A crucial evolutionary change in vertebrate history was the Palaeozoic (Devonian 419–359 million years ago) water-to-land transition, allowed by key morphological and physiological modifications including the acquisition of lungs. Nonetheless, the origin and early evolution of vertebrate lungs remain highly controversial, particularly whether the ancestral state was paired or unpaired. Due to the rarity of fossil soft tissue preservation, lung evolution can only be traced based on the extant phylogenetic bracket. Here we investigate, for the first time, lung morphology in extensive developmental series of key living lunged osteichthyans using synchrotron x-ray microtomography and histology. Our results shed light on the primitive state of vertebrate lungs as unpaired, evolving to be truly paired in the lineage towards the tetrapods. The water-to-land transition confronted profound physiological challenges and paired lungs were decisive for increasing the surface area and the pulmonary compliance and volume, especially during the air-breathing on land.

Coelacanths are lobe-finned fishes known from the Devonian to Recent that were long considered extinct, until the discovery of two living species in deep marine waters of the Mozambique Channel and Sulawesi. Despite extensive studies, the pulmonary system of extant coelacanths has not been fully investigated. Here we confirm the presence of a lung and discuss its allometric growth inLatimeria chalumnae, based on a unique ontogenetic series. Our results demonstrate the presence of a potentially functional, well-developed lung in the earliest known coelacanth embryo, and its arrested growth at later ontogenetic stages, when the lung is clearly vestigial. The parallel development of a fatty organ for buoyancy control suggests a unique adaptation to deep-water environments. Furthermore, we provide the first evidence for the presence of small, hard, flexible plates around the lung inL. chalumnae, and consider them homologous to the plates of the ‘calcified lung’ of fossil coelacanths.

Fossils, including those that occasionally preserve decay-prone soft tissues, are mostly made of minerals. Accessing their chemical composition provides unique insight into their past biology and/or the mechanisms by which they preserve, leading to a series of developments in chemical and elemental imaging. However, the mineral composition of fossils, particularly where soft tissues are preserved, is often only inferred indirectly from elemental data, while X-ray diffraction that specifically provides phase identification received little attention. Here, we show the use of synchrotron radiation to generate not only X-ray fluorescence elemental maps of a fossil, but also mineralogical maps in transmission geometry using a two-dimensional area detector placed behind the fossil. This innovative approach was applied to millimetre-thick cross-sections prepared through three-dimensionally preserved fossils, as well as to compressed fossils. It identifies and maps mineral phases and their distribution at the microscale over centimetre-sized areas, benefitting from the elemental information collected synchronously, and further informs on texture (preferential orientation), crystallite size and local strain. Probing such crystallographic information is instrumental in defining mineralization sequences, reconstructing the fossilization environment and constraining preservation biases. Similarly, this approach could potentially provide new knowledge on other (bio)mineralization processes in environmental sciences. We also illustrate that mineralogical contrasts between fossil tissues and/or the encasing sedimentary matrix can be used to visualize hidden anatomies in fossils.

The presence of a pulmonary organ that is entirely covered by true bone tissue and fills most of the abdominal cavity is hitherto unique to fossil actinistians. Although small hard plates have been recently reported in the lung of the extant coelacanthLatimeria chalumnae, the homology between these hard structures in fossil and extant forms remained to be demonstrated. Here, we resolve this question by reporting the presence of a similar histological pattern–true cellular bone with star-shaped osteocytes, and a globular mineralisation with radiating arrangement–in the lung plates of two fossil coelacanths (Swenzia latimeraeandAxelrodichthys araripensis) and the plates that surround the lung of the most extensively studied extant coelacanth species,L. chalumnae. The point-for-point structural similarity of the plates in extant and fossil coelacanths supports their probable homology and, consequently, that of the organ they surround. Thus, this evidence questions the previous interpretations of the fatty organ as a component of the pulmonary complex ofLatimeria.

Lungs are specialized organs originated from the posterior pharyngeal cavity and considered as plesiomorphic for osteichthyans, as they are found in extant basal actinopterygians (i.e.Polypterus) and in all major groups of extant sarcopterygians. The presence of a vestigial lung in adult stages of the extant coelacanthLatimeria chalumnaeis the result of allometric growth during ontogeny, in relation with long-time adaptation to deep water. Here, we present the first detailed histological and anatomical description of the lung ofLatimeria chalumnae, providing new insights into its arrested differentiation in an air-breathing complex, mainly represented by the absence of pneumocytes and of compartmentalization in the latest ontogenetic stages.