Molecular Ecology Practical Report
Assessment Notes: Analyse real-world data and report results
No. words: 1200-1500
Topic and analysis overview – Melichrus
You will conduct analyses (r studio) and write a report addressing the following topic.
Melichrus R.Br. is an Australian endemic genus of shrubs in the heather family, Ericaceae. There are currently six accepted species in the genus that have been described on the basis of morphological differences, four of which have broad distributions in eastern Australia. Morphological variability within those species (M. adpressus, M. urceolatus, M. erubescens and M. procumbens) suggest that there may be unrecognised species of Melichrus that will be revealed through integration of molecular and morphological methods. The two newest species, M. hirsutus and M. gibberagee, have very narrow distributions and appear to meet the criteria for conservation listing. If undiscovered species are also narrow endemics, they are unlikely to receive the protection they deserve unless they are recognised as distinct evolutionary lineages.
PhD student Helen Kennedy is revising the taxonomy of Melichrus using an integrative approach. They include a subset of her data focusing on populations that key out to four related species, with metadata describing their sampling locations and field determinations. With this data, you are to address the following questions:
1. Does molecular evidence support the current taxonomy? Which species are supported and which are not?
2. Are there distinctive genetic groups that may require description as new taxa?
3. Is there evidence of inbreeding, and does it represent a threat to any accepted or putative taxa?
4. Is there evidence of hybridisation, and does it represent a threat to any accepted or putative taxa?
You will need to examine the data, and/or appropriate subsets, using population summary statistics, ordination and non-hierarchical clustering to investigate these questions.
Field and laboratory methods (include this in your Methods section)
Population samples of the study group for this report (M. adpressus, M. gibberagee, M. hirsutus and M. urceolatus) were collected from 27 sites, and leaf samples for DNA analysis were freeze-dried or dried on silica gel. Additional samples of other species complexes and outgroup taxa were included in the 571 samples that were sent to Diversity Arrays (Canberra, Australia) for reduced-representation sequencing and genotyping via the DArTseq procedure. A total of 186 samples were extracted from the larger dataset to address our research questions. The resulting single nucleotide polymorphiosm (SNP) matrix was filtered using the statistical software R (R Core Development Team, 2020) and the package dartR (Gruber, Unmack, Berry, & Georges, 2018). Loci with repeatability of <97% were excluded, as were those with a call rate (i.e. non-missing genotypes) <95% and minor allele frequencies <0.05. Individuals with call rates less than 90% were also excluded, and ‘secondary’ SNPs within each DArTseq locus were removed, keeping the one with the highest minor allele frequency.
Practical report layout
Write a research report based on your results, in the following format. There should be no Abstract.
• The Introduction should be very brief (max. 250-300 words), but should put the study in context and state the research questions or hypotheses that will be addressed.
• The Methods section should give enough detail for the study to be replicated, but that can include references to other papers for details. Check the 'Field and laboratory methods' (below) section of the 'Topic and analysis overview' for more guidance. You need to state the samples used for each analysis, the origin of the methodology (i.e., the original paper in which it was published, which can usually be found in the software documentation), the software (and version), and the parameters or options used. It should also make it clear how each analysis addresses the research questions or hypotheses.
• In the Results section, show the results with text, figures and tables. Make sure that everything is clearly labelled, and both figures and tables are able to stand on their own; i.e. combined with its caption, each should have enough information to understand the results contained therein. The text should summarise the results and highlight those that are surprising, interesting or are of particular relevance to the hypotheses. All figures/tables must be referred to in the text, but focus on the important points, rather than just writing, for example, "The results of the STRUCTURE analyses are shown in Figure 3".
• The Discussion section should identify the key results, in relation to the research questions and hypotheses, and discuss their significance in the context of the study and more broadly. Any caveats relating to the design or analysis should also be considered. Finish with a concluding paragraph briefly stating the main findings and conclusions, and relating them back to the aims.
Cite any sources, including software (R studio), using the referencing style of Molecular Ecology (embedded link for your reference). As noted in the Author Guidelines, you need to look at a recent issue of the journal for reference formats. There is an Endnote Style for the journal, but there is no guarantee that it is correct (you still need to check each reference). N.B. For journal articles, give volume and page numbers, not web addresses. A small minority of journals are online-only, and those are an exception: find an example of an article citing a PLoS journal (PLoS One or PLoS Genetics).
Gruber, B., Unmack, P. J., Berry, O. F., & Georges, A. (2018). dartr: An R package to facilitate analysis of SNP data generated from reduced representation genome sequencing. Molecular Ecology Resources, 18(3), 691-699. doi:10.1111/1755-0998.12745
R Core Development Team. (2020). R: A Language and Environment for Statistical Computing. Version 4.0.2. Vienna, Austria: R Foundation for Statistical Computing. Retrieved from http://www.R-project.org
More instructions, r studio script, original data and marking rubric will be attached.