Journal articles on the topic 'Phylogenesi'
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Miyamoto, Michael M., and Walter M. Fitch. "Testing Species Phylogenies and Phylogenetic Methods with Congruence." Systematic Biology 44, no. 1 (March 1995): 64. http://dx.doi.org/10.2307/2413483.
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Borges, Rui, João Paulo Machado, Cidália Gomes, Ana Paula Rocha, and Agostinho Antunes. "Measuring phylogenetic signal between categorical traits and phylogenies." Bioinformatics 35, no. 11 (October 25, 2018): 1862–69. http://dx.doi.org/10.1093/bioinformatics/bty800.
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Abstract Motivation Determining whether a trait and phylogeny share some degree of phylogenetic signal is a flagship goal in evolutionary biology. Signatures of phylogenetic signal can assist the resolution of a broad range of evolutionary questions regarding the tempo and mode of phenotypic evolution. However, despite the considerable number of strategies to measure it, few and limited approaches exist for categorical traits. Here, we used the concept of Shannon entropy and propose the δ statistic for evaluating the degree of phylogenetic signal between a phylogeny and categorical traits. Results We validated δ as a measure of phylogenetic signal: the higher the δ-value the higher the degree of phylogenetic signal between a given tree and a trait. Based on simulated data we proposed a threshold-based classification test to pinpoint cases of phylogenetic signal. The assessment of the test’s specificity and sensitivity suggested that the δ approach should only be applied to 20 or more species. We have further tested the performance of δ in scenarios of branch length and topology uncertainty, unbiased and biased trait evolution and trait saturation. Our results showed that δ may be applied in a wide range of phylogenetic contexts. Finally, we investigated our method in 14 360 mammalian gene trees and found that olfactory receptor genes are significantly associated with the mammalian activity patterns, a result that is congruent with expectations and experiments from the literature. Our application shows that δ can successfully detect molecular signatures of phenotypic evolution. We conclude that δ represents a useful measure of phylogenetic signal since many phenotypes can only be measured in categories. Availability and implementation https://github.com/mrborges23/delta_statistic. Supplementary information Supplementary data are available at Bioinformatics online.
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Miyamoto, Michael M., and Walter M. Fitch. "Testing Species Phylogenies and Phylogenetic Methods with Congruence." Systematic Biology 44, no. 1 (March 1995): 64–76. http://dx.doi.org/10.1093/sysbio/44.1.64.
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Palmer, Marike, Stephanus N. Venter, Alistair R. McTaggart, Martin P. A. Coetzee, Stephanie Van Wyk, Juanita R. Avontuur, Chrizelle W. Beukes, 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 horizontal gene transfer and incomplete lineage sorting. Because of the huge effect that this could have on phylogenies, we evaluated the impact of phylogenetic conflict caused by organism-level evolutionary processes on the established species phylogeny for Pantoea, a member of the Enterobacterales. We explored the presence and distribution of phylogenetic conflict at the gene partition and nucleotide levels, by identifying putative inter-lineage recombination events that might have contributed to such conflict. Furthermore, we determined whether smaller, randomly constructed datasets had sufficient signal to reconstruct the current species tree hypothesis or if they would be overshadowed by phylogenetic incongruence. We found that no individual gene tree was fully congruent with the species phylogeny of Pantoea, although many of the expected nodes were supported by various individual genes across the genome. Evidence of recombination was found across all lineages within Pantoea, and provides support for organism-level evolutionary processes as a potential source of phylogenetic conflict. The phylogenetic signal from at least 70 random genes recovered robust, well-supported phylogenies for the backbone and most species relationships of Pantoea, and was unaffected by phylogenetic conflict within the dataset. Furthermore, despite providing limited resolution among taxa at the level of single gene trees, concatenated analyses of genes that were identified as having no signal resulted in a phylogeny that resembled the species phylogeny of Pantoea. This distribution of signal and noise across the genome presents the ideal situation for phylogenetic inference, as the topology from a ≥70-gene concatenated species phylogeny is not driven by single genes, and our data suggests that this finding may also hold true for smaller datasets. We thus argue that, by using a concatenation-based approach in phylogenomics, one can obtain robust phylogenies due to the synergistic effect of the combined signal obtained from multiple genes.
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Kim, Junhyong. "Large-Scale Phylogenies and Measuring the Performance of Phylogenetic Estimators." Systematic Biology 47, no. 1 (March 1, 1998): 43–60. http://dx.doi.org/10.1080/106351598261021.
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Aris-Brosou, Stéphane, and Xuhua Xia. "Phylogenetic Analyses: A Toolbox Expanding towards Bayesian Methods." International Journal of Plant Genomics 2008 (April 30, 2008): 1–16. http://dx.doi.org/10.1155/2008/683509.
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The reconstruction of phylogenies is becoming an increasingly simple activity. This is mainly due to two reasons: the democratization of computing power and the increased availability of sophisticated yet user-friendly software. This review describes some of the latest additions to the phylogenetic toolbox, along with some of their theoretical and practical limitations. It is shown that Bayesian methods are under heavy development as they offer the possibility to solve a number of long-standing issues and to integrate several steps of the phylogenetic analyses into a single framework. Specific topics include not only phylogenetic reconstruction, but also the comparison of phylogenies, the detection of adaptive evolution, and the estimation of divergence times between species.
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Hinchliff, Cody E., Stephen A. Smith, James F. Allman, J. Gordon Burleigh, Ruchi Chaudhary, Lyndon M. Coghill, Keith A. Crandall, et al. "Synthesis of phylogeny and taxonomy into a comprehensive tree of life." Proceedings of the National Academy of Sciences 112, no. 41 (September 18, 2015): 12764–69. http://dx.doi.org/10.1073/pnas.1423041112.
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Reconstructing the phylogenetic relationships that unite all lineages (the tree of life) is a grand challenge. The paucity of homologous character data across disparately related lineages currently renders direct phylogenetic inference untenable. To reconstruct a comprehensive tree of life, we therefore synthesized published phylogenies, together with taxonomic classifications for taxa never incorporated into a phylogeny. We present a draft tree containing 2.3 million tips—the Open Tree of Life. Realization of this tree required the assembly of two additional community resources: (i) a comprehensive global reference taxonomy and (ii) a database of published phylogenetic trees mapped to this taxonomy. Our open source framework facilitates community comment and contribution, enabling the tree to be continuously updated when new phylogenetic and taxonomic data become digitally available. Although data coverage and phylogenetic conflict across the Open Tree of Life illuminate gaps in both the underlying data available for phylogenetic reconstruction and the publication of trees as digital objects, the tree provides a compelling starting point for community contribution. This comprehensive tree will fuel fundamental research on the nature of biological diversity, ultimately providing up-to-date phylogenies for downstream applications in comparative biology, ecology, conservation biology, climate change, agriculture, and genomics.
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CRUICKSHANK, ROBERT H. "Exploring character conflict in molecular data." Zootaxa 2946, no. 1 (July 8, 2011): 45. http://dx.doi.org/10.11646/zootaxa.2946.1.10.
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Mooi & Gill (2010) have made a number of criticisms of statistical approaches to the phylogenetic analysis of molecular data as it is currently practiced. There are many different uses for molecular phylogenies, and for most of them statistical methods are entirely appropriate, but for taxonomic purposes the way that these methods have been used is questionable. In these cases it is necessary to introduce an extra step into the analysis – exploration of character conflict. Existing methods for exploring character conflict in molecular data such as spectral analysis, phylogenetic networks, likelihood mapping and sliding window analyses are briefly reviewed, but there is also a need for development of new tools to facilitate the analysis of large data sets. Incorporation of previous phylogenies as priors in Bayesian analyses could help to provide taxonomic stability, while still leaving room for new data to alter these conclusions if they contain sufficiently strong phylogenetic signal. Molecular phylogeneticists should make a clearer distinction between the different uses to which their phylogenies are put; methods suitable in one context may not be appropriate in others.
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DeBlasio, Dan F., and Jennifer H. Wisecaver. "SICLE: a high-throughput tool for extracting evolutionary relationships from phylogenetic trees." PeerJ 4 (August 23, 2016): e2359. http://dx.doi.org/10.7717/peerj.2359.
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We present the phylogeny analysis softwareSICLE(SisterCladeExtractor), an easy-to-use, high-throughput tool to describe the nearest neighbors to a node of interest in a phylogenetic tree as well as the support value for the relationship. The application is a command line utility that can be embedded into a phylogenetic analysis pipeline or can be used as a subroutine within another C++ program. As a test case, we applied this new tool to the published phylome ofSalinibacter ruber, a species of halophilic Bacteriodetes, identifying 13 unique sister relationships toS. ruberacross the 4,589 gene phylogenies.S. rubergrouped with bacteria, most often other Bacteriodetes, in the majority of phylogenies, but 91 phylogenies showed a branch-supported sister association betweenS. ruberand Archaea, an evolutionarily intriguing relationship indicative of horizontal gene transfer. This test case demonstrates howSICLEmakes it possible to summarize the phylogenetic information produced by automated phylogenetic pipelines to rapidly identify and quantify the possible evolutionary relationships that merit further investigation.SICLEis available for free for noncommercial use athttp://eebweb.arizona.edu/sicle/.
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Lloyd, Graeme T., and Graham J. Slater. "A Total-Group Phylogenetic Metatree for Cetacea and the Importance of Fossil Data in Diversification Analyses." Systematic Biology 70, no. 5 (January 28, 2021): 922–39. http://dx.doi.org/10.1093/sysbio/syab002.
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Abstract Phylogenetic trees provide a powerful framework for testing macroevolutionary hypotheses, but it is becoming increasingly apparent that inferences derived from extant species alone can be highly misleading. Trees incorporating living and extinct taxa are needed to address fundamental questions about the origins of diversity and disparity but it has proved challenging to generate robust, species-rich phylogenies that include large numbers of fossil taxa. As a result, most studies of diversification dynamics continue to rely on molecular phylogenies. Here, we extend and apply a recently developed meta-analytic approach for synthesizing previously published phylogenetic studies to infer a well-resolved set of species level, time-scaled phylogenetic hypotheses for extinct and extant cetaceans (whales, dolphins, and allies). Our trees extend sampling from the $\sim 90$ extant species to over 500 living and extinct species, and therefore allow for more robust inference of macroevolutionary dynamics. While the diversification scenarios, we recover are broadly concordant with those inferred from molecular phylogenies they differ in critical ways, notably in the relative contributions of extinction and speciation rate shifts in driving rapid radiations. The metatree approach provides the most immediate route for generating higher level phylogenies of extinct taxa and opens the door to re-evaluation of macroevolutionary hypotheses derived only from extant taxa.[Extinction; macroevolution; matrix representation with parsimony; morphology; supertree.]
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Brocklehurst, Neil, and Gemma Louise Benevento. "Dental characters used in phylogenetic analyses of mammals show higher rates of evolution, but not reduced independence." PeerJ 8 (March 24, 2020): e8744. http://dx.doi.org/10.7717/peerj.8744.
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Accurate reconstructions of phylogeny are essential for studying the evolution of a clade, and morphological characters are necessarily used for the reconstruction of the relationships of fossil organisms. However, variation in their evolutionary modes (for example rate variation and character non-independence) not accounted for in analyses may be leading to unreliable phylogenies. A recent study suggested that phylogenetic analyses of mammals may be suffering from a dominance of dental characters, which were shown to have lower phylogenetic signal than osteological characters and produced phylogenies less congruent with molecularly-derived benchmarks. Here we build on this previous work by testing five additional morphological partitions for phylogenetic signal and examining what aspects of dental and other character evolution may be affecting this, by fitting models of discrete character evolution to phylogenies inferred and time calibrated using molecular data. Results indicate that the phylogenetic signal of discrete characters correlate most strongly with rates of evolution, with increased rates driving increased homoplasy. In a dataset covering all Mammalia, dental characters have higher rates of evolution than other partitions. They do not, however, fit a model of independent character evolution any worse than other regions. Primates and marsupials show different patterns to other mammal clades, with dental characters evolving at slower rates and being more heavily integrated (less independent). While the dominance of dental characters in analyses of mammals could be leading to inaccurate phylogenies, the issue is not unique to dental characters and the results are not consistent across datasets. Molecular benchmarks (being entirely independent of the character data) provide a framework for examining each dataset individually to assess the evolution of the characters used.
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Simdyanov, Timur G., Laure Guillou, Andrei Y. Diakin, Kirill V. Mikhailov, Joseph Schrével, and Vladimir V. Aleoshin. "A new view on the morphology and phylogeny of eugregarines suggested by the evidence from the gregarine Ancora sagittata (Leuckart, 1860) Labbé, 1899 (Apicomplexa: Eugregarinida)." PeerJ 5 (May 30, 2017): e3354. http://dx.doi.org/10.7717/peerj.3354.
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Background Gregarines are a group of early branching Apicomplexa parasitizing invertebrate animals. Despite their wide distribution and relevance to the understanding the phylogenesis of apicomplexans, gregarines remain understudied: light microscopy data are insufficient for classification, and electron microscopy and molecular data are fragmentary and overlap only partially. Methods Scanning and transmission electron microscopy, PCR, DNA cloning and sequencing (Sanger and NGS), molecular phylogenetic analyses using ribosomal RNA genes (18S (SSU), 5.8S, and 28S (LSU) ribosomal DNAs (rDNAs)). Results and Discussion We present the results of an ultrastructural and molecular phylogenetic study on the marine gregarine Ancora sagittata from the polychaete Capitella capitata followed by evolutionary and taxonomic synthesis of the morphological and molecular phylogenetic evidence on eugregarines. The ultrastructure of Ancora sagittata generally corresponds to that of other eugregarines, but reveals some differences in epicytic folds (crests) and attachment apparatus to gregarines in the family Lecudinidae, where Ancora sagittata has been classified. Molecular phylogenetic trees based on SSU (18S) rDNA reveal several robust clades (superfamilies) of eugregarines, including Ancoroidea superfam. nov., which comprises two families (Ancoridae fam. nov. and Polyplicariidae) and branches separately from the Lecudinidae; thus, all representatives of Ancoroidea are here officially removed from the Lecudinidae. Analysis of sequence data also points to possible cryptic species within Ancora sagittata and the inclusion of numerous environmental sequences from anoxic habitats within the Ancoroidea. LSU (28S) rDNA phylogenies, unlike the analysis of SSU rDNA alone, recover a well-supported monophyly of the gregarines involved (eugregarines), although this conclusion is currently limited by sparse taxon sampling and the presence of fast-evolving sequences in some species. Comparative morphological analyses of gregarine teguments and attachment organelles lead us to revise their terminology. The terms “longitudinal folds” and “mucron” are restricted to archigregarines, whereas the terms “epicystic crests” and “epimerite” are proposed to describe the candidate synapomorphies of eugregarines, which, consequently, are considered as a monophyletic group. Abolishing the suborders Aseptata and Septata, incorporating neogregarines into the Eugregarinida, and treating the major molecular phylogenetic lineages of eugregarines as superfamilies appear as the best way of reconciling recent morphological and molecular evidence. Accordingly, the diagnosis of the order Eugregarinida Léger, 1900 is updated.
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Coetzee, Martin, Brenda Wingfield, and Michael Wingfield. "Armillaria Root-Rot Pathogens: Species Boundaries and Global Distribution." Pathogens 7, no. 4 (October 24, 2018): 83. http://dx.doi.org/10.3390/pathogens7040083.
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This review considers current knowledge surrounding species boundaries of the Armillaria root-rot pathogens and their distribution. In addition, a phylogenetic tree using translation elongation factor subunit 1-alpha (tef-1α) from isolates across the globe are used to present a global phylogenetic framework for the genus. Defining species boundaries based on DNA sequence-inferred phylogenies has been a central focus of contemporary mycology. The results of such studies have in many cases resolved the biogeographic history of species, mechanisms involved in dispersal, the taxonomy of species and how certain phenotypic characteristics have evolved throughout lineage diversification. Such advances have also occurred in the case of Armillaria spp. that include important causal agents of tree root rots. This commenced with the first phylogeny for Armillaria that was based on IGS-1 (intergenic spacer region one) DNA sequence data, published in 1992. Since then phylogenies were produced using alternative loci, either as single gene phylogenies or based on concatenated data. Collectively these phylogenies revealed species clusters in Armillaria linked to their geographic distributions and importantly species complexes that warrant further research.
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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 (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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Pompei, Simone, Vittorio Loreto, and Francesca Tria. "Copystree." Language Dynamics and Change 8, no. 1 (June 22, 2018): 55–77. http://dx.doi.org/10.1163/22105832-00801003.
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AbstractThe reconstruction of phylogenies of cultural artefacts represents an open problem that mixes theoretical and computational challenges. Existing benchmarks rely on simulated phylogenies, where hypotheses on the underlying evolutionary mechanisms are unavoidable, or on real data phylogenies, for which no true evolutionary history is known. Here we introduce a web-based game, Copystree, where users create phylogenies of manuscripts through successive copying actions in a fully monitored setup. While players enjoy the experience, Copystree allows to build artificial phylogenies whose evolutionary processes do not obey any predefined theoretical mechanisms, being generated instead with the unpredictability of human creativity. We present the analysis of the data gathered during the first set of experiments and use the artificial phylogenies gathered for a first test of existing phylogenetic algorithms.
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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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Román Palacios, Cristian, April Wright, and Josef Uyeda. "treedata.table: a wrapper for data.table that enables fast manipulation of large phylogenetic trees matched to data." PeerJ 9 (November 26, 2021): e12450. http://dx.doi.org/10.7717/peerj.12450.
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The number of terminals in phylogenetic trees has significantly increased over the last decade. This trend reflects recent advances in next-generation sequencing, accessibility of public data repositories, and the increased use of phylogenies in many fields. Despite R being central to the analysis of phylogenetic data, manipulation of phylogenetic comparative datasets remains slow, complex, and poorly reproducible. Here, we describe the first R package extending the functionality and syntax of data.table to explicitly deal with phylogenetic comparative datasets. treedata.table significantly increases speed and reproducibility during the data manipulation steps involved in the phylogenetic comparative workflow in R. The latest release of treedata.table is currently available through CRAN (https://cran.r-project.org/web/packages/treedata.table/). Additional documentation can be accessed through rOpenSci (https://ropensci.github.io/treedata.table/).
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Golding, G. Brian. "Reconstructing the Prior Probabilities of Allelic Phylogenies." Genetics 161, no. 2 (June 1, 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 samples and for different phylogenies. This method is a straightforward extension of Ewens' sample distribution. The probability of obtaining each possible sample according to Ewens' distribution is further subdivided into each of the possible phylogenetic topologies. These probabilities depend not only on the identity of the alleles and on 4Nμ (four times the effective population size times the neutral mutation rate) but also on the phylogenetic relationships among the alleles. Illustrations of the algorithm are given to demonstrate how different phylogenies are favored under different conditions.
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Pylro, Victor Satler, Luciano de Souza Vespoli, Gabriela Frois Duarte, and Karla Suemy Clemente Yotoko. "Detection of Horizontal Gene Transfers from Phylogenetic Comparisons." International Journal of Evolutionary Biology 2012 (May 23, 2012): 1–7. http://dx.doi.org/10.1155/2012/813015.
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Bacterial phylogenies have become one of the most important challenges for microbial ecology. This field started in the mid-1970s with the aim of using the sequence of the small subunit ribosomal RNA (16S) tool to infer bacterial phylogenies. Phylogenetic hypotheses based on other sequences usually give conflicting topologies that reveal different evolutionary histories, which in some cases may be the result of horizontal gene transfer events. Currently, one of the major goals of molecular biology is to understand the role that horizontal gene transfer plays in species adaptation and evolution. In this work, we compared the phylogenetic tree based on 16S with the tree based on dszC, a gene involved in the cleavage of carbon-sulfur bonds. Bacteria of several genera perform this survival task when living in environments lacking free mineral sulfur. The biochemical pathway of the desulphurization process was extensively studied due to its economic importance, since this step is expensive and indispensable in fuel production. Our results clearly show that horizontal gene transfer events could be detected using common phylogenetic methods with gene sequences obtained from public sequence databases.
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MacLeod, Norman. "The role of phylogeny in quantitative paleobiological data analysis." Paleobiology 27, no. 2 (2001): 226–40. http://dx.doi.org/10.1666/0094-8373(2001)027<0226:tropiq>2.0.co;2.
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Phylogenies provide a rich source of information that should be exploited in designing quantitative hypothesis tests in paleobiological contexts. Viewing such data analysis problems through the prism of phylogenetically structured comparisons can help add realism and depth to paleobiological data-analysis strategies. Two examples of the importance of adopting a phylogenetic perspective are discussed. In the first example, a phylogenetic-comparative approach is used to test correlations between ecological, morphological, and biological characteristics of planktonic foraminifera. Results suggest that the presence of spines and photosynthetic symbionts in Neogene-Recent species are not adaptations to living in shallow-intermediate planktonic depth habitats. In the second, a phylogenetic-comparative approach is used to reveal the presence of morphological correlations with locomotor function in a mammalian carnivore data set. Paleontologists can play an active role in improving comparative data analyses by (1) helping to develop improved phylogenies, especially those that provide better estimates of branch lengths, and (2) helping to resolve a number of outstanding issues surround the question of ancestral character-state specification.
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Fleming, James F., Roberto Feuda, Nicholas W. Roberts, and Davide Pisani. "A Novel Approach to Investigate the Effect of Tree Reconstruction Artifacts in Single-Gene Analysis Clarifies Opsin Evolution in Nonbilaterian Metazoans." Genome Biology and Evolution 12, no. 2 (February 1, 2020): 3906–16. http://dx.doi.org/10.1093/gbe/evaa015.
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Abstract Our ability to correctly reconstruct a phylogenetic tree is strongly affected by both systematic errors and the amount of phylogenetic signal in the data. Current approaches to tackle tree reconstruction artifacts, such as the use of parameter-rich models, do not translate readily to single-gene alignments. This, coupled with the limited amount of phylogenetic information contained in single-gene alignments, makes gene trees particularly difficult to reconstruct. Opsin phylogeny illustrates this problem clearly. Opsins are G-protein coupled receptors utilized in photoreceptive processes across Metazoa and their protein sequences are roughly 300 amino acids long. A number of incongruent opsin phylogenies have been published and opsin evolution remains poorly understood. Here, we present a novel approach, the canary sequence approach, to investigate and potentially circumvent errors in single-gene phylogenies. First, we demonstrate our approach using two well-understood cases of long-branch attraction in single-gene data sets, and simulations. After that, we apply our approach to a large collection of well-characterized opsins to clarify the relationships of the three main opsin subfamilies.
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Veldkornet, D. A., J. B. Adams, J. S. Boatwright, and A. Rajkaran. "Barcoding of estuarine macrophytes and phylogenetic diversity of estuaries along the South African coastline." Genome 62, no. 9 (September 2019): 585–95. http://dx.doi.org/10.1139/gen-2018-0067.
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Plant DNA barcoding serves as an effective approach to building community phylogenies and increasing our understanding of the factors that determine plant community assemblages. The aims of the study were to (i) barcode macrophytes with high estuarine fidelity and (ii) to determine the phylogenetic diversity (PD) of selected South African estuaries for conservation prioritisation. Three DNA barcoding gene regions (rbcLa, matK, and trnH-psbA) were assessed, and community phylogenies were constructed for 270 estuaries. Generally, the matK barcode had the greatest discrimination success rate of 67.4% (parsimony informative sites = 418). Closely related species formed clades that also represent estuarine habitat types. Estuaries with high phylogenetic diversity along the southeast coast were associated with a combination of mangrove and salt marsh habitats. Species richness was strongly and significantly correlated with PD (r = 0.93; p < 0.000). Based on mean pairwise distance (MPD), more temperate estuaries (56) showed significant phylogenetic clustering compared to subtropical estuaries (24) (p < 0.05). Similarly, based on mean nearest taxon distance (MNTD), significant phylogenetic clustering was highest in temperate estuaries (50) compared to subtropical estuaries (12) (p < 0.05). This suggests that the coexistence of plant species in estuaries is structured by both biotic and abiotic interactions.
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Dolson, Emily, Alexander Lalejini, Steven Jorgensen, and Charles Ofria. "Interpreting the Tape of Life: Ancestry-Based Analyses Provide Insights and Intuition about Evolutionary Dynamics." Artificial Life 26, no. 1 (April 2020): 58–79. http://dx.doi.org/10.1162/artl_a_00313.
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Fine-scale evolutionary dynamics can be challenging to tease out when focused on the broad brush strokes of whole populations over long time spans. We propose a suite of diagnostic analysis techniques that operate on lineages and phylogenies in digital evolution experiments, with the aim of improving our capacity to quantitatively explore the nuances of evolutionary histories in digital evolution experiments. We present three types of lineage measurements: lineage length, mutation accumulation, and phenotypic volatility. Additionally, we suggest the adoption of four phylogeny measurements from biology: phylogenetic richness, phylogenetic divergence, phylogenetic regularity, and depth of the most-recent common ancestor. In addition to quantitative metrics, we also discuss several existing data visualizations that are useful for understanding lineages and phylogenies: state sequence visualizations, fitness landscape overlays, phylogenetic trees, and Muller plots. We examine the behavior of these metrics (with the aid of data visualizations) in two well-studied computational contexts: (1) a set of two-dimensional, real-valued optimization problems under a range of mutation rates and selection strengths, and (2) a set of qualitatively different environments in the Avida digital evolution platform. These results confirm our intuition about how these metrics respond to various evolutionary conditions and indicate their broad value.
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Jones, Nick S., and John Moriarty. "Evolutionary inference for function-valued traits: Gaussian process regression on phylogenies." Journal of The Royal Society Interface 10, no. 78 (January 6, 2013): 20120616. http://dx.doi.org/10.1098/rsif.2012.0616.
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Biological data objects often have both of the following features: (i) they are functions rather than single numbers or vectors, and (ii) they are correlated owing to phylogenetic relationships. In this paper, we give a flexible statistical model for such data, by combining assumptions from phylogenetics with Gaussian processes. We describe its use as a non-parametric Bayesian prior distribution, both for prediction (placing posterior distributions on ancestral functions) and model selection (comparing rates of evolution across a phylogeny, or identifying the most likely phylogenies consistent with the observed data). Our work is integrative, extending the popular phylogenetic Brownian motion and Ornstein–Uhlenbeck models to functional data and Bayesian inference, and extending Gaussian process regression to phylogenies. We provide a brief illustration of the application of our method.
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Gastauer, M., and J. A. A. Meira-Neto. "An enhanced calibration of a recently released megatree for the analysis of phylogenetic diversity." Brazilian Journal of Biology 76, no. 3 (April 19, 2016): 619–28. http://dx.doi.org/10.1590/1519-6984.20814.
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Abstract Dated or calibrated phylogenetic trees, in which branch lengths correspond to evolutionary divergence times between nodes, are important requirements for computing measures of phylogenetic diversity or phylogenetic community structure. The increasing knowledge about the diversification and evolutionary divergence times of vascular plants requires a revision of the age estimates used for the calibration of phylogenetic trees by the bladj algorithm of the Phylocom 4.2 package. Comparing the recently released megatree R20120829.new with two calibrated vascular plant phylogenies provided in the literature, we found 242 corresponding nodes. We modified the megatree (R20120829mod.new), inserting names for all corresponding nodes. Furthermore, we provide files containing age estimates from both sources for the updated calibration of R20120829mod.new. Applying these files consistently in analyses of phylogenetic community structure or diversity serves to avoid erroneous measures and ecological misinterpretation.
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BORKENT, ART. "The State of Phylogenetic Analysis: Narrow Visions and Simple Answers—Examples from the Diptera (flies)." Zootaxa 4374, no. 1 (January 17, 2018): 107. http://dx.doi.org/10.11646/zootaxa.4374.1.7.
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The order Diptera is remarkably diverse, not only in species but in morphological variation in every life stage, making them excellent candidates for phylogenetic analysis. Such analysis has been hampered by methods that have severely restricted character state interpretation. Morphological-based phylogenies should be based on a deep understanding of the morphology, development and function of character states, and have extensive outgroup comparisons made to determine their polarity. Character states clearly vary in their value for determining phylogenetic relationships and this needs to be studied and utilized. Characters themselves need more explicit discussion, including how some may be developmentally or functionally related to other characters (and potentially not independent indicators of genealogical relationship). The current practice by many, of filling a matrix with poorly understood character states and highly limited outgroup comparisons, is unacceptable if the results are to be a valid reflection of the actual history of the group.Parsimony analysis is not an objective interpretation of phylogenetic relationships when all characters are treated as equal in value. Exact mathematical values applied to characters are entirely arbitrary and are generally used to produce a phylogeny that the author considers as reasonable. Mathematical appraisal of a given node is similarly inconsequential because characters do not have an intrinsic mathematical value. Bremer support, for example, provides values that have no biological reality but provide the pretence of objectivity. Cladists need to focus their attention on testing the validity of each synapomorphy proposed, as the basis for all further phylogenetic interpretation, rather than the testing of differing phylogenies through various comparative programs.Current phylogenetic analyses have come to increasingly depend on DNA sequence-based characters, in spite of their tumultuous history of inconsistent results. Until such time as sequences can be shown to produce predictive phylogenies (i.e., using Hennigian logic), independent of morphological analysis, they should be viewed with caution and certainly not as a panacea as they are commonly portrayed.The purported comprehensive analyses of phylogenetic relationships between families of Diptera by Wiegmann et al. (2011) and Lambkin et al. (2013) have serious flaws and cannot be considered as the “Periodic Table” of such relationships as originally heralded.Systematists working on Diptera have a plethora of complex and informative morphological synapomorphies in every life stage, either described or awaiting study. Many lineages have the potential of providing a wealth of evolutionary stories to share with other biologists if we produce stable phylogenies based on weighted synapomorphies and interpreted to elucidate the zoogeographic and bionomic divergence of the group. Some lineages are devoid of convincing synapomorphies and, in spite of our desires, should be recognized as being largely uninterpretable.
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CAMIER, MARIE, and ANDRE NEL. "The oldest fungus gnat of the tribe Exechiini in the lowermost Eocene Oise amber (Diptera: Mycetophilidae)." Zootaxa 4722, no. 1 (January 10, 2020): 91–98. http://dx.doi.org/10.11646/zootaxa.4722.1.9.
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Eoexechia gallica gen. n. and sp. n., oldest record of the fungus gnat tribe Exechiini, is described from the Lowermost Eocene amber of France. It falls as sister group of all the extant Exechiini after its addition to the morphological phylogenetic analysis of the tribe. Its discovery suggests a Paleocene age for the Exechiini, in accordance with the current phylogenetic dating. This new discovery will help to date the whole clade in future phylogenies.
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Cunningham, C. W., H. Zhu, and D. M. Hillis. "Best-Fit Maximum-Likelihood Models for Phylogenetic Inference: Empirical Tests with Known Phylogenies." Evolution 52, no. 4 (August 1998): 978. http://dx.doi.org/10.2307/2411230.
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Cunningham, C. W., H. Zhu, and D. M. Hillis. "BEST-FIT MAXIMUM-LIKELIHOOD MODELS FOR PHYLOGENETIC INFERENCE: EMPIRICAL TESTS WITH KNOWN PHYLOGENIES." Evolution 52, no. 4 (August 1998): 978–87. http://dx.doi.org/10.1111/j.1558-5646.1998.tb01827.x.
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Cammarano, Piero, Simonetta Gribaldo, and Andre Johann. "Updating Carbamoylphosphate Synthase (CPS) Phylogenies: Occurrence and Phylogenetic Identity of Archaeal CPS Genes." Journal of Molecular Evolution 55, no. 2 (August 1, 2002): 153–60. http://dx.doi.org/10.1007/s00239-002-2312-6.
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Begonia Phylogeny Group, Wisnu Ardi, Lucia Campos, Kuo Fang Chung, Wen-Ke Dong, Eleanor Drinkwater, Danny Fuller, et al. "RESOLVING PHYLOGENETIC AND TAXONOMIC CONFLICT IN BEGONIA." Edinburgh Journal of Botany 79 (August 18, 2022): 1–28. http://dx.doi.org/10.24823/ejb.2022.1928.
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Begonia is the world’s fastest-growing genus and a focus of intense taxonomic research. To support this, a stable and useful sectional classification is needed. This paper reviews the feasibility and challenges of creating an infrageneric classification for Begonia based on phylogenetic data, and how to overcome phylogenetic and taxonomic conflict. In particular, it (i) tests genus-wide patterns of incongruence between phylogenies based on the nuclear, chloroplast and mitochondrial genomes; (ii) explains organelle inheritance and its contribution to phylogenetic incongruence, and (iii) presents a manifesto for a workable and stable subgeneric classification in light of the above and lays the foundation for a collaborative Begonia Phylogeny Group.
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Yu, Yan, Christopher Blair, and Xingjin He. "RASP 4: Ancestral State Reconstruction Tool for Multiple Genes and Characters." Molecular Biology and Evolution 37, no. 2 (October 31, 2019): 604–6. http://dx.doi.org/10.1093/molbev/msz257.
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Abstract With the continual progress of sequencing techniques, genome-scale data are increasingly used in phylogenetic studies. With more data from throughout the genome, the relationship between genes and different kinds of characters is receiving more attention. Here, we present version 4 of RASP, a software to reconstruct ancestral states through phylogenetic trees. RASP can apply generalized statistical ancestral reconstruction methods to phylogenies, explore the phylogenetic signal of characters to particular trees, calculate distances between trees, and cluster trees into groups. RASP 4 has an improved graphic user interface and is freely available from http://mnh.scu.edu.cn/soft/blog/RASP (program) and https://github.com/sculab/RASP (source code).
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Chelo, Ivo M., Líbia Zé-Zé, and Rogério Tenreiro. "Congruence of evolutionary relationships inside the Leuconostoc–Oenococcus–Weissella clade assessed by phylogenetic analysis of the 16S rRNA gene, dnaA, gyrB, rpoC and dnaK." International Journal of Systematic and Evolutionary Microbiology 57, no. 2 (February 1, 2007): 276–86. http://dx.doi.org/10.1099/ijs.0.64468-0.
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The phylogenetic structure of the Leuconostoc–Oenococcus–Weissella clade was evaluated by comparison of 16S rRNA gene, dnaA, gyrB, rpoC and dnaK sequence analysis. Phylogenies obtained with the different genes were in overall good agreement and a well-supported, almost fully resolved phylogenetic tree was obtained when the combined data were analysed in a Bayesian approach. A rapid basal diversification of the three genera is suggested. Evolutionary rates of the 16S rRNA gene in these genera seem to be different and specifically related to the evolution of this group, revealing the importance of this sequence in the constitution of the present taxonomy, but preventing its straightforward use in phylogenetic inference.
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Young, Colin, Sarah Meng, and Niema Moshiri. "An Evaluation of Phylogenetic Workflows in Viral Molecular Epidemiology." Viruses 14, no. 4 (April 8, 2022): 774. http://dx.doi.org/10.3390/v14040774.
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The use of viral sequence data to inform public health intervention has become increasingly common in the realm of epidemiology. Such methods typically utilize multiple sequence alignments and phylogenies estimated from the sequence data. Like all estimation techniques, they are error prone, yet the impacts of such imperfections on downstream epidemiological inferences are poorly understood. To address this, we executed multiple commonly used viral phylogenetic analysis workflows on simulated viral sequence data, modeling Human Immunodeficiency Virus (HIV), Hepatitis C Virus (HCV), and Ebolavirus, and we computed multiple methods of accuracy, motivated by transmission-clustering techniques. For multiple sequence alignment, MAFFT consistently outperformed MUSCLE and Clustal Omega, in both accuracy and runtime. For phylogenetic inference, FastTree 2, IQ-TREE, RAxML-NG, and PhyML had similar topological accuracies, but branch lengths and pairwise distances were consistently most accurate in phylogenies inferred by RAxML-NG. However, FastTree 2 was the fastest, by orders of magnitude, and when the other tools were used to optimize branch lengths along a fixed FastTree 2 topology, the resulting phylogenies had accuracies that were indistinguishable from their original counterparts, but with a fraction of the runtime.
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Navas, Alfonso, and Pilar Flores-Romero. "Enhancing taxonomic resolution: distribution dependent genetic diversity in populations of Meloidogyne." Nematology 7, no. 4 (2005): 517–30. http://dx.doi.org/10.1163/156854105774384831.
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AbstractRoot-knot nematodes (Meloidogyne) are one of the most damaging agricultural pests. The polyploid apomictic M. arenaria, M. javanica and M. incognita are particularly ubiquitous and exhibit an extreme polyphagy. The taxonomic position of these three species remains unclear, as does the phylogenetic relationships between them. To characterise phenotype variants among these three species, allozyme electrophoresis (α-EST, MDH, CAT, GPI, DIA, GOT, and SOD) was performed in populations from the Iberian Peninsula. A total of 50 multilocus enzyme electrophoresis (MLEE) phenotype variants were detected of which, according to the esterase pattern, 24 corresponded to M. arenaria, 15 to M. javanica and 11 to M. incognita. The phylogenetic relationships of these 50 MLEE variants were studied following the Neighbour-Joining (NJ) distance method based on an allelic frequencies matrix built using two different methodologies. In addition, Maximum-Parsimony (MP) and Maximum-Likelihood (ML) phylogenetic methods were done in order to corroborate the phylogenies obtained. Our results showed a great disparity in the NJ trees obtained, thus indicating that the monophyly of the parthenogenetic Meloidogyne spp. would seem to depend on the methodology used. Evolutionary and epidemiological implications of the recovered phylogenies are discussed.
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Yang, Zhen, Guixi Wang, Qinghua Ma, Wenxu Ma, Lisong Liang, and Tiantian Zhao. "The complete chloroplast genomes of three Betulaceae species: implications for molecular phylogeny and historical biogeography." PeerJ 7 (January 25, 2019): e6320. http://dx.doi.org/10.7717/peerj.6320.
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Background Previous phylogenetic conclusions on the family Betulaceae were based on either morphological characters or traditional single loci, which may indicate some limitations. The chloroplast genome contains rich polymorphism information, which is very suitable for phylogenetic studies. Thus, we sequenced the chloroplast genome sequences of three Betulaceae species and performed multiple analyses to investigate the genome variation, resolve the phylogenetic relationships, and clarify the divergence history. Methods Chloroplast genomes were sequenced using the high-throughput sequencing. A comparative genomic analysis was conducted to examine the global genome variation and screen the hotspots. Three chloroplast partitions were used to reconstruct the phylogenetic relationships using Maximum Likelihood and Bayesian Inference approaches. Then, molecular dating and biogeographic inferences were conducted based on the whole chloroplast genome data. Results Betulaceae chloroplast genomes consisted of a small single-copy region and a large single copy region, and two copies of inverted repeat regions. Nine hotspots can be used as potential DNA barcodes for species delimitation. Phylogenies strongly supported the division of Betulaceae into two subfamilies: Coryloideae and Betuloideae. The phylogenetic position of Ostryopsis davidiana was controversial among different datasets. The divergence time between subfamily Coryloideae and Betuloideae was about 70.49 Mya, and all six extant genera were inferred to have diverged fully by the middle Oligocene. Betulaceae ancestors were probably originated from the ancient Laurasia. Discussions This research elucidates the potential of chloroplast genome sequences in the application of developing molecular markers, studying evolutionary relationships and historical dynamic of Betulaceae.It also reveals the advantages of using chloroplast genome data to illuminate those phylogenies that have not been well solved yet by traditional approaches in other plants.
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Schierup, Mikkel H., and Jotun Hein. "Consequences of Recombination on Traditional Phylogenetic Analysis." Genetics 156, no. 2 (October 1, 2000): 879–91. http://dx.doi.org/10.1093/genetics/156.2.879.
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Abstract We investigate the shape of a phylogenetic tree reconstructed from sequences evolving under the coalescent with recombination. The motivation is that evolutionary inferences are often made from phylogenetic trees reconstructed from population data even though recombination may well occur (mtDNA or viral sequences) or does occur (nuclear sequences). We investigate the size and direction of biases when a single tree is reconstructed ignoring recombination. Standard software (PHYLIP) was used to construct the best phylogenetic tree from sequences simulated under the coalescent with recombination. With recombination present, the length of terminal branches and the total branch length are larger, and the time to the most recent common ancestor smaller, than for a tree reconstructed from sequences evolving with no recombination. The effects are pronounced even for small levels of recombination that may not be immediately detectable in a data set. The phylogenies when recombination is present superficially resemble phylogenies for sequences from an exponentially growing population. However, exponential growth has a different effect on statistics such as Tajima's D. Furthermore, ignoring recombination leads to a large overestimation of the substitution rate heterogeneity and the loss of the molecular clock. These results are discussed in relation to viral and mtDNA data sets.
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FERNANDEZ, JULIO C. C., MARIANELA GASTALDI, GERMÁN ZAPATA-HERNÁNDEZ, LUIS M. PARDO, FABIANO L. THOMPSON, and EDUARDO HAJDU. "New species of Crella (Pytheas) Topsent, 1890 and Crellomima Rezvoi, 1925 (Crellidae, Poecilosclerida, Demospongiae) from Chilean shallow and Argentinean deep waters, with a synthesis on the known phylogenetic relationships of crellid sponges." Zootaxa 5052, no. 3 (October 15, 2021): 353–79. http://dx.doi.org/10.11646/zootaxa.5052.3.3.
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Here, we describe four new species of Crellidae Dendy, 1922 and discuss characters and relationships from published molecular phylogenies including crellid sponges. New species proposed are Crella (Pytheas) chiloensis Fernandez, Gastaldi, Pardo & Hajdu, sp. nov., from southern Chile (15 m depth), C. (P.) desventuradae Fernandez, Gastaldi, Zapata-Hernández & Hajdu, sp. nov., from Desventuradas Archipelago (10–20 m depth), Crella (P.) santacruzae Fernandez, Gastaldi, Thompson & Hajdu, sp. nov., from deep waters off Argentina (750 m depth) and Crellomima sigmatifera Fernandez, Gastaldi & Hajdu, sp. nov., from the Chilean fjords region (ca. 20 m depth). These new species are set apart from each other and from known species mainly due to aspects of their spiculation. Chelae microscleres and acanthostyles supply characters that might be used to infer phylogenetic relationships and to verify the monophyly of Crella Gray, 1867 and Crellidae, which has seemingly been contradicted by preliminary molecular data available in the systematics’ literature. Our own interpretation of phylogenetic affinities, in the light of morphological characters from previous taxonomic studies, argues for a classification reassessment of materials (vouchers) included in these molecular phylogenies, especially in the case of Crella incrustans (Carter, 1885). We argue that currently available molecular phylogenetic outcomes for crellid sponges are not supportive of the polyphyly of Crella and Crellidae.
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Romeiro-Brito, Monique, Milena Cardoso Telhe, Danilo Trabuco Amaral, Fernando Faria Franco, and Evandro Marsola Moraes. "A target Capture Probe Set Useful for Deep- and Shallow-Level Phylogenetic Studies in Cactaceae." Genes 13, no. 4 (April 17, 2022): 707. http://dx.doi.org/10.3390/genes13040707.
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The molecular phylogenies of Cactaceae have enabled us to better understand their systematics, biogeography, and diversification ages. However, most of the phylogenetic relationships within Cactaceae major groups remain unclear, largely due to the lack of an appropriate set of molecular markers to resolve its contentious relationships. Here, we explored the genome and transcriptome assemblies available for Cactaceae and identified putative orthologous regions shared among lineages of the subfamily Cactoideae. Then we developed a probe set, named Cactaceae591, targeting both coding and noncoding nuclear regions for representatives from the subfamilies Pereskioideae, Opuntioideae, and Cactoideae. We also sampled inter- and intraspecific variation to evaluate the potential of this panel to be used in phylogeographic studies. We retrieved on average of 547 orthologous regions per sample. Targeting noncoding nuclear regions showed to be crucial to resolving inter- and intraspecific relationships. Cactaceae591 covers 13 orthologous genes shared with the Angiosperms353 kit and two plastid regions largely used in Cactaceae studies, enabling the phylogenies generated by our panel to be integrated with angiosperm and Cactaceae phylogenies, using these sequences. We highlighted the importance of using coalescent-based species tree approaches on the Cactaceae591 dataset to infer accurate phylogenetic trees in the presence of extensive incomplete lineage sorting in this family.
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Byrne, Margaret, and Daniel J. Murphy. "The origins and evolutionary history of xerophytic vegetation in Australia." Australian Journal of Botany 68, no. 3 (2020): 195. http://dx.doi.org/10.1071/bt20022.
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The xeromorphic vegetation is a significant component of the Australian flora and phylogenetic and phylogeographic analysis of xeromorphic plants provides a basis for understanding the origins and evolutionary history of the Australian vegetation. Here we expand on previous reviews of the origins and maintenance of the Australian flora with an emphasis on the xeromorphic component. Phylogenetic evidence supports fossil evidence for evolution of sclerophyll and xeromorphic vegetation from the Eocene with lineages becoming more common in the Oligocene and Miocene, a time of major change in climate and vegetation in Australia. Phylogenetic evidence supports the mesic biome as ancestral to the arid zone biome in Australia in phylogenies of key groups. The diversification and radiation of Australian species shows single origins of xeromorphic group mainly at deeper levels in phylogenies as well as multiple origins of arid occurring species at shallower levels. Divergence across the Nullarbor is also evident and speciation rates in south-western Australia were higher than in the south-east in several plant families. Estimates of timing of diversification generally show either constant rates of diversification or increased diversification from the mid to late Miocene. Phylogeographic studies consistently demonstrate high localised genetic diversity and geographic structure in xeromorphic species occupying both mesic and arid biomes.
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Smith, Andrew B. "Stratigraphy in phylogeny reconstruction." Journal of Paleontology 74, no. 5 (September 2000): 763–66. http://dx.doi.org/10.1017/s0022336000032996.
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Access to the dimension of time makes paleontology unique as a discipline, and it is stratigraphical data that allows paleontologists to tackle a wide range of evolutionary questions unanswerable by neontologists. Some of these need only a vague and imprecise hypothesis of evolutionary relationships. For example, considerable headway has been made in documenting the evolution of morphological disparity with only the crudest of phylogenetic information (Foote, 1997). However, it is undoubtedly true that more precise and probing questions can be formulated if accurate phylogenies were available. But how do we construct such phylogenies?
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Kamilar, Jason M., and Natalie Cooper. "Phylogenetic signal in primate behaviour, ecology and life history." Philosophical Transactions of the Royal Society B: Biological Sciences 368, no. 1618 (May 19, 2013): 20120341. http://dx.doi.org/10.1098/rstb.2012.0341.
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Examining biological diversity in an explicitly evolutionary context has been the subject of research for several decades, yet relatively recent advances in analytical techniques and the increasing availability of species-level phylogenies, have enabled scientists to ask new questions. One such approach is to quantify phylogenetic signal to determine how trait variation is correlated with the phylogenetic relatedness of species. When phylogenetic signal is high, closely related species exhibit similar traits, and this biological similarity decreases as the evolutionary distance between species increases. Here, we first review the concept of phylogenetic signal and suggest how to measure and interpret phylogenetic signal in species traits. Second, we quantified phylogenetic signal in primates for 31 variables, including body mass, brain size, life-history, sexual selection, social organization, diet, activity budget, ranging patterns and climatic variables. We found that phylogenetic signal varies extensively across and even within trait categories. The highest values are exhibited by brain size and body mass, moderate values are found in the degree of territoriality and canine size dimorphism, while low values are displayed by most of the remaining variables. Our results have important implications for the evolution of behaviour and ecology in primates and other vertebrates.
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Hong, Jason C., David J. Norman, David L. Reed, M. Timur Momol, and Jeffrey B. Jones. "Diversity Among Ralstonia solanacearum Strains Isolated from the Southeastern United States." Phytopathology® 102, no. 10 (October 2012): 924–36. http://dx.doi.org/10.1094/phyto-12-11-0342.
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This is the first comprehensive study of a collection of Ralstonia solanacearum strains from the southeastern United States to be characterized based on biovar, pathogenicity, hypersensitive reaction on tobacco, and phylogenetic analyses of the egl sequence. Rigorous phylogenetic analysis of the commonly used egl gene produced robust phylogenies that differed significantly from a neighbor-joining tree differed from and previously published phylogenies for R. solanacearum strains. These robust trees placed phylotype IV within the phylotype I clade, which may suggest that phylogenies based solely on egl may be misleading. As a result of phylogenetic analyses in this study, we determined that U.S. strains from Georgia, North Carolina, South Carolina, and older Florida strains isolated from solanaceous crops all belong to phylotype II sequevar 7. However, many strains recently isolated in Florida from tomato and other crops were more diverse than the southeastern United States population. These unique Florida strains grouped with strains mostly originating from the Caribbean and Central America. One of the exotic strains, which in a previous study was determined to be established in northern Florida, was characterized more extensively. Upon using Musa-specific multiplex polymerase chain reaction, this strain produced a unique banding pattern, which has not previously been reported. Inoculation of this strain into Musa spp. did not result in wilt symptoms; however, the plants were stunted and root masses were significantly reduced. Furthermore, following root inoculation, the bacterium, unlike a typical Florida race 1 biovar 1 strain, was recovered from the roots and stems, indicating systemic movement. This is the first report of an R. solanacearum strain isolated in the United States that is deleterious to the growth of Musa plants.
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Presti, Alessandra Lo, Federica Del Chierico, Annamaria Altomare, Francesca Zorzi, Eleonora Cella, Lorenza Putignani, Michele Pier Luca Guarino, et al. "Exploring the genetic diversity of the 16S rRNA gene of Akkermansia muciniphila in IBD and IBS." Future Microbiology 14, no. 17 (November 2019): 1497–509. http://dx.doi.org/10.2217/fmb-2019-0175.
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Aim: The human gastrointestinal tract harbors diverse, abundant microbiota and Akkermansia muciniphila is involved in this community. The aim of this study is to characterize 16 new A. muciniphila 16S ribosomal RNA sequences selected from a metagenomic database from stools of patients with irritable bowel syndrome (IBS), inflammatory bowel diseases and control (CTRLs) subjects by a phylogenetic approach. Materials & methods: A phylogenetic approach was used to study the genetic diversity and SNPs in 16 A. muciniphila 16S ribosomal RNA sequences from stools of 107 individuals, 36 of which were patients affected by IBS, 30 by inflammatory bowel disease and 41 were CTRLs. Results: Phylogenetic analysis confirmed the subdivision into different supported clusters. An increase of variability in IBS has been identified. Conclusion: The genetic variation combined to the relative abundance, contribute to the protective role of A. muciniphila. Phylogenesis represent an additional approach to investigate genetic variability.
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Housworth, Elizabeth A., and Emília P. Martins. "Random Sampling of Constrained Phylogenies: Conducting Phylogenetic Analyses When the Phylogeny Is Partially Known." Systematic Biology 50, no. 5 (September 1, 2001): 628–39. http://dx.doi.org/10.1080/106351501753328776.
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Pleijel, F., U. Jondelius, E. Norlinder, A. Nygren, B. Oxelman, C. Schander, P. Sundberg, and M. Thollesson. "Phylogenies without roots? A plea for the use of vouchers in molecular phylogenetic studies." Molecular Phylogenetics and Evolution 48, no. 1 (July 2008): 369–71. http://dx.doi.org/10.1016/j.ympev.2008.03.024.
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Stamatakis, Alexandros. "RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies." Bioinformatics 30, no. 9 (January 21, 2014): 1312–13. http://dx.doi.org/10.1093/bioinformatics/btu033.
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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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Sansom, Robert S., Peter G. Choate, Joseph N. Keating, and Emma Randle. "Parsimony, not Bayesian analysis, recovers more stratigraphically congruent phylogenetic trees." Biology Letters 14, no. 6 (June 2018): 20180263. http://dx.doi.org/10.1098/rsbl.2018.0263.
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Reconstructing evolutionary histories requires accurate phylogenetic trees. Recent simulation studies suggest that probabilistic phylogenetic analyses of morphological data are more accurate than traditional parsimony techniques. Here, we use empirical data to compare Bayesian and parsimony phylogenies in terms of their congruence with the distribution of age ranges of the component taxa. Analysis of 167 independent morphological data matrices of fossil tetrapods finds that Bayesian trees exhibit significantly lower stratigraphic congruence than the equivalent parsimony trees. As such, taking stratigraphic data as an independent benchmark indicates that parsimony analyses are more accurate for phylogenetic reconstruction of morphological data. The discrepancy between simulated and empirical studies may result from historic data peaking practices or some complexities of empirical data as yet unaccounted for.
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Rehner, Stephen A., and Gary J. Samuels. "Molecular systematics of the Hypocreales: a teleomorph gene phylogeny and the status of their anamorphs." Canadian Journal of Botany 73, S1 (December 31, 1995): 816–23. http://dx.doi.org/10.1139/b95-327.
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Phylogenetic relationships among 40 species in the Hypocreales and Clavicipitales were inferred from sequence data obtained from the nuclear large-subunit ribosomal DNA. Cladistic analysis of these data support the monophyly of the Hypocreales, with the Clavicipitales derived from within the Hypocreales. Four groupings were resolved and are informally designated as the Hypocrea, Claviceps, Bionectria, and Nectria groups. Phylogenetic placement of teleomorphs including Melanospora and cleistothecial taxa, such as Heleococcum, Mycoarachis, and Roumegueriella, demonstrate the facility of molecular phylogenies to accommodate taxa with highly modified morphologies. Similarly, the hypocrealean origins of the anamorph species Verticillium lecanii and Acremonium chrysogenum illustrate the potential of the molecular phylogenetic approach to accommodate anamorph isolates within the context of a teleomorph phylogeny. Together these results suggest that a comprehensive classification of the Hypocreales, inclusive of teleomorph and anamorph states, is attainable through a molecular phylogenetic approach. Key words: Ascomycotina, Clavicipitaceae, Hypocreales, phylogeny, pyrenomycete, rDNA.