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Journal articles on the topic 'Phylogenetic'

Author: Grafiati

Published: 4 June 2021

Last updated: 25 May 2024

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1

Liu, Guo-Qing, Lian Lian, and Wei Wang. "The Molecular Phylogeny of Land Plants: Progress and Future Prospects." Diversity 14, no. 10 (September 21, 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. At present, the phylogenetic framework of land plants at the order and familial levels has been well built. Problematic deep-level relationships within land plants have also been well resolved by phylogenomic analyses. We pointed out five major aspects of molecular phylogenetics of land plants, which are nowadays being studied and will continue to be goals moving forward. These five aspects include: (1) constructing the genus- and species-level phylogenies for land plant groups, (2) updating the classification systems by combining morphological and molecular data, (3) integrating fossil taxa into phylogenies derived from living taxa, (4) resolving deep-level and/or rapidly divergent phylogenetic relationships using phylogenomic data, and (5) building big trees using the supermatrix method. We hope that this review paper will promote the development of plant molecular phylogenetics and other related areas.

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2

Ziegler, Willi, and Charles A. Sandberg. "Conodont Phylogenetic-Zone Concept." Newsletters on Stratigraphy 30, no. 2 (July 14, 1994): 105–23. http://dx.doi.org/10.1127/nos/30/1994/105.

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3

LI, JIA-XIN, MAO-QIANG HE, and RUI-LIN ZHAO. "Three new species of Micropsalliota (Agaricaceae, Agaricales) from China." Phytotaxa 491, no. 2 (March 19, 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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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 phylogenetic signal using the phylogenetic mixed model. I also identified clades with distinctive milks through nonparametric tests (KSI) and PhylogeneticEM evolutionary modeling. Results In addition to the previously reported diet effects, I found increasingly aquatic mammals have milk that this is lower in sugar and higher in fat. Phylogenteic heritabilities for each concentration were high and phylogenetic correlations were moderate to strong indicating coevolution among the concentrations. Primates and pinnipeds had the most outstanding milks according to KSI and PhylogeneticEM, with perissodactyls and marsupials as other noteworthy clades with distinct selection regimes. Discussion Mammalian milks are diverse but often characteristic of certain higher taxa. This complicates identifying the ecological and life history correlates of milk composition using common phylogenetic comparative methods because those traits are also conservative and clade-specific. Novel methods, careful assessment of data quality and hypotheses, and a “phylogenetic natural history” perspective provide alternatives to these traditional tools.

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Zhang, Xiaorong. "Teaching molecular phylogenetics through investigating a real-world phylogenetic problem." Journal of Biological Education 46, no. 2 (June 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 (March 10, 2016): 937–46. http://dx.doi.org/10.1111/2041-210x.12547.

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Agorreta, Ainhoa, Diego San Mauro, Ulrich Schliewen, James L. Van Tassell, Marcelo Kovačić, Rafael Zardoya, and Lukas Rüber. "Molecular phylogenetics of Gobioidei and phylogenetic placement of European gobies." Molecular Phylogenetics and Evolution 69, no. 3 (December 2013): 619–33. http://dx.doi.org/10.1016/j.ympev.2013.07.017.

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FAITH, DANIEL P., FRANK KÖHLER, LOUISE PUSLEDNIK, and J. W. O. BALLARD. "Phylogenies with Corroboration Assessment." Zootaxa 2946, no. 1 (July 8, 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 these problems in phylogenetic inference.

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Petersen, G., and O. Seberg. "Phylogenetic Analysis of allopolyploid species." Czech Journal of Genetics and Plant Breeding 41, Special Issue (July 31, 2012): 28–37. http://dx.doi.org/10.17221/6129-cjgpb.

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10

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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11

Kuhn, Kristen L., and Thomas J. Near. "Phylogeny of Trematomus (Notothenioidei: Nototheniidae) inferred from mitochondrial and nuclear gene sequences." Antarctic Science 21, no. 6 (December 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 both increased taxon sampling and an expanded dataset which includes DNA sequences from two mitochondrial genes (ND2 and 16S rRNA) and one single-copy nuclear gene (RPS7). The Bayesian phylogeny resulting from the analysis of the combined mitochondrial and nuclear gene datasets was well resolved and contained more interspecific nodes supported with significant Bayesian posteriors than either the mitochondrial or nuclear gene phylogenies alone. This demonstrates that the addition of nuclear gene sequence data to mitochondrial data can enhance phylogenetic resolution and increase node support. Additionally, the results of the combined mitochondrial and nuclear Bayesian analyses provide further support for the inclusion of species previously classified as Pagothenia and Cryothenia in Trematomus.

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Gamage, Gihan, Nadeeshan Gimhana, Indika Perera, Shanaka Bandara, Thilina Pathirana, Anuradha Wickramarachchi, and Vijini Mallawaarachchi. "Phylogenetic Tree Construction Using K-Mer Forest- Based Distance Calculation." International Journal of Online and Biomedical Engineering (iJOE) 16, no. 07 (June 19, 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 to find genetic relatedness of different species. In this paper we propose a novel alignment-free, pairwise, distance calculation method based on k-mers and a state of art machine learning-based phylogenetic tree construction mechanism. With the proposed approach we can convert longer DNA sequences into compendious k-mer forests which gear up the efficiency of comparison. Later we construct the phylogenetic tree based on calculated distances with the help of an algorithm build upon k-medoid clustering, which guaranteed significant efficiency and accuracy compared to traditional phylogenetic tree construction methods.

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Baños, Hector, Nathaniel Bushek, Ruth Davidson, Elizabeth Gross, Pamela E. Harris, Robert Krone, Colby Long, Allen Stewart, and Robert Walker. "Phylogenetic trees." Journal of Software for Algebra and Geometry 11, no. 1 (January 23, 2021): 1–7. http://dx.doi.org/10.2140/jsag.2021.11.1.

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14

Brower, A. V. "Phylogenetic Analysis." Science 276, no. 5317 (May 30, 1997): 1317b—1321. http://dx.doi.org/10.1126/science.276.5317.1317b.

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15

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

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16

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

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17

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

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Menet, Hugo, Vincent Daubin, and Eric Tannier. "Phylogenetic reconciliation." PLOS Computational Biology 18, no. 11 (November 3, 2022): e1010621. http://dx.doi.org/10.1371/journal.pcbi.1010621.

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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 (June 15, 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 networks. We develop here an efficient recursive algorithm to compute the phylogenetic variance matrix of a trait on a network, in only one preorder traversal of the network. We then extend the standard PCM tools to this new framework, including phylogenetic regression with covariates (or phylogenetic ANOVA), ancestral trait reconstruction, and Pagel’s $\lambda$ test of phylogenetic signal. The trait of a hybrid is sometimes outside of the range of its two parents, for instance because of hybrid vigor or hybrid depression. These two phenomena are rather commonly observed in present-day hybrids. Transgressive evolution can be modeled as a shift in the trait value following a reticulation point. We develop a general framework to handle such shifts and take advantage of the phylogenetic regression view of the problem to design statistical tests for ancestral transgressive evolution in the evolutionary history of a group of species. We study the power of these tests in several scenarios and show that recent events have indeed the strongest impact on the trait distribution of present-day taxa. We apply those methods to a data set of Xiphophorus fishes, to confirm and complete previous analysis in this group. All the methods developed here are available in the Julia package PhyloNetworks.

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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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Alvarez-González, Ernesto. "Modelo de estimación de pesos de árbol filogenético para un cuartet, aplicando conjugación de Hadamard." Tequio 4, no. 11 (January 27, 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. Based on this, a likelihood function is built for a quartet associated with an alignment of four nucleotide sequences.

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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 (June 30, 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 different abundance levels, three fully mapped 1-ha plots were established in Cuc Phuong National Park. Methods considering the phylogenetic community and nearest neighbor statistics were applied to identify how community structure changes during S. macrophyllus encroachment. Results showed that phylogenetic distance, phylogenetic diversity, and mean phylogenetic distance increased when species diversity increased and the abundance of S. macrophyllus decreased in forest communities. Net related index values were positive, which indicates a clustered phylogenetic structure among all sampled forest communities. S. macrophyllus trees were mixed well with heterospecifics and had regular to aggregated distributions, whereas the species showed evidence of being a strong competitor with its neighbors. Competition could be a major ecological process regulating forest communities encroached by S. macrophyllus. According to the forest disturbance effects, phylogenetic community properties showed the loss of phylogenetic relatedness when S. macrophyllus increased in abundance. To our knowledge, S. macrophyllus encroaches tropical rain forest communities as a disturbance-adapted species.

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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 (December 7, 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 and Chromadoria with the aim of clarifying the position of several taxa. The results show which parts of the Nematode tree are well resolved and understood, and which parts require more research, either by adding taxa that have not been included yet (increasing taxon coverage), or by changing the phylogenetic approach (improving data quality, using different types of data or different methods of analysis). The currently used classification of the phylum Nematoda in many cases does not reflect the phylogeny and in itself requires numerous improvements and rearrangements.

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Wang, Liangliang, Shijia Wang, and Alexandre Bouchard-Côté. "An Annealed Sequential Monte Carlo Method for Bayesian Phylogenetics." Systematic Biology 69, no. 1 (June 6, 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 with other computational Bayesian phylogenetic methods, in particular, different marginal likelihood estimation methods. Unlike previous SMC methods in phylogenetics, our annealed method can utilize standard Markov chain Monte Carlo (MCMC) tree moves and hence benefit from the large inventory of such moves available in the literature. Consequently, the annealed SMC method should be relatively easy to incorporate into existing phylogenetic software packages based on MCMC algorithms. We illustrate our method using simulation studies and real data analysis.

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Wiesemüller, Bernhard, and Hartmut Rothe. "New World Monkeys - A Phylogenetic Study." Zeitschrift für Morphologie und Anthropologie 82, no. 2-3 (June 9, 1999): 115–57. http://dx.doi.org/10.1127/zma/82/1999/115.

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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 introns and exons and ITS region containing the internal transcribed spacer regions 1 and 2 and the 5.8S rDNA, as potential genetic markers to infer phylogenetic relationships among different Phoma taxa. Twelve different Phoma species sequences were analysed together with the closely related Ascochyta ones. The constructed phylogenetic trees, based on tef1 and ITS sequences, do not support the traditional Phoma sections based on morphological characterization. However, we managed to distinguish between the Phoma strains and Ascochyta species by comparing their tef1 sequences through parsimony analysis. We proved that a tef1 can be a useful phylogenetic marker to resolve phylogenetic relationships at species level in Phoma genus.Both parsimony sequence analyses confirmed that the Phyllosticta sojicola species is identical to the Phoma exigua var. exigua species as Kövics et al. (1999) claimed. However, the evolutionary distance by ITS sequences within Phoma species is too small to get well based consequences for the phylogenetic relationships of Phoma genus.Further investigations would be necessary to clarify whether the tef1 and ITS sequences as phylogenetic molecular markers are well suited for the classification of Phoma species.

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Allman, Elizabeth S., John A. Rhodes, and Seth Sullivant. "When Do Phylogenetic Mixture Models Mimic Other Phylogenetic Models?" Systematic Biology 61, no. 6 (September 10, 2012): 1049–59. http://dx.doi.org/10.1093/sysbio/sys064.

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Balasubramaniam, K. N., K. Dittmar, C. M. Berman, M. Butovskaya, M. A. Cooper, B. Majolo, H. Ogawa, G. Schino, B. Thierry, and F. B. M. de Waal. "Hierarchical steepness and phylogenetic models: phylogenetic signals in Macaca." Animal Behaviour 83, no. 5 (May 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 (February 2012): 242–47. http://dx.doi.org/10.1890/11-1360.1.

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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 (January 4, 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 methods, and reduced representation techniques), providing solutions to different evolutionary questions regarding European earthworms. Molecular phylogenetics have led to significant advances being made in Lumbricidae systematics, such as the redefinition or discovery of new genera (Galiciandrilus, Compostelandrilus, Vindoboscolex, Castellodrilus), delimitation and revision of previously existing genera (Kritodrilus, Eophila, Zophoscolex, Bimastos), and changes to the status of subspecific taxa (such as the Allolobophorachaetophora complex). These approaches have enabled the identification of problems that can be resolved by molecular phylogenetics, including the revision of Aporrectodea, Allolobophora, Helodrilus, and Dendrobaena, as well as the examination of small taxa such as Perelia, Eumenescolex, and Iberoscolex. Similar advances have been made with the family Hormogastridae, in which integrative systematics have contributed to the description of several new species, including the delimitation of (formerly) cryptic species. At the family level, integrative systematics have provided a new genus system that better reflects the diversity and biogeography of these earthworms, and phylogenetic comparative methods provide insight into earthworm macroevolution. Despite these achievements, further research should be performed on the Tyrrhenian cryptic complexes, which are of special eco-evolutionary interest. These examples highlight the potential value of applying molecular phylogenetic techniques to other earthworm families, which are very diverse and occupy different terrestrial habitats across the world. The systematic implementation of such approaches should be encouraged among the different expert groups worldwide, with emphasis on collaboration and cooperation.

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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 (May 20, 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 multi-labelled phylogenetic networks, a more generic graph structure than phylogenetic networks where the reticulations are also labelled, to a polynomial ring. We prove that the separability condition allows us to characterize, via the polynomial, the phylogenetic networks with the same number of leaves and same number of reticulations by considering their internally labelled versions. While the invariant for trees is a polynomial in Z [ x 1 , … , x n , y ] where n is the number of leaves, the invariant for internally multi-labelled phylogenetic networks is an element of Z [ x 1 , … , x n , λ 1 , … , λ r , y ], where r is the number of reticulations in the network. When the networks are considered without leaf labels the number of variables reduces to r + 2.

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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 (February 5, 2016): 800–805. http://dx.doi.org/10.1111/2041-210x.12529.

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Losos, Jonathan B. "Phylogenetic niche conservatism, phylogenetic signal and the relationship between phylogenetic relatedness and ecological similarity among species." Ecology Letters 11, no. 10 (October 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 (February 14, 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, snakes, mosasaurs), and then compare the influence of lagerstätten deposits on phylogenetic information content and taxon selection in phylogenetic analyses to other fossil-bearing deposits. We find that groups that preserve a high amount of phylogenetic information in their global fossil record (e.g., non-avian theropods) are less vulnerable to a “lagerstätten effect” that leads to disproportionate representation of fossil taxa from one geologic unit in an evolutionary tree. Additionally, for each taxonomic group, we find comparable amounts of phylogenetic information in lagerstätten deposits, even though corresponding morphological character datasets vary greatly. Finally, we unexpectedly find that ancient sand dune deposits of the Late Cretaceous Gobi Desert of Mongolia and China exert an anomalously large influence on the phylogenetic information available in the squamate fossil record, suggesting a “lagerstätten effect” can be present in units not traditionally considered lagerstätten. These results offer a phylogenetics-based lens through which to examine the effects of exceptional fossil preservation on biological patterns through time and space, and invites further quantification of evolutionary information in the rock record.

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Posada, David, and Keith A. Crandall. "Felsenstein Phylogenetic Likelihood." Journal of Molecular Evolution 89, no. 3 (January 13, 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 (January 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 technique finds the related variables only once at the beginning of the algorithm, and not through the generations. This paper shows that the proposed technique is more efficient than the well known EDA called Extended Compact Genetic Algorithm (ECGA), especially for large-scale systems which are commonly found in real world problems.

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Ebach, Malte C., Christopher J. Humphries, and David M. Williams. "Phylogenetic biogeography deconstructed." Journal of Biogeography 30, no. 9 (August 22, 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 (October 1, 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 (April 1, 2007): 222–31. http://dx.doi.org/10.1080/10635150701311362.

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Salipante, S. J., and M. S. Horwitz. "Phylogenetic fate mapping." Proceedings of the National Academy of Sciences 103, no. 14 (March 28, 2006): 5448–53. http://dx.doi.org/10.1073/pnas.0601265103.

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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 (August 7, 2017): 384–99. http://dx.doi.org/10.1093/sysbio/syx066.

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Nehring, Klaus, and Clemens Puppe. "Modelling phylogenetic diversity." Resource and Energy Economics 26, no. 2 (June 2004): 205–35. http://dx.doi.org/10.1016/j.reseneeco.2003.11.008.

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Zavada, Michael S., and Muyeol Kim. "Phylogenetic analysis ofUlmaceae." Plant Systematics and Evolution 200, no. 1-2 (1996): 13–20. http://dx.doi.org/10.1007/bf00984745.

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Cornwell, Will, and Shinichi Nakagawa. "Phylogenetic comparative methods." Current Biology 27, no. 9 (May 2017): R333—R336. http://dx.doi.org/10.1016/j.cub.2017.03.049.

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McDiarmid, Colin, Charles Semple, and Dominic Welsh. "Counting Phylogenetic Networks." Annals of Combinatorics 19, no. 1 (January 21, 2015): 205–24. http://dx.doi.org/10.1007/s00026-015-0260-2.

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Morrison, David A. "Phylogenetic tree-building." International Journal for Parasitology 26, no. 6 (June 1996): 589–617. http://dx.doi.org/10.1016/0020-7519(96)00044-6.

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Moulton, Vincent, and Mike Steel. "Peeling phylogenetic ‘oranges’." Advances in Applied Mathematics 33, no. 4 (November 2004): 710–27. http://dx.doi.org/10.1016/j.aam.2004.03.003.

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Adams, Dean C. "PHYLOGENETIC META-ANALYSIS." Evolution 62, no. 3 (March 2008): 567–72. http://dx.doi.org/10.1111/j.1558-5646.2007.00314.x.

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