Supplemental File 2: Fossil calibration schemes The soft explosive model of placental mammal evolution Matthew J. Phillips*,1 and Carmelo Fruciano1 1School of Earth, Environmental and Biological Sciences, Queensland University of Technology, Brisbane, Australia *Corresponding author: E-mail: [email protected] Contents Fossil Calibration schemes ......................................................................................................... 1 Table S2 .................................................................................................................................. 1 New calibrations ..................................................................................................................... 3 Figure S2 ................................................................................................................................ 7 References ............................................................................................................................ 10 Calibration schemes Table S2. Soft-bound calibrations employed for the MCMCtree analyses of the 122-taxon, 128- taxon, and 57-taxon empirical datasets. Calibrations among placental mammals are largely based on dos Reis et al. [1], hence the designations dR32 and dR40 (numbers indicating the number of calibrations). Several new calibrations, including some inspired by Springer et al. [2], are described below the table. Also note that the 122-taxon dR40, 128-taxon and 57-taxon analyses employ bounds as listed below, whereas the dR32 analyses, which are intended to be directly comparable with Phillips [3] use a previous chronostratigraphic timescale, with slightly different bounds. The Campanian maximum bound has moved from 84.2 Ma to 83.8 Ma, minimum Selandian bound from 61.5 Ma to 61.6 Ma, maximum Selandian bound from 61.7 Ma to 61.6 Ma, maximum Eocene bound from 55.6 Ma to 56.0 Ma, and the KPg boundary is set to 66.0 Ma (previously min 65.2 Ma, max 65.8 Ma). Clade Bounds Reference 122-taxon 128-taxon 57-taxon (Ma) analyses analyses analysis dR32 dR40 Placentalia <131.5 [1] Xenarthra >55.6 [1] Xenarthra >47.8 New Folivora 15.97-41.3 [2] Afrotheria >55.6 [1]a Afrotheria >59.2 New Fereuungulata >62.5 [1]b Carnivora 39.68-66 [1] Feliformia 28.1-41.3 New Musteloidea 24.8-41.3 New Erinaceidae- >57.8 [3] Soricidae Haplorrhini >33.9 [1]c Primates 56-61.6 Min [1] Max [3] Strepsirrhini 37.8-56 [1] Archonta >61.6 [1] d Glires >61.6 [1] 1 Rodentia 56-61.6 Min [1] Max [3] Myomorpha- 52.5-59.2 [1] Hystricomorpha Myomorpha- 40.2-56.0 [1] Castorimorpha Caviomorpha- >35.8 New Phiomorpha Chinchilloidea- >28.1 New Octodontoidea Chiroptera 45.0-59.2 [3] Rhinolophidae- 33.9-53.0 New Hipposideridae Theria 124.0-171.2 [1] Mammalia 162.9-191.1 [1] Mammalia 162.9-208.5 New Suina- 50.0-61.6 New Cetruminatia Ruminantia >33.9 New Osteichthyes 416-425.4 [4] Tetrapoda 330.4-377.1 [4] Amniota 312.3-347.4 [4] Sauropsida 255.9-299.8 [4] Neognathae 66-86.5 [4] Caenolestidae 0.0-15.97 [4] Australidelphia- 65.18-84.2 [4] Didelphimorphia Australidelphia- 54.55-83.8 New Didelphimorphia Marsupialia 54.55-83.8 New Didelphimorphia 11.608-66 [4] Didelphidae 11.608-28.5 [4] Peramelidae 4.36-23.8 [4] Peramelemorphia 4.36-54.65 [4] Dasyuromorphia 15.97-54.65 [4] 2 Phalangeridae- 25-54.65 [4] Burramyidae Petauridae- 25.5-54.65 [4] Pseudocheiridae Macropodoidea 24.7-54.65 [4] Macropodoidea 17.79-54.65 New Macropodiformes 24.7-54.65 New Vombatiformes 25.5-54.65 [4] ados Reis et al. [1] and Phillips [3] used this bound for elephant/hyrax. With elephants excluded from the 122-taxon and 128-taxon analyses, instead of deleting the calibration we used the minimum bound only, for the next deepest included node (Afrotheria). bdos Reis et al. [1] and Phillips [3] used this bound for horse/cat (Zoomata). With perissodactyls excluded from the 122-taxon and 128-taxon analyses, instead of deleting the calibration we used the minimum bound only, for the next deepest included node (Fereuungulata). cdos Reis et al. [1] and Phillips [3] used this bound for new/old world monkeys (Anthropoidea). With Catarrhini excluded from the 122-taxon and 128-taxon analyses, instead of deleting the calibration we used the minimum bound only for the next deepest included node, Haplorrhini (tarsier/new world monkeys). dFor the 57-taxon analyses the bound is for Primatomorpha. New calibrations Fourteen calibrations in Table S2 are listed as “New”, and are described below. In many cases these are minor modifications of previously suggested calibration priors. Even more minor are changes that update several stratigraphic boundaries to the International Stratigraphic Chart (v.2016/10). The dates listed in Table S2 are for the 122-taxon dR40, 128-taxon, and 57-taxon analyses. 1. Xenarthra (armadillo-sloth): minimum bound only, >47.8 Ma. This follows Springer et al. [2], and acknowledges the uncertainty in the dating of the Itaborai Fauna, which includes Riostegotherium. The placement of Riostegotherium with armadillos is also somewhat questionable, being based on osteoderms, which are also known from some extinct sloths. However, the date is further supported by Astegotherium likely being late Early Eocene [5]. 3 Astegotherium osteoderms are also found in association with slightly younger jaw material, and so this reference taxon is preferable to Riostegotherium. For now we use Springer et al.’s [2] minimum bound, although radiometric dates (47.89 ± 1.21 Ma, [6]) overlying the Laguna Fría fossils could provide a more secure minimum age. 2. Afrotheria (elephant-tenrec): minimum bound only, >59.2 Ma. Here we follow Springer et al. [2] on the updated, late Selandian age of Eritherium [7, 8]. Although Cooper et al. [9] found that Eritherium may not be a stem proboscidean as was favoured by Gheerbrant [7], it is clearly a crown afrotherian. 3. Feliformia (cat-African palm civet): 28.1-41.3 Ma. This calibration is based on Proailurus and Stenogale for the minimum bound, and the absence of putative feliforms from well-sampled European and North American Bartonian carnivoran faunas for the maximum bound. Springer et al. [2] used both taxa as (stem felid) reference fossils for the shallower Felidae-Prionodontidae clade, however, there are no studies that place these fossil taxa within this clade with solid statistical support, while other studies (e.g. Spaulding and Flynn [10] place them outside the feliform clade that includes felids, herpestids, hyaenas and viverrids, and hence also euplerids and Prionodon. The thesis of Holliday [11] that Springer et al. [2] cite provides a highly unstable phylogeny. Both Proailurus and Stenogale are placed on the felid stem in an analysis that includes poorly sampled taxa (≥ 20% character completeness). However, in the more complete (≥ 50% character completeness) analysis, Proailurs falls well outside Felidae and into an implausibly shallow placement among euplerids. Stenogale was excluded for the more complete analysis, but its sister taxon in the 20% completeness analysis, Herpestides, also fell outside Felidae (among viverrids) in the more complete analysis. It is nevertheless generally agreed that Proailurus and Stenogale are feliforms. 4. Musteloidea (skunk-badger): 24.8-41.3 Ma. The minimum bound follows Springer et al. [2], and is based on Promartes (e.g. Finarelli [12]). In a combined DNA-morphology analysis Finarelli [12] nested Promartes implausibly, well within crown Mustelidae, a clade that is less than half the age of the fossil [13]. Some other studies also place oligobunines (which include Promartes) outside musteloids (e.g. [10, 14]). Thus, further investigation is warranted. However, 4 we maintain the bound for now, given that another musteloid, Amphictis is known from similar aged deposits among the Quercy Phosphorites [15, 16]. We extend Springer et al.’s [2] maximum bound from 38 Ma to 41.3 Ma, to account for the perhaps unlikely event that Mustelavus (which is known from Priabonian sites) is a crown Musteloid. Our maximum bound acknowledges that putative musteloids are absent from well- sampled Bartonian and older carnivoran faunas. 5. Caviomorpha-Phiomorpha (Guinea pig-naked mole rat): minimum bound only, >35.8 Ma, based on Cachiyacuy contamanensis [17]. Phillips [18] tentatively suggested a minimum age of 40.94 Ma, in line with Antoine et al.’s [17] 40Ar/39Ar dating of biotite grains overlying the fossil- bearing sediments (43.44 ± 2.5 Ma), but cautioned against a hard bound, because of potential radiometric dating incongruence with biocorrelation for the fauna, and absence of rodents from well-sampled younger faunas. Further concerns with the radiometric dating of the Contamana fauna have been raised by Bond et al. [19], particularly around the distant association of the dated biotite grains to the fossiliferous strata, the high variance of the date estimates, and the possibility of reworking. At present we prefer to employ Antoine et al.’s [17] more cautions biocorrelation minimum (35.8 Ma). 6. Chinchilloidea-Octodontoidea (Chinchilla-degu): minimum bound only, >28.1 Ma, based on Eoviscaccia frassinettii from the Tiguiririca Fauna of Chile [20]. There is some uncertainty in the age of these fossils, because they were from a site on the opposite side of the Tinguirirca River (and without outcrop continuity) from sites with underlying 31.5 Ma dates. Nevertheless, mammal fossil bicorrelation indicates at least an Early