Mapping epigenetic divergence in the massive radiation of Lake Malawi cichlid fishes

Epigenetic variation modulates gene expression and can be heritable. However, knowledge of the contribution of epigenetic divergence to adaptive diversification in nature remains limited. The massive evolutionary radiation of Lake Malawi cichlid fishes displaying extensive phenotypic diversity despite extremely low sequence divergence is an excellent system to study the epigenomic contribution to adaptation. Here, we present a comparative genome-wide methylome and transcriptome study, focussing on liver and muscle tissues in phenotypically divergent cichlid species. In both tissues we find substantial methylome divergence among species. Differentially methylated regions (DMR), enriched in evolutionary young transposons, are associated with transcription changes of ecologically-relevant genes related to energy expenditure and lipid metabolism, pointing to a link between dietary ecology and methylome divergence. Unexpectedly, half of all species-specific DMRs are shared across tissues and are enriched in developmental genes, likely reflecting distinct epigenetic developmental programmes. Our study reveals substantial methylome divergence in closely-related cichlid fishes and represents a resource to study the role of epigenetics in species diversification.

The limits of convergence: the roles of phylogeny and dietary ecology in shaping non-avian amniote crania

Cranial morphology is remarkably varied in living amniotes and the diversity of shapes is thought to correspond with feeding ecology, a relationship repeatedly demonstrated at smaller phylogenetic scales, but one that remains untested across amniote phylogeny. Using a combination of morphometric methods, we investigate the links between phylogenetic relationships, diet and skull shape in an expansive dataset of extant toothed amniotes: mammals, lepidosaurs and crocodylians. We find that both phylogeny and dietary ecology have statistically significant effects on cranial shape. The three major clades largely partition morphospace with limited overlap. Dietary generalists often occupy clade-specific central regions of morphospace. Some parallel changes in cranial shape occur in clades with distinct evolutionary histories but similar diets. However, members of a given clade often present distinct cranial shape solutions for a given diet, and the vast majority of species retain the unique aspects of their ancestral skull plan, underscoring the limits of morphological convergence due to ecology in amniotes. These data demonstrate that certain cranial shapes may provide functional advantages suited to particular dietary ecologies, but accounting for both phylogenetic history and ecology can provide a more nuanced approach to inferring the ecology and functional morphology of cryptic or extinct amniotes.

The Influence of Habitat on Viral Diversity in Neotropical Rodent Hosts

Rodents are important reservoirs of numerous viruses, some of which have significant impacts on public health. Ecosystem disturbances and decreased host species richness have been associated with the emergence of zoonotic diseases. In this study, we aimed at (a) characterizing the viral diversity in seven neotropical rodent species living in four types of habitats and (b) exploring how the extent of environmental disturbance influences this diversity. Through a metagenomic approach, we identified 77,767 viral sequences from spleen, kidney, and serum samples. These viral sequences were attributed to 27 viral families known to infect vertebrates, invertebrates, plants, and amoeba. Viral diversities were greater in pristine habitats compared with disturbed ones, and lowest in peri-urban areas. High viral richness was observed in savannah areas. Differences in these diversities were explained by rare viruses that were generally more frequent in pristine forest and savannah habitats. Moreover, changes in the ecology and behavior of rodent hosts, in a given habitat, such as modifications to the diet in disturbed vs. pristine forests, are major determinants of viral composition. Lastly, the phylogenetic relationships of four vertebrate-related viral families (Polyomaviridae, Flaviviridae, Togaviridae, and Phenuiviridae) highlighted the wide diversity of these viral families, and in some cases, a potential risk of transmission to humans. All these findings provide significant insights into the diversity of rodent viruses in Amazonia, and emphasize that habitats and the host’s dietary ecology may drive viral diversity. Linking viral richness and abundance to the ecology of their hosts and their responses to habitat disturbance could be the starting point for a better understanding of viral emergence and for future management of ecosystems.

Molar biomechanical function in South African hominins Australopithecus africanus and Paranthropus robustus

Diet is a driving force in human evolution. Two species of Plio-Pleistocene hominins, Paranthropus robustus and Australopithecus africanus , have derived craniomandibular and dental morphologies which are often interpreted as P. robustus having a more biomechanically challenging diet. While dietary reconstructions based on dental microwear generally support this, they show extensive dietary overlap between species, and craniomandibular and dental biomechanical analyses can yield contradictory results. Using methods from anthropology and engineering (i.e. anthroengineering), we quantified the molar biomechanical performance of these hominins to investigate possible dietary differences between them. Thirty-one lower second molars were 3D printed and used to fracture gelatine blocks, and Bayesian generalized linear models were used to investigate the relationship between species and tooth wear, size and shape, and biomechanical performance. Our results demonstrate that P. robustus required more force and energy to fracture blocks but had a higher force transmission rate. Considering previous dietary reconstructions, we propose three evolutionary scenarios concerning the dietary ecologies of these hominins. These evolutionary scenarios cannot be reached by investigating morphological differences in isolation, but require combining several lines of evidence. This highlights the need for a holistic approach to reconstructing hominin dietary ecology.

A comprehensive review of dietary strategies of sigmodontine rodents of central-eastern Argentina: linking diet, body mass and stomach morphology

Information on dietary ecology plays a key role in a wide array of biological research and conservation decisions, but its availability is biased towards large and charismatic taxa, whereas small mammals are underrepresented. Of the scarce publications on the Neotropical sigmodontine rodents, most are concentrated in central-eastern Argentina, and, up until now, no revision of the totality of these data has been made available. In this work, we performed a thorough review of the dietary information from over 50 publications on 22 species, finding omissions and errors propagated up to the present time. This resulted in a robust database, the proposal of a posteriori dietary categories, and a list of the species that have been neglected in feeding ecology research. In turn, we used that database to test whether the patterns which associate diet and morphology in medium and large mammals could be replicated in these small rodents, despite their overall generalist habits and the restrictions characteristic to their size. We found that larger species tend towards a low-protein diet. Additionally, we identified some stomach types which are restricted to specific diets. These results are consistent with the observations for larger species and shed light on the biology of small mammals.

Dental wear patterns reveal dietary ecology and season of death in a historical chimpanzee population

Dental wear analyses have been widely used to interpret the dietary ecology in primates. However, it remains unclear to what extent a combination of wear analyses acting at distinct temporal scales can be beneficial in interpreting the tooth use of primates with a high variation in their intraspecific dietary ecology. Here, we combine macroscopic tooth wear (occlusal fingerprint analysis, long-term signals) with microscopic 3D surface textures (short-term signals) exploring the tooth use of a historical western chimpanzee population from northeastern Liberia with no detailed dietary records. We compare our results to previously published tooth wear and feeding data of the extant and continually monitored chimpanzees of Taї National Park in Ivory Coast. Macroscopic tooth wear results from molar wear facets of the Liberian population indicate only slightly less wear when compared to the Taї population. This suggests similar long-term feeding behavior between both populations. In contrast, 3D surface texture results show that Liberian chimpanzees have many and small microscopic wear facet features that group them with those Taї chimpanzees that knowingly died during dry periods. This coincides with historical accounts, which indicate that local tribes poached and butchered the Liberian specimens during dust-rich dry periods. In addition, Liberian females and males differ somewhat in their 3D surface textures, with females having more microscopic peaks, smaller hill and dale areas and slightly rougher wear facet surfaces than males. This suggests a higher consumption of insects in Liberian females compared to males, based on similar 3D surface texture patterns previously reported for Taї chimpanzees. Our study opens new options for uncovering details of feeding behaviors of chimpanzees and other living and fossil primates, with macroscopic tooth wear tracing the long-term dietary and environmental history of a single population and microscopic tooth wear addressing short-term changes (e.g. seasonality).

Insights from macroevolutionary modelling and ancestral state reconstruction into the radiation and historical dietary ecology of Lemuriformes (Primates, Mammalia)

Background Lemurs once rivalled the diversity of rest of the primate order despite thier confinement to the island of Madagascar. We test the adaptive radiation model of Malagasy lemur diversity using a novel combination of phylogenetic comparative methods and geometric methods for quantifying tooth shape. Results We apply macroevolutionary model fitting approaches and disparity through time analysis to dental topography metrics associated with dietary adaptation, an aspect of mammalian ecology which appears to be closely related to diversification in many clades. Metrics were also reconstructed at internal nodes of the lemur tree and these reconstructions were combined to generate dietary classification probabilities at internal nodes using discriminant function analysis. We used these reconstructions to calculate rates of transition toward folivory per million-year intervals. Finally, lower second molar shape was reconstructed at internal nodes by modelling the change in shape of 3D meshes using squared change parsimony along the branches of the lemur tree. Our analyses of dental topography metrics do not recover an early burst in rates of change or a pattern of early partitioning of subclade disparity. However, rates of change in adaptations for folivory were highest during the Oligocene, an interval of possible forest expansion on the island. Conclusions There was no clear phylogenetic signal of bursts of morphological evolution early in lemur history. Reconstruction of the molar morphologies corresponding to the ancestral nodes of the lemur tree suggest that this may have been driven by a shift toward defended plant resources, however. This suggests a response to the ecological opportunity offered by expanding forests, but not necessarily a classic adaptive radiation initiated by dispersal to Madagascar.