Download The evolution of sex chromosomes: similarities and differences

The evolution of sex chromosomes:
similarities and differences between
plants and animals
Deborah Charlesworth
Institute of Evolutionary Biology, University of Edinburgh
Male
Silene dioica male
Female
Papaya female
Silene latifolia female
Classical sex chromosomes
Humans
Y is ~ 1/3 of
the size of
the X
X ~ 1,098 genes
Y 24 genes
Y
X
Male-specific Y region PseudoMSY
autosomal region
without recombination PAR
In Drosophila, the Y is about the same size as the X,
but the X has several thousand genes, while the Y has
around 20. No X gene has a Y homologue.
Sex chromosomes have been known to geneticists for a
long time, but many important things have only become
clear very recently, and great progress is occurring
•
Muller (1914): reviewed evidence for X-Y pairing (indicating their homology)
and Y genetic degeneration (suggested by C.W. Metz) and discussed
recessive loss of function mutations as the cause of degeneration
•
Haldane (1922, p. 107): “If sex were determined by a single factor, it is very
difficult to see what advantage there could be in its being linked with other
factors)”
– Nei (1969, 1970): models for lack of recombination and consequent
accumulation of detrimental mutations leading to degeneration
– BC, DC (1978) : evolution of sex-determining region with two loci (driving
selection for less recombination)
•
An excellent review of the classical work is JJ Bull!s 1983 book “Evolution
of Sex Determining Mechanisms”
•
Lahn and Page (1999): human genome sequence reveals sequences of
genes shared between X and Y, often highly diverged. Carvalho (2001):
Drosophila Y-linked genes
•
Recent data are starting to help us understand why and how recombination
gets stopped between the X and Y (and what the consequences are)
• 1. WHAT are sex chromosomes?
– and what are NOT sex chromosomes
• 2. WHY do sex chromosomes evolve loss of
recombination?
• 3. WHEN did sex chromosomes of some
important species evolve?
– and when did recombination stop?
• and 4. HOW did recombination stop?
• 5. WHERE are the sex-determining loci in relation
to the regions where recombination is absent?
• 6. WHAT are the consequences for sex
chromosomes of stopping recombination?
1. What are sex chromosomes?
• “Classical” sex chromosomes
– Non-recombining over a large genome region, with
small “pseudo-autosomal region(s)”
• Mammal and Drosophila X and Y, bird and Lepidopteran Z
and W
– Genetically degenerated
• loss of genes relative to the X (and lower function, see later)
– Rearranged relative to the X
• BUT sex chromosomes are more diverse than
this
• I shall take a (molecular) evolutionary
perspective
The human MSY region genes
Many Human Y
genes have male
functions
Genes on Y only
Y genes with male functions
can be kept on the Y because
the sex chromosomes don’t
recombine across much of
their length. These genes are
probably prevented from
degenerating
Genes on X and Y
Heterochromatin
There are a few
X-Y gene pairs (X
homologous genes),
even in the nonrecombining regions
(NRY)
Mammalian Y chromosomes
have many fewer genes than the
X, and are more rearranged
X
There are complex genome rearrangements in
the human Y due to duplications in a a 4.5-Mb
functional region close to the heterochromatic
region that includes AZFc
Kuroda-Kawaguchi
et al. 2001 Nature
Genetics: 29, 279 286
Y
Heterochromatin (no
functional genes)
Diversity of sex chromosome types (see
Bull’s 1983 book)
• CLASSICAL
– Non-recombining over a large genome region, with small “pseudoautosomal region(s)”
– Genetically degenerated
• loss of genes relative to the X (or lower function — see later)
• The Y can sometimes be totally lost (X0 systems)
– Y is enriched in male-function genes, and is rearranged relative to the X
• “LOCAL SEX-DETERMINING REGION”
– Chromosome is largely pseudo-autosomal
– The same properties as classical sex chromosomes, in a restricted region of
genome
• HAPLOID
– Haploid male genotype is Y and female is X
• NOT SEX CHROMOSOMES
– fungal and algal incompatibility regions (but have some similar properties)
– inversions
The genus Silene
Dioecious
(independent
evolution)
Gynodioecious
Hermaphrodite Female
PAR
Y
Dioecious
X
Silene latifolia has classical
sex chromosomes
Hermaphrodite
Estimated from ITS sequences by Desfeux, C., et al. 1996. Proc. Roy. Soc. Lond. B. 263:409-414
Recent work with more nuclear genes supports these phylogenetic relationships
MSY
region
Some other plants have small sex-determining regions
Several plant ‘sex
chromosomes’ have the sexdetermining genes located
within a small region (blue;
only 10% of chromosome 1 of
papaya) where recombination
does not occur (Liu et al. 2004)
– Some fish sex chromosomes
may be similar
– Does small size mean young,
or primitive?
Other plants have
heteromorphic sex
chromosomes like those of
humans and Drosophila, or
neo-sex chromosomes
neo-sex chromosomes also occur in plants
Liu et al. 2004.
Nature 427:348-352
Haploid sex chromosomes in a bryophyte with
separate sexes (Ceratodon purpureus)
Meiosis
2n ! n
288 spores genotyped
59% male Y
41% female X
Haploid
Diploid
sporophyte XY AA
NOTE No XX
Fertilization
n ! 2n
YA
Male
gametophyte
XA
Female
gametophyte
McDaniel et al. 2007
Genetics 176:2489-2500
C. purpureus genetic map showing 15 linkage groups, including the
XY pair of sex chromosomes
124 markers (121 AFLP, 3 genic)
This species
has a small
sexdetermining
region
MSY
Another bryophyte, Marchantia polymorpha (haploid) has
highly heteromorphic sex chromosomes
Yamato et al. (2007) Proc. Natl. Acad. Sci. USA 104, 6472-6477
X
Y
Fusions/translocations, neo-sex chromosomes
X
Y
Autosome
Y-autosome
fusion
X-autosome
fusion
neo-X
Y1
X1
neo-Y or Y2
neo-X or X2
neo-Y
Chromosome(s) transmitted to female progeny
Chromosome(s) transmitted to male progeny
In Drosophila, there is no recombination in males
Thus, both kinds of fusion create non-recombining neo-sex chromosomes
Chromosome fusions can lead to heteromorphism
Fusion can also occur in X0 systems
Neo sex chromosomes in
the genus Drosophila
Complete
degeneration of
the ancestral Y
Carvalho, A. B., and A. G. Clark. 2005. Y chromosome of D. pseudoobscura is
not homologous to the ancestral Drosophila Y. Science 307:108-110.
• The Y can be lost entirely if genes required for male fertility
can move to a different chromosome
• Some species have X/0 male genotype, but males are still
fertile.
– e.g. Drosophila affinis
• In D. pseudo-obscura, the sex chromosomes have been
fused to an autosome, and the Y has lost all male fertility
genes
– So, even if the Y chromosome degenerates, we do not need to
worry about a future without males
• Clearly, the Y cannot be lost unless the sex-determination
function is replaced by a new gene (or the Y gene moves to
another chromosome)
– Such changes are theoretically possible: e.g. DOORN, G. V., and M.
KIRKPATRICK, 2007 Turnover of sex chromosomes induced by
sexual conflict. Nature 449: 909-912.
Neo-sex chromosomes occur in many species
Rowell, D. (1985).
Complex sex-linked fusion
heterozygosity in the
Australian huntsman spider
Delena cancerides
(Araneae: Sparassidae).
Chromosoma 93, 169-176.
RENS et al., 2004 PNAS
101: 16257-16261
GRÜZNER et al., 2004
Nature 432: 913-917.
2. WHY does recombination stop on
sex chromosomes?
•
Haldane (1922, p. 107): “If sex were determined by a single factor, it is very
difficult to see what advantage there could be in its being linked with other
factors)” (Sex ratio and unisexual sterility in hybrid animals. J. Genetics 12:101-109)
– Nei (1969, 1970): models for lack of recombination and consequent
accumulation of detrimental mutations leading to degeneration
– Nei, M. 1969. Linkage modification and sex difference in recombination.
Genetics 63:681-699; 1970. Accumulation of nonfunctional genes on sheltered
chromosomes. American Naturalist 104:311-322.
•
Many modern authors are much less clear e.g. “heteromorphic sex
chromosomes have evolved ….when one autosome develops a dominant
sex-determining mutation”
– Itoh et al. 2007. Molecular cloning of zebra finch W chromosome repetitive
sequences: evolution of the avian W chromosome. Chromosoma 117:111-121.
• There is no selection to reduce recombination
unless at least 2 genes interact
•
Qvarnstrom & Bailey. 2009. Heredity 102:4-15 are completely wrong!
–
The evolution of identifiable heteromorphic sex chromosomes is initiated by the spread of a
sex-determining gene (SDG). This occurs when a new mutation at a locus leads all its carriers
to become the same (subsequently heterogametic) sex, with the chromosome carrying this
mutation becoming the Y/W chromosome (see main text). In eutherian mammals, for
example, the development of males is controlled by the SRY gene found only on the Y
chromosome
• To understand why the sex chromosomes don’t recombine, we need
to understand WHY interacting genes are involved, which requires
understanding HOW separate sexes evolved, and what kinds of
genes were involved
– BC, DC (1978) : evolution of sex-determining region with two loci (driving
selection for less recombination)
• A model for the evolution of dioecy and gynodioecy. Amer. Nat. 112:975-997
• This is a separate question from: how is recombination lost?
– i.e. questions like
• whether it was it in a single step when the sex chromosomes
orginated or a gradual process, with several successive steps?
• and were inversions involved?
• The question of what gene interactions have selected for loss of
recombination is still not fully answered
The argument for two or more evolutionary steps
1
M
f
M
f
cosexual
(hermaphrodite or
monoecious) or
environmental sex det
Female-sterility
mutation
f !"F
Male-sterility mutation
M !"m
Hermaphrodites and males
(androdioecy, very rare)
Hermaphrodites and females
(gynodioecy,
present in 5% of angiosperms)
2
Dominant femalesuppressing
mutation(s) f !"F
proto-Y
proto-X
Gynodioecy in
Silene vulgaris
Males
M F
m
f
Females
m f
m
f
proto-X
proto-X
Hermaphrodite Female
In S. latifolia, sex-determination is genetically simple: Males
and females are simply hermaphrodites with parts missing
Mutants support the hypothesis that at least 2 genes are involved
1: loss of stamen promoting factor, SPF, in females X (M! recessive m)
2: suppression of female functions by proto-Y-linked GSF (Suf ! dominant SuF)
Genotype at
second locus
Suf/Suf
(no female
suppressio n )
Hermaphrodite
Genotype at locus that mutates first
M/M or M/m
Loss of stamen
promoting factor (SPF
or M) creates females
Hermaphrodite
Gynoecium suppressing
factor (GSF or SuFemale)
reduces female functions
SuFemale/Suf
m /m
"
! Female
"
! Neuter
Male
(male fertility increase d )
Picture from
Shigeyuki Kawano
The simple 2 gene evolutionary model actually suggests that sex
determining loci must initially be linked for separate sexes to evolve
Once females are
present, hermaphrodites
are selected to re-allocate
more to male and less to
female functions
1
2
M SuFemale
“proto-Y”
“proto-X”
m f
Selection should then act to reduce recombination between the initial 2
genes
slightly older
Female
M2
M Su
proto-Y,
with MSY region
3. WHEN did sex chromosome systems evolve?
• Some classical sex chromosomes are probably old
– We don’t yet know how long it takes for the full set of features to
evolve
• It is often assumed that all other systems are young
CLASSICAL (heteromorphic)
SMALL SEX-DETERMINING REGIONS
(no heteromorphism)
NEO SEX CHROMOSOMES
Old
Young,
Maybe some are old
Young
• but we need data. It is now possible to get evidence, using
DNA sequences, estimating divergence between homologous
X and Y sequences, and assuming a molecular clock
– heteromorphism can evolve rapidly, e.g. by chromosome fusions
• For most species, it is difficult to get the genes for such studies
• To estimate ages of sex chromosomes, and to study degeneration,
we need to find genes and study alignable orthologous X and Y
gene pairs.
• There are few known mutant phenotypes (as Muller realised)
• Molecular methods are needed (Muller realised this too, in 1922)
– These methods also allow one to estimate ages and study degeneration
• Even with “complete” genome sequences of important “model
organisms” there are still great difficulties
– The gene content of the Y chromosomes of important “model organisms”
have only recently been determined
• Drosophila: Carvalho et al. 2001 PNAS 98:13225-13230
• Humans: SKALETSKYet al., 2003 Nature 423: 825 - 837, BHOWMICK et
al, 2007 Genome Res. 17: 441-450
• The mouse Y is still not well characterized
• and “model organisms” for sex chromosome work are only now
starting to be studied
– e.g. Dreyer et al. 2007. ESTs and EST-linked polymorphisms for genetic
mapping and phylogenetic reconstruction in the guppy, Poecilia
reticulata. BMC GENOMICS 8:269.
Why is it difficult to sequence Y chromosomes?
• Low gene density makes finding genes very difficult.
• Rearrangements: one homolog cannot used to help align the
other, unlike the autosomes
– Y can be sequenced from a single individual
• Their intergenic regions and introns contain large amounts of
repetitive sequence, so it is difficult to find the different parts
of the same gene
• Assembly of highly repetitive genomes is very difficult
– it requires large sequenced regions, such as BAC clones, but these may be
difficult to sequence if they contain repetitive sequences
• These are sometimes unstable when cloned, and so cannot be sequenced
• They may compete in PCR reactions, so that some copies fail to amplify
• If the repetitive sequences are AT-rich, poor strand separation may impede
sequencing reactions
Human X-Y divergence
Stratum 1
Many “X-degenerate”
genes still detectable on
the Y
Stratum 3
Stratum 2
Stratum 4
X-Y divergence, Ks
LAHN & PAGE, 1999 Four evolutionary strata on
the human X chromosome. Science 286: 964-967.
SKALETSKY et al. 2003. Nature 423:825 - 837.
Mostly old part of X (all but 2 genes present
in marsupial X chromosomes). Few genes on
the X are still detectable on the Y
Autosomal in
marsupials
(added to X
and Y by
transposition.
Xp
Xq
recent transposition
PAR1
2 genes transposed very
recently to the Y
What about
plants?
I emphasized how helpful it is to
identify genes, not just anonymous
markers or sequences
BUT finding orthologous X and Y
gene pairs in non-model species is
very difficult, and the S. latifolia
genome is awfully big!
Maybe one should sequence the genome?
Overview of the Marchantia
polymorpha YR2 region — so far in
this species mainly Y chromosome
data, not X and Y. This species is
expected to have an old Y chromosome
50 Y-linked housekeeping genes are
also found in females (presumably nondegenerated genes, with autosomal or
X-linked copies)
14 Y-linked genes are unique to males,
and expressed only in reproductive
organs
G = genes (indicated by arrows )
P = pseudogenes
O= organelle sequence
T = transposable element
How else can one find sex-linked loci?
• Testing linkage of known genes in families
• MROS3-X and -Y (Dave Guttman, 1998)
• Genes involved in flower development
– SlAp3-Y (Sachi Matsunaga, 2003)
• cDNA probing of micro-dissected Y chromosomes
– SlX/Y1 (Delichère et al. , 1999)
– SlX/Y4 (Atanassov et al., 2001)
– SlX/Y3 (Nicolas et al. 2005
• Genes discovered from cDNA libraries and EST sequences
–
–
–
–
–
SlSS-X/Y
SlCyp-X/Y
Sl8-Y only
Sl6a and b X/Y
Sl7X/Y
– RB11 and RB18
Dmitry Filatov
Roberta Bergero
Isomerase, cyclophilin type
Roberta Bergero
Mono-oxygenase/haem binding protein
Roberta Bergero
Unknown protein (2 Y and X copies)
Roberta Bergero
Unknown protein
Roberta and Vera Kaiser
• Differential display
• DD44 (Moore et al., 2003)
EST sequences were used to obtain sequences
Intron positions of genes at low copy number were determined from the
Arabidopsis thaliana and rice genomes
PCR primers were designed to cross introns to find length variants to do genetics
Parents
F1 progeny
Y-linked 1830 bp
730 bp
maternal X
2072 bp
700 bp
500 bp
510 bp
maternal X
590 bp
paternal X
590 bp
paternal X
X- and Y-linkage for locus Sl6
Roberta’s ISVS method
Forward primer
Intron region
Exon A
Exon B
Reverse primer
FAM
Incorporation of labeled universal
primer after the first PCR cycles
FAM
For product sizes >
450-500 bp, digest FAM
with restriction
enzyme
MboI
FAM
MboI
HaeIII
FAM
MboI
HaeIII
Analysis by
capillary
electrophoresis
Evidence for X/Y linkage of the SlCyp gene
Intron 3 variants, showing Y-linkage
of 438 bp band
Intron 2 variants , showing X-linkage
of 259 and 260 bp bands
2 male and 2 female
F1 plants
Parents
260Xm
257Y
260Xm
447bp
259Xp
257Y
447 bp
438 bp in
males only
447 bp
259Xp
260Xm
Possible strata in organisms other than humans
(X versus Y)
Human
(Z versus W)
(X versus Y)
(X versus Y)
PAR1
transposition
Autosomal in
Mostly old part of X
marsupials
(all but 2 genes
(added to X
present in
and Y by
marsupial X
transposition)
chromosomes)
PAR
inversion
Lawson-Handley et al., 2004
Genetics 167: 367-376
Nam & Ellegren. 2008.
Genetics 180: 1131 - 1136
PAR
Bergero et al., 2007
Genetics 175: 1945-1954
Phylogenetic analysis of bird Z and W chromosomes also
suggests that recombination between them stopped at
different times
Pseudoautosomal
end
Chicken Z
Genes that stopped
recombining after split
of taxa
Genes in region where ZW recombination stopped
before split of major bird
taxa
Some bird taxa probably
have small sexdetermining regions
from LAWSON-HANDLEY et al., 2004 Genetics 167: 367-376
Gradual evolution of bird sex chromosomes is also evident
when different taxa are compared — some taxa have not
undergone all the steps that others have taken
Giemsa
staining
C-bands
G-bands
by BrdU
Painting with Locations of
chicken Z
markers
probe
Z W
Non-recombining
region has
probably remained
small
Ostrich
Large nonrecombining
region
Chicken
Markers:
Z chromosomes of both taxa share several markers
Thus they probably had the same ancestral sex chromosome
Recombination has been suppressed only in the chicken lineage (including other
neognathae), and not in palaeognathous birds
Nishida-Umehara et al. 2007 Chromosome Research 15:721-734
Nanda, I et al.. 2008. Cytogenet Genome Res 122:150-156.
Gradual
evolution of
snake sex
chromosomes
P. molurus
(Pythonidae)
Females are WZ
E. quadrivirgata
(Colubridae)
Matsubara et al. (2006)
PNAS 103: 18190
Many (11/11) genes
shared between Z
and W (small sexdetermining region)
3/11 genes
No genes shared
shared between
between Z and W
Z and W
(W has lost most genes)
T. flavoviridis
(Viperidae)
Summary of some of the evolutionary changes that can
occur after a small sex determining region evolves
Starting state cosexual
or environmental sex determination
Males
M F
YA
XA
(5) Change to ZW system
W
Z
m
X
Y
f
Females
m f
m f
(2) Loss of recombination in
new region (e.g.mammalian,
chicken and viper lineages) (4) New sexdetermining
gene arises
old Y
old X
(3) Neo-sex chromosome(s)
X
XA
XA
(1) Recombination
continues in most of
the W (e.g. in ostrich
and python lineages)
Neo-Y
“Y”
“X”
A change from XY to ZW system in different populations of
the same species
An example of the use of genes to demonstrate that the
XY pair of chromosomes changed into a ZW pair
Uno et al. 2008. Comparative chromosome
mapping of sex-linked genes and identification
of sex chromosomal rearrangements in the
Japanese wrinkled frog (Rana rugosa,
Ranidae) with ZW and XY sex chromosome
systems. Chromosome Research:1217-7
Ks values in 6 X and Y Marchantia polymorpha
genes suggest that this sex chromosome system is old
(Ks is uncorrected synonymous or silent site divergence)
Ks
• If we had a good molecular clock, we could translate Ks values into times
when X-Y recombination stopped
• It is not yet possible to tell whether there are strata in this plant, or if the Y
and/or X is degenerated
Is papaya (with a small MSY) a young system?
Divergence is low between papaya
X and Y gene sequences
X and Y from hermaphrodite (Yh, YU et al, 2007 Plant Journal
53: 124-132)
Ks values in 4
papaya genes
from a BAC clone
X and Y from male (YU et al, 2008 Tropical Plant Biology 1: 49-57)
It is not yet possible to tell whether there are strata in this plant, because only 2 BACs
were sequenced (< 150 kb, whereas the size of the MSY is ~ 10 Mb)
WHY are there strata?
Why don’t organisms stop
recombination across the entire sex
chromosomes?
2
The simplest 2 gene evolutionary
model above suggested that sex
determining loci must initially be
linked for separate sexes to evolve
1
3
M SuFemale
“proto-Y”
“proto-X”
m f
Other genes may be added to the system in a 3rd step (and so on)
“proto-Y”
sexually antagonistic male-enhancer
“Y”
M2
M SuFemale
Reduced recombination
between initial 2 genes
Recombination suppression probably eventually
evolves across the whole Y chromosome because,
once free from the burden of female functions, males
keep on becoming better males
In hermaphrodites,
pressures to increase
male and female
functions are balanced
SuFemale
m f
m f
m f
In male-like hermaphrodites (with
lowered female function)
the balance at other loci
changes towards male
functions
m f
In males, only male functions matter
• The hypothesis of sexually antagonistic male-enhancers
is plausible, but all evidence to date is indirect, and no
such genes have yet been identified
– without sexual antagonism, there should be no selective
pressure converting hermaphrodites into males (the female
functions of hermaphrodites could be maintained unchanged
while male functions improve).
– Mank et al. (2008 American Naturalist 171:35-43) wanted to test
for antagonistic genes in chicken and mouse
• genes with different male and female expression patterns
• many of these will NOT have antagonistic effects, but, as a whole,
the set of such genes should include genes with antagonistic effects
– They found that this set of are less likely to be expressed in
multiple tissues (with the potential for conflicting selection
pressures) than the genome average, even after excluding sexlinked genes; however, a difference in tissue-specificity could be
explained without sexually antagonistic effects
• Drosophila experiments that
allowed selection in males only
show that female fitness
indeed declines
• This is consistent with a tradeoff between the sex functions,
but it could be due just to
stopping selection in females
Fertility of female offspring
High fertility
female parents
Low fertility
female parents
Fertility of male offspring
• Reversal in quality of progeny,
depending on whether they
had high or low fertility parents,
is clear evidence for trade-offs,
but it does not prove intralocus sexual conflict
Low fertility
female parents
High fertility
female parents
Low
High
Fertility of male parents
Pischedda & Chippindale (2006, PLoS Biology 4:e356)
• The best evidence so far for sexually antagonistic male-enhancers
is in the guppy fish, Poecilia reticulata
– Guppy males are highly polymorphic for color patterns and their genetics has
been studied analysis since 1927 (Winge, Journal of Genetics 18, 1, 1927)
– The guppy has 23 pairs of chromosomes — 22 are autosomal and one sex
determining. Males are heterogametic (the sex determination mechanism is
XX/XY, and the YY genotype is viable)
– Almost all the genes determining guppy colour patterns (except for body color)
are sex-linked or sex limited (unlike what is found in other teleosts)
– though usually not fully sex-linked
•
Winge, O. 1927. The location of eighteen genes in Lebistes reticulatus. Journal of Genetics 18,. A
peculiar mode of inheritance and its cytological explanation. Journal of Genetics 12:137.
• With the possibility of using naturally occurring polymorphic
sequence variants as genetic markers, it is now possible to make a
more detailed genetic linkage map and find out if the Y has an
excess of male attractiveness factors
• Molecular markers have now been found on the Y chromosome,
closely (but none fully) linked to the sex-determining region, SdR.
– Shen et al (2007, Aquaculture 271:178-187) mapped the sex locus and nine
AFLP markers and four microsatellite DNA markers
•
Overall, the results suggest that the non-recombining MSY region may not
be very large, and that the colour variants may be controlled by
polymorphic genes in the PAR
4. HOW did recombination stop, how do MSY regions expand?
BUT the known
inversions on the
Y occurred
relatively recently,
and these cannot
be involved in
stopping
recombination
(since, in most of
the Y, it stopped
long ago)
SRY/
SOX3
Translocation
• "..there is little evidence demonstrating the importance of [chromosome
rearrangements versus genes modifying recombination] in the
evolution of X-Y crossover suppression! (Bull 1983)
• There are many inversions on the mammalian Y
Lahn & Page’s suggested evolutionary history
of the mammalian sex-chromosomes
Heterochromatic
region
X chromosomes
Human
Mammalian X chromosome gene
arrangements are stable, while Y
chromosomes are highly rearranged
PAR1 Yp
BUT inversions occurred since humans (or
split from chimpanzees
PSA)
and modifier genes can also change
recombination rates during evolution
NRY regions
recently transposed from the X
degenerated copies of X genes
“Ampliconic”
(duplications)
degenerated X
genes
inverted
PSA2
Yq
inverted
Chimpanzee
The most recent strata in the human MSY already has several inversions
• Stratum 5 may involve an inversion, but stratum 4 includes several inversions (
)
• The AMEL locus may span the ancestral boundary between human strata 3 and 4 , but the
X and Y genes are intact (Marais & Galtier. 2003. Curr. Biol. 13:R641-643)
• Rearrangements may thus be a consequence of lack of recombination
Stratum 5
PAR1
Ross et al.
2005. Nature
434:325-337
Stratum 4
Stratum 3
• The papaya MSY
regions have already
been rearranged, even
in just the two BACs so
far studied
• It is not known whether
these inversions caused
recombination to stop,
but the region is only a
small part of the MSY
• The rearrangement in
this region is shared by
the Y and Yh, and
differentiates both of
them from the X
• Thus it pre-dates the
evolution of
hermaphrodites
X from
hermaphrodite
Y from hermaphrodite
(Yh)
6.5 Mb
Y from male
Y from
hermaphrodite (Yh)
6.5 Mb
X from male
Y from male
X-Y divergence
(%)
13 - 19
2-4
10 - 13
Yu et al. 2008. Tropical Plant Biology 1: 49-57
Did X-Y recombination stop in S. latifolia due to inversions?
Y chromosome deletion map of the Y, based on 3 parental plants
A
C
B
In one parent plant, the Y
chromosomes gene SlY1 is in
a different location
In two parent plants the Y
chromosomes gene SlY6b is absent
Possible rearrangements in the Y, relative
to the X
Present X
gene order
Pseudoautosomal
Proto-Y1
Proto-Y2
Present Y
gene order
p arm
M
M
m
Suf
q arm
SuFemale
SuFemale
Paracentric
inversion
Pericentric
inversion
These results show that inversions happened after
X-Y recombination stopped
6. Why does stopping recombination lead to sex
chromosome degeneration?
•
It has been known since 1918 that classical Y chromosomes are degenerated
chromosomes
– Muller, H. J. 1918. Genetic variability, twin hybrids and constant hybrids, in a case
of balanced lethal factors. Genetics 3:422-499.
•
“It is probably needless to point out that the W and especially the Y
chromosome ….. show the expected evidences of …. degeneration and
differentiation from their homologues, both genetically and cytologically. The
evidences are now as follows:
– X-linked mutations affecting visible phenotypes are manifested in XY males
• therefore the Y does not carry alleles that can cover up mutations
– Infrequent dominant Y (and W) linked mutations”
– “Great variations in their own size and shape even in closely related species”
– Synaptic attraction between them and their homologues
• “but the sex chromosomes in the heterozygous sex tend to remain condensed during the
growth period, while the autosomes are spinning out for intimate conjugation, and there is
frequently delayed synapsis”
• “also lack of crossing over between them and their homologues, even …. where other
chromosomes are undergoing crossing over”
Y chromosome degeneration
• Loss of genes
– Well illustrated by classical sex chromosomes
• for example, the human X region that has been non-recombining longest has
the lowest proportion of intact genes on the Y (at most, 5), whereas the
probable number carried on the X chromosome is 734 (based on a count done
by Gabriel Marais, using Ensembl version 47)
• Worse gene function
– amino acid substitutions that reduce functioning
– less use of optimal codons
– expression levels changed relative to X (presumably wrong levels)
• Transposable element insertion is often included as an aspect of Y
degeneration, and degeneration may indeed be caused partly by
transposable element insertions, but we don’t actually know this
– it is possible that these insertions are neutral
– they could insert after genes or the sequences controlling their expression
have degenerated
DNA
content
(Mb)
Species
Human
Total
3,286
X 164 (5%)
Y 59 (1.8%)
Euchromatic
(Mb)
genes
> 3,000
150
~ 78
40,000
1148
21
11
7
0.35
114
76 for euchromatin
118
1-2
Drosophila
Total
180
> 120
13,600
X
Y
33
20
22
0
~ 2600
20 ???
Estimated number of
genes/Mb
CpG islands/Mb
Region and
stratum
Humans: we can
now compare
homologous X and
Y gene regions
6-43; mean 10.5
6
2.9
Numbers of
functional
genes
(numbers
ampliconic)
X and Y copies (X-degenerate)
1 (old X)
5 (4)
Genetic
degeneration
of Y
chromosomes
Pseudogene
numbers
Numbers with
male function
Numbers
with
ubiquitous
expression
0
4 (3 ampliconic)
1 (nonampliconic)
1
1 (ampliconic)
1 (ampliconic)
2
6
2
Regions added to X about 120 MYA (p arm)
Stratum 2
3 (1)
0
Stratum 3
7 (1)
3
Stratum 4
7
6 (2)
Recently X-transposed genes
—
3 (0)
0
1
0
Other genes on the Y but not the X
—
3 (3)
0
3
0
• NOTE that most of the genes
present on the Y are found in the
youngest stratum of the X (strata 3
and 4 in the initial paper on strata)
• This indicates that the older strata
are genetically degenerated and
have lost most of the genes that
were once on the Y
• Notice how helpful it is to have
identified genes, not just
anonymous markers or sequences
LAHN & PAGE, 1999 Four evolutionary strata on
the human X chromosome. Science 286: 964-967
G C T
A T
Leaf
X/Y4
Flower
Leaf
X/Y3
X/Y7
Leaf
CypX/Y
DD44
Gene
X/Y1
Leaf
Flower
Differences between X and Y
homologues, estimated using PCR
with primers recognising the same
sequence in X and Y alleles, and
flanking an intron
Pyrosequencing
Expression studies in S.
latifolia give some direct
evidence of low Y
function
C A
pyrosequencing primer
SlCypY AATTTGCACACCAACAAAGCATCACG
SlCypX AATTTGCACACCAACAAAGTATCACG
Work of Michael Nicolas
and Roberta Bergero
TE insertions do NOT necessarily cause loss of function
Two Silene latifolia Y genes
DD44
Y
S. latifolia
X
Work of Gabriel Marais
Blastn Y3 / Y3
Blastn Genbank
RepeatMasker (Repbase)
Blastx prot TEs Arabidopsis
S. vulgaris
(not sex-linked)
SlXY3
Y
X
Introns
LTR retrotransposon
Exons
Non-LTR retrotransposon
DNA transposon
Inverted repeats
Direct repeats
Another sign of
low effectiveness of
selection is
accumulation of
repetitive DNA on
Y chromosomes
Autosomes
Accumulation of retrotransposons on the
Drosophila miranda neo-Y chromosome
neo-Y chromosome
BACHTROG, D., 2003. Mol.
Biol. Evol. 20: 173-181.
Drosophila miranda
Transposable elements
Genes
The neo-Y is turning into heterochromatin
Active MITE insertions were
detected by searching for
polymorphic inserts in introns of
Silene latifolia genes
EITRI: 11-bp terminal inverted
repeats (5'-CTAGGTAGCAC-3') and
8-bp target site duplications (TSDs,
like hAT or P elemenst)
A Tourist-like element
M
Roberta Bergero & DC, in
press in Genetics
GAAATTCTTT//Sl-To1//TAGTTTC
GAAATT--------------TAGTTTC
GAACTTCTTC-----------AGTTTC
GAACTTCTTC-----------AGTTTC
GAACTTCTTC-----------AGTTTC
GAACTTCTTC-----------AGTTTC
Silene latifolia
Not Y-linked (none fixed)
Genetic mapping allows us to
find ones that are Y-linked
As predicted from population
genetics theory, MITE
insertions are generally at low
frequencies, but on the Y
chromosome they reach high
frequencies
Y-linked (3/25 fixed)
• Accumulation of transposable element
on Y chromosomes may promote
rearrangements
• Loss of a gene in primates: Nakayama &
Ishida. 2006 Genome Res. 16:485-490.
• Rearrangements may make it difficult to
Cytogenetic maps of the threespine
stickleback X and Y chromosomes,
based on FISH with genes
X
Y
detect X-Y heteromorphism
• Gene conversion between paralogs in the
human Y: Bosch et al. 2004. Genome
Res. 14:835-844.
inversion
X
Y
X
Y
Heteromorphic X-Y pair
deletion of part of Y
inversion on Y and/or insertion, making
heteromorphism hard to detect
deletion
Ross and Peichel. Genetics
2008;179:2173-2182
6. WHY are Y chromosomes degenerated?
I. The ‘sheltering hypothesis’ (the Y is
always heterozygous with an X)
•
“The reason for this rapid decay of things Y-chromosomal is thought to be
quite simple: once the Y chromosome became sex-determining, its
presence was limited to the heterogametic sex (in our case, males).
Because the Y chromosome was never found in the absence of an X
chromosome, there was presumably little selection against the
mutational inactivation of those genes on the Y chromosome that were
also present on the X chromosome. Thus, over evolutionary time,the Y
chromosome gradually lost most of its functional genes by the accumulation
of deleterious mutations, resulting in that little dab of male-determining
chromatin that we have today.”
– HAWLEY, R., 2003 The human Y chromosome: Rumors of its death
been greatly exaggerated. Cell 113: 825-828.
•
This is wrong — it ignores the central importance of the lack of
recombination
have
• It is a challenge to evolutionary biologists that a common
observation such as degenerate Y chromosomes is still
so far from being understood! (Bull 1983, p. 258)
• Genetic degeneration is probably NOT caused by the
fact that Y chromosomes are always heterozygous (as
Hawley assumed)
– Allowing recessive deleterious mutations to arise without major
effects on fitness
• but, more likely, by lack of X-Y recombination in a large
genome region
• To answer the important questions
– Why does lack of recombination lead to degeneration?
– How long does it take?
• we need to model non-recombining genomes, and such
models have largely answered Bull’s challenge
Evidence from modelling: the importance of loss of recombination
There are now several other theories for degeneration when there is no recombination
Selection for advantageous mutations causes fixation of
deleterious mutations , which reduces the effective population size
Many different sequences, one
carrying the deleterious mutation
Only a single sequence, i.e. all
carry the deleterious mutation
several
generations
Deleterious mutations prevent spread of advantageous
mutations unless their selective advantage is large
several
generations
Muller’s ratchet (probably less important)
10 different sequences
Genotype
number
1
2
3
4
5
6
7
8
9
Selection against
mutations reduces
the effective size
After many generations with stable
numbers of deleterious mutations
4 ancestral sequences
Ancestral
genotype
number
1
4
7
Loss of mutant-free class
8
Data from non-degenerated genes can
provide indirect evidence that degeneration
is occurring
• Degeneration is thought to be caused by lack of
recombination
– This changes evolutionary processes in several ways
– The different processes all cause lower “effective population size”
and thus they lead to low genetic variation
• Diversity studies can thus detect these processes
– If degeneration is happening, we should find lower diversity of Ylinked than X-linked genes
– We must take into account that the population size of X-linked genes
is 3 time higher than for Y-linked genes
This is expected if the effective size of
the Y is low
More autosomal genes are needed (we
cannot yet exclude the possibility that X
diversity is unusually high)
S. latifolia Y diversity is low compared
with homologous X-linked or
autosomal genes
Nucleotide diversity values (%)
To estimate subdivision for Y
and X genes within S. latifolia,
we sampled plants from 23
European populations, and
sequenced Y and X alleles
SlXY4
Y-linked
X-linked or autosomal
DD44
-XY SlXY1
SlXY7
Cyp-XY
It is expected that all Y diversity
estimates are similar— all nonrecombining parts of the Y have the
same recent history
Type of site
SlAp3
(Y vs.A)
Studying Y gene degeneration
(ii) Molecular evolutionary comparisons of X, Y and outgroup
sequences allows one to test whether the X or Y has changed, again
using non-degenerated genes
Outgroup
species
X
Y
chromosome chromosome
G
A
A
A G
substitution
Ancestral sequence
X chromosome
nucleotide
Y chromosome
nucleotide
Outgroup
nucleotide
X or Y changed
G
A
G
T
T
C
C
T
C
T
C
A
G
G
C
C
T
C
C
G
A
T
A
G
A
T
C
C
G
T
A
T
C
X
X
Y
X
Y
Y
Y
Y
Inferring the causes of degeneration
Maladaptation inferred from divergence
• If the neo-Y genes are acquiring harmful mutations that impair
their functionality, we expect to find more changes in functionally
significant sequences in the ancestry of the neo-Y copies than the
neo-X copies (e.g. more non-synonymous substitutions).
The opposite is true if the neo-X
genes experience adapt more
than the neo-Y
We can test this by sequence
comparisons (X-Y
or along the
2 lineages
)
Y
X
outgroup
A consistent pattern in X-Y divergence
across many genes in D. miranda is
difficult to explain by a higher Ka than
Ks due to molecular adaptation of the
Y (it would be strange if all Y genes
were adapting)
Bachtrog, D. 2005. Genome
Research 15:1393-1401
Chicken compared with turkey
Chicken Z
Turkey Z
Chicken W
Turkey W
The W chromosome (restricted to females) has relatively more
non-synonymous substitutions (higher Ka/Ks) than the Z
Berlin & Ellegren. 2006. Journal of Molecular Evolution 62:66-72
In Silene latifolia genes, Gabriel Marais sees both failure of selection to
prevent deleterious substitutions, and favorable changes switching to neutral
Gene
(Numbers of
codons
analyzed)
Site model
indicates purifying
selection at all loci
Branch model
X versus Y
dN/dSX dN/dSY
Significance
Branch-site analysis suggests
weak efficacy of selection on Y
% of codons suggesting degeneration, and
changes in Y versus X and outgroup (to
neutral evolution or positive selection)
SlX1/Y1 (458)
100% ! <<1
10-4
0.11
X < Y***
6%
No significant switching
SlCypX/Y (519)
94% ! <<1
6% w~1
0.14
0.14
X=Y
10%
No significant switching
SlssX/Y (259)
97% ! <<1
3% ! >1
0.18
0.23
X < Y ns
0
No significant switching
63% ! <<1
36% ! ~1, 1% ! > 1
0.13
0.90
dNX=dNY=dSY
(all low values)
5.5% under positive selection (!=14.8)
Significant switching to positive selection
SlX3/Y3 (318)
95% ! <<1
5% ! ~1
0.04
0.13
X < Y*
4% under positive selection (! =3.5)
Significant switching to positive selection
SlX7/Y7 (246)
88% ! <<1
12% ! ~1
0.08
0.11
X < Y ns
4%
No significant switching
SlX4/Y4 (362)
92% ! <<1
6% ! ~ 1, 2% ! > 1
0.11
0.25
X < Y*
14%
Significant switching to neutrality
DD44X/Y (217)
Significance of differences in LR tests: ns = non-significant, * p < 0.05, *** p < 0.0005
Male sterility, m
Female fertility
Summary of steps in the
evolution of the Y
Maleness factor, M
Female suppressor, SuF
Proto-X and Y
1
Addition of male function
genes, further recombination
suppression,
rearrangements Loss of parts
of Y
M2
small
MSY
region
MSY
Evolution of a sexSuF
determining region in
M
Suppressed
an ancestral
recombination on
chromosome pair,
part of proto-Y
forming a nonTransposable element
heteromorphic pair
2
The simplest evolutionary
model suggests that males
and females evolved from
hermaphrodites by loss of
functions
Newest SuF
stratum M
Oldest
stratum
PAR
accumulation and
Some plants,
expanded MSY
fish, snakes
region
3
4
m
M2
Y X
Classical
(humans and
Drosophila)
5
Some consequences of sex chromosome
evolution
•
In species with XY systems
– The Y chromosome may acquire genes with male functions
– Genes with male functions may also evolve more readily on the X than the
autosomes, because the X spends a higher proportion of its evolutionary history
in males than females
•
If degeneration has occurred, then, at most X-linked loci XY males have
only one gene copy, compared with XX females’ two copies
– except for a few housekeeping genes on both X and Y
•
•
Some species have evolved control of levels of expression so that levels of
X-linked gene products are correct, relative to expression of other genes:
dosage compensation
The X must therefore undergo considerable evolutionary change
•
The compensation mechanisms are different in different organisms
inactivation of one X
The simplest
solution is overexpression of the X
in males
2X 2A X 2A
Females
Males
Mammals
low expression
of both Xs
Dosage compensation mechanisms in different organisms
2X 2A X 2A 2X 2A XO 2A
Females Males
Drosophila
“Females” Males
C. elegans
The Chimpanzee Sequencing
and Analysis Consortium 2005
Nature 437: 69-87.
Number of 1 MB
windows
Human-chimpanzee
divergence
Over all sites, genes on the
mammalian X evolve more slowly
than autosomal genes (indicating
selective constraints, which are
more important on the X because
of hemizygosity in males) and the
Y evolves unusually fast (because
there is a higher mutation rate in
males, due to multiple cell
divisions in spermatogenesis)
Autosomes
X
Human-chimpanzee divergence
Y
X
•
•
The PSA recombines at a much
higher frequency than the rest of the
X, increasingly so as its size is
restricted by evolution of new strata
High recombination may also cause
a high mutation rate (if recombination
causes mutations)
The PSA is smaller in
humans than other
mammals, because the
boundary has moved
towards the tip,
compare with its
location in bovine X
chromosomes
and in mice it is small
due to movement of
genes off the X
Van Laere A. et.al. Genome Res. 2008;18:1884-1895
7. What about other non-recombining systems?
• WHY did recombination stop, and what are the consequences, e.g. do
these genome regions degenerate?
• Some fungal incompatibility systems
– Different loci (pheromones and receptors) are involved at some of these
“loci”, and are sometimes present in inverted regions, but the selective
reason for lack of recombination is unknown
• Lee et al. 1999. The mating-type and pathogenicity locus of the fungus Ustilago hordei
spans a 500-kb region. PNAS 96:15026-15031.
– Some seem to have undergone degeneration. Allelic forms of the genome
region each lack genes found in the other orthologous region
– TEs are sometimes abundant (50% in U. hordei, maybe accumulated, but
comparisons with other genome regions should be made)
• Bakkeren et al. 2006. Fungal Genetics and Biology 43: 655-666
• Angiosperm self-incompatibility systems (SI, S-allele systems)
– Alleles at two different loci (encoding pollen and pistil function proteins) must
be present in the correct combinations, which would lead to selection
against recombination, but it is not yet certain whether these regions do
have unusually low recombination
– Studies testing whether homozygotes for the same allelic form at these “loci”
are disfavoured (suggesting “linked load”) are not yet conclusive
Fungal and algal mating type loci are NOT sex chromosomes,
but they show some very similar evolutionary behaviour, e.g.
the mating-type locus of Cryptococcus fungi
FRASER et al.,
2004 PLoS
Biology 2: 22432255
" type
Rearranged regions
a type
Non-diverged
region
Regions of high a-"
divergence
Non-diverged
region
This is like a neosex chromosome
system — a part
was added recently
NOTE: incorrect use of the word
‘rate’ (they mean ‘divergence’)
• In Neurospora tetrasperma, there is a non-recombining
region whose function is to link the incompatibility gene
region to the centromere, guaranteeing first division
segregation and thus compatibility among pairs of
meiotic products (a mechanism for self-fertilisation)
• This region has expanded
– Divergence between genes in the two haplotypes varies in a
pattern like the sex chromosome strata
• Menkis et al. 2008. The mating-type chromosome in the
filamentous ascomycete Neurospora tetrasperma represents a
model for early evolution of sex chromosomes. PLoS Genetics 4
– The expansion is due to an inversion and the effects of
modifier genes
• Jacobson 2005. Blocked recombination along the mating-type
chromosomes of Neurospora tetrasperma involves both structural
heterozygosity and autosomal genes. Genetics 171:839-843.
Frequency-dependent selection in plant selfincompatibility maintains many alleles
• Genotypes’ survival or fertility (or both, often,
for brevity, called “fitness”) depend on the
frequencies in the population
• e.g. plant self-incompatibility
– When an allele is rare, it will usually land on
stigmas of plants that do not have that allele,
and will thus be compatible with most of the
population. Rare alleles have a fertility
advantage
• Frequency dependent selection also occurs in
the interactions between plant defence genes
and pathogens
Two linked incompatibility loci (S-genes) are involved
Sporophytic
system Sloci in
Arabidopsis
species
SRK
SCR
Physical
map after
Kusaba et
al., 2001
NOTE: Differences in gene copy numbers and arrangement in Arabidopsis (and
Brassica) suggest suppressed recombination.
Gametophytic
system S-loci
0.6
0.5
Silent site diversity
#s
0.4
0.3
of diversity
between SRK classes
Kat
0.8
0.6
0.4
0.2
0
-0.2
0.6
0.5
Proportion of diversity
between actual populations, Kst
**
**
0.4
0.3
***
*
0.2
0.1
S8
SRK
S12
B160
-0.1
Aly8
0
B80
– Diversity and subdivision between
alleles are low (there are no
associations between SRK alleles and
those at the distant loci)
– But subdivision between populations
of this species is high (for unlinked
reference loci, Kst values between
European populations is ~ 0.65)
******
***
Proportion
1
SRK
• But far from the SRK locus
0
S4
– diversity within types is low, but overall
diversity is high, because subdivision
between alleles is high (Kat values),
but unusually low between populations
0.1
B70
• Close to SRK
0.2
S2
• Treating SRK alleles as “populations”,
we measured diversity within each
allele type, and “subdivision” between
them
B120
• In Arabidopsis lyrata, there is
evidence that a region around the Slocus has low recombination
Gene
Significance
tested by K*
using
randomization
• Even if the S-locus region has low recombination, it may be too
small (contain too few genes to drive the processes described
earlier) to undergo genetic degeneration
• The possibilities were reviewed by Uyenoyama, M. K. 2005.
Evolution under tight linkage to mating type. New Phytologist
165: 63-70.
• Some empirical tests have suggested that individuals identical
by descent for S alleles may have low survival
• BUT it is difficult to test more than a few alleles
– one has to compare homozygotes and heterozygotes, matching
their inbreeding coefficients, I.e. ensuring that both sets are noninbred (otherwise inbreeding depression might be the cause of
lower survival of homozygotes)
– it is also hard to rule out an early effect of the incompatibility
(which might slow the growth of the pollen that would generate
homozygotes, and might lead the maternal plant to abort those
zygotes)