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Journal articles on the topic 'PhyloNext'

Author: Grafiati

Published: 5 June 2025

Last updated: 2 August 2025

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1

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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2

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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3

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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7

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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8

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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9

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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10

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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11

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). http://dx.doi.org/10.3897/rio.10.e124988.

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Abstract:

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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12

Than, Cuong, Derek Ruths, and Luay Nakhleh. "PhyloNet: a software package for analyzing and reconstructing reticulate evolutionary relationships." BMC Bioinformatics 9, no. 1 (2008). http://dx.doi.org/10.1186/1471-2105-9-322.

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13

Yan, Zhi, Zhen Cao, Yushu Liu, Huw A. Ogilvie, and Luay Nakhleh. "Maximum Parsimony Inference of Phylogenetic Networks in the Presence of Polyploid Complexes." Systematic Biology, October 4, 2021. http://dx.doi.org/10.1093/sysbio/syab081.

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Abstract Phylogenetic networks provide a powerful framework for modeling and analyzing reticulate evolutionary histories. While polyploidy has been shown to be prevalent not only in plants but also in other groups of eukaryotic species, most work done thus far on phylogenetic network inference assumes diploid hybridization. These inference methods have been applied, with varying degrees of success, to data sets with polyploid species, even though polyploidy violates the mathematical assumptions underlying these methods. Statistical methods were developed recently for handling specific types of

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14

Pang, Xiao-Xu, and Da-Yong Zhang. "Detection of Ghost Introgression Requires Exploiting Topological and Branch Length Information." Systematic Biology, January 15, 2024. http://dx.doi.org/10.1093/sysbio/syad077.

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Abstract In recent years, the study of hybridization and introgression has made significant progress, with ghost introgression—the transfer of genetic material from extinct or unsampled lineages to extant species—emerging as a key area for research. Accurately identifying ghost introgression, however, presents a challenge. To address this issue, we focused on simple cases involving three species with a known phylogenetic tree. Using mathematical analyses and simulations, we evaluated the performance of popular phylogenetic methods, including HyDe and PhyloNet/MPL, and the full-likelihood metho

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15

Guo, Weijian, Di Sun, Yang Cao, et al. "Extensive Interspecific Gene Flow Shaped Complex Evolutionary History and Underestimated Species Diversity in Rapidly Radiated Dolphins." Journal of Mammalian Evolution, November 17, 2021. http://dx.doi.org/10.1007/s10914-021-09581-6.

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AbstractRecently diverged taxa are often characterized by high rates of hybridization, which can complicate phylogenetic reconstruction. For this reason, the phylogenetic relationships and evolutionary history of dolphins are still not very well resolved; the question of whether the genera Tursiops and Stenella are monophyletic is especially controversial. Here, we performed re-sequencing of six dolphin genomes and combined them with eight previously published dolphin SRA datasets and six whole-genome datasets to investigate the phylogenetic relationships of dolphins and test the monophyly hyp

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16

Hibbins, Mark, and Matthew Hahn. "Distinguishing Between Histories of Speciation and Introgression Using Genomic Data." Bulletin of the Society of Systematic Biologists 3, no. 1 (2024). http://dx.doi.org/10.18061/bssb.v3i1.9227.

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Introgression creates complex, non-bifurcating relationships among species. At individual loci and across the genome, both introgression and incomplete lineage sorting interact to produce a wide range of different gene tree topologies. These processes can obscure the history of speciation among lineages, and, as a result, identifying the history of speciation vs. introgression remains a challenge. Here, we use theory and simulation to investigate how introgression can mislead multiple approaches to species tree inference. We find that arbitrarily low amounts of introgression may potentially mi

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17

Wang, Shuaibin, Junping Gao, Zhaowu Li, Kai Chen, Wenxuan Pu, and Chen Feng. "Phylotranscriptomics supports numerous polyploidization events and phylogenetic relationships in Nicotiana." Frontiers in Plant Science 14 (July 28, 2023). http://dx.doi.org/10.3389/fpls.2023.1205683.

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IntroductionNicotiana L. (Solanaceae) is of great scientific and economic importance, and polyploidization has been pivotal in shaping this genus. Despite many previous studies on the Nicotiana phylogenetic relationship and hybridization, evidence from whole genome data is still lacking.MethodsIn this study, we obtained 995 low-copy genes and plastid transcript fragments from the transcriptome datasets of 26 Nicotiana species, including all sections. We reconstructed the phylogenetic relationship and phylogenetic network of diploid species.ResultsThe incongruence among gene trees showed that t

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18

Cui, Xingyong, Enze Li, Jian He, et al. "Ancient hybridization drives arid adaptation and species diversification in Caragana (Fabaceae)." New Phytologist, July 8, 2025. https://doi.org/10.1111/nph.70360.

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Summary The genus Caragana (Fabaceae), comprising predominantly xerophytic shrubs, is ecologically important in arid ecosystems across Asia and Eastern Europe. Hybridization is increasingly recognized as a critical evolutionary mechanism, yet its role in arid adaptation and lineage diversification remains underexplored. Here, we test the hypothesis that ancient hybridization‐facilitated ecological expansion and diversification in Caragana. We generated a chromosome‐level genome assembly for Caragana arborescens and conducted genome‐wide resequencing of 98 individuals across 73 species, represe

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19

Hlavatá, Kristýna, Eliška Záveská, Jana Leong-Škorničková, et al. "Ancient hybridization and repetitive element proliferation in the evolutionary history of the monocot genus Amomum (Zingiberaceae)." Frontiers in Plant Science 15 (April 19, 2024). http://dx.doi.org/10.3389/fpls.2024.1324358.

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Genome size variation is a crucial aspect of plant evolution, influenced by a complex interplay of factors. Repetitive elements, which are fundamental components of genomic architecture, often play a role in genome expansion by selectively amplifying specific repeat motifs. This study focuses on Amomum, a genus in the ginger family (Zingiberaceae), known for its 4.4-fold variation in genome size. Using a robust methodology involving PhyloNet reconstruction, RepeatExplorer clustering, and repeat similarity-based phylogenetic network construction, we investigated the repeatome composition, analy

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20

Lyu, Rudan, Jian He, Yike Luo, et al. "Natural Hybrid Origin of the Controversial “Species” Clematis × pinnata (Ranunculaceae) Based on Multidisciplinary Evidence." Frontiers in Plant Science 12 (October 12, 2021). http://dx.doi.org/10.3389/fpls.2021.745988.

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Interspecific hybridization is common and has often been viewed as a driving force of plant diversity. However, it raises taxonomic problems and thus impacts biodiversity estimation and biological conservation. Although previous molecular phylogenetic studies suggested that interspecific hybridization may be rather common in Clematis, and artificial hybridization has been widely applied to produce new Clematis cultivars for nearly two centuries, the issue of natural hybridization of Clematis has never been addressed in detail. In this study, we tested the hybrid origin of a mesophytic and cold

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21

Kong, Sungsik, David L. Swofford, and Laura S. Kubatko. "Inference of Phylogenetic Networks from Sequence Data using Composite Likelihood." Systematic Biology, October 10, 2024. http://dx.doi.org/10.1093/sysbio/syae054.

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Abstract While phylogenies have been essential in understanding how species evolve, they do not adequately describe some evolutionary processes. For instance, hybridization, a common phenomenon where interbreeding between two species leads to formation of a new species, must be depicted by a phylogenetic network, a structure that modifies a phylogenetic tree by allowing two branches to merge into one, resulting in reticulation. However, existing methods for estimating networks become computationally expensive as the dataset size and/or topological complexity increase. The lack of methods for s

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22

Yang, Fengmao, Jia Ge, Yongjie Guo, Richard Olmstead, and Weibang Sun. "Deciphering complex reticulate evolution of Asian Buddleja (Scrophulariaceae): insights into the taxonomy and speciation of polyploid taxa in the Sino-Himalayan region." Annals of Botany, February 1, 2023. http://dx.doi.org/10.1093/aob/mcad022.

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Abstract Background and Aims Species of the genus Buddleja in Asia are mainly distributed in the Sino-Himalayan region and forms a challenging taxonomic group with extensive hybridization and polyploidization. A phylogenetic approach to unraveling the history of reticulation in this lineage will deepen our understanding of the speciation in biodiversity hotspots. Methods For this study, we obtained 80 accessions representing all the species in the Asian Buddleja clade, and the ploidy level of each taxon was determined by flow cytometry analyses. Whole plastid genomes, nuclear ribosomal DNA, si

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23

Lei, Xie. "Natural Hybrid Origin of the Controversial "Species" Clematis pinnata (Ranunculaceae) Based on Multidisciplinary Evidence." August 11, 2021. https://doi.org/10.5281/zenodo.5179896.

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Interspecific hybridization is common and has often been viewed as a driving force of plant diversity. However, it raises taxonomic problems and thus impacts biodiversity estimation and biological conservation of species. Although previous molecular phylogenetic studies suggested that interspecific hybridization may be rather common in <em>Clematis</em>, and artificial hybridization has been widely applied to produce new <em>Clematis</em> cultivars for nearly two centuries, the issue of natural hybridization of <em>Clematis</em> has never been addressed in detail. In this study, we tested the

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24

Dias, Guilherme Rezende, Eduardo Guimarães Dupim, Thyago Vanderlinde, Beatriz Mello, and Antonio Bernardo Carvalho. "A phylogenomic study of Steganinae fruit flies (Diptera: Drosophilidae): strong gene tree heterogeneity and evidence for monophyly." BMC Evolutionary Biology 20, no. 1 (2020). http://dx.doi.org/10.1186/s12862-020-01703-7.

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Abstract Background The Drosophilidae family is traditionally divided into two subfamilies: Drosophilinae and Steganinae. This division is based on morphological characters, and the two subfamilies have been treated as monophyletic in most of the literature, but some molecular phylogenies have suggested Steganinae to be paraphyletic. To test the paraphyletic-Steganinae hypothesis, here, we used genomic sequences of eight Drosophilidae (three Steganinae and five Drosophilinae) and two Ephydridae (outgroup) species and inferred the phylogeny for the group based on a dataset of 1,028 orthologous

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25

Ren, Chen, Long Wang, Ze-Long Nie, et al. "Complex but Clear Allopolyploid Pattern of Subtribe Tussilagininae (Asteraceae: Senecioneae) Revealed by Robust Phylogenomic Evidence, with Development of a Novel Homeolog-Sorting Pipeline." Systematic Biology, July 25, 2024. http://dx.doi.org/10.1093/sysbio/syae046.

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Abstract Polyploidy is a significant mechanism in eukaryotic evolution and is particularly prevalent in the plant kingdom. However, our knowledge about this phenomenon and its effects on evolution remains limited. A major obstacle to the study of polyploidy is the great difficulty in untangling the origins of allopolyploids. Due to the drastic genome changes and the erosion of allopolyploidy signals caused by the combined effects of hybridization and complex post-polyploid diploidization processes, resolving the origins of allopolyploids has long been a challenging task. Here we revisit this i

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