Sarcopterygii

Sarcopterygii (from Greek sarx, "flesh," and pteryx, "fin") is the major clade of bony vertebrates (Osteichthyes) that comprises two living groups of lobe-finned fishes—Actinistia (the two living species of deep-water coelacanths, Latimeria chalumnae and Latimeria menadoensis) and Dipnoi (the six living species of obligate or facultative air-breathing lungfishes: Neoceratodus, Protopterus, and Lepidosiren)—together with Tetrapoda (all four-limbed terrestrial vertebrates: amphibians and amniotes).

Whereas ray-finned fishes (Actinopterygii) articulate their pectoral and pelvic fins with the shoulder/pelvic girdle via a broad row of three or more small basal radials, sarcopterygians are united by a monobasal endoskeletal fin axis: each paired pectoral and pelvic fin articulates with the girdle via a single proximal long bone—the humerus (in the forelimb) or femur (in the hindlimb)—surrounded by intrinsic appendicular muscles inside a fleshy, scale-covered lobe. This conserved three-part proximal-to-distal endoskeletal architecture (stylopod → zeugopod → autopod) provided the exact biomechanical scaffolding for the Devonian water-to-land transition (~385–360 Ma).

Following the sensational discovery of a living coelacanth (Latimeria chalumnae) off East London, South Africa, in December 1938 by museum curator Marjorie Courtenay-Latimer and ichthyologist J. L. B. Smith (believed extinct since the Late Cretaceous 66 million years ago!), paleontologists and molecular biologists long debated which living sarcopterygian fish—coelacanths (Actinistia) or lungfishes (Dipnoi)—is the true sister group (Rhipidistia) to Tetrapoda.

Whole-genome sequencing of the African coelacanth (Latimeria chalumnae, ~2.86 Gb; Amemiya et al., 2013) and the giant 43-gigabase genome of the Australian lungfish (Neoceratodus forsteri) and 40-gigabase genome of the African lungfish (Protopterus annectens) by Axel Meyer, Manfred Schartl, Guojie Zhang, and colleagues (2021) settled the question unequivocally:

• Dipnoi (Lungfishes) + Tetrapoda form the clade Dipnotetrapodomorpha (Rhipidistia), while Actinistia (Coelacanths) branched off earlier as the basal sister group to all other living sarcopterygians (~415 Ma).
• The Largest Sequenced Animal Genomes: Driven by relentless, uninhibited proliferation of LINE retrotransposons over 300 million years, the Australian lungfish (Neoceratodus forsteri, ~43 Gb—14 times the size of the human genome) and the South American lungfish (Lepidosiren paradoxa, ~91 Gb—30 times the human genome!) possess the largest genomes in the animal kingdom, yet preserve remarkably intact ancestral vertebrate chromosome macro-synteny and pre-adapted genes for pulmonary surfactant, pentadactyl limb enhancers, and terrestrial olfaction (vomeronasal and OR receptors).

Between the Middle and Late Devonian (Givetian–Famennian, ~385–360 Ma), tetrapodomorph lobe-finned fishes evolved step-by-step across tropical deltaic floodplains and shallow weed-choked rivers, documented by a classic series of transitional fossils:

Two Paradigm-Shifting Paleontological Discoveries

1. Tiktaalik roseae (2006): Predicted from geological maps of 375-million-year-old Frasnian river deposits of the Fram Formation on Ellesmere Island (Canadian High Arctic) and discovered in 2004 by Neil H. Shubin, Edward B. Daeschler, and Farish A. Jenkins Jr., Tiktaalik ("large freshwater fish" in Inuktitut) possesses fish scales, fin rays (lepidotrichia), and gill bars alongside a flat tetrapod-like head, a mobile neck (allowing the head to turn independently of the shoulders), overlapping weight-bearing ribs, and a functional bending wrist joint inside its pectoral fin.
2. Digits Evolved Before Vertebrates Left the Water (Acanthostega): Prior to the 1990s, Alfred Sherwood Romer's "drying pond" hypothesis assumed that fish crawled onto land on fins first and only later evolved fingers and toes (digits) for terrestrial walking. When Jennifer A. Clack and Michael I. Coates (1990–1996) prepared complete articulated skeletons of Acanthostega gunnari from Greenland, they discovered that Acanthostega already had 8 fully formed digits on each hand, yet retained internal fish-like gills, a lateral line system, a broad tail fin supported by dermal fin rays, and wrists/ankles incapable of bearing the animal's weight out of water—proving that digits and limbs evolved first in the water to navigate root-choked Devonian shallows, and that the canonical pentadactyl (5-digit) ground plan stabilized only later in Carboniferous crown-tetrapods!

How did developmental evolution transform the distal margin of a sarcopterygian fin (which builds collagenous actinotrichia and bony dermal lepidotrichia fin rays) into a digit-bearing tetrapod hand and foot (autopod)? Comparative embryology and CRISPR functional genomics by Denis Duboule, Neil Shubin, Igor Schneider, Marie Kmita, and Guillaume Andrey identified two decisive genetic switches:

1. Biphasic Regulation of HoxA and HoxD across a TAD Boundary Switch: In both fishes and tetrapods, the HoxD cluster is flanked by two opposing Topologically Associating Domains (TADs):
   • Early Phase (Proximal Limb — Stylopod & Zeugopod): Enhancers in the 3′ telomeric TAD (T-DOM) activate Hoxd9, Hoxd10, and Hoxd11 to build the humerus, radius, and ulna.
   • Late Phase (Distal Limb — The Autopod): In mouse and chick limb buds, CTCF-mediated chromatin looping switches the 5′ genes (Hoxd13 and Hoxa13) over to a battery of 7 island enhancers inside the 5′ centromeric TAD (C-DOM / Global Control Region), driving a strong, sustained wave of Hoxa13 and Hoxd13 across the distal paddle that interacts with the Sonic hedgehog (Shh) ZPA morphogen via a Turing reaction–diffusion mechanism (BMP–Sox9–Wnt) to pattern periodic cartilage condensations (digits). Remarkably, spotted gar, zebrafish, and lungfish already possess the early C-DOM autopod enhancers—showing that the digit-patterning regulatory landscape originated in bony fishes to pattern distal fin radials and was amplified in tetrapods.
2. Deletion of the Fin-Ray Structural Genes (Actinodin 1–4): As shown by Jing Zhang, Marie-Andrée Akimenko, and colleagues (2010), teleost fishes, gars, and coelacanths build the flexible embryonic scaffolding of their finfold out of actinodin proteins encoded by the and1–and4 gene family. During the transition from Tiktaalik to Acanthostega, the entire actinodin gene family was lost from the tetrapod genome, truncating the apical ectodermal fold into a compact Apical Ectodermal Ridge (AER) that prolongs mesenchymal proliferation to build endochondral digits instead of dermal fin rays.

How does the African lungfish (Protopterus) survive up to 4 years encased in dried mud without water or food?

When seasonal rivers dry up across sub-Saharan Africa, Protopterus annectens burrows into the mud, curls its tail over its eyes, and secretes a waterproof mucus cocoon (rich in antimicrobial peptides and neutrophil extracellular traps), entering terrestrial estivation for 1 to 4 years. During estivation, the lungfish breathes air solely through its paired alveolar lungs via a breathing hole, drops its metabolic rate by 80%, converts toxic ammonia into urea via an upregulated ornithine-urea cycle (reaching >200–400 mM plasma urea without uremic toxicity), and catabolizes its own tail musculature for energy until seasonal rains dissolve the cocoon.

Why does the coelacanth (Latimeria) have a hinged joint right across the middle of its braincase?

Latimeria is the only living animal that retains the intracranial joint—a biomechanical hinge dividing the neurocranium into an anterior ethmosphenoid block and a posterior otico-occipital block bridged by the massive, oil-filled, unsegmented notochord and operated by paired basicranial muscles. This intracranial hinge was universal among Devonian sarcopterygian fishes (Eusthenopteron), before the two halves of the braincase fused solidly together in Panderichthys, Tiktaalik, and tetrapods.

1. Daeschler, E. B., Shubin, N. H., & Jenkins, F. A. (2006). A Devonian tetrapod-like fish and the evolution of the tetrapod body plan. Nature, 440(7085), 757–763. doi:10.1038/nature04639
2. Coates, M. I., & Clack, J. A. (1990). Polydactyly in the earliest known tetrapod limbs. Nature, 347(6288), 66–69. doi:10.1038/347066a0
3. Amemiya, C. T., Alföldi, J., Lee, A. P., Fan, S., Philippe, H., MacCallum, I., ... & Lindblad-Toh, K. (2013). The African coelacanth genome provides insights into tetrapod evolution. Nature, 496(7445), 311–316. doi:10.1038/nature12027
4. Meyer, A., Schloissnig, S., Franchini, P., Du, K., Woltering, J. M., Irisarri, I., ... & Schartl, M. (2021). Giant lungfish genome elucidates the conquest of land by vertebrates. Nature, 590(7845), 284–289. doi:10.1038/s41586-021-03198-8
5. Zhang, J., Wagh, P., Guay, D., Sanchez-Pulido, L., Padhi, B. K., Korzh, V., ... & Akimenko, M. A. (2010). Loss of fish actinotrichia proteins and the fin-to-limb transition. Nature, 466(7303), 234–237. doi:10.1038/nature09137