Jane: a new tool for the cophylogeny reconstruction problem

<p>Abstract</p> <p>Background</p> <p>This paper describes the theory and implementation of a new software tool, called <it>Jane</it>, for the study of historical associations. This problem arises in parasitology (associations of hosts and parasites), molecular systematics (associations of orderings and genes), and biogeography (associations of regions and orderings). The underlying problem is that of reconciling pairs of trees subject to biologically plausible events and costs associated with these events. Existing software tools for this problem have strengths and limitations, and the new <it>Jane </it>tool described here provides functionality that complements existing tools.</p> <p>Results</p> <p>The <it>Jane </it>software tool uses a polynomial time dynamic programming algorithm in conjunction with a genetic algorithm to find very good, and often optimal, solutions even for relatively large pairs of trees. The tool allows the user to provide rich timing information on both the host and parasite trees. In addition the user can limit host switch distance and specify multiple host switch costs by specifying regions in the host tree and costs for host switches between pairs of regions. <it>Jane </it>also provides a graphical user interface that allows the user to interactively experiment with modifications to the solutions found by the program.</p> <p>Conclusions</p> <p><it>Jane </it>is shown to be a useful tool for cophylogenetic reconstruction. Its functionality complements existing tools and it is therefore likely to be of use to researchers in the areas of parasitology, molecular systematics, and biogeography.</p

The Cophylogeny Reconstruction Problem is NP-Complete

The cophylogeny reconstruction problem arises in the study of host-parasite relationships. Specif- ically, we are given a host tree H, a parasite tree P, and a function \u27 mapping the leaves (extant taxa) of P to the leaves of H. Four biologically plausible operations are considered: cospeciation, duplication, host switching, and loss (Figure 1). A host switch is permitted in conjunction with a duplication event but not with a cospeciation event [1]

Jane: A New Tool for the Cophylogeny Reconstruction Problem

Background This paper describes the theory and implementation of a new software tool, called Jane, for the study of historical associations. This problem arises in parasitology (associations of hosts and parasites), molecular systematics (associations of orderings and genes), and biogeography (associations of regions and orderings). The underlying problem is that of reconciling pairs of trees subject to biologically plausible events and costs associated with these events. Existing software tools for this problem have strengths and limitations, and the new Jane tool described here provides functionality that complements existing tools. Results The Jane software tool uses a polynomial time dynamic programming algorithm in conjunction with a genetic algorithm to find very good, and often optimal, solutions even for relatively large pairs of trees. The tool allows the user to provide rich timing information on both the host and parasite trees. In addition the user can limit host switch distance and specify multiple host switch costs by specifying regions in the host tree and costs for host switches between pairs of regions. Jane also provides a graphical user interface that allows the user to interactively experiment with modifications to the solutions found by the program. Conclusions Jane is shown to be a useful tool for cophylogenetic reconstruction. Its functionality complements existing tools and it is therefore likely to be of use to researchers in the areas of parasitology, molecular systematics, and biogeography

Deciphering the origin and evolution of Hepatitis B viruses by means of a family of non-enveloped fish viruses

Hepatitis B viruses (HBVs), which are enveloped viruses with reverse-transcribed DNA genomes, constitute the family Hepadnaviridae. An outstanding feature of HBVs is their streamlined genome organization with extensive gene overlap. Remarkably, the ∼1,100 bp open reading frame (ORF) encoding the envelope proteins is fully nested within the ORF of the viral replicase P. Here, we report the discovery of a diversified family of fish viruses, designated nackednaviruses, which lack the envelope protein gene, but otherwise exhibit key characteristics of HBVs including genome replication via protein-primed reverse-transcription and utilization of structurally related capsids. Phylogenetic reconstruction indicates that these two virus families separated more than 400 million years ago before the rise of tetrapods. We show that HBVs are of ancient origin, descending from non-enveloped progenitors in fishes. Their envelope protein gene emerged de novo, leading to a major transition in viral lifestyle, followed by co-evolution with their hosts over geologic eras

Mainstreaming Climate Change Education in UK Higher Education Institutions

Key messages• Mainstreaming Climate Change Education (CCE) across all learning and operational activities enables Higher Education Institutions (HEIs) to better serve their core purpose of preparing learners for their roles in work and wider society, now and in the future.• Student and employer demand for climate change education is growing, not just in specialist subjects but across all degree pathways.• The attitudes, mindsets, values and behaviours that graduates need to engage with climate change include the ability to deal with complexity, work collaboratively across sectors and disciplines and address challenging ethical questions.• The complexity of the climate crisis means all disciplines have a role to play in delivering education for the net-zero transition. Embedding interdisciplinarity is crucial to ensuring that our response to climate change makes use of all of the expertise HEIs have to offer and promotes knowledge exchange and integration for students and staff.• Student-centered CCE, including peer-to-peer learning, is a powerful tool for facilitating an inclusive and empowering learning experience, and developing graduates as change agents for the climate and ecological crisis.• HEIs should develop learning outcomes for CCE that include understanding the scale, urgency, causes, consequences and solutions of climate change; how social norms and practices are driving the climate crisis; and the ability to identify routes to direct involvement in solutions via every discipline.• Pedagogical approaches to teaching CCE should enable learners to engage with, and respond to, climate change as a “real-world” problem, such as through experiential learning.• Further recommendations for the HEI sector include developing a strategy for aligning CCE teaching provision with governance structures; partnering with industry, government and third sector organisations to enable context-specific CCE; and working with trade unions and accreditation bodies to enable curriculum reform