1 Electronic Supplementary Material, Appendix S1. R script to assess the effects of species 2 selection, immigration, and anagenetic change on mean mammalian body size change 3 across the latest Paleocene and earliest Eocene in the Bighorn and Clarks Fork basins of 4 Wyoming using the extended Price equation. Each of the provided datasets (see 5 electronic supplementary material, dataset S1-S4) centers on a single boundary between 6 two time faunal intervals (e.g., latest Clarkforkian/earliest Wasatchian), and must be 7 analyzed with the provided script separately. 8 9 ######################################################## 10 ###Extended Price equation for a single boundary 11 ######################################################## 12 #Read in csv file 13 dat<-read.csv(file.choose()) 14 ancestors<-c(dat[,5]) 15 16 #Identify taxa with ancestors within the dataset 17 has_ancestor<-function(num) {if (num>0){return(1)} else if (num==0){return(0)}} 18 19 #Zero the counting variable 20 count<-0 21 22 #Count and store the number of ancestor/descendant relationships within the dataset 23 for (a in ancestors){count<-count+has_ancestor(a)} 1 24 links<-count 25 26 #Count the number of taxon occurrences (i.e., total number of occurrences in both the 27 #older or younger time intervals) 28 countn<-function(num){length(num[!is.na(num)])} 29 30 #Count the number of descendants in the older time interval and the number of ancestors 31 #in the younger time interval 32 desc_i<-countn(dat[,4]) 33 anc_j<-countn(dat[,3]) 34 35 #Calculate the mean body size of ancestors and the mean body size of descendants, 36 #omitting missing data 37 mean_anc_size_i<-mean(dat[,3], na.rm=TRUE) 38 mean_desc_size_j<-mean(dat[,4], na.rm=TRUE) 39 40 #Calculate the difference between the mean ancestor and mean descendant sizes 41 xbar_anc_desc<-mean_anc_size_i-mean_desc_size_j 42 43 #Set the index variable to the first column of the dataset 44 index<-c(dat[,1]) 45 46 #Calculate the number of ancestors for each taxon 2 47 for (x in index){dat[x, "no_anc"]<-has_ancestor(c(dat[x,5]))} 48 49 #Separate immigrants in dataset 50 dat$no_anc<-ifelse((!is.na(dat$size_i==TRUE)&(dat$ancestor==0)),NA,(dat$no_anc)) 51 52 #Calculate the number of descendants for each taxon 53 for (x in index) {if 54 ((!is.na(dat[x,"size_i"])==FALSE)&&((!is.na(dat[x,"size_j"])==TRUE))) 55 {dat[x,"no_desc"]<-NA} else {dat[x, "no_desc"]<-nrow(dat[dat$ancestor==x,])}} 56 57 #Restrict the dataset to taxa with ancestors 58 non_missing_ancs<-na.omit(as.numeric(dat[,"no_anc"])) 59 60 #Calculate average number of ancestors, omitting missing data 61 average_ancestors<-mean(non_missing_ancs) 62 63 #Remove taxa with no descendants 64 non_missing_desc<-na.omit(as.numeric(dat[,"no_desc"])) 65 66 #Calculate the average number of ancestors, omitting missing data 67 average_descendants<-mean(non_missing_desc) 68 69 #Calculate relative fitness for each taxon 3 70 for (x in index) {dat[x, "rel_fitness"]<-dat[x,"no_desc"]/average_descendants} 71 72 #Create separate column for ancestor size 73 for (x in index) {if (dat[x,"ancestor"]>0) {dat[x,"anc_size"]<- 74 dat[(dat[x,"ancestor"]),"size_i"]}} 75 76 #Calculate the difference in mean body size between descendants and ancestors 77 dat$size_diff<-dat$size_j-dat$anc_size 78 79 #Calculate the contribution of anagenetic changes (i.e., term three of the extended Price 80 #equation) 81 transmission_bias<-mean(dat$size_diff, na.rm=TRUE) 82 83 #Calculate the difference between the number of descendants in the older time interval 84 #and mean number of descendants per ancestor in the older time interval 85 dat$diff_desc_i_mean<-as.numeric(dat$no_desc) - average_descendants 86 87 #Calculate the difference between the number of ancestors of the younger time interval 88 #and mean number of ancestors per descendant in the younger time interval 89 dat$diff_anc_j_mean<-as.numeric(dat$no_anc) - as.numeric(average_ancestors) 90 91 dat$diff_anc_size_i_mean <-(dat$size_i)-mean_anc_size_i 92 4 93 dat$anc_i_covar_contr<-(dat$diff_desc_i_mean)*(dat$diff_anc_size_i_mean) 94 dat$diff_desc_size_j_mean<-(dat$size_j)-mean_desc_size_j 95 dat$desc_j_covar_contr<-(dat$diff_anc_j_mean)*(dat$diff_desc_size_j_mean) 96 97 #Remove missing data to calculate the covariance of the ancestor contribution 98 nonmissing_covar_anc<-na.omit(as.numeric(dat[,"anc_i_covar_contr"])) 99 100 #Remove missing data to calculate the covariance of the descendant contribution 101 nonmissing_covar_desc<-na.omit(as.numeric(dat[,"desc_j_covar_contr"])) 102 103 #Calculate the contribution of species selection (i.e., term one of the extended Price 104 #equation) 105 covar_term_1<-(sum(nonmissing_covar_anc)/anc_j)/(links/anc_j) 106 107 #Calculate the contribution of immigration (i.e., term two of the extended Price 108 #equation) 109 covar_term_2<-(sum(nonmissing_covar_desc)/desc_i)/(links/desc_i)*-1 110 111 112 113 114 115 5 116 117 Electronic Supplementary Material, Appendix S2. The three terms of the Price equation are not best thought of as statistical 118 estimates of unknown population parameters. The Price equation does not treat the 119 observed data as sample data, and does not depend on any assumptions about the 120 sampling process (e.g., regarding randomness and independence of observations, the 121 distribution from which the observations were sampled, etc.). Rather, the Price equation 122 takes the observed data as given and reveals what those data imply about the species 123 selection, immigration, and anagenetic change. Rice [1,2] developed a prospective 124 extension of the Price equation in which phenotypes and fitnesses are unknown and so 125 are treated as random variables described by probability distributions; however, this 126 approach does not apply to fossil data describing evolution that has already occurred. 127 Nevertheless, our results are subject to various sources of uncertainty. 128 Quantifying these various sources of uncertainty is desirable in principle but difficult in 129 practice for our dataset. In order to quantify uncertainty in the terms of the Price 130 equation, it would be necessary to quantify sources of error in the observed data, and then 131 propagate those errors through the Price equation. For instance, we estimated the body 132 size of each species as the mean of the natural logarithm of lower first or second molar 133 area. These means are subject to sampling error, with the measured molars of each 134 species being a sample from the population of molars. In principle, this sampling error 135 could be quantified by bootstrapping. Resampling with replacement from the molar 136 measurements of each species would generate bootstrap replicates, each of which could 137 be analyzed with the Price equation, yielding a bootstrapped distribution for each Price 138 equation term. In practice, however, this cannot be accomplished since measurements of 6 139 individual fossils are unavailable for some species, and because some species are known 140 from only a single specimen or only a few specimens at our study site (see electronic 141 supplementary material, table S2). Other sources of error are more difficult to quantify. 142 New fossil discoveries that added new species to our dataset, or altered the timing of 143 species’ first and last appearances would alter our results. So would revisions to species’ 144 ancestor-descendant relationships and classification. 145 Assessing whether the observed values of species selection, anagenesis, and non- 146 random immigration across the PETM are different than would be expected under some 147 “null” model with a randomization test is another possibility. However, a biologically- 148 relevant “null” hypothesis is impossible to define. For instance, randomly shuffling body 149 sizes among species and then applying the extended Price equation to the randomized 150 data sets would provide the distribution of results expected under a “null” model in which 151 all species are equally likely to speciate, go extinct, or change in size by any amount. It 152 would not be scientifically informative to either reject this model, or fail to reject it, 153 because this model obviously is biologically implausible. Similarly, randomly shuffling 154 which descendant species descended from which ancestral species would provide the 155 distribution of results expected under an implausible null model in which all ancestor- 156 descendant links are equally probable. In principle, it would be informative to simulate 157 data expected under alternative plausible evolutionary scenarios. The available data, 158 however, are insufficient to guide and constrain development of models of different 159 scenarios. 160 161 7 162 Electronic Supplementary Data, Table S1. Latest Palaeocene and earliest Eocene 163 mammals from the Bighorn and Clarks Fork Basins, Wyoming, USA, studied to examine 164 the macroevolution of mean body size using the extended Price equation. Lineages, with 165 respective sources, are: Palaeanodon [3], Esthonyx [3, unpublished data], Azygonyx [3,4], 166 Macrocranion [4,5, unpublished data], Phenacolemur [6], Niptomomys [4,7], Carpolestes 167 [8,9], Teilhardina [4,10,11], Tetonius [12], Cantius [3,4, unpublished data], Arfia [3], 168 Galecyon [13], Didymictis [14], Viverravus [4,14], Chriacus [3,4], Hyopsodus [15], 169 Haplomylus [16], Phenacodus [4,17], Ectocion [3,4,17], Copecion [17], Diacodexis [3,4, 170 unpublished data], Sifrhippus sandrae/Arenahippus grangeri [3,4,18, unpublished data], 171 and Paramys [19]. 172 173 174 175 176 177 178 179 180 181 182 183 184 8 185 Order ?Pholidota Suborder Palaeanodonta Family Metacheiromyidae Genus Palaeanodon Cimolesta Tillodonta Esthonychidae Esthonyx Azygonyx Lipotyphla Erinaceomorpha Amphilemuridae Macrocranion Primates Plesiadapiformes Paromomyidae Phenacolemur Microsyopsidae Carpolestidae Niptomomys Carpolestes Omomyidae Teilhardina Notharctidae Tetonius Cantius Creodonta Hyaenodontidae Arfia Carnivora Viverravidae Galecyon Didymictis Condylarthra Arctocyonidae Viverravus Chriacus Phenacodontidae Ectocion Euprimates Copecion Phenacodus Hyopsodontidae Hyopsodus Haplomylus Artiodactyla Diacodexeidae Diacodexis Perissodactyla Equidae Sifrhippus Arenahippus Paramys Rodentia Sciuromorpha Ischyromyidae Species Palaeanodon parvulus Palaeanodon nievelti Esthonyx spatularius Azygonyx xenicus Azygonyx anyclion Azygonyx latidens Azygonyx grangeri Azygonyx gunnelli Azygonyx sp. Macrocranion junnei Macrocranion nitens Phenacolemur pagei Phenacolemur praecox Niptomomys doreenae Carpolestes nigridens Carpolestes simpsoni Teilhardina brandti Teilhardina gingerichi Teilhardina americana Tetonius matthewi Cantius torresi Cantius ralstoni Cantius mckennai Arfia junnei Arfia zele Arfia shoshoniensis Galecyon peregrinus Didymictis proteus Didymictis leptomylus Didymictis protenus Viverravus politus Chriacus sp. Chriacus badgleyi Ectocion osbornianus Ectocion parvus Copecion brachypternus Copecion davisi Phenacodus intermedius Phenacodus trilobatus Phenacodus vortmani Hyopsodus loomisi Haplomylus palustris Haplomylus simpsoni Haplomylus zalmouti Haplomylus speirianus Diacodexis illicis Diacodexis metasiacus Sifrhippus sandrae Arenahippus grangeri Paramys taurus 186 187 9 188 Electronic Supplementary Data, Table S2. Mean of the natural logarithm of the first or 189 second molar area (mm) of latest Palaeocene and earliest Eocene mammals from the 190 Bighorn and Clarks Fork Basins, Wyoming, USA, studied to examine the macroevolution 191 of mean body size using the extended Price equation. Sample sizes are provided in 192 parentheses. 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 10 211 Species Palaeanodon parvulus Palaeanodon nievelti Esthonyx spatularius Azygonyx xenicus Azygonyx anyclion Azygonyx latidens Azygonyx grangeri Azygonyx gunnelli Azygonyx sp. Macrocranion junnei Macrocranion nitens Phenacolemur pagei Phenacolemur praecox Niptomomys doreenae Carpolestes nigridens Carpolestes simpsoni Teilhardina brandti Teilhardina gingerichi Teilhardina americana Tetonius matthewi Cantius torresi Cantius ralstoni Cantius mckennai Arfia junnei Arfia zele Arfia shoshoniensis Galecyon peregrinus Didymictis proteus Didymictis leptomylus Didymictis protenus Viverravus politus Chriacus sp. Chriacus badgleyi Ectocion osbornianus Ectocion parvus Copecion brachypternus Copecion davisi Phenacodus intermedius Phenacodus trilobatus Phenacodus vortmani Hyopsodus loomisi Haplomylus palustris Haplomylus simpsoni Haplomylus zalmouti Haplomylus speirianus Diacodexis illicis Diacodexis metasiacus Sifrhippus sandrae Arenahippus grangeri Paramys taurus Cf1 Cf2 3.09 (2) Cf3 3.24 (2) Wa0 Wa1/2 2.80 (2) 3.69 (2) 2.82 (6) 3.77 (27) 4.25 (2) 4.45 (4) 0.68 (3) 4.45 (3) 3.88 (2) 4.03 (2) 4.18 (4) 4.42 (6) 4.72 (5) 0.73 (1) 1.43 (1) 1.01 (7) 1.53 (3) 1.07 (5) 0.85 (4) 1.49 (5) 1.66 (4) 1.78 (1) 0.06 (3) 1.76 (15) 0.40 (6) 0.84 (11) 1.09 (9) 1.29 (1) 1.13 (20) 1.55 (4) 2.32 (3) 2.46 (163) 2.55 (67) 2.88 (4) 3.69 (3) 3.94 (13) 3.98 (9) 3.15 (1) 2.53 (2) 3.01 (1) 2.98 (4) 3.19 (2) 3.59 (37) 3.55 (46) 3.50 (157) 2.89 (1) 3.61 (3) 2.89 (1) 3.19 (3) 3.46 (18) 3.30 (3) 3.79 (13) 4.32 (5) 3.20 (5) 3.16 (2) 2.93 (8) 3.54 (181) 3.17 (35) 3.56 (1) 3.61 (2) 4.77 (10) 4.80 (14) 4.82 (31) 4.39 (2) 4.24 (2) 4.23 (5) 1.82 (6) 1.98 (11) 3.56 (11) 3.20 (4) 4.72 (4) 4.17 (4) 2.10 (33) 4.67 (9) 4.55 (11) 4.07 (20) 2.30 (215) 1.58 (1) 1.17 (7) 1.65 (162) 2.38 (14) 2.55 (174) 3.44 (87) 1.85 (1) 1.93 (2) 1.95 (4) 3.55 (294) 1.89 (1) 212 213 214 11 215 Electronic Supplementary Data, Figure S1. The number of descendant species descended 216 from each ancestral species, as a function of mean ancestral body size, approximated 217 from the natural logarithm of the lower first or second molar area for (a) the early to 218 middle Clarkforkian, (b) middle to late Clarkforkian, (c) late Clarkforkian to earliest 219 Wasatchian, and (d) earliest Wasatchian to early Wasatchian. Each point gives data for 220 one ancestral species. Lines are linear regressions. Insets provide the three 221 subcomponents of species selection (equation 2): the selection gradient (regression slope) 222 β, the variance in body size among ancestral species, σ2, and the mean number of 223 descendant species to which an ancestral species gives rise, 𝑦̅. 224 225 226 227 228 229 230 231 232 233 234 235 236 237 12 3 2 β = -0.14 σ² = 1.67 ÓŻ = 1. 11 (a) Carpolestes 1 1 Number of descendants per ancestor 3 2 3 (b) 4 5 Azygonyx Phenacolemur 2 6 β = 0.14 σ² = 1.46 ÓŻ = 1. 14 1 1 3 2 3 4 5 6 β = 0.11 σ² = 1.46 Azygonyx ÓŻ = 0.69 (c) 2 1 Carpolestes 1 3 2 3 4 5 Didymictis 2 6 β = -0.01 σ² = 1.44 ÓŻ = 0.88 (d) Cantius 1 1 2 3 4 5 6 Ancestral body size (mean ln molar area (mm)) 238 239 13 240 Electronic Supplementary Data, Figure S2. The number of ancestors for each descendant 241 species, as a function of mean descendant body size, approximated as the natural 242 logarithm of the lower first or second molar area, for (a) the early to middle Clarkforkian, 243 (b) late Clarkforkian to earliest Wasatchian, and (c) earliest Wasatchian to early 244 Wasatchian. The middle to late Clarkforkian boundary is omitted because there was no 245 immigration across this boundary. Each point gives data for one descendant species. 246 Lines are linear regressions. Insets provide the three subcomponents of the effect of non- 247 random immigration (equation 3): the regression slope β, the variance in body size among 248 descendant species, σ2, and the mean number of ancestral species per descendant species, 249 𝑦̅ (equal to the proportion of descendant species that are not immigrants, and so have one 250 ancestor in the dataset). 251 252 253 254 255 256 257 258 259 260 261 262 14 Number of ancestors per descendant (0 = immigrant, 1 = non-immigrant) 1 (a) β = 0.02 σ² = 1.46 ÓŻ = 0.71 1 1 2 3 4 5 6 (b) β = 0.16 σ² = 1.45 ÓŻ = 0.46 1 1 2 3 4 5 6 (c) β = -0.04 σ² = 1.33 ÓŻ = 0.85 1 2 3 4 5 6 Descendant body size (mean ln molar area (mm)) 263 264 15 265 References 266 267 1. Rice SH. 2008 A stochastic version of the Price equation reveals the interplay of 268 deterministic and stochastic processes in evolution. BMC Evol. Biol. 8, 262. 269 (doi:10.1186/1471-2148-8-262) 270 271 2. 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Ivy LD. 1990 Systematics of the late Paleocene and early Eocene Rodentia 337 (Mammalia) from the Clarks Fork Basin, Wyoming. Contrib. Mus. Paleontol. Univ. 338 Mich. 28, 21-70. 339 340 Captions for Electronic Supplementary Material, Datasets 341 Electronic Supplementary Material, Dataset S1. Mean body sizes, approximated from the 342 natural logarithm of the lower first or second molar area, and the proposed evolutionary 343 relationships between mammalian genera from the early and middle Clarkforkian (Cf1 to 344 Cf2) of the Bighorn and Clarks Fork Basins, Wyoming, USA. Notably, each taxon is 345 assigned an index number (i.e., ‘Index’ column). The mean body size of each taxon is 346 provided for each of the time intervals that the taxon occurs (i.e., ‘size_i’ is the mean 347 body size of the taxon in the older time interval and ‘size_j’ is the mean body size of the 348 taxon in the younger time interval; NA indicates that the taxon does not occur in that time 349 interval). Evolutionary relationships are indicated with specific reference to the index 350 number of taxa, with a number in the ‘ancestor’ column indicating that the taxa is a 351 descendant of the referenced index number; zeros in the ‘ancestor’ columns indicates that 352 there is no ancestor for that taxon in the dataset. For instance, Haplomylus_palustris (i.e., 353 Index taxon 1) does not have an ancestor in the dataset and a zero is recorded within the 19 354 ‘ancestor’ column for this taxon. However, in the same dataset, Haplomylus_simpsoni 355 (i.e., Index taxon 2) does have an ancestor in the dataset; this ancestor is 356 Haplomylus_palustris and a 1 is recorded in ‘ancestor’ column referring to the index 357 number of Haplomylus_palustris. 358 359 Electronic Supplementary Material, Dataset S2. Mean body sizes, approximated from the 360 natural logarithm of the lower first or second molar area, and the proposed evolutionary 361 relationships between mammalian genera from the middle and late Clarkforkian (Cf2 to 362 Cf3) of the Bighorn and Clarks Fork Basins, Wyoming, USA. For details of the dataset 363 see caption for electronic supplementary material, dataset S1. 364 365 Electronic Supplementary Material, Dataset S3. Mean body sizes, approximated from the 366 natural logarithm of the lower first or second molar area, and the proposed evolutionary 367 relationships between mammalian genera from the late Clarkforkian and earliest 368 Wasatchian (Cf3 to Wa0) of the Bighorn and Clarks Fork Basins, Wyoming, USA. For 369 details of the dataset see caption for electronic supplementary material, dataset S1. 370 371 Electronic Supplementary Material, Dataset S4. Mean body sizes, approximated from the 372 natural logarithm of the lower first or second molar area, and the proposed evolutionary 373 relationships between mammalian genera from the earliest to early Wasatchian (Wa0 to 374 Wa1/2) of the Bighorn and Clarks Fork Basins, Wyoming, USA. For details of the 375 dataset see caption for electronic supplementary material, dataset S1. 376 20