Unraveling the evolutionary history of the nematode Pristionchus pacificus: from lineage diversification to island colonization
Version of Record online: 7 FEB 2013
© 2013 The Authors. Ecology and Evolution published by Blackwell Publishing Ltd.
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Ecology and Evolution
Volume 3, Issue 3, pages 667–675, March 2013
How to Cite
Ecology and Evolution 2013; 3(3): 667–675
- Issue online: 11 MAR 2013
- Version of Record online: 7 FEB 2013
- Manuscript Accepted: 8 JAN 2013
- Manuscript Revised: 4 JAN 2013
- Manuscript Received: 24 SEP 2012
Table S1. List of the Pristionchus pacificus samples used in the “Réunion” analyses of this study, and their relevant collection information, including sampling location, host beetle species, and population code (based on mtDNA and STR data from 16 loci). See Herrmann et al. 2010 and Morgan et al. 2012 for additional strain information about the “world” dataset strains.
Figure S1. Graphic to demonstrate the 24 colonization scenarios tested in DIYABC using STR and mt markers; our models examined all possible island colonization orders following the lineage diversification (lineages A, B, C, and D, diverging away from an unsampled source population, “U”) order U>D>A>C>B. Island colonization (i.e. sub-populations a, b, c, and d, diverging away from their respective lineages) was modeled by following the divergence of the island population away from the ancestral lineage with an immediate decrease in population size (i.e. a foundation bottleneck). In the presented examples, lineage diversification proceeds through times t5–t8, and is followed by colonization of populations at times t1–t4; colonization orders in the figure are presented with a, b, c, and d first for (a), (b), (c), and (d). In each case, the bottleneck is represented as population size changes (colored bars in figure; N5, N6, N7, and N8), and the bottleneck duration is the same for each population (db = 5 generations). The time axis is to relative scale only. Refer to 'Materials and Methods' and 'Results' for further information.
Figure S2. Observed distribution of pairwise differences (i.e. MMD) between mt haplotypes in the four selected populations (a, b, c, d, corresponding to (a), (b), (c), and (d) in the figure) of Pristionchus pacificus on La Réunion Island. Expected distributions were calculated both numerically (i.e. observed data; dark blue bars in figure) and with simulated data (light blue lines in figure) using mtDNA in Arlequin. The observed (unimodal) distributions for populations b, c, and d are consistent with the spatial expansion model, while the SSD and raggedness values given above each distribution plot are consistent with the spatial expansion model for all populations.
Figure S3. Principal component analysis (PCA) of the 1% of simulated datasets generated in DIYABC that were closed to the observed dataset in terms of summary statistics (see 'Materials and Methods') for the most likely colonization scenarios (n = 6) in analyses using mt and STR markers for P. pacificus, showing that most observed summary statistics fall within the range of simulated ones. Initial tests examined all possible orders (n = 24) of island colonization under the lineage diversification scenario U>D/A>C>B, and subsequent analysis considered the six most likely scenarios (see Table S3). The final most likely colonization scenario (logistic regression value: 1.000) was: c>a>b>d. See 'Results' for further information.
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