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New FPT algorithms for finding the temporal hybridization number for sets of phylogenetic trees [article]

Sander Borst, Leo van Iersel, Mark Jones, Steven Kelk
2020 arXiv   pre-print
We study the problem of finding a temporal hybridization network for a set of phylogenetic trees that minimizes the number of reticulations.  ...  First, we introduce an FPT algorithm for this problem on an arbitrary set of m binary trees with n leaves each with a running time of O(5^k· n· m), where k is the minimum temporal hybridization number.  ...  Another important open problem is whether Temporal Hybridization is FPT for a set of more than two non-binary input trees.  ... 
arXiv:2007.13615v1 fatcat:ijkohjkgnrcd7fwa3dmbn2d4o4

Algorithms and Complexity in Phylogenetics (Dagstuhl Seminar 19443)

Magnus Bordewich, Britta Dorn, Simone Linz, Rolf Niedermeier, Michael Wagner
2020 Dagstuhl Reports  
Phylogenetics is the study of ancestral relationships between species. Its central goal is the reconstruction and analysis of phylogenetic trees and networks.  ...  Dagstuhl Seminar 19443 on Algorithms and Complexity in Phylogenetics aimed at bringing together researchers from phylogenetics and theoretical computer science to enable an exchange of expertise, facilitate  ...  Our group began attempted to find a general FPT algorithm for Hybridization Number on arbitrary number of trees with unbounded outdegree.  ... 
doi:10.4230/dagrep.9.10.134 dblp:journals/dagstuhl-reports/BordewichDLN19 fatcat:nypkd3nzjvg5jdsd3cidktwyei

Efficient parsimony-based methods for phylogenetic network reconstruction

G. Jin, L. Nakhleh, S. Snir, T. Tuller
2007 Bioinformatics  
Maximum parsimony is one of the most commonly used criteria for phylogenetic tree inference. Roughly speaking, inference based on this criterion seeks the tree that minimizes the amount of evolution.  ...  Results: In the present work we prove that the problem of scoring the parsimony of a phylogenetic network is NP-hard and provide an improved fixed parameter tractable algorithm for it.  ...  ACKNOWLEDGEMENTS This work was supported in part by the Rice Terascale Cluster funded by NSF under grant EIA-0216467, Intel, and HP. S. S. was supported in part by NSF grant CCR-0105533.  ... 
doi:10.1093/bioinformatics/btl313 pmid:17237079 fatcat:qvghmrfjmrhx5k6cnfhhp7qp7y

Combining Networks using Cherry Picking Sequences [article]

Remie Janssen and Mark Jones and Yukihiro Murakami
2019 arXiv   pre-print
Phylogenetic networks are important for the study of evolution. The number of methods to find such networks is increasing, but most such methods can only reconstruct small networks.  ...  We characterize this complexity via a restricted problem, Tree-child Network Hybridization, and we present an FPT algorithm to efficiently solve this restricted problem.  ...  Cherry picking: a characterization of the temporal hybridization number for a set of phylogenies. Bulletin of mathematical biology, 75(10):1879– 1890, 2013. 6.  ... 
arXiv:1912.03999v1 fatcat:qfwgounklbgmnbnxvodkz6cvgq

Combining Networks Using Cherry Picking Sequences [chapter]

Remie Janssen, Mark Jones, Yukihiro Murakami
2020 Lecture Notes in Computer Science  
Phylogenetic networks are important for the study of evolution. The number of methods to find such networks is increasing, but most such methods can only reconstruct small networks.  ...  We characterize this complexity via a restricted problem, Tree-child Network Hybridization, and we present an FPT algorithm to efficiently solve this restricted problem.  ...  An Algorithm for Tree-Child Network Hybridization In this section, we give an FPT algorithm for Tree-child Network Combination.  ... 
doi:10.1007/978-3-030-42266-0_7 fatcat:2jsnhhabprarhompzz3baokvhy

Parameterized Algorithms in Bioinformatics: An Overview

Laurent Bulteau, Mathias Weller
2019 Algorithms  
Aside from reporting the state of the art, we give challenges and open problems for each topic.  ...  This work surveys recent developments of parameterized algorithms and complexity for important NP-hard problems in bioinformatics.  ...  Finally, we thank the anonymous reviewers for their helpful and productive comments. Conflicts of Interest: The authors declare no conflict of interest.  ... 
doi:10.3390/a12120256 fatcat:4dhjdnpibzh43iifgan2fu6bwa

Deciding the existence of a cherry-picking sequence is hard on two trees [article]

Janosch Döcker, Leo van Iersel, Steven Kelk, Simone Linz
2019 arXiv   pre-print
The hardness result also greatly strengthens previous inapproximability results for the minimum temporal-hybridization number problem.  ...  This is the optimization version of the problem where we wish to construct a temporal phylogenetic network that topologically embeds two given rooted binary phylogenetic trees and that has a minimum number  ...  Simone Linz was supported by the New Zealand Marsden Fund.  ... 
arXiv:1712.02965v2 fatcat:mqpr5pibxffmja5utgmabsfyte

Who is Who in Phylogenetic Networks: Articles, Authors and Programs [article]

Tushar Agarwal, Philippe Gambette, David Morrison
2016 arXiv   pre-print
The phylogenetic network emerged in the 1990s as a new model to represent the evolution of species in the case where coexisting species transfer genetic information through hybridization, recombination  ...  "Who is Who in Phylogenetic Networks" comprises more than 600 publications and 500 authors interlinked with a rich set of more than 200 keywords related to phylogenetic networks.  ...  , hybridization and horizontal gene transfer, which the simple tree-based model fails to do.  ... 
arXiv:1610.01674v1 fatcat:h2nzslpm4va3lem7okcs225une

Reconstructing phylogenetic networks using maximum parsimony

L. Nakhleh, G. Jin, F. Zhao, J. Mellor-Crummey
2005 2005 IEEE Computational Systems Bioinformatics Conference (CSB'05)  
In a great majority of the cases in our experiments, the parsimony criterion accurately predicts the numbers and placements of non-tree events.  ...  Various methods and criteria have been introduced for phylogenetic tree reconstruction.  ...  Given a set S of sequences, the parsimony problem is to find a maximum parsimony phylogenetic tree T for the set S.  ... 
doi:10.1109/csb.2005.47 dblp:conf/csb/NakhlehJZM05 fatcat:uyubigbmvzh7vlbxveulshcfqy

Evolutionary radiation of Asteromyia carbonifera (Diptera: Cecidomyiidae) gall morphotypes on the goldenrod Solidago altissima (Asteraceae)

JOHN O. STIREMAN, ERIC M. JANSON, TIMOTHY G. CARR, HILARY DEVLIN, PATRICK ABBOT
2008 Biological Journal of the Linnean Society  
We assess the likely history of this radiation and use the results of phylogenetic analyses along with ecological data on phenology and parasitism rates to evaluate potential hypotheses for the mode of  ...  In some cases, however, divergence is associated with the use of alternative host-plant organs of a single host species. The basis of within-host radiations such as these remains poorly understood.  ...  Royer for aiding in molecular work and gall dissection and Brenda L. Wells for collecting phenological and parasitism data. J. J. Heath shared insights and unpublished data on Asteromyia biology.  ... 
doi:10.1111/j.1095-8312.2008.01101.x fatcat:x42urhzpjrgp3ptwdiezs4by2a

Abstracts Submitted for Presentation at the 2012 APS Annual Meeting

2012 Phytopathology  
the DNA sequences, we obtain trees with splits that set different distribution for studied species.  ...  The prospects for azole fungicides in controlling European M. graminicola populations in the future are discussed in the context of these new findings.  ...  All of the tested organisms significantly reduced numbers of cysts formed, but did not significantly reduce numbers of nematodes in other stages.  ... 
doi:10.1094/phyto-102-7-s4.1 fatcat:pwsd2yi2s5f33c7x2i6gc4bzca

Dagstuhl Reports, Volume 9, Issue 10, October 2019, Complete Issue

2020
Our group began attempted to find a general FPT algorithm for Hybridization Number on arbitrary number of trees with unbounded outdegree.  ...  In fact, FPT algorithms are known for Hybridization Number when either the number of trees or the maximum outdegree of any tree is bounded.  ...  We have a sketch of a polynomial-time algorithm for the temporal case.  ... 
doi:10.4230/dagrep.9.10 fatcat:4dvf4zjt4nhafhwb4ot23au3ua

Placing problems from phylogenetics and (quantified) propositional logic in the polynomial hierarchy [article]

Janosch Otto Döcker, Universitaet Tuebingen, Dorn, Britta (Apl. Prof. Dr.)
2021
They can be considered as a structure that embeds a whole set of phylogenetic trees which is called the display set of the network.  ...  Another interesting question concerns the reconstruction of networks: given a set T of phylogenetic trees, can we construct a phylogenetic network with certain properties that embeds all trees in T?  ...  Acknowledgments The authors are grateful for the diligent report and the useful hints -in particular for the findings presented in Section 3 -of an anonymous referee which improved (and shortened) the  ... 
doi:10.15496/publikation-60076 fatcat:odzek7qjy5cdxn4zop3ffn54cy

Rainbow trout (Oncorhynchus mykiss) habitat overlap with wild Atlantic salmon (Salmo salar) and brook trout (Salvelinus fontinalis) in natural streams: do habitat and landscape factors override competitive interactions?

Scott D. Roloson, Kyle M. Knysh, Michael R.S. Coffin, Karen L. Gormley, Christina C. Pater, Michael R. van den Heuvel
2018 Canadian Journal of Fisheries and Aquatic Sciences  
Their work laid the groundwork for all of today's successes.  ...  I am grateful for all of the anglers and conservationists for leading me into their watersheds and doing the hard work of restoring native trout and their ecosystems.  ...  Thus, we began to use a previously tested approach for estimating species' ecological niches, the Genetic Algorithm for Rule-set Prediction (GARP; Stockwell and Peters, 1999; Anderson et al., 2003) to  ... 
doi:10.1139/cjfas-2017-0342 fatcat:ulbpgjgnwjdrplf4yyvrlnffdy

Proceedings of the 2022 Joint Workshop of the German Research Training Groups in Computer Science

Felix Freiling, Helmut Seidl, 2022 2022 Joint Workshop Of The German Research Training Groups In Computer Science June 12–June 15
2022
(DFG) in the field of computer science returns to Schloss Dagstuhl --– Leibniz Center for Informatics, one of the world's premier venues for computer science-related seminars.  ...  The meeting featured the usual sequence of research presentations by funded researchers, networking meetings for PIs and RTG coordinators, as well as two invited talks, one by Professor Martina Seidl (  ...  We develop FPT algorithms for several parameters including the vertex cover number of the underlying graph plus the number of layers and the maximum number of connected components in any layer.  ... 
doi:10.25593/opus4-fau-19321 fatcat:ry4vd32xxbgldirrvymuaxxqwi
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