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Journal articles on the topic 'Phylogeney'

Author: Grafiati

Published: 18 May 2024

Last updated: 31 July 2025

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1

Zeb, Umar, Xiukang Wang, Sajid Fiaz, et al. "Novel insights into Pinus species plastids genome through phylogenetic relationships and repeat sequence analysis." PLOS ONE 17, no. 1 (2022): e0262040. http://dx.doi.org/10.1371/journal.pone.0262040.

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Pinus is one of the most economical and ecological important conifers, model specie for studying sequence divergence and molecular phylogeney of gymnosperms. The less availability of information for genome resources enable researchers to conduct evolutionary studies of Pinus species. To improve understanding, we firstly reported, previously released chloroplast genome of 72 Pinus species, the sequence variations, phylogenetic relationships and genome divergence among Pinus species. The results displayed 7 divergent hotspot regions (trnD-GUC, trnY-GUA, trnH-GUG, ycf1, trnL-CAA, trnK-UUU and trn

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YU, YONG-XIU, YU-HANG LU, QING TIAN, and ASHA J. DISSANAYAKE. "Byssosphaeria vaginata, a new species of Melanommataceae from Magnolia officinalis in Sichuan Province, China." Phytotaxa 705, no. 1 (2025): 35–49. https://doi.org/10.11646/phytotaxa.705.1.3.

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During an investigation of ascomycetous fungi on Magnolia officinalis (Magnoliaceae) in Sichuan Province, Southwest China, a novel species, Byssosphaeria vaginata, is introduced. The taxonomic placement of the species was confirmed based on morphology and muti-gene phylogeney. Though our new species resembles B. clematidis, it differs from the type species (B. clematidis) in having larger ascomata with pale yellowish pigment around the pore and wider and shorter ascospores with clear mucilaginous sheaths. The phylogenetic analysis based on LSU, SSU, ITS, and tef1-α sequence data generated from

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LÖRZ, ANNE-NINA. "Deep-sea Rhachotropis (Crustacea: Amphipoda: Eusiridae) from New Zealand and the Ross Sea with key to the Pacific, Indian Ocean and Antarctic species." Zootaxa 2482, no. 1 (2010): 22. http://dx.doi.org/10.11646/zootaxa.2482.1.2.

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The amphipod genus Rhachotropis has a worldwide distribution. Four species new to science are described, increasing the total number of Rhachotropis species to 59. Only one species was previously known from New Zealand and none from the Ross Sea. Two species Rhachotropis chathamensis sp. nov. and R. delicata sp. nov. were collected at the same station in 420 m depth off eastern New Zealand; R. rossi sp. nov. and R. abyssalis sp. nov. were collected below 3000 m depth in the Ross Sea, Antarctica. Investigation of recently collected material as well as historic material from the NIWA Invertebrat

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Gawel, Nick J., Rory Mellinger, Eric Stout, and R. Sauve. "RAPD Analysis of Acer." HortScience 30, no. 4 (1995): 813F—813. http://dx.doi.org/10.21273/hortsci.30.4.813f.

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DNA from 27 Acer species was used for RAPD analysis. A relatively high number of phylogenically informative polymorphisms were detected, as would be expected in intraspecific comparisons. Principle coordinates analysis was used to discern groupings among the species and a RAPD-based phylogeny was constructed. As expected when making comparisons among species, very high levels of polymorphism were found. Cultivars that grouped together in the principle components analysis also grouped together in the phylogenic analysis. Parts of the phylogenic analysis do not agree with morphology-based phylog

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Kulman, Ethan, Rui Kuang, and Quaid Morris. "Orchard: Building large cancer phylogenies using stochastic combinatorial search." PLOS Computational Biology 20, no. 12 (2024): e1012653. https://doi.org/10.1371/journal.pcbi.1012653.

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Phylogenies depicting the evolutionary history of genetically heterogeneous subpopulations of cells from the same cancer, i.e., cancer phylogenies, offer valuable insights about cancer development and guide treatment strategies. Many methods exist that reconstruct cancer phylogenies using point mutations detected with bulk DNA sequencing. However, these methods become inaccurate when reconstructing phylogenies with more than 30 mutations, or, in some cases, fail to recover a phylogeny altogether. Here, we introduce Orchard, a cancer phylogeny reconstruction algorithm that is fast and accurate

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Ma, Tengfei, Haijiao Liu, Yafei Chen, et al. "Familial Reclassification Within Order Lysobacterales and Proposal of Four Novel Species." Microorganisms 13, no. 6 (2025): 1212. https://doi.org/10.3390/microorganisms13061212.

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The order Lysobacterales consists of three families (Rhodanobacteraceae, Lysobacteraceae and Marinicellaceae), many members of which are important pathogenic and beneficial bacteria. Previous classifications of members within order Lysobacterales have relied heavily on 16S rRNA gene sequences, leading to taxonomic ambiguities at the familial level. With the advancement of sequencing technologies, an increasing number of whole-genome sequences have been available, providing an opportunity to revisit the taxonomy of families in Lysobacterales. In this study, we revisited the taxonomy of Lysobact

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Golding, G. Brian. "Reconstructing the Prior Probabilities of Allelic Phylogenies." Genetics 161, no. 2 (2002): 889–96. http://dx.doi.org/10.1093/genetics/161.2.889.

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Abstract In general when a phylogeny is reconstructed from DNA or protein sequence data, it makes use only of the probabilities of obtaining some phylogeny given a collection of data. It is also possible to determine the prior probabilities of different phylogenies. This information can be of use in analyzing the biological causes for the observed divergence of sampled taxa. Unusually “rare” topologies for a given data set may be indicative of different biological forces acting. A recursive algorithm is presented that calculates the prior probabilities of a phylogeny for different allelic samp

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Stadler, Tanja, and Jana Smrckova. "Estimating shifts in diversification rates based on higher-level phylogenies." Biology Letters 12, no. 10 (2016): 20160273. http://dx.doi.org/10.1098/rsbl.2016.0273.

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Macroevolutionary studies recently shifted from only reconstructing the past state, i.e. the species phylogeny, to also infer the past speciation and extinction dynamics that gave rise to the phylogeny. Methods for estimating diversification dynamics are sensitive towards incomplete species sampling. We introduce a method to estimate time-dependent diversification rates from phylogenies where clades of a particular age are represented by only one sampled species. A popular example of this type of data is phylogenies on the genus- or family-level, i.e. phylogenies where one species per genus or

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Palmer, Marike, Stephanus N. Venter, Alistair R. McTaggart, et al. "The synergistic effect of concatenation in phylogenomics: the case in Pantoea." PeerJ 7 (April 16, 2019): e6698. http://dx.doi.org/10.7717/peerj.6698.

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With the increased availability of genome sequences for bacteria, it has become routine practice to construct genome-based phylogenies. These phylogenies have formed the basis for various taxonomic decisions, especially for resolving problematic relationships between taxa. Despite the popularity of concatenating shared genes to obtain well-supported phylogenies, various issues regarding this combined-evidence approach have been raised. These include the introduction of phylogenetic error into datasets, as well as incongruence due to organism-level evolutionary processes, particularly horizonta

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Purvis, Andy, Susanne A. Fritz, Jesús Rodríguez, Paul H. Harvey, and Richard Grenyer. "The shape of mammalian phylogeny: patterns, processes and scales." Philosophical Transactions of the Royal Society B: Biological Sciences 366, no. 1577 (2011): 2462–77. http://dx.doi.org/10.1098/rstb.2011.0025.

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Mammalian phylogeny is far too asymmetric for all contemporaneous lineages to have had equal chances of diversifying. We consider this asymmetry or imbalance from four perspectives. First, we infer a minimal set of ‘regime changes’—points at which net diversification rate has changed—identifying 15 significant radiations and 12 clades that may be ‘downshifts’. We next show that mammalian phylogeny is similar in shape to a large set of published phylogenies of other vertebrate, arthropod and plant groups, suggesting that many clades may diversify under a largely shared set of ‘rules’. Third, we

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Purvis, Andy, Susanne A. Fritz, Jesús Rodríguez, Paul H. Harvey, and Richard Grenyer. "The shape of mammalian phylogeny: patterns, processes and scales." Philosophical Transactions of the Royal Society B: Biological Sciences 366, no. 1577 (2011): 2462–77. https://doi.org/10.5281/zenodo.13434697.

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(Uploaded by Plazi for the Bat Literature Project) Mammalian phylogeny is far too asymmetric for all contemporaneous lineages to have had equal chances of diversifying. We consider this asymmetry or imbalance from four perspectives. First, we infer a minimal set of 'regime changes'—points at which net diversification rate has changed—identifying 15 significant radiations and 12 clades that may be 'downshifts'. We next show that mammalian phylogeny is similar in shape to a large set of published phylogenies of other vertebrate, arthropod and plant groups, suggesting that many clades may diversi

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Purvis, Andy, Susanne A. Fritz, Jesús Rodríguez, Paul H. Harvey, and Richard Grenyer. "The shape of mammalian phylogeny: patterns, processes and scales." Philosophical Transactions of the Royal Society B: Biological Sciences 366, no. 1577 (2011): 2462–77. https://doi.org/10.5281/zenodo.13434697.

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(Uploaded by Plazi for the Bat Literature Project) Mammalian phylogeny is far too asymmetric for all contemporaneous lineages to have had equal chances of diversifying. We consider this asymmetry or imbalance from four perspectives. First, we infer a minimal set of 'regime changes'—points at which net diversification rate has changed—identifying 15 significant radiations and 12 clades that may be 'downshifts'. We next show that mammalian phylogeny is similar in shape to a large set of published phylogenies of other vertebrate, arthropod and plant groups, suggesting that many clades may diversi

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Purvis, Andy, Susanne A. Fritz, Jesús Rodríguez, Paul H. Harvey, and Richard Grenyer. "The shape of mammalian phylogeny: patterns, processes and scales." Philosophical Transactions of the Royal Society B: Biological Sciences 366, no. 1577 (2011): 2462–77. https://doi.org/10.5281/zenodo.13434697.

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Abstract:

(Uploaded by Plazi for the Bat Literature Project) Mammalian phylogeny is far too asymmetric for all contemporaneous lineages to have had equal chances of diversifying. We consider this asymmetry or imbalance from four perspectives. First, we infer a minimal set of 'regime changes'—points at which net diversification rate has changed—identifying 15 significant radiations and 12 clades that may be 'downshifts'. We next show that mammalian phylogeny is similar in shape to a large set of published phylogenies of other vertebrate, arthropod and plant groups, suggesting that many clades may diversi

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14

Purvis, Andy, Susanne A. Fritz, Jesús Rodríguez, Paul H. Harvey, and Richard Grenyer. "The shape of mammalian phylogeny: patterns, processes and scales." Philosophical Transactions of the Royal Society B: Biological Sciences 366, no. 1577 (2011): 2462–77. https://doi.org/10.5281/zenodo.13434697.

Full text

Abstract:

(Uploaded by Plazi for the Bat Literature Project) Mammalian phylogeny is far too asymmetric for all contemporaneous lineages to have had equal chances of diversifying. We consider this asymmetry or imbalance from four perspectives. First, we infer a minimal set of 'regime changes'—points at which net diversification rate has changed—identifying 15 significant radiations and 12 clades that may be 'downshifts'. We next show that mammalian phylogeny is similar in shape to a large set of published phylogenies of other vertebrate, arthropod and plant groups, suggesting that many clades may diversi

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Purvis, Andy, Susanne A. Fritz, Jesús Rodríguez, Paul H. Harvey, and Richard Grenyer. "The shape of mammalian phylogeny: patterns, processes and scales." Philosophical Transactions of the Royal Society B: Biological Sciences 366, no. 1577 (2011): 2462–77. https://doi.org/10.5281/zenodo.13434697.

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Abstract:

(Uploaded by Plazi for the Bat Literature Project) Mammalian phylogeny is far too asymmetric for all contemporaneous lineages to have had equal chances of diversifying. We consider this asymmetry or imbalance from four perspectives. First, we infer a minimal set of 'regime changes'—points at which net diversification rate has changed—identifying 15 significant radiations and 12 clades that may be 'downshifts'. We next show that mammalian phylogeny is similar in shape to a large set of published phylogenies of other vertebrate, arthropod and plant groups, suggesting that many clades may diversi

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16

Xie, Pingxuan, Lilei Tang, Yanzhen Luo, Changkun Liu, and Hanjing Yan. "Plastid Phylogenomic Insights into the Inter-Tribal Relationships of Plantaginaceae." Biology 12, no. 2 (2023): 263. http://dx.doi.org/10.3390/biology12020263.

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Plantaginaceae, consisting of 12 tribes, is a diverse, cosmopolitan family. To date, the inter-tribal relationships of this family have been unresolved, and the plastome structure and composition within Plantaginaceae have seldom been comprehensively investigated. In this study, we compared the plastomes from 41 Plantaginaceae species (including 6 newly sequenced samples and 35 publicly representative species) representing 11 tribes. To clarify the inter-tribal relationships of Plantaginaceae, we inferred phylogenic relationships based on the concatenated and coalescent analyses of 68 plastid

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Mehregan, I., K. Ghanbarpour, and M. M. Shamsabad. "EVOLUTION OF PERICARP SURFACE STRUCTURE IN NEPETA S. S. (LAMIACEAE) AS INFERRED FROM ANALYSIS OF ITS DATA." Acta Botanica Hungarica 64, no. 3-4 (2022): 369–90. http://dx.doi.org/10.1556/034.64.2022.3-4.9.

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Nutlet pericarp structure is important in the taxonomy of Lamiaceae (Labiatae) at different taxonomic levels. Within the family it has also been found that variation in pericarp structure is strongly correlated with the phylogenic results obtained from molecular DNA analyses. The genus Nepeta L., with more than 200 species mainly centred in SW Asia, is one of the taxonomically most complex genera within the family. Traditional taxonomic treatments of Nepeta are mainly based on gross morphology. As in other groups of Lamiaceae, pericarp structure provides some of the diagnostic characters in th

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Etienne, Rampal S., Bart Haegeman, Tanja Stadler, et al. "Diversity-dependence brings molecular phylogenies closer to agreement with the fossil record." Proceedings of the Royal Society B: Biological Sciences 279, no. 1732 (2011): 1300–1309. http://dx.doi.org/10.1098/rspb.2011.1439.

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The branching times of molecular phylogenies allow us to infer speciation and extinction dynamics even when fossils are absent. Troublingly, phylogenetic approaches usually return estimates of zero extinction, conflicting with fossil evidence. Phylogenies and fossils do agree, however, that there are often limits to diversity. Here, we present a general approach to evaluate the likelihood of a phylogeny under a model that accommodates diversity-dependence and extinction. We find, by likelihood maximization, that extinction is estimated most precisely if the rate of increase in the number of li

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CASIRAGHI, M., T. J. C. ANDERSON, C. BANDI, C. BAZZOCCHI, and C. GENCHI. "A phylogenetic analysis of filarial nematodes: comparison with the phylogeny of Wolbachia endosymbionts." Parasitology 122, no. 1 (2001): 93–103. http://dx.doi.org/10.1017/s0031182000007149.

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Infection with the endosymbiotic bacteria Wolbachia is widespread in filarial nematodes. Previous studies have suggested concordance between the phylogeny of Wolbachia with that of their nematode hosts. However, there is only one published molecular phylogenetic study of filarial species, based on the 5S rRNA gene spacer. The phylogeny proposed by this study is partially incongruent with previous classifications of filarial nematodes, based on morphological characters. Furthermore, both traditional classifications and molecular phylogenies are, in part, inconsistent with the phylogeny of Wolba

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Hidayati, R. Misrianti, and A. Ali. "Phylogenetic tree of Kuantan cattle by DNA barcoding." Jurnal Ilmu Ternak dan Veteriner 21, no. 1 (2016): 41. http://dx.doi.org/10.14334/jitv.v21i1.1351.

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<p>Kuantan cattle is one of local beef cattle breed of Riau Province which its origin was unknown. Kuantan cattle are commonly found in Indragiri Hulu and Kuantan Singingi Regency. Based on phenotype characterizations, kuantan cattles are similar with pesisir cattle (West Sumatera beef cattle). Historically, kuantan cattle were pesisir cattle brought by “minang” immigrants (Immigrant from West Sumatera) to this region. The purpose of this study was to analyze the origin of the kuantan cattle through genetic diversity analysis using DNA barcode. DNA barcode used was Cytochrome oxidase sub

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Koirala, Amrit, and Volker S. Brözel. "Phylogeny of Nitrogenase Structural and Assembly Components Reveals New Insights into the Origin and Distribution of Nitrogen Fixation across Bacteria and Archaea." Microorganisms 9, no. 8 (2021): 1662. http://dx.doi.org/10.3390/microorganisms9081662.

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The phylogeny of nitrogenase has only been analyzed using the structural proteins NifHDK. As nifHDKENB has been established as the minimum number of genes necessary for in silico prediction of diazotrophy, we present an updated phylogeny of diazotrophs using both structural (NifHDK) and cofactor assembly proteins (NifENB). Annotated Nif sequences were obtained from InterPro from 963 culture-derived genomes. Nif sequences were aligned individually and concatenated to form one NifHDKENB sequence. Phylogenies obtained using PhyML, FastTree, RapidNJ, and ASTRAL from individuals and concatenated pr

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Temu, Stella G., Philippe Clerc, Miko R. A. Nadel, Leif Tibell, Donatha D. Tibuhwa, and Sanja Tibell. "Molecular, morphological and chemical variation of the Usnea pectinata aggregate from Tanzania, São Tomé and Príncipe." Lichenologist 54, no. 5 (2022): 291–98. http://dx.doi.org/10.1017/s0024282922000251.

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AbstractThis study investigated the molecular, chemical and morphological variation in the Usnea pectinata aggregate using 42 specimens, 22 from Tanzania and 20 from São Tomé and Príncipe. A total of 31 sequences (13 ITS, 13 nuLSU and 5 RPB1) were generated. The results are presented in two phylogenies: first a three-markers ‘backbone’ phylogeny for the U. pectinata aggregate, where six distinct, strongly supported subclades indicate considerable genetic variation in the dataset; and second, an ITS phylogeny with 47 terminals along with a mapping of morphological and chemistry data. Several we

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Christensen, Henrik, Peter Kuhnert, John Elmerdahl Olsen, and Magne Bisgaard. "Comparative phylogenies of the housekeeping genes atpD, infB and rpoB and the 16S rRNA gene within the Pasteurellaceae." International Journal of Systematic and Evolutionary Microbiology 54, no. 5 (2004): 1601–9. http://dx.doi.org/10.1099/ijs.0.03018-0.

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Phylogenies of housekeeping gene and 16S rRNA gene sequences were compared to improve the classification of the bacterial family Pasteurellaceae and knowledge of the evolutionary relationships of its members. Deduced partial protein sequences of the housekeeping genes atpD, infB and rpoB were compared in 28, 36 and 28 representative taxa of the Pasteurellaceae, respectively. The monophyly of representatives of the genus Gallibacterium was recognized by analysis of all housekeeping genes, while members of Mannheimia, Actinobacillus sensu stricto and the core group of Pasteurella sensu stricto f

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Yan, Zhi, Zhen Cao, and Luay Nakhleh. "Polyphest: fast polyploid phylogeny estimation." Bioinformatics 40, Supplement_2 (2024): ii20—ii28. http://dx.doi.org/10.1093/bioinformatics/btae390.

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Abstract Motivation Despite the widespread occurrence of polyploids across the Tree of Life, especially in the plant kingdom, very few computational methods have been developed to handle the specific complexities introduced by polyploids in phylogeny estimation. Furthermore, methods that are designed to account for polyploidy often disregard incomplete lineage sorting (ILS), a major source of heterogeneous gene histories, or are computationally very demanding. Therefore, there is a great need for efficient and robust methods to accurately reconstruct polyploid phylogenies. Results We introduce

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Schwery, Orlando, and Brian C. O’Meara. "MonoPhy: a simple R package to find and visualize monophyly issues." PeerJ Computer Science 2 (March 30, 2016): e56. http://dx.doi.org/10.7717/peerj-cs.56.

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Background.The monophyly of taxa is an important attribute of a phylogenetic tree. A lack of it may hint at shortcomings of either the tree or the current taxonomy, or can indicate cases of incomplete lineage sorting or horizontal gene transfer. Whichever is the reason, a lack of monophyly can misguide subsequent analyses. While monophyly is conceptually simple, it is manually tedious and time consuming to assess on modern phylogenies of hundreds to thousands of species.Results.The R packageMonoPhyallows assessment and exploration of monophyly of taxa in a phylogeny. It can assess the monophyl

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Malik, Ashar J., Anthony M. Poole, and Jane R. Allison. "Structural Phylogenetics with Confidence." Molecular Biology and Evolution 37, no. 9 (2020): 2711–26. http://dx.doi.org/10.1093/molbev/msaa100.

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Abstract For evaluating the deepest evolutionary relationships among proteins, sequence similarity is too low for application of sequence-based homology search or phylogenetic methods. In such cases, comparison of protein structures, which are often better conserved than sequences, may provide an alternative means of uncovering deep evolutionary signal. Although major protein structure databases such as SCOP and CATH hierarchically group protein structures, they do not describe the specific evolutionary relationships within a hierarchical level. Structural phylogenies have the potential to fil

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Zhang, Jing, Qian Cong, Jinhui Shen, Paul A. Opler, and Nick V. Grishin. "Genomics-guided refinement of butterfly taxonomy." Taxonomic Report of The International Lepidoptera Survey 9, no. 3 (2021): 1–55. https://doi.org/10.5281/zenodo.5630311.

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The authors use all protein-coding genes as they are retrieved from the whole genome shotgun sequences of butterflies for phylogeny construction. Analysis of these genome-scale phylogenies projected onto the taxonomic classification and the knowledge about butterfly phenotypes suggests further refinements of butterfly taxonomy.

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Fensome, Robert A., Juan F. Saldarriaga, and “Max” F. J. R. Taylor. "Dinoflagellate phylogeny revisited: reconciling morphological and molecular based phylogenies." Grana 38, no. 2-3 (1999): 66–80. http://dx.doi.org/10.1080/00173139908559216.

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Varón-González, Ceferino, Simon Whelan, and Christian Peter Klingenberg. "Estimating Phylogenies from Shape and Similar Multidimensional Data: Why It Is Not Reliable." Systematic Biology 69, no. 5 (2020): 863–83. http://dx.doi.org/10.1093/sysbio/syaa003.

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Abstract In recent years, there has been controversy whether multidimensional data such as geometric morphometric data or information on gene expression can be used for estimating phylogenies. This study uses simulations of evolution in multidimensional phenotype spaces to address this question and to identify specific factors that are important for answering it. Most of the simulations use phylogenies with four taxa, so that there are just three possible unrooted trees and the effect of different combinations of branch lengths can be studied systematically. In a comparison of methods, squared

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Kennedy, Martyn, and Roderic D. M. Page. "Seabird Supertrees: Combining Partial Estimates of Procellariiform Phylogeny." Auk 119, no. 1 (2002): 88–108. http://dx.doi.org/10.1093/auk/119.1.88.

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Abstract The growing use of comparative methods to address evolutionary questions has generated an increased need for robust hypotheses of evolutionary relationships for a wide range of organisms. Where a phylogeny exists for a group, often more than one phylogeny will exist for that group, and it is uncommon that the same taxa are in each of the existing trees. The types of data used to generate evolutionary trees can also vary greatly, and thus combining data sets is often difficult or impossible. To address comparative questions for groups where multiple phylogenetic hypotheses already exis

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Beutel, Rolf G., and Frank Friedrich. "The Phylogeny of Archostemata (Coleoptera) and new Approaches in Insect Morphology Zur Phylogenie der Archostemata (Coleoptera) und neue Ansätze zur Insektenmorphologie." Entomologia Generalis 31, no. 2 (2008): 141–54. http://dx.doi.org/10.1127/entom.gen/31/2008/141.

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Duchen, Pablo. "Métodos de reconstrucción filogenética I: máxima verosimilitud." Tequio 4, no. 11 (2021): 69–79. http://dx.doi.org/10.53331/teq.v4i11.3953.

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Phylogenetic inference is widely used in evolutionary biology, aiming to find evolutionary relationships between different species and report the result in the form of a phylogenetic tree (phylogeny). There are several statistical methods used for phylogenetic inference. In this review, the method of maximum likelihood for phylogenetic reconstruction is presented. This technique consists of finding the likelihood of multiple candidate phylogenies, and report the one with the highest likelihood as a representative of the evolutionary relationships of a group of species. In this paper, the likel

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Dong, Quan-Ying, Yao Wang, Zhi-Qin Wang, Yan-Fang Liu, and Hong Yu. "Phylogeny and Systematics of the Genus Tolypocladium (Ophiocordycipitaceae, Hypocreales)." Journal of Fungi 8, no. 11 (2022): 1158. http://dx.doi.org/10.3390/jof8111158.

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The taxonomy and phylogeny of the genus Tolypocladium are herein revised based on the most comprehensive dataset to date. Two species-level phylogenies of Tolypocladium were constructed: a single-gene phylogeny (ITS) of 35 accepted species and a multigene phylogeny (nrSSU, nrLSU, tef-1α, rpb1, and rpb2) of 27 accepted species. Three new species, Tolypocladium pseudoalbum sp. nov., Tolypocladium subparadoxum sp. nov., and Tolypocladium yunnanense sp. nov., are described in the present study. The genetic divergences of four markers (ITS, tef-1α, rpb1 and rpb2) among Tolypocladium species are als

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Grismer, L. Lee, Perry L. Wood, Jr., Nikolay A. Poyarkov, et al. "Phylogenetic partitioning of the third-largest vertebrate genus in the world, Cyrtodactylus Gray, 1827 (Reptilia; Squamata; Gekkonidae) and its relevance to taxonomy and conservation." Vertebrate Zoology 71 (March 16, 2021): 101–54. http://dx.doi.org/10.3897/vertebrate-zoology.71.e59307.

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The gekkonid genus Cyrtodactylus is the third most speciose vertebrate genus in the world, containing well over 300 species that collectively range from South Asia to Melanesia across some of the most diverse landscapes and imperiled habitats on the planet. A genus-wide phylogeny of the group has never been presented because researchers working on different groups were using different genetic markers to construct phylogenies that could not be integrated. We present here Maximum likelihood and Bayesian inference mitochondrial and mito-nuclear phylogenies incorporating of 310 species that includ

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Grismer, L. Lee, Perry L. Wood, Jr., Nikolay A. Poyarkov, et al. "Phylogenetic partitioning of the third-largest vertebrate genus in the world, Cyrtodactylus Gray, 1827 (Reptilia; Squamata; Gekkonidae) and its relevance to taxonomy and conservation." Vertebrate Zoology 71 (March 16, 2021): 101–54. http://dx.doi.org/10.3897/vz.71.e59307.

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The gekkonid genus Cyrtodactylus is the third most speciose vertebrate genus in the world, containing well over 300 species that collectively range from South Asia to Melanesia across some of the most diverse landscapes and imperiled habitats on the planet. A genus-wide phylogeny of the group has never been presented because researchers working on different groups were using different genetic markers to construct phylogenies that could not be integrated. We present here Maximum likelihood and Bayesian inference mitochondrial and mito-nuclear phylogenies incorporating of 310 species that includ

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O'Keefe, F. Robin, and P. Martin Sander. "Paleontological paradigms and inferences of phylogenetic pattern: a case study." Paleobiology 25, no. 4 (1999): 518–33. http://dx.doi.org/10.1017/s0094837300020364.

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In this paper we reconstruct the phylogeny of a clade of pachypleurosaurs (Reptilia: Sauropterygia) occurring in Triassic-age deposits in the Monte San Giorgio region, Switzerland. We also present the phylogeny of this clade as a case study for two paradigms of phylogeny reconstruction: cladistics and phenetic/stratigraphic methods. While this dichotomy is not held rigidly by all workers, its advancement by cladists leads us to retain it initially for rhetorical purposes. We review the philosophical bases of species, species concepts, and speciation, as well as cladograms and phylogenies, befo

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Grover, Siddhant, Alexey Markin, Tavis K. Anderson, and Oliver Eulenstein. "Phylogenetic diversity statistics for all clades in a phylogeny." Bioinformatics 39, Supplement_1 (2023): i177—i184. http://dx.doi.org/10.1093/bioinformatics/btad263.

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Abstract The classic quantitative measure of phylogenetic diversity (PD) has been used to address problems in conservation biology, microbial ecology, and evolutionary biology. PD is the minimum total length of the branches in a phylogeny required to cover a specified set of taxa on the phylogeny. A general goal in the application of PD has been identifying a set of taxa of size k that maximize PD on a given phylogeny; this has been mirrored in active research to develop efficient algorithms for the problem. Other descriptive statistics, such as the minimum PD, average PD, and standard deviati

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Pearse, William D. "Animating and exploring phylogenies with fibre plots." F1000Research 5 (April 5, 2017): 2790. http://dx.doi.org/10.12688/f1000research.10274.3.

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Despite the progress that has been made in many other aspects of data visualisation, phylogenies are still represented in much the same way as they first were by Darwin. In this brief essay, I give a short review of what I consider to be some recent major advances, and outline a new kind of phylogenetic visualisation. This new graphic, the fibre plot, uses the metaphor of sections through a tree to describe change in a phylogeny. I suggest it is a useful tool in gaining an rapid overview of the timing and scale of diversification in large phylogenies.

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Suntsov, Victor V. "Molecular phylogenies of the plague microbe <i>Yersinia pestis</i>: an environmental assessment." AIMS Microbiology 9, no. 4 (2023): 712–23. http://dx.doi.org/10.3934/microbiol.2023036.

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<abstract> <p>Two approaches are applied to studies of the phylogeny of the plague microbe <italic>Yersinia pestis</italic>, i.e., the reconstruction of its history: Molecular genetic (MG) and ecological (ECO). The MG approach dominates. Phylogenies created with MG and ECO methods are not congruent. MG conclusions contradict the known facts and patterns of ecology, biogeography, paleontology, etc. We discuss some obvious contradictions and inconsistencies and suggest that real phylogenies of the plague microbe can be constructed only on the basis of the integration of M

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Vidal-Hosteng, Amandine, Christophe Thébaud, Rampal S. Etienne, and Robin Aguilée. "Effects of archipelago geo-environmental dynamics on phylogenetic tree shape." Frontiers of Biogeography 18 (May 16, 2025): e146650. https://doi.org/10.21425/fob.18.146650.

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In archipelagic environments, the successive emergence and submergence of islands induces changes in area, spatial structure and isolation. Here, we aim to understand how such geo-environmental dynamics, by altering immigration, speciation and extinction over time, may influence phylogenetic patterns. We use a neutral, stochastic, individual-based model which simulates a community evolving in an archipelago where four islands emerge and submerge consecutively. We record each birth, death and immigration event, allowing us to build the complete phylogeny at any time, from which we extract the p

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Beutel, Rolf G., Hans Pohl, Evgeny V. Yan, et al. "The phylogeny of Coleopterida (Hexapoda) - morphological characters and molecular phylogenies." Systematic Entomology 44, no. 1 (2018): 75–102. http://dx.doi.org/10.1111/syen.12316.

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Stettler, Jason M., Mikel R. Stevens, Lindsey M. Meservey, et al. "Improving phylogenetic resolution of the Lamiales using the complete plastome sequences of six Penstemon species." PLOS ONE 16, no. 12 (2021): e0261143. http://dx.doi.org/10.1371/journal.pone.0261143.

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The North American endemic genus Penstemon (Mitchell) has a recent geologic origin of ca. 3.6 million years ago (MYA) during the Pliocene/Pleistocene transition and has undergone a rapid adaptive evolutionary radiation with ca. 285 species of perennial forbs and sub-shrubs. Penstemon is divided into six subgenera occupying all North American habitats including the Arctic tundra, Central American tropical forests, alpine meadows, arid deserts, and temperate grasslands. Due to the rapid rate of diversification and speciation, previous phylogenetic studies using individual and concatenated chloro

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Guyeux, Christophe, Stéphane Chrétien, Nathalie M. L. Côté, and Jacques M. Bahi. "Systematic investigations of gene effects on both topologies and supports: An Echinococcus illustration." Journal of Bioinformatics and Computational Biology 15, no. 05 (2017): 1750019. http://dx.doi.org/10.1142/s0219720017500196.

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In this paper, we propose a high performance computing toolbox implementing efficient statistical methods for the study of phylogenies. This toolbox, which implements logit models and LASSO-type penalties, gives a way to better understand, measure, and compare the impact of each gene on a global phylogeny. As an application, we study the Echinococcus phylogeny, which is often considered as a particularly difficult example. Mitochondrial and nuclear genomes (19 coding sequences) of nine Echinococcus species are considered in order to investigate the molecular phylogeny of this genus. First, we

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Crandall, K. A., and A. R. Templeton. "Empirical tests of some predictions from coalescent theory with applications to intraspecific phylogeny reconstruction." Genetics 134, no. 3 (1993): 959–69. http://dx.doi.org/10.1093/genetics/134.3.959.

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Abstract Empirical data sets of intraspecific restriction site polymorphism in Drosophila have been gathered in order to test hypotheses derived from coalescent theory. Three main ideas are tested: (1) haplotype frequency in the sample contains information on the topological position of a given haplotype in a cladogram, (2) the frequency of a haplotype is related to the number of mutational connections to other haplotypes in the cladogram and (3) geographic location can be used to infer topological positioning of haplotypes in a cladogram. These relationships can then be used to better estimat

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Duchen, Pablo. "Métodos de reconstrucción filogenética II: inferencia bayesiana." Tequio 4, no. 11 (2021): 81–89. http://dx.doi.org/10.53331/teq.v4i11.0055.

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Phylogenetic reconstruction through Bayesian inference is currently widely used. The main advantage of this method is the direct output of posterior probabilities for each clade on the final phylogeny. Thus, it does not require bootstrapping as a measure of uncertainty. Moreover, Bayesian inference is perfectly fit for dating phylogenies through molecular clocks. In this paper, the basics of Bayesian inference applied to phylogenetic reconstruction are described, starting with an explanation of Bayes’ theorem. Then, the use of the Metropolis-Hastings algorithm to sample topologies from the pos

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Guégan, Jean-François, and Jean-François Agnèse. "Parasite evolutionary events inferred from host phylogeny: the case of Labeo species (Teleostei, Cyprinidae) and their dactylogyrid parasites (Monogenea, Dactylogyridae)." Canadian Journal of Zoology 69, no. 3 (1991): 595–603. http://dx.doi.org/10.1139/z91-089.

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Independent phylogenies of West African Labeo (Teleostei, Cyprinidae) and their gill parasites of the genus Dactylogyrus (Monogenea, Dactylogyridae) are proposed. The phylogeny of Labeo is based on allele characters, whereas the phylogeny of the parasites is based on morphometric features. The comparison of host and parasite phylogenies did not correlate completely with predictions made by using Fahrenholz's rule. Parasites encountered on L. coubie and L. senegalensis seem to have evolved in parallel with their host, or by sequential colonizations between these two related hosts. Whatever the

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Patrick, Lorelei E., and Richard D. Stevens. "Investigating sensitivity of phylogenetic community structure metrics using North American desert bats." Journal of Mammalogy 95, no. 6 (2014): 1240–53. https://doi.org/10.5281/zenodo.13437102.

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(Uploaded by Plazi for the Bat Literature Project) A relatively recent approach to characterizing structure of natural communities is to use phylogenies of species pools to compare patterns of relatedness between real and simulated communities. Such an approach can provide mechanistic insights into structure. Despite popularity of phylogenetic approaches, we do not yet fully understand how phylogenetic community structure (PCS) metrics might be impacted by changes to the phylogeny or community membership data from which they are calculated. We investigate metric sensitivity and examine PCS of

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Patrick, Lorelei E., and Richard D. Stevens. "Investigating sensitivity of phylogenetic community structure metrics using North American desert bats." Journal of Mammalogy 95, no. 6 (2014): 1240–53. https://doi.org/10.5281/zenodo.13437102.

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Abstract:

(Uploaded by Plazi for the Bat Literature Project) A relatively recent approach to characterizing structure of natural communities is to use phylogenies of species pools to compare patterns of relatedness between real and simulated communities. Such an approach can provide mechanistic insights into structure. Despite popularity of phylogenetic approaches, we do not yet fully understand how phylogenetic community structure (PCS) metrics might be impacted by changes to the phylogeny or community membership data from which they are calculated. We investigate metric sensitivity and examine PCS of

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49

Patrick, Lorelei E., and Richard D. Stevens. "Investigating sensitivity of phylogenetic community structure metrics using North American desert bats." Journal of Mammalogy 95, no. 6 (2014): 1240–53. https://doi.org/10.5281/zenodo.13437102.

Full text

Abstract:

(Uploaded by Plazi for the Bat Literature Project) A relatively recent approach to characterizing structure of natural communities is to use phylogenies of species pools to compare patterns of relatedness between real and simulated communities. Such an approach can provide mechanistic insights into structure. Despite popularity of phylogenetic approaches, we do not yet fully understand how phylogenetic community structure (PCS) metrics might be impacted by changes to the phylogeny or community membership data from which they are calculated. We investigate metric sensitivity and examine PCS of

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50

Patrick, Lorelei E., and Richard D. Stevens. "Investigating sensitivity of phylogenetic community structure metrics using North American desert bats." Journal of Mammalogy 95, no. 6 (2014): 1240–53. https://doi.org/10.5281/zenodo.13437102.

Full text

Abstract:

(Uploaded by Plazi for the Bat Literature Project) A relatively recent approach to characterizing structure of natural communities is to use phylogenies of species pools to compare patterns of relatedness between real and simulated communities. Such an approach can provide mechanistic insights into structure. Despite popularity of phylogenetic approaches, we do not yet fully understand how phylogenetic community structure (PCS) metrics might be impacted by changes to the phylogeny or community membership data from which they are calculated. We investigate metric sensitivity and examine PCS of

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