19. Animal biomass (Brazilian rainforest)
Mammals
Birds
Reptiles
Other insects Amphibians
from Fittkau & Klinge 1973
!
Earthworms
!
!
Spiders
Soil fauna excluding
earthworms,
ants & termites
Ants & termites
20. We use modern technologies to
understand insect societies.
• evolution of social behaviour
• molecules involved in social behaviour
• consequences of environmental change
21. Major transitions:
eusociality
• Solitary lifestyle --> Eusociality
1. Reproductive division of labor
2. Overlapping generations (older
offspring help younger offspring)
3. Cooperative care of young
Eg: ants, bees, wasps, termites. But also:
naked mole rats, a beetle, a shrimp...
26. Major transitions: eusociality !
Hamilton’s rule: genes for altruistic behavior increase in frequency when:
r ₒ > C
indirect fitness benefits to the receiver (B) ,
reduced by the coefficient of relatedness (r)
Hamilton, 1964
B
between altruist & receiver,
exceeds costs to the altruist (C).
General framework: Kin selection: can favor the reproductive success of
an organism's relatives (ie. indirect fitness), even at a cost to the
organism's own survival and reproduction.
27.
28.
29. Downloaded from www.sciencemag.org on March 12, 2013 Solenopsis invicta fire ants are
REPORTS
a big problem!
very well studied!
Ascunce et al 2011
30. Solenopsis invicta fire ant:
two social forms
Single-queen form: Multiple-queen form:
!
•1 large queen
•Independent founding
•Highly territorial
•Many sizes of workers
!
•2-100 smaller queens
•Dependent founding
•No inter-colony
aggression
•All workers similar size
32. Allozyme screen Social form associated to Gp-9 locus
Frequency of
the most
common allele!
Ddh-1!
Pro-5!
Locus!
1.0!
0.9!
0.8!
0.7!
0.6!
0.5!
0.4!
0.3!
Single queen!
Multiple queen!
Est-4!
G3pdh-1! Ca-4!
Est-6!
Pgm-4!
Acy-1!
Pgm-1!
acoh-1!
Pgm-3!
Acoh-5!
Aat-2!
Gp-9!
Ken Ross and colleagues
Laurent Keller and colleagues
33. Social form completely associated to Gp-9 locus
Single queen form Multiple queen form
Ken Ross and colleagues
Laurent Keller and colleagues
34. Social form completely associated to Gp-9 locus
Single queen form Multiple queen form
BB BB Bb bb
Ken Ross and colleagues
Laurent Keller and colleagues
35. Social form completely associated to Gp-9 locus
Single queen form Multiple queen form
x
BB BB Bb bb
Gp-9 bb females rare
Ken Ross and colleagues
Laurent Keller and colleagues
36. Social form completely associated to Gp-9 locus
Single queen form Multiple queen form
BB BB Bb
Ken Ross and colleagues
Laurent Keller and colleagues
37. Social form completely associated to Gp-9 locus
Single queen form Multiple queen form
BB BB Bb
x
Ken Ross and colleagues
Laurent Keller and colleagues
38. Social form completely associated to Gp-9 locus
Single queen form Multiple queen form
BB BB Bb
x x
Ken Ross and colleagues
Laurent Keller and colleagues
39. Social form completely associated to Gp-9 locus
Single queen form Multiple queen form
(< 5% ) (>15% )
BB BB Bb
x x x
Ken Ross and colleagues
Laurent Keller and colleagues
41. Social form completely associated to Gp-9 locus
•Is this gene the single überregulator?
•Only 14 allozyme markers were used
maybe 1/14th of the genome?
Ddh-1!
Pro-5!
Locus!
1.0!
0.9!
0.8!
0.7!
0.6!
0.5!
0.4!
0.3!
Single queen!
Multiple queen!
Est-4!
G3pdh-1! Ca-4!
Est-6!
Pgm-4!
Acy-1!
Pgm-1!
acoh-1!
Pgm-3!
Acoh-5!
Aat-2!
Gp-9!
42. This changes
454 everything.
Illumina
Solid...
Any lab can
sequence anything!
43.
44. Are other genes linked to Gp-9?
Sequenced:
•a Gp-9 B ♂ genome
!
!
45. The genome of a Gp-9 B ♂ fire ant
Sequencing from haploid males (for easier assembly):
Single ♂:
His brothers:
45× (330bp-insert paired reads) + (normal single-end reads)
B 20x
11×
4×
(8,000 & 20,000bp-insert paired reads)
46.
47. The genome of a Gp-9 B ♂ fire ant
Sequencing from haploid males (for easier assembly):
Single ♂:
His brothers:
45× (330bp-insert paired reads) + (normal single-end reads)
B 20x
11×
4×
(8,000 & 20,000bp-insert paired reads)
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
→ Total: 350,000,000 bp assembled. The rest: repeats
10,000 scaffolds (100 biggest scaffolds: 50% of genome)
Wurm et al 2011
50. Lepidoptera 29
The genome of the fire ant
Some findings:
Diptera 404
Paraneoptera 577
Arachnida 50
Deuterostomia 173
Cnidaria 100
Not assigned 274
★ Expansion of lipid-processing gene families (for Cuticular Hydrocarbons)
3
SiOR03038
SiOR04609+SiOR06843+420 putative olfactory receptors 1 1
SiOR06723+12
★ SiOR04648+(more than any other insect!)
SiOR00899+6 ★ Functional DNA-methylation system
SiOR02694+4
★Ant-specific duplication and subfunctionalization
of vitellogenin (in bees: involved in reproduction & division of labor)
SiOR00899+8 SiOR04648+7
SiOR04648+6
SiOR04171+17
SiOR04171+29
SiOR04171+14
SiOR00330+14SiOR02694+38 SiOR04609+8
SiOR04609+5
SiOR01321
SiOR04609+19
SiOR00899+12 SiOR05901+1
SiOR04171+3
12 SiOR01224+SiOR04510+SiOR04510+16 13
SiOR04171+25 SiOR06577
SiOR04171+24
SiOR01629+3 SiOR01968+26
SiOR04171+21 SiOR06792+6
SiOR02883+2
SiOR05431+SiOR01858+1 1
SiOR05431+4
SiOR04510+7 SiOR01968+21
SiOR05431+3 SiOR04510+6
SiOR01629+1
SiOR01968+7 SiOR01629+6
SiOR05285+2
SiOR03663
SiOR00899+13
Wurm et al 2011
significance of these duplication events in vitellogenins, odor
perception genes, and a family of lipid-processing genes. We also
discuss additional features of interest in the fire ant genome rel-evant
to the complex social biology of this species, including sex
determination genes, DNA methylation genes, telomerase, and
the insulin and juvenile hormone pathways.
Vitellogenins. In contrast to other insects that mainly have only one
or two vitellogenins, the fire ant genome harbors four adjacent
regulation of life span (27, 28) and division of labor (29). Quanti-tative
RT-PCRshows that Vg1 and Vg4 are preferentially expressed
in workers and Vg2 and Vg3 in queens (Fig. 3C, SI Materials and
Methods, and Table S1G). Vitellogenin expression in S. invicta
workers is surprising because they lack ovaries. Given the super-organism
properties of ant societies, the expression patterns sug-gest
that vitellogenins underwent neo- or subfunctionalization
after duplication to acquire caste-specific functions.
Odor Perception. Consistent with studies in other insects, we find
a single S. invicta ortholog to DmOr83b, a broadly expressed ol-factory
receptor (OR) required to interact with other ORs for
Drosophila and Tribolium castaneum olfaction (30–32). Beyond
OR83b, OR number varies greatly between insect species. Blast
searches and GeneWise searches using an HMM profile con-structed
with aligned ORs from N. vitripennis (33) and Pogono-myrmex
barbatus identified more than 400 loci in the S. invicta
genome with significant sequence similarity to ORs. Preliminary
work on gene model reconstruction identified 297 intact full-length
proteins. Many S. invicta ORs are in tandem arrays (Fig.
S2A) and derive from recent expansions. S. invicta may thus har-bor
the largest identified insect OR repertoire because there are
10 ORs in Pediculus humanus (34), 60 in Drosophila, 165 in
A. mellifera, 225 in N. vitripennis (33), and 259 in T. castaneum
(32). The large numbers of N. vitripennis and T. castaneum ORs
are thought to be due to current or past difficulties in host and
food finding. As has been suggested for A. mellifera (35), the large
number of S. invicta ORs may result from the importance of
chemical communication in ants. The odorant-binding proteins
(OBPs) are another family of genes also known to play roles in
chemosensation in Drosophila (36). Intriguingly, the social orga-nization
of S. invicta colonies is completely associated with se-
Eumetazoa
No hits 3424
Coelomata
Bilateria
Nematoda 25
Fig. 2. Taxonomic distribution of best blastp hits of S. invicta proteins to the
nonredundant (nr) protein database (E < 10−5). Results were first plotted
using MEGAN software (22) and then branches with fewer than 20 hits were
removed, branch lengths were reduced for compactness, and tree topology
was adjusted to reflect consensus phylogenies (23, 24).
2,330,000 bp 2,360,000 bp A
Vg4 Vg1 Vg3 Vg2
B Solenopsis Vg1 C
Solenopsis Vg4
Solenopsis Vg2
Solenopsis Vg3
Apis Vg
Bombus Vg
Nasonia Vg1
Pteromalus Vg
Nasonia Vg2
Encarsia Vg
Pimpla Vg
Athalia Vg
Apocrita
Tenthedinoidea
Vespoidea
Apoidea
Aculeata
Chalcidoidea
25000 Vg2 Vg3
20000
15000
10000
5000
Vg1 Vg4
* ***
600
500
400
300
200
100
Ichneumonoidea 0
*** ***
Q W Q W Q W Q W
142 389 1 40 17820 1.4 9269 0.6
0
EVOLUTION
0.05
SiOR04648+10
SiOR01968+4
SiOR00899+7
SiOR02814+3
SiOR04171+6
SiOR04609+4
SiOR00330+28
SiOR02694+25
SiOR04609+20
SiOR05285+6
25
SiOR04510+15
SiOR00330+18 SiOR04609+23
SiOR01968+23
SiOR03952+4
SiOR04648+16
SiOR05901+2
SiOR02944+4
SiOR01968+5
SiOR04171+19SiOR04648+5
SiOR10535+3
SiOR06723+2
SiOR01968+9
SiOR02883+1
SiOR00899+3
SiOR04171+1
SiOR01629+11
SiOR04171+10
SiOR04171+13
SiOR02694+3
SiOR04171+20
SiOR02694+35
SiOR04171+15
SiOR04609+7
SiOR05118+2
SiOR07837+2
SiOR02694+27
SiOR01968+10
SiOR04648+17
SiOR01968+19
SiOR02694+17
13
SiOR01968+6
SiOR00330+20
SiOR02648+2
SiOR02659+2
SiOR01968+16
SiOR00899+11
SiOR02974
SiOR04171+2
SiOR03952+2
SiOR06792+2
SiOR04510+4
SiOR04171+28
SiOR05285+5
SiOR05285+9 SiOR00899+15 SiOR04648+3
SiOR02694+36
SiOR10535+1
SiOR02694+19
SiOR02694+23
SiOR02694+1
SiOR04609+14
SiOR01122
9
SiOR02694+34
SiOR01629+8
SiOR04648+8
SiOR04510+8
SiOR06573
SiOR02944+1
26
SiOR00330+1
SiOR02694+15
SiOR05285+7
SiOR00899+5
SiOR04609+10
SiOR04609+3 SiOR04339
SiOR08068
SiOR04510+2
SiOR05285+8
SiOR01573+4
SiOR04171+8
SiOR01858+2 SiOR01968+2
SiOR01968+1
SiOR02694+5
SiOR01968+3
SiOR06723+3
SiOR01968+15
SiOR05285+1
SiOR00899+4
SiOR04609+22
SiOR04171+9
SiOR02694+9 SiOR02648+1
SiOR06792+3
SiOR01573+2
SiOR02694+20
SiOR10542
SiOR04609+15
SiOR02694+8
SiOR00330+16
SiOR00899+2
SiOR02694+10
SiOR04510+9
SiOR05285+3
SiOR04609+2
SiOR05285+11 SiOR02694+14
SiOR01573+1
SiOR00613
SiOR01968+22
SiOR00899+9
SiOR06843+2
SiOR02694+37
SiOR00899+1
SiOR04609+9
SiOR05431+2 SiOR10535+2
SiOR00330+15
SiOR02694+18
SiOR01224+2
SiOR04510+11
SiOR00330+23
SiOR02694+29
SiOR05416
SiOR05285+10 SiOR02694+2
SiOR01629+9
SiOR08341 SiOR02694+22
SiOR01224+1
SiOR01968+12
SiOR02694+7
SiOR02944+2
SiOR03952+3
SiOR01968+8
SiOR04609+24
SiOR02694+30
SiOR01629+10
SiOR04510+14
SiOR00565 SiOR05118+3
SiOR04171+16
SiOR10455
SiOR04609+16
SiOR04609+21
SiOR02694+28 SiOR02659+1
SiOR04171+5 SiOR00330+29
SiOR01968+14
SiOR03983
SiOR00330+27
SiOR05285+4
SiOR04510+1
SiOR04609+17 SiOR00330+5
SiOR02694+21
SiOR02814+4
SiOR00330+7
SiOR02694+31
SiOR04648+2
SiOR02694+39
SiOR01968+25
SiOR04609+11
SiOR02694+11
SiOR06792+1
SiOR04171+4
SiOR01629+5
SiOR00330+21
SiOR04648+15
SiOR00330+6
SiOR02694+16
11
SiOR04648+4
SiOR00330+3
SiOR06535
SiOR04171+7
SiOR10493
SiOR02694+32
SiOR06792+4
SiOR04510+3
SiOR06890
SiOR01968+20
SiOR04609+12
SiOR04171+3
SiOR01968+18
SiOR01968+11
SiOR04609+13
SiOR01629+12
SiOR00330+22
SiOR02694+33
SiOR00330+13
SiOR01573+3
SiOR05118+1
SiOR02944+3
SiOR04171+26
SiOR00899+14
SiOR02694+13
SiOR00330+24
SiOR00330+19
SiOR04171+27
SiOR02694+24
SiOR04510+5
SiOR07090
SiOR03952+1
SiOR04510+10
SiOR00330+17
SiOR02694+26
SiOR02814+2
SiOR00330+11
SiOR04171+18
SiOR01968+17
SiOR00330+10
SiOR00330+9
SiOR01629+2
SiOR04171+11
SiOR04510+12
SiOR00330+8
SiOR02694+6
SiOR01968+13
SiOR00330+4 SiOR04609+18
SiOR00899+10
SiOR00330+12
SiOR00330+31
SiOR06843+1
SiOR07837+1
SiOR00330+2
SiOR01629+4
SiOR04648+1
SiOR01968+24
SiOR04171+23
SiOR01629+7 SiOR04648+14
SiOR06792+5
SiOR02883+3
SiOR02694+12
SiOR05118+4
SiOR04171+22
SiOR01080 SiOR04609+6
SiOR02814+1
SiOR00330+30
SiOR05285+12
51. Are other genes linked to Gp-9?
Social form completely associated to Gp-9 locus
Single queen form Multiple queen form
(< 5% ) (>15% )
BB BB Bb
x x x
52. Are other genes linked to Gp-9?
Sequenced:
•a Gp-9 B ♂ genome
!
!
•a Gp-9 b ♂ genome
RAD sequencing
“Next Generation Genotyping.”
53. RAD sequencing
“Next Generation Genotyping.”
Bb
unfertilised eggs
haploid ♂
Gp-9 B Gp-9 b Gp-9 B Gp-9 b Gp-9 b Gp-9 B
38 B♂ & 38 b♂
55. RAD sequencing discovery o&f gheanpolotiydp i♂ng for SNP
EcoR1 EcoR1 EcoR1
Gp-9 B
AACTG
AACTG
AACTG
AACTG
Gp-9 B
56. RAD sequencing discovery o&f gheanpolotiydp i♂ng for SNP
Gp-9 B
AACTG
Gp-9 B
Gp-9 B
GGCCT
Gp-9 B
Gp-9 B
AAGGT
Gp-9 B
Gp-9 b
CCAGT
Gp-9 b
Gp-9 b
TAAAT
Gp-9 b
Gp-9 b
GGAAT
Gp-9 b
38 Gp-9 B
males
38 Gp-9 b
males
57. RADseq: sequencing the same 0.01% of the
genome in many individuals
Identify polymorphism
individual x locus
genotype table
A B C D E F
L1 A C A A C C
L2 G G T - T G
L3 - A G A - G
L4 C - - G G C
L5 T T C T C -
L6 G A A - - G
2419 loci
38 B♂ & 38 b♂
PCA: Principal Component Analysis
Amount of variance explained per principal component
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20+
% Variance Explained
0 5 10 15 20 25 30
12.7%
6.1% 5.4% 4.8% 4.7% 3.9% 3.5% 3.2% 3.1% 2.9% 2.8% 2.6% 2.4% 2.3% 2.2% 2.0% 1.9% 1.7% 1.6%
30.2%
58. Principal Components: PC2 vs PC3
pc: 2 % variance: 6.073
pc: 3 % variance: 5.441
0.2
0.1
0.0
-0.1
-0.2
-0.2 -0.1 0.0 0.1 0.2
Gp-9 B ♂
Gp-9 b ♂
59. Principal Components: PC1 vs PC2
pc: 1 % variance: 12.666
pc: 2 % variance: 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 ♂
63. Why non-recombining? Structural differences
using Flourescence in situ Hybridization
Gp-9B
genetic map
SB Sb
a Gp-9 B male A22
A22
Gp-9 b male
9 B male Gp-9 b male
E17
E3
Gp-9 B male SB Sb
Gp-9B
genetic map
A22
A22
E17
E17
E3
SB Sb
Gp-9B
genetic map
E3
b SB Sb
Gp-9B
genetic map
E17
E3
Gp-9 b male
John Wang @ Taipei
64. X
ʁ
ʂ
X X Y
Single queen colony Multiple queen colony
SB SB SB Sb
Maybe several
rearrangements
Predictions:
•genes in S are responsible for phenotype?
65. Most BB vs Bb gene expression
differences map to S
Non-recombing region of S contains 800 genes
Gene Expression Patterns for a Social Trait
Gene expression: Gp-9 Bb vs BB workers in multiple queen colonies
29 sign i f i c a n t 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
66. ʂ
Single queen colony Multiple queen colony
SB SB SB Sb
Predictions:
•genes in S are responsible for phenotype?
•Sb is degenerating?
probably!
⟹ directional (antagonistic?) selection?
X
ʁ
X X Y
Maybe several
rearrangements
67. Is Sb degenerating?
Actually quite similar to SB:
(Almost) no SB or Sb-specific sequence
99.8% of non-gap sequences are identical
genes seem to be intact in Sb
But clearly: relaxation of purifying selection
Sb contains more small repeats
SB
Sb
Introns bigger in Sb than SB
68. Sb is degenerating:
repeats cause bad assembly
[a] vs. [c]: p < 10-7
[b] vs. [c]: p < 10-4
Gp-9B male Gp-9b male
6,000,000
5,000,000
4,000,000
3,000,000
2,000,000
1,000,000
Region:
Genome assembly:
Normally recombining
regions from all 16
linkage groups
Normally recombining
regions from all 16
linkage groups
Sb region without
recombination
in Gp-9 Bb queens
SB region without
recombination
in Gp-9 Bb queens
Scaffold length (bp)
0
[a] [a], [b] [a] [c]
SB Sb
69. Is Sb degenerating?
(Almost) no SB or Sb-specific sequence
99.8% of non-gap sequences are identical
genes seem to be intact in Sb
Sb contains more big repeats ⟹ bad assembly
dN/dS bigger in S than rest of the genome
Probably ♂ haploidy = strong purifying selection
⟹ slower degeneration
Actually quite similar to SB:
But clearly: relaxation of purifying selection
Sb contains more small repeats
Introns bigger in Sb than SB
70. Age of the region based on dS
250
250
200
200
150
150
100
100
50
50
0
0
leafcutterdS
0.00 0.05 0.10 0.15 0.20 leafcutterDndsSubset$dS
count
leafcutterdS
0.00 0.05 0.10 0.15 0.20 leafcutterDndsSubset$dS
Leafcutter common ancestor: 8,000,000-10,000,000 years ago
150
150
100
count
gp9linkedSolenopsisdS
count
100
0.00 0.05 0.10 0.15 0.20 subset(dndsdata, gp9linked == TRUE)$dS count
50
50
0
0.00 0.05 0.10 0.15 0.20 subset(dndsdata, gp9linked == TRUE)$dS gp9linkedSolenopsisdS
0
Maximum Likelihood Estimation of SB/Sb age:280,000-425,000
⟹ little time for degeneration
## Min. 1st Qu. Median Mean 3rd Qu. Max.
## Min. 1st Qu. Median Mean 3rd Qu. Max.
71. Summary
Ants are cool.
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
Structural differences between SB and Sb ➔ no recombination
SB and Sb stopped recombining ~400,000 years ago.
some relaxation of purifying selection
but haploid males ➔ strong purifying selection
72. Formica selysi
Alpine silver ant
Single vs Multiple-queen colonies
Convergent social chromosome architecture
Purcell et al 2014
J Meunier
73. ≠ social chromosomes
Purcell et al 2014
Solenopsis
invicta social
chromosome
Formica selysi
social
chromosome
75. QMUL lab (Rodrigo, Brunoet al)
Lausanne lab (L KELLER, J
WANG, D SHOEMAKER
ORIBA-GROGNUZ
MINGKWAN NIPITWATTANAPHON
!
Ecology & Evolution & Vital-IT
@ Lausanne
Evolve & Psych @ Queen Mary
y.wurm@qmul.ac.uk
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
76. Research themes
Social evolution
Pollinator health
• Biomedical approaches
• International population genomics surveys
• Monitoring via sequencing
• Responses to environmental challenges
Modern Bioinformatics for Genomics
• Reproducibility
• Accuracy
• Sustainability
• Versioning
• Agile & efficient
data handling
• Major social transitions
» social chromosomes
» convergence
» eusociality, queen number, parasitism...
• 100-fold intra-specific variation in lifespan
• Strengths of selection
• Candidate genes/pathway
77.
78. Gp-9 is an odorant binding protein
Hypothesis: influences queen odor & how workers « smell » queens
Krieger & Ross