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Academic literature on the topic 'PhyloNext'

Author: Grafiati

Published: 5 June 2025

Last updated: 2 August 2025

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Journal articles on the topic "PhyloNext"

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Mikryukov, Vladimir, Kessy Abarenkov, Thomas Jeppesen, Dmitry Schigel, and Tobias Frøslev. "Prototype Biodiversity Digital Twin: Phylogenetic Diversity." Research Ideas and Outcomes 10 (June 11, 2024): e124988. https://doi.org/10.3897/rio.10.e124988.

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Phylogenetic diversity (PD) represents a fundamental measure of biodiversity, encapsulating the extent of evolutionary history within species groups. This measure, pivotal for understanding biodiversity's full dimension, has gained recognition by major environmental and scientific organisations, including the Intergovernmental Science-Policy Platform on Biodiversity and Ecosystem Services. Unlike traditional taxonomic richness, PD offers a comprehensive, evolutionary perspective on biodiversity, essential for conservation planning and biodiversity management. This manuscript describes the deve

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Wen, Dingqiao, Yun Yu, Jiafan Zhu, and Luay Nakhleh. "Inferring Phylogenetic Networks Using PhyloNet." Systematic Biology 67, no. 4 (2018): 735–40. http://dx.doi.org/10.1093/sysbio/syy015.

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Zhu, Jiafan, Xinhao Liu, Huw A. Ogilvie, and Luay K. Nakhleh. "A divide-and-conquer method for scalable phylogenetic network inference from multilocus data." Bioinformatics 35, no. 14 (2019): i370—i378. http://dx.doi.org/10.1093/bioinformatics/btz359.

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Abstract Motivation Reticulate evolutionary histories, such as those arising in the presence of hybridization, are best modeled as phylogenetic networks. Recently developed methods allow for statistical inference of phylogenetic networks while also accounting for other processes, such as incomplete lineage sorting. However, these methods can only handle a small number of loci from a handful of genomes. Results In this article, we introduce a novel two-step method for scalable inference of phylogenetic networks from the sequence alignments of multiple, unlinked loci. The method infers networks

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Pospekhov, V. V., and K. V. Kusenko. "NEMATODES OF GENUS PHILONEMA (PHILONEMIDAE) FROM SOCKEYE SALMON AND WHITESPOTTED CHAR FROM LAKE KISI (OLA RIVER BASIN, OKHOTSK SEA)." Izvestiya TINRO 197 (July 5, 2019): 194–207. http://dx.doi.org/10.26428/1606-9919-2019-197-194-207.

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Morphology of phylonems infesting whitespotted char Salvelinus leucomaenis and sockeye salmon Oncorhynchus nerka in Lake Kisi at the northern coast of the Okhotsk Sea is described for the first time. Sockeye was infected with adults of Philonema oncorhynchi Kuitunen-Ekbaum, 1933 and larvae of other nematode species (Philonema sp. II), and char — with adult dracunculoid nematode designated as Philonema sp. I. This Philonema sp. I differs considerably from Ph. oncorhynchi by number of reproductive papillae, their distribution, and structure of cuticular appendices on the caudal end of males. Lar

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He, Jian, Mingyang Li, Huanyu Wu, Jin Cheng, and Lei Xie. "Unraveling the Ancient Introgression History of Xanthoceras (Sapindaceae): Insights from Phylogenomic Analysis." International Journal of Molecular Sciences 26, no. 4 (2025): 1581. https://doi.org/10.3390/ijms26041581.

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Ancient introgression is an infrequent evolutionary process often associated with conflicts between nuclear and organellar phylogenies. Determining whether such conflicts arise from introgression, incomplete lineage sorting (ILS), or other processes is essential to understanding plant diversification. Previous studies have reported phylogenetic discordance in the placement of Xanthoceras, but its causes remain unclear. Here, we analyzed transcriptome data from 41 Sapindaceae samples to reconstruct phylogenies and investigate this discordance. While nuclear phylogenies consistently placed Xanth

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Ma, Chi, Yu Lin, Junjun Yin, Lijuan Zhu, Jinkai Fang, and Dan Zhang. "Phylogenetic Analysis and Expression Patterns of Triterpenoid Saponin Biosynthesis Genes in 19 Araliaceae Plants." International Journal of Molecular Sciences 26, no. 7 (2025): 3439. https://doi.org/10.3390/ijms26073439.

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The Araliaceae family has significant economic and medicinal value. However, the phylogenetic relationships and the expression patterns of key genes of the active triterpenoid substance within this family are still unclear. In this study, we employed comparative transcriptomics to analyze the transcriptomes of 19 species from 11 genera of Araliaceae, aiming to elucidate the evolutionary history of the family and the expression patterns of key genes in the ginsenoside biosynthesis pathway. Our results divide Araliaceae into two subfamilies: Aralioideae and Hydrocotyloideae. Aralioideae is furth

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Pospekhov, V. V., and V. P. Nikishin. "Unusual form of relationship between parasitic nematodes of the genus Philonema (Philonemidae) and salmonids." Russian Journal of Parasitology 14, no. 4 (2020): 24–33. http://dx.doi.org/10.31016/1998-8435-2020-14-4-24-33.

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The purpose of the research is studying the relationship between nematodes of the genus Philonema (Philonemidae) and salmonids at the organismic level and justification for their interpretation as a peculiar form of encapsulation.Materials and methods. We studied the sockeye salmon, as well as the freshwater white-spotted char and Dolly Varden trout from lakes Kisi and Chistoye (basin of the Ola River, Taui Bay, Sea of Okhotsk). 7 males for breeding sockeye salmon, 39 freshwater white-spotted chars and 16 Dolly Varden trouts were dissected for infection by Philonema. We used well-known general

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Rabier, Charles-Elie, Vincent Berry, Marnus Stoltz, et al. "On the inference of complex phylogenetic networks by Markov Chain Monte-Carlo." PLOS Computational Biology 17, no. 9 (2021): e1008380. http://dx.doi.org/10.1371/journal.pcbi.1008380.

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For various species, high quality sequences and complete genomes are nowadays available for many individuals. This makes data analysis challenging, as methods need not only to be accurate, but also time efficient given the tremendous amount of data to process. In this article, we introduce an efficient method to infer the evolutionary history of individuals under the multispecies coalescent model in networks (MSNC). Phylogenetic networks are an extension of phylogenetic trees that can contain reticulate nodes, which allow to model complex biological events such as horizontal gene transfer, hyb

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Olave, Melisa, and Axel Meyer. "Implementing Large Genomic Single Nucleotide Polymorphism Data Sets in Phylogenetic Network Reconstructions: A Case Study of Particularly Rapid Radiations of Cichlid Fish." Systematic Biology 69, no. 5 (2020): 848–62. http://dx.doi.org/10.1093/sysbio/syaa005.

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Abstract The Midas cichlids of the Amphilophus citrinellus spp. species complex from Nicaragua (13 species) are an extraordinary example of adaptive and rapid radiation ($&lt;$24,000 years old). These cichlids are a very challenging group to infer its evolutionary history in phylogenetic analyses, due to the apparent prevalence of incomplete lineage sorting (ILS), as well as past and current gene flow. Assuming solely a vertical transfer of genetic material from an ancestral lineage to new lineages is not appropriate in many cases of genes transferred horizontally in nature. Recently devel

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Mikryukov, Vladimir, Kessy Abarenkov, Shawn Laffan, et al. "PhyloNext: a pipeline for phylogenetic diversity analysis of GBIF-mediated data." BMC Ecology and Evolution 24, no. 1 (2024). http://dx.doi.org/10.1186/s12862-024-02256-9.

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Abstract Background Understanding biodiversity patterns is a central topic in biogeography and ecology, and it is essential for conservation planning and policy development. Diversity estimates that consider the evolutionary relationships among species, such as phylogenetic diversity and phylogenetic endemicity indices, provide valuable insights into the functional diversity and evolutionary uniqueness of biological communities. These estimates are crucial for informed decision-making and effective global biodiversity management. However, the current methodologies used to generate these metric

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Book chapters on the topic "PhyloNext"

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Zikri, Nir Ben, and Andrei Sharf. "PhyLoNet: Physically-Constrained Long-Term Video Prediction." In Computer Vision – ACCV 2022. Springer Nature Switzerland, 2023. http://dx.doi.org/10.1007/978-3-031-26293-7_34.

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Cao, Zhen, Xinhao Liu, Huw A. Ogilvie, Zhi Yan, and Luay Nakhleh. "Practical Aspects of Phylogenetic Network Analysis Using PhyloNet." In Species Tree Inference. Princeton University Press, 2023. http://dx.doi.org/10.2307/j.ctv2wr4wdf.11.

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Cao, Zhen, Xinhao Liu, Huw A. Ogilvie, Zhi Yan, and Luay Nakhleh. "CHAPTER 5 Practical Aspects of Phylogenetic Network Analysis Using PhyloNet." In Species Tree Inference. Princeton University Press, 2023. http://dx.doi.org/10.1515/9780691245157-009.

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Conference papers on the topic "PhyloNext"

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Panahiazar, Maryam, Ajith Ranabahu, Vahid Taslimi, et al. "PhylOnt: A domain-specific ontology for phylogeny analysis." In 2012 IEEE International Conference on Bioinformatics and Biomedicine (BIBM). IEEE, 2012. http://dx.doi.org/10.1109/bibm.2012.6392677.

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