Computing the blocks of a quasi-median graph

Quasi-median graphs are a tool commonly used by evolutionary biologists to visualise the evolution of molecular sequences. As with any graph, a quasi-median graph can contain cut vertices, that is, vertices whose removal disconnect the graph. These vertices induce a decomposition of the graph into blocks, that is, maximal subgraphs which do not contain any cut vertices. Here we show that the special structure of quasi-median graphs can be used to compute their blocks without having to compute the whole graph. In particular we present an algorithm that, for a collection of $n$ aligned sequences of length $m$, can compute the blocks of the associated quasi-median graph together with the information required to correctly connect these blocks together in run time $\mathcal O(n^2m^2)$, independent of the size of the sequence alphabet. Our primary motivation for presenting this algorithm is the fact that the quasi-median graph associated to a sequence alignment must contain all most parsimonious trees for the alignment, and therefore precomputing the blocks of the graph has the potential to help speed up any method for computing such trees.Comment: 17 pages, 2 figure

Quasi-median hulls in Hamming space are Steiner hulls

AbstractA Hamming space Λn consists of all sequences of length n over an alphabet Λ and is endowed with the Hamming distance. In particular, any set of aligned DNA sequences of fixed length constitutes a subspace of a Hamming space with respect to mismatch distance. The quasi-median operation returns for any three sequences u,v,w the sequence which in each coordinate attains either the majority coordinate from u,v,w or else (in the case of a tie) the coordinate of the first entry, u; for a subset of Λn the iterative application of this operation stabilizes in its quasi-median hull. We show that for every finite tree interconnecting a given subset X of Λn there exists a shortest realization within Λn for which all interior nodes belong to the quasi-median hull of X. Hence the quasi-median hull serves as a Steiner hull for the Steiner problem in Hamming space

Combinatorial Optimization

This report summarizes the meeting on Combinatorial Optimization where new and promising developments in the field were discussed. Th

LIPIcs, Volume 244, ESA 2022, Complete Volume

LIPIcs, Volume 244, ESA 2022, Complete Volum

LIPIcs, Volume 261, ICALP 2023, Complete Volume

LIPIcs, Volume 261, ICALP 2023, Complete Volum

Monitoring and mitigation of the sound effects of hydrocarbon exploration activities on marine mammal populations

Offshore Exploration and Production (E&P) activities, such as seismic surveys and drilling, generate sound that can affect marine mammals in different ways. These effects range from permanent or temporary auditory impacts to disturbance or behavioral changes, and communication masking. Depending on the intensity and duration of these effects, and without implementation of appropriate mitigation measures, this can result in population-level consequences. The overarching objective of this study was to advance the protection of marine mammals during the implementation of E&P activities through the following themes: (1) enhancement of the state of knowledge of risk management, (2) efficacy of mitigation, (3) advanced monitoring technology, (4) implementation of advanced industry monitoring and mitigation measures and (5) measurement of heretofore unassessed E&P activities. In this study several marine mammal monitoring and mitigation programs associated with E&P projects are presented to further advance these themes. Topics being addressed include the use of autonomous camera systems for aerial monitoring of a narwhal population, long-term photo-identification studies of western gray whales to better understand site fidelity to their summer feeding grounds, mitigation of gray whales’ behavioral responses to a seismic survey near these feeding grounds and use of Passive Acoustic Monitoring to characterize seismic pulses and drilling activity as well as marine mammal presence in remote arctic areas. A synthesis of the main findings is provided that includes identification of future research needs. Conclusions and specific recommendations are made that will contribute to our ability to assess and mitigate risks of E&P sound to marine mammals