A Satisfiability-based Approach for Embedding Generalized Tanglegrams on Level Graphs

A tanglegram is a pair of trees on the same set of leaves with matching leaves in the two trees joined by an edge. Tanglegrams are widely used in computational biology to compare evolutionary histories of species. In this paper we present a formulation of two related combinatorial embedding problems concerning tanglegrams in terms of CNF-formulas. The first problem is known as planar embedding and the second as crossing minimization problem. We show that our satisfiability formulation of these problems can handle a much more general case with more than two, not necessarily binary or complete, trees defined on arbitrary sets of leaves and allowed to vary their layouts

A broadscale analysis of host-symbiont cophylogeny reveals the drivers of phylogenetic congruence

This is the final version. Available on open access from Wiley via the DOI in this recordData availability statement: A copy of the source data and R code used in this study have been deposited at figshare.com: https://doi.org/10.6084/m9.figshare.14393309 This article has earned Open Data and Open Materials badges. Data and materials are available at: https://figshare.com/articles/dataset/Dataset_for_ELE_EV_ELE13757/14393309?file=27503576 and https://figshare.com/articles/dataset/Dataset_for_ELE_EV_ELE13757/14393309?file=27503579Symbioses exert substantial biological influence, with great evolutionary and ecological relevance for disease, major evolutionary transitions, and the structure and function of ecological communities. Yet, much remains unknown about the patterns and processes that characterise symbioses. A major unanswered question is the extent to which symbiont phylogenies mirror those of their hosts and if patterns differ for parasites and mutualists. Addressing this question offers fundamental insights into evolutionary processes, such as whether symbionts typically codiverge with their hosts or if diversity is generated via host switches. Here, we perform a meta-analysis of host-symbiont phylogenetic congruence, encompassing 212 host-symbiont cophylogenetic studies that include ~10,000 species. Our analysis supersedes previous qualitative assessments by utilising a quantitative framework. We show that symbiont phylogeny broadly reflects host phylogeny across biodiversity and life-history, demonstrating a general pattern of phylogenetic congruence in host-symbiont interactions. We reveal two key aspects of symbiont life-history that promote closer ties between hosts and symbionts: vertical transmission and mutualism. Mode of symbiosis and mode of transmission are intimately interlinked, but vertical transmission is the dominant factor. Given the pervasiveness of symbioses, these findings provide important insights into the processes responsible for generating and maintaining the Earth's rich biodiversity.Kungliga Fysiografiska Sällskapet i LundAustralian Research Council (ARC

Comments on Allard and Carpenter (1996), or the "aquatic ape" hypothesis revisited

The results of Allard and Carpenter's (Cladistics 12, 183-198, 1996) paper on weighting and congruence among mammalian mitochondrial genes are an artefact of errors in their data matrix; their "blue whale" ATPASE8 sequence is human, the actual blue whale sequence is assigned to the grey seal, and the "horse" sequence is that of the harbor seal. When these errors are corrected there is no evidence that the mitochondrial genes are incongruent

Chimpanzee adenovirus vaccine provides multispecies protection against Rift Valley fever

Rift Valley Fever virus (RVFV) causes recurrent outbreaks of acute life-threatening human and livestock illness in Africa and the Arabian Peninsula. No licensed vaccines are currently available for humans and those widely used in livestock have major safety concerns. A ‘One Health’ vaccine development approach, in which the same vaccine is co-developed for multiple susceptible species, is an attractive strategy for RVFV. Here, we utilized a replication-deficient chimpanzee adenovirus vaccine platform with an established human and livestock safety profile, ChAdOx1, to develop a vaccine for use against RVFV in both livestock and humans. We show that single-dose immunization with ChAdOx1-GnGc vaccine, encoding RVFV envelope glycoproteins, elicits high-titre RVFV-neutralizing antibody and provides solid protection against RVFV challenge in the most susceptible natural target species of the virus-sheep, goats and cattle. In addition we demonstrate induction of RVFV-neutralizing antibody by ChAdOx1-GnGc vaccination in dromedary camels, further illustrating the potency of replication-deficient chimpanzee adenovirus vaccine platforms. Thus, ChAdOx1-GnGc warrants evaluation in human clinical trials and could potentially address the unmet human and livestock vaccine needs

Modelling nutritional interactions: from individuals to communities

International audienc