Journal of Biogeography
SUPPORTING INFORMATION
Mediterranean origin and Miocene–Holocene Old World diversification of meadow
fescues and ryegrasses (Festuca subgenus Schedonorus and Lolium)
Luis A. Inda, Isabel Sanmartín, Sven Buerki and Pilar Catalán
Appendix S1 Supplementary tables. Table S1 lists the taxa and sequences included in this
study. Table S2 shows the dispersal connectivity matrices used in the LAGRANGE stratified
analysis. Table S3 indicates some numeric results and characteristics from the individual and
combined plastid and nuclear analyses.
Appendix S2 Expanded Materials and Methods. (a) Detailed description of the phylogenetic
inference analyses, with associated references. (b) Description of the methodological settings
used in the BEAST dating analysis.
Appendix S3 Supplementary figures. Figures S1 and S2 show the phylogenetic trees from the
maximum parsimony, maximum likelihood and Bayesian (MRBAYES) analyses of the ITS–
cpDNA dataset. Figure S3 shows the BEAST analysis of the more inclusive Loliinae dataset.
Figure S4 shows the effect of different sampling strategies on date estimates. Figure S5 shows
the results from the LAGRANGE unconstrained M1 analysis.
1
Appendix S1: Supplementary tables
Table S1 List of Schedonorus–Lolium complex (Festuca subgenus Schedonorus, Lolium, Micropyropsis) and outgroup taxa used in this study.
GenBank accession numbers of newly generated sequences are highlighted in bold.
Taxon
Origin
Distribution
Source and voucher
GenBank accession numbers
ITS
trnL–F
trnT–L
Schedonorus–Lolium group
Festuca subgen. Schedonorus(P. Beauv.) Peterm.
Festuca apennina de Not. (1)
Switzerland: Valais: Gletsch
Eurosiberian
UZ J. Müller 9683
AF548028
AF533041
EF378991
Festuca apennina de Not. (15)
Italy
Eurosiberian
USDA Pullman PI 577108
EF379048
EF378952
EF378992
Festuca arundinacea Schreber (1)
Spain: Lugo: Láncana
Eurosiberian
UZ J.A. Lopez Rodriguez 1081
AF519976
AY098995
DQ367405
US P. Peterson 14896
EF379049
UZ M. Pimentel s.n.
EF379050
EF378954
EF378994
UZ M. Pimentel s.n.
-
GU573744
GU573745
JACA 9939 P. Auquier
EF379058
-
EF378999
Mahgrebian
ABY-BN 867.1974U
EF379051
EF378955
EF378995
Mahgrebian
ABY-BN 1304.0000U
EF379057
EF378956
EF378996
E Med + SW Asian
Festuca arundinacea Schreber (3)
Venezuela (introduced)
Eurosiberian
EF378953
EF378993
E Med + SW Asian
Festuca arundinacea Schreber (4)
Spain: La Coruña: Torre
Eurosiberian
E Med + SW Asian
Festuca arundinacea Schreber (5)
Spain: La Coruña: Ferrol
Eurosiberian
E Med + SW Asian
Festuca arundinacea Screber (9)
Belgium
Eurosiberian
E Med + SW Asian
Festuca arundinacea Schreber var. atlantigena Morocco (cultivar, UK)
(St.-Yves) Auquier (10) ('F. atlantigena')
Festuca arundinacea Schreber var. atlantigena Morocco (cultivar, Belgium)
2
(St.-Yves) Auquier (14) ('F. atlantigena')
Festuca arundinacea Screber var. corsica France: Corsica
W Mediterranean
ABY-BN 1170.0000U
EF379052
EF378957
EF378997
Mahgrebian
ABY-BN 400.1967U
EF379056
EF378960
EF378998
Eurosiberian
UZ I.Aizpuru P.Catalán 1331.88
AF303416
AF533043
EF379003
UZ D. Stancik 24.6.01
EF379059
EF378961
EF379004
UZ J. Müller 9947
EF379060
EF378962
EF379005
DNA, Fjellheim et al. 2006
EF379061
-
-
(Hack.) Richt. (11) ('F. corsica')
Festuca
arundinacea
Screber
var. Morocco (cultivar, UK)
letourneuxiana (St. Yves) Torrecilla & Catalan
('F. letourneuxiana')
Festuca gigantea (L.) Villars (1)
Spain: Navarra: Arce
E Med + SW Asian
Festuca gigantea (L) Villars (3)
Czech Republic
Eurosiberian
E Med + SW Asian
Festuca gigantea (L.) Villars (4)
Germany: Thuringen
Eurosiberian
E Med + SW Asian
Festuca gigantea (L.) Villars (5)
Norway
Eurosiberian
E Med + SW Asian
Festuca fontqueri St. Yves
Morocco: Rif mountains
W Mediterranean
UZ P. Catalan s.n.
AF303404
AF533044
DQ631486
Festuca fenas Lag. (1)
Spain: Segovia: Castilnovo
W Mediterranean
UZ J.A. Lopez Rodriguez s.n.
AF532951
AF533042
EF379000
Festuca fenas Lag. (3)
Spain: Mallorca
W Mediterranean
UZ L. Saenz s.n.
EF379055
-
-
Festuca fenas Lag. (7)
Spain: Huesca: Benabarre
W Mediterranean
JACA 243698 J.V. Ferrandez
EF379053
EF378958
EF379001
Festuca fenas Lag. (12)
France
W Mediterranean
ABY-BN 354.1974U
EF379054
EF378959
EF379002
Festuca pratensis Huds. (1)
UK: England: Wilshire:Calne
Eurosiberian
UZ P.Catalan
AF303421
AF478503
EF379007
UZ R.Soren 6025
AF532948
EF378949
EF379008
JACA 544795 J.V. Ferrández
EF379042
E Med + SW Asian
Festuca pratensis Huds. (2)
USA: Alaska
Eurosiberian
E Med + SW Asian
Festuca pratensis Huds. (3)
Spain: Huesca: Abizanda
Eurosiberian
-
-
E Med + SW Asian
3
Festuca pratensis Huds. (4)
Kazakhstan
Eurosiberian
USDA Pullman W6 13201 930
EF379043
EF378950
EF379009
USDA Pullman PI 289011 85i
EF379044
-
EF379010
UZ J. Müller 9683
EF379045
EF378951
EF379011
DNA, Fjellheim et al. 2006
EF379046
-
-
DNA, Fjellheim et al. 2006
EF379047
-
EF379012
Mahgrebian
UAM 4064
AF303424
AY098996
EF379006
E Med + SW Asian
Festuca pratensis Huds. (5)
Hungary
Eurosiberian
E Med + SW Asian
Festuca pratensis Huds. (6)
Germany: Thuringen
Eurosiberian
E Med + SW Asian
Festuca pratensis Huds. (7)
Norway
Eurosiberian
E Med + SW Asian
Festuca pratensis Huds. (8)
France
Eurosiberian
E Med + SW Asian
Festuca mairei St. Yves
Morocco: Marrakech:
Oukaimeden
Festuca simensis Hochst. ex A. Rich. (1)
Uganda: Uchuya: Kabale
E & W Trop. African
MHU 1608 M. Namaganda 204K
GU573752
GU573746
GU573777
Festuca simensis Hochst. ex A. Rich. (2)
Uganda: Elgon Mnt, bamboo forest
E & W Trop. African
MHU 1568 M. Namaganda 234K
GU573753
GU573748
GU573749
Festuca simensis Hochst. ex A. Rich. (3)
Uganda: Elgon Mnt, Mongongo
E & W Trop. African
MHU 1577 M. Namaganda 282K
GU573754
GU573750
GU573751
Lolium canariense Steud. (1)
Spain: Tenerife: Teno
Macaronesian
UZ A. Santos 13.3.02
EF379062
EF378963
EF379014
Lolium canariense Steud. (3)
Spain: Canarias: La Palma
Macaronesian
UZ P. Catalan 2002
EF379063
EF378964
EF379015
Lolium canariense Steud. (4)
Portugal: Madeira: Ponte Santo
Macaronesian
UZ M Sequeira s.n.
EF379064
EF378965
EF379016
Lolium canariense Steud. (5)
Spain: Canarias
Macaronesian
USDA Pullman PI 320544 82i
EF379065
EF378966
EF379017
Lolium L.
Lolium
edwardii
Scholz,
Stierstorfer
& Spain: Canarias: El Hierro
Macaronesian
DNA, Scholz (Berlin 24-3)
EF379066
EF378967
EF379018
Scholz,
Stierstorfer
& Spain: Canarias: El Hierro
Macaronesian
DNA, M. Gaisberg (Germany)
EF379067
EF378968
EF379019
Macaronesian
MADS 06842
EF379068
-
-
Gaisberg (1)
Lolium
edwardii
Gaisberg (2)
Lolium lowei Menezes
Portugal: Madeira: Porto Santo
4
Lolium multiflorum Lam. (1)
Italy
Eurosiberian
USDA_Pullman PI 239804 86 i
EF379069
EF378969
EF379020
USDA_Pullman PI 343155
EF379070
EF378970
EF379021
USDA_Pullman PI 222526
EF379071
EF378971
EF379022
JACA 394790 A. Martinez
EF379072
EF378972
EF379023
USDA Pullman PI 619001
EF379073
EF378973
EF379024
USDA Pullman PI 440475
EF379074
EF378974
EF379025
USDA Pullman PI547390
KF454873
KF454874
KF454875
JACA 402293 E. Carreira
EF379075
-
EF379026
E Med + SW Asian
Lolium multiflorum Lam. (2)
Egypt (introduced)
Eurosiberian
E Med + SW Asian
Lolium multiflorum Lam. (3)
Iran
Eurosiberian
E Med + SW Asian
Lolium multiflorum Lam. (4)
Spain: Zaragoza: Chodes
Eurosiberian
E Med + SW Asian
Lolium perenne L. (1)
UK: Wales
Eurosiberian
E Med + SW Asian
Lolium perenne L. (2)
Russia
Eurosiberian
E Med + SW Asian
Lolium perenne L. (3)
Iran
Eurosiberian
E. Med + SW Asian
Lolium perenne L. (6)
Spain: Lugo: Lugo
Eurosiberian
E Med + SW Asian
Lolium persicum Boiss. & Hoh. (1)
Afghanistan: Tarbulock
E Med + SW Asian
USDA Pullman PI 3174.50 88i
EF379076
EF378975
EF379027
Lolium persicum Boiss. & Hoh. (2)
Turkey
E Med + SW Asian
USDA Pullman PI 545661
EF379077
EF378976
EF379028
Lolium persicum Boiss & Hoh. (3)
Georgia
E Med + SW Asian
USDA Pullman PI 314446
EF379078
EF378977
EF379029
Lolium remotum Schrank (1)
France
Eurosiberian
USDA Pullman PI 283611 82i
EF379079
EF378978
EF379030
USDA Pullman PI 233613
EF379080
EF378979
EF379031
USDA Pullman PI 545604 90i
EF379081
EF378980
EF379032
E Med + SW Asian
Lolium remotum Schrank (2)
Sweden
Eurosiberian
E Med + SW Asian
Lolium rigidum Gaud. (1)
Turkey: Saparozu
W Mediterranean
E Med + SW Asian
5
Lolium rigidum Gaud. (2)
Iran
W Mediterranean
USDA Pullman PI 239794
EF379082
EF378981
EF379033
ABY-BA 9166.1999U
EF379083
EF378982
EF379034
ABY-BA 9936.1999U
EF379084
EF378983
EF379035
JACA 61195 P. Montserrat
EF379085
EF378984
EF379036
USDA Pullman PI 197310 82i
EF379086
-
-
USDA Pullman PI 195000
EF379087
USDA Pullman PI 302664
EF379088
EF378986
EF379038
USDA Pullman PI 477121
EF379089
EF378987
EF379039
USDA Pullman PI 545635 90i
EF379090
E Med + SW Asian
Lolium rigidum Gaud. (3)
France
W Mediterranean
E Med + SW Asian
Lolium rigidum Gaud. (4)
France
W Mediterranean
E Med + SW Asian
Lolium rigidum Gaud. (5)
Spain
W Mediterranean
E Med + SW Asian
Lolium rigidum Gaud. (6)
Argentina (introduced)
W Mediterranean
E Med + SW Asian
Lolium temulentum L. (1)
Ethiopia
Eurosiberian
EF378985
EF379037
E Med + SW Asian
Lolium temulentum L. (2)
India
Eurosiberian
E Med + SW Asian
Lolium temulentum L. (3)
Germany
Eurosiberian
E Med + SW Asian
Lolium temulentum L. (4)
Turkey
Eurosiberian
EF378988
EF379040
E Med + SW Asian
x Festulolium Asch. & Graebn.
Festulolium braunii (Richt.) Camus
Spain: Lerida
Eurosiberian
JACA 80158
EF379092
-
-
Festulolium holmbergii (Dörfl.) Fourn.
France
Eurosiberian
JACA P. Auquier s.n.
EF379091
EF378989
EF379041
Spain: Huelva: Almonte
W Mediterranean
UZ J.A. Lopez Rodriguez s.n.
AF532943
AF533037
Micropyropsis Romero-Zarco et Cabezudo
Micropyropsis tuberosa Rom.-Zarco &Cabez.
EF379013
Other Broad-leaved Festuca
6
Festuca sect. Subbulbosae Nyman ex Hack.
Festuca paniculata (L.) Schinz & Thell.
France: Mont Aigoual
W Mediterranean
UZ P. Catalan s.n.
AF303407
AF533046
DQ336858
Festuca durandoi Clauson
Spain: Segovia: Riaza
W Mediterranean
UZ J.A. Lopez Rodriguez 6.6.00
AF543514
AF533047
Festuca ovina L.
Germany: Thuringen
Eurosiberian
UZ J. Müller 6879
AF532959
AF533063
DQ367406
Festuca rubra L. (1)
Rumania (Cultivar UK)
Eurosiberian
UZ P. Catalan s. n.
AF303422
AY118098
-
Festuca rubra L. (2)
Switzerland: Valais: Desses
Eurosiberian
UZ J. Müller 8060
AF118088
AY118099
DQ336857
Spain: Zaragoza: Zaragoza
Eurosiberian
UZ P. Catalan 14.2000
AF393012
AF488773
DQ367407
USA: Colorado
Eurosiberian
UZ P. Catalan 730.93
AF532929
AF533026
DQ631507
USA (cultivar)
E Med + SW Asian
UZ P.Torrecilla P. Catalan s.n.
AF303400
AF478501
DQ336856
Slovenia: Ljubljana
W Mediterranean
UZ P.Torrecilla P. Catalan s.n.
AF303399
AF478500
DQ336855
EF378990
Fine-leaved Festuca
Festuca subgen. Festuca
Less related outgroups
Poa L.
Poa infirma Kunth
Deschampsia Beauv.
Deschampsia cespitosa (L.) Beauv.
Secale L.
Secale cereale L.
Brachypodium P. Beauv.
Brachypodium distachyon (L) P. Beauv.
E Med + SW Asian
7
Table S2 Dispersal rate matrices reflecting the palaeogeographic connectivity among
the study areas in each historical scenario (time slices TSI, TSII, TSIII). Areas: (A)
Eurosiberia; (B) Eastern Mediterranean
and
Southwest
Asia;
(C) Western
Mediterranean; (D) Atlas (continental north-western Africa); (E) Eastern and Western
Tropical Africa; and (F) Macaronesia.
TSI Late Miocene: Tortonian (11–7 Ma)
A
B
C
D
E
F
A
-
0.5
0.5
0.1
0.1
0.1
B
0.5
-
0.5
0.1
0.1
0.1
C
0.1
0.5
-
0.1
0.1
0.5
D
0.1
0.1
0.1
-
0.5
0.5
E
0.1
0.1
0.1
0.5
-
1.0
F
0.1
0.1
0.5
0.5
-
TSII Late Miocene: Messinian–early Pliocene (7–3.5 Ma)
A
B
C
D
E
F
A
-
0.5
0.5
0.5
0.5
0.1
B
0.5
-
1.0
1.0
1.0
0.1
C
0.5
1.0
-
1.0
0.5
1.0
D
0.5
1.0
1.0
-
0.7
1.0
E
0.5
1.0
0.5
0.7
-
0.5
F
0.1
0.1
1.0
1.0
0.5
-
8
TSIII Mid Pliocene–present (3.5–0 Ma)
A
B
C
D
E
F
A
-
1.0
1.0
0.5
0.1
0.1
B
1.0
-
0.7
0.1
0.1
0.1
C
1.0
0.7
-
0.7
0.1
1.0
D
0.5
0.1
0.7
-
0.5
1.0
E
0.1
0.1
0.1
0.5
-
0.1
F
0.1
0.1
1.0
1.0
0.1
-
9
Table S3 Numeric results from independent and combined maximum parsimony (MP)
and maximum likelihood (ML) phylogenetic analyses of nuclear ITS, cpDNA and
combined ITS+cpDNA data of the Schedonorus–Lolium group (ML analysis was
conducted only on the combined dataset).
Dataset
ITS
cpDNA
ITS+cpDNA
Total characters
654
1907
2561
Informative characters
147
214
361
Number of taxa
72
59
58
Number of MPTs found
31951
2945700
8552
Length (L)
510
789
1292
Consistency index (CI)
0.72
0.73
0.71
Retention index (RI)
0.84
0.69
0.74
Likelihood value (−Ln)
-
-
-10340.033710
MPT = most parsimonious trees.
10
Appendix S2: Expanded Materials and Methods
(a) Phylogenetic inference
Maximum parsimony (MP) analysis was conducted in
PAUP*
4.0 beta10 (Swofford,
2002), using two heuristic strategies: (1) Mulpars on, closest and tree bisection–
reconnection (TBR) branch swapping, and (2) 10,000 random-order-entry trees, TBR
and saving no more than 10 trees of length equal or shorter than 10 per replicate. A
strict and a 50% majority rule consensus tree were computed from the most
parsimonious trees obtained in these searches. Branch support was estimated through
1000 bootstrap replicates using the TBR-M (tree bisection–reconstruction swapping,
MULPARS OFF) strategy of DeBry & Olmstead (2000). Potentially informative
gaps were coded as binary characters and used in the MP analyses. Maximum
likelihood (ML) analysis was conducted in RAxML 7.2.8 (Stamatakis, 2006;
http://phylobench.vital-it.ch/raxml-bb/index.php), Stamatakis et al. (2008), using the
GTR nucleotide substitution model and leaving the program to estimate the model
parameters. Bootstrap support values were based on 100 rapid replicates using a
GTRMIX model. Bayesian inference (BI) analyses were performed in MRBAYES
v.3.2.1 (Ronquist et al., 2012). First, MRMODELTEST 2.3 (Nylander, 2004) was used
to select the optimal nucleotide substitution model for each marker, based on the
Akaike information criterion (AIC); a GTR model with a gamma parameter to
account for among-site rate variation and a proportion of invariant sites (GTR+G+I)
was selected for all markers. Two parallel runs with four coupled chains each were
run for 5 million generations, sampling every 1000 generations. Convergence and
mixing of the Markov chain Monte Carlo (MCMC) was assessed using the effective
sampling size (ESS > 200) criterion in TRACER v. 1.6 and by monitoring cumulative
split frequencies in MRBAYES. Post-burn-in samples (approximately 7500 trees)
were pooled into a 50% majority rule consensus tree to approximate the posterior
distribution of the phylogeny.
(b) Estimating lineage divergence times
Phylogenetic dating was performed using the Bayesian relaxed-clock model
implemented in
BEAST
v.1.5.2 (Drummond and Rambaut 2007) in the reduced
combined ITS-cpDNA dataset. Bayes factor comparisons were used to select the best
11
clock model (strict versus uncorrelated lognormal) and tree prior model (Yule versus
birth–death). The ucld.mean was assigned a uniform prior distribution of upper = 10E4; lower = 10E-1, initial value = 10E-4). The rest of the parameters were assigned
default prior distributions (exponential: ucld.stdev, gamma priors for parameters of the
substitution model). Two MCMC chains were run for 10 million generations, sampling
parameters every 1000 generations. We used TRACER to verify stationarity and
convergence among chains, and the ESS values were > 200 for all parameters. Postburn-in trees were summarized into a maximum clade credibility tree (MCC) with mean
values and 95% confidence intervals for nodal ages, using TREEANNOTATOR v. 1.6.1.
BEAST
found an intermediate level of substitution rate variation across the sampled
sequences (e.g. marginal posterior probability of the coefficient of variation of rates:
mean = 0.526; 95% highest posterior density (HPD) interval = (0.319, 0.738) and no
evidence of rate autocorrelation between neighbouring branches (e.g. marginal posterior
probability of rate covariance (mean = 0.009; 95% HPD interval = (−0.195, 0.209),
supporting the choice of an uncorrelated clock over the strict molecular clock. All
secondary calibration points were assigned a normal prior distribution with mean and
95% confidence intervals obtained from the more inclusive analysis, following Ho &
Phillips (2009).
REFERENCES
DeBry, R.W. & Olmstead, R.G. (2000) A simulation study of reduced tree-search effort
in bootstrap resampling analysis. Systematic Biology, 49, 171-179.
Drummond, A.J., Ho, S.Y.H., Rawlence, H.N. & Rambaut, A. (2007) A rough guide to
BEAST 1.4. Available at: http://beast.bio.ed.ac.uk/Main_Page (accessed 15th August
2012).
Ho, S.Y. & Phillips, M.J. (2009) Accounting for calibration uncertainty in
phylogenetic estimation of evolutionary divergence times. Systematic Biology, 58,
367-80.
Nylander, J.A. (2004) MrModeltest v2. Program distributed by the author.
Evolutionary Biology Centre, Uppsala University, Uppsala.
12
Ree, R.H. & Smith, S.A. (2008) Maximum likelihood inference of geographic range
evolution by dispersal, local extinction, and cladogenesis. Systematic Biology, 57, 4–14.
Ronquist, F., Teslenko, M., van der Mark, P., Ayres, D.L., Darling, A., Höhna, S.,
Larget, B., Liu, L., Suchard, M.A., Huelsenbeck, J.P. (2012) MrBayes 3.2: efficient
Bayesian phylogenetic inference and model choice across a large model space.
Systematic Biology, 61, 539–542.
Stamatakis, A. (2006) RAxML-VI-HPC: maximum likelihood-based phylogenetic
analyses with thousands of taxa and mixed models. Bioinformatics, 22, 2688-90.
Stamatakis, A, Hoover, P. & Rougemont, J. (2008) A rapid bootstrap algorithm for the
RAxML Web servers. Systematic Biology, 57, 758-71.
Swofford, D.L. (2002) PAUP*: phylogenetic analysis using parsimony and others
methods. Version 4.0. beta test. Sinauer, Sunderland, MA.
13
Appendix S3: Supplementary figures
Figure S1 Maximum parsimony analysis: 50% majority-rule consensus tree of 8552
MP trees found in the heuristic search of the combined ITS+cpDNA dataset (n = 58
sequences) of the Schedonorus–Lolium complex plus outgroup taxa. Brachypodium
distachyon was used to root the tree. Numbers above branches correspond to bootstrap
support values.
14
Figure S2 (a) Maximum likelihood analysis: optimal ML tree (−ln = −10340.0337)
found in the heuristic RAXML search of the combined ITS+cpDNA dataset (n = 58) of
the Schedonorus–Lolium complex plus outgroup taxa. Brachypodium distachyon was
used to root the tree. Numbers above branches correspond to bootstrap support values.
15
Figure S2 (b) Bayesian inference analysis (MRBAYES): 50% majority-rule consensus
tree of 7500 trees from the post-burn-in posterior distribution obtained from the
Bayesian analysis of the combined ITS+cpDNA sequences (n = 58) of the
Schedonorus–Lolium complex plus outgroup taxa. Brachypodium distachyon was used
to root the tree. Numbers correspond to nodal posterior probability support values.
16
Figure S3 Divergence time estimation (BEAST): maximum clade credibility (MCC) chronogram obtained from the analysis of the combined
ITS+cpDNA dataset (n = 57, F. arundinacea excluded) of the Schedonorus–Lolium complex plus outgroup taxa (Brachypodium distachyon was
pruned from the tree). Numbers correspond to the estimated mean nodal ages.
17
Figure S4 Effect of uneven sampling effort across species on divergence time estimations. Ages of key nodes in the phylogeny estimated with
BEAST
by randomly removing infraspecific samples from the original dataset to create new reduced datasets with one/two/or three individuals per
species, representing 30% (21 taxa), 70% (35 taxa), 90% (44 taxa) of the original number of sequences. The logarithmic lines reflect the expected
development with the addition of more infraspecific sampling. Node numbers as in Fig. 5. The table above the figure shows the original data used
for the diagram, and compares it with age node statistics calculated from the original dataset (all taxa included).
Percentage of taxa included
Node 50
Node 51
Node 97
Node 90
Node 52
Node 53
Node 83
Node 54
Node 55
Node 73
Node 56
Node 57
Node 68
Mean
21one1
21one2
35two1
35two2
35two5
44three1 44three2 44three5 Original
10.4931
10.4237
10.3918
10.432
10.5702
10.5504
10.4801
10.5483
10.545
9.3992
9.3057
9.415
9.2869
9.1607
9.2254
9.2989
9.229
9.1844
2.5613
2.4702
2.5091
2.4827
2.5309
2.524
2.516
2.501
2.6427
4.4669
4.7477
4.6446
4.8877
4.9007
4.8754
4.8813
4.9102
4.9341
5.3754
5.3033
5.5363
5.3753
5.6127
5.8244
5.498
5.7495
5.769
4.5367
4.4341
4.7486
4.5245
4.8289
5.0816
4.7593
4.9871
5.1844
3.6361
3.7168
3.6564
3.5572
3.9036
3.9552
3.7592
3.9247
3.982
3.8415
3.7
4.0721
3.8083
4.1272
4.3304
4.0271
4.2614
4.407
3.5145
3.3813
3.7832
3.5357
3.7882
3.995
3.7493
3.9069
4.1067
2.1025
2.3128
2.5227
2.3937
2.5541
2.7372
2.5842
2.619
2.8828
3.2365
3.0279
3.4779
3.1792
3.4313
3.6435
3.3763
3.566
3.729
2.1802
1.3446
2.2858
2.2943
2.4596
2.6764
2.2551
2.5878
2.7785
1.5579
1.7715
2.1229
2.4572
1.8002
2.0284
2.8661
1.9706
3.1317
4.3770615 4.3030462 4.5512615 4.4780538 4.5898692 4.7267154
4.6193 4.6739615 4.8674846
12
Estimated ages based on original dataset
Mean
10.545
9.1844
2.6427
4.9341
5.769
5.1844
3.982
4.407
4.1067
2.8828
3.729
2.7785
3.1317
Lowe r bound Uppe r bound
8.2086
13.062
7.0434
11.3932
0.963
5.3575
2.8932
7.091
3.8455
8.1062
3.4326
7.2008
2.8922
2.68
1.6387
2.4279
1.7072
1.916
6.2886
5.8157
4.1563
5.3578
4.0522
4.6416
Ages of key nodes estimated from reduced matrices
18
4.5367
3.6361
3.8415
3.5145
2.1025
3.2365
2.1802
1.5579
4.3770615
4.4341
4.7486
3.7168
3.6564
3.7
4.0721
3.3813
3.7832
2.3128
2.5227
3.0279
3.4779
1.3446
2.2858
1.7715
2.1229
4.3030462 4.5512615
4.5245
3.5572
3.8083
3.5357
2.3937
3.1792
2.2943
2.4572
4.4780538
4.8289
3.9036
4.1272
3.7882
2.5541
3.4313
2.4596
1.8002
4.5898692
5.0816
3.9552
4.3304
3.995
2.7372
3.6435
2.6764
2.0284
4.7267154
4.7593
3.7592
4.0271
3.7493
2.5842
3.3763
2.2551
2.8661
4.6193
4.9871
3.9247
4.2614
3.9069
2.619
3.566
2.5878
1.9706
4.6739615
5.1844
3.982
4.407
4.1067
2.8828
3.729
2.7785
3.1317
4.8674846
5.1844
3.982
4.407
4.1067
2.8828
3.729
2.7785
3.1317
3.4326
7.2008
2.8922
2.68
1.6387
2.4279
1.7072
1.916
6.2886
5.8157
4.1563
5.3578
4.0522
4.6416
Ages of key nodes estimated from reduced matrices
12
Node 50
10
Node 51
Node 97
8
Node 90
Node 52
Age (Ma)
Node 53
Node 83
Node 54
Node 55
Node 73
Node 56
Node 57
Node 68
Mean
Node 53
6
Node 54
Node 55
Node 73
4
Node 56
Node 57
Node 68
2
All Combined
Logarítmica
(Node 50)
0
0
2
4
6
8
10
12
Percentage of taxon deletion
14
16
18
Logarítmica
(Node 51)
Logarítmica
(Node 97)
Logarítmica
(Node 90)
19
Figure S5 Biogeographical scenarios for the Schedonorus–Lolium complex inferred by
the LAGRANGE unconstrained M1 model plotted onto the
Fig.
4).
Pie
chart
legends
correspond
to
BEAST
those
MCC chronogram (see
indicated
in
Fig.
5.
C F paniculata
C F durandoi
C F fenas3 7
C F fenas1
C F fenas12
C F corsica11
D F mairei
D F atlantigena10
D F atlantigena14
D F letournexiana13
CD F fontqueri
C M tuberosa
AB F gigantea1
AB F gigantea3
AB F gigantea4
A F apennina
A F apennina15
AB F pratensis2
AB F pratensis1
E F simensis3
E F simensis2
E F simensis1
B L persicum3
B L persicum2
B L persicum1
AB L temulentum1
AB L remotum1
AB L remotum2
AB L temulentum2
AB L temulentum4
AB L temulentum3
F L canariense3
F L edwardii1
F L edwardii2
F L canariense1
F L canariense4
F L canariense5
AB L perenne2
AB L perenne3
AB L perenne1
AB L multiflorum2
AB L multiflorum3
AB L multiflorum4
AB L multiflorum1
BC L rigidum1
BC L rigidum2
BC L rigidum4
BC L rigidum3
BC L rigidum5
20