Tracing the genetic footprints of vertebrate landing in non-teleost ray-finned fishes.

Rich fossil evidence suggests that many traits and functions related to terrestrial evolution were present long before the ancestor of lobe- and ray-finned fishes. Here, we present genome sequences of the bichir, paddlefish, bowfin, and alligator gar, covering all major early divergent lineages of ray-finned fishes. Our analyses show that these species exhibit many mosaic genomic features of lobe- and ray-finned fishes. In particular, many regulatory elements for limb development are present in these fishes, supporting the hypothesis that the relevant ancestral regulation networks emerged before the origin of tetrapods. Transcriptome analyses confirm the homology between the lung and swim bladder and reveal the presence of functional lung-related genes in early ray-finned fishes. Furthermore, we functionally validate the essential role of a jawed vertebrate highly conserved element for cardiovascular development. Our results imply the ancestors of jawed vertebrates already had the potential gene networks for cardio-respiratory systems supporting air breathing.

African lungfish genome sheds light on the vertebrate water-to-land transition.

Lungfishes are the closest extant relatives of tetrapods and preserve ancestral traits linked with the water-to-land transition. However, their huge genome sizes have hindered understanding of this key transition in evolution. Here, we report a 40-Gb chromosome-level assembly of the African lungfish (Protopterus annectens) genome, which is the largest genome assembly ever reported and has a contig and chromosome N50 of 1.60 Mb and 2.81 Gb, respectively. The large size of the lungfish genome is due mainly to retrotransposons. Genes with ultra-long length show similar expression levels to other genes, indicating that lungfishes have evolved high transcription efficacy to keep gene expression balanced. Together with transcriptome and experimental data, we identified potential genes and regulatory elements related to such terrestrial adaptation traits as pulmonary surfactant, anxiolytic ability, pentadactyl limbs, and pharyngeal remodeling. Our results provide insights and key resources for understanding the evolutionary pathway leading from fishes to humans.

The oldest complete jawed vertebrates from the early Silurian of China.

Molecular studies suggest that the origin of jawed vertebrates was no later than the Late Ordovician period (around 450 million years ago (Ma))1,2. Together with disarticulated micro-remains of putative chondrichthyans from the Ordovician and early Silurian period3-8, these analyses suggest an evolutionary proliferation of jawed vertebrates before, and immediately after, the end-Ordovician mass extinction. However, until now, the earliest complete fossils of jawed fishes for which a detailed reconstruction of their morphology was possible came from late Silurian assemblages (about 425 Ma)9-13. The dearth of articulated, whole-body fossils from before the late Silurian has long rendered the earliest history of jawed vertebrates obscure. Here we report a newly discovered Konservat-Lagerstätte, which is marked by the presence of diverse, well-preserved jawed fishes with complete bodies, from the early Silurian (Telychian age, around 436 Ma) of Chongqing, South China. The dominant species, a 'placoderm' or jawed stem gnathostome, which we name Xiushanosteus mirabilis gen. et sp. nov., combines characters from major placoderm subgroups14-17 and foreshadows the transformation of the skull roof pattern from the placoderm to the osteichthyan condition10. The chondrichthyan Shenacanthus vermiformis gen. et sp. nov. exhibits extensive thoracic armour plates that were previously unknown in this lineage, and include a large median dorsal plate as in placoderms14-16, combined with a conventional chondrichthyan bauplan18,19. Together, these species reveal a previously unseen diversification of jawed vertebrates in the early Silurian, and provide detailed insights into the whole-body morphology of the jawed vertebrates of this period.

A Silurian placoderm with osteichthyan-like marginal jaw bones.

The gnathostome (jawed vertebrate) crown group comprises two extant clades with contrasting character complements. Notably, Chondrichthyes (cartilaginous fish) lack the large dermal bones that characterize Osteichthyes (bony fish and tetrapods). The polarities of these differences, and the morphology of the last common ancestor of crown gnathostomes, are the subject of continuing debate. Here we describe a three-dimensionally preserved 419-million-year-old placoderm fish from the Silurian of China that represents the first stem gnathostome with dermal marginal jaw bones (premaxilla, maxilla and dentary), features previously restricted to Osteichthyes. A phylogenetic analysis places the new form near the top of the gnathostome stem group but does not fully resolve its relationships to other placoderms. The analysis also assigns all acanthodians to the chondrichthyan stem group. These results suggest that the last common ancestor of Chondrichthyes and Osteichthyes had a macromeric dermal skeleton, and provide a new framework for studying crown gnathostome divergence.

Bony-fish-like scales in a Silurian maxillate placoderm.

Major groups of jawed vertebrates exhibit contrasting conditions of dermal plates and scales. But the transition between these conditions remains unclear due to rare information on taxa occupying key phylogenetic positions. The 425-million-year-old fish Entelognathus combines an unusual mosaic of characters typically associated with jawed stem gnathostomes or crown gnathostomes. However, only the anterior part of the exoskeleton was previously known for this very crownward member of the gnathostome stem. Here, we report a near-complete post-thoracic exoskeleton of Entelognathus. Strikingly, its scales are large and some are rhomboid, bearing distinctive peg-and-socket articulations; this combination was previously only known in osteichthyans and considered a synapomorphy of that group. The presence in Entelognathus of an anal fin spine, previously only found in some stem chondrichthyans, further illustrates that many characters previously thought to be restricted to specific lineages within the gnathostome crown likely arose before the common ancestor of living jawed vertebrates.

Endocast and Bony Labyrinth of a Devonian "Placoderm" Challenges Stem Gnathostome Phylogeny.

Our understanding of the earliest evolution of jawed vertebrates depends on a credible phylogenetic framework for the jawed stem gnathostomes collectively known as "placoderms".1 However, their relationships, and whether placoderms represent a single radiation or a paraphyletic array, remain contentious.2-13 This uncertainty is compounded by an uneven understanding of anatomy across the group, particularly of the phylogenetically informative braincase and brain cavity-endocast. Based on new tomographic data, we here describe the endocast and bony labyrinth of Brindabellaspis stensioi from the Early Devonian of New South Wales.14 The taxon was commonly recovered as branching near the base of placoderms.5-9,11,12,15-17 Previous studies of Brindabellaspis emphasized its resemblances with fossil jawless fishes in the braincase anatomy14 and endocast proportions1,18 and its distinctive features were interpreted as autapomorphies, such as the elongated premedian region.19 Although our three-dimensional data confirmed the resemblance of its endocast to those of jawless vertebrates, we discovered that the inner ear and endolymphatic complex display a repertoire of previously unrecognized characters close to modern or crown-group jawed vertebrates, including a pronounced sinus superior and a vertical duct that connects the endolymphatic sac and the labyrinth cavity. Both parsimony and Bayesian analyses suggest that prevailing hypotheses of placoderm relationships are unstable, with newly revealed anatomy pointing to a radical revision of early gnathostome evolution. Our results call into question the appropriateness of arthrodire-like placoderms as models of primitive gnathostome anatomy and raise questions of homology relating to key cranial features.

A new Silurian fish close to the common ancestor of modern gnathostomes.

The Silurian Period occupies a pivotal stage in the unfolding of key evolutionary events, including the rise of jawed vertebrates.1-4 However, the understanding of this early diversification is often hampered by the patchy nature of the Silurian fossil record,5 with the articulated specimens of jawed vertebrates only known in isolated localities, most notably Qujing, Yunnan, China.6-9 Here, we report a new Silurian maxillate placoderm, Bianchengichthys micros, from the Ludlow of Chongqing, with a near-complete dermatoskeleton preserved in articulation. Although geographically separated, the new taxon resembles the previously reported Qilinyu in possessing a unique combination of dermatoskeletal characters. However, the dermal bone of the mandible in Bianchengichthys unexpectedly differs from those in both Qilinyu and Entelognathus and displays a broad oral lamina carrying a line of tooth-like denticles, in addition to the marginal toothless flange. The external morphology of the pectoral fin is preserved and reveals an extensively scale-covered lobate part, flanked by a fringe of lepidotrichia-like aligned scales. The phylogenetic analysis reveals that Bianchengichthys is positioned immediately below Entelognathus plus modern gnathostomes. The discovery significantly widens the distribution of Silurian placoderm-grade gnathostomes in South China and provides a range of morphological disparity for the outgroup comparison to the earliest evolution of jaws, dentitions, and pectoral fins in modern gnathostomes. We also demonstrate that the previously reported Silurian placoderms from central Vietnam10 are maxillate placoderms close to Qilinyu, Silurolepis, and Bianchengichthys, corroborating the paleogeographic proximity between the Indochina and South China blocks during the Middle Paleozoic.11.

Reappraisal of the Silurian placoderm Silurolepis and insights into the dermal neck joint evolution.

Silurolepis platydorsalis, a Silurian jawed vertebrate originally identified as an antiarch, is here redescribed as a maxillate placoderm close to Qilinyu and is anteroposteriorly reversed as opposed to the original description. The cuboid trunk shield possesses three longitudinal cristae, obstanic grooves on the trunk shield and three median dorsal plates, all uniquely shared with Qilinyu. Further preparation reveals the morphology of the dermal neck joint, with slot-shaped articular fossae on the trunk shield similar to Qilinyu and antiarchs. However, new tomographic data reveal that Qilinyu uniquely bears a dual articulation between the skull roof and trunk shield, which does not fit into the traditional 'ginglymoid' and 'reverse ginglymoid' categories. An extended comparison in early jawed vertebrates confirms that a sliding-type dermal neck joint is widely distributed and other types are elaborated in different lineages by developing various laminae. Nine new characters related to the dermal neck joint are proposed for a new phylogenetic analysis, in which Silurolepis forms a clade with Qilinyu. The current phylogenetic framework conflicts with the parsimonious evolution of dermal neck joints in suggesting that the shared trunk shield characters between antiarchs and Qilinyu are independently acquired, and the sliding-type joint in Entelognathus is reversely evolved from the dual articulation in Qilinyu.

A Devonian predatory fish provides insights into the early evolution of modern sarcopterygians.

Crown or modern sarcopterygians (coelacanths, lungfishes, and tetrapods) differ substantially from stem sarcopterygians, such as Guiyu and Psarolepis, and a lack of transitional fossil taxa limits our understanding of the origin of the crown group. The Onychodontiformes, an enigmatic Devonian predatory fish group, seems to have characteristics of both stem and crown sarcopterygians but is difficult to place because of insufficient anatomical information. We describe the new skull material of Qingmenodus, a Pragian (~409-million-year-old) onychodont from China, using high-resolution computed tomography to image internal structures of the braincase. In addition to its remarkable similarities with stem sarcopterygians in the ethmosphenoid portion, Qingmenodus exhibits coelacanth-like neurocranial features in the otic region. A phylogenetic analysis based on a revised data set unambiguously assigns onychodonts to crown sarcopterygians as stem coelacanths. Qingmenodus thus bridges the morphological gap between stem sarcopterygians and coelacanths and helps to illuminate the early evolution and diversification of crown sarcopterygians.

A Silurian maxillate placoderm illuminates jaw evolution.

The discovery of Entelognathus revealed the presence of maxilla, premaxilla, and dentary, supposedly diagnostic osteichthyan bones, in a Silurian placoderm. However, the relationship between these marginal jaw bones and the gnathal plates of conventional placoderms, thought to represent the inner dental arcade, remains uncertain. Here we report a second Silurian maxillate placoderm, which bridges the gnathal and maxillate conditions. We propose that the maxilla, premaxilla, and dentary are homologous to the gnathal plates of placoderms and that all belong to the same dental arcade. The gnathal-maxillate transformation occurred concurrently in upper and lower jaws, predating the addition of infradentary bones to the lower jaw.

The largest Silurian vertebrate and its palaeoecological implications.

An apparent absence of Silurian fishes more than half-a-metre in length has been viewed as evidence that gnathostomes were restricted in size and diversity prior to the Devonian. Here we describe the largest pre-Devonian vertebrate (Megamastax amblyodus gen. et sp. nov.), a predatory marine osteichthyan from the Silurian Kuanti Formation (late Ludlow, ~423 million years ago) of Yunnan, China, with an estimated length of about 1 meter. The unusual dentition of the new form suggests a durophagous diet which, combined with its large size, indicates a considerable degree of trophic specialisation among early osteichthyans. The lack of large Silurian vertebrates has recently been used as constraint in palaeoatmospheric modelling, with purported lower oxygen levels imposing a physiological size limit. Regardless of the exact causal relationship between oxygen availability and evolutionary success, this finding refutes the assumption that pre-Emsian vertebrates were restricted to small body sizes.