How Population Genetic Data Can Be

Published Date: 02 Nov 2017

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 structure. It attempts to explain such phenomena as adaptation and speciation.

Natural selection is the fact that some traits make it more likely for an organism to survive and reproduce. Population genetics describes natural selection by defining fitness as a propensity or probability of survival and reproduction in a particular environment.

Genetic drift is a change in allele frequencies caused by random sampling.[8] That is, the alleles in the offspring are a random sample of those in the parents.[9] Genetic drift may cause gene variants to disappear completely, and thereby reduce genetic variability. In contrast to natural selection, which makes gene variants more common or less common depending on their reproductive success,[10] the changes due to genetic drift are not driven by environmental or adaptive pressures, and may be beneficial, neutral, or detrimental to reproductive success.

Mutation is the ultimate source of genetic variation in the form of new alleles. Mutation can result in several different types of change in DNA sequences; these can either have no effect, alter the product of a gene, or prevent the gene from functioning. Studies in the fly Drosophila melanogaster suggest that if a mutation changes a protein produced by a gene, this will probably be harmful, with about 70 percent of these mutations having damaging effects, and the remainder being either neutral or weakly beneficial.[15] Mutations can involve large sections of DNA becoming duplicated, usually through genetic recombination.[16] These duplications are a major source of raw material for evolving new genes, with tens to hundreds of genes duplicated in animal genomes every million years.

Gene flow is the exchange of genes between populations, which are usually of the same species.[45] Examples of gene flow within a species include the migration and then breeding of organisms, or the exchange of pollen. Gene transfer between species includes the formation of hybrid organisms and horizontal gene transfer.

Migration into or out of a population can change allele frequencies, as well as introducing genetic variation into a population. Immigration may add new genetic material to the established gene pool of a population. Conversely, emigration may remove genetic material. Population genetic models can be used to reconstruct the history of gene flow between populations.[46]

Conservation biology is a multidisciplinary field dedicated to protecting global biodiversity and critical habitats. It incorporates biological approaches such as ecology, evolution, and behavior studies, as well as other disciplines, such as political science, law, economics, and cultural anthropology. One of the major goals of conservation biology is preserving critical habitats and the species that inhabit them. Genes can tell us something about how a particular habitat is used by species and populations. Genetic approaches are also used to identify and classify organisms and evaluate the extent of genetic diversity within a particular population.

Categories of Threatened Populations

The International World Conservation Union (IUCN) provides definitions of terms used to describe the status of a species in the wild, based on a number of factors, including the size of a particular population, whether the population is declining in number, and, if so, the extent to which the trend will continue, as well as the threats the population faces. Genetic approaches can play an essential role in helping to evaluate populations, species, and species designations.

The following categories currently cover the range of definitions for species status according to IUCN: Extinct, Extinct in the Wild, Critically Endangered, Endangered, Vulnerable, Lower Risk, and Data Deficient.

Threatened

Populations are considered critically endangered, endangered, or vulnerable when there is considerable concern, based on available evidence or a high level of uncertainty, that the population will survive. With any of these classifications, the species or population of concern is considered to be facing a high to very high risk of extinction in the wild.

Conservation Genetics Applications

The practical applications of conservation genetics include analyzing fragmented populations in nature, determining units of conservation in nature, and monitoring captive populations. In general, conservation genetics integrates these types of information on particular species and populations to help prioritize areas for conservation.

Conservation genetics also plays a major role in guiding relocation and reintroduction efforts, in prioritizing species for conservation, and in designing captive-breeding programs. Identifying natural units based on systematics and population genetics allows researchers and wildlife officials to track organisms in the wild and in zoos, and it lets them identify parts or products of endangered and threatened organisms that are used in illegal trade. Conservation geneticists may use genetic techniques to determine, for example, if certain individuals in the pet-trade were illegally taken from the wild versus bred from permitted captive breeding programs.

Some of the most common issues addressed by genetic techniques in conservation are those confronting small or fragmented populations. Genetic approaches in these cases allow researchers to assess the variability in these populations, as well as to assess whether there is any history or future danger of loss of genetic variability. Genetics can help conservation biologists do viability analyses (tests of how likely that a population will survive over time) by testing hypotheses concerning how long genetic variation might persist into the future. This might be done by examining current levels of genetic variation in a species or population, and integrating these pieces of information with demographic and life history models to examine what happens to genetic variation over time.

The use of a conservation genetics approach may be an effective way for assessing the status of populations and species in the wild. Populations that decrease in number while becoming increasingly fragmented by loss of habitat in the wild can experience a loss of genetic variation that could have a severe impact on their fitness and survival. Conservation genetics permits scientists to assess the impacts of habitat fragmentation and loss in the wild using both theoretical and empirical methods. Results from these studies allow managers to evaluate the viability of populations and design protected areas for conservation.

Sometimes conservation initiatives are also concerned with the translocation or reintroduction of animals to areas where they have been extirpated or severely depleted. Such reintroduction or translocation measures require a detailed understanding of the genetics of the populations being reintroduced in order to ensure there is compatibility between populations as well as to maximize genetic variation and minimize the chance of inbreeding among related animals.

Determining the extent of genetic variation among captive populations in zoological parks and botanical gardens is also essential, because captive populations must have sufficient genetic variation so that they persist into the future without suffering from reduced fitness due to inbreeding and other effects associated with small populations. In some cases, captive populations may be viewed as a source for improving genetically or numerically depleted wild populations. However, they must be managed to minimize the effects of inbreeding. Accredited zoos, aquariums, and botanical gardens work to manage populations and establish conservation programs that strive to carefully manage the breeding of a species in captivity. The primary goal is to maintain a healthy and self-sustaining captive population that is both genetically diverse and demographically stable. Captive breeding specialists usually attempt to maximize the genetic health of a population by reconstructing pedigrees of the animals in the captive populations in order to understand and minimize how much inbreeding might occur.

The Tools of Conservation Genetics

The technique that revolutionized modern molecular genetics is the polymerase chain reaction (PCR). PCR has had major implications for conservation genetics. This technique allows the amplification of minute amounts of DNA, which can then be used for analysis. Amplification is critical for the study of endangered species, because biological samples may be obtained from nontraditional sources, such as hair, feathers, sloughed skin, or feces from which only small amounts of DNA are generally available. Once DNA has been obtained, conservation geneticists are able to use a wide arsenal of tools to characterize the genetics of endangered and threatened species and populations.

When conservation genetics is used to decipher the evolutionary relationships among species, DNA sequence comparisons are often made. Sequencing a region of a gene and properly analyzing the data may lead to novel findings. Based on analyzing underlying genetic variation, there could be evidence to suggest that a revision of numbers of species might be warranted. What was once considered a single species with two populations, for example, might actually merit consideration for separate species status. The level of genetic differentiation detected could have significant implications for how they are protected in the wild and the measures that must be taken by local, state, and federal authorities. Alternatively, the data may indicate that these populations are not sufficiently genetically different to merit separate species designations. DNA sequences are also used to aid in diagnosing natural units for conservation in the wild. Detecting fixed nucleotide characters among DNA sequences between well-sampled populations can provide sufficient evidence for defining units of conservation that potentially merit separate species status under the Phylogenetic Species Concept. Several studies have used DNA sequence polymorphism shared by certain units to the exclusion of other groups to unequivocally define or diagnose species.

Population-level analyses use DNA sequences as well as another set of molecular markers, called microsatellites, a type of repetitive DNA element. Microsatellites are used to address many conservation genetics questions. They are short, tandem-repeated motifs of DNA sequences, such as a dinucleotide repeat (e.g., (AT)n), that usually vary in the number of repeats in a particular stretch of DNA. They are distributed throughout the genomes of plants and animals, are inherited in a Mendelian fashion, and have been found to be highly polymorphic. These genetic markers have proven to be useful in population studies for such purposes as estimating gene flow between populations, describing the genetic variation within and between populations, and examining the effects of hybridization between species. They are used in pedigree analysis to identify individuals based on a DNA sample, and they are used to decipher mating strategies and degrees of relatedness among members of a population.

Implication of Genetics for Conservation in the Wild

In the wild, populations that once were large and widespread are increasingly being reduced to small and fragmented isolates due to human activities. Habitat loss and fragmentation trigger processes that further threaten populations. Small populations often face greater demographic and genetic risks relative to large populations. When populations become fragmented and small, the genetic diversity of a population may be greatly affected. Conservation geneticists focus on the impact of such severe reductions, called bottlenecks, on endangered species.

When a bottleneck occurs, there is an increased chance of breeding among close relatives. This is termed inbreeding, and it may result in a reduction in fitness due to the expression of deleterious genes, in a process known as inbreeding depression. Inbreeding and the loss of genetic variation in small populations can lead to a genetically reduced or homogeneous population that is more sensitive to diseases and to the effects of habitat alteration. The interaction between genetic and demographic declines has been termed "extinction vortex." We include below several real examples of the use of genetics in conservation biology.

Bottlenecks, Cheetahs, and Right Whales

In small populations, inbreeding depression may be more common because random mating is less likely and breeding among related animals may have a greater cumulative effect. Low genetic diversity and inbreeding is not always deleterious, and some small populations may be stable while permanently maintaining low levels of genetic diversity. In general, however, avoidance of inbreeding is a major goal in the management of small populations, since it has been shown to cause a reduction in fitness in captive populations of endangered species.

Perhaps the most famous case of a putative bottleneck being examined in conservation genetics is the cheetah, as examined by Stephen J. O'Brien, a molecular geneticist at the National Cancer Institute. In this 1980s study, cheetahs were shown to have extremely low levels of genetic diversity, which the researchers attributed to a bottleneck that happened less than ten thousand years ago and that may have left only a few females alive. The bottleneck was so extreme that even the usually highly diverse genes of our immune system, genes of the major histocompatibility complex, showed amazingly low levels of diversity. The extreme loss of genetic diversity was attributed to difficulties associated with the species' breeding in captivity and in the wild, abnormal sperm counts, and susceptibility to disease. While it remains controversial whether cheetah populations went through a bottleneck and the extent to which reproductive issues can be attributed to reduced genetic variation, the example remains one of the most prominent in the field of conservation.

Other species, such as the North Atlantic right whale, have faced demographic decline and extremely low levels of genetic diversity since the end of legal commercial hunting for whales at the beginning of the twentieth century. The North Atlantic right whale has maintained a low level of genetic diversity since the 1930s, but recent studies suggest that some additional genetic variation may eventually be lost.

Units of Conservation and Dna Sequences

Using genetic data to evaluate or define species and/or units of conservation can also lead to novel findings and enhance conservation management. Right whales are found in the North Atlantic, North Pacific, and southern oceans. For over a hundred years, they have been considered as two species—one in the north (in the Pacific and Atlantic Oceans) and one in the south. DNA diagnosis methods have corroborated that the southern right whales are distinct from all the others. However, the DNA data also clearly demonstrate that the North Pacific and North Atlantic whales are distinct from each other and warrant distinct species status. The ramifications for the conservation plan of these whales have been taken into consideration by the appropriate management authorities, who have developed a revised plan for naming and protecting three distinct species of right whales.

Dna Detectives and Endangered Species

As discussed above, conservation genetics can aid in the identification of endangered and threatened animals that are traded illegally as commercial products. Researchers at the Wildlife Conservation Society used species-identification methods to detect caiman crocodile tissue in leather products and thus thwart their illegal importation into the United States. Other scientists have used species identification methods to detect whale meat in Japanese fish markets and thus have had an impact on the policing of whale hunting.

Rob DeSalle, a curator at The American Museum of Natural History, and colleagues have recently used species identification methods to verify or reject the labeling of caviar origin. Such tests have been instrumental in getting sturgeons (the source of caviar) listed on the Convention on International Trade in Endangered Species of Wild Fauna and Flora. Prior to the test's development, there was no way to verify the contents of a container of caviar, leading authorities to be wary of prosecuting the illegal importation of caviar. With the development of species-identification procedures based on analyzing the DNA from single caviar eggs, enforcement of importation regulations became possible.

Conservation genetics is the use of the knowledge obtained through genetics to improve the breeding stock and success of endangered populations, eg captive breeding programmes.

It is important because it can help us save some of the endangered animals like the Bengal Tiger. It can also improve the chance of a species survival in a new or unfamiliar territory.

Animals, plants, and other species become endangered when their normal habitats are lost or altered. Effective management of ecosystems can help preserve threatened species.

The science of Conservation Biology studies individuals and populations that have been affected by habitat loss, exploitation, and/or environmental change. That information is used to make informed decisions to ensure the survival of organisms in the future.

The science of Genetics is the study of inheritance and the investigation of the genes responsible for inherited traits.

Put the two together and you get the science of Conservation Genetics. Conservation in the past has been addressed from a mathematical, evolutionary, or taxonomic point of view. Genetic studies supply conservation scientists and ecological managers with new insights into the extent of diversity among the individuals in a population. Without using genetics, we may conserve the wrong population or waste valuable resources on a population that isn't endangered!

WHAT IS CONSERVATION GENETICS?

Conservation genetics is a mixture of ecology, molecular biology, population genetics, mathematical modeling and evolutionary systematics (the construction of family relationships). It is both a basic and an applied science. Scientists must first understand the genetic relationships of the organisms under study. Once this basic science is understood by scientists, management techniques must then be applied by wildlife managers to preserve biological diversity in these species.

The organisms under investigation are usually endangered or threatened populations. To develop a management strategy, scientists ask: what has brought these populations to the brink of extinction, and what steps can be taken to reverse this trend? Information about the genetic diversity of the animals under study helps scientists and managers in forming strategies to preserve and protect the diversity of plants and animals worldwide.

What is genetic diversity?

Genetic diversity is a measure of the possible choices of information provided by a gene. For example, a particular gene may determine the flower color of a plant. Different choices (alleles) may exist for that gene (i.e. a pink allele, a purple allele, a white allele). In each case, the same gene determines flower color, but the exact DNA sequence of the alleles of that gene are different. When all or nearly all the members of a population have the same allele at a gene, that population is said to have low genetic diversity at that gene. If many varients exist for a gene sequence, that population has high genetic diversity at that gene.

Why is genetic diversity so important?

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.

WHEN DO SCIENTISTS USE CONSERVATION GENETICS?

1) Habitat Destruction

When habitat destruction or other factors put a population at risk, scientists and conservation managers target that population for investigation. For example, a population of plants may be studied if it is known that a shopping mall will destroy its habitat. Duck and geese populations might be monitored because of new hunting regulations.

Obvious human interference is not the only danger to plants and other animal species. Populations can dwindle for natural or unknown reasons.

2) Change in Population Size

When the total population of a species becomes small, surveillance of that species becomes critical. A small population is much more susceptible to stochastic events (i.e., random or unpredictable events). Such events might be natural catastrophes, environmental changes or mutations. These sorts of events can cause sudden decreases in population size. When the population of a species is small to begin with, futher reduction of their remaining numbers can sharply reduce genetic diversity.

HOW DOES GENETIC DIVERSITY BECOME REDUCED?

How are gene variants lost?

Genetic drift is the name for a process by which the diversity of alleles in a new generation becomes different from that of the previous generation. Changes in migration, selective pressures, geographical isolation, establishment of a new population from only a few individuals (founder effect) all result in genetic drift. Each of these factors affects which individuals will be part of the new generation and therefore what the sample of alleles will be that determines the future of that species. A population is more susceptible to genetic drift when the number of individuals becomes small.

Sometimes a population can have many members but still undergo loss of genetic diversity. This can happen through geographical isolation. If a new geographical block is imposed (e.g. the new course of a river or the development of a subdivision creating houses, roads, and sidewalks on a previously empty meadow) a population of plants or animals may become separated into two groups. When this happens, the pool of gene variants in the two separated populations may differ from one another.

For example, a flower species may have two forms, and because of a new subdivision, they might become separated to two ends of the development. The first form, a tall, sturdy, but unattractive plant, may become isolated to the north end of the subdivision while the second form, a weaker, prettier plant, is isolated to the south end. Even though the new homeowners may preserve both populations on their various lots, the two types of plants are sufficiently isolated from each other that they can no longer exchange genes. In this situation, each type is exposed to environmental pressures without the ability to crossbreed with the other type to form plants with new, perhaps more advantageous, combinations of genes. The new pressures created by building the development may affect the two types of plants differently. For example, the weaker variety might dwindle away due to the lack of shade caused when nearby trees were cut down for the subdivision. If this form had been able to crossbreed with the tall, sturdy variety, plants with the prettier flower type might have survived. Since they were unable to do so, the gene responsible for the attractive flower might be lost permanently.

HOW IS CONSERVATION GENETICS DONE?

Conservation scientists use DNA evidence from an organism to make recommendations about how the organism should be managed. As in any scientific field, conservation scientists use a defined approach to their work, described below:

Identification, Inventory and Analysis

1. Define populations and areas of interest. Because there are so many species of organisms, endangered or threatened species usually take priority.

2. Observe the population. What are the known forms of the species? What are the morphological features used to classify the different species? What are known or suspected relatives of the species?

3. Form hypotheses about relationships between populations and/or species and test these hypotheses by examining genetic characteristics of the organisms (DNA or protein evidence).

4.Once the scientist has collected this information, mathematical models are used to analyze the data. The scientist determines how much diversity exists in separate populations of the same organism and the rate at which the exchange of genetic information (gene flow) is occurring between populations.

Interpretation and Management

Scientists and managers work together to decide whether the organism is endangered. To begin to develop a management strategy, the habitat of the organism is investigated.

1. The degree of adaptability of the organism to various temperatures, soils, and water conditions is examined.

2. Important factors that play roles in preserving genetic diversity, such as the identity and characteristics of plant pollinators, are examined. The health and welfare of pollinating species may be critical to the survival of endangered plant species.

3. Threats to the integrity of the habitat of the species due to human, climatic, or other factors are studied.