Review

Challenges and opportunities of genetic approaches to biological conservation

Richard Frankham
*
Department of Biological Sciences, Macquarie University, NSW 2109, Australia
Australian Museum, 6 College Street, Sydney, NSW 2010, Australia
a r t i c l e i n f o
Article history:
Received 17 March 2010
Received in revised form 12 May 2010
Accepted 18 May 2010
Available online 9 June 2010
Keywords:
Conservation genetics
Genetic management
Genomics
Fragmented populations
Outbreeding depression
Population viability analyses
a b s t r a c t
I discuss future challenges and opportunities in genetic approaches to biodiversity conservation. Resolv-
ing taxonomy uncertainties and identifying diverged evolutionary units within species are both bedev-
illed by a plethora of denitions: the challenge for the conservation community is to come to an
agreed denition of species and for a unit within species for conservation purposes. For genetic manage-
ment in the wild, the main challenge is to apply well-established genetic principles to management,
especially of fragmented populations. Fears about outbreeding depression are preventing rational use
of gene ow for genetic rescue; predicting the risk of outbreeding depression is the most important
unmet scientic challenge in the eld. The major challenge in genetic management of captive popula-
tions of threatened animal species is to institute explicit management to minimize genetic adaptation
to captivity, so that reintroduction success is maximized. The development of low cost genome sequenc-
ing offers many research opportunities and challenges. For example, there are opportunities to identify
genes involved in speciation and a major challenge is to devise molecular tests to predict reproductive
isolation between populations. Genomics offers opportunities to provide higher precision estimate for
many parameters of importance to conservation. A major challenge is to devise means to assess, on a gen-
ome-wide basis, genetic diversity that is important to adaptive evolution. There is a challenge to develop
simple inexpensive means to monitor genetic diversity of species on a global scale. Many of the most
important practical challenges concern application of current genetic knowledge to the management
of threatened species.
2010 Elsevier Ltd. All rights reserved.
Contents
1. Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1920
2. Resolving taxonomic uncertainties . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1920
2.1. Defining diverged evolutionary units with species . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1920
3. Genetic management of wild populations . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1920
4. Genetic management of captive populations . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1921
5. Addressing the conservation implications of global climate change. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1921
6. Contributions of genetics to management of invasive species and their impacts on threatened species. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1921
7. Consequences of different breeding systems in genetic management of threatened species . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1921
8. Application of molecular genetics to understand species biology. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1922
8.1. Use of molecular genetics in wildlife forensics . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1922
9. Conservation genomics . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1922
10. Global monitoring of changes in genetic diversity. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1923
11. Integrating genetics into conservation biology . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1924
12. Priorities in applications and research . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1925
Acknowledgements . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1925
References . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1925
0006-3207/$ - see front matter 2010 Elsevier Ltd. All rights reserved.
doi:10.1016/j.biocon.2010.05.011
* Address: Department of Biological Sciences, Macquarie University, NSW 2109, Australia. Tel.: +61 2 9850 8186; fax: +61 2 9850 8245.
E-mail address: rfrankha@science.mq.edu.au
Biological Conservation 143 (2010) 19191927
Contents lists available at ScienceDirect
Biological Conservation
j our nal homepage: www. el sevi er. com/ l ocat e/ bi ocon
1. Introduction
Conservation genetics is an applied science, involving the appli-
cation of evolutionary and molecular genetics to biodiversity con-
servation (see Allendorf and Luikart, 2006; Frankham et al., 2010).
IUCN recommends conservation of biological diversity at three le-
vel, genes, species and ecosystem diversity (McNeely et al., 1990).
Genetics contributes to all three levels. It is the focus of the rst.
For the second, genetic factors contribute to species extinction risk
through inbreeding depression, loss of genetic diversity and loss of
evolutionary potential (see Frankham, 2005). Third, genetic diver-
sity impacts on ecosystem survival, function and diversity (see
Reusch et al., 2005; Crutsinger et al., 2006). The main genetic activ-
ities in biological conservation are:
genetic contributions to resolving taxonomic uncertainties,
dening evolutionarily diverged units for separate manage-
ment within species,
genetic management to minimize inbreeding and loss of
genetic diversity in populations, and species extinction risk
in the wild,
genetic management of captive populations to minimize
inbreeding and loss of genetic diversity in captivity, and to
maximize reintroduction success,
contributions of genetics to management of invasive species
and their impacts on threatened species,
application of molecular genetics to obtain information
important to species conservation (sex, population size,
demographic history, mating system, population structure,
gene ow, parentage, diet, diseases),
use of molecular genetics in forensics,
integrating genetics with demographic and environmental
variables, catastrophes and human impacts to predict extinc-
tion risks and compare alternative options in species recovery
programs.
There has been substantial progress in conservation genetics
since its foundation in the late 1970s, including experimental val-
idation of most of the theories underlying genetic concerns in con-
servation biology (see Frankel and Soul, 1981; Frankham et al.,
2002, 2010; Allendorf and Luikart, 2006). I will briey consider
the current status of conservation genetics to provide context for
considering challenges and opportunities. This is a much expanded
version of a previous brief perspective (Frankham, 2010). My main
focus is on issues of importance to practical species conservation.
2. Resolving taxonomic uncertainties
Major genetic effort in conservation biology is directed towards
assisting in resolution of taxonomic uncertainties. This effort is
seriously compromised by the lack of an agreed denition for spe-
cies in biodiversity conservation. There are at least 22 denitions of
species (Claridge et al., 1997). Some denitions compromise popu-
lation and species persistence (see below). Further, the use of dif-
ferent denitions leads to controversies that undermine our
credibility in the broader community. There is an urgent need for
an IPPC-like organisation in conservation biology to reach a con-
sensus on a denition of species for our purposes. In my view,
the units that are relevant in conservation of sexual species are de-
ned by reproductive isolation and independent evolutionary
fates. Populations within species should be able to exchange genes
without adverse effects on reproduction or survival i.e. they should
not show serious outbreeding depression (a reduction in reproduc-
tion and/or survival in the rst or later generations upon crossing
populations; see Endler, 1977; Edmands, 2007). For example, the
biological species concept (BSC) meets these requirements and is
the denition used in the US Endangered Species Act. Conversely,
the ability to simply diagnose units as forming distinct groups, as
used in the phylogenetic species concept (PSC), is not appropriate
for the needs of conservation biology. In particular, it will often im-
pede genetic rescue of small inbred populations by preventing
gene ow between populations that are differentiated due to ge-
netic drift and inbred. Thus, using the PSC species denition is
likely to lead to unnecessarily high population extinction rates
and thus elevated species extinction rates. In the former case
(BSC), differentiation is determined primarily by natural selection
(adaptive evolutionary differences), as much evidence now points
to the predominant role of adaptive differentiation in the develop-
ment of reproductive isolation (see Coyne and Orr, 2004; Gavrilets,
2004; Funk et al., 2006; Langerhans et al., 2007; Rieseberg and Wil-
lis, 2007; Price, 2008; Nosil et al., 2009; Stelkens and Seehausen,
2009; Sobel et al., 2010; Thorpe et al., 2010; Wang and Summers,
2010). In the latter case (PSC), differentiation (especially in DNA
markers) is primarily determined by genetic drift (chance).
A major challenge is to devise molecular means to predict
reproductive isolation in crosses between populations. Interest-
ingly, Coleman (2009) suggested that sequence differences in a re-
gion of the internal transcribed spacer 2 (ITS2) of nuclear rRNA
genes predicts the occurrence of reproductive isolation. If this is
veried it will be a holy grail in relation to molecular tests to dis-
tinguish conservation species. On the research side, enhanced
opportunities exist to identify speciation genes and this should
be a priority pursuit within conservation genomics (see below).
2.1. Dening diverged evolutionary units with species
A closely related pursuit is to dene units within species that are
sufciently differentiated to require separate management. Evolu-
tionary signicant units and management units within species have
been dened and are being used in conservation biology (see Ryder,
1986; Moritz, 1994; Vogler and DeSalle, 1994; Waples, 1995;
Crandall et al., 2000). These units vary in the use of neutral markers
versus adaptive differentiation and reproductive isolation in the
criteria used. Again, there is need for an agreed denition for a unit
within species for conservation purposes. The most critical conser-
vation issue is the existence of elevated risks of outbreeding depres-
sion (partial reproductive isolation) in crosses between units, but
little risk within units. This risk is predominantly associated with
adaptive, rather than neutral, differentiation among units (see
above). The risk of outbreeding depression is a critical issue in the
genetic management of fragmented populations (see below).
3. Genetic management of wild populations
The application of genetics in the management of threatened
plant and animal species in the wild is in its infancy, compared
to that in captivity (see Husband and Campbell, 2004; Frankham
et al., 2010). There is now compelling evidence that inbreeding
and loss of genetic diversity compromise the viability of wild pop-
ulations (see Frankham, 2005). Lack of genetic management in
these populations is not due to a lack of scientic guidelines, but
due to failure to consider genetic issues in wild management.
The most important genetic challenge in conservation biology is
to address genetic issues in the management of fragmented wild
populations of threatened species. There are innumerable recently
fragmented populations across the planet being affected by genetic
erosion (inbreeding and loss of genetic diversity) and thus having
elevated extinction risks (see Aguilar et al., 2008). Augmentation
of gene ow between populations could alleviate this in many
cases. However, fears of outbreeding depression are impeding the
1920 R. Frankham/ Biological Conservation 143 (2010) 19191927
rational genetic management of fragmented populations; I am
aware of only 19 cases where gene ow between populations has
been re-established potentially for conservation purposes (Frank-
ham et al., draft manuscript). Thus, the major challenge and oppor-
tunity is to develop means for predicting the risk of outbreeding
depression. A group of us is currently working on such a proposal
(Frankham et al., draft manuscript). Our review of the literature
indicates that the risks of outbreeding depression are being exag-
gerated, and this is the view of most conservation geneticists.
An additional problem is that many people responsible for man-
aging wild animal and plant populations have inadequate genetics
training. A further challenge is to ensure that future conservation
and wildlife biologists receive adequate training in genetics, so that
they understand the genetic issues involved in managing threa-
tened populations.
4. Genetic management of captive populations
The primary focuses of genetic management of captive popula-
tions of outbreeding diploid (and amphidiploid) threatened animal
species are to maintain genetic diversity and minimize inbreeding
(see Frankham et al., 2010). Practical application of genetic princi-
ples to management of captive populations of threatened species
has been instituted and is being done in a scientically rational
manner (see Ballou et al., in press). Captive populations with ped-
igrees are typically managed to maximize the retention of genetic
diversity by minimizing mean kinship (Ballou and Lacy, 1995;
Fernndez et al., 2004). This is also effective in minimizing
inbreeding.
For many animal species in captivity, there is a desire to pre-
serve the option of eventual reintroduction into the wild. However,
genetic adaptation to captivity results in deleterious impacts on
wild tness (see Frankham, 2008). The most pressing challenge is
to explicitly manage populations to minimize genetic adaptation
to captivity so that its deleterious impacts on reintroductions are
minimized. We know in broad outline how to do this, mainly by
minimizing generations in captivity and/or using population
fragmentation (see Margan et al., 1998; Frankham, 2008). The chal-
lenge is to optimise procedures based upon simulations and labo-
ratory experiments and to apply them in practical management.
In species where pedigrees are unavailable due to multi-male
multi-female breeding groups, genetic management schemes have
been devised to manage groups, based on minimizing group
inbreeding (Princee, 1995; Wang, 2004). However, this is being
done in very few cases. The challenge is to apply these procedures
in managing group-breeding threatened species. Similar principles
could be applied to management of isolated fragmented popula-
tions in the wild, but I am unaware of any attempts to do so.
For plants, the issues in ex-situ genetic management are some-
what different (see Guerrant et al., 2004). Inbreeding and loss of
genetic diversity are important concerns. However, genetic adapta-
tion of captivity is generally a minor issue, as plants typically have
few generations in captivity, due to long-term seed storage or cryo-
preservation. Preserving adaptive genetic variation (often among
populations) is a more prominent issue in plants, as are systematic
strategies of sampling from a representative sample of seeds per
plant, individuals within populations and populations within the
species (see Husband and Campbell, 2004). Diversity of breeding
systems is more prominent issue in plants than animals and raises
additional issues (see Section 7).
Many estimates of molecular genetic diversity have been ob-
tained in threatened and non-threatened species (see Spielman
et al., 2004; Evans and Sheldon, 2008). However, the ability of spe-
cies to evolve is determined primarily by quantitative genetic var-
iation, rather than molecular variation for neutral and weakly
selected loci, and the two are weakly correlated (Reed and Frank-
ham, 2001). I am only aware of quantitative estimates of quantita-
tive genetic variation (heritability or additive genetic variation) in
two plant and three animal threatened species (Culley et al., 2006;
Frankham et al., 2010 pp. 108) and there is a need to provide esti-
mates for many threatened species. Pre-existing zoo records
should be suitable for estimating heritabilities in threatened ani-
mal species, especially for body weight and possibly for survival.
5. Addressing the conservation implications of global climate
change
Addressing the impacts of global climate change on biodiversity
and devising management to minimize impacts are major chal-
lenges that require both research and management actions. Some
species can adapt genetically to projected future environments
and other cannot (see Hoffmann et al., 2003; Umina et al., 2005;
Kellermann et al., 2006, 2009; Csszr et al., 2010). A crucial chal-
lenge is to distinguish species in the two categories and to deter-
mine the relative proportions.
Genetic issues need to be considered when designing means to
alleviate the impacts of climate change e.g. by managed transloca-
tions to keep pace with climate change. Which population or pop-
ulations should be used for such translocations? For example,
maximizing genetic diversity by crossing all available populations
is an attractive strategy for coping with translocations to human-
altered environments to which no single population is adapted,
but this strategy requires experimental evaluation.
6. Contributions of genetics to management of invasive species
and their impacts on threatened species
Invasion biology has recently risen to prominence and genetic
studies in the eld have increased correspondingly. For example,
genetic diversity has been shown to be lower, on average, in inva-
sive species, than in their native source populations (Dlugosch and
Parker, 2008). Evolutionary changes have been documented in sev-
eral invasive species (see Allendorf and Lundquist, 2003; Phillips
et al., 2006; Barrett et al., 2008; Suarez and Tsutsui, 2008; Phillips,
2009). The challenge is to delineate in what proportion of cases
evolutionary change is causally related to the development of inva-
siveness. A major challenge is to identify any genetic susceptibili-
ties that can aid in control of invasive species.
Several native species have shown evolutionary responses to
introduction of invasive species (Lee, 2002; Phillips and Shine,
2004, 2006; Freeman and Byers, 2006; Carroll, 2008), but it is un-
clear how often these responses will allow them to persist.
7. Consequences of different breeding systems in genetic
management of threatened species
The implications of different breeding systems for genetic man-
agement of threatened species have received limited attention (see
Frankham et al., 2010). The consequences of selng and obligate
asexual reproduction are relatively clear (see Hamrick and Godt,
1989). Further, we have growing understanding of the added sig-
nicance of loss of genetic diversity on self-incompatible (Richman
and Kohn, 1996; Young et al., 2000; Castric and Vekemans, 2004;
Pickup and Young, 2007) and haplo-diploid species (Cook and Cro-
zier, 1995; Pamilo and Crozier, 1997; Zayed et al., 2004; Zayed and
Packer, 2005). Haplo-diploid species with mixed mating systems
(high levels of sib mating) exhibit outbreeding depression within
populations, but little or no inbreeding depression (see Peer and
Taborsky, 2005; Greeff et al., 2009).
R. Frankham/ Biological Conservation 143 (2010) 19191927 1921
I am only aware of limited genetic management work on gyno-
dioecious plant species (populations containing a mixture of plants
with hermaphrodite and pistillate (female) owers), even though
these represent the second most common reproductive system in
owering plants (Richards, 1997). The frequencies of the two forms
are controlled by the combined effects of cytoplasmic male sterility
(determined by mtDNA variants) and dominant alleles at nuclear
restorer loci (Schnable and Wise, 1998). Such species are expected
to be more sensitive to population size reduction than hermaphro-
dite diploids, as they suffer from both inbreeding depression, and
elevated frequencies of pistillate plants with selng (resulting in
pollen shortage, fewer fertilized ovules and accelerated population
declines; Vilas and Garca, 2006).
Polyploids lose genetic diversity more slowly than equivalent
sized diploid populations (Brown and Young, 2000; Hardy and
Vekemans, 2001; Luttikhuizen et al., 2007). Theory suggests that
polyploids will be less affected by inbreeding depression than dip-
loids, but empirical evidence is insufcient to resolve this issue
(Ramsey and Schemske, 2002). There is a scientic opportunity
and a practical need to resolve this issue, for example by complet-
ing a meta-analysis.
In general, I am aware of few cases where the special features of
breeding systems are being taken into account in the genetic man-
agement of threatened species, especially in the haplo-diploid,
gynodioecious and self-incompatible cases. The challenges are to
identify the special features associated with different breeding sys-
tems and apply this information to practical management of such
threatened species. An additional concern in plants is the effects
of habitat fragmentation and other human disturbance on plant
mating systems, the usual effect being increased self-fertilization
(see Aguilar et al., 2008; Eckert et al., 2009).
8. Application of molecular genetics to understand species
biology
Much information important as background to conserving spe-
cies is difcult to obtain directly, especially for secretive, nocturnal
and fossorial species. Molecular genetic analyses of DNA from non-
invasive sampling allows much information of importance to con-
servation to be determined, including sex of individuals (in species
where sexes are morphologically indistinguishable), population
size, demographic history, mating and breeding systems, popula-
tion structure, gene ow, parentage, sites for reintroductions and
translocations, identity of disease organisms, diet (see Allendorf
and Luikart, 2006; Frankham et al., 2010). Much work has been
done in this area and the opportunities will increase with more
inexpensive and powerful molecular techniques, and improved
methods of analysis.
Some of the methods have proven less reliable than originally
claimed. For example, there is controversy about the reliability of
nested clade analyses for determining population structure and
inferring driving forces (Knowles and Maddison, 2002; Petit and
Grivet, 2002; Panchal and Beaumont, 2007; Beaumont and Pan-
chal, 2008; Petit, 2008; Templeton, 2008). Inferring selection by
identifying outlier loci has proven to be sensitive to population
structure and consequently more robust analyses have been rec-
ommended (Excofer et al., 2009). Similarly, potential biases have
been identied in Bayesian Markov chain Monte Carlo methods for
estimating DNA base substitution rates from populations with
structure (non-random mating) or that have suffered size bottle-
necks (Navascus and Emerson, 2009). Further, Balkenhol et al.
(2009) comparing 11 statistical methods for linking landscape
and genetic data and found that the most commonly applied tech-
niques had high type-1 error rates and that the different methods
showed only moderate levels of agreement. The burgeoning devel-
opment of methods has outstripped the quality control processes. I
suspect that other methods will also prove to be less than robust.
There are challenges and opportunities for research to evaluate
and compare the methods, typically by using computer simula-
tions. Where methods do not work as intended, more robust pro-
cedures need to be devised.
8.1. Use of molecular genetics in wildlife forensics
Scientic information forms a critical part of evidence in crim-
inal trials and it is now being used in conservation-related cases
and public shamings (see Linacre, 2009; Frankham et al., 2010).
For example, DNA analyses based on mtDNA have been used to dis-
tinguish threatened whales from minke whales in whale meat
from Japan and Korea (Baker and Palumbi, 1996; Dizon et al.,
2000). Further, whale meat on sale in sushi restaurants in Los
Angeles and Seoul, South Korea matched whales from Japan, indi-
cating illegal international trade in protected whales (Baker et al.,
2010). Methods have also been devised to identify tiger material
in Asian medicines and to identify species for shark ns (see Telet-
chea et al., 2005). The provenance of seized chimpanzees has also
been identied (Goldberg, 1997). Opportunities exist for increasing
the resolving power of forensic tests with improvements in statis-
tical techniques and inexpensive genome sequencing.
9. Conservation genomics
Conservation genomics is a new discipline that has arisen with
the sequencing of whole genomes (see Ryder, 2005; Primmer,
2009; Ouborg et al., 2010). A small number of threatened species
have already had their genomes sequenced, including chimpan-
zees, gorillas, orangutans and giant pandas (ENSEMBL, 2009; Li
et al., 2010). Many more will be sequenced in the near future, as
sequencing costs are rapidly decreasing. Genome sequencing
may be done either by sequencing the entire DNA, or by sequenc-
ing only the protein coding regions (transcriptome; also see ESTs
below). The latter is done by sequencing cDNAs created by reverse
transcribing bulk mRNA, as was done for the Glanville fritillary
buttery (Vera et al., 2008).
Many conservation research opportunities will arise from
sequencing of genomes of threatened species, but the challenge
will be to use this technology wisely for conservation purposes.
Whole genome sequencing will not provide a panacea for practical
management of threatened species. Genome sequence data for a
species provides basic information on genome structure and genet-
ic diversity. It allows us to determine the number of protein coding
loci, the proportion of the genome due to transposable elements, to
delineate copy number variants, to measure genetic diversity in
protein coding and non-coding regions and to detect chromosomal
variants (duplications, deciencies, inversions, and translocations).
The sequence of a single individual from a species provides only a
restricted window on genetic diversity for sequence and especially
chromosomal variants. However, sequence information aids in the
development of genetic marker, such as single nucleotide polymor-
phisms (SNPs) and microsatellites that can subsequently be geno-
typed on many individuals. It also allows cDNA expression
microarrays to be constructed for studying transcription rates for
many loci in the genome (Ranz and Machado, 2006).
Many threatened species exhibit elevated frequencies of alleles
causing recessively inherited diseases, as a result of genetic drift in
small populations (see Frankham et al., 2010 pp. 148 and 449). For
example, the California condor has a relatively high frequency of
chondrodystropy (an inherited dwarsm; Ralls et al., 2000; Ralls
and Ballou, 2004). Genome sequencing will aid in the development
of methods to detect carriers (heterozygotes). This offers the
1922 R. Frankham/ Biological Conservation 143 (2010) 19191927
opportunity to eliminated such diseases, but care must be taken to
preserve genetic diversity in the remainder of the genome (see
Frankham et al., 2010 pp. 226 and 450). Work to identify the chon-
drodystrophy locus in California condors is already underway and
is being aided by comparisons with the DNA sequence of the
domestic chicken (Romanov et al., 2009).
Whole genome sequencing studies will provide more precise
and unbiased estimates of effective population size, demographic
history, levels of inbreeding, rates of gene ow, differentiation
among populations and taxonomic status (Luikart et al., 2003). In
addition, they enhance opportunities to study multi-locus effects
such as associative overdominance, selective sweeps and back-
ground selection. For example, widespread non-neutral behaviour
of microsatellites due to selective sweeps has been found in animal
populations that adapted to captivity over 50 generations (Mont-
gomery et al., 2010).
The most important challenge in this area is to devise means to
measure adaptive genetic diversity on a genome-wide basis (see
Bustamante et al., 2005; Williamson et al., 2007). This variation
will be of three types (see Frankham et al., 2010). First, there will
be rare deleterious variants in mutation-selection balance that will
often consist of low activity alleles at many protein coding and reg-
ulatory loci. Second, more intermediate frequency alleles will occur
that are subject to balancing selection. Third, a small proportion of
alleles will be benecial and being driven towards xation by nat-
ural selection in populations well adapted to their environment.
This proportion is likely to be much higher in populations adapting
to new environments, such as populations adapting to captivity
(Montgomery et al., 2010), or climate change. Until recently, quan-
tication of adaptively important genetic diversity was largely re-
stricted to studies of MHC loci in vertebrates, self-incompatibility
loci in plants and sex loci in Hymenoptera (see Frankham et al.,
2010). These are subject to balancing selection, but represent only
a modest proportion of all adaptive genetic variation. Hohenlohe
et al. (2010) have used next generation sequencing to type over
45,000 SNPS in each of 100 individuals from two oceanic and three
freshwater populations of three spined stickleback sh (Gasteros-
teus aculeatus). Genomic regions exhibiting signatures of either
balancing selection or divergent selection were identied and were
remarkably consistent across independently derived populations.
Expressed sequence tags (ESTs) have been suggested as a means
for assessing adaptive genetic diversity (Yahara et al., 2010). These
sequences are derived from mRNA, by reverse transcribing it into
cDNA, followed by cloning and sequencing (Bouck and Vision,
2007). However, the regulatory regions that are important to func-
tion are missing. The sequence variation of particular ESTs is akin
to very high precision allozyme data and allozymes were not in
general successful in indicating adaptive genetic diversity, apart
from identication of some intermediate frequency adaptive poly-
morphisms. It may be possible using computational bioinformatics
to distinguish the three components of adaptive sequence varia-
tion. Consequently, there are opportunities to develop/enhance
and validate methods to obtain quantitative estimates of adaptive
genetic diversity from EST sequence variation. Variation in levels of
EST transcripts may be more informative, but genetic and environ-
mental causes of variation must be distinguished. cDNA expression
microarrays have been used widely to quantify transcription rates
(see Ranz and Machado, 2006; Whitehead and Crawford, 2006),
but are being replace by high-throughput RNA sequencing (see Ou-
borg et al., 2010). Transcription rates include many of the regula-
tory effects, but do not encompass regulation at the protein level.
I am not aware of EST or cDNA expression microarray variation
data being converted into quantitative assessments of adaptive
evolutionary potential in threatened species.
A recent surprising has been the discovery that epigenetic mod-
ication (in DNA methylation and DNA associated proteins such as
histones) can vary among individuals and populations of the same
species and that some of this variation is heritable (see Ouborg
et al., 2010). The role of epigenetic modication as a source of her-
itable variation, its persistence over generations, and its relevance
to conservation genetics is as yet unclear. There are clear chal-
lenges and opportunities to resolve its role.
Chromosomal variant polymorphisms (inversions, duplications
and deletions) are typically found in species genomes and are often
associated with adaptive differences. For example, genotypes for
polymorphic inversions in Drosophila typically differ in tness
(see Krimbas and Powell, 2000; Hoffmann et al., 2004). Chromo-
somal rearrangement polymorphisms in white-throated sparrows
are associated with variation in morphology, physiology, and
behaviour (Romanov et al., 2009). Further, large, rare chromosomal
deletions are associated with severe early-onset obesity in humans
(Bochukova et al., 2010). There are opportunities to characterise
chromosomal variant frequencies following genome sequencing
and to include them as part of the description of adaptive genetic
variation.
Genomics also provides realistic opportunities for detecting loci
subject to natural selection, and for identifying loci involved in spe-
ciation. Inevitably, improved markers and analytical tools will arise
from this work. It is to be hoped that genomic tools will be wisely
used to address important issues in conservation genetics (see Kris-
tensen et al., 2010; Wheat et al., 2010), rather than becoming a
bandwagon with a much trivial work, as happened with allozymes.
10. Global monitoring of changes in genetic diversity
It is widely recognized that monitoring changes in biodiversity
is desirable. Such monitoring is already underway at the species
and ecosystem levels, as reected in the IUCN Red List of Threa-
tened Species (IUCN, 2010), the WWF-Living Planet Index (2010),
Census of Marine Life (2010), Terrestrial Ecosystem Monitoring
Sites (2010). However, there is no routine global scale monitoring
of species genetic diversity over time (Laikre et al., 2009), although
a few species have been monitored over time (see Taylor et al.,
1994; Bouzat et al., 1998; Groombridge et al., 2000; Umina et al.,
2005; Schwartz et al., 2007; Laikre et al., 2008). Global monitoring
of genetic diversity in a broad array of taxa needs to be instituted
(Laikre et al., 2009; GEO BON, 2010). There are challenges to devis-
ing schemes, using both direct and indirect methods (Brown et al.,
1997; Schwartz et al., 2007; Laikre et al., 2008). A major challenge
will be to devise monitoring schemes that are sustainable over
100 years or more through nancial recessions and depressions,
climatic disasters, wars, changes of governments, changes in scien-
tic priorities. Notably economic indicators are often rather crude
and inexpensive to obtain (e.g. GDP, unemployment rates, and con-
dence opinion surveys). Economists often use data collected for
other purposes, even though economics has more ready access to
funds than biodiversity.
It will not be practical to monitor genetic diversity within spe-
cies over the long-term on any but a small sample of species, given
the short lifespan of research groups and funding constraints.
Brown et al. (1997) proposed seven indicator of genetic diversity
for State of the Environment Reporting in Australia (number of
sub-specic taxa, population size, numbers and isolation, environ-
mental amplitude of populations, genetic diversity at marker loci
within individual populations, quantitative genetic variation, in-
ter-population genetic structure, and mating (amount and pattern
of mating within populations, including mating system). However,
many of these do not provide quantitative estimates of changes in
genetic diversity.
Population size is an attractive option for an indirect and inex-
pensive monitor of genetic diversity. There are rm theoretical
R. Frankham/ Biological Conservation 143 (2010) 19191927 1923
grounds for expecting a causal relationship between heterozygos-
ity and population size (N) (see Wright, 1969). Further, high corre-
lations between heterozygosity and logN across species have been
found in empirical data (0.7 Soul, 1976; 0.81 Frankham, 1996). For
example, heterozygosity for neutral loci at generation t as a pro-
portion of initial heterozygosity (H
t
/H
0
) is related to effective pop-
ulation size in each generation (N
ei
), as follows (Crow and Kimura,
1970):
H
t
=H
0
p
t
i1
1 1=2N
ei
e
t=2Ne
1
where N
e
is the overall effective size over generations. N
e
is esti-
mated from the number of potentially breeding adults in each gen-
eration by multiplying by the average single generation estimate of
N
e
/N due to variance in family sizes and unequal sex ratios (0.35;
Frankham, 1995), and calculating the harmonic mean of these ad-
justed population sizes over generations (Wright, 1969). The pre-
dictions of Eq. (1) have been experimentally validated under
controlled laboratory conditions (see Borlase et al., 1993; Briton
et al., 1994; Woodworth et al., 1994; Frankham et al., 2010), but
evaluations of predictions from eld data (lacking information on
variance in family sizes and breeding sex-ratios) against cases
where actual heterozygosity data exists are also required to deter-
mine their practical utility.
It should be possible to infer likely changes in genetic diversity
from changes in population size (abundance), such as the informa-
tion collected for vertebrates for the WWF-Living Planet Index
(Hails et al., 2008). The Index is based on data from almost 5000
populations of 1686 species. Some of these data sets consist of esti-
mates of actual population sizes, so their primary data should al-
low estimates of changes in genetic diversity over the last
35 years for many vertebrate species, and allow further estimates
in the future. Similar approaches have already been used to infer
past population sizes in the nene (Paxinos et al., 2001) and north-
ern elephant seals (Hedrick, 1995; Hoelzel, 1999). Rauch and Bar-
Yam (2005) suggested that it was possible to infer changes in phy-
logenetic diversity from range size data in bacteria. However, this
method needs to be evaluated with data from higher eukaryotes.
Measures of allozyme genetic diversity have previously been
obtained on at least 1500 species of plants and animals (see Nevo
et al., 1984; Hamrick and Godt, 1989; Ward et al., 1992). The
opportunity exists to determine changes in genetic diversity since
these were measured (mostly in the 1970s1980s) by measuring
allozyme variation on current samples from the same species.
For species that have had their DNA sequenced, this can be done
by scoring appropriate DNA single nucleotide polymorphisms, as
done by Umina et al. (2005) in Drosophila melanogaster.
Direct measures of genetic diversity are required for a carefully
selected sub-set of species (see Laikre et al., 2008; GEO BON, 2010).
Challenges exist to decide upon means to do this and there are am-
ple opportunities to contribute to the undertaking. In brief, we
wish to measure and monitor neutral and adaptive genetic diver-
sity (as described in Section 9 above).
11. Integrating genetics into conservation biology
As genetics is only one of the considerations affecting popula-
tion viability, it is important to integrate it into an overall context
with demographic and environmental variables, catastrophes and
human impacts. While there is very limited information on the rel-
ative contributions of genetic factors to extinction risk, it appears
to make a substantial contribution. Saccheri et al. (1998) found
that inbreeding explained 26% of the deviance in extinction risk
for Glanville fritillary buttery (Melitaea cinixia) populations in Fin-
land when all other factors know to be affecting extinction risk
were included. Further, OGrady et al. (2006) found that inclusion
versus exclusion of inbreeding depression in population viability
analyses for 30 well-studied threatened vertebrate species reduced
median times to extinction by an average of 37% and was similar
for a range of habitat carrying capacities. There is a challenge
and opportunities to provide quantitative estimates of the relative
impacts of genetic versus other factors on extinction risk in a broad
array of taxa.
Population viability analyses (PVAs) are commonly applied to
study the combined impacts of all relevant variables to estimate
extinction risk and aid in prioritising management options in spe-
cies conservation (see Shaffer, 1981; Gilpin and Soul, 1986; Aka-
kaya and Sjgren-Gulve, 2000). Hundreds of PVAs have been
completed (Traill et al., 2007). Whilst there is extensive evidence
that inbreeding has deleterious effects on reproductive tness
(see Keller and Waller, 2002; Frankham, 2005), inbreeding depres-
Table 1
Priorities for applying pre-existing genetic knowledge in conservation biology.
1. Institute rational genetic management of threatened species in the wild, especially for fragmented populations
2. Agree upon an appropriate denition of species for conservation purposes
3. Agree on a denition of ESU for conservation purposes
4. Apply genetic principles in efforts to alleviate impacts of global climate change on biodiversity
5. Explicitly manage captive populations of threatened animal species to minimize genetic adaptation to captivity (along with minimizing loss of genetic diversity and
inbreeding)
6. Routinely include genetic factors (especially inbreeding depression) in PVAs and apply realistic levels of inbreeding depression to all aspects of the life cycle
7. Apply genetic principles to management of animal and plant species with diverse breeding systems
8. Apply group management to populations of threatened animal species that breed in multimale, multifemale groups (populations without pedigrees)
9. Apply genetic principles in assessing impacts of invasive species and in the control of invasive species
10. Estimate changes in genetic diversity over the past from abundance data for many species and publish an indicator of biodiversity change. Continue this activity into
the future
Table 2
Top priority areas in conservation genetics where additional data are required.
1. Collect extensive bodies of information on the occurrence of outbreeding depression and evaluate predictors of risk
2. Obtain many quantitative estimates of the cost of inbreeding in wild populations in nature
3. Obtain information on the relative contribution of genetic versus other factors to extinction risk for many species in the wild
4. Directly monitor genetic diversity on a carefully selected set of species and re-do this on a regular basis in the future
5. Obtain many estimates of quantitative genetic variation in threatened species
6. Update meta-analyses of Ne/N ratio in wild and tests for variables affecting the ratio (especially fecundity)
1924 R. Frankham/ Biological Conservation 143 (2010) 19191927
sion was only included in 57% of the models used for such assess-
ments (Traill et al., 2007). Even for those cases where inbreeding
depression was included in models, it was usually only applied
at a default level of 3.14 lethal equivalents derived from data on
juvenile survival in captive mammal populations (Traill et al.,
2007), rather than a more realistic 12 lethal equivalents across
the whole life cycle characteristic of wild populations (OGrady
et al., 2006). PVAs need to routinely include genetic factors, as
inbreeding depression typically has sizeable impacts on median
times to extinction (Brook et al., 2002; OGrady et al., 2006; Traill
et al., 2007). Further, realistic costs of inbreeding in the wild need
to be included. There are few estimates of the full impacts of
inbreeding depression in the wild and many more estimates are
required.
There is almost no empirical information on the long-term im-
pacts of loss of genetic variation (as distinct from inbreeding
depression) on extinction risk. Such information is sadly needed
and there is a challenge to devise experiments to provide such
information.
12. Priorities in applications and research
There are often disconnects between the highest priority scien-
tic needs in applied disciplines, what is technologically feasible,
and what is being implemented. Since resources are limited, I ad-
dress priorities for practical applications of current knowledge
and future research in conservation genetics. Table 1 lists my pri-
orities for applying current genetic knowledge within conservation
biology. Table 2 list priorities for collecting additional data on spe-
cic issues in conservation genetics. Priorities relating to new re-
search challenges are given in Table 3.
Acknowledgements
I thank the European Science Foundation Science Networking
Programme ConGen for nancial support to attend the 2009
Trondheim Conservation Genetics meeting where I rst spoke
about these issues, to NASA for funding my trip to the GEO BON
meeting in Asilomar where global monitoring of genetic diversity
was discussed, to D. Faith and T. Yahara for discussions concerning
that topic, and to L. Campbell and an anonymous reviewer for com-
ments on the manuscript.
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