For all three tasks of the project, we have provided a wealth of data that has been key to the project and will be an excellent resource for the research community. For the morphological task, 3D digital data of skulls were collected to characterise the evolutionary processes by which convergent tooth reduction occurs and how it has affected skull shape in the different ant-eating lineages. We show that convergent tooth loss in anteaters and pangolins resulted in a different fate for the mandibular canal, with anteaters retaining a neurovascular system (dorsal canaliculi) in the mandible, whereas pangolins did not. This suggests that the external similarities between anteater and pangolin mandibles have overshadowed the complex evolution of their internal morphology. The geometric morphometric data were used to examine cranial covariance patterns in convergently evolved myrmecophagous placentals. The results confirmed that morphological integration of the mammalian skull is highly constrained and may therefore rely on conserved developmental modules and underlying gene networks. For the genomic task, we overcame a major challenge of the project by demonstrating that a hybrid sequencing and assembly strategy could be successfully used to generate high quality genomes from roadkill. This resulted in nine new complete genomes of elusive myrmecophagous species and relatives, which we used to unravel the genomic mechanisms underlying convergent ant-eating phenotypes. An important result of this task concerns the evolution of chitinase genes (CHIAs), which encode enzymes capable of digesting the chitin of insect exoskeletons. By conducting a detailed comparative genomic survey of these genes, we were able to infer that the ancestor of placental mammals likely possessed five functional CHIA genes, which have undergone divergent evolutionary fates among myrmecophagous species. Indeed, anteaters, armadillos and aardvarks retain 4-5 functional CHIA genes, whereas pangolins and aardwolves have only one. Using comparative transcriptomics, we found that convergently evolved pangolins and anteaters express different chitinases in their hypertrophied salivary glands and other additional digestive organs. These results show that divergent molecular mechanisms underlie the convergent adaptation to myrmecophagy in pangolins and anteaters, highlighting the role of historical contingency and molecular tinkering of their chitin digestive enzyme toolkit. Finally, for the microbiome task, we use long-read metagenomics from field-collected faecal samples of nine myrmecophagous species to reconstruct more than 300 high-quality bacterial genomes. We show that more than a hundred of these carry chitinase genes, suggesting a potential role for the gut microbiota in insect prey digestion in myrmecophagous mammals. Furthermore, while some of the chitinolytic bacteria were recruited convergently across myrmecophagous species, others appeared to be host species specific. This sheds further light on the potential role of the holobiont in convergent adaptation to myrmecophagy.
