Localities of sponge specimens, museum voucher numbers, GB and ENA accession numbers used in this study.

<p>New sequences from this study are highlighted in bold.</p><p>*Fragment of holotype.</p><p>Abbreviations:</p><p>ZMA POR: Zoölogisch Museum van de Universiteit van Amsterdam.</p><p>QMG: Queensland Museum, Brisbane, Australia.</p><p>WAM: West Australian Museum.</p><p>ZMB Por: Museum for Natural History Humboldt Universität.</p><p>Mc: National Museums, Northern Ireland, Holywood.</p><p>UCMPW: University of California Museum of Paleontology, Berkeley, CA.</p><p>GW: Molecular Paleo- & Geobiology Munich, Germany.</p><p>ZMBN: Zoologisk Museum Bergen.</p><p>S/SAM: South Australian Museum, Adelaide.</p><p>MNHN: Muséum National d’Histoire Naturelle, Paris.</p><p>TAU: Steinhardt National Collection of Natural History, Zoological Museum at Tel Aviv University, Israel.</p><p>DH: Lab collections of Amir Szitenberg, Department of Zoology, Israel.</p><p>NIWA: National Institute of Water and Atmospheric Research, New Zealand.</p><p>Localities of sponge specimens, museum voucher numbers, GB and ENA accession numbers used in this study.</p

Various desma skeletons within lithistid demosponges.

<p>(A) tetraclone desmas (Phymatellidae); (B) tetraclone desmas (Theonellidae); (C–D) monaxial complex shaped desmas (Neopeltidae); (E) complex shaped desmas (Macandrewiidae) resembling tetraclones; (F) trider-like desmas of Desmanthidae; (G–H) trider-like desmas of Phymaraphiniidae.</p

The current molecular data for lithistid demosponges from GenBank, and their suggested reallocation of 9 of the 13 lithistid families to their closest non-lithistid relatives.

<p>Sequences not in GenBank are marked with an asterisk against the corresponding references.</p><p>The current molecular data for lithistid demosponges from GenBank, and their suggested reallocation of 9 of the 13 lithistid families to their closest non-lithistid relatives.</p

Illustration of different mega- and microscleres within lithistid demosponges. (A–F) different types of ectosomal spicules.

<p>(A): Monaxial ectosomal plate as found in the family of Neopeltidae. (B,C): Different phyllotriaenes within the family Theonellidae. (D,E): Two representatives of dichotriaenes (D): <i>Neophrissospongia</i>, (E): Corallistidae. (F): Discotriaene as found in the family Theonellidae. <b>(G–M) different types of microscleres.</b> (G): Amphiaster (Neopeltidae). (H): Metaster (Corallistidae). (I,J): Spiraster (Corallistidae). (K): Raphids (Azoricidae). (L): acanthorhabds (Scleritodermidae). (M): Exotylostyl (Siphonididae). (N,O) cross-sections of the ectosome and upper part of choanosome showing the skeleton architecture within the family Pleromidae. (N) <i>Pleroma turbinatum</i> collected during the Deep Down Under Expedition in 2009 at the deep fore-reef slopes of the Osprey Reef (Coral Sea, Australia).</p

Bayesian Inference (MrBayes, GTR+I+G model) phylogeny of a representative selection of demosponge taxa based on CO1.

<p>The maximum likelihood (RAxML) tree is congruent. Squares represent node supports. Black squares: PP = 0.95–1.00, BP = 75–100. Dark gray squares: PP = 0.75–0.94, BP = 60–74. White squares: PP<0.75, BP<60. Black triangle indicates lithistid families. Numbers behind taxon names are either voucher numbers or GenBank accession numbers. Self-generated sequences are in bold.</p

Summary of taxonomic changes from our present study and previous studies.

<p>Self-generated sequences, proposed reallocation from our data are marked in bold. PS for Present study.</p><p>Summary of taxonomic changes from our present study and previous studies.</p

Bayesian Inference (MrBayes, GTR+I+G model) phylogeny of a representative selection of demosponge taxa based on 28S rDNA (partition C1–D2).

<p>The maximum likelihood (RAxML) tree is congruent. Squares represent node supports. Black squares: PP = 0.95–1.00, BP = 75–100. Dark gray squares: PP = 0.75–0.94, BP = 60–74. White squares: PP<0.75, BP<60. Black triangle indicates lithistid families. Numbers behind taxon names are either voucher numbers or GenBank accession numbers. Self-generated sequences are in bold.</p

Additional file 1: of Divergence times in demosponges (Porifera): first insights from new mitogenomes and the inclusion of fossils in a birth-death clock model

Species list and ezRAD library information. (XLSX 52 kb

Additional file 5: of Divergence times in demosponges (Porifera): first insights from new mitogenomes and the inclusion of fossils in a birth-death clock model

Tracer statistics of turnover, diversification and sampling proportion of the two runs and the prior from BEAST analysis 2. (PNG 138 kb

Additional file 6: of Divergence times in demosponges (Porifera): first insights from new mitogenomes and the inclusion of fossils in a birth-death clock model

BEAST analysis 2 output log file. (LOG 106 kb