Supporting Information
Appendix S1. Current and Tertiary tree genus occurrences
Base dataset
We listed the present and fossil occurrence of tree genera (>8m maximum vegetative height) in the four
temperate forest regions of the northern hemisphere (Table S1), using appendix 26.1 of Latham and Ricklefs1
as a starting point. Genera were regarded as currently present in a region if represented by at least one typical
moist temperate forest tree species. We re-evaluated the present occurrences of all genera and applied a few
changes (Cupressus: no characteristic temperate forest trees in Europe and North America; Juniperus,
Pistacia and Kalmia: no characteristic temperate forest trees in Europe; Vaccinium: characteristic temperate
forest trees in East-central Asia; Yucca and Serenoa: no characteristic temperate forest trees in any region).
We also updated the taxonomy (Table S1). Finally, we conducted an extensive search for additional fossils
using palaeobotanical literature2-5 and the Paleobiology Database (http://paleobiodb.org). From the latter,
data were downloaded for all genera on 4 February, 2014, using the group name 'paleobotany' and the
following parameters: time interval = 65−2.6 Ma, continents (modern) = Europe + Asia + North America.
The records were then filtered manually to retain only those from within our study regions. The combined
literature and database search allowed us to add 78 fossil occurrences not listed by Latham and Ricklefs1.
The complete dataset used in our analyses is shown in Table S1.
Sensitivity analysis
Analyses based on fossils are always faced with uncertainties concerning fossil discovery and precise
identity. The presence of a fossil is a certain sign that a taxon was present but lack of fossils is no proof that
the taxon was not there; fossils might simply not have been found (false absence). To bracket this uncertainty
we used a conservative “fossil only” version of the dataset where Tertiary presence was recorded only where
fossils had been found (i.e., all absences were assumed to be true absences), and an "inferred fossil" version
where all genera that are present in a region today were assumed to have been present in the Tertiary, too
(Latham & Ricklefs 1993).The latter rests on the assumption that there has been no migration among the
regions within the past 2.6 Mya. Both assumptions are unlikely to be true, but they represent different
extremes. Of note, this approach focuses entirely on extinction and explicitly excludes the origin of new
genera, or migration of genera among regions, during the Quaternary. However, the fossil record and
phylogenetic studies suggest that these processes have been absent or very rare in temperate trees in the
Quaternary 2,6. Furthermore, fossils may represent non-tree members of a genus, or outlier populations of
species that are not characteristic for the moist temperate forest biome. To address that uncertainty we used a
“strict flora” version of the dataset where only characteristic temperate tree species were included in the
present floras, and a “liberal flora” version where genera were included in the present flora of a region even
if only represented by shrubs or marginal populations of species that otherwise occur outside the temperate
forest biome1. Thus, in total, four different combinations of the data were analysed: “fossil only – strict
flora”, “fossil only – liberal flora”, “inferred/fossil – strict flora”, and “inferred/fossil – liberal flora”. All
results presented in the main manuscript are based on the “inferred/fossil – strict flora” version; the other
results gave similar results and can be found in the Supplementary Information.
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Appendix S3. Exploring the effects of geographic and phylogenetic bias in the fossil record
Paleontological data are associated with a range of biases1,7. The probability of finding fossils is
geographically variable, depending on past conditions for fossilisation and present outcropping of relevant
strata in the regions of interest. Moreover, fossilisation or detection probability may depend on species' traits,
which may be related to phylogeny. We conducted several analyses of the fossil dataset to test for such
biases. In our dataset, the proportion of contemporary genera that are present in the Tertiary fossil record
varies among regions (Europe: 90%, Eastern Asia: 71%, Western North America: 89%, Eastern North
America: 58%). Assuming that currently present genera were also present in the Tertiary (see Appendix S1),
this is a crude indicator of the likelihood to recover fossils of Tertiary flora. Similarly, the number of relevant
fossils listed in the Paleobiology Database shows large regional variation (Europe: 2,682, Eastern Asia: 627,
Western North America: 136, Eastern North America: 112). This variation indicates that estimates of genus
loss may be biased by the likelihood of recovering fossils of genera that were present in the Tertiary, but are
absent today (Fig. S8a). However, randomly adding Tertiary occurrences proportional to the differences in
detection probability did not qualitatively change our results (Fig. S11c), probably because the most extreme
values are from regions with high putative detection probability (Europe and Asia). Moreover, detection
probability appeared to be unrelated to phylogeny. Measures of phylogenetic structure should only be biased
if detection probability is related to phylogeny. Genera with a low detection probability in the fossil record
(e.g. due to young age, small population sizes, or morphological or ecological features that decrease
fossilisation probability) should be more likely to be detected in regions with many fossils, such as Europe. If
detection probability is related to phylogeny, this non-random detection of fossils may change the
phylogenetic structure of the Tertiary flora, which serves as the genus pool in our phylogenetic structure
calculations. However, detection probability, approximated by the number of fossils listed in the
Paleobiology Database (Fig. S11B), was unrelated to phylogeny (Table S4).
Table S1: Present and fossil (65−2.6 Mya) occurrence of tree genera in Europe, East-central Asia, Pacific
North America, and Eastern North America (as defined in Fig. 1). Unless indicated otherwise by footnotes,
all occurrences are from R.E. Latham & R.E. Ricklefs (1993) Continental comparisons of temperate-zone
tree species diversity. P. 294−314 in: R.E. Ricklefs & D. Schluter (eds.) Species diversity in ecological
communities. University of Chicago Press, Chicago. “P” indicates genera that “do not attain tree height or [..]
rarely occur in the region’s flora, but do inhabit an adjoining biome and are characteristic members of moist
temperate tree floras in another region” (Latham & Ricklefs, 1993).
Northern,
central, and
eastern Europe
Order
Family
Genus
Fossil
Ginkgoales
Pinales
Ginkgoaceae
Cupressaceae
Ginkgo
Calocedrus
Chamaecyparis
Cryptomeria
Cunninghamia
Cupressus
Glyptostrobus
Juniperus
Metasquoia
Platycladus
Sequoia
Sequoiadendron
Taiwania
Taxodium
Thuja
Thujopsis
Abies
Keteleeria
Larix
Picea
Pinus
Pseudolarix
Pseudotsuga
Tsuga
Sciadopitys
Taxus
Torreya
Cephalotaxus
Illicium
Actinodaphne
Cinnamomum
Lindera
Litsea
Machilus
Neolitsea
Nothaphoebe
Persea
Phoebe
Sassafras
Umbellularia
Asimina
Liriodendron
Magnolia
Manglietia
x
x
x
x2,3
x
x3
x
x3
x
Pinaceae
Sciadopityaceae
Taxaceae
Austrobaileyales
Laurales
Magnoliales
Schisandraceae
Lauraceae
Annonaceae
Magnoliaceae
Present
East-central
Asia
Fossil
x
P
x
x
x
x
P
x
x
x
x
x
x
x
x
x
x
x2,3
x
x
x
x
x
x
x3
x3
x
x
x
x
x
x
x3,5
x
x
x
x
x
x
x5
x3
x
x
x
x
x
x
x
x
x
x3
x
x
x
x
x
x
x
x
x
Fossil
Present
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
Eastern North
America
Fossil
x
x
P
Pacific slope of
North America
x
x
Present
Present
x1
x
x
x
x3
x
x
x
x
x
x
x
x
x
x
x
x
x
x1
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x4
x
x
x
x
x
x
x
x4
P
x
x
x
x
x
x
x
x
x
x
x
P
x
x1,3
x1
x
P
P
x1,3
x1,3
x
x
x
x
x
x
x
x
x
x
x
x
x1,3
x
x
x
Sabiales
Fagales
Sabiaceae
Betulaceae
Fagaceae
Juglandaceae
Proteales
Ranunculales
Rosales
Myricaceae
Platanaceae
Eupteleaceae
Cannabaceae
Moraceae
Ulmeaceae
Saxifragales
Urticaceae
Altingiaceae
Cercidiphyllaceae
Daphniphyllaceae
Hamamelidaceae
Trochodendrales
Ericales
Trochodendraceae
Clethraceae
Cyrillaceae
Ebenaceae
Ericaceae
Myrsinaceae
Michelia
Meliosma
Alnus
Betula
Carpinus
Corylus
Ostrya
Castanea
Castanopsis
Cyclobalanopsis
Fagus
Lithocarpus
Quercus
Carya
Cyclocarya
Engelhardtia
Juglans
Platycarya
Pterocarya
Myrica
Platanus
Euptelea
Aphananthe
Celtis
Hemiptelea
Pteroceltis
Maclura*
Morus
Broussonetia
Ulmus
Zelkova
Planera
Oreocnide†
Altingia
Liquidambar
Cercidiphyllum
Daphniphyllum
Disanthus
Distylium
Fortuneria
Hamamelis
Loropetalum
Sinowilsonia
Tetracentron
Clethra
Cliftonia
Cyrilla
Diospyros
Arbutus
Elliottia
Enkianthus
Kalmia
Lyonia
Oxydendrum
Rhododendron
Vaccinium
Ardisia
Myrsine
x
x2,3
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
P
P
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x3
x
x3
x3
x
x
P
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
P
x
x
x
x
P
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x2
x
x
x
x
x
x
x
x
x
x
x
P
x1,3
x
x
x
x
x
x
x
x
x
P
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x1,3
x
x
x
x
x
x
x
x
P
x
x1,3
x
x
x
x
x
x
x5
x
x
x
x
x
x
x
x
x1
x
x
x
x1,3
x
x
x
x
x
x
x
x
x
x
x
P
x
x
x
x
x
x
x3
x
x2,3
x
x2,3
P
P
x
P
x
x
x6
x
x
x3
x
x
P
x
x
x
x
x
x
x
x
x
Sapotaceae
Styracaceae
Malpighiales
Symplocaceae
Salicaceae
Euphorbiaceae
Malvales
Malvaceae
Oxalidales
Theales
Elaeocarpaceae
Theaceae
Apiales
Aquifoliales
Buxales
Celastrales
Cornales
Crossosomatales
Fabales
Araliaceae
Torricelliaceae
Aquifoliaceae
Buxaceae
Celastraceae
Cornaceae
Hydrangeaceae
Staphyleaceae
Fabaceae
Garryales
Eucommiaceae
Garryaceae
Huerteales
Myrtales
Tapisciaceae
Lythraceae
Myrtaceae
Rhamnaceae
Rosales
Sideroxylon‡
Halesia
Pterostyrax
Styrax
Symplocos
Idesia
Poliothyrsis
Populus
Salix
Xylosma
Mallotus
Sapium
Firmiana
Tilia
Sloanea
Camellia
Franklinia
Gordonia
Stewartia
Ternstroemia
Eleutherococcus
Aralia
Dendropanax
Gamblea
Kalopanax
Schefflera
Torricellia
Ilex
Buxus
Euonymus
Alangium
Davidia
Nyssa
Cornus
Hydrangea
Staphylea
Turpinia
Cercis
Gleditsia
Albizia
Cladrastis
Dalbergia
Erythrina
Glymnocladus
Laburnum
Maackia
Ormosia
Robinia
Sophora
Eucommia
Aucuba
Macrocarpium
Tapiscia
Lagerstroemia
Szyzygium
Hovenia
Rhamnus
Ziziphus
x2
x
x5
x
x
x
x
x
x
x
x2
x
x3
x3
P
x
x
x
x
x2
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x3
x
x
x
x
x
x
x
x
x
x
x
x
x
x2
x2
x
x
x3
x
x
x
x
x3
x
x
x
x3
x
x
x
x
x
x
x3
x
x
x
x
x
x
x
x
x
x
x
x
x
x
P
x
x
x
x
x
x
x
x
x
x
P
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
P
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x1
x
x
x
x5
x
x5
x
x
x1,3
x
x
x
x1
x
x
x
x
x
x
x
P
x
x1,3
x
x
x3
x
x
x
x
x
x
x
x2
x
x
x
x
x
x
x2,3
x2,3
P
x
x
x
x1,3
x
x
x
x
x
x
x
x
x
x
x
x
x
P
x
P
x
x
x
x
Rosaceae
Santalales
Sapindales
Schoepfiaceae
Anacardiaceae
Meliaceae
Rutaceae
Sapindaceae
Simaroubaceae
Dipsacales
Gentianales
Lamiales
Adoxaceae
Rubiaceae
Bignoniaceae
Boraginaceae
Lamiaceae
Oleaceae
Arecales
Poales
1
Arecaceae
Poaceae
Amelanchier
Chaenomeles
Crataegus
Eriobotrya
Malus
Mespilus
Photinia
Prunus
Pyrus
Sorbus
Schoepfia
Choerospondias
Cotinus
Pistacia
Rhus
Toxicodendron
Cedrela
Phellodendron
Ptelea
Tetradium
Zanthoxylum
Acer
Aesculus
Dipteronia
Koelreuteria
Sapindus
Leitneria
Ailanthus
Picrasma
Sambucus
Viburnum
Adina
Cephalanthus
Emmenopterys
Pinckneya
Randia
Catalpa
Paulownia
Ehretia
Clerodendrum
Premna
Chionanthus
Forestiera
Fraxinus
Ligustrum
Osmanthus
Syringa
Sabal
Trachycarpus
Arundinaria
Phyllostachys
Semiarundinaria
x
x
x
x
x3
x
x
x
x
x
x
x3
x
x
x
x
x
x3
x
P
P
x
x
x3
x2,3
x3
x
x3
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x3
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
P
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x1
x
x
x
P
x
x
x
x
x
x
x
x5
x
x
x
x1,3
x
x
x
x
x3
x
x
x
x
x3
x1
x
x
x
x
x
x
x
x
x
x2,3
x
x
x2
x
x3
x
x
x
x2,3
x
x
P
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x3
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x
x1
x
x
Graham (1999), 2 Mai (1995), 3 The Paleobiology Database, 4 LePage & Basinger (1995), 5 Manchester et
al. (2009), 6 eFloras (2014), * including Cudrania, † as Villebrunea in Latham & Ricklefs (1993), ‡ as
Bumelia in Latham & Ricklefs (1993)
Table S2: Node ages8 used for calibrating the dated phylogenetic tree using the BLADJ algorithm9.
Node
Age [mya]
Node
Age [mya]
Spermatophyta
gymnosperms
Pinopsida
angiosperms
magnoliids
Magnoliales
Magnoliaceae
Manglietia/Magnolia
Sassafras/Cinmomum
Yucca
Arecales/Poales
Euptelea
Tetracentron
core-eudicots
Schoepfia
asteriids
Cornales
Alangium/Cornus
Ericales
Myrsiceae
Theales
Styraceae
Clethraceae
campanulids/lamiids
campanulids
Sambucus/Viburnum
lamiids
Garryales
Lamiales/Gentiales
Lamiales
Lamiaceae/Bignoniaceae
rosids/Saxifragales
Saxifragales
Altingiaceae
Hamamelidaceae
rosids
Sapindales/Malvales
Sapindales
Sapindaceae/Meliaceae
Sapindaceae
Sapindus/Koelreuteria
Aesculus/Acer
Simaroubaceae
fabids
Celastrales
Oxalidales/Malpighiales
Idesia
Salix/Populus
Fabales/Fagales
Fabales
Fagales/Rosales
Fagales
Fagus/Quercus
Alnus/Betula
299.4
187.8
158
172.7
140.5
62.4
36
11.13
13.4
113.4
106.7
144.2
139.2
133.5
126.1
115.7
86.3
67.3
90.5
82.1
69.5
37.6
57
107.5
73.7
32.9
104.1
76.6
91.5
74
60.8
128
103
7.3
18.3
118.1
98.9
67.7
64.2
35.6
26.7
25.1
53.7
109.6
103.3
102.4
47.9
31.1
98.9
62.7
95.8
55.5
31.2
19.5
Carya/Juglans
Rosales
Prunus/Photinia
Rhamceae
Ulmaceae
Morus/Celtis
4.4
84.9
33.3
75.9
66.3
51.3
Table S3: Net Relatedness index of present angiosperm/gymnosperm tree floras in temperate Europe, Asia,
Western North America, and Eastern North America, compared to their respective Tertiary floras.
marginal genus
fossils included
actual
inferred
fossils
fossils
Angiosperms
Europe
Asia
W North America
E North America
Gymnosperms
Europe
Asia
W North America
E North America
5.59 ***
1.21
1.26
0.28
0.88
-1.30
0.83
1.31
6.05 ***
0.92
1.82 *
0.56
0.87
-1.31
0.86
1.18
marginal genus
fossils excluded
actual
inferred
fossils
fossils
5.73 ***
1.15
1.42
0.75
1.00
-0.96
0.86
1.47
6.16 ***
0.93
1.95 *
1.11
1.03
-0.99
0.84
1.10
Table S4: Phylogenetic signal in detection probability (measured as relative frequency of fossils in the
Paleobiology Database). P-values are based on the variance of Phylogenetically Independent Contrasts
(phylosignal function in Picante).
Group
all genera
Angiosperms only
Gymnosperms only
Blomberg’s K
0.15
0.19
0.54
P
0.46
0.58
0.27
Figure S1: Phylogenetic tree of all genera listed in Table S1, based on APGIII10 with modifications.
Figure S2: Regional extinction and cold tolerance. Rank cold tolerance plots of tree genera in the Tertiary
floras of northern hemisphere forest areas. A−D: Angiosperms, E−H: Gymnosperms. A, E: Europe; B, F:
Eastern Asia; C, G: Western North America; D, H; Eastern North America. Only genera with cold tolerance
data from the Palaeoflora database are shown. Genera shown in red have survived to the present in the given
region, while genera shown in black are regionally extinct.
A
B
Figure S3: Phylogenetic signal (Pagel's λ) of cold tolerance and the frequency of regional extinction,
respectively, across angiosperm (A) and gymnosperm (B) genera. The density plots show the null
expectation of λ, the arrows indicate the observed values of lambda for cold tolerance ("cold") and the
frequency of regional extinction (ɛ).
A
B
C
D
Figure S4: Regional phylogenetic trees of Gymnosperms in the temperate forest biomes of Europe (A),
Eastern Asia (B), Western North America (C) and Eastern North America (D). Genera in red have survived
to the present.
A
B
C
D
Fig. S5: Relationship between lost genus diversity (intensity of extinction) and increase of phylogenetic
relatedness with four different versions of the data. A: fossil only – liberal flora, B: fossil only – strict flora,
C: inferred/fossil – liberal flora, D: inferred/fossil – strict flora.
A
B
C
D
Figure S6: Null distribution (histogram) and observed slope (red line) of the relationship between genus
diversity loss (δG) and change in phylogenetic relatedness (δMPD). Black lines indicate the 95%, 99%, and
99.9% quantiles of the null distribution. A: Angiosperms, fossil only, B: Angiosperms, inferred/fossil, C:
Gymnosperms, fossil only, D: Gymnosperms, inferred/fossil. A−D: liberal flora.
A
B
C
D
Figure S7: Null distribution (histogram) and observed slope (red line) of the relationship between genus
diversity loss (δG) and change in phylogenetic relatedness (δMPD). Black lines indicate the 95%, 99%, and
99.9% quantiles of the null distribution. A: Angiosperms, fossil only B: Angiosperms, inferred/fossil, C:
Gymnosperms, fossil only, D: Gymnosperms, inferred/fossil. A−D: strict flora.
A
B
Fig. S8: Null distribution (histogram) and observed slope (red line) of the relationship between genus
diversity loss (δG) and change in Faith's Phylogenetic Diversity (δPD). Black lines indicate the 95%, 99%, and
99.9% quantiles of the null distribution. A: Angiosperms, strict flora - inferred/fossil. B: Gymnosperms,
strict flora - inferred/fossil.
A
B
Figure S9: Hypothetical consequences of cold-driven extinction on the phylogenetic structure of
contemporary temperate tree floras relative to their Tertiary predecessors. In this scenario, the percentage of
extinct genera is as in the observed dataset; however, species are removed in the order of increasing cold
tolerance, so that only the most cold-tolerant species remain. A: Net Relatedness Index (***: P<0.001, *:
P<0.05). B: Relationship between extinction intensity (δG) and relative increase of phylogenetic relatedness
among the survivors (δMPD). For comparison, the regression lines from observed extinction events are shown
as dotted lines. The black dotted square outlines the scale of Figure 3B (main text) for comparison.
B
10 20 30 40 50 60 70
loss of genus diversity [%]
A
60
65
70
75
80
85
90
% current genera in fossil record
0.05
0.15
Angiosperms
Gymnosperms
-0.05
Increase in phyl. relatedness (
MPD)
C
0.0
0.2
0.4
0.6
Loss of genus diversity(
0.8
G)
Fig. S10: A: Relationship between the proportion of contemporary genera also known as fossils (a measure
of fossil detection probability, assuming no migration among regions since the end of the Tertiary) and the
proportion of genera lost during or after the Tertiary (a measure of intensity of extinction). B: Rankfrequency distribution of genera in the Paleobiology Database. C: Same analysis as in Figure 2B and S4A,
but after random addition of extra Tertiary fossils proportional to the differences in detection probability
(measured as % current genera in fossil record). Points show mean δMPD and δG values across 1000 random
additions of fossils; error bars show the range, tick marks the standard deviation. Regression lines are based
on mean values.
Supplementary references
1
2
3
4
5
6
7
8
9
10
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