Download Accelerated Evolution of Sex Chromosomes in

Accelerated Evolution of Sex Chromosomes in Aphids, an X0
System
Julie Jaquiéry,1,* Solenn Stoeckel,1 Claude Rispe,1 Lucie Mieuzet,1 Fabrice Legeai,1,2 and
Jean-Christophe Simon1
1
Institut National de Recherche Agronomique (INRA), Unité Mixte de Recherche 1099, Biology of Organisms and Populations
Applied to Plant Protection, Le Rheu, France
2
INRIA Centre Rennes—Bretagne Atlantique, GenOuest, Rennes, France
*Corresponding author: E-mail: [email protected].
Associate editor: John Parsch
Abstract
Key words: effective population size, faster-X effect, genetic diversity, inheritance, sex chromosome, X chromosome.
Introduction
Sex chromosomes exhibit several unusual properties such
as sex-specific inheritance patterns, hemizygosity, and reduced recombination (Vicoso and Charlesworth 2006).
Hence, these chromosomes are expected to differ from autosomes in their response to evolutionary factors (e.g., drift,
demography, and selection) and can help elucidate the relative importance of these forces to genome evolution. Several empirical studies outlined lower levels of genetic
diversity on the X relative to the autosomes in a wide range
of species and tried to disentangle the several possible
mechanisms that could account for this difference (e.g.,
Moriyama and Powell 1996; Begun and Whitley 2000;
Sundström et al. 2004; Geraldes et al. 2008; Ellegren
2009; see also table 1).
In XY systems, the effective population size of the X is
three-fourths that of the autosomes because under 1:1 sex
ratio and equal variance in reproductive success between
sexes, there are three copies of the X per mating pair but
four copies of the autosomes (Wright 1931; Caballero 1994,
1995). Thus, the X is more exposed to genetic drift, leading
to an expected X:A diversity ratio of three-fourths. However, this ratio might be further affected by several demo-
graphic factors. For example, a higher variance in male
reproductive success or female-biased dispersal will increase this ratio above three-fourths (the reverse would decrease it below three-fourths) since the Xs are more often
transmitted by females than males compared with the autosomes (Caballero 1995; Charlesworth 2001; Laporte and
Charlesworth 2002). Bottlenecks or population expansions
alter the X:A diversity ratio, too, because the effective population size determines the rate of convergence to the new
diversity equilibrium (Wall et al. 2002; Pool and Nielsen
2007). Additionally, both mutation and recombination
rates differ between the X and the autosomes. Given that
the X is transmitted more often through females than the
autosomes, male-biased mutation (i.e., a higher mutation
rate in males because of the large number of germ cells divisions required for spermatogenesis, Miyata et al. 1987; Li
et al. 2002) will lower mutation rate on the X and hence
X-linked diversity relative to autosomes (Ellegren 2007).
All else being equal, recombination is also predicted to be
lower on the X because autosomes recombine in both males
and females and the X only in females (Hedrick 2007) (but
note that recombination is predicted to be higher on the X
chromosome in Drosophila, since males do not recombine,
© The Author 2011. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. All rights reserved. For permissions, please
e-mail: [email protected]
Mol. Biol. Evol. 29(2):837–847. 2012 doi:10.1093/molbev/msr252
Advance Access publication October 13, 2011
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Research article
Sex chromosomes play a role in many important biological processes, including sex determination, genomic conflicts,
imprinting, and speciation. In particular, they exhibit several unusual properties such as inheritance pattern, hemizygosity,
and reduced recombination, which influence their response to evolutionary factors (e.g., drift, selection, and demography).
Here, we examine the evolutionary forces driving X chromosome evolution in aphids, an XO system where females are
homozygous (XX) and males are hemizygous (X0) at sex chromosomes. We show by simulations that the unusual mode of
transmission of the X chromosome in aphids, coupled with cyclical parthenogenesis, results in similar effective population
sizes and predicted levels of genetic diversity for X chromosomes and autosomes under neutral evolution. These results
contrast with expectations from standard XX/XY or XX/X0 systems (where the effective population size of the X is threefourths that of autosomes) and have deep consequences for aphid X chromosome evolution. We then localized 52
microsatellite markers on the X and 351 on autosomes. We genotyped 167 individuals with 356 of these loci and found
similar levels of allelic richness on the X and on the autosomes, as predicted by our simulations. In contrast, we detected
higher dN and dN/dS ratio for X-linked genes compared with autosomal genes, a pattern compatible with either positive or
relaxed selection. Given that both types of chromosomes have similar effective population sizes and that the single copy of
the X chromosome of male aphids exposes its recessive genes to selection, some degree of positive selection seems to best
explain the higher rates of evolution of X-linked genes. Overall, this study highlights the particular relevance of aphids to
study the evolutionary factors driving sex chromosomes and genome evolution.
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Jaquiéry et al. · doi:10.1093/molbev/msr252
Table 1. Factors Influencing X:A Diversity Ratio in Standard XX/XY or XX/X0 Systems and in Aphid-Like Systems.
Effect on X:A Diversity Ratio in Standard XX/XY or XX/XO
Systems
Effect on X:A Diversity Ratio in Aphid-Like Systems
(XX/X0)
Mechanisms
Mechanisms
Number of
chromosome
copies (X vs. A)
Yes (2)
NeX 5 3/4 NeA
No
NeX 5 NeA
Variance in
reproductive
success between
the sexes
Yes (1/2)
X is transmitted two-thirds of
the time by females; A half of the time
No
Both X and A are transmitted
half of the time by females
Sex-biased dispersal
Yes (1/2)
X is transmitted two-thirds of the
time by females; A half of the time
Noa
Both X and A are transmitted
half of the time by females
Bottleneck or
population expansion
Yes (1/2)
Ne determines the rate to reach
6 NeA
equilibrium 1 NeX ¼
No
Ne determines the rate to reach
equilibrium 1 NeX 5 NeA
Male-biased mutation
(i.e., higher mutation
rate m in males)
Yes (2)
X is transmitted two-thirds of the time
by females; A half of the time (so mX < mA)
No
Both X and A are transmitted
half of the time by females
(so mX 5 mA)
Recombination
rate r
Yes (1/2)
If only females recombine
(e.g., Drosophila):
d Both X and A recombine
only in females
No
In aphids, only females
recombine:
d Both X and A recombine
only in females
d Both X and A are transmitted
half of the time by females
0rX 5 rA
d X is transmitted two-thirds
of the time by females; A half of
the time
0rX > rA
Then selection similarly
affects diversity on the X and
autosomes through hitchhiking
effects because rX 5 rA
If both males and females
recombine (e.g., mammals):
d X recombines in females;
autosomes in both sexes
d X is transmitted two-thirds
of the time by females; A half of the time
0rX < rA
Then for both cases mentioned,
selection differentially affects linked
diversity on the X and autosomes through
hitchhiking effects because rX 6¼ rA
Positive or
background
selection on
new or standing
variation
Yes (1/2)
The hemizygosity of the X in
males exposes X-linked genes
to selection more than autosomal
genes
Yes (1/2)
The hemizygosity of the X in
males exposes X-linked genes to
selection more than autosomal genes
NOTE.—Signs in brackets show the direction of the effect.
a
A marginal effect (þ or ) can be expected under sex-biased dispersal combined to an extreme success of reproduction of migrant individuals.
Connallon 2007). Recombination in turn determines how
positive (Maynard-Smith and Haigh 1974) and background
selection (Charlesworth et al. 1993) impact on linked genes.
Furthermore, X-linked recessive alleles are exposed to selection in the heterogametic sex, whereas autosomal recessive
alleles are not exposed until they reach frequencies large
enough to allow them to appear as homozygote. Therefore,
selection is predicted to be more efficient on genes on the X
(Charlesworth et al. 1987; Vicoso and Charlesworth 2006),
and this will in turn increase or decrease the X:A diversity
ratio, depending on whether selection acts on standing variation or new mutations (Charlesworth et al. 1987; Orr and
838
Betancourt 2001; Betancourt et al. 2004). However, it is important to stress that the various evolutionary factors discussed here do interact (Ellegren 2009). Hence,
disentangling the evolutionary causes (e.g., drift, demography, and selection) of unequal diversity levels between
the X and the autosomes in XX/XY systems remains challenging.
In this context, organisms with alternative modes of inheritance of sex chromosomes can be valuable models to
better understand forces driving sex chromosome evolution.
For instance, the X chromosome of aphids shares some characteristics with the X of species with XX/XY sex-determining
Faster-X Evolution in Aphids · doi:10.1093/molbev/msr252
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FIG. 1. Annual life cycle of the pea aphid and ploidy levels for autosomes (A) and sexual chromosome (X). Overwintering eggs, diploid for both
types of chromosomes (AA and XX), give birth to an asexual female. After 10–20 generations of apomictic parthenogenesis, asexual females
produce (by parthenogenesis) sexual females and males. Males inherit the same autosomal genome as asexual females but receive only one of
the female Xs: hence, they are diploid for the autosomes and haploid for the X (represented as AAX0). Ovules (haploid for both the autosomes
and the X) are generated by a normal meiosis, but males produce only X-bearing sperm (AX). The fusion of male and female gametes restores
the diploid level at both the X and the autosomes and generates asexual females.
systems (e.g., the X is present in single copy in male aphids),
but its inheritance pattern is different; hence, the forces driving aphids’ X chromosome evolution must differ. Aphids
have an XX/X0 sex determination system whereby females
carry two X chromosomes and males only one (whereas
both sexes have three diploid autosomes) (fig. 1). A major
difference between aphids and other XX/XO organisms
such as some nematodes (e.g., Caenorhabditis elegans,
Pires-DaSilva 2007), insects (e.g., grasshopper, crickets, and
cockroaches, Tatsuta et al. 2006; Kaiser and Bachtrog
2010), or molluscs (Thiriot-Quievreux 2003) comes from
the peculiar pattern of inheritance of the aphid X chromosome in a life cycle combining sexual and asexual reproduction (see fig. 1). Indeed, the aphid life cycle involves several
rounds of apomictic parthenogenesis, followed by a single
event of sexual reproduction in autumn (fig. 1). Sexual individuals are produced by apomictic parthenogenesis, the
males inheriting randomly only one of the asexual female
Xs (Wilson et al. 1997; Caillaud et al. 2002). Since males produce exclusively X-bearing gametes (i.e., haploid for the X
and for the autosomes), the fusion of male and female gametes restores the diploidy of the X and autosomes to generate an asexual female (figs. 1 and 2). Therefore, in the
asexual progeny produced from sexual reproduction, half
of the autosomes and X chromosomes originate from the
mother and the other half from the father (fig. 2C). This differs from the pattern of X chromosome inheritance in standard XX/X0 or XX/XY systems whereby female offspring
receive one maternal and one paternal X chromosome,
but males only inherit the maternal X copy (fig. 2A and
B). Though a priori minor, this difference between aphids
and other standard systems has deep consequences
for the evolutionary trajectory of the aphid X chromosome
(table 1).
Since both male and sexual female aphids transmit one
set of autosomes and one of their X chromosomes to the
progeny during sexual reproduction, we predict similar effective population sizes for X chromosome and autosomes
(i.e., NeA 5 NeX), and so an X:A diversity ratio equal to one
(this hypothesis is validated by simulations in the present
study). Hence, bottlenecks or population expansions do
not affect differentially the genetic diversities on the X
and on the autosomes, since these diversities converge
to the new equilibrium at the same rate. In addition,
any variance in sex-specific reproductive success will have
NeX
the same effect on the X as on the autosomes, leaving Ne
A
unchanged. This result arises because the same proportion
(50%) of the X and autosomes in the progeny is paternally
inherited, so that both the X and the autosomes are similarly impacted by any sex-specific variance in reproductive
success. This contrasts to standard XX/XY or XX/XO systems where autosomes and X are differentially affected because half of the autosomes are paternally inherited in the
progeny but only 1/3 of the Xs. A similar argument can be
raised to explain why sex-biased dispersal similarly affects X
NeX
and the autosomes in aphids, also leaving Ne
unchanged.
A
Interestingly, we also expect male-biased mutation to similarly affect X chromosome and autosomes in aphids, since
the same proportion (50%) of autosomes and X chromosomes are paternally inherited and thus have experienced
the higher mutation rate occurring in males. Additionally,
we predict no a priori difference in recombination rate between X and autosomes in aphids. This prediction also differs from that for standard XX/XY systems, where the X is
predicted to recombine less than autosomes when males
recombine (Ellegren 2009) or more than autosomes in species with male achiasmy (e.g., Drosophila, Connallon 2007).
The aphid system resembles that of Drosophila because
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Jaquiéry et al. · doi:10.1093/molbev/msr252
FIG. 2. Inheritance of the X chromosome in XX/XY, standard XX/X0, and aphid-like XX/X0 sex-determining systems. Whereas males transmit
their X chromosome to only half of their progeny (i.e., only to daughters) in XX/XY (A) and standard XX/X0 sex-determining systems (B), male
aphids transmit their X to 100% of their progeny (C).
there is also no recombination during spermatogenesis
(Sloane et al. 2001; Hales et al. 2002). Nevertheless, we predict different X:A recombination rates between aphids and
Drosophila. The key point is not to consider the proportion
of Xs and autosomes that recombine in the parental generation (two-thirds of the Xs and half of the autosomes
recombine in the parents in both aphids and Drosophila)
but to consider the proportion of chromosomes actually
transmitted to the progeny that have recombined in the
parents. Indeed, in Drosophila, two-thirds of the Xs found
in the progeny have recombined (against half of the autosomes), resulting in a larger rate of recombination for the X.
By contrast, in aphids, the progeny from sexual crosses always inherits one X from the mother and the second from
the father since male aphids transmit their X to all their
progeny (fig. 2C). Autosomes are also evenly transmitted
by mothers and fathers. As a result, 50% of the Xs and
50% of the autosomes found in the progeny have recombined in the parents, leading to a 1:1 X:A expected recombination rate in aphids. Therefore, we expect X-linked and
autosomal diversities to be similarly eroded by positive or
background selection acting on linked genes. By contrast,
a shared feature between aphid X chromosome and the X
from standard XX/X0 and XX/XY systems is the hemizygosity of the X in males, which exposes X-linked recessive genes to selection. This in turn affects X:A diversity
ratio through the influence of selective sweeps or background selection on linked loci. Note also that the faster-X effect (i.e., an accelerated rate of evolution of Xlinked genes, Charlesworth et al. 1987) due to the fixation
of beneficial mutations is predicted to be particularly
strong in aphids that combine large effective population
NeX
sizes and a large Ne
ratio compared with other species
A
(Vicoso and Charlesworth 2009; Mank, Vicoso, et al.
840
2010). Overall, a difference in X:A diversity ratio would
be more straightforward to interpret in aphids than in
conventional XX/XY systems, since fewer factors affect
this ratio (table 1).
This study aims to disentangle the different evolutionary
factors driving X chromosome evolution in the pea aphid
(Acyrthosiphon pisum), whose genome has recently been sequenced (International Aphid Genomics Consortium 2010).
To this end, we first verified through simulations that the
effective population size of the X chromosome equals that
of autosomes in an aphid-like sex determination system. In
a second step, we assessed the genetic diversity in these two
types of chromosomes using 45 X-linked and 311 autosomal
microsatellite loci typed on 167 individuals. Finally, we compared the rate of evolution of genes on the X and on the
autosomes by identifying orthologs between A. pisum and
three other aphid species.
Materials and Methods
Assessing X and Autosome Effective Population
Sizes in Aphids
NeX
To compare the Ne
: NeX ratio in organisms with an aphidA
like XX/X0 system (e.g., aphids and the nematode Strongyloides ratti, Harvey and Viney 2001) and in those with an
XX/XY system, we simulated the action of genetic drift on
X-linked and autosomal genes in R (R Development Core
Team 2010). At cycle 0, two alleles at one X-linked locus
and one autosomal locus were randomly assigned to
100 asexual females (AA XX) from a uniform distribution
considering 30 possible allelic states. Then, the 10–20 generations of asexual reproduction occurring in spring and
summer (fig. 1) were modeled by drawing the number
of clones generated by each of the 100 initial female lineage
Faster-X Evolution in Aphids · doi:10.1093/molbev/msr252
from a geometric distribution with mean 5 0.02 (with this
value, each initial lineage produced 48.7 ± 49.1 [mean ±
standard deviation] asexual females that reached the last
generation before the production of sexual females and
males). Each of these newly generated asexual females then
produced on average (Poisson distribution) five sexual females and five males parthenogenetically (males randomly
lost one of their X chromosome). Finally, offspring (asexual
females) were generated by randomly drawing with replacement one female gamete and one male gamete produced by sexual individuals (see figs. 1 and 2). We repeated
this step until 100 offspring were generated, to start a new
cycle. Simulations were run for ten cycles (a cycle corresponds to several rounds of asexual reproduction followed
by one event of sexual reproduction, e.g., fig. 1), and 50,000
independent replicates were performed. Expected heterozygosities (Nei 1987) were computed for the autosomal
and the X-linked loci at every cycle t after sexual reproduction (HA,t and HX,t) and were then averaged over the 50,000
replicates. Effective population sizes (Nei) for both the autosomal (NeA) and the X-linked (NeX) loci were estimated
from the rate of loss of genetic diversity during the last cyHi;t
cle as Nei 5 2ðHi;t H
. In our simulations, fecundities were
i;tþ1 Þ
chosen within the lower tail of values observed in aphids to
ensure conservative results. By contrast, the number of allelic states and the size of the population do not influence
NeA:NeX ratio and were thus chosen arbitrarily. Since we
estimated NeA and NeX from the rate of loss of diversity
at one locus within one cycle in a small population (i.e.,
100 individuals), we expect a large variance for this estimate
because of the stochastic process of inheritance of alleles.
We therefore performed an important number of replicates (i.e., 50,000) to obtain an accurate estimation of mean
NeA and NeX (alternatively, we could have estimated Ne
over a larger number of cycles, but this would have led
to similar results).
We ran analogous simulations to compute effective population sizes for X-linked and autosomal loci in a standard
XX/XO or XX/XY system (i.e., where males transmit their X
chromosome only to their daughters). In that case, the adult
population consisted of 50 males and 50 females, and 100
offspring (50 males and 50 females) were randomly generated by drawing with replacement one female gamete (AX)
and one spermatozoid (either AX to generate females or AY
to generate males) from the pool of gametes generated by
the adults.
Comparison of Genetic Diversities on the X versus
Autosomes in Pea Aphid Populations
DNA extraction was carried out as in Peccoud et al. (2008)
on 167 individuals from nine European pea aphid populations collected on three different host plants (supplementary table S1, Supplementary Material online). Several
independent extractions of genetically identical individuals
(clones) from each of the 167 lineages were required to
obtain enough DNA to genotype these 167 individuals at
403 loci (for primer sequences, see supplementary table
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S2, Supplementary Material online). Three hundred and
seventeen of the microsatellite loci were located within
EST contigs or at an average distance of 1.4 kb from the closest predicted gene (International Aphid Genomics Consortium 2010) (hereafter referred to as loci in ‘‘coding region’’).
The 86 remaining loci were located at more than 30 kb
from any predicted genes (average distance to the closest
gene is 47 kb) (hereafter referred to as loci in ‘‘noncoding
region’’). Polymerase chain reaction (PCR) amplification
and genotyping for loci AlA09M, AlB07M, AlB12M,
ApF08M, ApH10M, and AlB08M were performed as in Peccoud et al. (2008). The 397 remaining loci were amplified
individually in 10 ll PCR. The mix included approximately
20 ng of DNA, 0.4 U of Taq, PCR buffer at 1 final concentration, 2 mM of MgCl2 (all products from Promega),
0.2 mM of each dNTP, 0.4 lM of forward and reverse primers, and 0.36 lM of a universal primer labeled with either
6-FAM, VIC, NED, or PET fluorescent dyes (DyeGTGCTGCAACATTTTGCTG) (Schuelke 2000). Amplifications were performed on Tetrad PTC-225 (MJ Research) or
C1000 (Biorad) Thermo Cyclers. Conditions of the PCR amplification are as follows: 95 °C (5 min), then 20 cycles at
95 °C (1 min)/58 °C (1 min)/72 °C (1 min 30 s), followed by
20 cycles 95 °C (1 min)/53 °C (1 min)/72 °C (1 min 30 s),
and a final extension at 72 °C for 10 min. Two microliters of
PCR product from four loci with nonoverlapping amplicon
sizes and each labeled with a different dye were added to
150 ll H2O. Two microliters of this solution were then
added to 5 ll of formamide and 0.05 ll of 500 Liz DNA
Ladder (Applied Biosystems). Samples were run on an
ABI 3730 or ABI 3130 and we determined allelic scores with
Genemapper 3.7 (Applied Biosystems). Allelic richness was
estimated for each of the nine populations assuming a minimal sample size of six individuals with FSTAT 2.9.4 (Goudet
2005) on the 356 loci (of 403) that successfully amplified in
most of the 167 individuals (see supplementary table S2,
Supplementary Material online). The chromosomal localization of each microsatellite marker was performed as in
Wilson et al. (1997) by looking at the pattern of inheritance
of alleles in 6–28 families made up of an asexual mother
and 2 of her sons (we used the families generated by Frantz
et al. 2006). Briefly, a heterozygote female will produce heterozygote sons at autosomal loci but her sons will appear
homozygote for X-linked loci since males inherit only one
of their mother Xs.
The effects of the chromosome (X chromosome vs. autosomes) and type of loci (within coding regions or not) on
allelic richness were assessed in R (R Development Core
Team 2010) using the following linear mixed-effect model
(R package Lme4, Bates and Sarkar 2007) fitted with REML
(REstricted Maximum Likelihood): Allelic richness ; Number of Repeats þ Motif Size þ Chromosome þ Type of Loci
þ Population þ Host Plant þ Loci. Population, Host Plant,
and Loci were set as random factors, accounting for the
structure of the data. The other effects, namely the Number
of Repeats (measured on the genome sequence of the pea
aphid, International Aphid Genomics Consortium 2010),
Motif Size (di-, tri-, or tetranucleotide), Chromosome,
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1
0
−1
−2
Residuals for allelic richness
2
3
Jaquiéry et al. · doi:10.1093/molbev/msr252
Autosomes
X
Within non−coding area
Autosomes
X
Within coding area
FIG. 3. Effects of chromosome type (X or autosomes) and locus
position (within coding areas or not) on allelic richness estimated as
residuals from the partial mixed-effects model.
and Type of Loci were set as fixed effects. The effect of
each variable was tested by likelihood ratio tests based on
the drop in Akaike’s information criterion following the
inclusion of the focal variable into the partial model comprising all other variables. Since Motif Size had no effect
of allelic richness (P 5 1), it was removed from the models. To graphically look at the effects of Chromosome (X
vs. autosomes) and Type of Loci (within coding regions or
not) on allelic richness (fig. 3) once other effects were
accounted for, residuals for allelic richness for each locus
were extracted from the partial model: Allelic richness ;
Number of Repeats þ Population þ Host Plant þ Loci.
Linkage disequilibrium between pairs of loci was calculated with FSTAT 2.9.4 (Goudet 2005). We then measured
the proportion of pairs showing significant linkage disequilibrium (at P , 0.05) for loci that were both located on 1)
the X or 2) autosomes (in that case, we are not able to
distinguish whether both loci are located on the same autosome). As a result, even under similar X and autosomes
recombination rates, we expect a slightly larger linkage disequilibrium for loci on the X than for those on autosomes.
Evolutionary Rates of Genes Located on the X
versus Autosomes
The 403 microsatellite loci that had been assigned to the X
(52 loci) or to the autosomes (351 loci) were then located
on the genome sequence of the pea aphid (Acyr 1.0 assembly, International Aphid Genomics Consortium 2010), allowing us to assign 47 scaffolds (genomic DNA
fragments) to the X chromosome and 323 to the autosomes. Orthologs between A. pisum genes located on these
scaffolds (International Aphid Genomics Consortium 2010)
and coding sequences (CDSs) reconstituted from ESTs databases from three aphid species (Acyrthosiphon kondoi:
842
23,046 ESTs, Myzus persicae: 27,728 ESTs, and Aphis gossypii:
88,851 ESTs) were then identified following reciprocal best
blast hit criterion (RBH). Translated sequences were aligned
using T-coffee (Notredame et al. 2000), nucleic sequences
being then aligned using the proteic alignment as a guide.
Alignments were trimmed using Gblocks (Castresana 2000;
Talavera and Castresana 2007) with default parameter
values. We then estimated maximum likelihood pairwise
synonymous (dS) and nonsynonymous (dN) evolutionary
rates for each gene, using a codon-based model (Codeml
from PAML, Yang 1997). For each species comparison,
genes located in the upper 5% tail for dS values (when considering X-linked and autosomal genes together) were eliminated as well as those with dN . 0.2. We combined these
two thresholds because it allowed eliminating paralogous
genes and those containing errors in their EST-based sequence. Overall, 26 genes (of 512) were eliminated for
the comparison between A. pisum and A. kondoi (50/
842 for A. pisum vs. M. persicae and 67/864 for A. pisum
vs. A. gossypii, respectively). The eliminated genes represented 5%, 5%, and 7% of autosomal loci and 4%, 15%,
and 12% of X-linked loci for comparisons between A.
pisum–A. kondoi, A. pisum–M. persicae, and A. pisum–A.
gossypii, respectively.
Differences between dN (dS and dN/dS, respectively) for
X-linked and autosomal genes were tested using two-sided
Mann–Whitney tests, independently for each pair of species. A global analysis (overall species) was also performed
using the following linear mixed-effects model (fitted with
REML): y ; Chromosome þ Gene Expression Level þ Gene
þ Species Comparison, where y is dN, dS, or dN/dS. Gene
and Species Comparison were set as random factors and
Chromosome (X vs. autosomes) as fixed. Gene Expression
Level (log[x þ 1] transformed) was included as a fixed-effect covariable and was roughly estimated by counting the
ESTs from A. pisum supporting each gene used for dN/dS
estimation by using Blastn between the published approximately 204,800 A. pisum ESTs and the 34,603 predicted
genes (International Aphid Genomics Consortium 2010).
The significance of Chromosome and Gene Expression
Level were tested by likelihood ratio tests.
Finally, we also tested for a difference in expression levels
(based on ESTs counts) between X-linked and autosomal
genes using a two-sided Mann–Whitney test.
Results
Similar X and Autosome Effective Population Sizes
in Aphid-Like Systems
From our simulations on an aphid-like sex determination
system, genetic diversities did not differ between X-linked
and autosomal loci after ten cycles (HX,t510 5 0.8566744,
HA,t510 5 0.8566305, two-sample t-test: P 5 0.85, n 5
50,000) (see also supplementary fig. S1, Supplementary Material online). Effective population sizes were estimated as
NeX
NeA 5 50.25 and NeX 5 49.72, providing a ratio of Ne
close
A
to 1 (0.99). By contrast, our simulations of genetic drift in
an XX/XY or standard XX/X0 system led to a smaller
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Table 2. Allelic Richness Averaged over Nine Populations for X-Linked and Autosomal Microsatellite Loci Located within Coding and
Noncoding Genomic Areas.
Type of
Chromosome
Number of
microsatellite loci
Mean number of
repeats (median 6 SD)
Mean allelic richness
(median 6 SD)
Mean allelic richness
(corrected for number
of microsatellite repeats)
(median 6 SD)
Within Noncoding Areas
Within Coding Areas
Autosomes
X Chromosome
Autosomes
X Chromosome
64
14
247
31
11.9 (10 6 4.8)
16.5 (14 6 8.3)
9.3 (9 6 3.1)
9.8 (9 6 3.4)
4.54 (4.59 6 1.43)
5.15 (5.21 6 1.35)
3.30 (3.15 6 1.18)
3.53 (3.52 6 1.06)
0.50 (0.43 6 1.04)
0.15 (0.38 6 1.49)
20.13 (20.25 6 0.86)
20.03 (20.08 6 0.91)
NOTE.—SD, standard deviation.
genetic diversity on the X than on autosomal loci (twosample t-test: n 5 50,000, P , 1015) and to an X:A ratio
of effective population sizes of 0.74, close to the threefourths expectation.
Similar Genetic Diversity on the X and Autosomes
Mean allelic richness (averaged over populations) reached
3.53 for X-linked and 3.30 for autosomal loci located within
coding regions, but allelic richness was slightly higher on
the X (5.15) than on the autosomes (4.54) for loci located
within noncoding areas. X-linked loci also had a higher
number of microsatellite repeats than loci on the autosomes (table 2) and more especially so for loci located
within noncoding regions. In contrast, when allelic richness
was corrected for the number of microsatellite repeats
(since both parameters covary: R2 5 0.43, P , 1015),
we observed no difference (P 5 1) of allelic richness between X-linked and autosomal loci (fig. 3). Loci located
within coding regions were less diverse (P , 106) than
those far from genes (fig. 3). We also showed that 17%
of the pairs of loci located on the X chromosome were significantly linked against 12% for pairs on autosomes. These
values suggest similar recombination rates on the X and
autosomes (for details, see Materials and Methods).
Faster Evolutionary Rates for X-Linked Genes
In the three pairs of aphid species, we found higher rates of
nonsynonymous mutations (dN) for X-linked genes than
for autosomal genes (two-sided Mann–Whitney test, P
, 0.04 for all comparisons, table 3). Synonymous rate of
substitution (dS) did not differ between X-linked and autosomal genes (P . 0.38 in all comparisons). Also, we found
higher dN/dS ratio for X-linked genes in all pairs of species,
the effect being significant in two pairs of species (P , 0.04)
but not in the third one (P 5 0.08) (table 3 and supplementary fig. S2, Supplementary Material online). The global
analysis (that accounted for Gene Expression Level, Gene,
and Species Comparison) also showed higher dN and dN/
dS ratio for X-linked genes (P 5 0.029 and P 5 0.034) but
no difference for dS values (P 5 0.42). We observed
particularly high dN/dS values for X-linked genes compared
dNX =dSX
with autosomes, with dN
reaching 1.76 for A. pisum–A.
A =dSA
kondoi, 1.45 for A. pisum–M. persicae, and 1.34 for A. pisum–A. gossypii. These values decreased with phylogenetic
distances between the pair of species compared, A. kondoi
being the closest from A. pisum and A. gossypii the more
distantly related (Ortiz-Rivas and Martinez-Torres 2010).
We also found a significant effect of gene expression levels
on dN/dS (P 5 103), dN (P 5 106), and dS (P 5 106), with
a negative relation between gene expression and evolutionary rates in all cases. The amount of explained variance was
nevertheless small (R2 , 0.005 for dN/dS, and ;0.035
for dN and dS). Finally, we observed slightly lower (but
not significantly) EST support for X-linked genes (mean:
19.8) compared with those on the autosomes (mean: 25.6;
Mann–Whitney test, n 5 1,188, P 5 0.07).
Discussion
Effective Population Size Does Not Differ between
Aphid X Chromosome and Autosomes
Here, we showed by simulations that the aphid X chromosome and autosomes have similar effective population sizes
because of the peculiar X chromosome inheritance. This
result contrasts with expectations from standard XX/XY
or XX/X0 systems, where NeX is only three-fourths of
NeA (assuming 1:1 sex ratio and equal variance in reproductive success between sexes) because of the sex-specific inheritance pattern of the X (Wright 1931; Caballero 1994,
1995). Consequently, in aphids, the rate of genetic drift
should not differ among the two categories of chromosomes, so that the ratio of X:A diversity should be 1. Interestingly, this result, coupled to the arguments presented
before, implies that the ratio of X:A diversity in aphids is
not affected by the various demographic (i.e., expansion, bottleneck, sex-biased dispersal, or mating systems) and genetic
(recombination and mutation) factors influencing the X:A
diversity ratio in XX/XY and standard XX/X0 (fig. 1). Indeed,
in such standard systems, several neutral factors such as the
number of chromosome copies (e.g., Begun and Whitley
2000; Schofl and Schlotterer 2004; Berset-Brändli et al.
2007), sex-biased dispersal (Laporte and Charlesworth
2002; Ellegren 2009), population demography (e.g., Andolfatto 2001; Schofl and Schlotterer 2004; Handley, Berset-Brandli
and Perrin 2006; Baines and Harr 2007), mating system (e.g.,
843
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Jaquiéry et al. · doi:10.1093/molbev/msr252
Table 3. Number of Genes, Median Values for Rates of Nonsynonymous (dN) and Synonymous (dS) Substitution, and Ratio of dN/dS for the
Three Pairs of Species Compared for X-Linked and Autosomal Genes (standard deviation in brackets).
Species Pair Comparison
Acyrthosiphon pisum–
Acyrthosiphon kondoi
Acyrthosiphon pisum–
Myzus persicae
Acyrthosiphon pisum–
Aphis gossypii
A
X
P
A
X
P
A
X
P
n
463
23
753
39
755
46
dN
0.008 (0.026)
0.014 (0.018)
0.038*
0.020 (0.031)
0.032 (0.035)
0.039*
0.031 (0.034)
0.043 (0.049)
0.032*
0.100
0.091
0.58
0.253
0.271
0.38
0.414
0.396
0.60
dS
(0.052)
(0.053)
(0.087)
(0.068)
(0.137)
(0.131)
dN/dS
0.088 (0.104)
0.155 (0.354)
0.040*
0.079 (0.121)
0.115 (0.181)
0.085
0.077 (0.095)
0.102 (0.105)
0.038*
NOTE.—P values from two-sided Mann–Whitney tests.
*P, 0.050
Baines and Harr 2007; Broquet et al. 2009), and mutation rate
(e.g., Handley et al. 2006; Qiu et al. 2010) must be accounted
for.SincetheaphidX:Adiversityratioisnotaffectedbyallthese
neutral evolutionary factors, aphids are ideal models to investigate the effects of selection on sex chromosome evolution.
Similar Levels of Diversity on Aphid X Chromosome
and Autosomes
We found similar genetic diversity on the X compared with
autosomes once the number of microsatellite repeats (that
was higher for X-linked loci, and particularly, so for those located within noncoding regions) was accounted for. Such
a correction was required since mutation rate, hence genetic
diversity, increases with the number of repeats (Ellegren 2000;
Xu et al. 2000; Seyfert et al. 2008), an effect also observed in
our data where repeat number accounted for 43% of the
variance in allelic richness. The larger number of microsatellite repeats observed on X-linked loci corroborates
previous evidence that aphid X chromosomes are enriched in heterochromatin and repetitive DNA sequences
compared with autosomes (Mandrioli and Borsatti 2007;
Monti et al. 2010).
The similar diversity on the X and autosomes corresponds to the 1:1 X:A diversity ratio predicted under neutral evolution. However, these results contrast with those of
Brisson et al. (2009) who used a smaller data set of noncoding DNA sequences and found that X-linked loci were
less diverse than autosomal ones in the pea aphid. Microsatellite markers have been widely used to compare X and autosomes diversities in other taxa (e.g., Payseur et al. 2002;
Schofl and Schlotterer 2004), but in aphids, these markers
may not be the most appropriate to investigate such patterns
because as mentioned above, aphid X chromosomes appear
to be enriched in repetitive DNA sequences compared with
the rest of the genome.
Faster Evolution of X-Located Genes: Relaxed or
Positive Selection?
We observed higher dN values and dN/dS ratio for X-linked
genes, whereas dS, that can be equated to the rate of
neutral substitution, did not differ between the X and
the autosomes. This suggests similar mutation rates for
genes located on these two types of chromosomes. A fast844
er-X effect (i.e., increased dN and dN/dS for X-linked genes)
can result from relaxed selection: this is indeed the case
when the X has a smaller effective population size than
autosomes (e.g., Mank, Nam, et al. 2010), resulting in a reduced effectiveness of selection against slightly deleterious
mutations. Alternatively, faster evolutionary rates on the X
could result from a higher efficiency of selection (because
of the haploid state of the X in males, Vicoso and Charlesworth 2006). As we found here, the similar effective population size between the X and the autosomes in aphids
argues against a role of drift and reduced efficiency of selection on the X (Vicoso and Charlesworth 2009). Second,
we observed no significant difference in EST supports of A.
pisum genes on the X and on the autosomes, suggesting
that X-linked genes do not evolve faster because they
are less expressed. Gene expression levels also explained less
than 0.5% of the variance in dN/dS. Therefore, positive selection seems to best explain the higher evolutionary rates
of X-linked genes. However, our measurements of evolutionary rates are only based on pairwise estimates of synonymous and nonsynonymous distances, and few pairwise
estimates of the dN/dS ratio were above 1, the usual criteria
to conclude that there has been positive selection at the
scale of the entire sequence. But such approach (based
on pairwise estimates) lacks power to actually detect positive selection (Yang et al. 2005), and a more complete set
of taxa and genes would help to better evaluate the potential for positive selection. Ongoing genome sequencing
projects in other aphid species will help filling this gap
in the near future. Also, positive selection often concerns
only specific regions or domains of a gene. With more sequences and taxa available, we will be able to test models of
site variation of the rates and to determine if X-linked genes
more often contain domains or regions under the influence
of positive selection.
Interestingly, Vicoso and Charlesworth (2009) showed
that the scope for faster-X effect due to the fixation of benNeX
eficial mutations increases when Ne
exceeds three-fourths,
A
with faster-X effect occurring for a wider range of dominance values (h) and the effects being stronger (fig. 2 in
Vicoso and Charlesworth 2009). Mank, Vicoso, et al.
(2010) and Vicoso and Charlesworth (2009) also showed
with a theoretical model that the fixation of X-linked
MBE
Faster-X Evolution in Aphids · doi:10.1093/molbev/msr252
beneficial mutation is predicted to increase with effective
population size. From these results, we expect aphid Xlinked genes to show a higher rate of evolution compared
NeX
with autosomal genes because 1) Ne
51 in aphids and 2)
A
aphid effective population size is large compared with
the effective population sizes of vertebrates. We indeed observed particularly high dN/dS values for X-linked genes
compared with autosomes, with X:A dN/dS ratio ranging
from 1.34 to 1.76 in the three pairs of aphid species. These
values are located within the upper tail of values generally
observed (ranging from 0.995 in some Drosophila species to
1.359 in rodents, Begun et al. 2007; Mank, Vicoso, et al. 2010).
We located genes on the X and on the autosomes in A.
pisum, but we ignore whether their orthologs in A. kondoi,
M. persicae, and A. gossypii are also X-linked. This is not
necessarily always the case, but the X is thought to be
the structurally most conserved chromosome among aphid
species (Wilson et al. 2004), possibly because it should be
clearly identified for its elimination in males. The hypothesis of high homology of the X between species is further
supported because most X-linked microsatellite loci amplify and remain X-linked across distantly aphid related
species (Wilson et al. 2004). Yet, any gene shuffling between
X and autosomes should reduce the X:A dN/dS ratio and
thus be conservative regarding our conclusions. Along this
line, we observed that the X:A dN/dS ratio decreases with
increasing phylogenetic distances between the pair of species compared, presumably because of increased probability of gene shuffling between the X and the autosomes.
Our data on effective population size and expression
rate suggest that positive selection (rather than relaxed selection) is responsible for increased rate of evolution of Xlinked genes. Yet, our diversity data from X-linked and autosomal microsatellite loci neither support nor refute this
hypothesis. Indeed, theoretical models have shown that
both increased and reduced levels of diversity can be expected on linked genes on the X relative to autosomes, depending on whether positive selection acts on newly arisen
or standing variation (Orr and Betancourt 2001; Betancourt
et al. 2004). Furthermore, even under the hypothesis of positive selection on new mutations, we still could expect similar levels of diversity between the X and the autosomes if
recombination rate is high and thus prevents hitchhiking
effect to act on linked loci. Interestingly and in contrast to
our results, Brisson et al. (2009) found lower rate of diversity on the X than on autosomes on a data set based on
noncoding DNA sequences obtained on the pea aphid, giving some support to the hypothesis of positive selection on
newly arisen mutations. Resolving the issue of the nature
of selection driving X chromosome evolution may be
achieved in the future when more extensive genomic data
sets from multiple aphid individuals and species will be
available. Then comparing within species patterns of polymorphism with patterns of divergence among species
(fixed substitutions)—using for example McDonald and
Kreitman tests (McDonald and Kreitman 1991)—could
provide key insights into the dominant selective forces that
influence X chromosome and autosomes.
Conclusion
This study highlights the relevance of organisms with
peculiar modes of inheritance of sex chromosomes, such
as aphids, as complementary models to disentangle the
various evolutionary forces that drive sex chromosome
evolution. Indeed, we have shown here that aphids are particularly well-suited for covering such an issue because 1)
clear predictions for X:A diversity ratio can be made under
neutral evolution because no factor (apart from selection)
should influence this ratio and 2) the similar effective population sizes of the X and autosomes allows to sort out
causes for faster-X evolution. Our study therefore highlights
the particular relevance of the aphid system to compare
the different evolutionary factors that drive sex chromosome and genome evolution in general.
Supplementary Material
Supplementary tables S1 and S2 and figures S1 and S2 are
available at Molecular Biology and Evolution online (http://
www.mbe.oxfordjournals.org/).
Acknowledgments
We thank L. Buechi, A. Juilland, G. Evanno, Y. Outreman,
the Jaquiéry, and Evanno families for help with sampling,
J. Bonhomme for rearing aphids, N. Bernard, A. Bonvoisin,
F. Mahéo, and N. Prunier-Leterme for help with lab work,
and M. Ollivier and J.-P. Gauthier for help with statistical
analyses. L. Handley, N. Perrin, D. Tagu, Associate Editor
J. Parsch, and two anonymous referees contributed constructive comments to a previous draft of this manuscript.
This work was supported by INRA-AIP BioRessources, the
Département INRA Santé des Plantes et Environnement,
the Genoscope, the Fondation pour la Recherche sur la Biodiversité, the ANR GW-Aphid, and the Swiss National Science Foundation (grant number PBLAA-122658 to J.J.).
References
Andolfatto P. 2001. Contrasting patterns of X-linked and autosomal
nucleotide variation in Drosophila melanogaster and Drosophila
simulans. Mol Biol Evol. 18:279–290.
Baines JF, Harr B. 2007. Reduced X-linked diversity in derived
populations of house mice. Genetics 175:1911–1921.
Bates D, Sarkar D. 2007. lme4: linear mixed-effects models using S4
classes. R package version 0.999375-28. Available from: http://
lme4.r-forge.r-project.org/
Begun DJ, Holloway AK, Stevens K, et al. (13 co-authors). 2007.
Population genomics: whole-genome analysis of polymorphism
and divergence in Drosophila simulans. PLoS Biol. 5:2534–2559.
Begun DJ, Whitley P. 2000. Reduced X-linked nucleotide polymorphism in Drosophila simulans. Proc Natl Acad Sci U S A.
97:5960–5965.
Berset-Brändli L, Jaquiéry J, Perrin N. 2007. Recombination is
suppressed and variability reduced in a nascent Y chromosome.
J Evol Biol. 20:1182–1188.
Betancourt AJ, Kim Y, Orr HA. 2004. A pseudohitchhiking model of
X vs. autosomal diversity. Genetics 168:2261–2269.
Brisson JA, Nuzhdin SV, Stern DL. 2009. Similar patterns of linkage
disequilibrium and nucleotide diversity in native and introduced
845
Jaquiéry et al. · doi:10.1093/molbev/msr252
populations of the pea aphid, Acyrthosiphon pisum. BMC Genet.
10:22.
Broquet T, Jaquiéry J, Perrin N. 2009. Opportunity for sexual
selection and effective population size in the lek-breeding
European treefrog (Hyla arborea). Evolution 63:674–683.
Caballero A. 1994. Developments in the prediction of effective
population-size. Heredity 73:657–679.
Caballero A. 1995. On the effective size of populations with separate
sexes, with particular reference to sex-linked genes. Genetics
139:1007–1011.
Caillaud MC, Boutin M, Braendle C, Simon JC. 2002. A sex-linked
locus controls wing polymorphism in males of the pea aphid,
Acyrthosiphon pisum (Harris). Heredity 89:346–352.
Castresana J. 2000. Selection of conserved blocks from multiple
alignments for their use in phylogenetic analysis. Mol Biol Evol.
17:540–552.
Charlesworth B. 2001. The effect of life-history and mode of
inheritance on neutral genetic variability. Genet Res. 77:153–166.
Charlesworth B, Coyne JA, Barton NH. 1987. The relative rates of
evolution of sex-chromosomes and autosomes. Am Nat. 130:
113–146.
Charlesworth B, Morgan MT, Charlesworth D. 1993. The effect of
deleterious mutations on neutral molecular variation. Genetics
134:1289–1303.
Connallon T. 2007. Adaptive protein evolution of X-linked and
autosomal genes in Drosophila: implications for faster-X
hypotheses. Mol Biol Evol. 24:2566–2572.
Ellegren H. 2000. Microsatellite mutations in the germline:
implications for evolutionary inference. Trends Genet. 16:
551–558.
Ellegren H. 2007. Characteristics, causes and evolutionary consequences of male-biased mutation. Proc R Soc B Biol Sci. 274:
1–10.
Ellegren H. 2009. The different levels of genetic diversity in sex
chromosomes and autosomes. Trends Genet. 25:278–284.
Frantz A, Plantegenest M, Simon JC. 2006. Temporal habitat
variability and the maintenance of sex in host populations of the
pea aphid. Proc R Soc B Biol Sci. 273:2887–2891.
Geraldes A, Basset P, Gibson B, Smith KL, Harr B, Yu HT, Bulatova N,
Ziv Y, Nachman MW. 2008. Inferring the history of speciation in
house mice from autosomal, X-linked, Y-linked and mitochondrial genes. Mol Ecol. 17:5349–5363.
Goudet J. 2005. FSTAT, a program to estimate and test gene
diversities and fixation indices. Version 294. Lausanne (Switzerland): University of Lausanne, Department of Ecology and
Evolution.
Hales DF, Wilson ACC, Sloane MA, Simon JC, Le Gallic JF,
Sunnucks P. 2002. Lack of detectable genetic recombination
on the X chromosome during the parthenogenetic production
of female and male aphids. Genet Res. 79:203–209.
Handley LJL, Berset-Brandli L, Perrin N. 2006. Disentangling reasons
for low Y chromosome variation in the greater white-toothed
shrew (Crocidura russula). Genetics 173:935–942.
Harvey SC, Viney ME. 2001. Sex determination in the parasitic
nematode Strongyloides ratti. Genetics 158:1527–1533.
Hedrick PW. 2007. Sex: differences in mutation, recombination,
selection, gene flow, and genetic drift. Evolution 61:2750–2771.
International Aphid Genomics Consortium. 2010. Genome sequence
of the pea aphid Acyrthosiphon pisum. PLoS Biol. 8:e1000313.
Kaiser VB, Bachtrog D. 2010. Evolution of sex chromosomes in
insects. Annu Rev Genet. 44:91–112.
Laporte V, Charlesworth B. 2002. Effective population size and
population subdivision in demographically structured populations. Genetics 162:501–519.
Li WH, Yi SJ, Makova K. 2002. Male-driven evolution. Curr Opin
Genet Dev. 12:650–656.
846
MBE
Mandrioli M, Borsatti F. 2007. Analysis of heterochromatic
epigenetic markers in the holocentric chromosomes of the
aphid Acyrthosiphon pisum. Chromosome Res. 15:1015–1022.
Mank JE, Nam K, Ellegren H. 2010. Faster-Z evolution is predominantly due to genetic drift. Mol Biol Evol. 27:661–670.
Mank JE, Vicoso B, Berlin S, Charlesworth B. 2010. Effective
population size and the faster-X effect: empirical results and
their interpretation. Evolution 64:663–674.
Maynard-Smith J, Haigh J. 1974. Hitch-hiking effect of a favorable
gene. Genet Res. 23:23–35.
McDonald JH, Kreitman M. 1991. Adaptive protein evolution at the
ADH locus in Drosophila. Nature 351:652–654.
Miyata T, Hayashida H, Kuma K, Mitsuyasu K, Yasunaga T. 1987.
Male-driven molecular evolution—a model and nucleotidesequence analysis. Cold Spring Harb Symp Quant Biol. 52:863–867.
Monti V, Manicardi GC, Mandrioli M. 2010. Distribution and
molecular composition of heterochromatin in the holocentric
chromosomes of the aphid Rhopalosiphum padi (Hemiptera:
Aphididae). Genetica 138:1077–1084.
Moriyama EN, Powell JR. 1996. Intraspecific nuclear DNA variation
in Drosophila. Mol Biol Evol. 13:261–277.
Nei M. 1987. Molecular evolutionary genetics. New York: Columbia
University Press.
Notredame C, Higgins DG, Heringa J. 2000. T-Coffee: a novel method
for fast and accurate multiple sequence alignment. J Mol Biol.
302:205–217.
Orr HA, Betancourt AJ. 2001. Haldane’s sieve and adaptation from
the standing genetic variation. Genetics 157:875–884.
Ortiz-Rivas B, Martinez-Torres D. 2010. Combination of molecular
data support the existence of three main lineages in the
phylogeny of aphids (Hemiptera: Aphididae) and the basal
position of the subfamily Lachninae. Mol Phylogenet Evol. 55:
305–317.
Payseur BA, Cutter AD, Nachman MW. 2002. Searching for evidence
of positive selection in the human genome using patterns of
microsatellite variability. Mol Biol Evol. 19:1143–1153.
Peccoud J, Figueroa CC, Silva AX, Ramirez CC, Mieuzet L,
Bonhomme J, Stoeckel S, Plantegenest M, Simon JC. 2008. Host
range expansion of an introduced insect pest through multiple
colonizations of specialized clones. Mol Ecol. 17:4608–4618.
Pires-DaSilva A. 2007. Evolution of the control of sexual identity in
nematodes. Semin Cell Dev Biol. 18:362–370.
Pool JE, Nielsen R. 2007. Population size changes reshape genomic
patterns of diversity. Evolution 61:3001–3006.
Qiu S, Bergero R, Forrest A, Kaiser VB, Charlesworth D. 2010.
Nucleotide diversity in Silene latifolia autosomal and sex-linked
genes. Proc R Soc B Biol Sci. 277:3283–3290.
R Development Core Team. 2010. R: a language and environment
for statistical computing. Vienna (Austria): R Foundation for
Statistical Computing.
Schofl G, Schlotterer C. 2004. Patterns of microsatellite variability
among X chromosomes and autosomes indicate a high frequency
of beneficial mutations in non-African D. simulans. Mol Biol Evol.
21:1384–1390.
Schuelke M. 2000. An economic method for the fluorescent labeling
of PCR fragments. Nat Biotechnol. 18:233–234.
Seyfert AL, Cristescu MEA, Frisse L, Schaack S, Thomas WK,
Lynch M. 2008. The rate and spectrum of microsatellite
mutation in Caenorhabditis elegans and Daphnia pulex. Genetics
178:2113–2121.
Sloane MA, Sunnucks P, Wilson ACC, Hales DF. 2001. Microsatellite
isolation, linkage group identification and determination of
recombination frequency in the peach-potato aphid, Myzus
persicae (Sulzer) (Hemiptera: Aphididae). Genet Res. 77:251–260.
Sundström H, Webster MT, Ellegren H. 2004. Reduced variation on
the chicken Z chromosome. Genetics 167:377–385.
Faster-X Evolution in Aphids · doi:10.1093/molbev/msr252
Talavera G, Castresana J. 2007. Improvement of phylogenies after
removing divergent and ambiguously aligned blocks from
protein sequence alignments. Syst Biol. 56:564–577.
Tatsuta H, Hoshizaki S, Bugrov AG, Warchalowska-Sliwa E,
Tatsuki S, Akimoto SI. 2006. Origin of chromosomal rearrangement: phylogenetic relationship between X0/XX and XY/XX
chromosomal races in the brachypterous grasshopper Podisma sapporensis (Orthoptera: Acrididae). Ann Entomol Soc Am.
99:457–462.
Thiriot-Quievreux C. 2003. Advances in chromosomal studies of
gastropod molluscs. J Molluscan Stud. 69:187–202.
Vicoso B, Charlesworth B. 2006. Evolution on the X chromosome:
unusual patterns and processes. Nat Rev Genet. 7:645–653.
Vicoso B, Charlesworth B. 2009. Effective population size and the
faster-X effect: an extended model. Evolution 63:2413–2426.
Wall JD, Andolfatto P, Przeworski M. 2002. Testing models of
selection and demography in Drosophila simulans. Genetics
162:203–216.
MBE
Wilson ACC, Massonnet B, Simon JC, et al. (11 co-authors). 2004.
Cross-species amplification of microsatellite loci in aphids:
assessment and application. Mol Ecol Notes. 4:104–109.
Wilson ACC, Sunnucks P, Hales DF. 1997. Random loss of X
chromosome at male determination in an aphid, Sitobion near
fragariae, detected using an X-linked polymorphic microsatellite
marker. Genet Res. 69:233–236.
Wright S. 1931. Evolution in Mendelian populations. Genetics
16:97–159.
Xu X, Peng M, Fang Z, Xu XP. 2000. The direction of microsatellite
mutations is dependent upon allele length. Nat Genet.
24:396–399.
Yang ZH. 1997. PAML: a program package for phylogenetic analysis
by maximum likelihood. Comput Appl Biosci. 13:555–556.
Yang ZH, Wong WSW, Nielsen R. 2005. Bayes empirical Bayes
inference of amino acid sites under positive selection. Mol Biol
Evol. 22:1107–1118.
847