Chapter 2 – Interspecific hybridisation and
introgression in animal taxa
Abstract
It has long been established that interspecific hybridisation, and consequently
introgression can play an important evolutionary role in plants, however, in animals
introgression has generally been considered absent or unimportant. This view was
due largely to the misconception that animals hybridise only rarely in nature, and to
the generally negative attitude towards animal hybrids. Here I aim to show that
hybridisation is more common between animal species than is generally realised,
and that this can lead to gene flow. I review the studies of interspecific hybridisation
and introgression to date, and suggest some limitations with these. Finally, I
examine the possible consequences of animal introgression for species definition,
evolution, phylogeny reconstruction, conservation and commercial applications and
suggest directions for future work in this area.
Introgression
Introgression was defined by Avise (1994) as “the movement of genes between
species (or other well-marked genetic populations) mediated by back-crossing”.
Here I will look at the process of introgressive hybridisation between animal
species, that is hybridisation between species, accompanied by gene flow.
44
Research bias on plants
In a database literature search under the terms ‘introgression’ and ‘gene’ (Web of
Science, 07/01/03), 718 references were returned. Of these studies, 68% were plant
studies, with only 32% of studies focusing on animals (Table 1). This demonstrates
the historical bias of introgression studies towards plant taxa.
It has long been accepted that interspecific hybridisation in plants can lead to
introgression of genetic material from one species to another, and that this can be
important in the evolution of plants (e.g. Stebbins, 1950; Mayr, 1963; Heiser, 1973).
Although the exact role that hybridisation and introgression plays in evolution is still
a subject of much debate (Arnold, 1997; Barton, 2001), it is clear that novel
combinations of genes arising in hybrids can act as a new resource for natural
selection to work on. Paradoxically, though these studies asserted the role
introgression plays in driving evolution in plant taxa, the same was not generally
thought to be true in animals, where introgression of genetic material has historically
been seen as unimportant. Part of this bias may due to the greater frequency with
which plant species hybridise (Stebbins, 1950; Grant, 1981). Another reason may be
that zoologists have often emphasised the negative aspects of hybridisation, whereas
botanists tend to view the process in a more positive light (Heiser, 1973).
Table 1 – Analysis of introgression studies. (From Web of Science 07/01/03).
Plants
Year
1981
0
Intraspecific
0
Study type
Animals
Drosophila
Commercial
0
0
Conservation
0
Other
1
45
1982
1986
1988
1989
1990
1991
1992
1993
1994
1995
1996
1997
1998
1999
2000
2001
2002
Totals
1
0
1
1
1
22
19
27
36
45
41
58
48
47
57
65
52
521
0
0
0
0
0
2
0
3
0
1
5
4
7
1
4
10
9
46
0
1
0
0
0
1
0
1
0
0
1
1
1
1
3
3
2
15
0
0
0
0
1
3
3
6
5
4
11
7
9
10
12
12
10
93
0
0
0
0
0
2
1
2
0
5
2
6
1
3
3
6
6
37
0
0
0
0
0
3
3
4
1
2
6
3
7
4
8
6
4
52
Hybridisation in animals is often seen as the breakdown of isolating mechanisms
brought about unnaturally by habitat destruction or human disturbance (Mayr,
1963). Many researchers have been unwilling to think of animals as capable of
interspecific hybridisation, a view summed up by this quote from Fisher (1958),
“The grossest blunder in sexual preference, which we can conceive of an animal
making, would be to mate with a species different from its own”.
Hybridisation in animal taxa
Natural hybridisation has often been thought of as insignificant in the evolution of
animals (Burke and Arnold, 2001). Hybrids between animal species were thought to
arise so infrequently as to be irrelevant, but recent studies on a range of animal taxa
have shown that this is not necessarily the case. Here we use Arnold et al’s (1991)
46
definition of hybrids as arising from matings between species (as opposed to races,
sub-species or geographically distinct populations).
There have been several attempts in recent years to quantify the percentages of
animal species that hybridise in nature. Grant and Grant (1992) found that 9.2% of
bird species hybridise with one or more relative, Guillaumin and Descimon (1976)
found that 11% of European butterflies hybridise, Sperling (1990) reported over 6%
of Papilio species hybridising and Mallet et al (2002) found that 29% of Heliconius
butterfly species produce viable hybrids with at least one other species. In the Great
Lakes of Africa, there are hundreds of closely related cichlid fish species which
hybridise probably naturally, although this is enhanced when the water turbidity
rises due to human disturbance (Seehausen et al, 1997; Turner et al, 2001). It is not
just birds, butterflies and fish that hybridise either. Wolves and coyotes hybridise
naturally (Hall, 1978), as do bison and domestic cattle (Templeton, 1991; Polziehn
et al, 1995), and Bullini and Nascetti (1990) document cases of speciation by
hybridisation in insects as diverse as stick insects, grasshoppers and black flies.
It has often been assumed that allopatric species will be more likely to hybridise if
brought into contact, than sympatric species, as this latter group will be expected to
have developed isolating mechanisms to prevent hybridisation. However, a number
of studies have shown that hybridisation can occur in sympatry (e.g. Vane-Wright
and Smith, 1992; Grant and Grant, 1992; Mallet et al, 2002).
Historically, it has been difficult to detect animal hybrids, as they often show little
morphological differentiation from one of the parental forms, or may fall within the
47
range of morphological traits for several species (Bullini and Nascetti, 1990; Hewitt,
1993; Barton, 2001). This has changed with the increasing use of molecular
techniques which have enabled hybrids to be identified more easily and reliably,
even when cryptic morphologically (Bullini, 1994; Rhymer et al, 1994; Allendorf et
al, 2001). However, even with molecular techniques, it can be difficult to
distinguish between evidence for hybridisation and lineage sorting (Sang and Zhong,
2000; Holder et al, 2001).
As a result of the recent advances in molecular techniques, the number of
documented cases of introgressive hybridisation between animal species is
increasing (Streit et al, 1994). It is clear from these studies that a high number of
animal species breed with close relatives to form hybrids in the wild. Given this
level of natural hybridisation between animal species, it seems likely that some
introgression of genetic material is likely to occur.
Animal introgression studies
In the literature search mentioned earlier, 32% of introgression studies were on
animal taxa. Of these, 6% dealt with intraspecific gene flow, with only 26% of all
papers dealing with gene flow between animal species.
Non-molecular studies
Early studies on hybridisation and gene flow used non-molecular techniques, many
of which are still used today. Some look at the introgression of morphological traits
(Bell, 1996; Bynum et al, 1997; Seehausen et al, 1997; Crespin et al, 1999; Faivre et
48
al, 1999), or other characters such as song (Lein and Corbin, 1990), cytotypes
(Michailova, 1996), or pheromone introgression (Hepburn et al, 1994).
Limitations of non-molecular studies
These studies have many limitations, as hybrids are defined using characters that are
intermediate between two forms. However, an intermediate may just be due to
natural variation within a taxon, rather than a true hybrid. Deciding whether an
individual has intermediate characteristics can also be very subjective, so that
designations of hybrid status may differ between researchers. Additionally, it is not
usually possible to distinguish between F1 hybrids, backcrosses or later stage
hybrids.
Molecular studies
The advent of techniques such as allozyme electrophoresis in the 1960s and the
polymerase chain reaction (PCR) in 1985 sparked a revolution in evolutionary
biology (Saiki et al, 1985; Mullis et al, 1986; Guyer and Koshland, 1990; Avise,
1994). These technological advances have allowed introgression to be studied using
a huge range of new markers (Harrison, 1990).
Allozyme electrophoresis has hitherto been a popular means of detecting gene flow
across the species boundary (e.g. Derr, 1991; Lee and Engstrom, 1991; Brown,
1995; Gardner, 1996; Lessios and Pearse, 1996; Jiggins et al, 1997; Spaak, 1997;
Berrebi et al, 2000; Cianchi et al, 2003). Allozyme data can indicate whether alleles
characteristic of one species are present at low levels in another species, providing
more direct evidence of interspecific gene flow, and an estimate of how often it
49
occurs. With further advances in molecular techniques, studies became more
detailed with more loci being analysed at a time. After allozymes came restriction
fragment length polymorphisms (RFLP), which essentially give information similar
to multiallelic allozyme data, although there are only two alleles at each site in a
given locus (e.g. Ferris et al, 1983; Aubert et al, 1997; Martinsen et al, 2001). With
the development of randomly amplified polymorphic DNA (RAPD), the number of
loci being analysed at a time rose to 20 or 30 (e.g. Deverno et al, 1998), and with
amplified fragment length polymorphisms (AFLP) that number rose to hundreds,
although both techniques deliver genetically dominant presence/absence band
markers at each single locus. Microsatellites provide another multiallelic genetic
marker technique which uses nucleotide repeats to produce PCR fragments of
different lengths according to the number of repeats there are (e.g. Chenuil et al,
2000; Noor et al, 2001a). Microsatellites are again scored using gel banding
patterns, although this time on a sequencing gel. These methods have revealed that
the extent of genetic variation in natural populations is huge; however the total
variation cannot be known without study at the DNA sequence level (Nei, 1987).
Many groups have looked for evidence of interspecific gene flow in animals at the
nucleotide level, by direct sequencing of PCR products. The vast majority of these
studies have used mitochondrial DNA (mtDNA), (e.g. Aubert et al, 1997; Garcia
and Powell, 1998; Garnery et al, 1998; Pilgrim et al, 1998; Davison et al, 1999;
Feder et al, 1999; Freeland and Boag, 1999; Sota et al, 2001; Saltzburger et al,
2002; Cianchi et al, 2003). This predominance of mitochondrial DNA based
phylogenies in the literature, is due largely to its haploid inheritance which makes
sequencing easy (no cloning is required), and many universal mtDNA primers are
50
available. The latest studies have used nuclear DNA sequence data to study
introgression. Studies using nuclear primers for studies of animal introgression are,
however rare (e.g. Wang et al, 1997; Vane-Wright et al, 1999, Kliman et al, 2000;
Ting et al, 2000; Saetre et al, 2001; Machado et al, 2002; Shaw, 2002).
Limitations of molecular studies to date
Allozymes, RFLP’s. RAPD’s, AFLP’s and microsatellites are all electrophoretic
techniques, based on scoring banding patterns. The results are often hard to read and
open to misinterpretation. It is usually possible to tell only that fragments are the
same length, but not whether they are equivalent. Two different fragments can have
the same mobility, and so can give false positives of hybridisation. If closely related
species are studied, it may not be possible to detect differences at a single base
polymorphism. This poses a major problem in introgression studies, as species will
usually be closely related if they hybridise. Allozymes often display low levels of
interspecific variation and are therefore of limited use in studies of closely related
species (Pacheco et al, 2002). Deverno et al, (1998) caution that for RAPD
technology “meticulous technique must be used to avoid artefacts”, and that
“variation of results among laboratories with different thermal cyclers is a limiting
factor in overall reproducibility and applicability”. Noor et al, 2001a urge caution in
using microsatellite data for phylogeny reconstruction or to infer divergences
between populations. In future, micro-array technology will allow a large sample of
the whole genome to be viewed rather than just a small subset of loci., raising the
potential for electrophoretic techniques as useful tools in introgression studies.
51
Direct sequencing of DNA provides many more characters and a seemingly more
reliable method for assessing potential introgression between species. Most studies
to date have used mitochondrial genes for this purpose, as they are easier to
manipulate, clonally inherited, rapidly-evolving, single copy, non-recombining and
are abundant (Simon et al, 1994). The problem with this is that, because of the lack
of recombination, the entire mitochondrial genome can effectively be seen as a
single locus, limiting its usefulness in phylogenetic studies (Moore, 1995). Pacheco
et al, 2002 note that “because mtDNA is inherited primarily matrilineally, it can be
used to identify maternal species; however it fails to detect male-mediated
introgression, so cannot be used to estimate rates of hybridisation or introgression”.
Single copy nuclear DNA (scnDNA) can be more useful because the nuclear
genome provides many, essentially independent loci to work with. Nuclear genes
have the advantage over mtDNA of providing numerous independent genealogies
which are under varying degrees of selective constraint, with different mechanisms
and rates of evolution, and with a biparental mode of inheritance (Degnan, 1993).
Hybrids can be detected using nuclear markers as they carry nuclear DNA from both
parental species (Pacheco et al, 2002). Nuclear introns offer a potentially rich source
of characters for detecting introgression between species (Hey and Kliman, 1993;
Slade et al, 1994; Palumbi and Cipriano, 1998; Friesen, 2000; Pacheco et al, 2002).
Because introns are non-coding, they accumulate mutations faster than coding
sequence, making them especially valuable for phylogeny reconstruction between
closely related species.
52
Many studies of animal introgression to date have been carried out at hybrid zones,
where hybrids are often found in large numbers (Barton and Hewitt, 1985; Harrison,
1990, 1993; Howard et al, 1993; Bullini, 1994; Jiggins et al, 1997; Dasmahapatra et
al, 2002). Hybrid zones can be seen as natural laboratories for studying speciation
and evolution (Arnold, 1997), but are not ideal for studying introgression between
species, as it could be argued that speciation has not really occurred yet. There are
in fact many examples of genes flowing between animal populations called
“separate species”, which are found adjacent to one another, but which don’t coexist
in sympatry; these taxa are, however, not the kind of species that contribute to local
diversity. There are examples in Drosophila where detailed statistical analysis has
revealed that gene flow occurring a long time ago is more probable than the
maintenance of ancestral polymorphisms, in order to explain why similar (but nonidentical) alleles are maintained within each species (e.g. Wang et al, 1997; Ting et
al, 2000; Noor et al, 2000; Machado et al, 2002). But there are few welldocumented examples in animals where two clearly genetically, ecologically, and
morphologically differentiated species coexist in sympatry, and currently exchange
some genes, but not others (e.g. Caccone et al. 1998; Thelwell et al. 2000; Gentile et
al, 2002; Cianchi et al, 2003).
Why does introgression occur?
Discerning whether hybridisation has arisen naturally or is due to human disturbance
is critical for conservation studies. Rates of interspecific hybridisation and
introgression have undoubtedly increased due to translocation and habitat
modification by humans (Allendorf et al, 2001). Habitat modification, purposeful
introduction of species and domestication can all lead to introgressive hybridisation
53
(Wiegand, 1935; Anderson and Stebbins, 1954; Atkinson, 1989). However,
introgressive hyridisation is not always caused by anthropogenic interference.
Geological events or climatic changes can lead to a break down in reproductive
isolation between species, resulting in the mixing of gene pools which can
eventually lead to the loss of genetically distinct populations (Bullini and Nascetti,
1990; Rhymer and Simberloff, 1996).
Where in the genome does introgression occur?
An interesting problem in speciation research is that before reproductive isolation is
complete, some parts of the genome are able to cross the species boundary, whereas
others are not (e.g. Wang et al, 1997; Butlin, 1998; Noor et al, 2001b; Beltrán et al,
2002). So what factors affect this differential ability of genes to flow between
species? Areas of the genome linked with barriers to gene exchange such as hybrid
sterility or sexual isolation would be expected to be unable, or at least unlikely to
introgress, whereas unlinked loci might be expected to flow between species more
readily. If there is female F1 hybrid sterility, then mtDNA introgression will be
impossible.
All other things being equal, introns and other non-coding regions might be more
likely to show introgression than coding regions, and, where exon variation occurs,
transferences will be most likely for variants at 3rd codon positions. If a locus is
disruptively selected, or linked to such e,g,. colour pattern genes, they will be
prevented from flowing and should not introgress. Conversely, if a mutation is
globally advantageous, it should be able to spread across the species barrier much
54
faster. All of these factors may be of importance when choosing gene regions to
sequence for introgression studies.
The consequences of introgression
Given the recent body of evidence for interspecific hybridisation and gene flow
between animal species in the wild, what are the possible consequences? To answer
this, it is perhaps best to start with a direct comparison with plants. In plants it is
known that introgressive hybridisation can cause problems for conservation of rare
species, species definition, and phylogeny reconstruction. Introgressive
hybridisation has clearly played a major role in plant evolution (Arnold, 1992); and
the potential of deliberately introgressing genetic material into plants has already
been harnessed for the improvement of crops. These consequences of introgression
are all equally important, although usually less well-studied in animals.
Implications – Conservation
A large part of the animal gene flow literature to date has focused on mammals and
birds of high conservation status. Introgression of genetic material between animals
has very important implications in conservation biology (Avise, 1994; Haig, 1998).
Genes from common or introduced species can enter the rarer or native species
genome by hybridisation, resulting in the eventual loss of ‘pure’ species by
homogenisation of genomes (e.g. Grant, 1981; O’Brien and Mayr, 1991; Rhymer
and Simberloff, 1996; Pilgrim et al, 1998; Seehausen et al, 1997; Davison et al,
1999; Allendorf et al, 2001; Randi et al, 2001; Turner et al, 2001). Indeed, Randler
(2002) has shown that in bird species at least, hybridisation is more common where
one of the two species is rare. Hybrids formed between a protected species and a
55
non-protected relative may also suffer through losing their protection status (see
species definition implications). It has been assumed that once a species hybridises,
it loses its identity, and therefore no longer requires protection (O’Brien and Mayr,
1991). However, rare species are the most likely to hybridise with other species and
in the most need of protection. In using this criterion for deciding which species to
protect, those most needy, rarest species are also likely to be most at risk from
hybridisation, and consequently will be most prone to removal from the endangered
list. Policies dealing with hybrids and introgression have been a subject of much
debate in recent years (e.g. Allendorf et al, 2001), but no general consensus has yet
been reached as to the appropriate legislation to enforce.
On the positive side, animal species suffering from genetic bottlenecks due to
restricted range size or isolation, may benefit from the deliberate introduction of
genetic material from different populations, or even species to prevent their decline
through inbreeding depression. One example of this is that genetic material from
the Texas cougar (Puma concolor stanleyana) has been used in an attempt to
prevent inbreeding depression in the Florida panther (P. c. coryi), (Maehr and
Caddick, 1995; Maehr and Lacy, 2002).
Implications - Species definition
The problem of species definition is central to the problems caused by hybridisation
and introgression between species, but links between conservation biologists and
systematists remain poor (Rojas, 1992).
56
Since the 18th century, the problem of how to define ‘species’ has been hotly
debated. Introgression of genetic material between species can cause especial
difficulties with regard to species definition: because species are defined on the
basis of the splitting of two evolutionary lineages into two distinct forms, problems
can arise when these two resulting forms hybridise with each other (Schwenk et al,
1995; Turner et al, 2001). In using the biological species concept to define species,
taxa which hybridise may become amalgamated into a single species. However, for
instance, some Eastern European wolves (Canis lupus) have mtDNA haplotypes
shared with domestic dogs (C. familiaris) (Randi et al, 2001; Randi and Lucchini,
2002), but these are normally thought of as separate species and worthy of
conservation, even though all dog breeds originate from domestication of wild
wolves. But this same problem of species definition can have dramatic conservation
consequences where hybridisation occurs in the wild. For example, the endangered
red wolf (Canis rufus) enjoyed full protective status until it was discovered that it
was really a natural hybrid population between Canis lupus and the coyote Canis
latrans, and is therefore not regarded as a ‘pure’ species in its own right (Wayne and
Jenks, 1991; Nowak, 1992; Phillips and Henry, 1992; Brownlow, 1996; Nowak et
al, 1998; Randi and Lucchini, 2002). Hybridising species are not recognised under
the U.S. Endangered species act (1973), also termed the ‘hybrid policy’, which lead
to confusion over the protection of the red wolf (O’Brien and Mayr, 1991).
Spence and Gooding (1991) suggest that that molecular techniques could be used to
determine the amount of gene exchange between a given set of species, and once
this has been assessed for a number of taxa, a rational decision may be made about
how to handle hybridising species. Hudson and Coyne (2002) suggest that a
57
genealogical species might be defined as one showing monophyly at 95% of
sampled nuclear loci, but this would result in many ‘good’ species being joined into
a single species. Recently there has been much interest, in both the scientific
literature and the media, about using molecular data as a form of ‘DNA barcode’ by
which species can be identified (Blaxter, 2003; Hebert et al, 2003; Mallet and
Willmott, 2003). This idea seems tempting as a quick-fix solution for identifying the
world’s biodiversity, but the existence of introgression and hybridisation mean that
these methods can be unreliable for closely related species.
Implications- Commercial
Introgression of genetic material in commercially important species has huge
financial implications, and therefore over 38% of the animal introgression papers
concern species of commercial importance.
Historically, commercial animal species have been selected for their beneficial traits
and crossed using artificial selection. With advances in recombinant DNA
technology, this has gone a stage further, with genes being deliberately introduced
into commercial animal species in order to improve certain traits (Yancovich et al,
1996; Golden, 2000); for instance, introgression of a plumage colour mutation into
commercial Japanese quail to allow for auto-sexing (Minvielle et al, 1999, 2000).
Other examples include introgressing genes to increase lamb production (Gootwine
et al, 2001; Weimann et al, 2001); using growth hormones to increase salmon size
(Hedrick, 2001); and introducing a gene to prevent fish from developing melanoma
(Anders et al, 1991). Ever since the 1990’s when commercial companies brought
these genetically modified organisms (GMOs) into the public forum, there has been
58
a large amount of concern, and questions have arisen regarding their safety (Arriola,
1997; Burrows, 1999; Ellstrand et al, 1999; Gliddon, 1999; Wolfenbarger and
Phifer, 2000; Nash, 2000; Pearce, 2000). Major concerns include the accidental
transfer of introduced genes to other organisms, the effects on non-target organisms
(for pest resistant transgenes), extinction of indigenous species, the health of humans
and animals and the adverse effects on wildlife due to change in farming practices
(Diamond, 1999; Perez et al, 2001). So far, the concern has been largely
concentrated on transgenic plants (but see Bruggemann, 1993; Levidow and Kahn,
1996), because of the commonly held belief that genetic material cannot pass from
one species to another in animals. Guidelines for evaluating the risk of transgenic
crops have been published (e.g. Rissler and Mellon, 1996), but so far no equivalent
set of guidelines exists for transgenic animals. Recent evidence from a number of
fish studies suggest that gene introgression has occurred between cultured and wild
populations (e.g. Cagigas et al, 1999; Garcia-Martin et al, 1999; Hansen et al, 2000;
Epifanio and Philipp, 2000; Utter, 2000; Allendorf et al, 2001; Martinez et al, 2001;
Campbell et al, 2002). Commercial breeders need to carefully balance the benefits
of introducing new stock, as introgression of alien genotypes with current gene
pools may result in the disruption of local adaptation, or in the loss of desirable
characteristics (e.g. Cronin et al, 1995; Teale et al, 1995; Conover, 1998).
Interspecific hybridisation can also disrupt the normal resistance of plant and animal
species to their parasites (Fritz et al, 1999).
Aside from breeding of animals, gene introgression has other commercial
applications such as pest control. Experiments are currently underway to test the
feasibility of introducing inducible fatality genes (IFG’s), or inducible sterility genes
59
(ISG’s) via transgenic individuals into a pest population to reduce numbers (Davis et
al, 1999).
Conversely, hybrids between species may well stabilise to become “hybrid species”.
Such species could become pests themselves due to an increased competitive ability
(e.g. Bullini and Nascetti, 1989). Additionally, natural introgression can cause pest
species to become more of a problem. For instance, chromosomal rearrangements,
mitochondrial haplotypes and kdr, a mutation responsible for resistance to
pyrethroid insecticides have all been shown to spread between sibling species and
geographic races of the Anopheles gambiae group of species through introgression
(Caccone et al, 1998; Thelwell et al, 2000; Weill et al, 2000; Gentile et al, 2002).
Implications – Evolution
The role that interspecific hybridisation and introgression may play in the evolution
of animal species has always been a subject of much debate. Mayr (1963) held the
view that introgression is unimportant, whereas Anderson (1949) felt that it
presented a means of introducing new gene combinations into species genomes,
which could be exploited. Some authors even implicated introgressive hybridisation
as having the potential to lead to the extinction of species (Rhymer and Simberloff,
1996; Allendorf et al, 2001). There is still much debate, but generally it is agreed
that interspecific hybridisation plays some role in the evolution of animal species,
although how much influence it has is still largely unknown (Heiser, 1973; Arnold,
1992, 2001; Dowling and Secor, 1997).
60
Introgression can have important implications for evolutionary biology, as
interspecific hybridisation provides favourable conditions for rapid and major
evolution (Grant and Grant, 1992). Hybridisation produces novel combinations of
genes and alleles, which can lead to greater adaptability and diversification (Barton
and Hewitt, 1985; Woodruff, 1989; Allendorf et al, 2001; Gerber et al, 2001). Even
a small amount of gene flow may be sufficient to override other evolutionary forces
such as mutation, drift and selection (Slatkin, 1987, Ellstrand et al, 1999).
Hybrids are often inferior in some way compared to parental forms (Coyne, 1992;
Wu and Davis, 1993; Wu and Palopoli, 1994). However, this is not necessarily
always the case (e.g. Barton and Hewitt, 1985; De Marais et al, 1992; Moore and
Price, 1993; Reiseberg et al, 1996; Arnold et al, 1999, 2001; Parris, 2001;
Hasselquist, 2001; Veen et al, 2001). There may even be hybrid vigour, where
hybrids fare better than either parent, particularly if the parental species are inbred
(Burke and Arnold, 2001; Grant and Grant, 1992). When both parents are welladapted to suit their own habitats, it would seem likely that a hybrid between the
two species will be less well adapted, being intermediate between the two. However,
this can make them more generalist and more able to exploit a range of available
habitats and resources, and may prove beneficial in a changing environment
(Anderson and Stebbins, 1954; Lewontin and Birch, 1966; Barton, 2001). This can
lead to the evolution of new species (e.g. Bullini and Nascetti, 1990).
Implications – Phylogeny reconstruction and biogeography
61
There has been much recent debate about how phylogenies should be constructed.
Historically, morphological characters have been used to identify species, and these
same characters were used in phylogeny reconstruction. Over the last few decades,
this has become problematic due to a lack of funding for ‘alpha taxonomy’ and a
decrease in the number of trained taxonomists. With the recent advances in
molecular techniques, and particularly with the advent of PCR, DNA sequence data
have been favoured as a technique for phylogeny reconstruction. DNA sequences
are particularly useful for this purpose as they give a virtually unlimited supply of
independent characters, whereas morphological characters are limited, have varying
but unknown degrees of non-independence, making phylogenies unreliable. Most
authors today use molecular data to construct trees, either using mitochondrial genes
alone (e.g. Dowling et al, 1992; Hebert et al, 2003), or a combination of
mitochondrial and nuclear loci (e.g. Saetre et al, 2001; Beltrán et al, 2002). Others
argue for an integrated approach using a combination of morphological characters
and DNA sequence data (e.g. Sota and Vogler, 2001). The literature on methods of
phylogeny reconstruction, and debates about gene trees versus species trees has been
reviewed recently by Brower et al, 1996.
Introgression can cause problems to arise when using gene genealogies to represent
the true organismal phylogeny. If there has been hybridisation in the past, there may
be introgression of genetic material at some loci, but not at others creating
discordant genealogies which can cause confusion (Smith, 1992; Brower et al, 1996;
Sang and Zhong, 2000; Tosi et al, 2000; Holder et al, 2001; Rosenberg, 2002).
Inclusion of hybrid taxa in a phylogeny may lead to increased amounts of
homoplasy which may disrupt the relationships of other taxa (McDade, 1995). If
62
speciation has been recent, this may result in incomplete lineage sorting with species
sharing ancestral haplotypes (e.g. Avise et al, 1990; Klicka et al, 1999).
Additionally, gene flow between species can cause problems when estimating
genetic divergence times as it can bias genetic distances (McKinnon and Rundle,
2002).
Neutral genes have often been proposed as the best to use in constructing
genealogies, as those under selection may converge when they are exposed to
similar environments (Clarke et al, 1998). This approach may, however be
misleading in sympatric species as introgression may occur, and therefore in this
situation it may be wise to use genes under divergent selection if possible. In any
case, rapidly-evolving gene regions are preferred for closely related taxa, as only the
most rapidly evolving nucleotide sites will have accumulated substitutions (Kocher
et al, 1989). Additionally, multiple unlinked loci should be used to ensure the best
topology is found (Ballard, 2000).
Single gene trees do not necessarily reflect the ‘true’ organismal tree. Introgression
between animal species means that traditional phylogenies based on morphological
characters may not accurately reflect the organismal tree, as hybridisation between
species will often go undetected phenotypically. Some authors believe that several
gene trees, along with morphological trees should be combined in order to elucidate
the best theory of relationships in a given set of taxa. For many cases this may be the
best solution, but needs to be assessed on a case by case basis, as highly discordant
genealogies may lead to a loss of resolution in the consensus tree (Ballard, 2000).
Kliman et al (2000) use a new method they term “divergence population genetics”
63
(DPG) to perform detailed population genetics analysis of species divergence at
multiple loci, coupled with analysis of common patterns among loci. This is a
potentially powerful technique for investigating species divergence where there is
gene flow at some, but not all loci.
Distinguishing introgression from ancestral polymorphism and balancing selection
is vital in establishing the reason for non-concordance of topologies (Avise and Ball,
1990; Goodman et al, 1999; Harrison and Bogdanowicz, 1997. Dobzhansky (1951)
noted that the presence of characters from two species in individuals does not
necessarily indicate hybridity but that the individuals may represent the remnants of
the ancestral population out of which the two species differentiated.
Biogeographical information may be useful in distinguishing whether nonconcordance of character sets is due to recent introgression or ancestral
polymorphism. Good et al (2003) used phylogeography to predict expected spatial
patterns in two species of chipmunks, and with this information were able to
attribute the given pattern to introgression. They used the assumption that
introgressed alleles are expected to be more common near to contact zones
(Barbujani et al, 1994).
Evidence for introgression within genealogies may elucidate the biogeography of a
set of taxa. For instance, in one study mtDNA introgression was found between two
species of Japanese land snail (Euhadra peliomphala and E.brandtii). Since recent
contact between the species was deemed unlikely, this was assumed to be evidence
64
of past hybridisation via a landbridge that existed in the early Pleistocene (Shimizu
and Ueshima, 2000).
Future directions
We know that there can be some flow of genetic material between closely related
animal species in the wild, and we understand that this can have many consequences
for fields as diverse as conservation, agriculture and systematics. The next question
might be: “where next?” Studies that have been carried out to date are limited and
specific to certain taxa, and use a limited subset of genetic loci. Many more taxa and
loci would be needed in order to quantify how widespread introgression really is in
the wild. Additionally, given that genes can successfully flow between animal
species, it would be advantageous to quantify this in terms of how much, how often
and the factors affecting which gene regions are most likely to introgress. More
extensive studies into the number of animal species which naturally form hybrids
would also be beneficial.
65
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