A median fin derived from the lateral plate mesoderm and the origin of paired fins.

The development of paired appendages was a key innovation during evolution and facilitated the aquatic to terrestrial transition of vertebrates. Largely derived from the lateral plate mesoderm (LPM), one hypothesis for the evolution of paired fins invokes derivation from unpaired median fins via a pair of lateral fin folds located between pectoral and pelvic fin territories. Whilst unpaired and paired fins exhibit similar structural and molecular characteristics, no definitive evidence exists for paired lateral fin folds in larvae or adults of any extant or extinct species.

An Fgf-Shh positive feedback loop drives growth in developing unpaired fins.

The origin and diversification of appendage types is a central question in vertebrate evolution. Understanding the genetic mechanisms that underlie fin and limb development can reveal relationships between different appendages. Here we demonstrate, using chemical genetics, a mutually agonistic interaction between Fgf and Shh genes in the developing dorsal fin of the channel catfish, .

Deploying Big Data to Crack the Genotype to Phenotype Code.

Mechanistically connecting genotypes to phenotypes is a longstanding and central mission of biology. Deciphering these connections will unite questions and datasets across all scales from molecules to ecosystems. Although high-throughput sequencing has provided a rich platform on which to launch this effort, tools for deciphering mechanisms further along the genome to phenome pipeline remain limited.

Deep evolutionary origin of limb and fin regeneration.

Salamanders and lungfishes are the only sarcopterygians (lobe-finned vertebrates) capable of paired appendage regeneration, regardless of the amputation level. Among actinopterygians (ray-finned fishes), regeneration after amputation at the fin endoskeleton has only been demonstrated in polypterid fishes (Cladistia). Whether this ability evolved independently in sarcopterygians and actinopterygians or has a common origin remains unknown.

Insights into electrosensory organ development, physiology and evolution from a lateral line-enriched transcriptome.

The anamniote lateral line system, comprising mechanosensory neuromasts and electrosensory ampullary organs, is a useful model for investigating the developmental and evolutionary diversification of different organs and cell types. Zebrafish neuromast development is increasingly well understood, but neither zebrafish nor is electroreceptive and our molecular understanding of ampullary organ development is rudimentary. We have used RNA-seq to generate a lateral line-enriched gene-set from late-larval paddlefish ().

HoxD expression in the fin-fold compartment of basal gnathostomes and implications for paired appendage evolution.

The role of Homeobox transcription factors during fin and limb development have been the focus of recent work investigating the evolutionary origin of limb-specific morphologies. Here we characterize the expression of HoxD genes, as well as the cluster-associated genes Evx2 and LNP, in the paddlefish Polyodon spathula, a basal ray-finned fish. Our results demonstrate a collinear pattern of nesting in early fin buds that includes HoxD14, a gene previously thought to be isolated from global Hox regulation.

Making teeth to order: conserved genes reveal an ancient molecular pattern in paddlefish (Actinopterygii).

Ray-finned fishes (Actinopterygii) are the dominant vertebrate group today (+30 000 species, predominantly teleosts), with great morphological diversity, including their dentitions. How dental morphological variation evolved is best addressed by considering a range of taxa across actinopterygian phylogeny; here we examine the dentition of Polyodon spathula (American paddlefish), assigned to the basal group Acipenseriformes. Although teeth are present and functional in young individuals of Polyodon, they are completely absent in adults.

The deep homology of the autopod: insights from hox gene regulation.

The evolution of tetrapod limbs from fish fins was a significant functional and morphological shift, but how significant was it in terms of the underlying genetic mechanisms? The fossil record provides insight into the morphological changes. However, to understand the underlying mechanisms, we must peer into the gene regulatory networks of living vertebrates. Analysis of HoxA/D expression in a basal actinopterygian, the North American paddlefish, Polyodon spathula, reveals patterns of expression long considered to be a unique developmental signature of the autopod (hands/feet, digits) and shown in tetrapods to be controlled by a "digit enhancer" regulatory landscape.

Electrosensory ampullary organs are derived from lateral line placodes in bony fishes.

Electroreception is an ancient subdivision of the lateral line sensory system, found in all major vertebrate groups (though lost in frogs, amniotes and most ray-finned fishes). Electroreception is mediated by 'hair cells' in ampullary organs, distributed in fields flanking lines of mechanosensory hair cell-containing neuromasts that detect local water movement. Neuromasts, and afferent neurons for both neuromasts and ampullary organs, develop from lateral line placodes.

An autopodial-like pattern of Hox expression in the fins of a basal actinopterygian fish.

Comparative analyses of Hox gene expression and regulation in teleost fish and tetrapods support the long-entrenched notion that the distal region of tetrapod limbs, containing the wrist, ankle and digits, is an evolutionary novelty. Data from fossils support the notion that the unique features of tetrapod limbs were assembled over evolutionary time in the paired fins of fish. The challenge in linking developmental and palaeontological approaches has been that developmental data for fins and limbs compare only highly derived teleosts and tetrapods; what is lacking are data from extant taxa that retain greater portions of the fin skeletal morphology considered primitive to all bony fish.

Sonic hedgehog function in chondrichthyan fins and the evolution of appendage patterning.

The genetic mechanisms regulating tetrapod limb development are well characterized, but how they were assembled during evolution and their function in basal vertebrates is poorly understood. Initial studies report that chondrichthyans, the most primitive extant vertebrates with paired appendages, differ from ray-finned fish and tetrapods in having Sonic hedgehog (Shh)-independent patterning of the appendage skeleton. Here we demonstrate that chondrichthyans share patterns of appendage Shh expression, Shh appendage-specific regulatory DNA, and Shh function with ray-finned fish and tetrapods.

Pectoral fin and girdle development in the basal actinopterygians Polyodon spathula and Acipenser transmontanus.

The pectoral fins of Acipenseriformes possess endoskeletons with elements homologous to both the fin radials of teleosts and the limb bones of tetrapods. Here we present a study of pectoral fin development in the North American paddlefish, Polyodon spathula, and the white sturgeon, Acipenser transmontanus, which reveals that aspects of both teleost and tetrapod endoskeletal patterning mechanisms are present in Acipenseriformes. Those elements considered homologous to teleost radials, the propterygium and the mesopterygial radials, form via subdivision of an initially chondrogenic plate of mesenchymal cells called the endoskeletal disc.