Buerki et al.
Evaluating parametric vs. parsimony-based methods in biogeography
APPENDIX S2 Supplementary tables.
Table S1. Contingency table showing number and type of biogeographical events (change in geographic range from ancestor to descendant) inferred by dispersal-vicariance analysis (DIVA) integrated over a
Bayesian sample of trees obtained from the posterior distribution of the phylogeny of Sapindaceae (i.e., a Bayes-DIVA analysis). Biogeographical events are sorted by time slice (see Fig. 2). Notice that DIVA does not
take into account the timing of divergence events between lineages (branch lengths). Biogeographical events are expressed as frequencies of range expansion (Dab), sometimes combined with vicariance events (V
a|b) according to the cost transition matrix represented in Figure 2. Fonts indicate different types of transition events between geographic ranges: italic: vicariance events; roman: range expansion; bold: vicariance
and range expansion or two range expansions; red + bold: not considered. See Materials and Methods for more details on areas and time slice definitions.
a
ab
ad
ag
From Area(s)
b
bc
bd
bg
c
cd
ce
cg
d
de
dg
e
eg
g
Time_slice
2
3
4
3
4
3
4
3
4
4
4
3
4
4
4
4
3
4
4
3
4
3
3
4
4
3
4
3
4
a
ab
abcd
abcdeg
ad
1 (Dad)
ade
af
ag
b
bc
To Area(s)
abcdeg
bcd
bd
bde
bg
c
cd
ce
cg
d
de
dg
e
eg
g
1 (Dag)
1 (Dab)
4 (Dad)
4 (Daf)
2 (Dab+Dac+Dad+Dae+Dag)
1 (Va¦b)
1 (Va¦b)
1 (Va¦d)
1 (Va¦d)
1 (Va¦g)
2 (Va¦g)
1 (Va¦b+Dbc)
1 (Va¦d)
1 (Va¦d)
1 (Va¦g+Dge)
1 (Va¦g+Dad)
2 (Va¦g)
1 (Dba+Dbc+Dbd)
4 (Dbc)
3 (Dbc+Dbd)
1 (Dbd) 1 (Dbd+Dbe)
2 (Vb¦c)
1 (Vb¦d)
1 (Vb¦d)
2 (Vb¦g)
2 (Vb¦c)
1 (Vb¦d)
1 (Vb¦d) 1 (Vb¦d+Dde)
2 (Vb¦g)
3 (Dcb)
1 (Vc¦d)
1 (Vc¦d)
1 (Vc¦e)
1 (Vc¦e)
1 (Vc¦g)
5 (Dda)
1 (Vc¦g)
1 (Ddb)
1 (Ddb)
2 (Dda+Dde)
1 (Dde)
1 (Dde)
1 (Vd¦e+Dec)
1 (Vd¦e+Ddg)
1 (Vd¦g)
1 (Vd¦g)
3 (Dea+Deb+Dec+Ded+Deg)
6 (Dea+Ded)
12 (Ded)
1 (Ve¦g+Dgc)
1 (Dgb)
1 (Dga)
1 (Dga+Dgb+Dgc+Dgd+Dge)
-1-
1 (Ve¦g+Ded)
2 (Deg)
1 (Ve¦g)
1 (Ve¦g)
2 (Ve¦g)
Buerki et al.
Evaluating parametric vs. parsimony-based methods in biogeography
Table S2. Contingency table showing number and type of transition events between geographic ranges (change in geographic range from ancestor to descendant) inferred by a non-stratified likelihood dispersal–
extinction–cladogenesis (DEC) model (Lagrange M1) on the Sapindaceae chronogram obtained with penalized likelihood. Transition events are sorted by time slice and expressed as rates of local extinction (Ea)
and/or range expansion (DAB), according to the Q transition probability matrix represented in Figure 2. Fonts indicate different types of transition events between geographical ranges: italic: local extinction (range
contraction); roman: dispersal (range expansion); bold: transitions between ranges that are separated by more than one dispersal or extinction event; according to the Q matrix, transitions involving dispersal (range
expansion) the rate is the sum of rates from areas in the starting range to the target area, e.g., DAB+DBC = DABC (Ree & Sanmartín, 2009); bold *: transitions that involve three or more events of range expansion and
for which there are uncertainty in the direction of dispersals or the transition is not present in the Q matrix (e.g., DABC to DBC); red: not considered. See Materials and Methods for more details on areas and time slice
definitions.
a
From Area(s)
abc
ad
ade
ae
af
b
bc
bcd
bd
c
cd
ce
cg
d
de
dg
e
g
Time slice
a
2
3
4
1
3
4
1 (Ed)
4
4
4
1 (Ef)
4
4
4
3
4
4
4
3
4
4
3
4
4
3
4
4
abcd
ad
1 (Dad)
ade
ae
af
b
bc
To Area(s)
bcd
bd
bde
c
cd
cg
d
de
dg
e
g
2 (Daf)
1 (Ea)*
1 (Ea)
1 (Ea)
1 (Ee)
2 (Dad+Ded)
1 (Dbc+Dbd+Dcd+Dba+Dca+Dda)
1 (Dbd)
1 (Ec)
1 (Ed+Ec)
1 (Ed)
1 (Ed)
1 (Dbg+Eb)
2 (Eb)
2 (Eb)
1 (Eb)
1 (Eb)
1 (Dbe+Dde+Eb)
2 (Dcb)
2 (Ed)
1 (Ec)
1 (Ec)
1 (Ee+Dcb)
1 (Eg)
2 (Ec)
1 (Ddb)
4 (Dda) 2 (Dda+Dde)*
1 (Dde+Ed)
1
1 (Ee)
3 (Ded+Dda)*
1
1 (Dgc)
1 (Dgb+Eg)
-2-
8 (Ded)
1 (Ed)
1 (Deg+Ee)
Buerki et al.
Evaluating parametric vs. parsimony-based methods in biogeography
Table S3. Contingency table showing number and type of transition events between geographic ranges (change in geographic range from ancestor to descendant) inferred by a non-stratified likelihood dispersal–
extinction–cladogenesis (DEC) model (Lagrange Str) on the Sapindaceae chronogram obtained with penalized likelihood. Transition events are sorted by time slice and expressed as rates of local extinction (Ea)
and/or range expansion (DAB), according to the Q transition probability matrix represented in Figure 2. Fonts indicate different types of transition events between geographical ranges: italic: local extinction (range
contraction); roman: dispersal (range expansion); bold: transitions between ranges that are separated by more than one dispersal or extinction event; according to the Q matrix, transitions involving dispersal (range
expansion) the rate is the sum of rates from areas in the starting range to the target area, e.g., DAB+DBC = DABC (Ree & Sanmartín, 2009); bold *: transitions that involve three or more events of range expansion and
for which there are uncertainty in the direction of dispersals or the transition is not present in the Q matrix (e.g., DABC to DBC); red: not considered. See Materials and Methods for more details on areas and time slice
From Area(s)
definitions.
Time slice
a
1
2
3
4
ab
4
abcdeg
4
ad
3
4
ade
4
af
3
b
4
bc
4
bd
3
4
bg
4
c
4
cd
4
d
3
4
de
3
4
e
4
eg
3
4
g
4
a
ab abc abcd abcde abcdeg
ad
ade
1 (Dad)
1 (Dad)
2 (Dad)
af
1 (Daf)
b
bc
bcd
To Area(s)
bcdeg
bd
bde
bg
c
cd
d
de
e
eg
g
1 (Dad+Ea)
1 (Daf)
1 (Dag+Ea)
1 (Eb)
1
1 (Ed)
1 (Ed)
1 (Ea+Dbc)
1 (Ea)
1 (Ea)
1 (Ea)
1 (Dae+Dde+Ea)
1 (Ee)
1 (Ef)
1
2 (Dbd)
1 (Ec)
1 (Ed)
2 (Ed)
2 (Eg)
1
1 (Dbg+Eb)
3 (Eb)
1 (Dbc+Ddc+Eb)
3 (Eb)
1 (Pbd+Dde)
1
2 (Eb)
4 (Dcb)
1 (Dcb+Ddb)
2 (Ed)
1 (Ec)
1 (Ddb)
4 (Dda)
1
2 (Dda+Dde)*
1 (Dde)
1
1 (Ddc)
2 (Dda)*
3 (Ded+Dda)*
1 (Ee)
11 (Ded)
1
3 (Dgb)
-3-
1 (Eg+Ded)
2 (Ed) 1 (Ed+Deg)
1 (Ed)
1 (Deg)
1 (Deg+Ee)
1 (Ee)
1 (Ee)
Buerki et al.
Evaluating parametric vs. parsimony-based methods in biogeography
Table S4. Frequency of dispersal events between areas sorted into time slices as inferred by Bayes-DIVA, Lagrange M1, and Lagrange Str for Sapindaceae. See text and Fig. 6 for more details.
Dispersals
Time
From-
Bayes-
Lagrange
slice
To
DIVA
M1
A-D
1
Lagrange Str
1
1
A-F
2
A-D
1
2
D-E
1
A-D
1
A-B
1
1
A-F
3
3
A-G
1
B-C
1
B-E
1
D-A
1
D-B
2
D-E
D-G
1
E-D
1
1
1
1
2
1
E-G
G-A
1
G-B
1
G-E
1
A-B
4
A-D
4
2
2
-4-
Buerki et al.
Evaluating parametric vs. parsimony-based methods in biogeography
A-F
4
1
1
A-G
B-C
5
B-D
2
1
1
2
B-E
1
B-G
1
1
C-B
3
3
5
D-A
12
9
11
D-B
1
D-C
1
D-E
4
3
2
E-D
18
13
15
E-G
2
1
2
1
3
G-B
G-C
1
1
Total
70
41
57
-5-