BackgroundCADM is a statistical test used to estimate the level of Congruence Among Distance Matrices. It has been shown in previous studies to have a correct rate of type I error and good power when applied to dissimilarity matrices and to ultrametric distance matrices. Contrary to most other tests of incongruence used in phylogenetic analysis, the null hypothesis of the CADM test assumes complete incongruence of the phylogenetic trees instead of congruence. In this study, we performed computer simulations to assess the type I error rate and power of the test. It was applied to additive distance matrices representing phylogenies and to genetic distance matrices obtained from nucleotide sequences of different lengths that were simulated on randomly generated trees of varying sizes, and under different evolutionary conditions.ResultsOur results showed that the test has an accurate type I error rate and good power. As expected, power increased with the number of objects (i.e., taxa), the number of partially or completely congruent matrices and the level of congruence among distance matrices.ConclusionsBased on our results, we suggest that CADM is an excellent candidate to test for congruence and, when present, to estimate its level in phylogenomic studies where numerous genes are analysed simultaneously.

Copulations lasting much longer than required to effect insemination are common throughout the Insecta, but their adaptive significance remains obscure. We address the hypothesis that prolonged copulations benefit male Aquarius remigis (Hemiptera, Gerridae) by influencing sperm use and storage following insemination. We describe the gynatrial complex of females and document sperm location immediately following 32 naturally terminated and 25 artificially terminated copulations. We also examine sperm storage in 22 females isolated from males for 2–10 days. Our results demonstrate that insemination occurs at the end of copulation, and therefore that prolonged copulation is not a post-insemination mate-guarding tactic, as was previously assumed. Sperm are transferred in a coherent, coiled mass and move rapidly to the spermathecal tube, the primary storage organ. However, a few sperm move directly to the fecundation canal and hence should be capable of immediate fertilization. Prolonged copulation is associated with increased filling of the spermathecal tube, which may indicate some form of copulatory courtship or sperm loading by males during the prolonged pre-insemination phase. We discuss this new interpretation of prolonged copulation in A. remigis in the context of the overall costs and benefits of prolonged copulation for both sexes under the natural conditions of polygynandry.

In phylogenetic analysis, one possible approach to minimize missing data in DNA supermatrices consists in sampling sequences from different species to obtain a complete sequence for all genes included in the study. We refer to those complete sequences as composite taxa because DNA sequences that are combined belong to different species. An alternative approach is to analyze incomplete supermatrices by coding unavailable DNA sequences as missing. The accuracy of phylogenetic trees estimated using matrices that include composite taxa has recently been questioned, and the best approach for analyzing incomplete supermatrices is highly debated. Through computer simulations, we compared the phylogenetic accuracy of the 2 competing approaches. We explored the effect of composite taxa when inferring higher level relationships, that is, relationships between monophyletic groups. DNA sequences were simulated on a 42-taxon model tree and incomplete supermatrices containing different percentages of missing data were generated. These incomplete supermatrices were analyzed either by coding the missing data with "?" or by reducing the amount of missing data through the combination of 2 or more taxa to generate composite taxa. Of 180 comparisons (18 simulation cases with 2 different inference methods and 5 levels of incompleteness), we observed significantly higher phylogenetic accuracies for composite matrices in 46 comparisons, whereas missing data matrices outperformed composites in 8 comparisons. In all other cases, the phylogenetic accuracy obtained with composite matrices was not significantly different from that of missing data matrices. This study demonstrates that composite taxa represent an interesting approach to minimize the amount of missing data in supermatrices and we suggest that it is the optimal approach to use in phylogenomic studies to reduce computing time.

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Incongruence, Power, Statistical test, Simulation, Type I error rate,