Online phylogenetic inference methods add sequentially arriving sequences to an inferred phylogeny without the need to recompute the entire tree from scratch. Some online method implementations exist already, but there remains concern that additional sequences may change the topological relationship among the original set of taxa. We call such a change in tree topology a lack of stability for the inferred tree. In this paper, we analyze the stability of single taxon addition in a Maximum Likelihood framework across 1, 000 empirical datasets. We find that instability occurs in almost 90% of our examples, although observed topological differences do not always reach significance under the AU-test. Changes in tree topology after addition of a taxon rarely occur close to its attachment location, and are more frequently observed in more distant tree locations carrying low bootstrap support. To investigate whether instability is predictable, we hypothesize sources of instability and design summary statistics addressing these hypotheses. Using these summary statistics as input features for machine learning under random forests, we are able to predict instability and can identify the most influential features. In summary, it does not appear that a strict insertion-only online inference method will deliver globally optimal trees, although relaxing insertion strictness by allowing for a small number of final tree rearrangements or accepting slightly suboptimal solutions appears feasible.
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http://dx.doi.org/10.1093/sysbio/syae059 | DOI Listing |
MycoKeys
December 2024
Yunnan Provincial Key Laboratory for Conservation and Utilization of In-forest Resource, the Key Laboratory of Forest Resources Conservation and Utilization in the Southwest Mountains of China Ministry of Education, Southwest Forestry University, Kunming 650224, China Southwest Forestry University Kunming China.
Three new fungal species, , and , are proposed based on a combination of the morphological features and molecular evidence. The taxon is characterized by the coriaceous basidiomata with a cream surface, cylindrical basidia, straight, 4-celled, subglobose or ovoid probasidia and thin-walled, narrowly cylindrical basidiospores with septa, measuring as 7-9 × 3.5-4.
View Article and Find Full Text PDFActa Parasitol
January 2025
Museum Zoologicum Bogoriense, Research Center for Biosystematics and Evolution, National Research and Innovation Agency (BRIN), Jl. Raya Jakarta-Bogor Km. 46, Cibinong, West Java, 16911, Indonesia.
Purpose: The present paper reports the nematodes of the suborder Trichostrongylina collected from the common spiny bandicoot, Echymipera kalubu, in Arso, Papua Indonesia. The description of Kalubustrongylus arsoensis gen. et sp.
View Article and Find Full Text PDFGlob Chang Biol
January 2025
School of Biological Sciences, The University of Hong Kong, Hong Kong, China.
Land use change threatens global biodiversity and compromises ecosystem functions, including pollination and food production. Reduced taxonomic α-diversity is often reported under land use change, yet the impacts could be different at larger spatial scales (i.e.
View Article and Find Full Text PDFFront Nutr
December 2024
College of Marine and Bioengineering, Yancheng Institute of Technology, Yancheng, China.
Introduction: Type 2 diabetes mellitus (T2DM) often leads to elevated blood glucose levels and lipid metabolism disorder, which is generally accompanied by dysbiosis of gut microbiota and metabolic dysfunction.
Methods: In this study, a mouse model of T2DM was established by feeding a high-fat/sucrose diet combined with injecting a low dose of streptozotocin. The aim of this study was to analyze the regulatory effect of Suaeda salsa extract (SSE) on T2DM and its effect on the intestinal flora of mice.
Vavilovskii Zhurnal Genet Selektsii
November 2024
Federal Scientific Center of the East Asia Terrestrial Biodiversity of the Far Eastern Branch of the Russian Academy of Sciences, Vladivostok, Russia.
During the study of algal diversity in pyroclastic deposits of the Kamchatka Peninsula, Chlorella-like green algae strains VCA-72 and VCA-93 were isolated from samples collected from along the Baydarnaya river bed on the Shiveluch volcano in 2018 and at the outlet of thermal vapors along the edge of the caldera on the southern slope of the Gorely volcano in 2020. Identification of the strains was carried out within the framework of an integrative approach using microscopic and molecular genetic methods, including preliminary taxon identification, obtaining nucleotide sequences of the small subunit and the internal transcribed spacer rRNA, reconstruction of phylogenetic trees and secondary structures of the ITS1 and ITS2 rRNA regions. On the phylogenetic tree, strain VCA-93 was clustered in the Micractinium thermotolerans species clade.
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