldin expression may indicate higher protein synthesis rates,possibly in relation to the relatively smaller size and highermetabolic rates of polygyne workers [42].
The pattern of expression of the six genes in the viral genecategory is consistent with the expectation that differences in socialorganization affect susceptibility to pathogens and parasites. In themonogyne form, there is intense selection against susceptibleinfected individuals during independent colony founding, a stagethat colonies of the polygyne form never display [26]. Accordingly,we found that workers in the polygyne form express moresequences corresponding to viral genes than their counterparts inthe monogyne form, presumably because of relaxed selection andgenerally greater susceptibility in the former (see also [43]). Basedon sequence similarity and correlated expression across ourexperiments, we identified six gene products that likely representthree different viruses, a ssRNA negative-strand (2) virus and twossRNA positive-strand (+) viruses, one of which is the SINV-2 virus[44]. All 20 polygyne study colonies showed evidence of infectionwith at least one virus (mean number of viral types per colony,2.560.67), whereas only three of the 20 monogyne coloniesshowed evidence of infection, in all cases by a single viral type.Finally, the pattern of expression of another socially-regulated
gene, this one encoding a defensin (a class of small proteinantibiotics active against viruses, bacteria, and fungi [45]), also isconsistent with greater selection for resistance in the monogyneform, as this gene was more highly expressed in monogyne thanpolygyne workers.
The numbers of genes differentially expressed in the genotype (39)and social form (91) comparisons are relatively low compared to thenumbers expected based on other published microarray experi-ments. There are several possible explanations for this. First, the useof whole worker bodies as the source of RNA may decrease theprobability of detecting genes whose level of expression varies amongcells or tissues. Second, our comparisons were performed on groupsof workers originating from different colonies, thus adding a colony-level effect to, and thus increasing the total variance in, geneexpression. Finally, workers of alternate genotype or social formapparently exhibit fewer phenotypic differences than queens[20,21,46,47], possibly reflecting the involvement of fewer differen-tially expressed genes in the former caste.
Remarkably, there was almost no overlap between genes whoselevel of expression was influenced by the focal workers’ Gp-9genotypes and genes whose expression was influenced by the socialenvironment, with only one of the 129 differentially expressedgenes appearing in both categories. This demonstrates an almostcomplete decoupling of the direct effects of the genomic regionmarked by Gp-9 and the indirect effects mediated by socialinteractions within colonies. Moreover, there is little indication ofan interaction between these direct and indirect effects; genes
Figure 1. Expression profiles between S. invicta adult workers with the BB and Bb genotypes of Gp-9. Expression profiles for 39differentially expressed genes are depicted (ANOVA, 10% false discovery rate [FDR]). Each row represents data for one gene, and each columnrepresents data for a pool of 7–10 nestmates with the same Gp-9 genotype sampled from each of twenty colonies of each social form. Colonies werecollected from Georgia (2004, checkered peach bar; 2006, solid peach bar) and Louisiana (2006, solid red bar), USA (data from each polygyne colonyare presented in the identical order for the alternate genotype groupings). Expression levels for each gene are depicted relative to the average levelacross all experimental samples (blue, low levels; yellow, high levels). Genes are arranged by hierarchical clustering. See Text S1 and Table S1 forconfirmation of selected gene expression results with quantitative RT-PCR (qRT-PCR).doi:10.1371/journal.pgen.1000127.g001
Gene Expression Patterns for a Social Trait
PLoS Genetics | www.plosgenetics.org 3 July 2008 | Volume 4 | Issue 7 | e1000127
Gene expression: Gp-9 Bb vs BB workers in multiple queen colonies
29 significant genes "are in the SB/Sb region
(p<10-10)
20 of
Similar for BB vs Bb queens; & for B vs b males. Wang et al 2008
Predictions: •genes in S are responsible for phenotype?
•Sb is degenerating?
probably!⟹ directional (antagonistic?) selection?
X
ʁ
X X Y
ʂ
Maybe several rearrangements
SBSB SB Sb
Single queen colony Multiple queen colony
Is Sb degenerating?
99.8% of non-gap sequences are identical
SB
Sb
(Almost) no SB or Sb-specific sequenceActually quite similar to SB:
But clearly: relaxation of purifying selectionSb contains more small repeats
genes seem to be intact in Sb
Introns bigger in Sb than SB
Sb is degenerating: repeats cause bad assembly
[b] vs. [c]: p < 10-4
[a] vs. [c]: p < 10-7
Gp-9B male Gp-9b male
Region:
Genome assembly:
Normally recombiningregions from all 16
linkage groups
Normally recombiningregions from all 16
linkage groups
Sb region without recombination
in Gp-9 Bb queens
SB region without recombination
in Gp-9 Bb queens
Sca
ffold
leng
th (b
p)
0
1,000,000
2,000,000
3,000,000
4,000,000
5,000,000
6,000,000
[a] [a], [b] [a] [c]
SB Sb
Is Sb degenerating?
Sb contains more big repeats ⟹ bad assemblydN/dS bigger in S than rest of the genome
Probably � haploidy = strong purifying selection ⟹ slower degeneration
99.8% of non-gap sequences are identical(Almost) no SB or Sb-specific sequence
Actually quite similar to SB:
But clearly: relaxation of purifying selectionSb contains more small repeats
genes seem to be intact in Sb
Introns bigger in Sb than SB
Age of the region based on dS
0
50
100
150
200
250
0.00 0.05 0.10 0.15 0.20 0.25leafcutterDndsSubset$dS
coun
tleafcutterdS
0
50
100
150
0.00 0.05 0.10 0.15 0.20 0.25subset(dndsdata, gp9linked == TRUE)$dS
coun
t
gp9linkedSolenopsisdS
## Min. 1st Qu. Median Mean 3rd Qu. Max.
## 0.00000 0.08160 0.10300 0.10559 0.12600 0.32190
Richard thinks the mega-dS values are likely not orthologs. WARNING: We still have some leafcutterD-ndsSubset dS > 1 here!!!!
1.3.4 Calculating age using mean based on dS
10000000 * median(subset(dndsdata, gp9linked == TRUE)$dS)/median(leafcutterDndsSubset$dS)
## [1] 330097.09
8000000 * median(subset(dndsdata, gp9linked == TRUE)$dS)/median(leafcutterDndsSubset$dS)
## [1] 264077.67
Richard Nichols says I can use Maximum Likelihood to compare such distributions. See section below.
1.3.5 Calculating age based on dN
What do my dN distributions look like?
multiplot(qplot(x = subset(leafcutterDndsSubset, dN < 0.1)$dN, binwidth = 0.002, main = "leafcutterdNs"), qplot(x = subset(dndsdata,
gp9linked == TRUE & dN < 0.1)$dN, binwidth = 0.0005, main = "gp9linkedSolenopsisdNs"), cols = 1)
3
0
50
100
150
200
250
0.00 0.05 0.10 0.15 0.20 0.25leafcutterDndsSubset$dS
coun
tleafcutterdS
0
50
100
150
0.00 0.05 0.10 0.15 0.20 0.25subset(dndsdata, gp9linked == TRUE)$dS
coun
t
gp9linkedSolenopsisdS
## Min. 1st Qu. Median Mean 3rd Qu. Max.
## 0.00000 0.08160 0.10300 0.10559 0.12600 0.32190
Richard thinks the mega-dS values are likely not orthologs. WARNING: We still have some leafcutterD-ndsSubset dS > 1 here!!!!
1.3.4 Calculating age using mean based on dS
10000000 * median(subset(dndsdata, gp9linked == TRUE)$dS)/median(leafcutterDndsSubset$dS)
## [1] 330097.09
8000000 * median(subset(dndsdata, gp9linked == TRUE)$dS)/median(leafcutterDndsSubset$dS)
## [1] 264077.67
Richard Nichols says I can use Maximum Likelihood to compare such distributions. See section below.
1.3.5 Calculating age based on dN
What do my dN distributions look like?
multiplot(qplot(x = subset(leafcutterDndsSubset, dN < 0.1)$dN, binwidth = 0.002, main = "leafcutterdNs"), qplot(x = subset(dndsdata,
gp9linked == TRUE & dN < 0.1)$dN, binwidth = 0.0005, main = "gp9linkedSolenopsisdNs"), cols = 1)
3
Leafcutter common ancestor: 8,000,000-10,000,000 years ago
Maximum Likelihood Estimation of SB/Sb age:280,000-425,000⟹ little time for degeneration
Summary
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•Gp-9 marks ~4% of genome"•social like sex chromosomes: SB is like X; Sb is like Y
some relaxation of purifying selection"but haploid males ➔ strong purifying selection
Structural differences between SB and Sb ➔ no recombination
Ants are cool.
SB and Sb stopped recombining ~400,000 years ago.
genome evolution social evolutionGenerally
Single- vs. Multiple queennessin fire antsin similar independent species
•one or many loci?"•one or many genes?"•convergence?
Social parasitism
Strengths of selection in social evolution
concepts & mechanisms
Medically relevant questionsQueen longevity? Candidate gene studies
VitellogeninSex determination genes
functional testing....
Tools for genomics work on emerging model organisms
Molecular response to social upheaval
AGATCCCCGCTGGGCGAATTCGGCTTAGAGAGGTGGAGTGCAGCCTGGTGCCACGGTGTCGTGTTCGCATTGTTAATTGGCCGGCCGTTtCATTTtCCGTTGCGGCGGCGTAACGTGAGAGACAGCGTAACGGGAAGCGAAACGACACGGCGCGTCGAGCGTGCACAGAGAAGTTGAATTATCGAGGGaGAAAAAGGGCGCGAGGGAGGGGCAGGACGGTCAAACACTGAGAAAGCAGGCAACATCCGCGAACCCGTAAATTAATTAGGGCCAACATAATAGCTGGGAATGGCTGGTAGTGGTGGTTCGTCTTCGTGGTCCAGCTTGCGGTTCCCGAGTGCCCTCGCAGTTCGCGCGGTCATGCCTCGGAAACTACACGATACACCTTGCGTCATCCTTACACGAGGATACCTGTTTGCGATCCCCTGAGGTATTAACGAGCGTATAAGCAGACTCAAAGTACGAACACACTGCTAGTTTCGCGTGCATGTTGCTCGTCGCCGTGCAGACGAGTTAGTACTGTCGACAAAGTAGTCGTAAAGTACGTAAGAGTCTTCCTCTAGTAGCGAGGACTAATCTCCCGGTACATTAATCTATGTATATTTTATGATATACACACCTGTATTTATCGAAAGTTTATGTTTATCTCGAAAATTAACGTTAATTTTCGAGGACGCAAAAGCTGTCGCAAGTTTaTTTAATTTTGTTTGtATTTTTTTTTCTTGCTCATTTTTATTTCGAAGTATGCAAATTGAATCTCTTGGTGGCATAACGAGAATTTTCGAAGCTTAAAGGGATCTGCGTTGGCGCGAAGAGAATGGGACTTGTTTTAAACTTTTCTTTCCAACGAACACCGTTTCCTTCATTGTAACGTAAAAATGGTGAGCTTCTGCGGCGCGATTGGTCTCATCTTTCCTCTCGTATCGTTCGTCATTTTGTCCGAGAGCGTGTAGATATTGTACCCGATAGAACGGAGACGGAATCACGCTATACGGTTCCCTCCCAAATGTTCGTTCCTCACGGGCAAAAGTACAAGTAAAAGTAGGAGGGTCCGACTTTATGACCCTACGAGGCACAATAAAGGTTGATGACTACTAAACGTAGAAGAACACGTATACAGTCCGACGTAAAGTTATTTTTCAATTCCGCGGTCCTCCGCCGCAGTCGTTTTGCCTTGACGTGGAAAAGGAAATTTCCCGGGTTCTAGTCGTCCGGTCTTCTTTtCGTTCTACTGACAATACCATAtTTTCGACATAGATCGATCTCCTTTtCTCTTtCTCTCTCTCTCTCTCTCTCTCTCTTGAAAATGAAAGCGCGGAAGAGCCGGATCGTGCAACGCACAATGCGAGGCCGCTTTGTACGAGGTACGAGGAGTCCGTCATGCGCCGTAAAACGCCGGAATATGCAATACTACTTTCGCAGCGACGGGGCTTGCACGAAGTAATATCGTGAAACGTAGAACCGTTCTTTTCATACGGATATGCGGGAGAAGTTGCTCGTCCGCCCTCCGGCGCATACACGTCGCGCGAGAGTATCGTGCATCCGAAACTCTGAGATGAAACTCTTCTGTAGTCGATATTCGTCGCGATAAATAGATAAGTCTCGGATAAGGTAGAGACATCGATAATTCCGTTACGAGAATACTCGAGAATAAGATCCAAGTGAAGTGATCACGCTCCATATGGTTTCAGATTAATCTCCAATCGGCTGACGAAGGAGGATCATCCTTTTACCGGTGGAAAATAGGGTGGATTGGCGGAGCAAGAAGGCTAAACAGAGAATAAACAGGAGCTATAGCCGAACGAGGGAGAAGGTAAGTAGATGCCTCGGAGAACGTGAGCGAAAAAAGGAAACGGGTACGAGAGAAAAAGAAACGGACGGAATAGCGGCTCGGGATTCGCATCCCAAGGAAAACCAAGGCTATACCGGGGTCTTGGATTATTCGAGGCACGACGACGATCTTCGAGTCAGCCGACTGTCTGTACCGTGAAAGTGGCACGTATCGATCGCACGGCTGGATTATCTTCCACTTCGATCTACGACGATTACTTCCGCCATCGTATATCCGGGCTTTGCACTAGCGAGGCTATTTAAAAATCTGCGCTCAGTAACTACTTATGATTTTTCCATCAGAAACGATTGTGGAGAGAAAAGAGGGAAAAAAAGAGATAGACAGCCTCTGGCTCGAAATGCTAATTTCGCAATCGAGAATTAAAATGCACTTCTTTGTATCTAAATTTTCGTAGAATTAAAATAAAATTGAATAAAGCAATGAATAAATTGAATAAACTAAAATATAGCTAAATATTTTTTCCTCTATACAAGGTGAATATAATTATCAAATATTTAAGTATGTAGATTGAATTTAAACAGCCTCGGAAGAGAAAAGAATCGGATAAACGAAATGCTTTTGCCTCTATTTTCAAGCACGTGACGAATAAAATCTAGCAAAGCTTTTCGACACAATATGTCGACGCAAATGTGGTCTATTTTGGCTAATGATTATTACCGGGAGTCCCGGGCACGGTGTGTCCGCGGCGCGATAAATTAGAGCGCGAATCGACTTCCACGGCCGTTGTAGAAGGTACTTTGGCAAACGTTATTTCTTCCTGTCTCGAAGGAAGCGCCACTCGAAAACTTGGAAAAGTTCGGCCAGCTGCACGCACCGCGATCTCGGGTCCGTTCTGGCTCGGTGGCGTGCGCAGGACGGTTGTGAGACGAGAGAAAGAGAGAAAGGAGGATAGAGCGCGAGAGGGAAAGAAGAGGGAACATCCGCGTGCGTGGTTGTATATGGCGTTAATGGCGGCGAGCATAAAGCATCCCCGcGCCTGCACGCTCGACCACGGTCGTTTACAGTGCCACTATTTATGTTGATAACTTCGGAATGGAGTCAGATACACGGTACCGAGTGCCGGCGGTTCGGCGGTGGTCCGGCAGCGGTCTGGTAGCACTTGCAAAGTATGGGAGAAGAAGGGGGATGGTGGATTCGCGGATCTTTTTGGTCGTGCAAGGAAGGCGGGTCGGTTAGGGTAGGTAGAGAGGAGACGAGCCGAGTCGAGAACAAGATTCAAGCGGAAAGTTTTGCGAGTTAATGGTGCGGAGGTAATGCCGCGGCCGCAACAGCAACAGCCATCCCCCTGCTTGTGTGTTCGCTCGCTCGCTCACTtCTTCCGTTCTCTCCTCTTCGCGCTAGTTCTCTCTCTCTCTCTCTCTCTCTCTCTGtCTTTCTTGGAATAGCCGTAGAAAAAaGGAAAAGAAAGAGAGAGAAAGAACGAGACTCCTTTCTCCCCACGAATTCTCTCCTCTCTTTAAGCACACTCTCTCTTCCTGCaccCCCCCCCcTCcTCTCTCTCTCTTTCTCTCTCTATTTTCTTGTCTTCCTCACTTGCATCATCCCTCGTCCATTTCCcTCTGGAGAACGTGCCACGTTCTCACTTCCTCGTTCGTCGCTACTTTTTTTCTTCTTTAGTTGTCTCCTCTCACACCCTCGAGACGGCCCGATCTTTTCCTCGTACAGCTCCTATCACGAACAGTCGCTAACAAGTGCATCGAATGCAAGTTGCCGACAAACTTCTTCCACCGATTTGTGCTTGTTCTCTGTGCATGCGCGGGCATGTATATCTCTATTAGGCGACATCTGCTCTCAGCTTTTTCATAACGAGGTAGCGCGGATTCGCGCTCCGAGAGACTTCACGAAGCACTTCCGATCTCGCTACAGTAGAATGCGTATTGTATTTTCTTGTCTCTCTCATTTACTCTTTTCTATCTTTCGTATCTAGCGTGAATACTCCCATGAGGAATGTAGAAACCAGATTTTGAAACGGCTTCTTCGTATCTAAATTTTCTTAACTATTTGTTCCTCAAAGTCCATTTTGACGTTATAAATTTTTATTTTTTAATGAGAATGTTTTTATGTGGAGAAGAAAAGTACAACTTTTTTCAAAATGCAATTAAATTTATACAAGACTACTAAGATAAAAAAAGATGCAAATAATAATGTTCAACTTACTAACTGCTATATTATTAAGGCCAAGTTAAATTACAGATTTATGATGTTGCAGAATATAATAGAAAAGTTTCAAGAAAAAAaCATTTTAAAGCTTAAAGAGTTTGTTTTCAAACCCATCAAATTTTTTtCTCTGGCAGTGCTGCTGCTCTGCGACGTCATTTTCAAGTCGATCAATGCAAAGTTAACAAAAGTATTTCAACTTTAAAATCATGCAGAAAGTTGGGAAAAATTTGTTTTCAATTTTACTTAAATTTTAGTTACATTTTTTCTAAAAGCTTAAAATCTCCTCTTTAAAATATGTCTTTAAAAATTGAGCTATGATTTTTCTTCACCGAGTTATCGTAATTTGAAATGGCCAATCGACGTTTTCTTTTCATCACTAGGAATAATGCCGGCGGATTTAAGCTTTCAGAAGATTCCAAGCAAAGTTGAAAACAATTTGTTTGAATTCCGCATGATCTCAAAGTTGAAGCTAAAAAAATTTCACAAGACTTTAAAAGACAAAAAGTCAATGTTGCACAATCGACTTGGAAATAACGCCACTTGGAGCAGAGAAGTATTGCCGAGAAAAAGCTTCGACCGGGTTTGAAAGCAGGATCTATAGGCTTCCAAACTTTTTTTTtGAAAAATGGAGCTTTAAGGTTACTTTTCACGAAATTGTATAAATTGTGTTTTGTTGtTTTTATCATCGATTCGAAATGATCCTTTCATTTTGTTCAAGAATGTATCATTAACTTAATGCAATGATATCTTTTAATAATTCAATACTTCTTACTAATTAGATTTAGAAAAGTTTCATGAACAATTTTAGAACGGTTATTGCTAATTATTCGCCAAAAACAGACGCCTTTCTTCGAGGAGTAACAACTCAAGCTGCATTCGCGGTTGACGGCTTTCCGCGGCGCGTCGCGGTAATATGGCTCCTATTTAATTACCCGGTCCTTTGGGAGCTTAAACCAGCCAGAGCTGGAACGGCTGCGCCGTTATTCTATCTAGACTCCTTTGCTTTCTCAAGCAGGCGCGCGATCAAACCTTCTCGCATAAAAGACAATCGCAGCTGGCAGTCGACGACGCGcGGGACAGTCGAATCATGACCCGCTCCTCTCTAGTTACCGCCGTCAGTCTGCTCTACTTCCAGACGCCGCGCGTAATCTATTCGACATTAGTTGCTTGATTGCACCGTAAAATGCGACGGCGACGTGAACGAGAACGACGACGACGACGACGACGACGACAACGACGACGACAATGACAACGACGACGACGACAAGAGTGGGTTCGTCGGTGCTCGATGGCGCCTCCGATTTCAACCGCAGCACGATGCAAGCCCATTACTATCGCCCGGAGCTAAACGGCACCCGGAGCTCGTGCCATTAAGGGAATCTAGGGTCCGATCCACCTCATTGAATTCCGTTcAATTGCGATTATGATAATGCGTGAACGATCGCCGTGGACGTGAGCTACGGaCAACgAGGGTGTTCGTTCTCGGCTCAGAGAAACGCAGCGATAAAATTATCAGTGACAGCTTCATTTTTGTTACATTTGACGTTGAAAAATTTGCGAAAGAAATGTGCATTATTCAACTACATTGACAATTGTAAATCTTACATGACCTTTTATTAATATACATATATGTAAGATATATGTTCCATCTCTAGTCTCGTTCGATAATGAAGAAATTATAGCTGCAACATAGACGCCGGATTATTCGCGGGGGAAACCGTTGATTATTTGGACTCCGTGGGCTCGGGGTCTGGTTTACTTCTTCCCTTATGTCCGGAGATAATGGACACTATTACCTTAACGAGGCCCCAGTCTCTTAGCCGGTAATTGCTTCGAGATATCCGAGAGAGCTCCGGCGTACGTTGCCGCCTGGTGTTGCAGGCAGAGAACCCaGACGGTATTATTGCCGCCGAGGCTACTCGCCCGTTTCATGGTGGTTATTGTTATGGGCCTGCGGCATTAAGATGTACACCGCACTCTCATACGGGACCCACCACCCCATATACGAGCTGCATATATACTTATGCGGGGAGGATTTCATTACGCCGCTTCATAACTGGCGGTCTTCAAAATCGCGATAAATCGGGATTGTCTTCCTTGTTAAATCAGCTCCCGTTCCCCTTCCTCATATCGCTGACGAAGCCAACGAGACGGATTAATCTGCGCGATTGAATGGCCTCTATGACGTAAGCGCACCGTTTACTGGCACGGCTCCTCGTGTTCACGTGAAACGATTTGCGTCGTAAATATTTTATTTTAACATCGCAACATCAAGACAGACGAGGATCGGCTATTGCCTCGTGATCCTAAAAGGGAGATTCTCAAGGCGGAATCGGGGTAACGCGTTCGTTGATCTCGCCAAACTACGGCATCTTGAGGACTAGTCTTAGaGGAAAAAAAGACGACGAGGAGACACGGTGAGCATTAGATGAGAAAGAGACGGCGCGGCGCGGTGCGGCGGAGCGAGACGGAAAGAGATCAAATCTGGATATCAGGATTAGGGTGGGTACGTAATCCGCAGGACGACGGGTGGTAGGAACGGTGGATCCGTCGGCAGATCTCATCGCGCGGAGGAACTCTGCGGGTACTTCGCCCGGCCAAATACGACAAGAGCAGCAGCCTAACTCGAGTAGAGCCGCCGAGATGGTTTACGGCTCGTCGCAAGTTGGTGAAATTTAAGAGCGCATTTAAAACTGGTTTGGCGCGATGCCCTGCGCCTCCCTGCAGCAGGTACTGCCGGCGAGAGATACCGCTGGGCTCCGACAGGAGTTTATCGCCCTAACATTCTTGGAAAGCTTCGGATGGATTTCCCTCCTCAACCCATTTCTTCCGGCAGCACCTCAAATCGTCGCTTCTTTCGAGCTCCCTGTGTCGTCCGTTCTTTCCCCTTGCCACGAAAATTCTTCCAACAGACTCGACACCAAATCGTCACGACGATCATCGGTCAAGATACCCGGAGAAACGTCGCGGACGATGTTACCGTCAGATCGGACGCTTTTAGCTCCGCATTGGAGCTTTTTCCTCGACCGTCTCGGAGGAGATTTAGCGGACCGACAACAAATGAAGGTCATCTTTCGCGCGAGAAAGCGTCTCACCTTGATTTCCGTCTCGTTTCTCCGGAAATTGGATATCAACCGGACGAACTGTAATGTGTACGTTAAATTGCCAATTATATATATAATGTAACAGCTGATTATCTCAAGTGTCCTAAAAACCATTATACTCTTAATTTCTGTGAAAAATGGCGAAAATAAAAAAGAAACCGATCTTAATAAAGATATTCTTCCTGATAGATGCCATGACCCACGTGGAAAACTTTTTAGTTTTGTACAGTGGTATTATACGTTATCTTCCGCTGAACGTAAGACGTGCCTATCGCGCAATTTCATCGCGACGTCGTCGTATAGCGATTATGGCTACTCCATTAAAAATGAATTTTATAAAGGCAATCTTTCCAAGCGATCGTTGTAGGAGAAAAAGGCGAAAGCCGGAGCCAAAGGGGATGAGGCCACTACCTTTGGCTGATCCACTTCGAATGATAATCACCTCTAGGAGACTCAATTTCGCCCTGCTCCGCGTCCTTACCCGTTCCTATCTTCGGAAGGTTCAACGCCGCAGCGGACTGCATCTTTCACTCCCTTCGTCACCACCGCCCTATTCCTATCGCCCTCCGCGCGCCTACCGCCCCTATATCCTTCCCTTCCTTCACtCCTAGACTATTCTGAACGACCTCTTCCCCCATTCGCCAACGCTCACTCCTAACTGATTGGAGTACCAATCAATGCGGCATTCAGGCGGCCGTGCTGAAaCTTTAGGAAATTAACTATTCACTCTCTGGAAATGGTTATTTGGAAGGCCGGAAAGGCAGTCGGGACTACGTTACGGAGAATATGAGCGAAAGGATATGGGCAGACGATGACGATAGATAAGACAGTTCAATTTTCAATTAGGCGTGGACGTAGCGCGCGTAGCTCGGCTCCTACCACGATGCTTACCACGCGTCCCATACGTTAGGAGGAATCCGA
But making it useable is hard.
Sequencing a genome is now cheap & easy.
Tools for genomics work on emerging model organisms
Antgenomes.org Sequenceserver.com: "BLAST made easy
1: identifying sequences.
Gene predictionDozens of software algorithms: dozens of predictions
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. Ya
ndell
& E
nce
2013
NRG
GTCTACAATGCGATTGTAAAATAGCACGAgAGGTGCATATGATGAACGACTATGTTCCACAACCACAGCTCATATATAACATGATTTtGTTTGCCGAATTCATACACGCATTACAACACACATTGAATTCAATAATAATATCAAATTCACATTCAAAGCTTTCAAGTTAGACAAAAGTTTTAATGCCGTTTTtACCTGTTTTtGAAAAGGTAATTTTCTTTAGATATATACAGTTTGTAATaTTAGGTATTTTATAAACAGTGTGTATATTTCTTACAATATAAAAGACACAATTGCAAACTAGCATGATTGTAAACAATTGCTAAACGGATCAATATAAATTAAAATTGTAATATTAAGTATCAAACCGATAATTTTTATTTATTGTTCATTGTTTGTTCTTTATTTTGTTATTTGTAAATAATGAAA
Evidence
Evidence
Consensus:
Monica Dragan https://github.com/monicadragan/GeneValidator
2.
Monica Dragan https://github.com/monicadragan/GeneValidator
2.
Gene predictionDozens of software algorithms: dozens of predictions
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. Ya
ndell
& E
nce
2013
NRG
GTCTACAATGCGATTGTAAAATAGCACGAgAGGTGCATATGATGAACGACTATGTTCCACAACCACAGCTCATATATAACATGATTTtGTTTGCCGAATTCATACACGCATTACAACACACATTGAATTCAATAATAATATCAAATTCACATTCAAAGCTTTCAAGTTAGACAAAAGTTTTAATGCCGTTTTtACCTGTTTTtGAAAAGGTAATTTTCTTTAGATATATACAGTTTGTAATaTTAGGTATTTTATAAACAGTGTGTATATTTCTTACAATATAAAAGACACAATTGCAAACTAGCATGATTGTAAACAATTGCTAAACGGATCAATATAAATTAAAATTGTAATATTAAGTATCAAACCGATAATTTTTATTTATTGTTCATTGTTTGTTCTTTATTTTGTTATTTGTAAATAATGAAA
Evidence
Consensus:
Begin
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Being curated
Curate
Being curated
Curate
Being curated
Curate
Submit Submit Submit
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http://afra.sbcs.qmul.ac.ukAnurag Priyam
3. Crowd-sourcing inspection & correction of gene predictions Scientific software + Facebook + Points + Badges + Redundancy
Ecology & Evolution & Vital-IT @ LausanneEvolve & Psych @ Queen Mary
LAURENT KELLER JOHN WANG DEWAYNE SHOEMAKER OKSANA RIBA-GROGNUZ MINGKWAN NIPITWATTANAPHON !
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
Anurag Priyam & Monica Dragan