Speciation genes
H Allen Orr, John P Masly and Daven C Presgraves
Until recently, the genes that cause reproductive isolation
remained black boxes. Consequently, evolutionary biologists
were unable to answer several questions about the identities
and characteristics of ‘speciation genes’. Over the past few
years, however, evolutionary geneticists have finally
succeeded in isolating several such genes, providing our first
glimpse at factors that are thought to be representative of
those underlying the origin of species. Evolutionary analysis
of these genes suggests that speciation results from positive
Darwinian selection within species. Molecular evolutionary
study of the genes causing reproductive isolation may
represent an important new phase in the study of speciation.
Addresses
Department of Molecular Biology & Genetics, Cornell University,
Ithaca, New York 14853, USA
e-mail: aorr@mail.rochester.edu
Current Opinion in Genetics & Development 2004, 14:675–679
This review comes from a themed issue on
Genomes and evolution
Edited by David Haig and Steve Henikoff
Available online 5th October 2004
0959-437X/$ – see front matter
# 2004 Elsevier Ltd. All rights reserved.
DOI 10.1016/j.gde.2004.08.009
Abbreviations
HMS hybrid male sterility
NPC nuclear pore complex
Introduction
The founders of the modern synthesis viewed speciation — the evolution of barriers to gene flow between
taxa — as a key issue in evolutionary genetics. The title of
Dobzhansky’s seminal book [1] was, after all, Genetics and
the Origin of Species. Despite this early enthusiasm, our
understanding of the genetics of speciation has lagged far
behind that of most other evolutionary phenomena. In
part, this reflects an obvious methodological problem: the
genetic study of speciation is, almost by definition, the
attempt to do genetics where it cannot be done —
namely, between species.
Until recently, our understanding of speciation was
restricted to comparative and classical genetic patterns.
It was clear, for example, that reproductive isolation
evolves gradually in most taxa (if we ignore polyploid
speciation in plants [2–8]). It was also clear that the
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‘postzygotic’ form of reproductive isolation — that is,
the sterility or inviability of hybrids — is caused by
epistatic interactions between alleles from different species at two or more loci: although such alleles function
well on their normal within-species genetic background,
they fail to interact properly in a hybrid genome [9,10].
Evolutionary biologists were not, however, able to identify the particular genes that cause postzygotic reproductive isolation. As a result, we were unable to address a
large set of fundamental questions about the factors that
cause reproductive isolation: are these factors ‘ordinary’
genes that have normal functions within species? If so, do
they typically belong to a particular functional class (e.g.
are they usually transcription factors)? Are these genes
rapidly diverging? And are they adaptively evolving?
Over the past several years, evolutionary geneticists,
capitalizing on the availability of genome sequences, have
finally succeeded in identifying and molecularly characterizing several genes that cause postzygotic reproductive
isolation. Here, we briefly review this recent work. As will
become clear, we consider that this research represents an
important new phase in the study of speciation, one that
unifies studies of the origin of species with studies of
molecular evolution.
Hybrid sterility
Several lines of evidence show that hybrid sterility
evolves faster than hybrid inviability. First, comparative
studies in various taxa have shown that sterility of hybrids
appears between diverging species earlier than does
inviability of hybrids [3,5,6,11]. Second, genetic studies
in Drosophila have shown that particular species pairs are
separated by more hybrid male sterility (HMS) genes
than either hybrid female sterility genes or hybrid inviability genes [12–15]. This excess of HMS genes might
arise as a byproduct of sexual selection [16], genetic
conflicts [14,17–21], or an intrinsic developmental sensitivity of spermatogenesis in hybrids [16]. The idea that
the genes causing HMS simply diverge faster between
species than do other types of genes is supported by the
more rapid evolution of both the DNA sequences and
expression levels of sex-related genes (or genes with sexbiased expression) relative to other genes [22–28]. There
would seem to be good reason, then, to expect a signature
of positive selection at the genes that cause hybrid
sterility.
The only HMS gene identified so far, Odysseus site homeobox (OdsH), causes sterility in male hybrids of Drosophila
simulans and Drosophila mauritiana. Using a classical
genetic approach, Coyne and Charlesworth [29] mapped
Current Opinion in Genetics & Development 2004, 14:675–679
676 Genomes and evolution
a segment of about 2 cM of the D. mauritiana X chromosome that causes HMS when introgressed into a D.
simulans genetic background. Using molecular markers,
Ting et al. [30] subsequently narrowed in on an 8.4kb
region including three exons. These three exons plus an
adjacent one encode OdsH, a protein that includes a
sequence of 60 amino acids characteristic of homeobox transcription factors. OdsH is a duplicate of unc-4,
which encodes a transcription factor expressed in the
embryo and in adult neural tissue. Although its function
within species remains unknown, OdsH has acquired
novel expression in testis. The homeobox motif of
OdsH suggests that it may cause HMS by misregulating
downstream target genes necessary for spermatogenesis.
Consistent with this, Michalak and Noor’s [31] recent
survey of gene expression has shown that backcross
hybrid males carrying a segment of D. mauritiana including OdsH show misexpression of at least five coordinately regulated loci, some of which function in
spermatogenesis.
Like many reproductive genes, OdsH has evolved rapidly.
The homeodomain alone has accumulated a remarkable
15 replacement substitutions (those that change the
amino acid encoded) in the roughly 0.25–1.00 million
years since D. simulans and D. mauritiana diverged from a
common ancestor [30]. The tenfold excess of replacement to silent substitutions in the lineage leading to
D. mauritiana strongly suggests that OdsH has evolved
by positive selection [30,32]. A burst of adaptive evolution of this magnitude is not seen in the lineage leading
to D. simulans, suggesting that selection pressures on
OdsH have differed in these two species.
When introgressed alone into D. simulans, the OdsH allele
from D. mauritiana causes a reduction in fertility of only
about 50%; to confer complete HMS, OdsH must be cointrogressed with unidentified but tightly linked factors
[30,33]. Findings from other genetic analyses also suggest
that HMS often has a polygenic basis [10,32]. There are,
however, exceptions. The tiny dot fourth chromosome of
D. simulans, for example, causes complete HMS when
introgressed into a Drosophila melanogaster genetic background [34,35]. Recent deletion mapping and complementation tests suggest (but do not prove) that the
D. simulans allele of a single gene causes this hybrid
sterility (JP Masly, unpublished).
Additional hybrid sterility loci will almost certainly be
identified in the near future. Tao et al. [19,36] have fine
mapped autosomal introgressions that cause both HMS
and hybrid meiotic drive in hybrids of D. mauritiana and
D. simulans. Similarly, Sawamura et al. [15,37] seem
poised to identify several hybrid sterility loci in hybrids
of D. melanogaster and D. simulans, in which five regions on
the second chromosome that cause HMS have been
localized by interspecific deletion mapping.
Current Opinion in Genetics & Development 2004, 14:675–679
Systems other than Drosophila may also soon yield hybrid
sterility loci. In Mus, for example, Dnahc8, an axonemal
dynein heavy chain expressed in testis, has been mapped
to the site of the Hybrid sterility 6 locus [38], which is
involved in HMS in hybrids of Mus domesticus and Mus
spretus. Thus, Dnahc8 represents a strong candidate hybrid
sterility locus.
Hybrid inviability
The evolutionary history of OdsH confirms what was
suspected from comparative and genetic data — namely,
that positive selection drives the rapid evolution of hybrid
sterility genes. The same comparative and genetic data
show, however, that hybrid inviability evolves more
slowly than does sterility in a range of taxa (see above).
It was therefore unclear whether positive selection would
also have a role in the evolution of hybrid inviability
genes; after all, hybrid incompatibilities could also evolve
through the slow accumulation of neutral or even slightly
deleterious substitutions. Although many evolutionary
details remain to be resolved for the first of the hybrid
inviability genes identified, two recently isolated genes
show clear signatures of adaptive evolution.
The first hybrid inviability gene to be identified was the
platyfish Xiphophorus melanoma receptor kinase 2 gene
(Xmrk2), which is located on the X chromosome [39–
41]. Xmrk2 encodes a novel receptor tyrosine kinase that
is overexpressed in some Xiphophorus hybrids, often causing lethal tumorigenesis. The evolutionary history of
Xmrk2 is complex. The gene originated more than 5
million years ago as a partial duplication and acquired a
novel 50 cis-regulatory region [42,43]. Although independently lost from several species, Xmrk2 persists as a
polymorphism in at least eight Xiphophorus species,
always in association with a tightly linked pigment pattern-encoding locus [43]. The persistence of this ancient
polymorphism through several speciation events and its
association with pigmentation patterning — a trait that is
known to influence mating success in these fish — may
indicate a history of balancing selection. Population
genetic analyses of the forces involved in the maintenance and evolution of Xmrk2 are needed.
The second hybrid inviability gene to be identified was
the Drosophila gene Hybrid male rescue (Hmr), which is
located on the X chromosome [44]. Crosses involving
D. melanogaster females and sibling species males (D.
simulans, Drosophila sechellia or D. mauritiana) yield dead
hybrid sons, whose development arrests at the larval–
pupal transition, and sterile hybrid daughters that die
when reared at high temperatures [45]. (Hmr also seems
to affect the fertility of hybrid daughters [46].) Hmr was
originally recovered in a screen for ‘rescue’ mutations in
D. melanogaster that can suppress hybrid inviability.
Nearly 20 years of effort have made Hmr the best characterized of all hybrid incompatibility genes. Genetic
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Speciation genes Orr, Masly and Presgraves 677
manipulations show that decreasing the Hmr dosage
suppresses the lethality of hybrid males and the temperature-dependent lethality of hybrid females, whereas
increasing Hmr dosage has the opposite effects [45,47].
Barbash et al. [44] found that Hmr encodes a protein
with two MADF DNA-binding domains similar to those
of myeloblastosis-related transcription factors. Recent
transgenic experiments confirm that the D. melanogaster
allele of Hmr has functionally diverged from those of
D. simulans and D. mauritiana [48].
The third hybrid inviability gene to be identified was the
Drosophila gene Nucleoporin-96 (Nup96), which is located
on the right arm of chromosome 3 [49]. The D. simulans
allele of Nup96 is incompatible with an unknown gene on
the X chromosome of D. melanogaster. Nup96 encodes 1 of
about 30 nuclear pore proteins (nucleoporins) that
together form nuclear pore complexes (NPCs), the
macromolecular structures that perforate nuclear membranes and conduct mRNA and protein trafficking
between the nucleus and cytoplasm. Nup96 is a one of
seven conserved interacting proteins of the Nup84 subcomplex [50,51]. From yeast to vertebrates, the Nup84
subcomplex is stably bound at the nuclear and cytoplasmic sides of the NPC, where it functions as a docking site
for dynamic nucleoporins that shuttle between the
nuclear interior and NPCs, delivering mRNA cargoes
for nuclear export [52].
It is worth considering the evolutionary histories of Hmr
and Nup96 together because they share several features.
First, both genes show clear evidence of adaptive protein
evolution: both have fixed more amino-acid-changing
substitutions between species than can be accommodated
by neutral models of evolution [48,49]. Second, both
genes have experienced adaptive evolution in the
D. melanogaster and D. simulans lineages. Last, these bouts
of adaptation seem to have been ancient because patterns
of polymorphism at both loci show no signs of a recent
selective sweep [48,49]. This does not, of course,
mean that adaptive evolution has necessarily ground to
a halt at these loci, only that no substitution has occurred
recently.
Future progress in hybrid inviability
Further progress in the molecular evolution and genetics
of hybrid inviability seems imminent. First, the success of
the Hmr work suggests that analogous analyses of other
hybrid rescue mutations should succeed. Second, Nup96
is only the first gene to emerge from a large deletionbased screen for autosomal D. simulans factors involved in
lethal incompatibilities with X-linked D. melanogaster
genes [53]. Nineteen other autosomal regions associated
with hybrid lethality have been mapped, and two of these
have been narrowed to single complementation groups
(DC Presgraves, unpublished). Last, conserved interactions among Nup84 subcomplex members [50,51] suggest
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natural candidates for the incompatible ‘partner’ molecules of Nup96. Once partners are identified for this and
other hybrid incompatibilities, evolutionary geneticists
can begin to analyze how coevolution among interacting
molecules within species ultimately gives rise to incompatible interactions between species.
Conclusions
Although it is too early to draw robust conclusions from
the small sample of ‘speciation genes’ isolated so far,
several facts seem reasonably clear. First, the factors that
cause postzygotic reproductive isolation are often ordinary genes that have normal functions within species.
Second, these genes are evolving rapidly. Last, and
perhaps most important, this rapid evolution is driven
by positive Darwinian selection. Recent molecular analyses of speciation genes thus support one of the central
tenets of the modern synthesis—namely, that reproductive isolation is an epiphenomenon of Darwinian selection within species.
We hasten to add, however, that the ecological basis of
this selection is often unclear. Indeed, we have no good
evidence that the relevant selection reflected adaptation
to the external environment at all, and it is entirely
possible that selection instead reflected adaptation to
the internal genetic ‘environment’, as posited by several
recent selfish gene theories of postzygotic isolation.
According to some of these theories, bouts of coevolution
between genes associated with meiotic drive and their
suppressors might drive the evolution of postzygotic
reproductive isolation [14,17–21].
One of the most important tasks facing speciation geneticists is therefore clear: we must connect the population
genetic signal of positive selection seen at speciation
genes to the biological basis of that selection. This goal
will require both the identification of more speciation
genes—a task facilitated by the increasing number of
genome sequences becoming available—and careful analyses of their normal functions within species.
Acknowledgements
This work was supported by a grant from the National Institutes
of Health (2R01GM51932) to HAO and by funding from the
Alexander von Humboldt Foundation to DCP.
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