2. Blog post authoring
• Decide your groups for authoring
• (must pair with different people than presentation!)
• cannot present and blog as part of same "theme"
• https://etherpad.mozilla.org/obVAlZUq5D
• Editors:
• determine who is responsible for which papers
• alert authors when their stuff is due
• determine who receives which review task when
•Web people need to decide on platform (e.g. tumblr & color
scheme etc), name, potential guidelines, and set up…
3. RAD? CNV? FST? WTF?
• New papers - specific question session
• Next Tuesday 9a.m. (all welcome)
• Additional needed?
• maybe: this Thursday 16:30 - fogg 5.03A
9. 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
10. Social form completely associated to Gp-9 locus
Single queen form Multiple queen form
Ken Ross and colleagues
Laurent Keller and colleagues
11. 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
12. 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
13. 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
14. 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
15. 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
16. 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
20. 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!
21. This changes
454
everything.
Illumina
Solid...
Any lab can
sequence
anything!
22.
23. Are other genes linked to Gp-9?
Sequenced:
•a Gp-9 B ♂ genome
!
!
24. 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)
25.
26. 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
29. Lepidoptera 29
The genome of the fire ant
Some findings:
Diptera 404
Paraneoptera 577
Arachnida 50
Deuterostomia 173
Cnidaria 100
★ Expansion of lipid-processing gene families (for Cuticular Hydrocarbons)
420 putative olfactory receptors 3
SiOR03038
SiOR04609+SiOR06843+1 1
SiOR06723+12
★ (more than any other insect!)
SiOR04648+★ Functional DNA-methylation system
SiOR00899+6 SiOR02694+4
★Ant-specific duplication and subfunctionalization
of vitellogenin (in bees: involved in reproduction & division of labor)
SiOR00899+8 SiOR04648+7
SiOR04648+6
SiOR04171+17
SiOR04171+29
SiOR04171+14
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
Not assigned 274
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
30. 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
31. Are other genes linked to Gp-9?
Sequenced:
•a Gp-9 B ♂ genome
!
!
•a Gp-9 b ♂ genome
RAD sequencing
“Next Generation Genotyping.”
32. 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♂
34. RAD sequencing discovery o&f gheanpolotiydp i♂ng for SNP
EcoR1 EcoR1 EcoR1
Gp-9 B
AACTG
AACTG
AACTG
AACTG
Gp-9 B
35. 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
36. 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%
37. 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 ♂
38. 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 ♂
42. 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
43. 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?
44. 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 fi 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
45. 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
46. 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
Introns bigger in Sb than SB
Sb
47. 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
48. 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
49. 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.
50. 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
51.
52. ARTICLE doi:10.1038/nature13151
Origins and functional evolution of Y
chromosomes across mammals
Diego Cortez1,2, Ray Marin1,2, Deborah Toledo-Flores3, Laure Froidevaux1, Ange´lica Liechti1, Paul D. Waters4, Frank Gru¨tzner3
& Henrik Kaessmann1,2
Ychromosomes underlie sex determination inmammals, but their repeat-rich nature has hampered sequencing and asso-ciated
evolutionary studies. Here we trace Y evolution across 15 representativemammals on the basis of high-throughput
genome and transcriptome sequencing. We uncover three independent sex chromosome originations in mammals and
birds (the outgroup). The original placental and marsupial (therian)Y, containing the sex-determining gene SRY, emerged
in the therian ancestor approximately 180 million years ago, in parallel with the first of five monotreme Y chromosomes,
carrying the probable sex-determining geneAMH. The avianWchromosomearose approximately 140 million years ago in
the bird ancestor.ThesmallY/Wgene repertoires, enrichedin regulatory functions,were rapidly defined following strati-fication
(recombination arrest) and erosion events and have remained considerably stable. Despite expression decreases
in therians, Y/Wgenes shownotable conservation of proto-sex chromosomeexpression patterns, althoughvariousYgenes
evolved testis-specificities through differential regulatory decay. Thus, although some genes evolved novel functions through
spatial/temporal expression shifts, most Ygenes probably endured, at least initially, because of dosage constraints.
In mostmammals, Y chromosomes are required to override the program
underlying development of the default sex, females1. Extant mammals
possess anXY(male heterogametic) sex chromosomesystem, with rare
exceptions that experienced secondary XY loss2, but sex chromosomes
male-specific genomic data with Yorthologues fromother species. The
genomic data also served to support theabsenceofancestralYgenes (that
is, their evolutionary loss).We validated our approach using large-scale
PCR/Sanger sequencing-based screening of male/female genomic DNA
53. LETTER OPEN
doi:10.1038/nature12326
Genomic evidence for ameiotic evolution in the
bdelloid rotifer Adineta vaga
Jean-François Flot1,2,3,4,5,6, Boris Hespeels1,2, Xiang Li1,2, Benjamin Noel3, Irina Arkhipova7, Etienne G. J. Danchin8,9,10,
Andreas Hejnol11, Bernard Henrissat12, Romain Koszul13, Jean-Marc Aury3, Vale´rie Barbe3, Roxane-Marie Barthe´le´my14,
Jens Bast15, Georgii A. Bazykin16,17, Olivier Chabrol14, Arnaud Couloux3, Martine Da Rocha8,9,10, Corinne Da Silva3,
Eugene Gladyshev7, Philippe Gouret14, Oskar Hallatschek6,18, Bette Hecox-Lea7,19, Karine Labadie3, Benjamin Lejeune1,2,
Oliver Piskurek20, Julie Poulain3, Fernando Rodriguez7, Joseph F. Ryan11, Olga A. Vakhrusheva16,17, Eric Wajnberg8,9,10,
Be´ne´dicteWirth14, Irina Yushenova7, Manolis Kellis21, Alexey S. Kondrashov16,22, David B. Mark Welch7, Pierre Pontarotti14,
Jean Weissenbach3,4,5, Patrick Wincker3,4,5, Olivier Jaillon3,4,5,21* & Karine Van Doninck1,2*
Loss of sexual reproduction is considered an evolutionary dead end
for metazoans, but bdelloid rotifers challenge this view as they
appear to have persisted asexually for millions of years1. Neither
male sex organs nor meiosis have ever been observed in these
microscopic animals: oocytes are formed through mitotic divi-sions,
with no reduction of chromosome number and no indica-tion
of chromosome pairing2. However, current evidence does not
exclude that they may engage in sex on rare, cryptic occasions. Here
we report the genome of a bdelloid rotifer, Adineta vaga (Davis,
1873)3, and show that its structure is incompatible with conven-tional
meiosis. At gene scale, the genome of A. vaga is tetraploid
and comprises both anciently duplicated segments and less diver-gent
allelic regions. However, in contrast to sexual species, the
allelic regions are rearranged and sometimes even found on the
same chromosome. Such structure does not allow meiotic pairing;
instead, we find abundant evidence of gene conversion, which may
limit the accumulation of deleterious mutations in the absence of
meiosis. Gene families involved in resistance to oxidation, car-bohydrate
metabolism and defence against transposons are signifi-cantly
expanded,whichmay explainwhy transposable elements cover
only 3%of the assembled sequence. Furthermore, 8%of the genes are
likely to be of non-metazoan origin and were probably acquired
horizontally. This apparent convergence between bdelloids and pro-karyotes
We assembled the genome of a clonal A. vaga lineage into separate
haplotypes with aN50 of 260 kilobases (kb) (that is, half of the assembly
was composed of fragments longer than 260 kb). Assembly size was
218 megabases (Mb) but 26 Mb of the sequence had twice the average
sequencing coverage, suggesting that some nearly identical regions
were not resolved during assembly (Supplementary Fig. 3); hence,
the total genome size is likely to be 244 Mb, which corresponds to
the estimate obtained independently using fluorometry (Supplemen-tary
Note C2). Annotation of the complete assembly (including all
haplotypes) yielded 49,300 genes. Intragenomic sequence comparisons
revealed numerous homologous blocks with conserved gene order
(colinear regions). For each such block we computed the per-site syn-onymous
divergence (Ks) and a colinearity metric defined as the frac-tion
of colinear genes. Colinear blocks fell into two groups (Fig. 2a): a
group characterized by high colinearity and low average synonymous
divergence, and a group characterized by lower colinearity and higher
synonymous divergence. The presence of two classes of colinear blocks
is consistent with a tetraploid structure comprised of alleles (recent
homologues) and ohnologues (ancienthomologues formed by genome
duplication). Allelic pairs of coding sequences are on average 96.2%
Adineta vaga (Rotifera: Bdelloidea)
LETTER doi:10.1038/Genomic evidence for ameiotic evolution in the
bdelloid rotifer Adineta vaga
Jean-François Flot1,2,3,4,5,6, Boris Hespeels1,2, Xiang Li1,2, Benjamin Noel3, Irina Arkhipova7, Etienne G. J. Danchin8,9,10,
Andreas Hejnol11, Bernard Henrissat12, Romain Koszul13, Jean-Marc Aury3, Vale´rie Barbe3, Roxane-Marie Barthe´le´my14,
Jens Bast15, Georgii A. Bazykin16,17, Olivier Chabrol14, Arnaud Couloux3, Martine Da Rocha8,9,10, Corinne Da Silva3,
Eugene Gladyshev7, Philippe Gouret14, Oskar Hallatschek6,18, Bette Hecox-Lea7,19, Karine Labadie3, Benjamin Lejeune1,2,
Oliver Piskurek20, Julie Poulain3, Fernando Rodriguez7, Joseph F. Ryan11, Olga A. Vakhrusheva16,17, Eric Wajnberg8,9,10,
Be´ne´dicteWirth14, Irina Yushenova7, Manolis Kellis21, Alexey S. Kondrashov16,22, David B. Mark Welch7, Pierre Pontarotti14,
Jean Weissenbach3,4,5, Patrick Wincker3,4,5, Olivier Jaillon3,4,5,21* & Karine Van Doninck1,2*
Loss of sexual reproduction is considered an evolutionary dead end
for metazoans, but bdelloid rotifers challenge this view as they
appear to have persisted asexually for millions of years1. Neither
male sex organs nor meiosis have ever been observed in these
microscopic animals: oocytes are formed through mitotic divi-sions,
with no reduction of chromosome number and no indica-tion
of chromosome pairing2. However, current evidence does not
exclude that they may engage in sex on rare, cryptic occasions. Here
we report the genome of a bdelloid rotifer, Adineta vaga (Davis,
1873)3, and show that its structure is incompatible with conven-tional
meiosis. At gene scale, the genome of A. vaga is tetraploid
and comprises both anciently duplicated segments and less diver-gent
allelic regions. However, in contrast to sexual species, the
allelic regions are rearranged and sometimes even found on the
same chromosome. Such structure does not allow meiotic pairing;
instead, we find abundant evidence of gene conversion, which may
limit the accumulation of deleterious mutations in the absence of
meiosis. Gene families involved in resistance to oxidation, car-bohydrate
metabolism and defence against transposons are signifi-cantly
expanded,whichmay explainwhy transposable elements cover
only 3%of the assembled sequence. Furthermore, 8%of the genes are
likely to be of non-metazoan origin and were probably acquired
horizontally. This apparent convergence between bdelloids and pro-karyotes
sheds new light on the evolutionary significance of sex.
With more than 460 described species4, bdelloid rotifers (Fig. 1)
represent the highest metazoan taxonomic rank in which males, her-maphrodites
We assembled the genome of a clonal A. vaga lineage into haplotypes with aN50 of 260 kilobases (kb) (that is, half of was composed of fragments longer than 260 kb). Assembly 218 megabases (Mb) but 26 Mb of the sequence had twice sequencing coverage, suggesting that some nearly identical were not resolved during assembly (Supplementary Fig. the total genome size is likely to be 244 Mb, which corresponds the estimate obtained independently using fluorometry (Note C2). Annotation of the complete assembly (haplotypes) yielded 49,300 genes. Intragenomic sequence revealed numerous homologous blocks with conserved (colinear regions). For each such block we computed the divergence (Ks) and a colinearity metric defined of colinear genes. Colinear blocks fell into two groups group characterized by high colinearity and low average divergence, and a group characterized by lower colinearity synonymous divergence. The presence of two classes of colinear is consistent with a tetraploid structure comprised of alleles homologues) and ohnologues (ancienthomologues formed duplication). Allelic pairs of coding sequences are on average Adineta vaga (Rotifera: Bdelloidea)
54. A worldwide survey of genome sequence variation
provides insight into the evolutionary history of the
honeybee Apis mellifera
Andreas Wallberg1, Fan Han1,10, Gustaf Wellhagen1,10, Bjørn Dahle2, Masakado Kawata3, Nizar Haddad4,
Zilá Luz Paulino Simões5, Mike H Allsopp6, Irfan Kandemir7, Pilar De la Rúa8, Christian W Pirk9 &
Matthew T Webster1
The honeybee Apis mellifera has major ecological and economic importance. We analyze patterns of genetic variation at 8.3 million
SNPs, identified by sequencing 140 honeybee genomes from a worldwide sample of 14 populations at a combined total depth
of 634×. These data provide insight into the evolutionary history and genetic basis of local adaptation in this species. We find
evidence that population sizes have fluctuated greatly, mirroring historical fluctuations in climate, although contemporary
populations have high genetic diversity, indicating the absence of domestication bottlenecks. Levels of genetic variation are
strongly shaped by natural selection and are highly correlated with patterns of gene expression and DNA methylation. We identify
genomic signatures of local adaptation, which are enriched in genes expressed in workers and in immune system– and sperm
motility–related genes that might underlie geographic variation in reproduction, dispersal and disease resistance. This study
provides a framework for future investigations into responses to pathogens and climate change in honeybees.
Insect pollination is necessary for one-third of our food and is a vital
part of the ecosystem. The honeybee A. mellifera is a key pollinator,
with its services to agriculture valued at >$200 billion per year world-wide1.
It is therefore a major cause of concern that honeybees have
faced huge and largely unexplained colony losses in recent decades2.
However, little is known about global patterns of genomic variation in
this species, which hold the key to an understanding of its evolution-ary
history, the biological basis of adaptation to different climates and
mechanisms governing resistance to disease.
major honeybee pathogen13,14. The genetic basis of this phenotypic
variation is largely unknown.
Humans began harvesting wax and honey from honeybee colonies
at least 7,000 years before the present15. Human activity has led to the
transportation of honeybee colonies all over the world, artificial selec-tion
for desirable traits and gene flow between native subspecies16,
including the expansion of hybrid strains of Africanized bees, known
for their highly aggressive stinging behavior, across the Americas17
after their introduction to Brazil. The effects of these processes on the
55. ECOLOGICAL GENOMICS
The genomic landscape underlying
phenotypic integrity in the face of
gene flow in crows
J. W. Poelstra,1* N. Vijay,1* C. M. Bossu,1* H. Lantz,2,3 B. Ryll,4 I. Müller,5,6 V. Baglione,7
P. Unneberg,8 M. Wikelski,5,6 M. G. Grabherr,3 J. B. W. Wolf 1†
The importance, extent, and mode of interspecific gene flow for the evolution of species
has long been debated. Characterization of genomic differentiation in a classic example of
hybridization between all-black carrion crows and gray-coated hooded crows identified
genome-wide introgression extending far beyond the morphological hybrid zone. Gene
expression divergence was concentrated in pigmentation genes expressed in gray
versus black feather follicles. Only a small number of narrow genomic islands exhibited
resistance to gene flow. One prominent genomic region (<2 megabases) harbored 81
of all 82 fixed differences (of 8.4 million single-nucleotide polymorphisms in total)
linking genes involved in pigmentation and in visual perception—a genomic signal reflecting
color-mediated prezygotic isolation. Thus, localized genomic selection can cause marked
heterogeneity in introgression landscapes while maintaining phenotypic divergence.
Genomic studies increasingly appreciate the
importance of interspecific gene flow in
the context of species diversification (1, 2),
cycles during the Pleistocene, when periods
of isolation in distinct southern refugia alter-nated
with periods of range expansion and sec-ondary
sequence table populations, between of evidence flow genetic variance) of carrion hooded fixation and table divergence]. crows was further S5 and and an isolation-signatures diversity Spanish The hybrid divergence (RNA-
56. (12, 33). Unless CDW recedes sufficiently to
reduce melt well below present levels, it is dif-ficult
16. J. Mouginot, E. Rignot, B. Scheuchl, Geophys. Res. Lett.
41, 1576–1584 (2014).
27 November 10.1126/Stick Insect Genomes Reveal Natural
Selection’s Role in Parallel Speciation
Víctor Soria-Carrasco,1* Zachariah Gompert,2* Aaron A. Comeault,1 Timothy E. Farkas,1
Thomas L. Parchman,3 J. Spencer Johnston,4 C. Alex Buerkle,5 Jeffrey L. Feder,6 Jens Bast,7
Tanja Schwander,8 Scott P. Egan,9 Bernard J. Crespi,10 Patrik Nosil1†
Natural selection can drive the repeated evolution of reproductive isolation, but the genomic basis
of parallel speciation remains poorly understood. We analyzed whole-genome divergence between
replicate pairs of stick insect populations that are adapted to different host plants and undergoing
parallel speciation. We found thousands of modest-sized genomic regions of accentuated
divergence between populations, most of which are unique to individual population pairs. We also
detected parallel genomic divergence across population pairs involving an excess of coding genes
with specific molecular functions. Regions of parallel genomic divergence in nature exhibited
exceptional allele frequency changes between hosts in a field transplant experiment. The results
advance understanding of biological diversification by providing convergent observational and
experimental evidence for selection’s role in driving repeatable genomic divergence.
Whether evolution is predictable and re-peatable
is difficult to test yet central
to our understanding of biological di-versification
(1–6). Instances of repeated, parallel
selection and can involve repeated divergence
at specific genes (7–9). Indeed, parallel evolution
of individual phenotypic traits has been esti-mated
to involve the same genomic regions 30 to
speciation) Although might contingencies genomic causes 1Department Sheffield, Utah of Biology, 4Department Station, of Wyoming, Biology, 7J. F. University Lausanne Evolutionary 10Department Burnaby,
