3.3 Reconstructing scenario of breeding site colonization
A split between ancestral Atlantic and Indian populations (Fig. 2a)
occurring 1.76 My ago (95% CI range 0.99-2.60) was inferred based on
all 9 gene trees (2.71 My ago (1.17-4.72) using only mitochondrial
markers). West and east Atlantic ancestral populations split around 1.38
My ago (0.78-2.04), baroli and boydi split at 0.85 My ago
(0.44-1.32), and nicolae and bailloni at 0.70 My ago
(0.33-1.13). The *BEAST analysis based on all nine markers showed the
same topology though with generally lower divergence times and higher
confidence intervals (Supplementary Material 8). ABC analyses also
supported a similar scenario of ancestral population divergence: best
retained topologies using mtDNA markers and all nine markers suggested,
starting from oldest to newest splits, nicolae being ancestral,
leading to the appearance of boydi (Fig 2d, Supplementary
Material 5). Then lherminieri diverged from boydi , andbaroli diverged from boydi . Finally, baillonidiverged from nicolae (Fig. 2d Supplementary Material 4). Our
phylogenetic trees placed the Central Pacific taxon dichrouswithin the Indian clade, thus supporting the putative scenario of
Atlantic lineages diversifying from Indian Ocean rather than from
Pacific ancestors (Fig. 2b,c). Within lherminieri , ABC analyses
suggested a northerly stepping stone colonization process, from
Martinique to the Bahamas (Supplementary Material 5). Similarly, the
most likely scenario of population divergence within baroli was
colonization from the Canaries to the more northerly Azores.
Finally, Bayesian Skyline analyses inferred current effective population
sizes to be around 104 individuals (see Supplementary
Material 10). Mean Ne seemed to increase slowly over time, but high
confidence intervals precluded detection of any sudden change in
population sizes. Confidence intervals on current population sizes were
also very large, in particular for the individuals breeding on Réunion
(see Supplementary Material 10). The demographic parameter estimations
were consistent with a constant population size over time for each
lineage, as suggested from Fu’s Fs results (which are more suitable than
Tajima’s D to estimate population expansion; Ramirez-Soriano et al.
2008; Supplementary Material 7).
Discussion