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Supplementary Note 1 : Melanin chemistry- background. Supplementary Note 2: Geological setting. Supplementary Note 3: Details of sulfur oxidation. Supplementary Figure 1. XRD analysis of the lateral fossil. Sedimentary matrix (brown profile) compared to the body of the fossil (black profile). Supplementary Figure 2. Correlation maps. Supplementary Figure 2. Correlation maps (cont.). Supplementary Figure 3. Individual SRS-XRF maps of selected elements in the lateral fossil. Supplementary Figure 4. SRS-XRF maps of the dorsal fossil. Supplementary Figure 5. Fits to the EXAFS data. Supplementary Figure 5 (continued). Fits to the EXAFS data. Supplementary Figure 6. Melanin in extant tissue. Supplementary Figure 7. Red human hair analyses. Supplementary Figure 8. SRS-XRF point analyses. Supplementary Figure 8 (continued). SRS-XRF point analyses. Supplementary Figure 9. SRS-XRF map of normally pigmented Mus musculus. Supplementary Figure 10. FTIR analyses. Supplementary Figure 11. ESEM analyses. Supplementary Figure 11 (continued). ESEM analyses. Supplementary Figure 12A. Optical images to show details of fossil separation. Supplementary Figure 12B (continued). Optical images to show details of fossil separation. Supplementary Figure 12C (continued). Optical images to show details of fossil separation. 25 Supplementary Figure 12C (continued). Optical images to show details of fossil separation. Optical photograph of the dorsal fossil [GZG.W.17393a, left] compared to its counterpart [GZG.W.17393b, right]. Scale bar in cm. A fourth region is highlighted for comparison to check whether uneven separation of soft tissue between part and counterpart could explain the lack of chemical residue in the scanned images. (Copyright for these photos: GZG Museum / G. Hundertmark.) Supplementary Figure 12D (continued). Optical images to show details of fossil separation. Supplementary Table 1. Sulfur speciation and quantification. Supplementary Table 2. Calibrated energies for dominant su

Agaresuchus fontisensis is an allodaposuchid crocodile from the Campanian–Maastrichtian (Late Cretaceous) of Lo Hueco (Cuenca, Spain). Allodaposuchidae is a clade of European basal eusuchians, which is considered a part of the stem group of Crocodylia. The holotype and paratype skulls of Agaresuchus fontisensis were scanned on computed tomography and their internal cavities, including those of the brain, nerves and blood vessels, as well as the paratympanic sinus system and the paranasal sinuses, digitally reconstructed. The cranial endocast and pneumatic sinuses were then compared with those of other crocodyliforms. The neuroanatomy of Agaresuchus fontisensis resembles those of other mesoeucrocodylians, sharing some morphological traits with extant crocodiles. The neurosensorial and cognitive capabilities inferred from the inner skull cavity reconstructions of Agaresuchus fontisensis are similar to those of other eusuchians. The olfactory acuity of Agaresuchus fontisensis is low by crocodylian standards, closer to that of the alligatoroids rather than to that of the crocodyloids. Its visual acuity is similar to that of Lohuecosuchus megadontos, a sympatric allodaposuchid also found in the fossil site of Lo Hueco.

Proa valdearinnoensis is a relatively large-headed and stocky iguanodontian dinosaur from the latest Early Cretaceous of Spain. Its braincase is known from three specimens. Similar to that of other dinosaurs, it shows a mosaic ossification pattern in which most of the bones seem to have fused together indistinguishably while a few (frontoparietal, basioccipital) might have remained loosely attached. The endocasts of the three specimens are described based on CT data and digital reconstructions. They show unmistakable morphological similarities with the endocast of closely related taxa, such as Sirindhorna khoratensis (which is close in age but from Thailand). This supports a high conservatism of the endocranial cavity. The issue of volumetric correspondence between endocranial cavity and brain in dinosaurs is analyzed. Although a brain-to-endocranial cavity (BEC) index of 0.50 has been traditionally used, we employ instead 0.73. This is indeed the mid-value between the situation in adults of Alligator mississippiensis and Gallus gallus, which are members of the extant bracketing taxa of dinosaurs (Crocodilia and Aves). We thence gauge the level of encephalization of P. valdearinnoensis through the calculation of the encephalization quotient (EQ), which remains valuable as a metric for assessing the degree of cognitive function in extinct taxa, especially those with fully ossified braincases like dinosaurs and other archosaurs. The EQ obtained for P. valdearinnoensis (3.611) suggests that this species was significantly more encephalized than most if not all extant nonavian, non-mammalian amniotes. Our work adds to the growing body of data concerning theo- retical cognitive capabilities in dinosaurs and supports the idea that an increasing encephalization was fostered not only in theropods but also in parallel in the shorter-lived lineage of ornithopods. P. valdearinnoensis was ill-equipped to respond to theropod dinosaurs and possibly lived in groups as a strategy to

In birds, the brain (especially the telencephalon) is remarkably developed, both in relative volume and complexity. Unlike in most early-branching sauropsids, the adults of birds and other archosaurs have a well-ossified neurocranium. In contrast to the situation in most of their reptilian relatives but similar to what can be seen in mammals, the brains of birds fit closely to the endocranial cavity so that their major external features are reflected in the endocasts. This makes birds a highly suitable group for palaeoneurological investigations. The first observation about the brain in a long-extinct bird was made in the first quarter of the 19th century. However, it was not until the 2000s and the application of modern imaging technologies that avian palaeoneurology really took off. Understanding how the mode of life is reflected in the external morphology of the brains of birds is but one of several future directions in which avian palaeoneurological research may extend. Although the number of fossil specimens suitable for palaeoneurological explorations is considerably smaller in birds than in mammals and will very likely remain so, the coming years will certainly witness a momentous strengthening of this rapidly growing field of research at the overlap between ornithology, palaeontology, evolutionary biology and neurosciences.

Despite continuous improvements, our knowledge of the palaeoneurology of sauropod dinosaurs is still deficient. This holds true even for Titanosauria, which is a particularly speciose clade of sauropods with representatives known from numerous Cretaceous sites in many countries on all continents. The data currently available regarding the palaeoneurology of titanosaurs is strongly biased towards Gondwanan forms (Argentina above all, but also India, Malawi and Australia). In contrast, the palaeoneurology of Laurasian titanosaurs is known only from a few taxa from Spain and Uzbekistan, despite the discovery in other countries of Laurasia of a number of neurocranial remains that would lend themselves well to investigations of this kind. To fill in this gap in our knowledge, we subjected a titanosaurian braincase from the uppermost Upper Cretaceous of southern France to X-ray computed tomographic scanning, allowing the generation of 3D renderings of the endocranial cavity enclosing the brain, cranial nerves and blood vessels, as well as the labyrinth of the inner ear. These reconstructions are used to clarify the phylogenetic position of the specimen from the Fox-Amphoux-Metisson site. A combination of characters, including the presence of two hypoglossal rami on the endocast, the average degree of development of the dorsal-head/caudal-middle-cerebral vein system and the relatively short and subequal lengths of the ipsilateral semicircular canals of the labyrinth, are particularly revealing in this respect. They suggest that, compared with the few other Laurasian titanosaurs for which in-depth palaeoneurological data are available, the French taxon is more derived than the distinctly more ancient, possibly non-lithostrotian titanosaur from the Uzbek site of Dzharakuduk but more basal than derived saltasaurids, such as the coeval or slightly more recent forms from the Spanish locality of Lo Hueco.

Recent progress has been made in paleontology with respect to resolving pigmentation in fossil material. Morphological identification of fossilized melanosomes has been one approach, while a second methodology using chemical imaging and spectroscopy has also provided critical information particularly concerning eumelanin (black pigment) residue. In this work we develop the chemical imaging methodology to show that organosulfur-Zn complexes are indicators of pheomelanin (red pigment) in extant and fossil soft tissue and that the mapping of these residual biochemical compounds can be used to restore melanin pigment distribution in a 3 million year old extinct mammal species (Apodemus atavus). Synchotron Rapid Scanning X-ray Fluorescence imaging showed that the distributions of Zn and organic S are correlated within this fossil fur just as in pheomelanin-rich modern integument. Furthermore, Zn coordination chemistry within this fossil fur is closely comparable to that determined from pheomelanin-rich fur and hair standards. The non-destructive methods presented here provide a protocol for detecting residual pheomelanin in precious specimens.

Karydomys is a rare and little diversified democricetodontine, of which only six species are currently recognized. This group of rodents is first recorded in the early Miocene (MN3) in China and spread quickly thereafter to Kazakhstan and Greece (MN4). Karydomys reached south-western and central Europe by early middle Miocene times (MN5), from where it became extinct shortly thereafter (MN6). A new species of Karydomys is here described from the Miocene Keramia Formation of Chios Island (north-eastern Aegean Sea). Karydomys strati sp. nov. is characterized by the presence of a labial spur on the anterolophule, the lack of anterior protolophule on the M1 and by the presence of a double metalophule on the M2. A cladistics analysis involving all the species of Karydomys and some closely related species of Democricetodon and Cricetodon show that Karydomys split early into two different lineages, an ‘eastern stock’, which includes the central Asian (K. debruijni and K. dzerzhinskii) and Greek (K. symeonidisi, K. boskosi and K. strati) species, and a ‘western lineage’ comprising the western and central European species (K. wigharti and K. zapfei). The evolutionary stage of Karydomys strati suggests that the lowermost part of the Keramia Formation, usually attributed to the middle Miocene, is older than previously thought.

Despite continuous improvements, our knowledge of the palaeoneurology of sauropod dinosaurs is still deficient. This holds true even for Titanosauria, which is a particularly speciose clade of sauropods with representatives known from numerous Cretaceous sites in many countries on all continents. The data currently available regarding the palaeoneurology of titanosaurs is strongly biased towards Gondwanan forms (Argentina above all, but also India, Malawi and Australia). In contrast, the palaeoneurology of Laurasian titanosaurs is known only from a few taxa from Spain and Uzbekistan, despite the discovery in other countries of Laurasia of a number of neurocranial remains that would lend themselves well to investigations of this kind. To fill in this gap in our knowledge, we subjected a titanosaurian braincase from the uppermost Upper Cretaceous of southern France to X-ray computed tomographic scanning, allowing the generation of 3D renderings of the endocranial cavity enclosing the brain, cranial nerves and blood vessels, as well as the labyrinth of the inner ear. These reconstructions are used to clarify the phylogenetic position of the specimen from the Fox-Amphoux-Métisson site. A combination of characters, including the presence of two hypoglossal rami on the endocast, the average degree of development of the dorsal-head/caudal-middle-cerebral vein system and the relatively short and subequal lengths of the ipsilateral semicircular canals of the labyrinth, are particularly revealing in this respect. They suggest that, compared with the few other Laurasian titanosaurs for which in-depth palaeoneurological data are available, the French taxon is more derived than the distinctly more ancient, possibly non-lithostrotian titanosaur from the Uzbek site of Dzharakuduk but more basal than derived saltasaurids, such as the coeval or slightly more recent forms from the Spanish locality of Lo Hueco.

Recent extensive field prospecting conducted in the Upper Miocene of Lebanon resulted in the discovery of several new fossiliferous localities. One of these, situated in the Zahleh area (Bekaa Valley, central Lebanon) has yielded a particularly diverse vertebrate fauna. Micromammals constitute an important part of this assemblage because not only do they represent the first Neogene rodents and insectivores from Lebanon, but they are also the only ones from the early Late Miocene of the Arabian Peninsula and circumambient areas. Analyses of the murines from Zahleh reveal that they belong to a small-sized early Progonomys, which cannot be assigned to any of the species of the genus hitherto described. They are, thereby, shown to represent a new species: Progonomys manolo. Morphometric analyses of the outline of the first upper molars of this species suggest a generalist and omnivorous diet. This record sheds new light onto a major phenomenon in the evolutionary history of rodents, which is the earliest dispersal of mice. It suggests that the arrival of murines in Africa got under way through the Levant rather than via southern Europe and was monitored by the ecological requirements of Progonomys.

Fossils of juvenile Mesozoic birds provide insight into the early evolution of avian development, however such fossils are rare. The analysis of the ossification sequence in these early-branching birds has the potential to address important questions about their comparative developmental biology and to help understand their morphological evolution and ecological differentiation. Here we report on an early juvenile enantiornithine specimen from the Early Cretaceous of Europe, which sheds new light on the osteogenesis in this most species-rich clade of Mesozoic birds. Consisting of a nearly complete skeleton, it is amongst the smallest known Mesozoic avian fossils representing post-hatching stages of development. Comparisons between this new specimen and other known early juvenile enantiornithines support a clade-wide asynchronous pattern of osteogenesis in the sternum and the vertebral column, and strongly indicate that the hatchlings of these phylogenetically basal birds varied greatly in size and tempo of skeletal maturation.

Monitor lizards (genus Varanus) inhabited Europe at least from the early Miocene to the Pleistocene. Their fossil record is limited to about 40 localities that have provided mostly isolated vertebrae. Due to the poor diagnostic value of these fossils, it was recently claimed that all the European species described prior to the 21st century are not taxonomically valid and a new species, Varanus amnhophilis, was erected on the basis of fragmentary material including cranial elements, from the late Miocene of Samos (Greece). We re-examined the type material of Varanus marathonensis Weithofer, 1888, based on material from the late Miocene of Pikermi (Greece), and concluded that it is a valid, diagnosable species. Previously unpublished Iberian material from the Aragonian (middle Miocene) of Abocador de Can Mata (Vallès-Penedès Basin, Barcelona) and the Vallesian (late Miocene) of Batallones (Madrid Basin) is clearly referable to the same species on a morphological basis, further enabling to provide an emended diagnosis for this species. Varanus amnhophilis appears to be a junior subjective synonym of V. marathonensis. On the basis of the most complete fossil Varanus skeleton ever described, it has been possible to further resolve the internal phylogeny of this genus by cladistically analyzing 80 taxa coded for 495 morphological and 5729 molecular characters. Varanus marathonensis was a large-sized species distributed at relatively low latitudes in both southwestern and southeastern Europe from at least MN7+8 to MN12. Our cladistic analysis nests V. marathonensis into an eastern clade of Varanus instead of the African clade comprising Varanus griseus, to which it had been related in the past. At least two different Varanus lineages were present in Europe during the Neogene, represented by Varanus mokrensis (early Miocene) and V. marathonensis (middle to late Miocene), respectively.