Electronic supplementary material from Mass extinction in tetraodontiform fishes linked to the Palaeocene Eocene thermal maximum

Integrative evolutionary analyses based upon fossil and extant species provide a powerful approach for understanding past diversification events and for assessing the tempo of evolution across the Tree of Life. Herein, we demonstrate the importance of integrating fossil and extant species for inferring patterns of lineage diversification that would otherwise be masked in analyses that examine only one source of evidence. We infer the phylogeny and macroevolutionary history of the Tetraodontiformes (triggerfishes, pufferfishes and allies), a group with one of the most extensive fossil records among fishes. Our analyses combine molecular and morphological data, based on an expanded matrix that adds newly coded fossil species and character states. Beyond confidently resolving the relationships and divergence times of tetraodontiforms, our diversification analyses detect a major mass-extinction event during the Palaeocene Eocene Thermal Maximum (PETM), followed by a marked increase in speciation rates. This pattern is consistently obtained when fossil and extant species are integrated, whereas examination of the fossil occurrences alone failed to detect major diversification changes during the PETM. When taking into account non-homogeneous models, our analyses also detect a rapid lineage diversification increase in one of the groups (tetraodontoids) during the middle Miocene, which is considered a key period in the evolution of reef fishes associated with trophic changes and ecological opportunity. In summary, our analyses show distinct diversification dynamics estimated from phylogenies and the fossil record, suggesting that different episodes shaped the evolution of tetraodontiforms during the Cenozoic

Stevardiinae trees

Stevardiinae phylogenies reconstructed with the software's: RAxML (concatenated and gene trees), Garli, STAR and TNT. Trees were rooted in Serrasalmus sp. and bootstraps support are shown when available

A new family of gymnodont fish (Tetraodontiformes) from the earliest Eocene of the Peri-Tethys (Kabardino-Balkaria, northern Caucasus, Russia)

<p>The environmental changes that occurred during the Paleocene–Eocene transition are crucial for the interpretation of the patterns and processes of diversification of vertebrate clades. A prominent increase of the number of vertebrate families occurred between the late Paleocene and early Eocene, resulting in the appearance of many in the earliest representatives of extant lineages, including a number of marine fish groups. Tetraodontiforms are a monophyletic group of derived teleost fishes encompassing a variety of bizarre morphologies. Even though the earliest members of this order appeared in the Late Cretaceous, most of the crown lineages date back to the Eocene. One of the crown tetraodontiform groups that appeared in the fossil record during the Eocene are the gymnodonts (pufferfishes, porcupinefishes, ocean sunfishes and their allies), which include a variety of species characterized by highly modified teeth incorporated into beak-like jaws and scales usually modified into prickly spines. Herein, we describe †<i>Balkaria histiopterygia</i> gen. et sp. nov., a gymnodont fish characterized by a strikingly peculiar morphology. The single available specimen in part and counterpart documented herein was recovered from the sapropelitic deposits that originated in the northern Peri-Tethys during the transition between the Paleocene and Eocene. Today, these deposits are exposed near the village of Gerpegezh, Republic of Kabardino-Balkaria, Russia. The skeletal structure reveals an extreme mosaicism of primitive and derived characters that result in a very bizarre and unexpected morphology. †<i>Balkaria histiopterygia</i> gen. et sp. nov. is unique among the extant and other fossil gymnodont fishes by, among many other features, the huge size of its spiny-dorsal fin and the position of these spines on the top of the head. †<i>Balkaria histiopterygia</i> gen. et sp. nov. is the earliest unequivocal gymnodont fish, representing the sole member of the new family †Balkariidae. More particularly, †<i>Balkaria histiopterygia</i> gen. et sp. nov. is shown herein to be the oldest and arguably the most informative fossil of the gymnodont suborder Tetraodontoidei. The phylogenetic placement of this new taxon has been assessed based on both morphology alone and on a combination of morphological and molecular data that strongly supports the close relationship of †<i>Balkaria</i> gen. nov. to the herein restricted Tetraodontoidei. However, its position within Tetraodontoidei is unstable depending on the type of method of phylogenetic inference. Significantly younger ages, during the Late Cretaceous, are estimated for the diversification of Tetraodontiformes than in previous tip-dating analyses (Jurassic and Early Cretaceous) using the fossilized birth-death process; these new age estimates are in better agreement with the tetraodontiform fossil record.</p> <p><a href="http://zoobank.org/urn:lsid:zoobank.org:pub:41764800-B0D8-4CA4-A111-5F4C4A281C37" target="_blank">http://zoobank.org/urn:lsid:zoobank.org:pub:41764800-B0D8-4CA4-A111-5F4C4A281C37</a></p

Stevardiinae concatenated alignment

Concatenated alignment with all sequences generated to reconstruct the phylogeny of Stevardiinae. The gene partitions are: myh6 = 1 - 621; ptr = 622 - 1158; rag1 = 1159 - 2520; rag2 = 2521 - 3291; coi = 3292 - 3813; 16s = 3814 - 4387; 12s = 4388 - 4816. Also, all taxa listed are identified by its name and voucher number

Trees_TD_ND

Trees_TD_N

MrBayes_ND_Commands

MrBayes_ND_Command

Supplementary_Files

Supplementary_File

Appendix_1

Appendix_

MCMCTreeFiles

Files for running divergence time estimation in MCMCTree. See Supplementary Appendix for list of fossil calibrations and details on our three calibration schemes

BGI-Sequencing-Results

Assembly metrics from BGI-sequenced transcriptomes for Fish T1