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

Transcription

1 Electronic Supplementary Materials Mammal body mass evolution in North America and Europe over million years: similar trends generated by different processes Shan Huang 1, *, Jussi T. Eronen 2, 3, Christine M. Janis, Juha J. Saarinen 2, 5, Daniele Silvestro 6, Susanne A. Fritz 1,7 1 Senckenberg Biodiversity & Climate Research Centre (BiK-F), Frankfurt am Main, Germany; 2 Department of Geosciences and Geography, University of Helsinki, Helsinki, Finland; 3 BIOS Research Unit, Helsinki, Finland; Department of Ecology and Evolutionary Biology, Brown University, Providence, USA; 5 Natural History Museum, London, UK; 6 Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden; 7 Institute of Ecology, Evolution and Diversity, Goethe University, Frankfurt am Main, Germany. * address: shan.huang@senckenberg.de

2 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 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 datasets, we ran million iterations (excluding the additional, 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 q and a correlation parameter αq 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 λ and extinction rate μ: 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 λ and μ) and 2) correlation parameters, αλ and αμ, that describe lineage-

3 specific deviations of origination and extinction rates respectively from the baseline rates due to variation in body size. Correlation parameters for preservation (αq), origination (αλ), and extinction rates (αμ) were assigned a normal prior distribution with mean m = (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.

4 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 Model 1 Model 2 Model 3 Europe (N = 161) AIC = 379 (.59) p =. AIC = 381 (.22) p =.7 AIC = 381 (.) p =. Artiodactyla North America (N = 1) AIC = 113 (.57) p =.71 AIC = 115 (.21) p =.7 AIC = 115 (.23) p =.71 Combined (N = 2) AIC = 87 (.5) p =.17 AIC = 89 (.) p =.3 AIC = 88 (.26) p =.17 Europe (N = 59) AIC = 78 (.62) p =.25 AIC = 8 (.23) p =.33 AIC = 81 (.15) p =.62 Perissodactyla North America (N = 57) AIC = 113 (.62) p =.75 AIC = 11 (.28) p =.93 AIC = 116 (.) p =.89 Combined (N = 119) AIC = 196 (.5) p =.1 AIC = 196 (.39) p =.23 AIC = 198 (.16) p =.31

5 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 [], originally compiled from [5] and [6] for North American occurrences and the NOW database [7] for European occurrences North America Longitude ( ) Latitude ( ) Europe Longitude ( ) Latitude ( ) NA log Body Mass (g)

6 7 North America Artiodactyla 15 5 Geologic time (Ma) 8 Artiodactyla Europe 15 5 Geologic time (Ma) Perissodactyla 15 5 Geologic time (Ma) Perissodactyla 15 5 Geologic time (Ma) Sampled Inferred Singleton 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 >.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.

7 log 2 Body mass (Kg) Median 25% 75% quantile Total range All species with body mass data Artiodactyla in N. America log 2 Body mass (Kg) Artiodactyla in Europe log 2 Body mass (Kg) Perissodactyla in N. America log 2 Body mass (Kg) Perissodactyla in Europe 15 5 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.

8 96 Artiodactyla in N. America 96 Artiodactyla in Europe Body mass (Kg, scaled in log 2 ) Anthracotheriidae Camelidae Protoceratidae Dromomerycidae Tayassuidae Merycoidodontidae Cervidae Antilocapridae Moschidae Leptomerycidae Body mass (Kg, scaled in log 2 ) Hippopotamidae Giraffidae Anthracotheriidae Palaeomerycidae Camelidae Suidae Bovidae Cervidae Tragulidae Sanitheriidae Palaeochoeridae Moschidae Andegamerycidae Early Mio Mid Mio Late Mio Plio Early Mio Mid Mio Late Mio Plio 15 5 Geologic 15 5 Geologic Body mass (Kg, scaled in log 2 ) Perissodactyla in N. America Teleoceratinae Schizotheriinae Aceratheriinae Diceratheriinae Menoceratinae Equinae Tapiridae Anchitheriinae Body mass (Kg, scaled in log 2 ) Perissodactyla in Europe Elasmotheriinae Rhinocerotinae Teleoceratinae Schizotheriinae Chalicotheriinae Aceratheriinae Menoceratinae Equinae Tapiridae Anchitheriinae Early Mio Mid Mio Late Mio Plio Early Mio Mid Mio Late Mio Plio 15 5 Geologic 15 5 Geologic Figure S 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;

9 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.

10 2. North America Europe Rates Rates Artiodactyla Geologic Geologic Rates Rates Origination Extinction Perissodactyla 15 5 Geologic 15 5 Geologic Figure S5 Temporal patterns of clade-wide baseline origination (λ) and extinction (μ) rates of Artiodactyla (upper) and Perissodactyla (lower) in Neogene North America (left) and Europe (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.

11 Additional references 1. Silvestro D., Salamin N., Schnitzler J. 1 PyRate: a new program to estimate speciation and extinction rates from incomplete fossil data. Methods in Ecology and Evolution 5(), (doi:.1111/1-2x.12263). 2. Silvestro D., Schnitzler J., Liow L.H., Antonelli A., Salamin N. 1 Bayesian estimation of speciation and extinction from incomplete fossil occurrence data. Syst Biol. (doi:.93/sysbio/syu6). 3. Silvestro D., Antonelli A., Salamin N., Quental T.B. 15 The role of clade competition in the diversification of North American canids. Proc Natl Acad Sci USA 112(28), (doi:.73/pnas ).. Fritz S.A., Eronen J.T., Schnitzler J., Hof C., Janis C.M., Mulch A., Böhning-Gaese K., Graham C.H. 16 Twenty-million-year relationship between mammalian diversity and primary productivity. Proc Natl Acad Sci USA. (doi:.73/pnas ). 5. Janis C.M., Scott K.M., Jacos L.L 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. 8 Evolution of Tertiary Mammals of North America: Volume 2, Small Mammals, Xenarthrans, and Marine Mammals. (Cambridge, UK, Cambridge University Press. 7. Fortelius M. (coordinator) 15 New and Old Worlds Database of Fossil Mammals (NOW). University of Helsinki. Date of access: November 1st, 15.