Download Sex chromosomes demonstrate complex evolutionary trajectories

2/3/2015
Sex chromosomes
demonstrate complex
evolutionary trajectories
across bird taxa
Sex is often determined by a pair of
heteromorphic sex chromosomes.
Doris Bachtrog
University of California, Berkeley
I. Introduction
Sex chromosomes evolve from autosomes
autosomes
XY
X
X
X
X
X
X
X
X
X
X
X
X
XY
XY
Sry
Sry
X
X
X
I. Introduction
Same evolutionary steps in ZW systems
XY
Sry
Sry
X
autosomes
Z W
X
X
X
X
X
X
X
X
X
X
X
X
ZW
ZW
DMRT1
DMRT1
X
X
X
ZW
DMRT1
DMRT1
X
- 1st step: Genetic sex determination
- Recombination suppression evolves in independent steps (evolutionary strata)
- X & Y differentiate; older evolutionary strata are more diverged
- 1st step: Genetic sex determination
- Recombination suppression evolves in independent steps (evolutionary strata)
- Z & W differentiate; older evolutionary strata are more diverged
- Y chromosomes degenerate and may accumulate male-specific genes
- X chromosomes often become dosage compensated and may evolve specialized
gene content (demasculinization)
- W chromosomes degenerate and may accumulate female-specific genes
- Z chromosomes evolve specialized gene content (masculinization) but no dosage
compensation has been found yet in ZW systems
I. Introduction
Sex chromosomes are at different stages of
differentiation in different lineages
XY
XY
X
X
X
X
X
X
X
X
X
homomorphic
sex chromosomes
X
X
X
X
ZW
XY
Sex chromosomes are at different stages of
differentiation in different strata
ZW
X
X
X
X
X
I. Introduction
X
heteromorphic
sex chromosomes
XY
XY
X
X
X
X
X
X
X
X
X
homomorphic
sex chromosomes
X
X
X
X
ZW
XY
ZW
X
X
X
X
X
X
heteromorphic
sex chromosomes
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2/3/2015
II. Bird sex chromosome evolution
Sex chromosome evolution in birds
Sex chromosomes in birds
autosomes
PALEOGNATHAE
X
X
X
X
X
X
X
Z W
ZW
ZW
X
X
X
X
X
X
X
ZW
DMRT1
DMRT1
DMRT1
DMRT1
X
?
- All birds have homologous sex chromosomes
NEOGNATHAE
- DMRT1 appears to be the master sex determining locus
- In emu/ostrich: large PAR’s
- In chicken: W fully degenerated, evolutionary strata; no dosage compensation of Z
I. Introduction
I. Introduction
Using male/female coverage to determine X-derived scaffolds
Identify sex-linked genes using genomic sequencing
Female and Male
PE reads
Scaffolds
I. De novo
Assembly
DNA
II. Map reads to scaffolds
& determine coverage
DNA
III. Map scaffolds to reference genome
& plot coverage
1 - de novo assembly of genome
2 – determine sex-linkage using male and female coverage
0.5
PAR
DR
PAR
Coverage
Coverage
Reference genome
1
Autosomal
I. Introduction
II. Bird sex chromosome evolution
Using male/female coverage to determine Y-derived scaffolds
Female and Male
PE reads
Sex chromosomes in birds
Scaffolds
I. De novo
Assembly
Paleognathae
Galloanserae
II. Map reads to scaffolds
& determine coverage
In collaboration with BGI:
Genome sequences of 18 bird
species from females (ZW system)
High-quality assemblies from ostrich
and chicken; other genomes were
scaffolded against ostrich genome
(for Paleognathae) or against
chicken (for Neognathae)
Neoaves
III. Map scaffolds to reference genome
& plot coverage
X-linked
Use coverage from females only to
identify sex-linked scaffolds
young stratum
IV. Y-linked scaffolds may show some
homology with X chromosome
Coverage
old stratum
Coverage
Reference genome
Y-linked
X-linked
Neognathae
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II. Bird sex chromosome evolution
Using male/female coverage to determine Z-derived scaffolds
Female and Male
PE reads
Scaffolds
I. De novo
Assembly
PAR’s
II. Map reads to scaffolds
& determine coverage
III. Map scaffolds to chicken / ostrich
Z & plot coverage
0.5
DR
PAR
PAR
(Pseudo)Autosomal
Z-linked
II. Bird sex chromosome evolution
Using male/female coverage to determine W-derived scaffolds
Female and Male
PE reads
Ostrich Z
Size of PARs varies dramatically
across lineages – independent
evolution of sex chromosomes
in different bird lineages
To reconstruct the evolutionary
history of sex chromosomes in
birds: Identify candidate Wregions as un-mapped scaffolds
with Z homology
Coverage
1
Coverage
Chicken/ostrich Z
DMRT1
II. Bird sex chromosome evolution
Coverage analysis along Z reveals dramatic differences in PAR among birds
Chicken Z
II. Bird sex chromosome evolution
W-linked fragments in birds
Scaffolds
I. De novo
Assembly
II. Map reads to scaffolds
& determine coverage
III. Map scaffolds to chicken /
ostrich Z
young stratum
IV. Infer strata based on sequence
homology between Z & W fragments
Coverage
old
Chicken/ostrich Z
Coverage
DMRT1
W-linked
Z-linked
II. Bird sex chromosome evolution
W-linked fragments in birds
II. Bird sex chromosome evolution
W-linked fragments reveal evolutionary strata
W-fragments differ in
density & ZW similarity
-> strata
Allow us to infer the
evolutionary history of
bird sex chromosomes:
Older strata: less
homology between Z & W
Not fully degenerate W’s
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II. Bird sex chromosome evolution
Are W-candidates indeed W-linked?
Exact same mapping pipeline applied to chromosome 1:
II. Bird sex chromosome evolution
Are W-candidates indeed W-linked?
Coverage of W-candidates, Z-linked sequences and autosomes in males and females
W-sequences are femalelimited
Z-sequences show half the
coverage in females
Autosomal sequences show
similar coverage in males
and females
- No differentiated region on chromosome 1
- Very little mapping of unmapped fragments
II. Bird sex chromosome evolution
Evolutionary strata of bird sex chromosomes
Age of strata and gene
synteny information allow
us to reconstruct
evolutionary history of
bird sex chromosomes
II. Bird sex chromosome evolution
Evolutionary strata of Paleognathae
Shared and lineage-specific strata in bird sex
chromosomes
S0 is shared among all birds
-
High overlap of gene content
Gametologs cluster by chromosome and not species
ZW divergence time exceeds species divergence time
Other strata in Palaeognaths are lineage-specific
-
- DMRT1 is in ancestral stratum in each species
Little overlap of gene content
Gametologs cluster by species and not chromosome
ZW divergence time is less than species divergence time
- Strata become progressively younger when moving from ancestral stratum to PAR
II. Bird sex chromosome evolution
Evolutionary strata of Neognathae
II. Bird sex chromosome evolution
Use synteny to infer if inversion contribute to strata formation
Shared and lineage-specific strata in bird sex
chromosomes
S1 is shared among all Neognathae
S2 is shared among all Neoaves but not Galloanserae
S3 is PAR / lineage-specific
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II. Bird sex chromosome evolution
Sex chromosome differentiation in birds
II. Bird sex chromosome evolution
Sex chromosome differentiation in birds
II. Bird sex chromosome evolution
Sex chromosome differentiation in birds
II. Bird sex chromosome evolution
Sex chromosome differentiation in birds
II. Bird sex chromosome evolution
Sex chromosome differentiation in birds
II. Bird sex chromosome evolution
Sex chromosomes of birds
Shared sex
chromosomes
but lineagespecific events
have generated
a diversity of
sex
chromosome
karyotypes!
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2/3/2015
II. Bird sex chromosome evolution
II. Bird sex chromosome evolution
W degeneration over time
W degeneration over time
How many genes are left on W
chromosomes?
Younger strata
contain more
intact genes
White-throated Tinamou
Z
W
2 strata with W-linked genes
II. Bird sex chromosome evolution
II. Bird sex chromosome evolution
W degeneration over time
Conclusions
 Avian sex chromosomes harbor diverse compositions of DR and PAR across taxa
 Avian W chromosomes showed great variation in their degree of degeneration
 the putative avian sex determining gene DMRT1 is consistently within the nonrecombining region of the sex chromosomes
 avian sex chromosomes have suppressed recombination through a series of
punctuated events (“strata”) with a gradient of ages, reflected by higher levels of
sequence homology between W and Z sequences as one moves towards the PAR and
away from DMRT1
 reconstruct the evolutionary history of recombination suppression and
differentiation across birds
 dynamics of W degeneration changes over time, with W-linked genes subject to
ongoing decay, and the tempo of W degeneration slowing down in older strata
Rate of gene loss is not linear over
time (but declines exponentially)
III. Snakes
Sex chromosomes of snakes
Sex chromosome evolution in snakes
- Species with homomorphic and heteromorphic sex chromosomes & some in between
autosomes
Z W
X
X
X
X
X
X
X
X
X
X
X
X
ZW
?
ZW
X
X
X
ZW
?
?
?
X
boas & pythons
colubridae
vipers & cobras
Closely related species (i.e. garter snakes; Colubridae) appear to have both
homomorphic and heteromorphic sex chromosomes
 Rapid evolution of sex chromosomes????
- All snakes have homologous ZW sex chromosomes
- In boas & pythons: largely undifferentiated sex chromosomes
- In Colubridae: various intermediate stages of differentiation which suggests that
ancestor of Colubrids had homomorphic sex chromosomes and many speciesspecific events created diverse sex chromosomes in Colubrids
- In vipers & cobras: fully degenerate W chromosomes; dosage compensation
status unknown
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III. Snakes
III. Snakes
Anolis genome to identify snake sex chromosomes
No dosage compensation in snakes
Anolis chromosome 6
corresponds to snake sex
chromosome
Less expression
from Z in female
rattlesnakes –
no dosage
compensation!
Boa
rattlesnake
- Boa has completely homomorphic sex chromosomes
- Sex chromosomes of rattlesnake and garter snake are completely differentiated
III. Snakes
Evolutionary strata on snake sex chromosomes
Evolutionary strata on snake sex chromosomes
No homology
between Z and
W at middle
region – central
part stared to
differentiate
first!
garter snake
2 or 3
evolutionary
strata on snake Z
chromosome!
rattlesnake
III. Snakes
x
x
x
x
x
x
x
x
x
no differentiation
in boas
x
x
x
x
x
x
x
x
cytogenetic data
gave wrong
impression of
variation among
sex chromosomes
in Colubridae
x
x
x
x
x
x
evidence for 2 shared
strata in garter snakes
& rattle snakes
IV. Flies
Basic karyotype in Diptera
Anopheles
In many Diptera families:
6 pairs of chromosomes
(5 rods, 1 dot)
IV. Flies
Basic karyotype in Diptera
Sex chromosome in
Drosophila &
Anopheles
In many Diptera families: Element A
Anopheles
6 pairs of chromosomes
(5 rods, 1 dot)
Element B
Element C
Element D
Element E
Gene content among
chromosomes conserved
Gene content among
chromosomes conserved
 Muller element’s
 Muller element’s
Drosophila
Element F
Drosophila
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IV. Flies
IV. Flies
Sex chromosome evolution across Diptera
crane flies
Coboldia fuscipes
dung midges
Maye ola destructor
Herme a illucens
Condylostylus pa bulatus
Megaselia abdita
Eristalis dimidiata
Themira minor
chironimids
black flies
mosquitoes
sand flies
Tipula oleracea
Trichoceridae sp.
crane flies
Coboldia fuscipes
dung midges
gall midges
Maye ola destructor
gall midges
solder
e fli s
robber flies
long-legged flie s
Herme a illucens
solder
e fli s
robber flies
long-legged flie s
de novo gain of sex chromosomes in some lineages
hump-back flies
hover fli s
scavenger flies
Megaselia abdita
hump-back flies
hover fli s
scavenger flies
some species have entirely lost sex chromosomes
Holcocephala fusca
Condylostylus pa bulatus
Eristalis dimidiata
Themira minor
true frui lies
Eutreta diana
Tephri s californica (ZW)
Trupanea negronis
Bactrocera oleae (XY)
true frui lies
Teleopsis dalmanni
Sphyracephala brevicornis
stalk-eyed flies
Teleopsis dalmanni
Sphyracephala brevicornis
stalk-eyed flies
Liriomyza trifolii
leaf miners
Liriomyza trifolii
leaf miners
Ephydra hians
Ephydra
e gracilis
Phor ca variegata
shoree fli s
Ephydra hians
Ephydra gracilis
Phor ca variegata
shoree fli s
Drosophila pseudoobscura
Drosophila miranda
Drosophila melanogaster
Drosophila busckii
Drosophila albomicans
BRACHYCERA
Eutreta diana
Tephri s californica (ZW)
Trupanea negronis
Bactrocera oleae (XY)
Drosophila
rela ves
Sex-linked
e
element(s)
A
B
C
D
E
F
Scaptodrosophila lebanonensis
Glossina morsitans
tsetse flies
Sarcophaga bullata
Sarcophagidae sp.
Lucilia sericata
Calliphora erythrocephala
flesh fli s
bot flies
bloweflies
Undifferen ated
Vicoso & Bachtrog, PLoS Biology, in press
Drosophila pseudoobscura
Drosophila miranda
Drosophila melanogaster
Drosophila busckii
Drosophila albomicans
Drosophila
rela ves
Scaptodrosophila lebanonensis
Glossina morsitans
tsetse flies
Sarcophaga bullata
Sarcophagidae sp.
Lucilia sericata
Calliphora erythrocephala
flesh fli s
bot flies
bloweflies
a dozen different sex chromosome karyotypes
NEMATOCERA
Tipula oleracea
Trichoceridae sp.
Holcocephala fusca
Chironomus riparius
Chaoborus trivi atus
Mochlonyx cinc pes
Anopheles gambiae
Aedes aegyp
Clogmia albipunctata
>30 species,
20 different families
>250 MY evolution
ancestral karyotype: dot chromosome as sex
chromosome or homomorphic sex chromosomes
some families have replaced sex chromosomes
with different Muller element
BRACHYCERA
chironimids
black flies
mosquitoes
sand flies
NEMATOCERA
Chironomus riparius
Chaoborus trivi atus
Mochlonyx cinc pes
Anopheles gambiae
Aedes aegyp
Clogmia albipunctata
Sex chromosome evolution across Diptera
some families have incorporated additional
chromosomes into their sex chromosomes
Muller element D is repeatedly used as a sex
chromosome
XY to ZW transition in Tephritidae
A
B
C
D
E
F
Undiff
IV. Flies
Conclusions
X chromosomes show partial dosage compensation
Transcriptome analysis of whole flies to study functional properties of sex chromosomes
P. variegata
T. minor
*
***
E. hians
L. trifolii
***
*
2
0.5
2
4
2
 Sex-chromosome turnover has occurred multiple times throughout Dipteran
evolution; bird & snake sex chromosomes are conserved but show signs of
evolutionary strata
-1
-3
-4
-1.0
-6
-1.5
-2
-2
-1.0
-2
-4
-2
-0.5
-1
-2
-0.5
0
0
0
0
0.0
0
0.0
1
2
0.5
1
2
0
Log2[M/F expression]
-2
-4
X
X=A
X
X=B
A
A
A
A
X
X=C,D,F
 Comparing male to female coverage can be a good approach to identify sexlinked sequences in non-model organisms, and combined with gene expression
analysis, this allows us to make general inferences on sex chromosomes biology
1.0
2
3
6
G. morsitans
4
M. destructor
1.0
***
1.5
T. dalmanni
***
4
D. melanogaster
AA
X
X=A
A
A
X
X=A,D,F
AA
X
X=D
A
A
X
X=D
A
A
X
X=D
A
A
 Dosage compensation has evolved in multiple Diptera families, through upregulation of the X in males; dosage compensation is lacking in snakes & birds
This provides a great sample in which to test hypothesis of sex-chromosome
evolution in a more systematic manner than has so far been possible.
Expression of single X in males in not half that of females!
 Always some level of dosage compensation, but perhaps some evidence of
specialized gene content as well.
Acknowledgements
UC Berkeley
Beatriz Vicoso
Qi Zhou
Chris Ellison
Wynn Meyers
Karen Wong
Tania Gurbich
Emily Brown
Lauren Giblisco
Shivani Mahajan
BGI
Jilin Zhang
Guojie Zhang
Zaak Walton
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