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Word limit: 2000, excluding references and tables
You will produce a conservation plan for a species of your choice which takes into account genetic factors.
Before Session 1
Choose a species of conservation importance which meets the criteria described in the instructions for Session 1. This may take some time (possibly over an hour), so do it before the first session in order to avoid frustration.
Many species are distributed over wide geographical ranges and occur in diverse habitats. Where populations are genetically isolated, natural selection may result in local adaptation. In this case, the loss of whole populations or subspecies may reduce the ability of a species to thrive across its entire range. In order to prevent this from happening, it is necessary to identify populations which have been reproductively isolated for long periods of time and therefore potentially have different adaptations. Such populations are termed Evolutionary Significant Units and can be identified through the existence of reciprocal monophyly in non-recombining sequences such as mitochondrial genes (see Lecture 11). Put simply, two populations show reciprocal monophyly where all sequences from one population are more similar to one another than any are to sequences from the other population. This will produce a phylogenetic tree showing a deep divergence between sequences drawn from the two populations.
In Session 1, you will be asked to choose a species of conservation importance and to download mitochondrial sequences from individuals of this species, from across its geographical range. You will align these sequences and then use them to produce a phylogenetic tree which you will examine for evidence of reciprocal monophyly between populations.
It is important to know the genetic diversity of populations. Genetically diverse populations are potentially more adaptable and are less likely to suffer from inbreeding depression and deleterious alleles. They can therefore be of greater value to conservation than populations which have become genetically depauperate. It is also important to know the degree of gene flow or connectivity between populations, since this provides us with important information on the spatial scale at which conservation effort should occur.
In Session 2 you will use the mitochondrial sequences that you aligned in Session 1 to compare the genetic diversity of different populations and to assess levels of gene flow between them.
Once you have characterised a species in terms of evolutionary significant units, genetic diversity and connectivity, you then need to make decisions regarding how its genetic diversity should be conserved. These will depend upon the life cycle and ecology of the species and the nature of the threats to its survival.
In Session 3, you will answer questions regarding the life cycle and ecology of your species and use your answers to formulate a genetic conservation plan for the species.
You must produce a report, outlining your genetic conservation plan for your species. The report must contain fewer than 2000 words (excluding references, tables and figures).
It should begin with an introduction, providing background on the species and threats to its survival (drawn from your answers to questions in session 3). Backed by peer-reviewed references, with explicit statement of aims and scope.
A methods section should follow, in which you summarise your analysis for sessions 1 and 2. This should not repeat the detailed instructions for the sessions but should assume that the reader knows how to use the various programmes and should focus on information specific to your particular data set (number of sequence sets, number of sequences in each set, locations from which sequences were collected, groups in AMOVA, etc.).
You should then produce a results section containing the following items along with written descriptions:
1. Phylogenetic tree (from session 1) – description and interpretation
2. Bar chart of genetic diversity and results of Tajima’s test (from session 2)
3. Table of pairwise HS values and results of permutation tests of HST (from session 2)
Finally, you should produce a discussion section, interpreting your results and using them, together with your background information, to devise a conservation plan for your species. The plan should conserve the species genetic diversity and capacity to evolve while taking into account other factors (e.g. its unique biology and the nature of the threats against it).
Breakdown of marks (total=40%):
Phylogenetic tree 4%
Genetic diversity indices, bar chart and Tajima’s test 7%
Genetic structure tables 4%