Parameters describing genetic differentiation among phylogroups.

<p>The following abbreviations were used:</p>*<p>significant with <i>P</i><0.05;</p>**<p>significant with P<0.01;</p>***<p>significant with P<0.001. “n/a” indicates that it was impossible to compute the corresponding test statistic because of the lack of relevant data.</p

Haplotype network and phylogenetic tree resulting from the analysis of the Fib7 dataset.

<p>The haplotype network reconstruction takes into account missing data and gaps, so that the inferred number of haplotypes is higher than the one presented in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0077815#pone-0077815-t004" target="_blank">Table 4</a>. Red values on nodes indicate the inferred number of mutation steps between haplotypes or ancestral haplotypes (symbolized by a red node). The absence of value means that the number of step is equal to 1. The phylogenetic tree corresponds to the results of a Bayesian inference analysis (see text for details); posterior probabilities (PP) are indicated for major nodes (values below<0.50 are not figured). On the right side, the general origin of <i>Arvicanthis niloticus</i> specimens is figured using circles filled with different colours that directly refer to the map presented in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0077815#pone-0077815-g001" target="_blank">Figure 1</a>.</p

Bayesian relaxed clock age estimates (Ma) based on three distinct calibration sets (fossil constraint with an ‘exponential distribution’, fossil constraint with a ‘lognormal distribution’, ‘secondary calibrations’).

<p>The median age and 95% HPD of major nodes are reported for each calibration set. Clades of interest are highlighted using bold characters.</p

Haplotype network and phylogenetic tree resulting from the analysis of the cytb dataset.

<p>The haplotype network reconstruction takes into account missing data and gap so the inferred number of haplotype I higher than the one presented in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0077815#pone-0077815-t004" target="_blank">Table 4</a>. Red values on nodes indicate the inferred number of mutation steps between haplotypes or ancestral haplotypes (symbolized by a red node). The absence of value means that the number of steps is inferior to 10. The phylogenetic tree corresponds to the results of a Bayesian inference analysis (see text for details); posterior probabilities (PP) are indicated for major nodes (values below<0.50 are not figured). On the right side, the general origin of <i>Arvicanthis niloticus</i> specimens is figured using circles filled with different colours that directly refer to the map presented in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0077815#pone-0077815-g001" target="_blank">Figure 1</a>.</p

Time-calibrated tree resulting from the partitioned Bayesian analysis of the combined dataset.

<p>Age estimates correspond to the results of the BRC analysis using the fossil constraint with an exponential distribution. Labels on nodes correspond to the nodes listed in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0077815#pone-0077815-t002" target="_blank">Table 2</a>. Posterior probabilities (left) and bootstrap values (right) are also indicated for major nodes (values below<0.50 are not figured). On the bottom left (lower panel), a map is included to figure the localities of almost all sampled <i>Arvicanthis niloticus</i> specimens (with the exception of the specimen from Ethiopia and the two specimens from Egypt). Additional information on mountain and hydrogeographic formations of interest is also provided. A red line is also used to figure the distribution limits of the two distinct <i>A. niloticus</i> cytotypes (ANI-1a and ANI-1b; see text for details). On the right side, the general origin of <i>Arvicanthis niloticus</i> specimens is represented using circles filled with colours corresponding to those used on the map. In addition, vertical sidebars highlight the three major lineages (A, B and C) and the four major clades within the lineage C (C-1, C-2, C-3 and C-4). On the bottom left again (upper panel), the simplified phylogenetic topology of <i>Arvicanthis</i> studied here is represented with corresponding geographic origin of extant lineages as well as of MRCA as inferred by the ancestral area optimization under Mesquite (see text for details).</p

Parameters describing genetic diversity and genetic differentiation.

<p>The following abbreviations were used: number of sequences per phylogroup (n); number of polymorphic sites (<i>S</i>); number of haplotypes (<i>h</i>); haplotypic diversity (<i>Hd</i>); nucleotide diversity (π); Tajima’s <i>D</i> statistic (<i>D</i>); Fu’s <i>F</i> statistic (<i>F</i>).</p

COI-based phylogenetic relationships of <i>Spodoptera</i> species.

<p>The tree on the left summarizes the results of ML analyses while the tree on the right summarizes the results of BI analyses. Black dots indicate nodes supported by bootstrap values ≥ 70% (ML tree) or supported by posterior probability ≥ 0.95 (BI tree).</p

List of evidences arguing in favor of a high level of differentiation between the two FAW strains.

<p>As indicated by the combination of pros and cons some results are more or less contradictory.</p><p>List of evidences arguing in favor of a high level of differentiation between the two FAW strains.</p

Putative species clusters corresponding to: (i) morphological delineations (column 1); (ii) PTP analyses using either the majority-rule consensus topology resulting from the BI analyses (column 2) or the best tree from the ML analyses (column 3); (iii) GMYC analyses based either on a strict clock and a BD model (column 4) or on a UCLN clock and a BD model (column 5).

<p>The reference tree used here corresponds to the tree resulting from the BI analyses carried out with MrBayes.</p

Likelihood scores, harmonic means and Bayes factors approximated under Tracer for each partitioning strategy of the MrBayes 3.1.2 analyses for the gene trees.

<p>The Bayes factors are given for each possible comparison of strategies in the three last columns of the table. The analyses with the partitioning strategies ‘12v3’ are the best analyses for both genes (COI and EF1-α). The analysis with the partitioning strategy ‘BySix’ is the best analysis for the combined dataset, and is chosen for the dating analyses as a tree prior.</p