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Artykuły w czasopismach na temat „Phylogenetic”

Autor: Grafiati

Data publikacji: 4 czerwca 2021

Data aktualizacji: 25 lipca 2025

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1

Villalobos, Fabricio, Thiago F. Rangel, and José Alexandre F. Diniz-Filho. "Phylogenetic fields of species: cross-species patterns of phylogenetic structure and geographical coexistence." Proceedings of the Royal Society B: Biological Sciences 280, no. 1756 (2013): 20122570. https://doi.org/10.5281/zenodo.14817416.

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(Uploaded by Plazi for the Bat Literature Project) Differential coexistence among species underlies geographical patterns of biodiversity. Understanding such patterns has relied either on ecological or historical approaches applied separately. Recently, macroecology and community phylogenetics have tried to integrate both ecological and historical approaches. However, macroecology is mostly non-phylogenetic, whereas community phylogenetics is largely focused on local scales. Here, we propose a conceptual framework to link macroecology and community phylogenetics by exploring the evolutionary c

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2

Liu, Guo-Qing, Lian Lian, and Wei Wang. "The Molecular Phylogeny of Land Plants: Progress and Future Prospects." Diversity 14, no. 10 (2022): 782. http://dx.doi.org/10.3390/d14100782.

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Phylogenetics has become a powerful tool in many areas of biology. Land plants are the most important primary producers of terrestrial ecosystems and have colonized various habitats on Earth. In the past two decades, tremendous progress has been made in our understanding of phylogenetic relationships at all taxonomic levels across all land plant groups by employing DNA sequence data. Here, we review the progress made in large-scale phylogenetic reconstructions of land plants and assess the current situation of phylogenetic studies of land plants. We then emphasize directions for future study.

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3

Ziegler, Willi, and Charles A. Sandberg. "Conodont Phylogenetic-Zone Concept." Newsletters on Stratigraphy 30, no. 2 (1994): 105–23. http://dx.doi.org/10.1127/nos/30/1994/105.

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LI, JIA-XIN, MAO-QIANG HE, and RUI-LIN ZHAO. "Three new species of Micropsalliota (Agaricaceae, Agaricales) from China." Phytotaxa 491, no. 2 (2021): 167–76. http://dx.doi.org/10.11646/phytotaxa.491.2.6.

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Species diversity of Micropsalliota in China remains poorly known, especially in southwestern China, a hotspot of biodiversity. Based on morphological characteristics and molecular phylogenetic analyses using ITS and nrLSU sequences, three new species named Micropsalliota delicatula, M. dentatomarginata and M. digitatocystis are introduced from China. Phylogenetc analyses results indicated the unique phylogenetic positions of three new species in Micropsalliota. Full descriptions, photo plates, illustrations and a phylogenetic tree to show the placement of three new species are presented.

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5

Blomquist, Gregory E. "Adaptation, phylogeny, and covariance in milk macronutrient composition." PeerJ 7 (November 13, 2019): e8085. http://dx.doi.org/10.7717/peerj.8085.

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Background Milk is a complicated chemical mixture often studied through macronutrient concentrations of fat, protein, and sugar. There is a long-standing natural history tradition describing interspecific diversity in these concentrations. However, recent work has shown little influence of ecological or life history variables on them, aside from maternal diet effects, along with a strong phylogenetic signal. Methods I used multivariate phylogenetic comparative methods to revisit the ecological and life history correlates of milk macronutrient composition and elaborate on the nature of the phyl

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6

Zhang, Xiaorong. "Teaching molecular phylogenetics through investigating a real-world phylogenetic problem." Journal of Biological Education 46, no. 2 (2012): 103–9. http://dx.doi.org/10.1080/00219266.2011.634018.

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Duarte, Leandro D. S., Vanderlei J. Debastiani, André V. L. Freitas, and Valério D. Pillar. "Dissecting phylogenetic fuzzy weighting: theory and application in metacommunity phylogenetics." Methods in Ecology and Evolution 7, no. 8 (2016): 937–46. http://dx.doi.org/10.1111/2041-210x.12547.

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8

Agorreta, Ainhoa, Diego San Mauro, Ulrich Schliewen, et al. "Molecular phylogenetics of Gobioidei and phylogenetic placement of European gobies." Molecular Phylogenetics and Evolution 69, no. 3 (2013): 619–33. http://dx.doi.org/10.1016/j.ympev.2013.07.017.

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9

FAITH, DANIEL P., FRANK KÖHLER, LOUISE PUSLEDNIK, and J. W. O. BALLARD. "Phylogenies with Corroboration Assessment." Zootaxa 2946, no. 1 (2011): 52. http://dx.doi.org/10.11646/zootaxa.2946.1.11.

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Mooi & Gill (2010) argued that careful character study and well-understood synapomorphies do not have the strong role that they deserve as the basis for evidence in phylogenetics. We agree, but suggest that the problem is even greater. Not only character synapomorphies, but also other forms of phylogenetic evidence, typically do not receive the critical assessment that would support phylogenetic inference. In this paper, our goal is to not simply to highlight problems but to suggest solutions. We will suggest that a stronger role for corroboration assessment in systematics could overcome t

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10

Shi, Huiyang. "How can statistical models improve the accuracy of phylogenetic tree reconstruction?" Theoretical and Natural Science 66, no. 1 (2024): 68–72. https://doi.org/10.54254/2753-8818/2024.17991.

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When building the phylogenetic tree, current methods for calculating phylogenetic trees often lack the desired level of accuracy. This research paper explores the role of statistical models in enhancing the precision of phylogenetic tree reconstruction. The phylogenetic tree plays an important role in phylogenetic analysis and evolutionary biology. An accurate phylogenetic tree underpins our understanding of the major transitions in evolution, such as the emergence of new body plans or metabolism. Recent advancements in statistical modeling have more elaborate improvements than traditional met

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11

Petersen, G., and O. Seberg. "Phylogenetic Analysis of allopolyploid species." Czech Journal of Genetics and Plant Breeding 41, Special Issue (2012): 28–37. http://dx.doi.org/10.17221/6129-cjgpb.

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12

Hegewald, Eberhard, and Nobutaka Hangata. "Phylogenetic studies on Scenedesmaceae (Chlorophyta)." Algological Studies/Archiv für Hydrobiologie, Supplement Volumes 100 (December 20, 2000): 29–49. http://dx.doi.org/10.1127/algol_stud/100/2000/29.

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13

Kuhn, Kristen L., and Thomas J. Near. "Phylogeny of Trematomus (Notothenioidei: Nototheniidae) inferred from mitochondrial and nuclear gene sequences." Antarctic Science 21, no. 6 (2009): 565–70. http://dx.doi.org/10.1017/s0954102009990253.

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AbstractThe biota of Antarctica is amazingly rich and highly endemic. The phylogenetics of notothenioid fishes has been extensively investigated through analyses of morphological characters, DNA sequences from mitochondrial genes, and single copy nuclear genes. These phylogenetic analyses have produced reasonably similar phylogenetic trees of notothenioids, however a number of phylogenetic questions remain. The nototheniid clade Trematomus is an example of a group where phylogenetic relationships remain unresolved. In this paper we revisit the phylogenetic relationships of Trematomus using bot

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14

S.L., Mosyakin, and Buyun L.I. "Modern views on phylogeny of Orchidaceae Juss. and the position of the family in the systems of monocots." Plant Introduction 30 (June 1, 2006): 3–14. https://doi.org/10.5281/zenodo.2567105.

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The article provides an overview of recent publications devoted to phylogeny and taxonomy of the family <em>Orchidaceae</em> Juss., with a special reference to molecular phylogenetics. Modern methods of molecular taxonomy and phylogenetics are powerful tools that clarified many long-debated problems in phylogenetic systematics of orchids. In the recent phylogenetic systems (APG, APG II and others) <em>Orchidaceae </em>are placed in or near the extended order <em>Asparagales</em>, most probably at the base of the asparagalean clade. Recent age estimations for major angiosperm groups yielded rat

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15

Gamage, Gihan, Nadeeshan Gimhana, Indika Perera, et al. "Phylogenetic Tree Construction Using K-Mer Forest- Based Distance Calculation." International Journal of Online and Biomedical Engineering (iJOE) 16, no. 07 (2020): 4. http://dx.doi.org/10.3991/ijoe.v16i07.13807.

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Phylogenetics is one of the dominant data engineering research disciplines based on biological information. More particularly here, we consider raw DNA sequences and do comparative analysis in order to come up with important conclusions. When representing evolutionary relationships among different organisms in a concise manner, the phylogenetic tree helps significantly. When constructing phylogenetic trees, the elementary step is to calculate the genetic distance among species. Alignment-based sequencing and alignment-free sequencing are the two main distance computation methods that are used

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16

Alvarez-González, Ernesto. "Modelo de estimación de pesos de árbol filogenético para un cuartet, aplicando conjugación de Hadamard." Tequio 4, no. 11 (2021): 41–52. http://dx.doi.org/10.53331/teq.v4i11.2942.

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The subject on this paper is that part of algebraic phylogenetics which proposes a method to infere the expected values of three kinds of nucleotide substitutions on the branches of a phylogenetic tree that explains the ancestral relations among an associated set of lineages. A tool known as Hadamard conjugation is presented, which –because it connects both the probability distribution of the different substitution patterns on the leaves of the phylogenetic tree, and the complete set of expected values of substitutions on its branches– may indeed be a resource to phylogenetic reconstruction. B

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17

Baños, Hector, Nathaniel Bushek, Ruth Davidson, et al. "Phylogenetic trees." Journal of Software for Algebra and Geometry 11, no. 1 (2021): 1–7. http://dx.doi.org/10.2140/jsag.2021.11.1.

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18

Brower, A. V. "Phylogenetic Analysis." Science 276, no. 5317 (1997): 1317b—1321. http://dx.doi.org/10.1126/science.276.5317.1317b.

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19

Hillis, David M. "Phylogenetic analysis." Current Biology 7, no. 3 (1997): R129—R131. http://dx.doi.org/10.1016/s0960-9822(97)70070-8.

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20

de Queiroz, Kevin, and Jacques Gauthier. "Phylogenetic Taxonomy." Annual Review of Ecology and Systematics 23, no. 1 (1992): 449–80. http://dx.doi.org/10.1146/annurev.es.23.110192.002313.

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21

Ellis, Chris. "Phylogenetic Memory." South African Family Practice 52, no. 1 (2010): 78. http://dx.doi.org/10.1080/20786204.2010.10873942.

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22

Menet, Hugo, Vincent Daubin, and Eric Tannier. "Phylogenetic reconciliation." PLOS Computational Biology 18, no. 11 (2022): e1010621. http://dx.doi.org/10.1371/journal.pcbi.1010621.

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23

Bastide, Paul, Claudia Solís-Lemus, Ricardo Kriebel, K. William Sparks, and Cécile Ané. "Phylogenetic Comparative Methods on Phylogenetic Networks with Reticulations." Systematic Biology 67, no. 5 (2018): 800–820. http://dx.doi.org/10.1093/sysbio/syy033.

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Abstract The goal of phylogenetic comparative methods (PCMs) is to study the distribution of quantitative traits among related species. The observed traits are often seen as the result of a Brownian Motion (BM) along the branches of a phylogenetic tree. Reticulation events such as hybridization, gene flow or horizontal gene transfer, can substantially affect a species’ traits, but are not modeled by a tree. Phylogenetic networks have been designed to represent reticulate evolution. As they become available for downstream analyses, new models of trait evolution are needed, applicable to network

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24

Wicke, Kristina, and Mareike Fischer. "Phylogenetic diversity and biodiversity indices on phylogenetic networks." Mathematical Biosciences 298 (April 2018): 80–90. http://dx.doi.org/10.1016/j.mbs.2018.02.005.

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25

Hai, Nguyen Hong, Yousef Erfanifard, Tran Quang Bao, Any Mary Petritan, Trinh Hien Mai, and Ion Catalin Petritan. "Phylogenetic Community and Nearest Neighbor Structure of Disturbed Tropical Rain Forests Encroached by Streblus macrophyllus." Forests 11, no. 7 (2020): 722. http://dx.doi.org/10.3390/f11070722.

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Although woody plant encroachment of tropical forest ecosystems has been related to altered disturbance regimes, its impacts on the nearest neighborhood structures and community phylogenetics are still poorly understood. Streblus macrophyllus is a light-demanding species during its early life stages and is shade-tolerant as a mature tree. S. macrophyllus can be found in tropical karst evergreen forests in northern Vietnam. It often regenerates at high densities in anthropogenic disturbed forest stands. To understand the structural patterns of disturbed forests encroached by S. macrophyllus at

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26

Ahmed, Mohammed, and Oleksandr Holovachov. "Twenty Years after De Ley and Blaxter—How Far Did We Progress in Understanding the Phylogeny of the Phylum Nematoda?" Animals 11, no. 12 (2021): 3479. http://dx.doi.org/10.3390/ani11123479.

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Molecular phylogenetics brought radical changes to our understanding of nematode evolution, resulting in substantial modifications to nematode classification implemented by De Ley and Blaxter and widely accepted now. Numerous phylogenetic studies were subsequently published that both improved and challenged this classification. Here we present a summary of these changes. We created cladograms that summarise phylogenetic relationships within Nematoda using phylum-wide to superfamily-wide molecular phylogenies published in since 2005, and supplemented with the phylogenetic analyses for Enoplia a

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27

Wang, Liangliang, Shijia Wang, and Alexandre Bouchard-Côté. "An Annealed Sequential Monte Carlo Method for Bayesian Phylogenetics." Systematic Biology 69, no. 1 (2019): 155–83. http://dx.doi.org/10.1093/sysbio/syz028.

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Abstract We describe an “embarrassingly parallel” method for Bayesian phylogenetic inference, annealed Sequential Monte Carlo (SMC), based on recent advances in the SMC literature such as adaptive determination of annealing parameters. The algorithm provides an approximate posterior distribution over trees and evolutionary parameters as well as an unbiased estimator for the marginal likelihood. This unbiasedness property can be used for the purpose of testing the correctness of posterior simulation software. We evaluate the performance of phylogenetic annealed SMC by reviewing and comparing wi

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28

Pereira, Islandia Silva, and Pedro Vasconcellos Eisenlohr. "It Is Neither the Environment Nor the Space, But Phylogeny, That Best Explains The Variation in Tree Species Composition in Brazil." Revista de Gestão Social e Ambiental 19, no. 2 (2025): e011087. https://doi.org/10.24857/rgsa.v19n2-041.

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Objective: This study aims to evaluate the relative importance of phylogenetic, environmental, and spatial components in explaining the floristic variation of tree communities, with the goal of understanding the different processes shaping tree assemblages in Brazil. Methodology: The methodology adopted for this research includes the construction of eigenvectors to operationalize the predictor variables (phylogeny, environment, and space) in our models. We employed variation partitioning using canonical models, predicting that the phylogenetic component would play a stronger role in explaining

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29

Wiesemüller, Bernhard, and Hartmut Rothe. "New World Monkeys - A Phylogenetic Study." Zeitschrift für Morphologie und Anthropologie 82, no. 2-3 (1999): 115–57. http://dx.doi.org/10.1127/zma/82/1999/115.

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Ferreira, Paola de Lima, Romina Batista, Tobias Andermann, Milton Groppo, Christine D. Bacon, and Alexandre Antonelli. "Target sequence capture of Barnadesioideae (Compositae) demonstrates the utility of low coverage loci in phylogenomic analyses." Molecular Phylogenetics and Evolution 169, no. - (2022): 107432. https://doi.org/10.5281/zenodo.5794675.

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Supplemental Matrices from the published article: Ferreira, P.L., Batista, R., Andermann , T., Groppo, M., Bacon, C.D. & Antonelli, A., 2022.<strong> </strong>Target sequence capture of Barnadesioideae (Compositae) demonstrates the utility of low coverage loci in phylogenomic analyses. Molecular Phylogenetics and Evolution. Volume 169, April 2022, 107432. DOI: https://doi.org/10.1016/j.ympev.2022.107432 email: paolaferreira@alumni.usp.br This dataset includes: <strong>Phylogenetic trees </strong>for each set of taxonomic completeness and phylogenetic inference; <strong>DNA matrices </stron

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31

Marchán, Daniel Fernández, Thibaud Decaëns, Jorge Domínguez, and Marta Novo. "Perspectives in Earthworm Molecular Phylogeny: Recent Advances in Lumbricoidea and Standing Questions." Diversity 14, no. 1 (2022): 30. http://dx.doi.org/10.3390/d14010030.

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Earthworm systematics have been limited by the small number of taxonomically informative morphological characters and high levels of homoplasy in this group. However, molecular phylogenetic techniques have yielded significant improvements in earthworm taxonomy in the last 15 years. Several different approaches based on the use of different molecular markers, sequencing techniques, and compromises between specimen/taxon coverage and phylogenetic information have recently emerged (DNA barcoding, multigene phylogenetics, mitochondrial genome analysis, transcriptome analysis, targeted enrichment m

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Pons, Joan Carles, Tomás M. Coronado, Michael Hendriksen, and Andrew Francis. "A polynomial invariant for a new class of phylogenetic networks." PLOS ONE 17, no. 5 (2022): e0268181. http://dx.doi.org/10.1371/journal.pone.0268181.

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Invariants for complicated objects such as those arising in phylogenetics, whether they are invariants as matrices, polynomials, or other mathematical structures, are important tools for distinguishing and working with such objects. In this paper, we generalize a complete polynomial invariant on trees to a class of phylogenetic networks called separable networks, which will include orchard networks. Networks are becoming increasingly important for their ability to represent reticulation events, such as hybridization, in evolutionary history. We provide a function from the space of internally m

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33

Irinyi, László, György Kövics, and Erzsébet Sándor. "Phylogenetic analysis of Phoma species." Acta Agraria Debreceniensis, no. 26 (July 16, 2007): 100–107. http://dx.doi.org/10.34101/actaagrar/26/3062.

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The cosmopolitan Phoma genus contains mainly phytopathogenic, opportunistic parasites, and saprophyte fungal species. Up to now, the characterization of Phoma species and other taxa of Phoma has been determined on the basis of morphology on standardized media, and gene sequence analysis was only used as a confirmative or distinctive complement.In this study, we tried to find molecular markers which can be used as phylogenetics markers in the molecular based classification in the Phoma genus.We employed a part of the translation elongation factor 1 subunit alpha (EF-1α=tef1) containing both int

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34

Allman, Elizabeth S., John A. Rhodes, and Seth Sullivant. "When Do Phylogenetic Mixture Models Mimic Other Phylogenetic Models?" Systematic Biology 61, no. 6 (2012): 1049–59. http://dx.doi.org/10.1093/sysbio/sys064.

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Balasubramaniam, K. N., K. Dittmar, C. M. Berman, et al. "Hierarchical steepness and phylogenetic models: phylogenetic signals in Macaca." Animal Behaviour 83, no. 5 (2012): 1207–18. http://dx.doi.org/10.1016/j.anbehav.2012.02.012.

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Davies, T. Jonathan, Nathan J. B. Kraft, Nicolas Salamin, and Elizabeth M. Wolkovich. "Incompletely resolved phylogenetic trees inflate estimates of phylogenetic conservatism." Ecology 93, no. 2 (2012): 242–47. http://dx.doi.org/10.1890/11-1360.1.

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Zambrano‐Vega, Cristian, Antonio J. Nebro, and José F. Aldana‐Montes. "MO ‐Phylogenetics: a phylogenetic inference software tool with multi‐objective evolutionary metaheuristics." Methods in Ecology and Evolution 7, no. 7 (2016): 800–805. http://dx.doi.org/10.1111/2041-210x.12529.

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38

Losos, Jonathan B. "Phylogenetic niche conservatism, phylogenetic signal and the relationship between phylogenetic relatedness and ecological similarity among species." Ecology Letters 11, no. 10 (2008): 995–1003. http://dx.doi.org/10.1111/j.1461-0248.2008.01229.x.

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Woolley, C. Henrik, David J. Bottjer, Frank A. Corsetti, and Nathan D. Smith. "Quantifying the effects of exceptional fossil preservation on the global availability of phylogenetic data in deep time." PLOS ONE 19, no. 2 (2024): e0297637. http://dx.doi.org/10.1371/journal.pone.0297637.

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Fossil deposits with exceptional preservation (“lagerstätten”) provide important details not typically preserved in the fossil record, such that they hold an outsized influence on our understanding of biodiversity and evolution. In particular, the potential bias imparted by this so-called “lagerstätten effect” remains a critical, but underexplored aspect of reconstructing evolutionary relationships. Here, we quantify the amount of phylogenetic information available in the global fossil records of 1,327 species of non-avian theropod dinosaurs, Mesozoic birds, and fossil squamates (e.g., lizards

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40

BOGARÍN, DIEGO, ADAM P. KARREMANS, and MELANIA FERNÁNDEZ. "Genus-level taxonomical changes in the Lepanthes affinity (Orchidaceae, Pleurothallidinae)." Phytotaxa 340, no. 2 (2018): 128. http://dx.doi.org/10.11646/phytotaxa.340.2.2.

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We propose a new classification of the Lepanthes affinity based on previous studies and our ongoing phylogenetic re-evaluation of the Pleurothallidinae. Fourteen genera are recognized as belonging to the affinity. They are found highly supported in a DNA-based phylogenetic inference of combined plastid (matK) and nuclear (nrITS) datasets. The necessary changes, including four novel generic concepts, needed to reorganize the Lepanthes affinity, are proposed here to insure monophyly. The integral discussion on the phylogenetics and biogeography of the group, together with morphological character

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Ai, Deqiang, Lingfei Peng, Daozheng Qin, and Yalin Zhang. "Characterization of Three Complete Mitogenomes of Flatidae (Hemiptera: Fulgoroidea) and Compositional Heterogeneity Analysis in the Planthoppers’ Mitochondrial Phylogenomics." International Journal of Molecular Sciences 22, no. 11 (2021): 5586. http://dx.doi.org/10.3390/ijms22115586.

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Although sequences of mitogenomes have been widely used for investigating phylogenetic relationship, population genetics, and biogeography in many members of Fulgoroidea, only one complete mitogenome of a member of Flatidae has been sequenced. Here, the complete mitogenomes of Cerynia lineola, Cromna sinensis, and Zecheuna tonkinensis are sequenced. The gene arrangements of the three new mitogenomes are consistent with ancestral insect mitogenomes. The strategy of using mitogenomes in phylogenetics remains in dispute due to the heterogeneity in base composition and the possible variation in ev

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42

Posada, David, and Keith A. Crandall. "Felsenstein Phylogenetic Likelihood." Journal of Molecular Evolution 89, no. 3 (2021): 134–45. http://dx.doi.org/10.1007/s00239-020-09982-w.

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Francis, Andrew, Daniel H. Huson, and Mike Steel. "Normalising phylogenetic networks." Molecular Phylogenetics and Evolution 163 (October 2021): 107215. http://dx.doi.org/10.1016/j.ympev.2021.107215.

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Veloso de Melo, Vinícius, Danilo Vasconcellos Vargas, and Marcio Kassouf Crocomo. "Phylogenetic Differential Evolution." International Journal of Natural Computing Research 2, no. 1 (2011): 21–38. http://dx.doi.org/10.4018/jncr.2011010102.

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This paper presents a new technique for optimizing binary problems with building blocks. The authors have developed a different approach to existing Estimation of Distribution Algorithms (EDAs). Our technique, called Phylogenetic Differential Evolution (PhyDE), combines the Phylogenetic Algorithm and the Differential Evolution Algorithm. The first one is employed to identify the building blocks and to generate metavariables. The second one is used to find the best instance of each metavariable. In contrast to existing EDAs that identify the related variables at each iteration, the presented te

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Ebach, Malte C., Christopher J. Humphries, and David M. Williams. "Phylogenetic biogeography deconstructed." Journal of Biogeography 30, no. 9 (2003): 1285–96. http://dx.doi.org/10.1046/j.1365-2699.2003.00928.x.

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Giannini, Norberto P. "Canonical Phylogenetic Ordination." Systematic Biology 52, no. 5 (2003): 684–95. http://dx.doi.org/10.1080/10635150390238888.

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Townsend, Jeffrey P. "Profiling Phylogenetic Informativeness." Systematic Biology 56, no. 2 (2007): 222–31. http://dx.doi.org/10.1080/10635150701311362.

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Mecham, Jesse, Mark Clement, Quinn Snell, Todd Freestone, Kevin Seppi, and Keith Crandall. "Jumpstarting phylogenetic analysis." International Journal of Bioinformatics Research and Applications 2, no. 1 (2006): 19. http://dx.doi.org/10.1504/ijbra.2006.009191.

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Tolkoff, Max R., Michael E. Alfaro, Guy Baele, Philippe Lemey, and Marc A. Suchard. "Phylogenetic Factor Analysis." Systematic Biology 67, no. 3 (2017): 384–99. http://dx.doi.org/10.1093/sysbio/syx066.

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