thibauldmichel/species-delimitation-using-beast

DISSECT trials using data from Species delimitation without prior knowledge, Toprak (2016)

Species-delimitation-using-BEAST

RAW DATA

#location of the working directory:

/home/thibauld/Documents/plantID_ressources/2018_11_22_PlantIDsummerschool/lectures/8_stacey_bengt_oxelman

In the publication 6 unlinked loci used in the study: NRPA2, NRPB2, EST04, EST14, EST24, rps16. In the data provided for the course, 5 different loci: EST04, EST09, EST14, EST24, RPA2.

75 individuals sampled.

For the Silene aegyptiaca group: S. fraudatrix -> fraud_fraud_fraud S. a. subsp. ruderalis -> aegyp_ruder_assyr S. a. subsp. aegyptiaca -> aegyp_aegyp_aegyp S. atocioides -> aegyp_aegyp_atoci S. d. subsp. delicatula -> delic_delic_delic S. d. subsp. pisidica -> delic_pisid_atoci

Sequences of the NEXUS format. Generated by multiple sequence alignment with MUSCLE in Geneious v5.4.6.

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NEXUS_taxa DATA FORMAT

#NEXUS begin taxa; dimensions ntax=56; taxlabels aegyp_ruder_assyr_17702_1_[&Created=Sun Oct 01 22:10:59 CEST 2017] aegyp_ruder_assyr_15256_0_[&Created=Sun Oct 01 22:10:59 CEST 2017] ...

aegyp_ruder_assyr_15256_0_	----------------ATTGTGACCTATTGGAGGAGGTTTGTGATTGGGTTAATGCAAAGG...

Each line (open in aliview, for example) is a sample. aegyp_ruder_assyr_15263_1_ Single specie_subspecie written. What is the number following The sequence ID? YES

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BEAUTi ANALYSIS

The nexus data are submitted to BEAUTi. User-friendly software setting up the model parameters for the BEAST analysis (and Markov Chain Monte Carlos analysis in general).

Inputs: NEXUS files (.nex) Outputs: 1 XML file (.xml)

Substitution model: Jukes-Cantor (JC69). Simpliest Continuous-time Markov process. Strict Clock selected, seems there is no choice here. prior=estimated probability distribution

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BEAST ANALYSIS

Inputs: XML file (.xml) Outputs: 2 files trace_log (.log) -> analysis in Tracer. tree_log (.tree) -> analysis in FigTree.