The ancient elasmobranchs (sharks + rays) have the potential to provide great insight into evolutionary processes over large timescales, but this potential is limited by a poor understanding of the relationships between living and extinct groups and the timing of major divergence events. In this project I will address these knowledge gaps by combining new 3D tomographic data on key Mesozoic elasmobranch body fossils with genomic and anatomical data from their living relatives. I will then use this and a dataset of 3D elasmobranch lower jaws to investigate the dynamics of elasmobranch macroevolution, using the rate and mode of lower jaw shape evolution as a case study. In doing so I will build on my existing background in palaeobiology and 3D methods by learning new skills in genomics-based phylogenetics and 3D geometric morphometrics, while developing my skills as a supervisor, communicator, and leader. These new skills, along with the scientific groundwork laid by this project, will give me the tools to pursue an independent programme of research in the longer term, investigating the early evolution of elasmobranchs by combining data from animals both living and extinct.

Of all the traits that define humans, bipedal locomotion likely evolved first. How and why bipedalism evolved in the fossil human (hominin) lineage are fundamental questions in palaeoanthropology. An underexplored dimension of “how” bipedalism evolved is its growth and development (ontogeny). Humans locomotion develops much slower than those of other apes. Modern humans are also fully terrestrial, while the other African apes transition from predominantly arboreal locomotion using their upper limbs as juveniles to predominantly terrestrial knuckle-walking as adults. The importance of arboreal locomotion throughout hominin evolution has remained debated since the 1980s. However, since all extant apes are most arboreal as juveniles, the answers to this debate are most likely found in juvenile hominins.We know little about hominin locomotor ontogeny and the behaviour of juveniles due to (1) a lack of fossils and (2) limited tools for behavioural reconstruction. CRAHL applies recent methodological advances to both well-studied and newly discovered fossils to overcome these limitations, and will be the first to investigate the evolutionary pattern of hominin locomotor development. Bones can dynamically adapt to changes in loading direction, magnitude, and frequency by altering the structure of trabecular bone, the 3D mesh-like structure found underneath joint surfaces. Trabecular structure can therefore provide a functional record of developmental variation in loading conditions as animals learn to locomote. By using state-of-the-art methods for analysing age-related changes in trabecular bone structure throughout the skeleton, CRAHL will reconstruct how quickly hominins learned to locomote and the variety of postures they assumed, including arboreal versus terrestrial locomotion. By combining state-of-the-art methods new fossil discoveries, CRAHL sheds new light on the evolution of two defining human traits: slow development and fully terrestrial bipedalism.

One of the most drastic impacts of man on Earth is species extinctions. We do not know how many species are extinct and how many will go extinct, but we may be experiencing a sixth mass extinction. Thus, actions to help protect species from extinction are urgently needed. These actions should be prioritized in biomes such as tropical forests that shelter enormous biodiversity but have increasingly been impacted. One example is the Atlantic Forest in South America. It shelters around 5% of world species, half of them being endemic. But 86% of its original extent has already been lost and only about 1% is effectively protected. To support the protection of the Atlantic Forest, this proposal has the following goals: (i) to assess the threat status of endemic Atlantic Forest trees (EAFT) based on all criteria of the International Union for Conservation of Nature (IUCN), (ii) to quantify the evolutionary uniqueness of globally threatened EAFT, (iii) provide guidelines to conserve threatened EAFT, including the identification of gaps of knowledge and priority areas for their conservation, and (iv) to involve the local society in species conservation through the proposal of a citizen science program. The proposed action is perfectly aligned with targets of the United Nations Strategic Plan for Biodiversity 2011-2020, the Global Strategy for Plant Conservation 2011-2020 and the IUCN Global Tree Specialist Group. It is multi-disciplinary with both scientific and applied components. It combines large datasets with high-resolution maps, up-to-date modelling techniques and the expertises of researchers from four different countries. It will also provide new information that can be readily used by conservation agencies. Finally, it will engage different social actors to launch a conservation and educational program based on the involvement of local people.

Sailors called it “burning of the sea”, Shakespeare described it as “pale fire” and Aristotle named it “cold light”. The glimmer they witnessed was light emitted by living organisms or bioluminescence. While it represents one of the most striking examples of convergent evolution across the tree of life, in Fungi it has a single origin in the Agaricales order, Basidiomycota. In particular, Mycena, a large genus of mushroom-forming fungi, includes most of known bioluminescent species together with hundreds of species that lost the ability to emit light. In GLiMMer, I will study the evolution of fungal bioluminescence and test the hypothesis that multiple, lineage-specific mechanisms led to the convergent loss of this trait, providing clues for its ecological relevance. To date, Mycena lacks a robust phylogenetic framework and is heavily under sampled. Fungarium collections, such as the one at Naturalis, preserved thousands of Mycena specimens over the past centuries. Thanks to new high-throughput sequencing methods these collections are being transformed in genomics resources, bridging taxonomy and evolution. In GLiMMer, my expertise in fungal genomics will serve to develop a genome-based classification of Mycena, that combines contemporary and museum specimens. I will generate assemblies of 100 representative species using short-read sequencing. Next, I will extract phylogenetically informative loci to design a target sequence capture method for recalcitrant museum specimens for the first time in mushrooms. Then, I will use the new classification to select reference species and obtain chromosomal-level assemblies using long-read sequencing. Finally, with genome-wide synteny analyses I will investigate the evolutionary circumstances that led to the birth and death of bioluminescence in Fungi. By integrating taxonomy, genomics and evolution, my project will create a paradigm shift in our knowledge on fungal biodiversity and ultimately contribute to its conservation.

Large-scale ocean changes, including ocean acidification (OA) and ocean warming (OW), are projected to occur over the next 50-100 years as a result of elevated atmospheric CO2. Living close to the atmosphere/ocean boundary, plankton are particularly vulnerable to, but also excellent indicators of these changes. Euthecosome pteropods (small swimming gastropods) have been highlighted as bio-indicators because their delicate aragonite shells are susceptible to OA. However complex feeding behaviours have impeded laboratory experiments on pteropods, limiting research to short term studies. The proposed action will apply an interdisciplinary approach to investigate the past, present and future effects of OA and OW upon the planktonic family Atlantidae, and to evaluate their use as bio-indicators. Atlantid heteropods are also small (max. 14 mm), aragonite shelled, planktonic gastropods that are sensitive to OA and OW. Unlike pteropods, atlantids are predatory and have the potential to be excellent experimental organisms with which to investigate the effects of these surface ocean changes. Atlantids also provide a unique opportunity to investigate the effect of OA and OW at an as-yet unstudied and potentially more sensitive trophic level. The Experienced Researcher has worked with atlantids for >8 years and is one of very few researchers able to identify atlantid species. As such, she is uniquely positioned to deliver the objectives of this interdisciplinary project. The proposed research will provide opportunities for the Researcher to advance her career and skill-set through specialist training and teaching opportunities. The proposed action will improve our appreciation of how surface ocean changes will affect zooplankton and produce high impact data that are relevant to a wide body of marine scientists. The atlantids are also beautiful, charismatic gastropods, and excellent ambassadors for engaging the public and policy makers with current ocean changes.