Table 1 Taxa included in this study with a summary of the calibration method for the molecular clock, type and number of markers used, divergences dates.

From: Ecological changes have driven biotic exchanges across the Indian Ocean

Taxon

Taxonomic level

Calibration method

Markers

Taxon age in m.y.a. (95% CI)

mtDNA/cpDNA

nDNA

Source

This study

Aves: Acrocephalidae

Family

Substitution rate

3

5

14 (12–16)

8 (6–9)

Aves: Anatini

Tribe

Fossil

5

0

 ~ 18

22 (18.5–26)

Aves: Falconidae

Family

Fossil

0

8

28 (23–35)

34 (29–38)

Aves: Palaeognathae

Infraclass

Fossil

1*

0

73 (63–84)

80 (73–89)

Aves: Psittacoidea

Superfamily

Fossil

3

4

59 (45–72)

50 (40–60)

Aves: Pycnonotidae

Family

Substitution rate, Secondary calibration

7

7

–

11 (9–13)

Crustacea: Atyidae

Family

Fossil, Secondary calibration

1

1

161 (69–257)

141.5 (125–158)

Lissamphibia: Caecilia

Order

Fossil

3

6

 ~ 109

178 (174–184)

Lissamphibia: Neobatrachia

Suborder

Fossil

0

95**

128 (120–135)

–

Mammalia: Emballonurinae

Subfamily

Fossil

1

1

56 (47.5–69)

54 (47–63)

Mammalia: Strepsirrhini

Suborder

Fossil

2

4

61 (55–67)

58 (50–65)

Mammalia: Pteropodidae

Family

Substitution rate, Secondary calibration

2

4

8 (5.5–11)

7 (5–8)2

Squamata: Boidae

Family

Fossil

1

5

77 (68–89)

72 (67–79)

Squamata: Chamaeleoninae

Subfamily

Fossil

3

10

65 (55–75)

66 (53–75)

Squamata: Gekkonidae

Family

Fossil, Secondary calibration

3

4

–

100 (97–103)

Squamata: Natricinae

Subfamily

Fossil

6

1

33 (28–40)

56 (48–66)

Squamata: Typhlopoidea

Superfamily

Fossil

0

5

106 (91–121)

108 (93–124)

Testudines: Testudinidae

Family

Fossil

3

2

–

50 (37–66)

Angiosperms: Aphananthe

Genus

Fossil

4

0

19 (12–27.5)

13 (9–16.5)

Angiosperms: Exacum

Genus

Secondary calibration

2

0

21 (8–36)

41 (32–50)

Angiosperms: Ficus

Genus

Fossil

0

4

70 (60–92.5)

68 (60–82)

Angiosperms: Loranthaceae

Family

Fossil

3

2

59 (53–66)

72 (71–72.5)

Angiosperms: Rubiaceae

Family

Secondary calibration1

4

0

25 (30–21)

25 (28–20)

  1. Ages are the most recent common ancestor for the given taxon. References of the articles on which the analyses were based are available in the Appendix S0. Some of the analyses include data from other sources and these are specified in Appendix S2.
  2. *The marker used was the entire mitogenome;
  3. **This dataset was very large and, thus, we had to reduce and restrain it to set up the analysis (see Appendices);
  4. 1To simplify the analysis, we separated the tribes that were present in diverse biogeographic regions (Coffeae, Bertiereae, Octotropideae, and Pavetteae) and built the trees independently;
  5. 2Age of TMRCA between Pteropus and Acerodon.
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