Empirical Analysis of Phylogenetic Quasi-Terraces

AbstractTerraces in phylogenetic tree space are, among other things, important for the design of tree space search strategies. While the phenomenon of phylogenetic terraces is already known for unlinked partition models on partitioned phylogenomic data sets, it has not yet been studied if an analogous structure is present under linked and scaled partition models. To this end, we analyze aspects such as the log-likelihood distributions, likelihood-based significance tests, and nearest neighborhood interchanges on the trees residing on a terrace and compare their distributions among unlinked, linked, and scaled partition models. Our study shows that there exists a terrace-like structure under linked and scaled partition models as well. We denote this phenomenon as quasi-terrace. Therefore quasi-terraces should be taken into account in the design of tree search algorithms as well as when reporting results on ‘the’ final tree topology in empirical phylogenetic studies.

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Systematic Exploration of the High Likelihood Set of Phylogenetic Tree Topologies

Systematic Biology ◽

10.1093/sysbio/syz047 ◽

2019 ◽

Vol 69 (2) ◽

pp. 280-293 ◽

Cited By ~ 1

Author(s):

Chris Whidden ◽

Brian C Claywell ◽

Thayer Fisher ◽

Andrew F Magee ◽

Mathieu Fourment ◽

...

Keyword(s):

Phylogenetic Tree ◽

Hash Table ◽

Tree Topology ◽

Hill Climbing ◽

Bayesian Posterior Probability ◽

Data Sets ◽

High Likelihood ◽

Tree Topologies ◽

Tree Space ◽

Local Topology

Abstract Bayesian Markov chain Monte Carlo explores tree space slowly, in part because it frequently returns to the same tree topology. An alternative strategy would be to explore tree space systematically, and never return to the same topology. In this article, we present an efficient parallelized method to map out the high likelihood set of phylogenetic tree topologies via systematic search, which we show to be a good approximation of the high posterior set of tree topologies on the data sets analyzed. Here, “likelihood” of a topology refers to the tree likelihood for the corresponding tree with optimized branch lengths. We call this method “phylogenetic topographer” (PT). The PT strategy is very simple: starting in a number of local topology maxima (obtained by hill-climbing from random starting points), explore out using local topology rearrangements, only continuing through topologies that are better than some likelihood threshold below the best observed topology. We show that the normalized topology likelihoods are a useful proxy for the Bayesian posterior probability of those topologies. By using a nonblocking hash table keyed on unique representations of tree topologies, we avoid visiting topologies more than once across all concurrent threads exploring tree space. We demonstrate that PT can be used directly to approximate a Bayesian consensus tree topology. When combined with an accurate means of evaluating per-topology marginal likelihoods, PT gives an alternative procedure for obtaining Bayesian posterior distributions on phylogenetic tree topologies.

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A Survey of VLSI Implementations of Tree Search Algorithms for MIMO Detection

Circuits Systems and Signal Processing ◽

10.1007/s00034-015-0218-y ◽

2015 ◽

Vol 35 (10) ◽

pp. 3644-3674 ◽

Cited By ~ 4

Author(s):

Ibrahim A. Bello ◽

Basel Halak ◽

Mohammed El-Hajjar ◽

Mark Zwolinski

Keyword(s):

Search Algorithms ◽

Tree Search ◽

Mimo Detection

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High-throughput implementation of tree-search algorithms for vector precoding

2011 IEEE International Conference on Acoustics, Speech and Signal Processing (ICASSP) ◽

10.1109/icassp.2011.5946825 ◽

2011 ◽

Cited By ~ 5

Author(s):

Maitane Barrenechea ◽

Luis Barbero ◽

Idoia Jimenez ◽

Egoitz Arruti ◽

Mikel Mendicute

Keyword(s):

High Throughput ◽

Search Algorithms ◽

Tree Search

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Using target enrichment sequencing to study the higher-level phylogeny of the largest lichen-forming fungi family: Parmeliaceae (Ascomycota)

IMA Fungus ◽

10.1186/s43008-020-00051-x ◽

2020 ◽

Vol 11 (1) ◽

Author(s):

Felix Grewe ◽

Claudio Ametrano ◽

Todd J. Widhelm ◽

Steven Leavitt ◽

Isabel Distefano ◽

...

Keyword(s):

Data Sets ◽

Target Enrichment ◽

Data Set ◽

Reduced Genome ◽

Genome Data ◽

Worldwide Distribution ◽

Phylogenetic Studies ◽

Genome Scale ◽

Scale Data ◽

Promising Avenue

AbstractParmeliaceae is the largest family of lichen-forming fungi with a worldwide distribution. We used a target enrichment data set and a qualitative selection method for 250 out of 350 genes to infer the phylogeny of the major clades in this family including 81 taxa, with both subfamilies and all seven major clades previously recognized in the subfamily Parmelioideae. The reduced genome-scale data set was analyzed using concatenated-based Bayesian inference and two different Maximum Likelihood analyses, and a coalescent-based species tree method. The resulting topology was strongly supported with the majority of nodes being fully supported in all three concatenated-based analyses. The two subfamilies and each of the seven major clades in Parmelioideae were strongly supported as monophyletic. In addition, most backbone relationships in the topology were recovered with high nodal support. The genus Parmotrema was found to be polyphyletic and consequently, it is suggested to accept the genus Crespoa to accommodate the species previously placed in Parmotrema subgen. Crespoa. This study demonstrates the power of reduced genome-scale data sets to resolve phylogenetic relationships with high support. Due to lower costs, target enrichment methods provide a promising avenue for phylogenetic studies including larger taxonomic/specimen sampling than whole genome data would allow.

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Utility of phylogenetic studies in the identification ofLeptospirastrains

Epidemiology and Infection ◽

10.1017/s095026880700800x ◽

2007 ◽

Vol 135 (8) ◽

pp. 1266-1273 ◽

Cited By ~ 5

Author(s):

G. RESCH ◽

M. AWAD-MASALMEH ◽

P. BAKOSS ◽

J. JAREKOVÁ

Keyword(s):

Phylogenetic Tree ◽

Central Europe ◽

Computer Software ◽

Digital Reading ◽

Phylogenetic Studies ◽

Wild Strains ◽

Software Programs ◽

Reference Strains

SUMMARYA phylogenetic tree, which distinguishes between the serovars and serogroups of leptospires common in Central Europe was constructed using an established RAPD procedure together with digital reading and evaluation (using different computer software programs) of the generated amplified DNA patterns. The application of this procedure has revealed a consistent correspondence between serogroup and genotype (position in constructed tree) in 69 cases, and serovar and genotype in 72 cases, of wild strains of leptospires. There was an agreement between serovar and genotype in cases of strains of Grippotyphosa, Pomona, Mozdok, Arborea and Sorexjalna as well as between serogroup and genotype in cases of Australis, Bataviae and Sejroe. With the procedure used in this study, it was not possible to distinguish between reference strains of serovars Jalna, Bratislava and Lora (all serogroup Australis) as well as between serovars Icterohaemorrhagiae and Copenhageni (both of serogroup Icterohaemorrhagiae). In contrast to this, wild strains belonging to serogroup Sejroe were distributed between Polonica, Istrica, Saxkoebing and Sejroe serovars. Endemic strains of leptospires tested, were also distinguishable.

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