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Assessing conservation status of populations

Summary

Here we give a brief overview of what is genetic diversity, what type of information we can get from doing genetic analyses of wild populations, how genetic variation is assessed and what conservation issues are linked to the genetic variation of populations and species.


1. Genetic diversity within species

2. Continuous or discrete structure

3. Differentiation due to genetic drift

4. Differentiation due to selection - local adaptation

5. Genetic diversity and ecosystem function

6. Genetic variation and population resilience

7. How to assess the genetic structure

8. Conservation issues


 

1. Genetic diversity within species

Diversity (or biodiversity) at the genetic level is a primary criteria for assessing the conservation status of a species, or a population of a particular species.

Biodiversity of a species is both the total amount of genetic variation in the species and how this variation is distributed among populations of a species. For example, some species have overall a very low level of genetic variation, which can be due to current or historical size bottlenecks (genetic variation is rapidly lost in very small populations). These species are usually considered to be more sensitive to environmental changes than other populations.

More common is that a species is subdivided into populations with more or less gene flow among them, that is, the species has a genetic structure characterized by genetic differences among populations. Differences between pairs of populations are usually indicated by the FST index varying between 1.0 and 0.0 with 0.0 indicating no differentiation at all. Most values of FST between populations of the same species lies in the range 0.001-0.1. It is possible to test if an FST value is statistically significant or not.

Eel is an example of a species with extremely low (and non-significant) values of FST among European samples indicating that all the eels found in Europe belong to one and the same random mating population (spawning in the Sargasso Sea).

Atlantic salmon is an example at the other extreme, with significant FST values between samples of salmon originating in different rivers. This species is highly genetically structured.

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2. Continuous or discrete structure

Genetic composition of samples may change continuously in space, simply due to successively less genetic exchange between individuals further and further apart.

Alternatively a species may be structured in discrete populations with partial barriers to genetic exchange (gene flow) caused by, for example, physical barriers or by species history (e.g. two or more refuge areas during the last glaciation).

Earlier assumptions for marine species were that most species had extensive gene flow over wide areas due to active migration (fish) or passive dispersal of larvae and spores. This assumption has turned out to be largely wrong. Most marine species are genetically structured and the minimum distance for finding significant genetic differences is <1 km for many common species of invertebrates and algae, and <100 km for many fish species.

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3. Differentiation due to genetic drift

Genetic differentiation between populations evolve by chance events if two populations are not exchanging genes or by natural selection (see below). The first process is named "genetic drift". As a rule of thumb if less than 1-2 individuals will migrate between two populations each generation these two populations will start to diverge and over time become genetically different. After some time (at balance) the FST value will actually indicate how many individuals that are exchanged between two populations each generation (under the assumption that the migrants contribute to reproduction). The relationship is outlined in the graph below.

 

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4. Differentiation due to selection - local adaptation

Genetic differentiation between populations evolve by chance events (see above) and by diversifying natural selection. If populations of a species live in different physical environments (e.g. different salinities) or under different biotic regimes (eg. presence of absence of a particular predator) natural selection may favour different genetic set ups in the different populations. When genetic differences are consistently correlated with specific environmental characteristics this suggests local adaptation. However, to identify the genes that are under natural selection is not trivial, as genes sitting close to each other on the chromosome will be linked to each other (becoming indicators) if one of them are under selection. Therefore, genes that are putatively under selection (but may alternatively be linked to selected genes) are usually denoted "candidate genes".

Typically, diversifying natural selection causes much stronger differentiation than do genetic drift and therefore candidate genes are often "outliers" when differentiation (FST values) of many different genes are compared. It may sometimes also be the case that stabilizing natural selection cause some genes to be less differentiated than genes only affected by genetic drift.

Natural selection may cause genetic differences in individual genes also in the presence of strong gene flow in other genes - that is, populations that are not genetically structured in neutral genes (genes not under selection) may be highly differentiated in selected genes. Thus measuring genetic differentiation using a small number of genetic markers such as microsatellites, allozymes, mitochondrial DNA (see below) will often not unveil differentiation in selected genes, but these methods are appropriate to estimate differentiation due to restricted gene flow among populations. (See below: How to measure genetic structure).

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5. Genetic diversity and ecosystem function

Species diversity affect ecosystem function. In the same way it has been shown for seagrass (Zostera marina) that meadows formed by many different clones have higher primary production, have more associated biodiversity and are more resistant to extreme weather conditions (Reusch TBH, Ehlers A, Hämmerli A, Worm B. Ecosystem recovery after climatic extremes enhanced by genotypic diversity. PNAS, USA  102:2826-2831. ).

In BaltGene we have experimentally showed that the partially clonal species, Fucus radicans, present in the northern Baltic Sea, have populations that are almost monoclonal in some areas, and these populations have much less variation among plants in inherited traits. This is likely to have short or longterm consequences on ecosystem function and resilience in this species. 

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6. Genetic variation and population resilience

In general, the more genetic variation that is present in a population (or a species) the higher chance has the population to survive a future change in the environment such as a temperature increase, a salinity decline or a new predator or grazer. Also genetic variation that do not currently contribute to increase fitness may be highly useful under new regimes of natural selection. Such genetic variation is sometimes referred to as "standing genetic variation" and this variation is characterized by alleles (gene variants) being carried by few individuals only (low frequency alleles).

One illustrative example is one allele that is rare in marine populations of sticklebacks (EDA allele, typically found in a few percent of the marine fishes) is crucial to survival in freshwater and increase to almost 100% in most freshwater populations (that has their origin in nearby marine populations).

With very few examples, we do not today have the knowledge about individual gene functions and can therefore not predict what genes will be important given a specified scenario of environmental change. This knowledge is, however, expected to grow during the coming years when more and more marine organisms will have their genomes investigated (see below under Genomics).

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7. How to assess the genetic structure

To get any information on genetic structure of a species samples (minimum number of individuals 20-30) from two spatially or temporally segregated populations are required. More commonly, many spatially separate samples of a species are taken to represent the whole or part of the species distribution.

Samples consist of either whole organisms or parts of organisms and tissue is maintained fresh, frozen (ideally -80C) or in alcohol (70-90%, not suitable for allozyme analysis). Genetic variation in a set of gene loci is assessed using methods available in research or commercial labs such a microsatellite analysis, allozyme analysis, sequencing of mitochondrial DNA, sequencing of nuclear genes). More advanced methods of analysis (not yet used more than in special cases for wild organism, include genome sequencing of random parts of the genome (eg. RAD) or whole genome resequencing (requires that the genome of the species is mapped). Analysing the primary data is not trivial and expertise (generally at the level of a scientist) is needed.

Assessing the genetic structure of species is most easily performed by finding a research lab that have the experience of the particular species and initiate a collaboration with them. In the future if genetic variation will be included in monitoring programs and similar, there may well be private consultancy firms that provide the services needed in running the sequencing and analysing the primary data for conservation and management purposes.

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8. Conservation issues

There are several important aspects of why genetic variation and genetic structure of species should be considered in management and conservation. The more important ones are briefly outlined here.

1. Local adaptation. Individuals of a population that has evolved local adaptation to a specific geographic area (small or large) have inherited traits that are more fit to live in this area than have other individuals of the same species. This means that if a locally adapted population goes extinct, there will most likely be problems to fill up this area again with individuals of the same species (from other populations). This is thus equivalent to local loss of a species. If this species is a foundation species, a key species or in other ways a very important species for the ecosystem, such a loss will have profound consequences on the ecosystem. If it is a rare species, the lost population may have represented unique genetic variation not present anywhere else in the species' distribution with possible consequences for the long-term survival of the species.

2. Population connectivity. Species are in most cases distributed over spatially separated populations that are connected by gene flow. In such a metapopulation structure some populations may be more important than others, being the sources for recruitment, while others are sinks. Genetic data will guide in assessing connectivity among populations of a species and will in this way provide suggestions to which populations should be prioritized in conservation.

3. Population size and long-term resilience. Populations (or whole species) will loose genetic variation by genetic drift (see above) if the size of the population is small. Importantly, it is not the census size (total size, N) but the so called effective population size (Ne) that is important. Ne is affected by how many of the individuals of the population contribute in reproduction, the relative contribution from each of them, and the balance between males and females. Basically, the more deviation there is from complete random mating among all adult individuals of a population, the less is the effective population size. Not uncommonly Ne is only a few percent of N.

With Ne below 50 a population will loose genetic variation and over time be less resistant to environmental changes (see above: Genetic variation and population resilience). With samples from two different generations of the same population it is possible to estimate effective population size and guide in decisions of conservation measures.

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CONTRIBUTOR 
Kerstin Johannesson, University of Gothenburg, Sweden


Responsible editor: Kerstin Johannesson, University of Gothenburg, Sweden 
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