Assessment of available anatomical characters for linking living mammals to fossil taxa in phylogenetic analyses

ORCID: 0000-0003-4919-8655© 2016 The Authors. Published by the Royal Society under the terms of the Creative Commons Attribution License http://creativecommons.org/licenses/by/4.0/, which permits unrestricted use, provided the original author and source are credited. The file attached is the published version of the article

Concepts and applications in functional diversity

The use of functional diversity analyses in ecology has grown exponentially over the past two decades, broadening our understanding of biological diversity and its change across space and time. Virtually all ecological sub-disciplines recognise the critical value of looking at species and communities from a functional perspective, and this has led to a proliferation of methods for estimating contrasting dimensions of functional diversity. Differences between these methods and their development generated terminological inconsistencies and confusion about the selection of the most appropriate approach for addressing any particular ecological question, hampering the potential for comparative studies, simulation exercises and meta-analyses. Two general mathematical frameworks for estimating functional diversity are prevailing: those based on dissimilarity matrices (e.g. Rao entropy, functional dendrograms) and those relying on multidimensional spaces, constructed as either convex hulls or probabilistic hypervolumes. We review these frameworks, discuss their strengths and weaknesses and provide an overview of the main R packages performing these calculations. In parallel, we propose a way for organising functional diversity metrics in a unified scheme to quantify the richness, divergence and regularity of species or individuals under each framework. This overview offers a roadmap for confidently approaching functional diversity analyses both theoretically and practically.Peer reviewe

Calculating functional diversity metrics using neighbor-joining trees

The study of functional diversity (FD) provides ways to understand phenomena as complex as community assembly or the dynamics of biodiversity change under multiple pressures. Different frameworks are used to quantify FD, either based on dissimilarity matrices (e.g. Rao entropy, functional dendrograms) or multidimensional spaces (e.g. convex hulls, kernel-density hypervolumes), each with their own strengths and limits. Frameworks based on dissimilarity matrices either do not enable the measurement of all components of FD (i.e. richness, divergence, and regularity), or result in the distortion of the functional space. Frameworks based on multidimensional spaces do not allow for comparisons with phylogenetic diversity (PD) measures and can be sensitive to outliers.We propose the use of neighbor-joining trees (NJ) to represent and quantify FD in a way that combines the strengths of current frameworks without many of their weaknesses. Importantly, our approach is uniquely suited for studies that compare FD with PD, as both share the use of trees (NJ or others) and the same mathematical principles.We test the ability of this novel framework to represent the initial functional distances between species with minimal functional space distortion and sensitivity to outliers. The results using NJ are compared with conventional functional dendrograms, convex hulls, and kernel-density hypervolumes using both simulated and empirical datasets.Using NJ, we demonstrate that it is possible to combine much of the flexibility provided by multidimensional spaces with the simplicity of tree-based representations. Moreover, the method is directly comparable with taxonomic diversity (TD) and PD measures, and enables quantification of the richness, divergence and regularity of the functional space

Endochondral bone in an Early Devonian ‘placoderm’ from Mongolia

Endochondral bone is the main internal skeletal tissue of nearly all osteichthyans—the group comprising more than 60,000 living species of bony fishes and tetrapods. Chondrichthyans (sharks and their kin) are the living sister group of osteichthyans and have primarily cartilaginous endoskeletons, long considered the ancestral condition for all jawed vertebrates (gnathostomes). The absence of bone in modern jawless fishes and the absence of endochondral ossification in early fossil gnathostomes appear to lend support to this conclusion. Here we report the discovery of extensive endochondral bone in Minjinia turgenensis, a new genus and species of ‘placoderm’-like fish from the Early Devonian (Pragian) of western Mongolia described using X-ray computed microtomography. The fossil consists of a partial skull roof and braincase with anatomical details providing strong evidence of placement in the gnathostome stem group. However, its endochondral space is filled with an extensive network of fine trabeculae resembling the endochondral bone of osteichthyans. Phylogenetic analyses place this new taxon as a proximate sister group of the gnathostome crown. These results provide direct support for theories of generalized bone loss in chondrichthyans. Furthermore, they revive theories of a phylogenetically deeper origin of endochondral bone and its absence in chondrichthyans as a secondary condition

Politiques publiques et gestions paysannes de l’arbre et de la forêt: alliance durable ou dialogue de dupes?

Les politiques du développement durable sont-elles favorables à la forêt des agriculteurs ? Malmenée par l’histoire, la forêt des agriculteurs (que nous avons qualifiée de forêt « domestique » ou « rurale ») est un objet orphelin indissociable de l’histoire des systèmes de production agricoles et des modes de vie paysans. Ses qualités hybrides, alliant à la fois production, qualités environnementales et bénéfices sociaux en font un exemple de choix pour le développement durable. Les crises actuelles la remettent au centre des stratégies rurales à travers des dynamiques de valorisation variées mettant en avant les synergies entre productions spécifiques, valeur environnementale, et développement social. Ces dynamiques permettent d’interroger l’un des grands chantiers du développement durable: la mise en avant du local comme caution et instruments d’une gestion durable des territoires. Dans les régions où les trajectoires locales vers la durabilité sont entravées par la marginalité économique, l’action publique, qui reconnait aujourd’hui la valeur du local après l’avoir longtemps dénigrée, estelle apte à accompagner sa mutation en suscitant de nouvelles synergies ? Ou bien, au contraire, va-telle accentuer le décalage qui a toujours existé entre les pratiques réelles, concrètes, mouvantes, des agriculteurs et l’appréciation qui en est faite ? Une approche dialectique de l’identité de la forêt domestique et de ses trajectoires de durabilité POPULAR a travaillé à travers le renforcement d’un réseau de recherche interdisciplinaire sur la forêt domestique permettant de mutualiser les expériences en approfondissant les questionnements sur la domestication, la résilience, la patrimonialisation, et en les synthétisant autour de la question du développement durable. La méthodologie globale est basée sur une approche comparative, cumulative et intégrative confrontant les trajectoires historiques et contemporaines de forêts affectées par des mesures publiques ou des dynamiques propres (valorisation de produits spécifiques liés à des savoirs locaux : Maroc, Corse et Cévennes, Languedoc ; mise en place de nouvelles gouvernances : Cameroun, Inde, Indonésie ; renforcement de gouvernances existantes : Maroc, Coteaux de Gascogne ; politiques agricoles : Pyrénées, ou foncières : Coteaux de Gascogne). La constitution d’une base de données et des monographies harmonisées comparées terme à terme ont permis la caractérisation de l’identité de la forêt domestique et de ses propriétés, dans les contextes locaux et politiques qui l’influencent. La confrontation de trois champs de conceptualisation théorique concernant les relations nature / société a permis de mieux comprendre le poids des nouvelles politiques publiques visant à assurer la durabilité de ces forêts. Résultats majeurs du projet : à travers une déclinaison spécifique du concept de domestication, pris dans le sens technique, environnemental et social, la forêt domestique propose un modèle original d’intégration socio environnementale dans la gestion des ressources naturelles qui éclaire de façon originale le rôle des interactions à différentes échelles entre processus écologiques, techniques, économiques et sociaux dans la durabilité des systèmes de gestion des ressources naturelles. Dans ses dynamiques actuelles, elle éclaire aussi les contradictions qui existent entre développement durable (plus faible sur la génération de revenu que sur le renforcement des qualités écologiques ou sociale), et développement tout court avec ses grandes forces d’évolution (marché, politiques de modernisation libérale). Production scientifique et brevets depuis le début du projet. Notre production scientifique s’est concentrée sur la rédaction d’articles et l’organisation de Colloques internationaux dédiés à la forêt rurale et à ses relations avec les politiques publiques, ainsi que sur les apports théoriques autour de la résilience, de la domestication, du patrimoine et de l’écologie politique. L’encadrement de thésards et de masters a constitué une part importante du travail. La valorisation se poursuit avec la production d’un numéro spécial de la revue en ligne Ecology and Society. L’année de la forêt constituera un point fort pour la diffusion des résultats auprès du grand publi

SIDER : an R package for predicting trophic discrimination factors of consumers based on their ecology and phylogenetic relatedness

KH acknowledges support from the Marie Curie Research Grants Scheme, grant [749594] and Science Foundation Ireland awarded to Yvonne Buckley. TG acknowledges support from European Research Council under the European Union’s Seventh Framework Programme (FP/2007–2013)/ERC Grant Agreement number 311092 awarded to Martin D. Brazeau. AJ was funded by a research scholarship administered by the Fulbright Commission of Ireland and in conjunction with the Marine Institute of Ireland. SB & RI are funded by an ERC consolidators grant (STATEMIG: 310820). The data used to fit the regression models, along with the code itself is bundled within the R package and is available on GitHub https://github.com/healyke/SIDER, with the data also on Figshare https://figshare.com/articles/Dataset_for_the_SIDER_R_package/4737481. Data available from the Dryad Digital Repository: http://dx.doi.org/10.5061/dryad.c6035 (Healy et al. 2017).Stable isotope mixing models (SIMMs) are an important tool used to study species' trophic ecology. These models are dependent on, and sensitive to, the choice of trophic discrimination factors (TDF) representing the offset in stable isotope delta values between a consumer and their food source when they are at equilibrium. Ideally, controlled feeding trials should be conducted to determine the appropriate TDF for each consumer, tissue type, food source, and isotope combination used in a study. In reality however, this is often not feasible nor practical. In the absence of species-specific information, many researchers either default to an average TDF value for the major taxonomic group of their consumer, or they choose the nearest phylogenetic neighbour for which a TDF is available. Here, we present the SIDER package for R, which uses a phylogenetic regression model based on a compiled dataset to impute (estimate) a TDF of a consumer. We apply information on the tissue type and feeding ecology of the consumer, all of which are known to affect TDFs, using Bayesian inference. Presently, our approach can estimate TDFs for two commonly used isotopes (nitrogen and carbon), for species of mammals and birds with or without previous TDF information. The estimated posterior probability provides both a mean and variance, reflecting the uncertainty of the estimate, and can be subsequently used in the current suite of SIMM software. SIDER allows users to place a greater degree of confidence on their choice of TDF and its associated uncertainty, thereby leading to more robust predictions about trophic relationships in cases where study-specific data from feeding trials is unavailable. The underlying database can be updated readily to incorporate more stable isotope tracers, replicates and taxonomic groups to further increase the confidence in dietary estimates from stable isotope mixing models, as this information becomes available.PostprintPeer reviewe

Innovation and elaboration on the avian tree of life

Widely documented, megaevolutionary jumps in phenotypic diversity continue to perplex researchers because it remains unclear whether these marked changes can emerge from microevolutionary processes. Here, we tackle this question using new approaches for modeling multivariate traits to evaluate the magnitude and distribution of elaboration and innovation in the evolution of bird beaks. We find that elaboration, evolution along the major axis of phenotypic change, is common at both macro- and megaevolutionary scales, whereas innovation, evolution away from the major axis of phenotypic change, is more prominent at megaevolutionary scales. The major axis of phenotypic change among species beak shapes at megaevolutionary scales is an emergent property of innovation across clades. Our analyses suggest that the reorientation of phenotypes via innovation is a ubiquitous route for divergence that can arise through gradual change alone, opening up further avenues for evolution to explore

Individual variation of the masticatory system dominates 3D skull shape in the herbivory-adapted marsupial wombats

BackgroundWithin-species skull shape variation of marsupial mammals is widely considered low and strongly size-dependent (allometric), possibly due to developmental constraints arising from the altricial birth of marsupials. However, species whose skulls are impacted by strong muscular stresses - particularly those produced through mastication of tough food items - may not display such intrinsic patterns very clearly because of the known plastic response of bone to muscle activity of the individual. In such cases, allometry may not dominate within-species shape variation, even if it is a driver of evolutionary shape divergence; ordination of shape in a geometric morphometric context through principal component analysis (PCA) should reveal main variation in areas under masticatory stress (incisor region/zygomatic arches/mandibular ramus); but this main variation should emerge from high individual variability and thus have low eigenvalues.ResultsWe assessed the evidence for high individual variation through 3D geometric morphometric shape analysis of crania and mandibles of three species of grazing-specialized wombats, whose diet of tough grasses puts considerable strain on their masticatory system. As expected, we found little allometry and low Principal Component 1 (PC1) eigenvalues within crania and mandibles of all three species. Also as expected, the main variation was in the muzzle, zygomatic arches, and masticatory muscle attachments of the mandibular ramus. We then implemented a new test to ask if the landmark variation reflected on PC1 was reflected in individuals with opposite PC1 scores and with opposite shapes in Procrustes space. This showed that correspondence between individual and ordinated shape variation was limited, indicating high levels of individual variability in the masticatory apparatus.DiscussionOur results are inconsistent with hypotheses that skull shape variation within marsupial species reflects a constraint pattern. Rather, they support suggestions that individual plasticity can be an important determinant of within-species shape variation in marsupials (and possibly other mammals) with high masticatory stresses, making it difficult to understand the degree to which intrinsic constraints act on shape variation at the within-species level. We conclude that studies that link micro- and macroevolutionary patterns of shape variation might benefit from a focus on species with low-impact mastication, such as carnivorous or frugivorous species

Disparities in the analysis of morphological disparity

Analyses of morphological disparity have been used to characterize and investigate the evolution of variation in the anatomy, function and ecology of organisms since the 1980s. While a diversity of methods have been employed, it is unclear whether they provide equivalent insights. Here, we review the most commonly used approaches for characterizing and analysing morphological disparity, all of which have associated limitations that, if ignored, can lead to misinterpretation. We propose best practice guidelines for disparity analyses, while noting that there can be no ‘one-size-fits-all’ approach. The available tools should always be used in the context of a specific biological question that will determine data and method selection at every stage of the analysis

Oncolytic Viruses-Interaction of Virus and Tumor Cells in the Battle to Eliminate Cancer.

Oncolytic viruses (OVs) are an emerging treatment option for many cancer types and have recently been the focus of extensive research aiming to develop their therapeutic potential. The ultimate aim is to design a virus which can effectively replicate within the host, specifically target and lyse tumor cells and induce robust, long lasting tumor-specific immunity. There are a number of viruses which are either naturally tumor-selective or can be modified to specifically target and eliminate tumor cells. This means they are able to infect only tumor cells and healthy tissue remains unharmed. This specificity is imperative in order to reduce the side effects of oncolytic virotherapy. These viruses can also be modified by various methods including insertion and deletion of specific genes with the aim of improving their efficacy and safety profiles. In this review, we have provided an overview of the various virus species currently being investigated for their oncolytic potential and the positive and negative effects of a multitude of modifications used to increase their infectivity, anti-tumor immunity, and treatment safety, in particular focusing on the interaction of tumor cells and OVs.This work was supported by the MRC DPFS grant (MR/M015696/1 and MR/N027655/1)