802
Journal of Paleontology 91(4):799–814
Diversification produces a tree with branching and extinction events and random sampling of nodes. Sampling events are indicated by dots. (2)A ‘reconstructed’ phylogenetic tree produced by pruning all of the unsampled lineages in 1.1. Thus, only the observed portion of samples participating in the macroevolutionary process is depicted. Note that some sampled nodes represent ancestors.
Figure 1. The set of stochastic branching, extinction, and sampling
events for a single FBD process gives rise to a ‘complete’ phylogeny with generating parameters π = (p, q, r, ε, to) (Fig. 1.1). The ‘sampled’ FBD phylogeny is obtained when all lineages with unsampled descendants produced by the process are pruned from the tree and therefore represents the reconstructed tree topology and divergence times implied by the sampled taxa (Fig. 1.2). Trees sampled from the FBD process are called sampled ancestor phylogenetic trees (even if no ancestors were sampled), and their nodes can be labeled to summarize their unique history of macroevolutionary and sampling events (Gavryushkina et al., 2014). Equations for calculating the probability density of f Ψj π
FBD parameters p, q, r, and ε can be derived by modifying birth–death sampling models used to study virus transmissions in epidemiology (Stadler, 2010; Stadler et al., 2012; Gavryush- kina et al., 2014; Zhang et al., 2016), and their details are discussed in the Appendix.
½ given the
Taxon sampling, characters analyzed, and specimens examined
The character matrix analyzed herein was constructed as part of a larger project resolving phylogenetic relationships among Paleozoic crinoids. I updated, modified, and expanded the character list of Ausich et al. (2015) to include an ensemble of new characters to better capture variation among post- Ordovician taxa, particularly among ‘cladids’ (Ausich et al., 2015; Wright and Ausich, 2015). Because the taxonomic diversity of fossil crinoids is formidably high for comprehensive analysis, taxon sampling was restricted to Ordovician through Devonian species and multiple exemplars were sampled at pertinent taxonomic scales appropriate to the present analysis (Brusatte, 2010). The matrix was constructed in an attempt to maximize sampling across the broad spectrum of taxonomic, morphologic, and preservation gradients while keeping rigorous analysis tractable (Wagner, 2000c; Carlson and Fitzgerald, 2007; Heath et al., 2008).
Illustration of the fossilized birth–death process. (1) A full realization of the FBD process from time t in the past to the end of the process.
The data set contains representative species fromOrdovician, Silurian, and Devonian families of nominal ‘cladids’ (including
cyathocrines and dendrocrines), disparids, hybocrinids, and flexibles (all taxa sensuMoore and Laudon, 1943). Species chosen as exemplars were typically the type species of a type genus that well characterizes the distribution of morphologic traits for each higher taxon, but sometimes geologically older species and/or more complete specimens were sampled instead (Table 1). Characters, plate homologies, and terminology are after Ubaghs (1978) and Ausich et al. (2015), with updates from Webster and Maples (2006) andWright (2015). All but four traits were treated as unordered binary ormultistate characters (SupplementalData 1). These four characters were ordered based on known patterns of crinoid development, and arguments for ordering these traits are discussed byWright (2015) andWebster andMaples (2006, 2008). Unknown and inapplicable character stateswere coded as missing. This new compilation of more than 3,000 specimen-based observations is the largest and most comprehensive morpho- logic data matrix ever constructed sampling Ordovician and post-Ordovician fossil crinoids (Supplemental Data 2). In the final matrix, a total of 87 discrete morphologic
characters comprisingmore than 300 character states were sampled across 42 species of non-camerate crinoids (SupplementalData 2). Camerateswere not included in the analysis because they diverged from non-camerate crinoids by at least the earliest Ordovician (Guensburg and Sprinkle, 2003; Guensburg, 2012; Ausich et al., 2015; Cole, 2017). Although tip-dating analyses do not per se require use of an outgroup (Ronquist et al., 2012), there are several reasons I used the Tremodocian species Apektocrinus ubaghsi Guensburg and Sprinkle, 2009 to assist rooting the tree. Apektocrinus was originally described as a tentative cladid that featured traits intermediate between protocrinoids and nominal cladids (Guensburg and Sprinkle, 2009). Protocrinoids were originally considered basal crinoids stemward of the divergence between camerates and non-camerates (Guensburg and Sprinkle, 2003). However, Guensburg (2012) subsequently placed protocrinoids within the Camerata, and later analyses by Ausich et al. (2015) recovered protocrinoids to be closer to non-camerates than to camerates. Regardless of the labile phylogenetic position of
Page 1 |
Page 2 |
Page 3 |
Page 4 |
Page 5 |
Page 6 |
Page 7 |
Page 8 |
Page 9 |
Page 10 |
Page 11 |
Page 12 |
Page 13 |
Page 14 |
Page 15 |
Page 16 |
Page 17 |
Page 18 |
Page 19 |
Page 20 |
Page 21 |
Page 22 |
Page 23 |
Page 24 |
Page 25 |
Page 26 |
Page 27 |
Page 28 |
Page 29 |
Page 30 |
Page 31 |
Page 32 |
Page 33 |
Page 34 |
Page 35 |
Page 36 |
Page 37 |
Page 38 |
Page 39 |
Page 40 |
Page 41 |
Page 42 |
Page 43 |
Page 44 |
Page 45 |
Page 46 |
Page 47 |
Page 48 |
Page 49 |
Page 50 |
Page 51 |
Page 52 |
Page 53 |
Page 54 |
Page 55 |
Page 56 |
Page 57 |
Page 58 |
Page 59 |
Page 60 |
Page 61 |
Page 62 |
Page 63 |
Page 64 |
Page 65 |
Page 66 |
Page 67 |
Page 68 |
Page 69 |
Page 70 |
Page 71 |
Page 72 |
Page 73 |
Page 74 |
Page 75 |
Page 76 |
Page 77 |
Page 78 |
Page 79 |
Page 80 |
Page 81 |
Page 82 |
Page 83 |
Page 84 |
Page 85 |
Page 86 |
Page 87 |
Page 88 |
Page 89 |
Page 90 |
Page 91 |
Page 92 |
Page 93 |
Page 94 |
Page 95 |
Page 96 |
Page 97 |
Page 98 |
Page 99 |
Page 100 |
Page 101 |
Page 102 |
Page 103 |
Page 104 |
Page 105 |
Page 106 |
Page 107 |
Page 108 |
Page 109 |
Page 110 |
Page 111 |
Page 112 |
Page 113 |
Page 114 |
Page 115 |
Page 116 |
Page 117 |
Page 118 |
Page 119 |
Page 120 |
Page 121 |
Page 122 |
Page 123 |
Page 124 |
Page 125 |
Page 126 |
Page 127 |
Page 128 |
Page 129 |
Page 130 |
Page 131 |
Page 132 |
Page 133 |
Page 134 |
Page 135 |
Page 136 |
Page 137 |
Page 138 |
Page 139 |
Page 140 |
Page 141 |
Page 142 |
Page 143 |
Page 144 |
Page 145 |
Page 146 |
Page 147 |
Page 148 |
Page 149 |
Page 150 |
Page 151 |
Page 152 |
Page 153 |
Page 154 |
Page 155 |
Page 156 |
Page 157 |
Page 158 |
Page 159 |
Page 160 |
Page 161 |
Page 162 |
Page 163 |
Page 164 |
Page 165 |
Page 166 |
Page 167 |
Page 168 |
Page 169 |
Page 170 |
Page 171 |
Page 172 |
Page 173 |
Page 174 |
Page 175 |
Page 176 |
Page 177 |
Page 178 |
Page 179 |
Page 180 |
Page 181 |
Page 182 |
Page 183 |
Page 184 |
Page 185 |
Page 186 |
Page 187 |
Page 188 |
Page 189 |
Page 190 |
Page 191 |
Page 192 |
Page 193 |
Page 194 |
Page 195 |
Page 196 |
Page 197 |
Page 198 |
Page 199 |
Page 200 |
Page 201 |
Page 202 |
Page 203 |
Page 204 |
Page 205 |
Page 206 |
Page 207 |
Page 208 |
Page 209 |
Page 210 |
Page 211 |
Page 212 |
Page 213 |
Page 214 |
Page 215 |
Page 216 |
Page 217 |
Page 218 |
Page 219 |
Page 220 |
Page 221 |
Page 222 |
Page 223 |
Page 224 |
Page 225 |
Page 226 |
Page 227 |
Page 228 |
Page 229 |
Page 230 |
Page 231 |
Page 232 |
Page 233 |
Page 234 |
Page 235 |
Page 236 |
Page 237 |
Page 238 |
Page 239 |
Page 240 |
Page 241 |
Page 242 |
Page 243 |
Page 244 |
Page 245 |
Page 246 |
Page 247 |
Page 248 |
Page 249 |
Page 250 |
Page 251 |
Page 252 |
Page 253 |
Page 254 |
Page 255 |
Page 256 |
Page 257 |
Page 258 |
Page 259 |
Page 260 |
Page 261 |
Page 262 |
Page 263 |
Page 264 |
Page 265 |
Page 266 |
Page 267 |
Page 268 |
Page 269 |
Page 270 |
Page 271 |
Page 272 |
Page 273 |
Page 274 |
Page 275 |
Page 276 |
Page 277 |
Page 278 |
Page 279 |
Page 280 |
Page 281 |
Page 282 |
Page 283 |
Page 284 |
Page 285 |
Page 286 |
Page 287 |
Page 288
