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Supporting Information Near et al. 10.1073/pnas.1304661110 SI Text and SD of 0.8 to set 57.0 Ma as the minimal age offset and 65.3 Ma as the 95% soft upper bound. Fossil Calibration Age Priors † Here we provide, for each fossil calibration prior, the identity of Calibration 7. Trichophanes foliarum, calibration 13 in Near et al. the calibrated node in the teleost phylogeny, the taxa that rep- (1). Prior setting: a lognormal prior with the mean of 1.899 and resent the first occurrence of the lineage in the fossil record, SD of 0.8 to set 34.1 Ma as the minimal age offset and 59.0 Ma as a description of the character states that justify the phylogenetic the 95% soft upper bound. placement of the fossil taxon, information on the stratigraphy of Calibration 8. †Turkmene finitimus, calibration 16 in Near et al. the rock formations bearing the fossil, and the absolute age es- (1). Prior setting: a lognormal prior with the mean of 2.006 and timate for the fossil; outline the prior age setting used in the SD of 0.8 to set 55.8 Ma as the minimal age offset and 83.5 Ma as BEAST relaxed clock analysis; and provide any additional notes the 95% soft upper bound. on the calibration. Less detailed information is provided for 26 of the calibrations used in a previous study of actinopterygian di- Calibration 9. †Cretazeus rinaldii, calibration 14 in Near et al. (1). vergence times, as all the information and prior settings for these Prior setting: a lognormal prior with the mean of 1.016 and SD of calibrations is found in the work of Near et al. (1). Each cali- 0.8 to set 70.6 Ma as the minimal age offset and 80.9 Ma as the bration is numbered, and the phylogenetic placement of the 95% soft upper bound. calibration is highlighted in Fig. S2. Calibration 10. †Zenopsis clarus †Zenopsis tyleri and †Zenopsis † , , Calibration 1. Rubiesichthys gregalis, calibration 6 in Near et al. hoernesi, calibration 15 in Near et al. (1). Prior setting: a log- (1). Prior setting: a lognormal prior with the mean of 1.51 and normal prior with the mean of 0.231 and SD of 0.8 to set 32.0 Ma SD of 0.8 to set 133.9 Ma as the minimal age offset and 150.8 Ma as the minimal age offset and 36.7 Ma as the 95% soft upper as the 95% soft upper bound. bound. † Calibration 2. Estesesox foxi, calibration 9 in Near et al. (1). Prior Calibration 11. †Hoplopteryx simus and †Hoplopteryx lewesiensis, setting: a lognormal prior with the mean of 1.091 and SD of 0.8 calibration 17 in Near et al. (1). Prior setting: a lognormal prior to set 76.4 Ma as the minimal age offset and 87.5 Ma as the 95% with the mean of 0.479 and SD of 0.8 to set 93.6 Ma as the soft upper bound. minimal age offset and 105.8 Ma as the 95% soft upper bound. † Calibration 3. Eosalmo driftwoodensis, calibration 10 in Near Calibration 12. †Gephyroberyx robustus,calibration19inNear et al. (1). Prior setting: a lognormal prior with the mean of 1.618 et al. (1). Prior setting: a lognormal prior with the mean of and SD of 0.8 to set 51.8 Ma as the minimal age offset and 76.4 0.231 and SD of 0.8 to set 32.0 Ma as the minimal age offset Ma as the 95% soft upper bound. and 36.7 Ma as the 95% soft upper bound. Calibration 4. Node: stem lineage Alepisauroidei, dating the most Calibration 13. †Eoholocentrum macrocephalum, †Berybolcensis recent common ancestor (MRCA) of Bathypterois and all other leptacanthus,and†Tenuicentrum pattersoni,calibration18in † sampled Aulopiformes. First occurrence: Enchodus zimapan- Near et al. (1). Prior setting: a lognormal prior with the mean ensis La Negra horizon, El Doctor Formation, Muhi quarry, of 0.672 and SD of 0.8 to set 50.0 Ma as the minimal age offset Zimapán, Hidalgo, Mexico (2), Enchodus brevis Ein-Yabrud, and 57.3 Ma as the 95% soft upper bound. Jerusalem, Israel (3), Enchodus venator Jebel Tselfat, Morocco (4), Enchodus marchesettii Hakel and Hadjula, Lebanon (5), and Calibration 14. †Gasterorhamphosus zuppichinii, calibration 20 in Enchodus mecoanalis Namoura, Lebanon (6). Resolution in Near et al. (1). Prior setting: a lognormal prior with the mean of phylogenetic analyses: maximum parsimony analysis of 87 mor- 1.016 and SD of 0.8 to set 70.6 Ma as the minimal age offset and phological characters resolve Synodus as the sister lineage of all 80.9 Ma as the 95% soft upper bound. other sampled Aulopiformes including †Enchodus (figure 1 of ref. 7). Character states: pharyngeal toothplates bearing large Calibration 15. †“Syngnathus” heckeli and †Prosolenostomus lessi- teeth, known from congeneric Enchodus longidens from the nii, calibration 22 in Near et al. (1). Prior setting: a lognormal Santonian of Sahel Alma, Lebanon (figure 68 of ref. 8); slender prior with the mean of 0.672 and SD of 0.8 to set 50.0 Ma as the maxilla; palatine dominant tooth-bearing bone of upper jaw; first minimal age offset and 57.3 Ma as the 95% soft upper bound. epipleural originates on first centrum (8–10). Stratigraphy: lower Cenomanian. Absolute age estimate: 99.6 Ma (11). Prior setting: Calibration 16. †Paramphisile weileri and †Paraeoliscus robinetae, an exponential prior with the mean of 2.86 to set 99.6 Ma as the calibration 21 in Near et al. (1). Prior setting: a lognormal prior minimal age offset and 108.2 Ma as the 95% soft upper bound. with the mean of 0.672 and SD of 0.8 to set 50.0 Ma as the The upper bound is based on the calculation of fossil age (FA)95 minimal age offset and 57.3 Ma as the 95% soft upper bound. following Marshall (12). Calibration 17. Node: crown lineage Exocetoidei, dating the MRCA of Calibration 5. †Homonotichthys dorsalis, calibration 11 in Near Arrhamphus and Dermogenys. First occurrence: †Rhamphexocoetus et al. (1). Prior setting: a lognormal prior with the mean of 0.476 volans Pesciara beds of “Calcari nummulitici,” Bolca, Italy (13). and SD of 0.8 to set 93.6 Ma as the minimal age offset and 99.6 Resolution in phylogenetic analyses: none. Character states: Ma as the 95% soft upper bound. lower jaw symphysis extended; ventral lobe of caudal fin enlarged relative to dorsal lobe; pectoral fins greatly expanded (14–16). Calibration 6. †Massamorichthys wilsoni, calibration 12 in Near Stratigraphy: upper Ypresian [Paleogene calcareous nannofossil et al. (1). Prior setting: a lognormal prior with the mean of 0.525 zone (NP)14] (17). Absolute age estimate: 50 Ma (17). Prior set- Near et al. www.pnas.org/cgi/content/short/1304661110 1of20 ting: a lognormal prior with the mean of 0.672 and the SD of 0.8 to the minimal age offset and 63.9 Ma as the 95% soft upper set 50.0 Ma as the minimal age offset and 57.3 Ma as the 95% soft bound. The upper bound is based on the calculation of FA95 upper bound. The upper bound is based on the calculation of FA95 following Marshall (12). following Marshall (12). Calibration 26. †Archoplites clarki, calibration 36 in Near et al. (1). Calibration 18. †Eobothus minimus, calibration 27 in Near et al. Prior setting: a lognormal prior with the mean of 0.1 and SD of (1). Prior setting: a lognormal prior with the mean of 0.672 and 0.5 to set 15.5 Ma as the minimal age offset and 17.8 Ma as the SD of 0.8 to set 50.0 Ma as the minimal age offset and 57.3 Ma as 95% soft upper bound. the 95% soft upper bound. Calibration 27. †Euleiognathus tottori, calibration 32 in Near et al. Calibration 19. †Oligobothus pristinus, calibration 29 in Near et al. (1). Prior setting: a lognormal prior with the mean of 1.602 and (1). Prior setting: a lognormal prior with the mean of 0.165 and SD of 0.8 to set 11.6 Ma as the minimal age offset and 23.1 Ma as SD of 0.8 to set 30.0 Ma as the minimal age offset and 34.4 Ma as the 95% soft upper bound. the 95% soft upper bound. Calibration 28. Chaetodontidae cf. Chaetodon (tholichthys-stage † † Calibration 20. Eobuglossus and Turahbuglossus, calibration 28 larvae), calibration 30 in Near et al. (1). Prior setting: a lognormal in Near et al. (1). Prior setting: a lognormal prior with the mean prior with the mean of 0.165 and SD of 0.8 to set 30.1 Ma as the of 0.946 and SD of 0.8 to set 40.4 Ma as the minimal age offset minimal age offset and 34.5 Ma as the 95% soft upper bound. and 50 Ma as the 95% soft upper bound. Calibration 29. †Avitoluvarus dianae, †Avitoluvarus mariannae, † Calibration 21. Archaeus oblongus, calibration 23 in Near et al. †Kushlukia permira,and†Luvarus necopinatus, calibration 25 in (1). Prior setting: a lognormal prior with the mean of 0.776 and Near et al. (1). Prior setting: a lognormal prior with the mean of SD of 0.8 to set 55.8 Ma as the minimal age offset and 63.9 Ma as 0.776 and SD of 0.8 to set 55.8 Ma as the minimal age offset the 95% soft upper bound.
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  • Ecography ECOG-05049 Marques, V., Guérin, P.-É., Rocle, M., Valentini, A., Manel, S., Mouillot, D

    Ecography ECOG-05049 Marques, V., Guérin, P.-É., Rocle, M., Valentini, A., Manel, S., Mouillot, D

    Ecography ECOG-05049 Marques, V., Guérin, P.-É., Rocle, M., Valentini, A., Manel, S., Mouillot, D. and Dejean, T. 2020. Blind assessment of vertebrate taxonomic diversity across spatial scales by clustering environmental DNA metabarcoding sequences. – Ecography doi: 10.1111/ ecog.05049 Supplementary material Appendix 1 Fig. A1 Sampling map for the 196 samples, in 103 distinct sites, with a mean of 2 samples per site. family Frequency Frequency 0 10 20 30 40 50 0 10000 20000 30000 40000 0 10 20 30 40 50 60 70 0 20 40 60 80 intrasapecific distance intersapecific distance genus 100 150 Frequency Frequency 50 0 0e+00 1e+05 2e+05 3e+05 0 10 20 30 40 50 60 70 0 20 40 60 80 intrasapecific distance intersapecific distance species 15 10 Frequency Frequency 5 0 0e+00 2e+05 4e+05 6e+05 8e+05 1e+06 0 1 2 3 4 5 0 20 40 60 80 intrasapecific distance intersapecific distance Fig. A2 Fish genetic distance depending on taxa level using the 12S teleo primer, from an in silico PCR on all available sequences in the European Nucleotide Archive. Fig. A3 Effects of LULU parameters (minimum percentage of similarity and co-occurrence) on the number of discarded MOTUs with A) making only the similarity percentage vary between 80 and 100% and a co-occurrence value of 95% and B) making both co-occurrence and identity percentage vary. Table A1: The 12 species detected only with the European Nucleotide Archive (ENA) at 100% similarity, with their main country location compared to its assignment using the local reference database and associated location.