Supplementary Material 1.Contingency table showing the number of individuals cross- classified by morphological categories, mtDNA and nuclear phylogenetic clades.
mtDNA clustering
ITS2 clustering
genitalic
morphology M1 M2 M3 M4 M5 M6 M7 Total
N0 alpestris α 1 5 6
alpestris β 15 15
speciosa 9 11 2 19 61 102
Total N0 10 11 2 39 61 123
N1 ganglbaueri 5 5
Total N1 5 5
N2 alpestris α 8 1 6 10 25
alpestris β 5 5
Total N2 8 1 6 15 30
Total 8 5 11 17 17 39 61 158
A.O. alpestris
K2P distance
Occurrence
0.00 0.02 0.04 0.06 0.08
050100150200250
B.O. speciosa
K2P distance
Occurrence
0.00 0.02 0.04 0.06 0.08
050010001500
C.O. ganglbaueri
K2P distance
Occurrence
0.00 0.02 0.04 0.06 0.08
0.00.51.01.52.02.53.0
Supplementary Material 2. Detailed K2P barcoding distances within each species (O. alpestris, O. speciosa, O. ganglbaueri).
1.0
VS2b-SPE
VS4e-SPE*
AUT1d-SPE HR2b-SPE
AI1b-SPE FR1a-SPE
GR1c-ALPα AUT1c-SPE*
FR14a-SPE HR4b-SPE
AUT5c-SPE*
IT8a-SPE
FR5b-GAN PL2c-ALPβ
MON2b-ALPα VALa-SPE
FR11b-SPE*
SLO8c-SPE
O. cacaliae IT9b-SPE*
IT5a-SPE HR4c-SPE
SW3b-ALPα
AUT5a-SPE*
VALb-SPE
SLO8d-SPE IT11b-SPE
RO1b-ALP*
VD1b-ALPα HR2c-SPE
IT3a-SPE
SLO9b-SPE SURa-SPE SLO9a-SPE
BE1a-ALPα HR4a-SPE
AUT2b-SPE LOTa-SPE
RO2a-ALPβ AUT5d-SPE*
DOL2b-SPE GRHb-SPE*
IT11c-SPE
PL2a-ALP*
SUSb-SPE IT8b-SPE DOL3b-SPE
CZ4a-ALPα VS8b-SPE*
GR1a-ALPα VS4a-SPE SLO2b-SPE*
O. cacaliae VS4d-SPE FR16a-SPE
CZ4c-ALP*
AI1a-SPE
IT5c-SPE PL2b-ALPβ
VD1a-ALPα VS2a-SPE VS4f-SPE*
VS5a-SPE*
JU1c-SPE
VS2c-SPE
AI1b-ALPα IT8c-SPE HR2a-SPE BE1a-SPE VS4b-SPE
SER1a-ALPα AUT1b-SPE*
IT5b-SPE DOL3a-SPE
IT2a-ALPα SLO10a-SPE
FR16b-SPE
FR5a-GAN
SLO8a-SPE FR1c-SPE SURb-SPE*
SP1b-GAN SO1d-SPE IT1b-SPE
RO1a-ALPα
MON2c-ALPα SER1c-ALPα SLO2a-SPE
IT12b-SPE
IT2c-ALPα SW3a-ALPα AUT2a-SPE
GRHa-SPE
SP1a-GAN DOL2a-SPE
SUSa-SPE SW3c-ALPα
BE1b-ALPα
SLO10c-SPE AUT1a-SPE
IT12c-SPE FR13c-SPE
VALa-ALPα SLO8b-SPE FR13b-SPE AUT2c-SPE*
GR1a-SPE
CZ4b-ALPβ
VD1c-ALPα FR13a-SPE
JU1a-SPE IT9a-SPE IT4a-SPE
O. bifrons VS7a-SPE
SER1b-ALPα IT1c-SPE
IT11a-SPE SLO2c-SPE*
VS8a-SPE
GR1b-ALPα AUT3a-ALP*
VALb-ALPα FR1b-SPE
RO2b-ALPβ
O. liturata LOTb-SPE
FR5c-GAN AUT5b-SPE*
VS4c-SPE
VD1a-SPE
VS6a-SPE
O. gloriosa SO1g-SPE
SLO10b-SPE VS6b-SPE GL1a-SPE
IT1a-SPE
MON2a-ALPα AI1a-ALPα
O. bifrons FR11a-SPE
SLO9c-SPE
O. gloriosa IT12a-SPE AI1c-SPE
IT2b-ALPα VS7b-SPE
1 / 0.93 1 / 0.61
1 / 0.81 3 / 1.00
1 / 0.94
2 / 1.00
2 / 0.97
8 / 0.68 0 / 0.58
2 / 0.60
3 / 0.98
2 / 0.94
2 / 0.91 1 / 0.72
2 / 0.97
1 / 0.65
2 / 0.97
16 / 1.00 0 / 0.54
3 / 1.00
1 / 0.51 1 / 0.92
1 / 0.88
2 / 1.00
6 / 1.00
3 /1.00 1 / 0.63
3 / 0.59
3 / 1.00 2 / 0.99
1 / 0.81
1 / 0.51
1 / 0.92
1 / 0.71 0 / 0.81
4 / 0.92 1 / 0.70 2 / 0.89
2 / 0.99
1 / 0.71 2 / 1.00
1 / 0.74 4 / 0.96
1 / 0.86
24 / 1.00 1 / 0.59 0 / 0.52
1 / 0.51 0 / 0.50
6 / 1.00 10 / 1.00
1 / 0.79
1 / 0.67
14 / 1.00
2 / 0.86
6 / 0.98
0 / 0.91
2 / 0.87 2 / 1.00
5 / 0.89
0 / 0.54
1 / 0.63
Outgroups M1 M2 M3 M4 M5 M6 M7
IT11c SPE
S
IT5c SPE
FR5c GAN
AI1b ALPα ABZ2a-ALPα EURa-ALPβ
ABZ5a-ALPα ABZ1a-ALPα
ABZ5b-ALPα FR3b-ALPβ
ABZ1c-ALP*
SP1b-ALP*
FR3a-ALPβ
FR4c-ALPβ FR3c-ALPβ
FR9c-SPE FR4b-ALPβ
ABZ1b-ALPα
FR8b-SPE SP1a-ALPβ
ABZ2b-ALPβ FR4a-ALPβ
ABZ2c-ALPβ SP1c-ALPβ EURb-ALPβ
1 / 0.99 5 / 1.00 2 / 0.78 2 / 0.61
4 / 1.00 3 / 0.99
7 / 1.00 2 / 0.63
3 / 0.96
2 / 0.83
VD1c-SPE
FR14c-SPE VD1b-SPE SO1a-SPE
NE1b-SPE NE1a-SPE
IT7a-ALPβ FR8c-SPE SO1e-SPE
FR9a-SPE JU1b-SPE
VS6c-SPE
FR8a-SPE SO1f-SPE
FR9b-SPE FR14b-SPE SO1b-SPE
IT7b-ALPβ SO1c-SPE
NE1c-SPE*
BE1b-SPE*
IT7c-ALPβ VS5b-SPE*
1 / 0.53
5 / 1.00 5 / 1.00
7 / 1.00
3 / 0.99
2 / 0.86
4 / 1.00
3 / 1.00 0 / 0.57
2 / 0.99 2 / 0.70
§ a b c d e
Supplementary Material 3. Half-compatible topology of the MrBayes analysis, with the corresponding BPP and Bremer support values on each node. Major clades from the MP analysis are shown at the right of the topology.
The group indicated by a '§' switched position between the MP and the Bayesian analyses (see Fig. 4). Codes correspond to populations detailed in Table 1.
Supplementary Material 4. All-in-one geographical distribution of each mtDNA clade identified in the MP analysis (see Fig. 4). Colors refer to clades as in Figure 4 and codes correspond to populations detailed in Table 1.
/UTGROUPS
- - - -
-
-
-
-YA
Supplementary Material 5. Biogeographic history of the Oreina AGS complex inferred from the likelihood method implemented in Mesquite and represented on the PL dated Majority-rule consensus tree. On each node is represented a pie-chart indicating the ancestral reconstruction of biogeographic areas (see text for more details). See Fig. 4 for clade definition and color legends. The red lines represent the mean and 95% interval of confidence for the shift in diversification rate (see Fig. 8).
Supplementary Material 6. Summary of the biogeographic scenarios of the OreinaAGS complex inferred from the MP-DIVA and Mesquite ancestral area reconstructions (see text for more details on the protocol to extract biogeographic events from the reconstructions).
The table is subdivided into two parts: (A) “main story” from the root to the definition of the clades and (B) “within-clade” summarizing events occurring in clades M1 to M7. This table was used to reconstruct the biogeographic scenario from Fig. 7 where only events shared by the two methods (in bold) were represented. Abbreviations: in roman: events unique to one of the method; in grey: events not represented on Fig. 7 due to their high level of uncertainty; in bold: events shared between the two methods (represented on Fig. 7). Finally the star (*) indicates events that are shared between the two methods but occurred at different time scales:
either the main story for MP-DIVA or within-clade for Mesquite. These events were represented on Fig. 7 using dashed lines. The occurrence of each event is represented in the column “Times”. See Fig. 4 for area definitions.
Clade Event Times Event Times
Main story B-->C (clade 1) 1 B-->C (clade 1) 1 B-->I (clade 2) 1 B-->I (clade 2) 1
B-->G (clade 5) 1 - -
B-->A (clade 6) 1 - -
B-->E (clade 6) 1 - -
B-->J (clade 6) 1 - -
Clade M1 - - C-->B 2
Clade M2 Stays in I - Stays in I -
Clade M3 B-->G 1 B-->G 1
Clade M4 Stays in B - Stays in B -
Clade M5 B-->F 2 B-->F 3
B-->G 1 B-->G 2
D-->B 1 D-->B 1
F-->D 1 F-->D 1
Clade M6 A-->J 1 - -
- - B-->A 1
- - B-->E 1
- - B-->G 2
B-->H 1 B-->H 1
B-->J 1 B-->J 2
E-->I 1 E-->I 1
E-->J 1 - -
G-->B 1 G-->B 2
- - G-->J 2
J-->G 1 J-->G 1
Clade M7 B-->C 2 B-->C 6
B-->G 2 B-->G 4
23 35
MP-DIVA Mesquite
Number of dispersals:
Supplementary Material 7.
Tajima’s D test parameters for each biogeographic region. All tests were non-significant, indicating no signature of recent range expansion or retraction.
Neutrality test Abruzzi
Appenines Alps Balkanic Range
Black Forest
Cantabric Range
Carpathians
& Sudetes Jura Ligurian
Appenines Pyrenees Massif
Central Mean Standard deviation Sample size 8 112 12 3 2 10 16 3 14 6 18.6 33.17027
S 5 152 29 1 14 10 67 1 40 26 34.5 46.10435
Pi 2.143 19.799 11.061 1.333 14.000 3.689 17.500 0.667 17.813 11.533 9.954 7.428 Tajima's D 0.504 -1.053 0.682 0.000 0.000 -0.058 -0.570 0.000 1.810 0.081 0.140 0.763 Tajima's D p-value 0.754 0.129 0.789 0.989 1 0.525 0.285 0.986 0.987 0.534 0.6978 0.31709
Supplementary Material 8.
Geographic events for each of the ten nodes included in the 5-95% inflexion-point interval of the diversification rate (see Figure 8), as
highlighted in Figure 4. Areas’ codes also refer to codes used in Figure 4. Both events that arose from the anterior node and events that happened towards the posterior node(s) are addressed, respectively on the left and on the right of the column informing on the focal node (in bold in the centre). We distinguished among three different types of geographical events: dispersal, vicariance, and no change. When for a given node, there was a high level of biogeographic uncertainty (i.e., the maximum probability of the most likely area was not higher than 0.5), no events could be inferred. Besides each area, the DIVA probability is given in brackets. In three cases (in italics), we did not duplicate information and just referred to the line above. In total, we could retrieve six vicariance and four dispersal events, all but one implying the Alps (b).
anterior node 5-95% inflexion point interval posterior node(s)
Areas [DIVA probability] « from » event
Node (clade) Areas [DIVA probability] « to » event
Areas [DIVA probability]
c [1]
b [1] dispersal (b Æ c) I (M7) bc [1] vicariance (b│c)
b [0.927]
b [1] no biogeographic change II (M7) b [1] see « from » event to node I just above g [1]
j [1]
j [1]
g [1]
g [1]
b [1]
j [0.724] no inference possible III (M6) high level of biogeographic
uncertainty no inference possible
bg [0.51]
b [1]
high level of
biogeographic uncertainty no inference possible IV (M6) bh [1] vicariance (b│h)
h [1]
e [1]
high level of
biogeographic uncertainty no inference possible V (M6) ae [1] vicariance (a│e)
a [1]
a [1]
a [1]
high level of
biogeographic uncertainty no inference possible VI (M6) a [1] no biogeographic change
a [1]
b [1]
b [0.947] dispersal (b Æ f) VII (M5) bf [1] vicariance (b│f)
f [1]
see « from » event to node VII just above dispersal (b Æ g) bg [0.612]
b [1]
b [1]
bg [0.969] vicariance (b│g) VIII (M5) b [0.947]
no biogeographic change
b [1]
b [0.974] dispersal (b Æ g) IX (M5) bg [0.969] see « from » event to node VIII just above i [1]
bi [1] vicariance (b│i) X (M2) i [1] no biogeographic change
i [1]
