Electronic Supplementary Material, Appendix S1. R script to assess

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Electronic Supplementary Material, Appendix S1. R script to assess the effects of species
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selection, immigration, and anagenetic change on mean mammalian body size change
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across the latest Paleocene and earliest Eocene in the Bighorn and Clarks Fork basins of
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Wyoming using the extended Price equation. Each of the provided datasets (see
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electronic supplementary material, dataset S1-S4) centers on a single boundary between
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two time faunal intervals (e.g., latest Clarkforkian/earliest Wasatchian), and must be
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analyzed with the provided script separately.
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########################################################
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###Extended Price equation for a single boundary
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########################################################
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#Read in csv file
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dat<-read.csv(file.choose())
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ancestors<-c(dat[,5])
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#Identify taxa with ancestors within the dataset
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has_ancestor<-function(num) {if (num>0){return(1)} else if (num==0){return(0)}}
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#Zero the counting variable
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count<-0
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#Count and store the number of ancestor/descendant relationships within the dataset
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for (a in ancestors){count<-count+has_ancestor(a)}
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links<-count
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#Count the number of taxon occurrences (i.e., total number of occurrences in both the
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#older or younger time intervals)
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countn<-function(num){length(num[!is.na(num)])}
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#Count the number of descendants in the older time interval and the number of ancestors
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#in the younger time interval
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desc_i<-countn(dat[,4])
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anc_j<-countn(dat[,3])
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#Calculate the mean body size of ancestors and the mean body size of descendants,
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#omitting missing data
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mean_anc_size_i<-mean(dat[,3], na.rm=TRUE)
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mean_desc_size_j<-mean(dat[,4], na.rm=TRUE)
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#Calculate the difference between the mean ancestor and mean descendant sizes
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xbar_anc_desc<-mean_anc_size_i-mean_desc_size_j
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#Set the index variable to the first column of the dataset
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index<-c(dat[,1])
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#Calculate the number of ancestors for each taxon
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for (x in index){dat[x, "no_anc"]<-has_ancestor(c(dat[x,5]))}
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#Separate immigrants in dataset
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dat$no_anc<-ifelse((!is.na(dat$size_i==TRUE)&(dat$ancestor==0)),NA,(dat$no_anc))
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#Calculate the number of descendants for each taxon
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for (x in index) {if
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((!is.na(dat[x,"size_i"])==FALSE)&&((!is.na(dat[x,"size_j"])==TRUE)))
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{dat[x,"no_desc"]<-NA} else {dat[x, "no_desc"]<-nrow(dat[dat$ancestor==x,])}}
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#Restrict the dataset to taxa with ancestors
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non_missing_ancs<-na.omit(as.numeric(dat[,"no_anc"]))
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#Calculate average number of ancestors, omitting missing data
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average_ancestors<-mean(non_missing_ancs)
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#Remove taxa with no descendants
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non_missing_desc<-na.omit(as.numeric(dat[,"no_desc"]))
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#Calculate the average number of ancestors, omitting missing data
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average_descendants<-mean(non_missing_desc)
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#Calculate relative fitness for each taxon
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for (x in index) {dat[x, "rel_fitness"]<-dat[x,"no_desc"]/average_descendants}
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#Create separate column for ancestor size
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for (x in index) {if (dat[x,"ancestor"]>0) {dat[x,"anc_size"]<-
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dat[(dat[x,"ancestor"]),"size_i"]}}
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#Calculate the difference in mean body size between descendants and ancestors
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dat$size_diff<-dat$size_j-dat$anc_size
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#Calculate the contribution of anagenetic changes (i.e., term three of the extended Price
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#equation)
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transmission_bias<-mean(dat$size_diff, na.rm=TRUE)
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#Calculate the difference between the number of descendants in the older time interval
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#and mean number of descendants per ancestor in the older time interval
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dat$diff_desc_i_mean<-as.numeric(dat$no_desc) - average_descendants
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#Calculate the difference between the number of ancestors of the younger time interval
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#and mean number of ancestors per descendant in the younger time interval
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dat$diff_anc_j_mean<-as.numeric(dat$no_anc) - as.numeric(average_ancestors)
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dat$diff_anc_size_i_mean <-(dat$size_i)-mean_anc_size_i
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dat$anc_i_covar_contr<-(dat$diff_desc_i_mean)*(dat$diff_anc_size_i_mean)
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dat$diff_desc_size_j_mean<-(dat$size_j)-mean_desc_size_j
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dat$desc_j_covar_contr<-(dat$diff_anc_j_mean)*(dat$diff_desc_size_j_mean)
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#Remove missing data to calculate the covariance of the ancestor contribution
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nonmissing_covar_anc<-na.omit(as.numeric(dat[,"anc_i_covar_contr"]))
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#Remove missing data to calculate the covariance of the descendant contribution
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nonmissing_covar_desc<-na.omit(as.numeric(dat[,"desc_j_covar_contr"]))
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#Calculate the contribution of species selection (i.e., term one of the extended Price
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#equation)
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covar_term_1<-(sum(nonmissing_covar_anc)/anc_j)/(links/anc_j)
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#Calculate the contribution of immigration (i.e., term two of the extended Price
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#equation)
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covar_term_2<-(sum(nonmissing_covar_desc)/desc_i)/(links/desc_i)*-1
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Electronic Supplementary Material, Appendix S2.
The three terms of the Price equation are not best thought of as statistical
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estimates of unknown population parameters. The Price equation does not treat the
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observed data as sample data, and does not depend on any assumptions about the
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sampling process (e.g., regarding randomness and independence of observations, the
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distribution from which the observations were sampled, etc.). Rather, the Price equation
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takes the observed data as given and reveals what those data imply about the species
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selection, immigration, and anagenetic change. Rice [1,2] developed a prospective
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extension of the Price equation in which phenotypes and fitnesses are unknown and so
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are treated as random variables described by probability distributions; however, this
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approach does not apply to fossil data describing evolution that has already occurred.
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Nevertheless, our results are subject to various sources of uncertainty.
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Quantifying these various sources of uncertainty is desirable in principle but difficult in
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practice for our dataset. In order to quantify uncertainty in the terms of the Price
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equation, it would be necessary to quantify sources of error in the observed data, and then
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propagate those errors through the Price equation. For instance, we estimated the body
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size of each species as the mean of the natural logarithm of lower first or second molar
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area. These means are subject to sampling error, with the measured molars of each
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species being a sample from the population of molars. In principle, this sampling error
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could be quantified by bootstrapping. Resampling with replacement from the molar
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measurements of each species would generate bootstrap replicates, each of which could
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be analyzed with the Price equation, yielding a bootstrapped distribution for each Price
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equation term. In practice, however, this cannot be accomplished since measurements of
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individual fossils are unavailable for some species, and because some species are known
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from only a single specimen or only a few specimens at our study site (see electronic
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supplementary material, table S2). Other sources of error are more difficult to quantify.
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New fossil discoveries that added new species to our dataset, or altered the timing of
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species’ first and last appearances would alter our results. So would revisions to species’
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ancestor-descendant relationships and classification.
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Assessing whether the observed values of species selection, anagenesis, and non-
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random immigration across the PETM are different than would be expected under some
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“null” model with a randomization test is another possibility. However, a biologically-
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relevant “null” hypothesis is impossible to define. For instance, randomly shuffling body
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sizes among species and then applying the extended Price equation to the randomized
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data sets would provide the distribution of results expected under a “null” model in which
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all species are equally likely to speciate, go extinct, or change in size by any amount. It
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would not be scientifically informative to either reject this model, or fail to reject it,
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because this model obviously is biologically implausible. Similarly, randomly shuffling
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which descendant species descended from which ancestral species would provide the
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distribution of results expected under an implausible null model in which all ancestor-
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descendant links are equally probable. In principle, it would be informative to simulate
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data expected under alternative plausible evolutionary scenarios. The available data,
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however, are insufficient to guide and constrain development of models of different
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scenarios.
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Electronic Supplementary Data, Table S1. Latest Palaeocene and earliest Eocene
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mammals from the Bighorn and Clarks Fork Basins, Wyoming, USA, studied to examine
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the macroevolution of mean body size using the extended Price equation. Lineages, with
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respective sources, are: Palaeanodon [3], Esthonyx [3, unpublished data], Azygonyx [3,4],
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Macrocranion [4,5, unpublished data], Phenacolemur [6], Niptomomys [4,7], Carpolestes
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[8,9], Teilhardina [4,10,11], Tetonius [12], Cantius [3,4, unpublished data], Arfia [3],
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Galecyon [13], Didymictis [14], Viverravus [4,14], Chriacus [3,4], Hyopsodus [15],
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Haplomylus [16], Phenacodus [4,17], Ectocion [3,4,17], Copecion [17], Diacodexis [3,4,
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unpublished data], Sifrhippus sandrae/Arenahippus grangeri [3,4,18, unpublished data],
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and Paramys [19].
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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
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Electronic Supplementary Data, Table S2. Mean of the natural logarithm of the first or
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second molar area (mm) of latest Palaeocene and earliest Eocene mammals from the
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Bighorn and Clarks Fork Basins, Wyoming, USA, studied to examine the macroevolution
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of mean body size using the extended Price equation. Sample sizes are provided in
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parentheses.
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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)
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Electronic Supplementary Data, Figure S1. The number of descendant species descended
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from each ancestral species, as a function of mean ancestral body size, approximated
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from the natural logarithm of the lower first or second molar area for (a) the early to
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middle Clarkforkian, (b) middle to late Clarkforkian, (c) late Clarkforkian to earliest
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Wasatchian, and (d) earliest Wasatchian to early Wasatchian. Each point gives data for
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one ancestral species. Lines are linear regressions. Insets provide the three
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subcomponents of species selection (equation 2): the selection gradient (regression slope)
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β, the variance in body size among ancestral species, σ2, and the mean number of
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descendant species to which an ancestral species gives rise, 𝑦̅.
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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))
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Electronic Supplementary Data, Figure S2. The number of ancestors for each descendant
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species, as a function of mean descendant body size, approximated as the natural
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logarithm of the lower first or second molar area, for (a) the early to middle Clarkforkian,
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(b) late Clarkforkian to earliest Wasatchian, and (c) earliest Wasatchian to early
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Wasatchian. The middle to late Clarkforkian boundary is omitted because there was no
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immigration across this boundary. Each point gives data for one descendant species.
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Lines are linear regressions. Insets provide the three subcomponents of the effect of non-
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random immigration (equation 3): the regression slope β, the variance in body size among
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descendant species, σ2, and the mean number of ancestral species per descendant species,
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𝑦̅ (equal to the proportion of descendant species that are not immigrants, and so have one
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ancestor in the dataset).
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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))
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References
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Mich. 28, 21-70.
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Captions for Electronic Supplementary Material, Datasets
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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
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relationships between mammalian genera from the early and middle Clarkforkian (Cf1 to
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Cf2) of the Bighorn and Clarks Fork Basins, Wyoming, USA. Notably, each taxon is
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assigned an index number (i.e., ‘Index’ column). The mean body size of each taxon is
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provided for each of the time intervals that the taxon occurs (i.e., ‘size_i’ is the mean
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body size of the taxon in the older time interval and ‘size_j’ is the mean body size of the
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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
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number of taxa, with a number in the ‘ancestor’ column indicating that the taxa is a
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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
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‘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
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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
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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.
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