Huang, S., Eronen, J., Janis, C., Saarinen, J., Silvestro, D., & Fritz, S. (2017).Mammal body size evolution in North America and Europe over 20 Myr:similar trends generated by different processes. Proceedings of the RoyalSociety B: Biological Sciences, 284(1849), [20162361].https://doi.org/10.1098/rspb.2016.2361

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Mammal body size evolution in North America and Europe over 20 million years: 1

Similar trends generated by different processes 2

3

Shan Huang1,*, Jussi T. Eronen2, 3, Christine M. Janis4, Juha J. Saarinen2, 5, Daniele 4

Silvestro6, Susanne A. Fritz1,7 5

6

1Senckenberg Biodiversity & Climate Research Centre (BiK-F), Frankfurt am Main, 7

Germany; 8

2Department of Geosciences and Geography, University of Helsinki, Helsinki, Finland; 9

3BIOS Research Unit, Helsinki, Finland; 10

4Department of Ecology and Evolutionary Biology, Brown University, Providence, USA; 11

5Natural History Museum, London, UK; 12

6Department of Biological and Environmental Sciences, University of Gothenburg, 13

Gothenburg, Sweden; 14

7Institute of Ecology, Evolution and Diversity, Goethe University, Frankfurt am Main, 15

Germany. 16

17

*e-mail address: shan.huang@senckenberg.de 18

19

20

ABSTRACT 21

Because body size interacts with many fundamental biological properties of a species, body 22

size evolution can be an essential component of the generation and maintenance of 23

biodiversity. Here we investigate how body size evolution can be linked to the clade-specific 24

diversification dynamics in different geographic regions. We analyze an extensive body size 25

dataset of Neogene large herbivores (covering ~50% of the 970 species in the orders 26

Artiodactyla and Perissodactyla) in Europe and North America in a Bayesian framework. We 27

reconstruct the temporal patterns of body size in each order on each continent independently, 28

and find significant increases of minimum size in three of the continental assemblages (except 29

European perissodactyls), suggesting an active selection for larger bodies. Assessment of 30

trait-correlated birth-death models indicates that the common trend of body size increase is 31

generated by different processes in different clades and regions. Larger-bodied artiodactyl 32

species on both continents tend to have higher origination rates, and both clades in North 33

America show strong links between large bodies and low extinction rate. Collectively, our 34

results suggest a strong role of species selection and perhaps of higher-taxon sorting in 35

driving body size evolution, and highlight the value of investigating evolutionary processes in 36

a biogeographic context. 37

38

Keywords: species body mass, diversification, biogeography, species selection, Cope’s rule, 39

higher-taxon sorting. 40

41

42

Body size has been considered one of the most important traits of an organism, a species or 43

higher taxon, because it co-varies with a wide range of morphological, physiological, and 44

ecological traits [1-3, 4 and references therein]. Therefore, the study of broad-scale spatial and 45

temporal patterns of body size, central to ecology and evolutionary biology, can shed light 46

onto underlying processes shaping biodiversity patterns [5, 6], for which the rich body of 47

literature on body size biology provides a solid basis. Here, we present a cross-continent 48

investigation of the temporal dynamics of species body size in relation to the means of 49

generation and maintenance of biodiversity over 20 million years (myr). 50

Large-scale assessments comparing a range of taxa often found a variety of 51

trajectories of body size evolution, including directional changes, stasis, and range expansion 52

to contain both larger and smaller sizes through time [4, 7-11]. Particularly in the geologic 53

past, many taxa evolved to have larger bodies, a pattern referred to broadly as Cope's rule, 54

often coinciding with a cooling climate [12-15]. The current and projected climate change and 55

human impact are thus anticipated to cause higher stress for large-bodied species [16-18] and 56

lead to general dwarfism of the present-day fauna [19]. However, a spatially-explicit 57

framework has been suggested essential for sensible prediction [20, 21], and the variation in 58

patterns calls for mechanistic explanations and a deeper understanding of the 59

macroevolutionary processes behind body size change through time. 60

Several different macroevolutionary processes can generate an increasing trend of 61

body size through time. If body size is generally irrelevant to diversification processes of 62

lineages, the temporal pattern of body size should mimic a diffusive process, perhaps 63

asymmetrically bounded by a limit on the minimum size for a viable animal body (a passive 64

evolutionary process) [4, 22-24]. This passive process gives rise to an increasing maximum, 65

and if given enough time, an increasing median body size without raising the minimum. In 66

contrast, more active evolutionary processes like species selection (general correlation of 67

body size with species origination and/or extinction rates), higher-taxon sorting (turnover of 68

higher taxa with different body sizes), and a within-lineage tendency of smaller ancestors 69

giving rise to larger descendants (Cope’s rule in a strict sense) should affect the minimum 70

body size of a clade and diversification processes at relevant scales [4, 22-25]. Assessments of 71

the relationship between body size and diversification processes cannot rely on molecular 72

phylogenies alone, because separating changes in speciation and extinction is difficult without 73

including the extinct lineages [26, 27]. The fossil record serves as a direct window to the long 74

history of biodiversity, and can thus provide an excellent opportunity for investigating 75

evolutionary processes [e.g. 12, 13, 28-30]. Specifically in Cenozoic mammals, Raia et al. 76

attributed apparent size increases in several clades to frequent expansions into new niches 77

favoring large bodies, with the finding of generally later appearances of larger-bodied clades 78

in the fossil record [12]. Within closely related species pairs, however, large-bodied species 79

appeared earlier in the fossil record than their small-bodied relatives in the same geographic 80

region, rejecting the hypothesis of within-lineage evolution towards larger sizes but also 81

raising the question of potential sampling bias against small bodies in older fossils at a fine 82

scale. The context-related heterogeneity shown in their findings invites further investigation 83

of clade-specific dynamics in a biogeographic context. 84

In this study, we investigate whether clade-specific body size variation can be 85

associated with differential origination and/or extinction rates, and can thus be directly linked 86

to the clade-specific diversification dynamics in different geographic regions. We focus on 87

the two extant orders of ungulates, Artiodactyla and Perissodactyla, which have an excellent 88

fossil record of their high diversity throughout the Neogene (around 23–2 million years ago; 89

Ma), allowing a cross-clade, cross-region comparison of evolutionary processes. To derive 90

robust results from the fossil record, we analyze our paleontological data in a Bayesian 91

framework that accounts for the heterogeneous preservation potential. We analyze the two 92

orders separately in two major continental faunas, Europe and North America (thus four 93

groups of continental assemblages in total). We expect an apparent increase of body size in all 94

four of our focal groups with a backdrop of climate cooling during the Neogene [12, 13, 31, 95

32], and we further distinguish whether this trend is generated by a bounded diffusive process 96

or by an active evolutionary process due to selection for large-bodied species. To explain the 97

active process suggested in some groups, we further investigate whether large bodies were 98

selected through elevated origination rate and/or reduced extinction rate (i.e. species 99

selection), whether family/subfamily replacements could have contributed to substantial body 100

size changes (i.e. higher-taxon sorting), and/or whether there is a within-genus tendency of 101

larger species appearing later than smaller species (i.e. strict Cope’s rule). 102

103

Materials and methods 104

We combined data of 6432 fossil occurrences for 970 ungulate species (Orders: Artiodactyla 105

and Perissodactyla) from two sources for Europe (the NOW database [33]) and North 106

America [34, 35] respectively (see figure S1 for sample locations and [36] for a standardized 107

and taxonomically unified dataset), throughout the last ~21 myr, excluding the last ~2 myr 108

(after Gelasian). The geologic ages (reported in Ma) of all fossil data are based on the 109

continental time units for each continent: the Mammal Neogene (MN) units for European 110

occurrences (as followed by the NOW database for their European data [37]), and the North 111

American Land Mammal Ages (NALMAs) for the North American occurrences [38]. We 112

complemented the body mass data available from the initial data sources (NOW and [34, 35]) 113

with additional estimates from the published literature and measurements from museum 114

collections (average across specimen when multiple were measured). Specimen-specific 115

dating was usually not possible for considering temporal intra-specific variation. Our final 116

dataset contains species-level average body mass for 483 of the included species (~50%) (data 117

used in our analyses available at: [Senckenberg data archive address available once the 118

manuscript is accepted]). Despite the common belief that fossil data tend to be more complete 119

close to the Recent, we did not find such bias in our data (see figure S2 and statistics in the 120

figure caption). In addition, an increase of body size towards Recent is the opposite 121

expectation of a biased fossil record – small-bodied animals are more likely to be 122

underrepresented in older, poorly sampled fossil collections but more abundant in the younger 123

record [39, 40]. To assess potential sampling bias against small-bodied species within the two 124

focal orders, we also included preservation rate in our models and tested for a correlation with 125

body size (see below). 126

We analyzed the fossil data in a Bayesian framework to simultaneously estimate the 127

origination and extinction times of each species, the preservation rate (the average expected 128

number of fossil records per species per myr), and parameters of a birth-death model 129

describing the diversification dynamics of an entire clade including correlation of body mass 130

with origination and extinction rates (expected number of origination/extinction events per 131

lineage per myr) using the Python program PyRate [41, 42]. For each order in each 132

continental fauna, we generated 99 replicate datasets to sample random occurrences within 133

the geological time bins [following the procedure in 41, 43], and with each of these 99×4 134

datasets, we ran 10 million iterations (excluding the additional 50,000 burn-in iterations), 135

using Birth-Death Markov Chain Monte Carlo to sample the parameters from their posterior 136

distribution for a covar birth-deadth model of the correlation of body size (!) with the 137

preservation rate (#), origination rate ($) and extinction rate (%; see more details of the 138

methods in ESM). Because we are interested in the first-order processes generating the 139

temporal trend of body size in a biogeographic context, we do not distinguish in-situ 140

origination and extinction from range dynamics (i.e. invasion from outside the focal region 141

and regional extinction due to emigration). However, the long duration and coarse temporal 142

resolution examined here probably decreases impacts of short-term range dynamics. 143

To compare body size patterns with higher taxa replacement, we reconstructed 144

temporal patterns of relative diversities in families (in Artiodactyla) and subfamilies (in 145

Perissodactyla) using the origination and extinction times estimated from the PyRate analyses. 146

To test for within-genus tendency of body size increase from older to younger species, we fit 147

linear mixed-effect models to the relationship between species body size and their order of 148

origination (fixed effect), with genus assignment as a random effect. We compared three 149

models for each group (Artiodactyla and Perissodactyla in Europe and North America) based 150

on AIC: one model with genus effect on the intercepts, one on the slopes, and one on both. 151

Without further evidence from a phylogenetic analysis, a positive correlation between body 152

size and order of origination within a genus can be considered partial support for the tendency 153

of smaller ancestors giving rise to larger descendants. 154

The PyRate analyses were conducted in Python 2.7 (available at 155

http://www.python.org). All additional analyses and data visualizations were conducted in R 156

3.2.2 [44], with the package CODA [45] for summarizing MCMC iteration logs and the 157

packages lme4 [46] and lmerTest [47] for testing and interpreting linear models with mixed 158

effects. 159

160

Results 161

We summarized the body size distribution of species in each geologic time bin (using the 162

continent-specific geologic time scales, see Methods) based on the estimated species 163

origination and extinction times (summarized in: [Senckenberg data archive address available 164

once the manuscript is accepted]) for each order in Europe and North America respectively 165

(thus four groups in total), as well as in a combination of the two regions (figure 1 and S3; 166

table 1). In North America, both Artiodactyla and Perissodactyla increased significantly in 167

minimum body size through time, although only artiodactyls showed a significant increase of 168

median size. However, comparisons of artiodactyl family and perissodactyl subfamily 169

diversities show no consistent replacement of smaller-bodied clades by larger ones (figure 2). 170

In the Neogene of Europe, only artiodactyls increased significantly in minimum, 171

median and maximum body size (table 1), which coincided with apparent declines of several 172

small-bodied families (e.g. Tragulidae, Moschidae, and Cainotheriidae), diversity increase of 173

the larger-bodied Bovidae, and arrivals of even larger hippos and camels (figure 2). European 174

perissodactyls only expanded their range of body size to include a larger maximum over time 175

(table 1). Compared with the other groups, European perissodactyl species already had 176

relatively large bodies owing to the large diversity of rhinos and chalicotheres (figure 2) at the 177

beginning of the Neogene (figure 1 and S3), and as a group, remained large throughout 178

Neogene despite the rises and falls seen in different subclades (figure 2); the lack of 179

significant trend in body size is also apparent at the family level (figure S4). When we 180

combined the two regional faunas, our results suggest significant increases in both minimum 181

and maximum body size, masking the variation between regional patterns (table 1). 182

Although similar trends of increasing body size are shared between the continental 183

faunas, we found different relationships between body size and diversification dynamics 184

among the groups we examined. In the North American fauna, larger body sizes were 185

associated with significantly lower extinction rates in both Artiodactyla (mean !% = -0.16) 186

and Perissodactyla (mean !% = -0.21, although the credible interval’s upper bound falls 187

slightly above 0 at 0.005), and with significantly higher origination rates in Artiodactyla 188

(mean !$ = 0.21; see the posterior distributions in figure 3 and effects illustrated in figure 4). 189

Neither of the groups showed a correlation between body size and preservation rate. Among 190

European artiodactyl species, larger bodies are also strongly associated with higher 191

origination rates (mean !$ = 0.20), as well as lower preservation rates (mean !# = -0.33), an 192

unexpected pattern opposite from the commonly assumed sampling bias against small-bodied 193

animals (see Discussion). 194

For all four groups we examined for within-genus relationship between species body 195

size and origination order, the model including a random effect of genus on the intercept was 196

always the best model, although the differences in AIC were marginal (table S1). Based on 197

the best models, we found no correlation between species body size and order of origination 198

within a genus in any of the groups (p ³ 0.20; table S1). 199

200

Discussion 201

We find significant increases in minimum, median, and/or maximum body size in all four 202

focal groups (artiodactyls and perissodactyls in North America and Europe), but this common 203

trend seems to have been generated by different processes in different groups and regions. 204

Three groups (except European perissodactyls) show significant increases in minimum size 205

through time, so their overall body size trends are generated by selection for large bodies, 206

rather than a bounded diffusive process. Our finding of significant correlations of body size 207

with speciation rate (positively) in Artiodactyla on both continents, but with extinction rate 208

(negatively) in both orders in the North American fauna, further supports the idea of a driven 209

evolution towards larger body sizes through species selection, and highlights phylogenetic as 210

well as regional differences in evolutionary processes. The turnover of higher taxa, especially 211

the temporal variation in relative diversities of families in European Artiodactyla, also plays a 212

role in driving the body size patterns. The fourth group, the European perissodactyls, 213

maintained their large sizes throughout the Neogene, except for a temporary drop of their 214

median size with the rise of the Equinae. Notably, the maximum body size in this group 215

increased through time (with the addition of several large rhino species), implying a diffusion-216

like process bounded by selection against smaller sizes. We found no evidence of consistent 217

within-genus evolutionary trends towards larger bodies, thus no support for the strict-sense 218

Cope’s rule to be the dominant process of body size evolution. 219

Further sampling effort for fossil data is unlikely to alter the patterns, as our analyses 220

did not find larger bodies associated with higher preservation rates in any of our groups. In 221

only one group, the European artiodactyls, we found larger bodies to be associated with lower 222

preservation rates, a trend opposite from the expectation of large bodies to be overrepresented 223

in the fossil record [39, 40, 48, 49]. Larger bodies also coincide with lower population density 224

in the extant artiodactyl species that are classified as Least Concern in terms of extinction risk 225

by the IUCN Red List (Spearman’s r = -0.24, p =0.043, n = 93 species, data from [20]; see 226

also [50]), which might have reduced the chance of entering the fossil record [48, 51]. 227

Capturing this trend is probably a signal of extensive sampling for the European fauna. The 228

trend of body size increase towards the present in this group can only change if additional 229

large species had been under-sampled so far and were added into the beginning of our focal 230

time period, i.e. Early-Mid Miocene (by ~12 myr ago). Such addition is highly unlikely given 231

the already higher coverage of body size data for the European species in our dataset (57% 232

artiodactyls and 58% perissodactyls, compared with 38% and 42% respectively in North 233

America). Nevertheless, adding large species to the Early-Mid Miocene cannot change the 234

pattern of increasing minimum body size in European Artiodactyla, and thus cannot reject the 235

hypothesis that larger bodies were preferentially generated in this group. 236

The link between larger bodies and higher origination rates in mammals has been 237

suggested by previous studies examining multiple clades collectively based on fossil body 238

size [12] or based on inferred body size from extant relatives [52], but we only find this link 239

in Artiodactyla. In addition, we also find that both of our focal clades tend to have lower 240

extinction rates for larger-sized species in North America, contradicting previous results [12, 241

52]. In other words, while baseline extinction rates tend to increase towards the Recent (Fig. 242

S5), the elevation of extinction rate affected small-sized species more strongly than large 243

ones. Previous studies hypothesized that adopting new life styles, and thus entering new niche 244

space, allowed some large-bodied lineages to rapidly diversify, implying a role of higher-245

taxon sorting [12, 15, 53, 54]. Our results indicate that this process might be specific to 246

artiodactyls, which show consistently higher origination rates of large-bodied species on both 247

continents. Comparisons of artiodactyl family diversities also show expanding of some large-248

bodied families (e.g. Hippopotamidae and Camelidae) and the thriving of Bovidae in Europe, 249

but little obvious change in North America except for the expansion of Camelidae in the 250

Pliocene (figure 2). However, the niche-opening hypothesis cannot explain the removal of 251

small-bodied species (indicated by the increase in minimum body size and declines of small-252

bodied families such as Tragulidae, Moschidae, and Cainotheriidae in Europe), especially in 253

North America where the lower extinction rate in large-bodied artiodactyls and perissodactyls 254

is more likely to be related to survivorship in face of reportedly less productive habitats since 255

Late Miocene [55, 56] within the continent’s biogeographic setup (see below). Large bodies 256

are evidently associated with (a) capability of tracking suitable conditions due to longer 257

dispersal distance [2] and larger geographic ranges [57, 58], and (b) relaxation of 258

physiological constraints due to larger gut size (especially the hindgut in the case of 259

perissodactyls) for digesting larger quantities of low-nutrient plant materials [59] and larger 260

volume-to-surface ratio for preserving energy [2] and thus improving fasting endurance [60, 261

61], all of which can contribute to resisting extinction. 262

Variation exists not only between the two clades, but also between the two focal 263

regions we examine, suggesting different mechanisms generated the apparently similar trend 264

of body size increase shared by regions. Compared with the European fauna, the North 265

American fauna shows stronger signals of extinction rate in driving body size evolution of 266

both clades we examine. One important biogeographic distinction between the two continents 267

is that, before the initial rise of the Isthmus of Panama at ~6 Ma [62], North America lacked a 268

southern pathway for frequent migration out of the region and later return. The tapering shape 269

of the North American continent also contributes to restricting dispersal towards lower 270

latitudes while the climate transitioned to a colder state. With changes in physical conditions 271

as well as biotic interactions, North American species might be more prone to selective 272

extinction than European species, where more dynamic ranges are possible with access to 273

surrounding regions. Spatial dynamics can thus be another key process shaping the 274

evolutionary history of body size and macroevolutionary patterns in general [30, 55, 63, 64]; 275

comparisons of its role with those of in-situ origination and extinction in further investigation 276

will be valuable. Further, metabolic theory predicts that large bodies are favored in colder 277

climates in various environmental scenarios [13, 14, 19, 54, 65], so that an increase of body 278

size in both temperate regions is not surprising along a generally cooling trajectory of the 279

global climate during the Neogene [32, 66, 67]. However, there is substantial heterogeneity of 280

the climatic conditions across space at all times [56, 68-70], and the resulting 281

appearance/disappearance of habitats (e.g. mid-latitude savannas) can affect faunal 282

composition greatly. It is also possible that body size was not the only trait that was selected 283

for but was entangled in a composite morphological and functional evolution, especially traits 284

tightly related to interaction with the ever-changing environments, and we propose a future 285

direction of assessing how traits interact to play different roles in driving diversification 286

dynamics in different environments. 287

As discussed above, higher-taxon sorting might also have contributed to shaping the 288

body size trends, but the patterns shown here are more complex than clear. In particular, 289

North American perissodactyls show increases in minimum and (marginally) maximum body 290

size but not in the median, suggesting a change in the shape of their size distribution through 291

time rather than a systematic tendency towards larger bodies (a pattern more likely for 292

artiodactyls, shown in figure 1 and S3). The replacement (in terms of relative diversities) of, 293

for example, the generally smaller-bodied subfamily Anchitheriinae by the larger Equinae, 294

might contribute to shaping the patterns in this group, but Anchitheriinae as a clade also 295

appears to have increased in body size through time to an extent that Late Miocene 296

anchitheres were larger than the contemporaneous equines in North America (figure S4). 297

Further, the increase in body size of the smaller-bodied subfamilies (Equinae, Anchitheriinae, 298

and the family Tapiridae) might have contributed to the general increase in minimum body 299

size of North American Perissodactyla throughout the record. There are also other taxa 300

turnover patterns that complicate the picture, such as the early disappearance of the large-301

bodied subfamily Schizotheriinae from the region by Mid-Miocene and the persistence of the 302

generally small-bodied Equinae (figure 2 & S4). The variety of temporal trajectories for 303

family body size shown in figure S4 suggest that within an order, the families might have 304

undergone different evolutionary processes, but species selection might still be an important 305

mechanism in family body size evolution given the general negative correlation between body 306

size and extinction rates, and the lack of evidence for a strict Cope’s rule. Further 307

distinguishing (and comparing) the roles of cross-clade species selection and higher-taxon 308

sorting in shaping the larger-scale body size evolutionary pattern is difficult with current data 309

(the coverage is less satisfactory when analyzed at the family or subfamily level), but a 310

fruitful next step will be rigorous analyses using fossil phylogenies to investigate the 311

phylogenetic distributions of origination and extinction events in relation to phenotypic 312

evolution in similar biogeographical contexts. 313

314

Conclusion 315

A general trend of increasing body size through time is frequently found and discussed in 316

mammalian studies, although not without exceptions [4, 12, 13]. Results from this study 317

suggest species selection and potentially higher-taxon sorting are the most likely driving 318

mechanism for active evolution of larger body size. Passive evolution, a diffusive process 319

bounded by the minimum requirement, is also supported in one group, the European 320

Perissodactyla. The variety of patterns and processes we have identified in the Neogene 321

ungulates from Europe and North America, and others found in different study systems [e.g. 7, 322

10, 14], points to the importance of scale for studying macroevolutionary dynamics [71]. 323

More importantly, similar macroevolutionary trends shared among clades in different regions 324

might actually be generated by different processes – even one single trait (i.e. body size, 325

though admittedly a composite one) can associate with the origination and extinction rates 326

differently across clades and regions, perhaps even differently at different levels of the 327

taxonomic hierarchy [63, 71]. As evolution takes place within the biogeographic setup, 328

apparent patterns are products of the interaction between the focal clade and the regional 329

environment, including the regional topography, climatic conditions, and other biotic 330

components such as vegetation and infectious disease in the system [55, 72, 73]. Therefore, 331

both the clade’s biology and regional environment must be considered to fully understand the 332

evolution of body size, and in general, macroevolutionary patterns [74-76]. 333

334

Data accessibility 335

The data with the average body mass, estimated origination time and estimated extinction 336

time for each species are available at [Senckenberg data archive address available once the 337

manuscript is accepted]. 338

339

Authors’ contributions 340

S.H., J.T.E. and S.A.F. designed the study; S.H., J.J.S. and C.M.J. collected data; S.H., D.S. 341

and S.A.F. performed analyses; S.H. wrote the first draft of the manuscript; all authors 342

contributed to interpretation of data and revisions. 343

344

Competing interests 345

We declare we have no competing interests. 346

347

Funding 348

S.H. is supported by Alexander von Humboldt Foundation through a postdoc fellowship. 349

J.T.E. was supported by Kone Foundation during this work. J.S. was funded by Oskar 350

Huttunen Foundation, Helsinki, Finland (year 2015) and by Jenny and Antti Wihuri Fund, 351

Helsinki, Finland (year 2016). D.S. received funding from the Swedish Research Council 352

(2015-04748). S.F. is funded by the DFG (German Research Foundation grant FR 3246/2-1). 353

This article is a contribution to the integrative Climate Change Biology (iCCB) programme. 354

355

Acknowledgement 356

We thank C. Weiland at the Senckenberg Data Center for technical assistance with the cluster 357

server, the Böhning-Gaese working group at Senckenberg BiK-F for discussion at various 358

stages of the project, and collection accesses (and assistance by personnel in parentheses) at 359

Natural History Museum of Vienna, Austria (U. Göhlich); Natural History Museum, London, 360

UK (A. Currant and P. Brewer); Torquay Museum, Torquay, UK (B. Chandler and C. Jones); 361

British Geological Survey, Nottingham, UK (L. Neep and P. Shepherd); Sedgwich Museum 362

(M. Riley) and University Museum of Zoology (M. Lowe), Cambridge, UK; Staatliches 363

Museum für Naturkunde, Stuttgart, Germany (R. Ziegler); Staatliches Museum für 364

Naturkunde, Karlsruhe, Germany (D. Schreiber); Research Station of Quaternary 365

Palaeontology of the Senckenberg Institute, Weimar, Germany (R.-D. Kahlke); National 366

Museums of Kenya, Nairobi, Kenya (M. Muungu), and Field Natural History Museum (W. F. 367

Simpson). We also thank F. Smith and two anonymous reviewers for constructive comments. 368

369

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Table and figure legends

Table 1 Temporal trends of body size of Artiodactyla and Perissodactyla in Europe and North

America. The relationship between body size and time to Recent is tested using Spearman’s

rank-order correlation test (n = 14 time bins for all cases); a negative correlation indicates an

increase of body size towards Recent. The combined data set is based on the European

geologic time scale, but results are qualitatively consistent when using the North American

time scale. The number of species with body size data (N) is given for each order on each

continent. Results are qualitatively consistent with Bonferroni correction of the p-values

except for the maximum size in European Artiodactyla (adjusted-p = 0.09).

Body size variables

Artiodactyla Perissodactyla All

combined Europe

(N = 223)

North America (N = 101)

Combined Europe (N = 86)

North America (N = 72)

Combined

Minimum r = -0.973 p < 0.001

r = -0.982 p < 0.001

r = -0.935 p < 0.001

r = -0.103 p = 0.727

r = -0.837 p < 0.001

r = -0.837 p < 0.001

r = -0.935 p < 0.001

Median r = -0.998 p < 0.001

r = -0.844 p < 0.001

r = -0.987 p < 0.001

r = -0.330 p = 0.250

r = -0.198 p = 0.497

r = -0.068 p = 0.816

r = -0.952 p < 0.001

Maximum r = -0.550 p = 0.042

r = -0.987 p < 0.001

r = -0.987 p < 0.001

r = -0.827 p < 0.001

r = -0.485 p = 0.079

r = -0.955 p < 0.001

r = -0.965 p < 0.001

Figure 1 Temporal trends of body size of Artiodactyla and Perissodactyla in Neogene Europe

(left) and North America (right), based on their species’ origination and extinction times

estimated in PyRate analyses (excluding species without body size data). Lines indicate

median size in each time bin and color shades represent the 25%-75% quantiles for between-

clade comparisons. See statistical results of the trends in Table 1 and full range of body size

through time in Figure S3. Geologic epochs (Early-, Mid-, and Late-Miocene, and Pliocene)

following the time scale by Gradstein et al [77] are indicated for reference.

Figure 2 Temporal patterns of relative diversity (proportion of species) in artiodactyl families

(upper) and perissodactyl subfamilies (lower) in relation to the median body size of their

species, ordered (for both the polygons and the legends) as increasing in size from the bottom

(i.e. larger-bodied families are towards the top). Family (and subfamily) duration are based on

their species’ origination and extinction times estimated in PyRate analyses. Color similarity

loosely illustrates the commonly assumed phylogenetic relationship among the families and

subfamilies (see caption for Figure S4 for taxonomic details), with the same color scheme

applied in Europe [left] and North America [right]. Families and subfamilies without any

species body size data are indicated with an asterisk (*), and the white space represents

species without sufficient information for family assignment (position not indicative of their

body size). See Figure S4 for the temporal trend of family or subfamily median body size.

Figure 3 Posterior distributions of the correlation parameter estimates (Covar model)

between body size and three rates: origination rate (!$, left), extinction rate (!%, middle) and

preservation rate (!#, right) in Artiodactyla and Perissodactyla in Europe and North America

respectively. Solid lines indicate the mean estimate and color-filled bars represent the 95%

credible intervals.

Figure 4 The differential origination (white) and extinction rates (grey) in relation to

variation in body size in Artiodactyla and Perissodactyla in Europe and North America

respectively, illustrated using the highest rates during the Neogene (based on the mean

temporal trajectory of all posterior rates from the PyRate analysis, see figure S5) as the

baseline rates ($0 and %0). The baseline rates were then corrected for lineages sized at the

10% and 90% quantiles of all body sizes (b10 and b90, in Kg) in each group, based on the

posterior distribution of the correlative parameters (shown in figure 3) from the Covar model.

Therefore, the bars representing the corrected rates show that artiodactyls of different sizes

are expected to have different origination rates ($10 and $90) in on both continents (the upper

row) and different extinction rates (%10 and %90) in both clades in North America (the left

column). Origination rate of larger-sized artiodactyls could be twice as high as small-sized

ones in Europe.

20 15 10 5Geologic Time (Ma)

PlioLate−MioMid−MioEarly−MioNorth America

Artiodactyla Perissodactyla

20 15 10 5Geologic Time (Ma)

PlioLate−MioMid−MioEarly−Mio

Europe4

6

8

10

log 2

Bod

y m

ass

(Kg)

4

6

8

10

15 10 50.0

0.2

0.4

0.6

0.8

1.0

Geologic Time (Ma)

Prop

ortio

nal d

ivers

ityN. American Artiodactyla

Entelodontidae*Hypertragulidae*Gelocidae*LeptomerycidaeMoschidaeAntilocapridaeCervidaeBovidaeMerycoidodontidaeTayassuidaeDromomerycidaeProtoceratidaeCamelidaeAnthracotheriidae

Increasing median body size

15 10 50.0

0.2

0.4

0.6

0.8

1.0

Geologic Time (Ma)

Prop

ortio

nal d

ivers

ity

European Artiodactyla

Hoplitomerycidae*Haplobunodontidae*CainotheriidaeAndegamerycidaeMoschidaePalaeochoeridaeSanitheriidaeTragulidaeCervidaeBovidaeSuidaeCamelidaePalaeomerycidaeAnthracotheriidaeGiraffidaeHippopotamidae

Increasing median body size

15 10 50.0

0.2

0.4

0.6

0.8

1.0

Geologic Time (Ma)

Prop

ortio

nal d

ivers

ity

N. American Perissodactyla

AnchitheriinaeTapiridaeEquinaeMenoceratinaeDiceratheriinaeAceratheriinaeSchizotheriinaeTeleoceratinae

Increasing median body size

15 10 50.0

0.2

0.4

0.6

0.8

1.0

Geologic Time (Ma)

Prop

ortio

nal d

ivers

ity

European Perissodactyla

AnchitheriinaeTapiridaeEquinaeMenoceratinaeAceratheriinaeChalicotheriinaeSchizotheriinaeTeleoceratinaeRhinocerotinaeElasmotheriinae

Increasing median body size

Den

sity

(%)

−0.6 −0.4 −0.2 0.0 0.2 0.4 0.60

1

2

3

4

5North AmericanArtiodactyla

Den

sity

(%)

−0.6 −0.4 −0.2 0.0 0.2 0.40

1

2

3

4

5

Den

sity

(%)

−3 −2 −1 0 1 2 30.0

0.5

1.0

1.5

2.0

2.5

3.0D

ensi

ty (%

)

−0.6 −0.4 −0.2 0.0 0.2 0.4 0.60

1

2

3

4North AmericanPerissodactyla

Den

sity

(%)

−0.6 −0.4 −0.2 0.0 0.2 0.40

1

2

3

Den

sity

(%)

−3 −2 −1 0 1 2 30.0

0.5

1.0

1.5

2.0

2.5

Den

sity

(%)

−0.6 −0.4 −0.2 0.0 0.2 0.4 0.60

1

2

3

4 EuropeanArtiodactyla

Den

sity

(%)

−0.6 −0.4 −0.2 0.0 0.2 0.40

2

4

6

8

Den

sity

(%)

−3 −2 −1 0 1 2 30

1

2

3

Den

sity

(%)

−0.6 −0.4 −0.2 0.0 0.2 0.4 0.60

1

2

3EuropeanPerissodactyla

Den

sity

(%)

−0.6 −0.4 −0.2 0.0 0.2 0.40

1

2

3

Den

sity

(%)

−3 −2 −1 0 1 2 30.00.51.01.52.02.53.03.5

Correlation with origination rate (αλ) Correlation with extinction rate (αµ) Correlation with preservation rate (αq)

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λ10 λ90 µ10 µ900

1

2

3

Size

cor

rect

ed ra

tes

North American Artiodactylaλ0 = 0.48µ0 = 0.83b10 = 16b90 = 441µ = mm

Origination (λ)Extinction (µ)

λ10 λ90 µ10 µ90

0.5

1.0

1.5

2.0

Size

cor

rect

ed ra

tes

European Artiodactylaλ0 = 0.35µ0 = 0.58b10 = 14b90 = 584µ = mm

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λ10 λ90 µ10 µ900.0

0.2

0.4

0.6

0.8

1.0

Size

cor

rect

ed ra

tes

North American Perissodactylaλ0 = 0.42µ0 = 0.75µ = mm

b10 = 81b90 = 1159µ = mm

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λ10 λ90 µ10 µ900.0

0.2

0.4

0.6

0.8

1.0

Size

cor

rect

ed ra

tes

European Perissodactylaλ0 = 0.36µ0 = 0.73b10 = 138b90 = 1688µ = mm

Electronic Supplementary Materials

Mammal body mass evolution in North America and Europe over 20 million years:

similar trends generated by different processes

Shan Huang1,*, Jussi T. Eronen2, 3, Christine M. Janis4, Juha J. Saarinen2, 5, Daniele

Silvestro6, Susanne A. Fritz1,7

1Senckenberg Biodiversity & Climate Research Centre (BiK-F), Frankfurt am Main,

Germany;

2Department of Geosciences and Geography, University of Helsinki, Helsinki, Finland;

3BIOS Research Unit, Helsinki, Finland;

4Department of Ecology and Evolutionary Biology, Brown University, Providence, USA;

5Natural History Museum, London, UK;

6Department of Biological and Environmental Sciences, University of Gothenburg,

Gothenburg, Sweden;

7Institute of Ecology, Evolution and Diversity, Goethe University, Frankfurt am Main,

Germany.

*e-mail address: shan.huang@senckenberg.de

Supplementary information on the PyRate analysis

This study presents a cross-continent investigation of the temporal dynamics of species body

size in relation to the means of generation and maintenance of biodiversity over 20 million

years (myr). We analysed the fossil data in a Bayesian framework using the Python program

PyRate [1, 2]. For each order in each continental fauna, we generated 99 replicate datasets to

sample random occurrences within the geological time bins [following the procedure in 1, 3],

and with each of these 99×4 datasets, we ran 10 million iterations (excluding the additional

50,000 burn-in iterations), using Birth-Death Markov Chain Monte Carlo to sample the

parameter distributions. We modeled preservation as a stochastic Poisson process, in which

the preservation rate is heterogeneous among species [2] and may change as a function of

body size. Two parameters were needed to define the preservation process: a baseline

preservation rate ! and a correlation parameter "! determining how preservation rate

correlates with body size across lineages. To assess the temporal trend of body size evolution

for each group, we summarized the overall body size distribution in each geologic time bin

using the absolute origination and extinction times estimated by PyRate and averaged over the

99 replicates. For each group, we tested for significant trend through time based on the

Spearman’s rank-order correlations of the minimum, median, and maximum body size with

the time to Recent (at the mid-point of each time bin).

To further assess the relationship between body size and the diversification history of

each clade on each continent respectively, we used the Covar birth-death model with

temporally variable rates described in [1] (also implemented in PyRate [1]). The Covar

analysis jointly estimates two forms of heterogeneity in the origination rate # and extinction

rate $: changes through time by implementing clade-wide rate shifts through time and

variation among lineages as a function of body size. Thus, the birth-death model implemented

in our PyRate analyses inferred 1) the temporal dynamics of origination and extinction rates

(baseline rates # and $) and 2) correlation parameters, "#and "$, that describe lineage-

specific deviations of origination and extinction rates respectively from the baseline rates due

to variation in body size. Correlation parameters for preservation ("!), origination ("#), and

extinction rates ("$) were assigned a normal prior distribution with mean m = 0 (i.e. no

correlation) and precision (1/variance) = τ. We treated τ as a free parameter with a gamma

hyperprior [τ ~ Γ(2,2)] and estimated it from the data, a very important procedure allowing

definition of informative priors based on the data, rather than on an arbitrary choice. We

evaluated the correlations between body size and the various rates based on the posterior

distribution from all iterations.

Supplementary tables & figures

Table S1 The relationship between species body size and origination order within each genus,

assessed in linear mixed-effect models. In addition to the fixed effect of origination order

(significance indicated by the p-value), we included genus assignment as a random effect on

the intercept (model 1), the slope (model 2) and both (assumed uncorrelated, model 3). Only

genera with more than 1 species are included, so that the sample sizes are different from the

number of species reported in Table 1 for each assemblage. Using AIC as the model

comparison criterion, model 1 is the best model (in bold) for all cases (AIC weights shown in

parentheses) and shows no evidence for Cope’s rule as the dominant process driving body

size evolution in any of the assemblages. The only signal of Cope’s rule is seen in model 2

(DAIC = 2 log units higher than in the best model) for Artiodactyla when its two continental

assemblages were combined, but inference of the whole-clade evolutionary scenario must be

made with caution considering the biogeographic barrier between the two continents.

Models

Artiodactyla Perissodactyla

Europe (N = 161)

North America (N = 41)

Combined (N = 202)

Europe (N = 59)

North America (N = 57)

Combined (N = 119)

Model 1 AIC = 379

(0.59) p = 0.20

AIC = 113 (0.57)

p = 0.71

AIC = 487 (0.54)

p = 0.17

AIC = 78 (0.62)

p = 0.25

AIC = 113 (0.62)

p = 0.75

AIC = 196 (0.45)

p = 0.14

Model 2 AIC = 381

(0.22) p = 0.07

AIC = 115 (0.21)

p = 0.47

AIC = 489 (0.20)

p = 0.03

AIC = 80 (0.23)

p = 0.33

AIC = 114 (0.28)

p = 0.93

AIC = 196 (0.39)

p = 0.23

Model 3 AIC = 381

(0.20) p = 0.20

AIC = 115 (0.23)

p = 0.71

AIC = 488 (0.26)

p = 0.17

AIC = 81 (0.15)

p = 0.62

AIC = 116 (0.10)

p = 0.89

AIC = 198 (0.16)

p = 0.31

Figure S1 The distribution of our fossil samples in North America (left) and Europe (right),

with a color gradient indicating species body mass (occurrences of species without body mass

data are in black). Slight noises were added to the georeferenced locations of all occurrences

to illustrate multiple samples from the same or nearby sites. Detailed location information can

be found in [4], originally compiled from [5] and [6] for North American occurrences and the

NOW database [7] for European occurrences.

−120 −100 −80 −70

10

20

30

40

50

60North America

Longitude (°)

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ude

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2.8

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●NA

log 1

0 Bod

y M

ass

(g)

Figure S2 The number of species based on recorded occurrences in each time bin (sampled

data, circles with solid lines) and based on species durations between first and last

appearances in the fossil record (inferred data, crosses with dashed lines). No correlation was

found between time to Recent and the difference between the two lines (p > 0.29 in

Spearman’s rank order correlation tests for all four cases). In addition, we report the number

of singletons (triangles with dotted lines) which indicates no temporal bias of sampling effort.

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20 15 10 50

10203040506070

Geologic time (Ma)

Num

ber o

f spe

cies Artiodactyla

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20 15 10 50

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Geologic time (Ma)

Num

ber o

f spe

cies Artiodactyla

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20 15 10 50

10

20

30

40

50

Geologic time (Ma)

Num

ber o

f spe

cies Perissodactyla

●

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20 15 10 50

10

20

30

40

Geologic time (Ma)

Num

ber o

f spe

cies Perissodactyla

North America Europe

● Sampled Inferred Singleton

Figure S3 Temporal patterns of body size (left) and species richness (right) based on the

origination and extinction times estimated in PyRate analyses. Only the focal time period is

represented here.

20 15 10 52

4

6

8

10

12

Time (Ma)

log 2

Bod

y m

ass

(Kg)

20 15 10 50

20

40

60

80

100

Time (Ma)

Num

ber o

f spe

cies

Artiodactyla in N. America

20 15 10 5

0

2

4

6

8

10

Time (Ma)

log 2

Bod

y m

ass

(Kg)

20 15 10 50

50

100

150

Time (Ma)

Num

ber o

f spe

cies

Artiodactyla in Europe

20 15 10 5

5

6

7

8

9

10

11

Time (Ma)

log 2

Bod

y m

ass

(Kg)

20 15 10 50

20

40

60

Time (Ma)

Num

ber o

f spe

cies

Perissodactyla in N. America

20 15 10 5

7

8

9

10

11

12

Time (Ma)

log 2

Bod

y m

ass

(Kg)

20 15 10 50

10

20

30

40

50

60

Time (Ma)

Num

ber o

f spe

cies

Perissodactyla in Europe

Median 25%−75% quantile Total range All species with body mass data

Figure S4 The temporal distribution of artiodactyl families and perissodactyl subfamilies

(except for Tapiridae which does not have subfamily splitting) in relation to their median

body size. Family (and subfamily) appearances and disappearances in the record are based on

their species’ origination and extinction times estimated in PyRate analyses, but only species

with body size data are included; the lines therefore might not represent the complete lifespan

of the family or subfamily. The colors correspond to the color scheme in Figure 2, loosely

indicating the commonly assumed phylogenetic relationship among families and subfamilies,

with the legend ordered to reflect the median body size in the record (increasing in size from

the bottom, i.e. larger-bodied families at the top, similar to figure 2). In Perissodactyla, the

subfamilies Teleoceratinae, Elasmotheriinae, Diceratherinae, Menoceratinae, Rhinocerotinae

and Aceratheriinae are in the family Rhinocerotidae; the Schizotheriinae and Chalicotheriinae

in the Chalicotheriidae; and the Anchitheriinae and Equinae in the Equidae. In the

Artiodactyla, the families Anthracotheriidae, Haplobunodontindae, Hippopotamidae and

Entelodontidae are distinctive from others and traditionally included in the suborder Suina;

20 15 10 5

Geologic Time (Ma)

Body

mas

s (K

g, s

cale

d in

log 2

)

4

16

64

256

1024

4096

PlioLate−MioMid−MioEarly−Mio

Artiodactyla in N. America

LeptomerycidaeMoschidaeAntilocapridaeCervidaeMerycoidodontidaeTayassuidaeDromomerycidaeProtoceratidaeCamelidaeAnthracotheriidae

20 15 10 5

Geologic Time (Ma)

Body

mas

s (K

g, s

cale

d in

log 2

)

4

16

64

256

1024

4096

PlioLate−MioMid−MioEarly−Mio

Artiodactyla in Europe

AndegamerycidaeMoschidaePalaeochoeridaeSanitheriidaeTragulidaeCervidaeBovidaeSuidaeCamelidaePalaeomerycidaeAnthracotheriidaeGiraffidaeHippopotamidae

20 15 10 5

Geologic Time (Ma)

Body

mas

s (K

g, s

cale

d in

log 2

)

4

16

64

256

1024

4096

PlioLate−MioMid−MioEarly−Mio

Perissodactyla in N. America

AnchitheriinaeTapiridaeEquinaeMenoceratinaeDiceratheriinaeAceratheriinaeSchizotheriinaeTeleoceratinae

20 15 10 5

Geologic Time (Ma)

Body

mas

s (K

g, s

cale

d in

log 2

)

4

16

64

256

1024

4096

PlioLate−MioMid−MioEarly−Mio

Perissodactyla in Europe

AnchitheriinaeTapiridaeEquinaeMenoceratinaeAceratheriinaeChalicotheriinaeSchizotheriinaeTeleoceratinaeRhinocerotinaeElasmotheriinae

the Tayassuidae, Suidae, Sanitheriidae, and Palaeochoeridae in the Suoidea within the Suina;

the Camelidae, Protoceratidae, Merycoidodontidae and Cainotheriidae in the Tylopoda; the

Tragulidae, Hypertragulidae, Leptomerycidae and Andegamerycidae are in the Tragulina

within the Ruminantia; and the Dromomerycidae, Gelocidae, Bovidae, Cervidae,

Antilocapridae, Moschidae, Giraffidae and Palaeomerycidae are in the Pecora within the

Ruminantia.

Figure S5 Temporal patterns of clade-wide baseline origination (#) and extinction ($) rates of

Artiodactyla (upper) and Perissodactyla (lower) in Neogene Europe (left) and North America

(right), until 3 million years ago (Ma). Solid lines represent the mean in each million-year

interval, and shaded area indicate the 95% credible interval. The PyRate analysis also allows

variation among lineages (see Supplementary information for methods), which was modeled

in relation to body size and is illustrated in Figure 4.

20 15 10 50.0

0.5

1.0

1.5

2.0

Geologic Time (Ma)

Rate

s

20 15 10 50.0

0.2

0.4

0.6

0.8

Geologic Time (Ma)

Rate

s

20 15 10 5

0.2

0.4

0.6

0.8

1.0

Geologic Time (Ma)

Rate

s

20 15 10 5

0.5

1.0

1.5

Geologic Time (Ma)

Rate

s

OriginationExtinction

North America EuropePerissodactyla

Artiodactyla

Additional references

1. Silvestro D., Salamin N., Schnitzler J. 2014 PyRate: a new program to estimate

speciation and extinction rates from incomplete fossil data. Methods in Ecology and Evolution

5(10), 1126-1131. (doi:10.1111/2041-210X.12263).

2. Silvestro D., Schnitzler J., Liow L.H., Antonelli A., Salamin N. 2014 Bayesian

estimation of speciation and extinction from incomplete fossil occurrence data. Syst Biol.

(doi:10.1093/sysbio/syu006).

3. Silvestro D., Antonelli A., Salamin N., Quental T.B. 2015 The role of clade

competition in the diversification of North American canids. Proc Natl Acad Sci USA

112(28), 8684-8689. (doi:10.1073/pnas.1502803112).

4. Fritz S.A., Eronen J.T., Schnitzler J., Hof C., Janis C.M., Mulch A., Böhning-Gaese

K., Graham C.H. 2016 Twenty-million-year relationship between mammalian diversity and

primary productivity. Proc Natl Acad Sci USA. (doi:10.1073/pnas.1602145113).

5. Janis C.M., Scott K.M., Jacos L.L. 1998 Evolution of Tertiary Mammals of North

America: Volume 1, Terrestrial Carnivores, Ungulates, and Ungulate Like Mammals.

(Cambridge, UK, Cambridge University Press.

6. Janis C.M., Gunnell G.F., Uhen M.D. 2008 Evolution of Tertiary Mammals of North

America: Volume 2, Small Mammals, Xenarthrans, and Marine Mammals. (Cambridge, UK,

Cambridge University Press.

7. Fortelius M. (coordinator) 2015 New and Old Worlds Database of Fossil Mammals

(NOW). University of Helsinki. Date of access: November 1st, 2015.