Table 3.
The haplotypes and corresponding accession numbers for GenBank per sequenced sample per gene
| asl | clpc | coI | cytb | |||||
|---|---|---|---|---|---|---|---|---|
| ind. | ht. | acc. nb. | ht. | acc. nb. | ht. | acc. nb. | ht. | acc. nb. |
| 104 | Pmu1 | JN990725 | Pmu1 | JN990723 | Pmu1 | JN990718 | Pmu1 | JN990712 |
| 114 | Pmu1 | .. | Pmu2 | JN990724 | - | - | Pmu1 | .. |
| 156 | Pmu1 | .. | Pmu1 | .. | Pmu2 | JN990719 | Pmu2 | JN990713 |
| A2111 | - | Pme3 | JN990720 | Pme3 | JN990714 | Pme3 | JN990708 | |
| A2112 | Pme2 | JN990726 | Pme4 | JN990721 | Pme4 | JN990715 | Pme4 | JN990709 |
| A2113 | - | - | Pme5 | JN990722 | Pme5 | JN990716 | Pme5 | JN990710 |
| A2114 | - | - | - | - | Pme6 | JN990717 | Pme6 | JN990711 |
Samples 104, 114 and 156 are Polychromophilus murinus, sampled from Myotis daubentoni and shared some haplotypes. The samples A2111-A2114 are Polychromophilus melanipherus from Miniopterus schreibersii and never shared haplotypes. For each unique haplotype, the GenBank accession number is mentioned only once in the table. '..': accession number already mentioned. '-': sequencing was unsuccessful.
None of the topologies obtained by independent analyses of the separate genes conflicted with the topology resulting from the concatenated alignment (Kishino-Hasegawa tests: cytb: Δlnl = 2.8, pKH = 0.432, coI: Δlnl = 12.1, pKH = 0.234, clpc: Δlnl = 9.3, pKH = 0.270), except for asl (Δlnl = 81.0, pKH < 0.001). Despite this strong rejection, both the ML and BI trees of asl had only few supported nodes and only closely related pairs were recovered (data not shown). A possible cause of the incongruence detected could be positive selection events in the evolution of the asl nuclear sequence [34]. However, analyses performed with Codeml [33] did not show signs of positive selection on the nuclear gene.