Conservation genetics

For molecular conservation in genetics see: conservation (genetics). For the scientific journal Conservation Genetics, see Conservation Genetics (journal).

Conservation genetics is an interdisciplinary science that aims to apply genetic methods to the conservation and restoration of biodiversity. Researchers involved in conservation genetics come from a variety of fields including population genetics, molecular ecology, biology, evolutionary biology, and systematics. Genetic diversity is one of the three fundamental levels of biodiversity, so it is directly important in conservation of biodiversity, though genetic factors are also important in the conservation of species and ecosystem diversity. Conservation of genetic variability is important to the overall health of populations because decreased genetic variability leads to increased levels of inbreeding, and reduced fitness.

Genetic diversity

Genetic diversity is the variability of genes in a species. It can be estimated by the mean levels of heterozygosity in a population, the mean number of alleles per locus, or the percentage of polymorphic loci.

Importance of genetic diversity

If genetic diversity becomes low at many genes of a species, that species becomes increasingly at risk. It has only one possible choice of information at all or nearly all of its genes—in other words, all the individuals are nearly identical. If new pressures (such as environmental disasters) occur, a population with high genetic diversity has a greater chance of having at least some individuals with a genetic makeup that allows them to survive. If genetic diversity is very low, none of the individuals in a population may have the characteristics needed to cope with the new environmental conditions. Such a population could be suddenly wiped out.

The genetic diversity of a species is always open to change. No matter how many variants of a gene are present in a population today, only the variants that survive in the next generation can contribute to species diversity in the future. Once gene variants are lost, they cannot be recovered.

Contributors to extinction

1. Inbreeding and inbreeding elevation which reduces the fitness of populations.
2. The accumulation of deleterious mutations
3. A decrease in frequency of heterozygotes in a population, or heterozygosity, which decreases a species’ ability to evolve to deal with change in the environment.
4. Outbreeding depression
5. Fragmented populations
6. Taxonomic uncertainties, which can lead to a reprioritization of conservation efforts
7. Genetic drift as the main evolutionary process, instead of natural selection
8. Management units within species
9. Use of molecular techniques, such as allozymes as molecular markers, to analyze species in depth

Techniques

Specific genetic techniques are used to assess the genomes of a species regarding specific conservation issues as well as general population structure. This analysis can be done in two ways, with current DNA of individuals or historic DNA.

Techniques for analysing the differences between individuals and populations include

1. Alloenzymes
2. Random Fragment Length Polymorphisms
3. Amplified Fragment Length Polymorphisms
4. Random Amplification of Polymorphic DNA
5. Single strand conformation polymorphism
6. minisatellites
7. microsatellites .
8. Single-nucleotide polymorphisms
9. Sequence analysis
10. DNA fingerprinting

These different techniques focus on different variable areas of the genomes within animals and plants. The specific information that is required determines which techniques are used and which parts of the genome are analysed. For example, mitochondrial DNA in animals has a high substitution rate, which makes it useful for identifying differences between individuals. However, it is only inherited in the female line, and the mitochondrial genome is relatively small. In plants, the mitochondrial DNA has very high rates of structural mutations, so is rarely used for genetic markers, as the chloroplast genome can be used instead. Other sites in the genome that are subject to high mutation rates such as the Major Histocompatibility Complex, and the microsatellites and minisatellites are also frequently used.

These techniques can provide information on long-term conservation of genetic diversity and expound demographic and ecological matters such as taxonomy.

Another technique is using historic DNA for genetic analysis. Historic DNA is important because it allows geneticists to understand how species reacted to changes to conditions in the past. This is a key to understanding the reactions of similar species in the future.

Techniques using historic DNA include looking at preserved remains found in museums and caves. Museums are used because there is a wide range of species that are available to scientists all over the world. The problem with museums is that, historical perspectives are important because understanding how species reacted to changes in conditions in the past is a key to understanding reactions of similar species in the future. Evidence found in caves provides a longer perspective and does not disturb the animals.

Another technique that relies on specific genetics of an individual is noninvasive monitoring, which uses extracted DNA from organic material that an individual leaves behind, such as a feather. This too avoids disrupting the animals and can provide information about the sex, movement, kinship and diet of an individual.

Other more general techniques can be used to correct genetic factors that lead to extinction and risk of extinction. For example, when minimizing inbreeding and increasing genetic variation multiple steps can be taken. Increasing heterozygosity through immigration, increasing the generational interval through cryopreservation or breeding from older animals, and increasing the effective population size through equalization of family size all helps minimize inbreeding and its effects. Deleterious alleles arise through mutation, however certain recessive ones can become more prevalent due to inbreeding. Deleterious mutations that arise from inbreeding can be removed by purging, or natural selection. Populations raised in captivity with the intent of being reintroduced in the wild suffer from adaptations to captivity.

Inbreeding depression, loss of genetic diversity, and genetic adaptation to captivity are disadvantageous in the wild, and many of these issues can be dealt with through the aforementioned techniques aimed at increasing heterozygosity. In addition creating a captive environment that closely resembles the wild and fragmenting the populations so there is less response to selection also help reduce adaptation to captivity.

Solutions to minimize the factors that lead to extinction and risk of extinction often overlap because the factors themselves overlap. For example, deleterious mutations are added to populations through mutation, however the deleterious mutations conservation biologists are concerned with are ones that are brought about by inbreeding, because those are the ones that can be taken care of by reducing inbreeding. Here the techniques to reduce inbreeding also help decrease the accumulation of deleterious mutations.

Applications

These techniques have wide ranging applications. One application of these specific molecular techniques is in defining species and sub-species of salmonids. Hybridization is an especially important issue in salmonids and this has wide ranging conservation, political, social and economic implications. In Cutthroat Trout mtDNA and alloenzyme analysis, hybridization between native and non-native species was shown to be one of the major factors contributing to the decline in their populations. This led to efforts to remove some hybridized populations so native populations could breed more readily. Cases like these impact everything from the economy of local fishermen to larger companies, such as timber. Specific molecular techniques led to a closer analysis of taxonomic relationships, which is one factor that can lead to extinctions if unclear.

Implications

New technology in conservation genetics has many implications for the future of conservation biology. At the molecular level, new technologies are advancing. Some of these techniques include the analysis of minisatellites and MHC. These molecular techniques have wider effects from clarifying taxonomic relationships, as in the previous example, to determining the best individuals to reintroduce to a population for recovery by determining kinship. These effects then have consequences that reach even further. Conservation of species has implications for humans in the economic, social, and political realms. In the biological realm increased genotypic diversity has been shown to help ecosystem recovery, as seen in a community of grasses which was able to resist disturbance to grazing geese through greater genotypic diversity. Because species diversity increases ecosystem function, increasing biodiversity through new conservation genetic techniques has wider reaching effects than before.

A short list of studies a conservation geneticist may research include:

1. Phylogenetic classification of species, subspecies, geographic races, and populations, and measures of phylogenetic diversity and uniqueness.
2. Identifying hybrid species, hybridization in natural populations, and assessing the history and extent of introgression between species.
3. Population genetic structure of natural and managed populations, including identification of Evolutionary Significant Units (ESUs) and management units for conservation.
4. Assessing genetic variation within a species or population, including small or endangered populations, and estimates such as effective population size (Ne).
5. Measuring the impact of inbreeding and outbreeding depression, and the relationship between heterozygosity and measures of fitness (see Fisher's fundamental theorem of natural selection).
6. Evidence of disrupted mate choice and reproductive strategy in disturbed populations.
7. Forensic applications, especially for the control of trade in endangered species.
8. Practical methods for monitoring and maximizing genetic diversity during captive breeding programs and re-introduction schemes, including mathematical models and case studies.
9. Conservation issues related to the introduction of genetically modified organisms.
10. The interaction between environmental contaminants and the biology and health of an organism, including changes in mutation rates and adaptation to local changes in the environment (e.g. industrial melanism).
11. New techniques for noninvasive genotyping.

References

• Avise, John C & Hamrick James L, (eds); Conservation Genetics Springer ISBN 0-412-05581-3
• Frankham, Richard. “Conservation Genetics.” Annual Review of Genetics 29(1995):305–27
• Frankham, Richard. “Genetics and Conservation Biology.” Comptes Rendus Biologies 326(2003):S22-S29
• Frankham, Richard. “Eosystem recovery enhanced by genotypic diversity.” Heredity 95.183(2005)
• Haig, Susan M.. “Molecular Contributions to Conservation.” Ecology 79.2(1998):413–25
• Wayne, Robert; Morin, Phillip. “Conservation genetics in the new molecular age.” Front Ecol. Environment 2.2(2004):89–97. The Ecological Society of America.
• Woodworth, Lynn; Montgomery, Margaret; Briscoe, David; Frankham, Richard. “rapid genetic deterioration in captive populations:causes and conservation implications.” Conservation Genetics 3(2002):277–88. Kluwer Academic Publishers
• Allendorf, F.W. and G. Luikart. 2007. Conservation and the Genetics of Populations. Wiley-Blackwell. Pp. 642.

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