Conservation genetics
Encyclopedia
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
.
is the variability of a 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.
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.
Techniques for analysiing the differences between individuals and populations include
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 minisatellite
s 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 non invasive 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.
s 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:
Genetics
Genetics , a discipline of biology, is the science of genes, heredity, and variation in living organisms....
methods to the conservation and restoration of biodiversity
Biodiversity
Biodiversity is the degree of variation of life forms within a given ecosystem, biome, or an entire planet. Biodiversity is a measure of the health of ecosystems. Biodiversity is in part a function of climate. In terrestrial habitats, tropical regions are typically rich whereas polar regions...
. Researchers involved in conservation genetics come from a variety of fields including population genetics
Population genetics
Population genetics is the study of allele frequency distribution and change under the influence of the four main evolutionary processes: natural selection, genetic drift, mutation and gene flow. It also takes into account the factors of recombination, population subdivision and population...
, molecular ecology
Molecular ecology
Molecular ecology is a field of evolutionary biology that is concerned with applying molecular population genetics, molecular phylogenetics, and more recently genomics to traditional ecological questions...
, biology
Molecular biology
Molecular biology is the branch of biology that deals with the molecular basis of biological activity. This field overlaps with other areas of biology and chemistry, particularly genetics and biochemistry...
, evolutionary biology, and systematics
Systematics
Biological systematics is the study of the diversification of terrestrial life, both past and present, and the relationships among living things through time. Relationships are visualized as evolutionary trees...
. Genetic diversity
Genetic diversity
Genetic diversity, the level of biodiversity, refers to the total number of genetic characteristics in the genetic makeup of a species. It is distinguished from genetic variability, which describes the tendency of genetic characteristics to vary....
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
Inbreeding
Inbreeding is the reproduction from the mating of two genetically related parents. Inbreeding results in increased homozygosity, which can increase the chances of offspring being affected by recessive or deleterious traits. This generally leads to a decreased fitness of a population, which is...
, and reduced fitness
Fitness (biology)
Fitness is a central idea in evolutionary theory. It can be defined either with respect to a genotype or to a phenotype in a given environment...
.
Genetic Diversity
Genetic diversityGenetic diversity
Genetic diversity, the level of biodiversity, refers to the total number of genetic characteristics in the genetic makeup of a species. It is distinguished from genetic variability, which describes the tendency of genetic characteristics to vary....
is the variability of a genes in a species. It can be estimated by the mean levels of heterozygosity in a population, the mean number of alleles per locus
Locus (genetics)
In the fields of genetics and genetic computation, a locus is the specific location of a gene or DNA sequence on a chromosome. A variant of the DNA sequence at a given locus is called an allele. The ordered list of loci known for a particular genome is called a genetic map...
, or the percentage of polymorphic
Polymorphism (biology)
Polymorphism in biology occurs when two or more clearly different phenotypes exist in the same population of a species — in other words, the occurrence of more than one form or morph...
loci.
The importance of genetic diversity
If genetic diversityGenetic diversity
Genetic diversity, the level of biodiversity, refers to the total number of genetic characteristics in the genetic makeup of a species. It is distinguished from genetic variability, which describes the tendency of genetic characteristics to vary....
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
- InbreedingInbreedingInbreeding is the reproduction from the mating of two genetically related parents. Inbreeding results in increased homozygosity, which can increase the chances of offspring being affected by recessive or deleterious traits. This generally leads to a decreased fitness of a population, which is...
and inbreeding elevation which reduces the fitness of populations. - The accumulation of deleterious mutations
- 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.
- Adapting to conditions in captivity
- Outbreeding depressionOutbreeding depressionA concept in selective breeding and zoology, outbreeding depression refers to cases when offspring from crosses between individuals from different populations have lower fitness than progeny from crosses between individuals from the same population....
- Fragmented populationsHabitat fragmentationHabitat fragmentation as the name implies, describes the emergence of discontinuities in an organism's preferred environment , causing population fragmentation...
- Taxonomic uncertainties, which can lead to a reprioritization of conservation efforts
- Genetic driftGenetic driftGenetic drift or allelic drift is the change in the frequency of a gene variant in a population due to random sampling.The alleles in the offspring are a sample of those in the parents, and chance has a role in determining whether a given individual survives and reproduces...
as the main evolutionary process, instead of natural selectionNatural selectionNatural selection is the nonrandom process by which biologic traits become either more or less common in a population as a function of differential reproduction of their bearers. It is a key mechanism of evolution.... - Management units within species
- Use of molecular techniques, such as allozymes as molecular markers, to analyze species in depth
Techniques
Specific genetic techniques are used to assess the genetics 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 analysiing the differences between individuals and populations include
- Alloenzymes
- Random Fragment Length Polymorphisms
- Amplified Fragment Length PolymorphismsAflpAFLP may refer to:*amplified fragment length polymorphism, a highly sensitive tool used in molecular biology to detect DNA polymorphisms*acute fatty liver of pregnancy, a life-threatening liver condition that may occur during pregnancy...
- Random Amplification of Polymorphic DNARAPDRAPD stands for random amplification of polymorphic DNA. It is a type of PCR reaction, but the segments of DNA that are amplified are random. The scientist performing RAPD creates several arbitrary, short primers , then proceeds with the PCR using a large template of genomic DNA, hoping that...
- Single strand conformation polymorphismSingle strand conformation polymorphismSingle-strand conformation polymorphism , or single-strand chain polymorphism, is defined as conformational difference of single-stranded nucleotide sequences of identical length as induced by differences in the sequences under certain experimental conditions...
- minisatelliteMinisatelliteA minisatellite is a section of DNA that consists of a short series of bases 10-60 bp. These occur at more than 1,000 locations in the human genome...
s - microsatellites .
- Single-nucleotide polymorphisms
- Sequence analysisDNA sequencingDNA sequencing includes several methods and technologies that are used for determining the order of the nucleotide bases—adenine, guanine, cytosine, and thymine—in a molecule of DNA....
- 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
Mitochondrial DNA
Mitochondrial DNA is the DNA located in organelles called mitochondria, structures within eukaryotic cells that convert the chemical energy from food into a form that cells can use, adenosine triphosphate...
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
Major histocompatibility complex
Major histocompatibility complex is a cell surface molecule encoded by a large gene family in all vertebrates. MHC molecules mediate interactions of leukocytes, also called white blood cells , which are immune cells, with other leukocytes or body cells...
, and the microsatellites and minisatellite
Minisatellite
A minisatellite is a section of DNA that consists of a short series of bases 10-60 bp. These occur at more than 1,000 locations in the human genome...
s 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 non invasive 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
Cryopreservation
Cryopreservation is a process where cells or whole tissues are preserved by cooling to low sub-zero temperatures, such as 77 K or −196 °C . At these low temperatures, any biological activity, including the biochemical reactions that would lead to cell death, is effectively stopped...
or breeding from older animals, and increasing the effective population size
Effective population size
In population genetics, the concept of effective population size Ne was introduced by the American geneticist Sewall Wright, who wrote two landmark papers on it...
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 minisatelliteMinisatellite
A minisatellite is a section of DNA that consists of a short series of bases 10-60 bp. These occur at more than 1,000 locations in the human genome...
s and MHC
MHC
-Biology:*Myosin heavy chain - part of the motor protein myosin's quaternary protein structure*Major histocompatibility complex - a highly polymorphic region on chromosome 6 with genes particularly involved in immune functions-Colleges:...
. 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:
- PhylogeneticPhylogeneticsIn biology, phylogenetics is the study of evolutionary relatedness among groups of organisms , which is discovered through molecular sequencing data and morphological data matrices...
classification of species, subspecies, geographic races, and populations, and measures of phylogenetic diversityPhylogenetic diversityPhylogenetic diversity is a measure of biodiversity which incorporates taxonomic difference between species. It is defined and calculated as "the sum of the lengths of the all the branches that are members of the corresponding minimum spanning path", in which 'branch' is a segment of a cladogram,...
and uniqueness. - Identifying hybrid species, hybridization in natural populations, and assessing the history and extent of introgression between species.
- Population genetic structure of natural and managed populations, including identification of Evolutionary Significant UnitEvolutionary Significant UnitAn Evolutionarily Significant Unit is a population of organisms that is considered distinct for purposes of conservation. Delineating ESUs is important when considering conservation action.This term can apply to any species, subspecies, geographic race, or population...
s (ESUs) and management units for conservation. - Assessing genetic variation within a species or population, including small or endangered populations, and estimates such as effective population size (Ne).
- Measuring the impact of inbreedingInbreeding depressionInbreeding depression is the reduced fitness in a given population as a result of breeding of related individuals. It is often the result of a population bottleneck...
and outbreeding depressionOutbreeding depressionA concept in selective breeding and zoology, outbreeding depression refers to cases when offspring from crosses between individuals from different populations have lower fitness than progeny from crosses between individuals from the same population....
, and the relationship between heterozygosity and measures of fitness (see Fisher's fundamental theorem of natural selectionFisher's fundamental theorem of natural selectionIn population genetics, R. A. Fisher's fundamental theorem of natural selection was originally stated as:Or, in more modern terminology:- History :...
). - Evidence of disrupted mate choice and reproductive strategy in disturbed populations.
- Forensic applications, especially for the control of trade in endangered species.
- Practical methods for monitoring and maximizing genetic diversity during captive breeding programs and re-introduction schemes, including mathematical models and case studies.
- Conservation issues related to the introduction of genetically modified organisms.
- The interaction between environmental contaminants and the biology and health of an organism, including changes in mutation rates and adaptationAdaptationAn adaptation in biology is a trait with a current functional role in the life history of an organism that is maintained and evolved by means of natural selection. An adaptation refers to both the current state of being adapted and to the dynamic evolutionary process that leads to the adaptation....
to local changes in the environment (e.g. industrial melanism). - New techniques for noninvasive genotypingNoninvasive genotypingAdvances in molecular DNA sequencing in some cases allow researchers to obtain high-quality DNA samples from small quantities of hair, feathers, scales, or other body parts. These so-called noninvasive samples are an improvement over older allozyme and DNA sampling techniques that often required...
.