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No phylogenomic support for a Cenozoic origin of the "living fossil" Isoetes
<p class="western"><span><span><span><strong><span>Premise:</span></strong></span></span></span><span><span><span><span> The isoetalean lineage has a rich fossil record that extends to the Devonian, but the age of the living clade is unclear. Recent results indicate that it is young, from the Cenozoic, whereas earlier work based on less data from a denser taxon sample yielded Mesozoic median ages.</span></span></span></span></p> <p class="western"><span><span><span><strong><span>Methods:</span></strong></span></span></span><span><span><span><span> We investigated node ages in </span></span></span></span><span><span><span><em><span>Isoetes</span></em></span></span></span><span><span><span><span> using two genomic datasets (plastome and nuclear ribosomal cistron) analyzed using three different clock models implemented in MrBayes (ILN, WN and TK02 models) and a conservative approach to calibration.</span></span></span></span></p> <p class="western"><span><span><span><strong><span>Key results:</span></strong></span></span></span><span><span><span><span> While topological results are consistently resolved in </span></span></span></span><span><span><span><em><span>Isoetes</span></em></span></span></span><span><span><span><span>, estimated crown group ages range from the latest Paleozoic (mid-Permian) to the Mesozoic depending on datatype and clock model. The oldest estimates were retrieved using the autocorrelated TK02 clock model. An (early) Cenozoic age was only obtained under one specific condition (plastome data analyzed with the uncorrelated ILN clock model). That same plastome dataset also yielded the oldest (mid-Permian) age estimate when analyzed with the autocorrelated TK02 clock model. Adding the highly divergent recently established sister species </span></span></span></span><span><span><span><em><span>Isoetes wormaldii</span></em></span></span></span><span><span><span><span> to the dataset approximately doubled the </span></span></span></span><span><span><span><span>average median node depth to the </span></span></span></span><span><span><span><em><span>Isoetes</span></em></span></span></span><span><span><span><span> crown group</span></span></span></span><span><span><span><span>.</span></span></span></span></p> <p class="western"><span><span><span><strong><span>Conclusions:</span></strong></span></span></span><span><span><span><span> There is no consistent support for a Cenozoic origin of the living clade </span></span></span></span><span><span><span><em><span>Isoetes</span></em></span></span></span><span><span><span><span>. We obtained seemingly well-founded, yet strongly deviating results, depending on datatype and clock model. The single most important future improvement is probably to add calibration points, which requires an improved understanding of the isoetalean fossil record or alternative bases for calibration.</span></span></span></span></p>
Hidden species diversity in an iconic living fossil vertebrate
<p><span>Ancient, species-poor lineages persistently occur across the Tree of Life. These unique lineages are likely to contain unrecognized species diversity masked by the low rates of morphological evolution that characterize living fossils. Halecomorphi is a lineage of ray-finned fishes that diverged from its closest relatives over 200 million years ago and is represented by only one living species in eastern North America, the Bowfin <em>Amia calva Linnaeus</em>. We use double digest restriction-site associated DNA (ddRAD) sequencing and morphology to illuminate recent speciation in bowfins. Our results support the delimitation of a second living species of <em>Amia </em>with the timing of diversification dating to the Plio-Pleistocene. This delimitation expands the species diversity of an ancient lineage that is integral to studies of vertebrate genomics and development, yet is facing growing conservation threats driven by the caviar fishery.</span></p>
Phylogenetic classification of living and fossil ray-finned fishes (Actinopterygii)
<p>Classification of the tremendous diversity of ray-finned fishes (Actinopterygii) began with the designation of taxonomic groups based on morphological similarity. Starting in the late 1960s morphological phylogenetics became the basis for the classification of Actinopterygii but failed to resolve many relationships, particularly among lineages within the hyperdiverse Percomorpha. The introduction of molecular phylogenetics led to a dramatic reconfiguration of actinopterygian phylogeny. Refined phylogenetic resolution afforded by molecular studies revealed an uneven diversity among actinopterygian lineages, resulting in a proliferation of redundant group names in Linnean-ranked classifications. Here we provide an unranked phylogenetic classification for actinopterygian fishes based on a summary phylogeny of 830 lineages of ray-finned fishes that includes all currently recognized actinopterygian taxonomic families and 287 fossil taxa. We provide phylogenetic definitions for 90 clade names and review seven previously defined names. For each of the 97 clade names we review the etymology of the clade name, clade species diversity and constituent lineages, clade diagnostic morphological apomorphies, a review of synonyms, and discuss the clade's nomenclatural and systematic history. The new classification is free of redundant group names and includes only one new name among the 97 clade names we review and describe, yielding a comprehensive classification that is based explicitly on the phylogeny of ray-finned fishes that has emerged in the 21st century and rests on the foundation of the previous 200 years of actinopterygian systematic research.</p>
Data for: Reliable biogeography requires fossils: Insights from a new species-level phylogeny of extinct and living carnivores
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Phylogenetic classification of living and fossil ray-finned fishes (Actinopterygii)
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Hidden species diversity in an iconic living fossil vertebrate
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Supporting data for: The de novo genome of the Black-necked Snakefly (Venustoraphidia nigricollis Albarda, 1891): A resource to study the evolution of living fossils
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No phylogenomic support for a Cenozoic origin of the “living fossil” Isoetes
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Data from: Evolutionary tempo, supertaxa and living fossils
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Data from: Macroevolutionary patterns in Rhynchocephalia: is the tuatara (Sphenodon punctatus) a living fossil?
The tuatara, Sphenodon punctatus, known from 32 small islands around New Zealand, has often been noted as a classic 'living fossil' because of its apparently close resemblance to its Mesozoic forebears and because of a long, low-diversity history. This designation has been disputed because of the wide diversity of Mesozoic forms and because of derived adaptations in living Sphenodon. We provide a testable definition for 'living fossils' based on a slow rate of lineage evolution and a morphology close to the centroid of clade morphospace. We show that through their history since the Triassic, rhynchocephalians had heterogeneous rates of morphological evolution and occupied wide morphospaces during the Triassic and Jurassic, and these then declined in the Cretaceous. In particular, we demonstrate that the extant tuatara underwent unusually slow lineage evolution, and is morphologically conservative, being located near the centre of the morphospace for all Rhynchocephalia.
Figure 7. Phylogeny. A in The evolutionary diversity of barnacles, with an updated classification of fossil and living forms
Figure 7. Phylogeny. A summary of the phylogenetic relationships amongst the Thecostraca families, with major groups labelled on the right and on the branches within the Thoracica. All families are considered monophyletic, except where specifically noted in the text. In Rhizocephala, families with an akentrogonid type of host invasion are coloured blue. Drawings representing the different groups are, from the top: Facetotectan y-cyprid; Dendrogaster; Trypetesa; Clistosaccus; Sacculina; Ibla; Pollicipes; Lepas; Neolepas; Verruca; Catophragmus; Xenobalanus; Balanus.
Figure 6. Fossil Thoracica. A in The evolutionary diversity of barnacles, with an updated classification of fossil and living forms
Figure 6. Fossil Thoracica. A, Stramentum pulchellum, Stramentidae, Upper Cretaceous, Turonian, UK. B, Archaeolepas redtenbacheri, Archaeolepadidae, Upper Jurassic, Tithonian, Germany. C, Eolepas bathonica, Eolepadidae, Middle Jurassic, France. D, E, Witherscalpellum aptiensis, Cretiscalpellidae, Lower Cretaceous, UK; capitulum, in lateral (D) and dorsal (E) views. F, G, Brachylepas naissanti, Brachylepadidae, Upper Cretaceous, UK, in apical (F) and lateral (G) views. H, Etcheslepas durotrigensis, Zeugmatolepadidae, Upper Jurassic, UK. I, J, Proverruca vinculum, Proverrucidae, Upper Cretaceous, UK, in apical (I) and lateral (J) views. K, L, Q, R, Eoverruca hewitti, Eoverrucidae, Upper Cretaceous, UK; K, L, calcified basis with imbricating scales; and Q, R, fixed and moveable scuta. M–P, Myolepas scanica, Myolepadidae, Upper Cretaceous, Sweden; external (M) and internal (O) views of tergum; and external (N) and internal (P) views of scutum. S–AE, fossil whale barnacles, Coronula. Scale bars: 5 mm in A–H; 2 mm in M–P; 1 mm in I–L; 0.5 mm in Q, R, AE.
Figure 9 in The evolutionary diversity of barnacles, with an updated classification of fossil and living forms
Figure 9. Timeline of Thoracican evolution. Generic diversity of the Thoracica from the latest Triassic to the present. Early forms are entirely phosphatic, followed by calcitic pedunculated forms. Balanomorphans (acorn barnacles) appeared in the Cretaceous, but they radiated only after a low-diversity period following the Cretaceous– Palaeogene (K–Pg) extinction. The diversification starting in the Neogene is still ongoing. Living genera shown include only forms with shell plates, in order to compare with the fossil record. Further explanation is given in the main text. (1) Eolepadomorpha, Eolepadidae, Eolepas; (2) Eolepadomorpha, Eolepadidae, Toarcolepas; (3) Pollicipedomorpha, Zeugmatolepadidae, Concinnalepas; (4) Archaeolepadomorpha, Archaeolepadidae, Archaeolepas; (5) Calanticomorpha, Cretiscalpellidae, Witherscalpellum; (6) Scalpelloidea, Scalpellidae, Arcoscalpellum; (7) Brachylepadomorpha, Brachylepadidae, Pycnolepas; (8) Verrucomorpha, Verrucidae, Altiverruca; (9) Balanomorpha, Catophragmidae, Catomerus; (10) Lepadoidea, Lepadidae, Lepas; (11) Neolepadomorpha, Neolepadidae, Stipilepas.
Figure 2. Ascothoracida. A–D in The evolutionary diversity of barnacles, with an updated classification of fossil and living forms
Figure 2. Ascothoracida. A–D, larval diversity of selected Ascothoracida. A, an early, live Baccalaureus nauplius larva. B, an early, live Zibrowia nauplius larva. C, D, a Tessmann's larva or a-cypris (C), with hooked antennules (D). E–N, adult diversity of selected Ascothoracida. E–G, the coral Turbinaria, showing the galls formed by the ascothoracidan Petrarca. Insert in E shows the galls in cross-section, with red Petrarca inside the coral skeleton. F, Petrarca. G, magnified view of Petrarca. H, Synagoga arabesque, with extended, hooked first antennules. I, J, Ascothorax rybakovi on the brittle star Ophiacantha pacifica. K, a free Dengrogaster sp. L–N, the zoanthid Palythoa with Baccalaureus sp. inside. Abbreviation: a1, first antennule. Fig 2C photographed by ND and Dr. Jørgen Olesen, Natural History Museum of Denmark.
Figure 5. Thoracica. A in The evolutionary diversity of barnacles, with an updated classification of fossil and living forms
Figure 5. Thoracica. A, nauplius larva of Balanus improvisus. Note the presence of frontal horns. B, cypris larva of Amphibalanus amphitrite, showing the pair of extended first antennules and six pairs of thoracopods. C, Anelasma squalicola, a parasite of deep-sea lantern sharks (Etmopterus). The cirri are rudimentary, and the base of the peduncle has a root-like structure embedded inside the tissue of the shark to absorb nutrients. D, Fistulobalanus albicostatus, common on mangrove tree trunks. E, the family Pyrgomatidae are associated with scleratinian corals, and the bases are embedded in the coral skeleton. Cantellius sp. extending the cirri. F, Ibla cumingi, which is located at the most basal position on the molecular phylogenetic tree of thoracican barnacles. G, Megabalanus, Amphibalanus and Lepas inhabiting the capitulum of a penduculated barnacle. H, Capitulum mitella, a stalked barnacle inhabiting rocky shores. In molecular phylogenetic analyses, it is the sister to Anelasma (see C). I, Conchoderma, a stalked barnacle with reduced shell plates, epibiotic on many marine taxa, mostly crabs and whales. J, An early dwarf male settled on the surface of an adult Heteralepas. K, Octolasmis cor lives exclusively on the surface of crab gills. L, Scalpellum scalpellum, a stalked barnacle epibiotic with hydroids. The inserts in LM (upper) and SEM (lower) shows the hermaphrodite receptacles, which can house dwarf males. Inserts show a dwarf male with extended penis (upper) and an SEM micrograph of the receptacle structure. M, Waikalasma is a deep-sea inhabitant, having a row of imbricating plates on the base of shells. N, Chthamalus malayensis is common on intertidal shores. O, Tetraclita, with four shell plates, common on rocky and tropical shores.
Figure 8 in The evolutionary diversity of barnacles, with an updated classification of fossil and living forms
Figure 8. Thoracica phylogenetic hypotheses. Comparison of four recent hypotheses on the phylogenetic relationships among recent Thoracica. Note the overall similarity in topology. Major discordances are highlighted by colour. Note especially the difference in the precise position of the genera Capitulum, Lithotrya and Pollicipes, but also that these taxa always appear 'close together' (highlighted in yellow) in the trees. In the analysis by Herrera et al. (2015), these genera are nested inside the Balanomorpha (dotted square). See detailed explanation in the main text.
Figure 4. Rhizocephala. A–H in The evolutionary diversity of barnacles, with an updated classification of fossil and living forms
Figure 4. Rhizocephala. A–H, life cycle stages and larval morphology of selected Rhizocephala. A, nauplius larva of Sacculina carcini. B, male cyprid of S. carcini. C, settled male cyprid of Lernaeodiscus porcellanae in the mantle aperture of a virginal female reproductive body (externa). Box D indicates the receptacle holding the trichogon. D, male trichogon of S. carcini dissected from the mantle cavity of a virginal female externa. E, female cypris of S. carcini. F, kentrogon of S. carcini, inside the empty cuticle of the spent female cyprid, in the process of injecting the primordial parasite. G, vermigon of Loxothylacus panopaei. H, scanning electron micrograph of Peltogaster curvata, showing the reproductive sac (externa) connected to the ramified internal root system. I–P, diversity of selected Rhizocephala externae. I, Peltogasterella sulcata on its host, Pagurus cuanensis. J, Briarosaccus auratum on its host, Lithodes aequispinus. K, Parthenopea subterranea on its host, Calianassa subterranea. L, Sacculina carcini on its host, Carcinus manaeas. M, Thompsonia sp. on its host, Thyraplax truncata, courtesey of Peter Castro. N, Sylon hippolytes on its host, Spirontocaris lilljeborgi. O, Heterosaccus dollfusi on its host, Charybdis longicollis. P, Polyascus gregarius on its host, Eriocheir japonica.
Figure 11 in The evolutionary diversity of barnacles, with an updated classification of fossil and living forms
Figure 11. Moulting and growth in Thoracica. Moulting occurs in the cuticular zones separating shell plates. A, new cuticle is formed by infolded epidermis in a narrow growth zone between two adjacent shell plates. B, old cuticle is shed only above the growth zone. The broken-off cuticle leaves distinct growth lines on either side of the growth zone. C, the new cuticle expands by outfolding; the growth zone is not distinct during intermoults. D, a new growth zone forms for the next moult; the shell plate can now expand laterally under the cuticle; older growth lines can thereby be included on top of the plate. Constructed from descriptions by Mahmoud (1959, 1960), Bourget & Crisp (1975) and Blomsterberg et al. (2004).
Phylogeny and systematics of Sphaeriusidae (Coleoptera: Myxophaga): minute living fossils with underestimated past and present-day diversity
<p>Complete specimen morphology data and sequences used for the analyses.</p>
FIGURES 26–27. Steginoporella discors n in Living and fossil Steginoporellidae (Bryozoa: Cheilostomata) from New Zealand
FIGURES 26–27. Steginoporella discors n. sp. from Terra Nova station 944 (NHMUK1967.2.8.127). 26, autozooids; 27, operculum, showing marginal cuticular teeth. Scalebars respectively 1 mm, 0.2 mm.
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