Journal articles: 'Maximum Parsimony Analysis'

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Weng, J. F., I. Mareels, and D. A. Thomas. "Probability Steiner trees and maximum parsimony in phylogenetic analysis." Journal of Mathematical Biology 64, no. 7 (June 25, 2011): 1225–51. http://dx.doi.org/10.1007/s00285-011-0442-4.

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Balogh, Gábor, Stephan H. Bernhart, Peter F. Stadler, and Jana Schor. "A probabilistic version of Sankoff’s maximum parsimony algorithm." Journal of Bioinformatics and Computational Biology 18, no. 01 (February 2020): 2050004. http://dx.doi.org/10.1142/s0219720020500043.

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The number of genes belonging to a multi-gene family usually varies substantially over their evolutionary history as a consequence of gene duplications and losses. A first step toward analyzing these histories in detail is the inference of the changes in copy number that take place along the individual edges of the underlying phylogenetic tree. The corresponding maximum parsimony minimizes the total number of changes along the edges of the species tree. Incorrectly determined numbers of family members however may influence the estimates drastically. We therefore augment the analysis by introducing a probabilistic model that also considers suboptimal assignments of changes. Technically, this amounts to a partition function variant of Sankoff’s parsimony algorithm. As a showcase application, we reanalyze the gain and loss patterns of metazoan microRNA families. As expected, the differences between the probabilistic and the parsimony method is moderate, in this limit of [Formula: see text], i.e. very little tolerance for deviations from parsimony, the total number of reconstructed changes is the same. However, we find that the partition function approach systematically predicts fewer gains and more loss events, showing that the data admit co-optimal solutions among which the parsimony approach selects biased representatives.

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Kasap, Server, and Khaled Benkrid. "High Performance Phylogenetic Analysis With Maximum Parsimony on Reconfigurable Hardware." IEEE Transactions on Very Large Scale Integration (VLSI) Systems 19, no. 5 (May 2011): 796–808. http://dx.doi.org/10.1109/tvlsi.2009.2039588.

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Tamura, K., D. Peterson, N. Peterson, G. Stecher, M. Nei, and S. Kumar. "MEGA5: Molecular Evolutionary Genetics Analysis Using Maximum Likelihood, Evolutionary Distance, and Maximum Parsimony Methods." Molecular Biology and Evolution 28, no. 10 (May 4, 2011): 2731–39. http://dx.doi.org/10.1093/molbev/msr121.

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Hill, Tobias, Andor Lundgren, Robert Fredriksson, and Helgi B. Schiöth. "Genetic algorithm for large-scale maximum parsimony phylogenetic analysis of proteins." Biochimica et Biophysica Acta (BBA) - General Subjects 1725, no. 1 (August 2005): 19–29. http://dx.doi.org/10.1016/j.bbagen.2005.04.027.

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Riemann, O., A. Kieneke, and W. H. Ahlrichs. "Phylogeny of Dicranophoridae (Rotifera: Monogononta) - a maximum parsimony analysis based on morphological characters." Journal of Zoological Systematics and Evolutionary Research 47, no. 1 (February 2009): 61–76. http://dx.doi.org/10.1111/j.1439-0469.2008.00482.x.

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Bhattacharya, Debashish. "Analysis of the Distribution of Bootstrap Tree Lengths Using the Maximum Parsimony Method." Molecular Phylogenetics and Evolution 6, no. 3 (December 1996): 339–50. http://dx.doi.org/10.1006/mpev.1996.0084.

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Puttick, Mark N., Joseph E. O'Reilly, Alastair R. Tanner, James F. Fleming, James Clark, Lucy Holloway, Jesus Lozano-Fernandez, et al. "Uncertain-tree: discriminating among competing approaches to the phylogenetic analysis of phenotype data." Proceedings of the Royal Society B: Biological Sciences 284, no. 1846 (January 11, 2017): 20162290. http://dx.doi.org/10.1098/rspb.2016.2290.

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Morphological data provide the only means of classifying the majority of life's history, but the choice between competing phylogenetic methods for the analysis of morphology is unclear. Traditionally, parsimony methods have been favoured but recent studies have shown that these approaches are less accurate than the Bayesian implementation of the Mk model. Here we expand on these findings in several ways: we assess the impact of tree shape and maximum-likelihood estimation using the Mk model, as well as analysing data composed of both binary and multistate characters. We find that all methods struggle to correctly resolve deep clades within asymmetric trees, and when analysing small character matrices. The Bayesian Mk model is the most accurate method for estimating topology, but with lower resolution than other methods. Equal weights parsimony is more accurate than implied weights parsimony, and maximum-likelihood estimation using the Mk model is the least accurate method. We conclude that the Bayesian implementation of the Mk model should be the default method for phylogenetic estimation from phenotype datasets, and we explore the implications of our simulations in reanalysing several empirical morphological character matrices. A consequence of our finding is that high levels of resolution or the ability to classify species or groups with much confidence should not be expected when using small datasets. It is now necessary to depart from the traditional parsimony paradigms of constructing character matrices, towards datasets constructed explicitly for Bayesian methods.

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Krauss, Siegfried L. "A Phylogeographic Analysis of Allozyme Variation among Populations of Persoonia mollis (Proteaceae)." Australian Journal of Botany 46, no. 6 (1998): 571. http://dx.doi.org/10.1071/bt97051.

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The phylogeography of 18 populations representing all nine subspecies within Persoonia mollis R.Br. (Proteaceae) was estimated from allozyme frequency data. Trees were constructed using UPGMA, maximum likelihood (CONTML) and maximum parsimony (FREQPARS) procedures. Major differences in topology between the UPGMA tree and other trees indicated that evolutionary rates are probably heterogeneous in different lineages in P. mollis, and that the UPGMA tree is inaccurate as it assumes constant evolutionary rates in all lineages. The maximum likelihood and maximum parsimony trees produced near-identical topologies. The major patterns produced by these trees included the early differentiation of subspecies maxima, the well-supported clade of all other P. mollis populations and, within this clade, the split into two clades that, although distinct, was weakly differentiated at their base. Within these two clades, there is a strong correlation between geographical distance between populations and the position of populations on the tree. These trees are consistent with a scenario of range expansion along two distinct paths in a southerly direction from northern refugia since the last glacial maximum, which is supported by data on the vegetation history of the area. These southern paths currently terminate in populations that share a hybrid zone of apparently secondary origin west of the Budawang Range.

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Fraix-Burnet, Didier, Mauro D’Onofrio, and Paola Marziani. "Maximum parsimony analysis of the effect of the environment on the evolution of galaxies." Astronomy & Astrophysics 630 (September 23, 2019): A63. http://dx.doi.org/10.1051/0004-6361/201935604.

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Context. Galaxy evolution and the effect of the environment are most often studied using scaling relations or regression analyses around a given property. However, these approaches do not take into account the complexity of the physics of the galaxies and their diversity. Aims. We here investigate the effect of the cluster environment on the evolution of galaxies through multivariate, unsupervised classification and phylogenetic analyses applied to two relatively large samples from the Wide-field Nearby Galaxy-cluster Survey (WINGS), one of cluster members and one of field galaxies (2624 and 1476 objects, respectively). Methods. These samples are the largest ones ever analysed with a phylogenetic approach in astrophysics. To be able to use the maximum parsimony (cladistics) method, we first performed a pre-clustering in 300 clusters with a hierarchical clustering technique, before applying it to these pre-clusters. All these computations used seven parameters: B − V, log(Re), nV, ⟨μ⟩e, Hβ, D4000, and log(M*). Results. We have obtained a tree for the combined samples and do not find different evolutionary paths for cluster and field galaxies. However, the cluster galaxies seem to have accelerated evolution in the sense that they are statistically more diversified from a primitive common ancestor. The separate analyses show a hint of a slightly more regular evolution of the variables for the cluster galaxies, which may indicate they are more homogeneous compared to field galaxies in the sense that the groups of the latter appear to have more specific properties. On the tree for the cluster galaxies, there is a separate branch that gathers rejuvenated or stripped-off groups of galaxies. This branch is clearly visible on the colour-magnitude diagram, going back from the red sequence towards the blue one. On this diagram, the distribution and the evolutionary paths of galaxies are strikingly different for the two samples. Globally, we do not find any dominant variable able to explain either the groups or the tree structures. Rather, co-evolution appears everywhere, and could depend itself on environment or mass. Conclusions. This study is another demonstration that unsupervised machine learning is able to go beyond simple scaling relations by taking into account several properties together. The phylogenetic approach is invaluable in tracing the evolutionary scenarios and projecting them onto any bivariate diagram without any a priori modelling. Our WINGS galaxies are all at low redshift, and we now need to go to higher redshfits to find more primitive galaxies and complete the map of the evolutionary paths of present day galaxies.

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TSCHOPP, Emanuel, and Paul UPCHURCH. "The challenges and potential utility of phenotypic specimen-level phylogeny based on maximum parsimony." Earth and Environmental Science Transactions of the Royal Society of Edinburgh 109, no. 1-2 (March 2018): 301–23. http://dx.doi.org/10.1017/s1755691018000877.

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ABSTRACTSpecimen-level phylogenetic approaches are widely used in molecular biology for taxonomic and systematic purposes. However, they have been largely ignored in analyses based on morphological traits, where phylogeneticists mostly resort to species-level analyses. Recently, a number of specimen-level studies have been published in vertebrate palaeontology. These studies indicate that specimen-level phylogeny may be a very useful tool for systematic reassessments at low taxonomic levels. Herein, we review the challenges when working with individual organisms as operational taxonomic units in a palaeontological context, and propose guidelines of how best to perform a specimen-level phylogenetic analysis using the maximum parsimony criterion. Given that no single methodology appears to be perfectly suited to resolve relationships among individuals, and that different taxa probably require different approaches to assess their systematics, we advocate the use of a number of methodologies. In particular, we recommend the inclusion of as many specimens and characters as feasible, and the analysis of relationships using an extended implied weighting approach with different downweighting functions. Resulting polytomies should be explored using a posteriori pruning of unstable specimens, and conflicting tree topologies between different iterations of the analysis should be evaluated by a combination of support values such as jackknifing and symmetric resampling. Species delimitation should be consistent among the ingroup and based on a reproducible approach. Although time-consuming and methodologically challenging, specimen-level phylogenetic analysis is a highly useful tool to assess intraspecific variability and provide the basis for a more informed and accurate creation of species-level operational taxonomic units in large-scale systematic studies. It also has the potential to inform us about past speciation processes, morphological trait evolution, and their potential intrinsic and extrinsic drivers in pre-eminent detail.

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Sookias, Roland B. "The relationships of the Euparkeriidae and the rise of Archosauria." Royal Society Open Science 3, no. 3 (March 2016): 150674. http://dx.doi.org/10.1098/rsos.150674.

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For the first time, a phylogenetic analysis including all putative euparkeriid taxa is conducted, using a large data matrix analysed with maximum parsimony and Bayesian analysis. Using parsimony, the putative euparkeriid Dorosuchus neoetus from Russia is the sister taxon to Archosauria + Phytosauria. Euparkeria capensis is placed one node further from the crown, and forms a euparkeriid clade with the Chinese taxa Halazhaisuchus qiaoensis and ‘ Turfanosuchus shageduensis ’ and the Polish taxon Osmolskina czatkowicensis . Using Bayesian methods, Osmolskina and Halazhaisuchus are sister taxa within Euparkeriidae, in turn sister to ‘ Turfanosuchus shageduensis ’ and then Euparkeria capensis . Dorosuchus is placed in a polytomy with Euparkeriidae and Archosauria + Phytosauria. Although conclusions remain tentative owing to low node support and incompleteness, a broad phylogenetic position close to the base of Archosauria is confirmed for all putative euparkeriids, and the ancestor of Archosauria +Phytosauria is optimized as similar to euparkeriids in its morphology. Ecomorphological characters and traits are optimized onto the maximum parsimony strict consensus phylogeny presented using squared change parsimony. This optimization indicates that the ancestral archosaur was probably similar in many respects to euparkeriids, being relatively small, terrestrial, carnivorous and showing relatively cursorial limb morphology; this Bauplan may have underlain the exceptional radiaton and success of crown Archosauria.

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Crespo, Ana, and Oscar F. Cubero. "A Molecular Approach to the Circumscription and Evaluation of Some Genera Segregated from Parmelia S. Lat." Lichenologist 30, no. 4-5 (July 1998): 369–80. http://dx.doi.org/10.1006/lich.1998.0156.

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AbstractNew sequences have been produced of the ITS rDNA region of twenty-nine species of Parmeliaceae and analysed by neighbour-joining maximum likelihood distance analysis, and maximum parsimony analysis. Twelve monophyletic groups have been identified, most of which correspond to proposed generic segregated from Parmelia s. lat. Parmelia and Parmelina, Melanelia, and Punctelia appear as independent monophyletic groups; the type species of the two latter genera were, however, not included in the analysis. The parsimony analysis does not support Xanthoparmelia as a monophyletic group separate from Neofuscelia, and Rimelia reticulate is nested within Parmotrema. Parmelinopsis horrescens is more closely related to Hypotrachyna revolute than to Parmelina. Genetic distance values suggest that Flavoparmelia caperata is closer to Parmotrema than to other taxa included, and that Platismatia glauca and Hypogymnia tubulosa are closer to Parmelia s. lat. than to the Physciaceae. However, there is no conclusive support for any of thelatter groupings in the parsimony analysis. We conclude that the ITS region contains valuable information for studying generic delimitations within the family Parmeliaceae, but our study suggests that this region will not conclusively resolve within-family relationships in this group.

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NASCIMENTO, ELYNTON ALVES DO, TAMIRES DINIZ BRESSAN, and MILADA BOCAKOVA. "Currhaeus, a new genus of net-winged beetles and phylogenetic analysis of Eurrhacini (Coleoptera: Lycidae: Lycinae)." Zootaxa 4869, no. 3 (November 3, 2020): 387–403. http://dx.doi.org/10.11646/zootaxa.4869.3.5.

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A new genus of Neotropical Lycidae, Currhaeus gen. nov., is herein proposed as the second Eurrhacini genus lacking parameres in male genitalia. Seven new species are described: Currhaeus striatus sp. nov., C. nigroapicalis sp. nov., C. championi sp. nov., C. tabascensis sp. nov., C. ruschii sp. nov., C. polegattoi sp. nov., and C. paranaensis sp. nov. Illustrations of diagnostic characters and a key to species identification are presented. Parsimony and maximum likelihood analyses of morphological data demonstrated that Currhaeus gen. nov. belongs in the crown Eurrhacini. Implied weighting parsimony trees recovered Currhaeus as sister to Eurrhacus Waterhouse.

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Lyson, Tyler R., and Walter G. Joyce. "A new species of Palatobaena (Testudines: Baenidae) and a maximum parsimony and Bayesian phylogenetic analysis of Baenidae." Journal of Paleontology 83, no. 3 (May 2009): 457–70. http://dx.doi.org/10.1666/08-172.1.

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New Palatobaena material from the Hell Creek Formation (Maastrichtian), including the first skull and shell association, from southwestern North Dakota represents a new species named herein Palatobaena cohen. the material consists of 4 skulls, 2 lower jaws, and 2 shells and represents a true biological population (spatially and temporally restricted), which provides unprecedented access to ontogenetic and other intraspecific variation found in this taxon. the skull's round shape and lack of a lingual ridge on the greatly expanded triturating surface indicate its Palatobaena affinities, but it differs from both previously existing Palatobaena taxa in a number of features. the addition of shell characters to the most inclusive baenid phylogenetic analyses (Maximum parsimony and Bayesian) to date indicate that Pa. cohen is sister taxon to the other Palatobaena taxa. Notably, both the maximum parsimony analysis and Bayesian analysis provide strong support for Plesiobaena antiqua as sister to the Palatobaena clade. in addition, both analyses provide strong support for Stygiochelys estesi as sister to the Eocene clade of Baena arenosa and Chisternon undatum, which significantly reduces this clades' ghost lineage. the baenid topology reveals a demonstrably homoplastic trend towards the reduction of the temporal emargination and unique thickening of the posterior portion of the parietals that corresponds with the K/T boundary and is hypothesized to have provided limited protection from increasingly effective mammalian predators.

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Joshi, Anagha, and Berthold Göttgens. "Maximum parsimony analysis of gene expression profiles permits the reconstruction of developmental cell lineage trees." Developmental Biology 353, no. 2 (May 2011): 440–47. http://dx.doi.org/10.1016/j.ydbio.2011.02.013.

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Steel, Mike, Larry Goldstein, and Michael S. Waterman. "A central limit theorem for the parsimony length of trees." Advances in Applied Probability 28, no. 04 (December 1996): 1051–71. http://dx.doi.org/10.1017/s0001867800027555.

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In phylogenetic analysis it is useful to study the distribution of the parsimony length of a tree under the null model, by which the leaves are independently assigned letters according to prescribed probabilities. Except in one special case, this distribution is difficult to describe exactly. Here we analyze this distribution by providing a recursive and readily computable description, establishing large deviation bounds for the parsimony length of a fixed tree on a single site and for the minimum length (maximum parsimony) tree over several sites. We also show that, under very general conditions, the former distribution converges asymptotically to the normal, thereby settling a recent conjecture. Furthermore, we show how the mean and variance of this distribution can be efficiently calculated. The proof of normality requires a number of new and recent results, as the parsimony length is not directly expressible as a sum of independent random variables, and so normality does not follow immediately from a standard central limit theorem.

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Steel, Mike, Larry Goldstein, and Michael S. Waterman. "A central limit theorem for the parsimony length of trees." Advances in Applied Probability 28, no. 4 (December 1996): 1051–71. http://dx.doi.org/10.2307/1428164.

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In phylogenetic analysis it is useful to study the distribution of the parsimony length of a tree under the null model, by which the leaves are independently assigned letters according to prescribed probabilities. Except in one special case, this distribution is difficult to describe exactly. Here we analyze this distribution by providing a recursive and readily computable description, establishing large deviation bounds for the parsimony length of a fixed tree on a single site and for the minimum length (maximum parsimony) tree over several sites. We also show that, under very general conditions, the former distribution converges asymptotically to the normal, thereby settling a recent conjecture. Furthermore, we show how the mean and variance of this distribution can be efficiently calculated. The proof of normality requires a number of new and recent results, as the parsimony length is not directly expressible as a sum of independent random variables, and so normality does not follow immediately from a standard central limit theorem.

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Ray, Jesse W., Richard B. King, Melvin R. Duvall, Jace W. Robinson, Collin P. Jaeger, Michael J. Dreslik, Bradley J. Swanson, and Diane Mulkerin. "Genetic Analysis and Captive Breeding Program Design for the Eastern Massasauga Sistrurus catenatus catenatus." Journal of Fish and Wildlife Management 4, no. 1 (June 1, 2013): 104–13. http://dx.doi.org/10.3996/032012-jfwm-026.

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Abstract The eastern massasauga Sistrurus catenatus catenatus is a declining species for which a captive breeding program was established in 2006. To effectively manage wild and captive populations, an understanding of genetic diversity within the species is necessary. We analyzed mitochondrial DNA sequences of 186 individuals: 109 wild snakes from 34 U.S. and Canadian counties and districts, all 52 breeding program members (23 of known and 29 of unknown origin), 18 other captives of unknown origin, and 7 outgroup representatives of desert massasauga S. c. edwardsii, and western massasauga, S. c. tergeminus. Statistical parsimony, maximum likelihood, and maximum parsimony analyses all identified eastern massasaugas as divergent from western and desert massasaugas. We found 18 different haplotypes among eastern massasaugas, comprising three geographically and genetically differentiated NADH dehydrogenase II (ND2) subunits that potentially reflect post-Pleistocene range expansion from unglaciated into formerly glaciated regions. Snakes of unknown origin could all be assigned unambiguously to these ND2 subunits. To maintain natural genetic variation, preserve diversity in captive lineages, and allow future augmentation or reintroduction, the Association of Zoos and Aquariums is managing these three geographic ND2 subunits separately within the Eastern Massasauga Species Survival Plan breeding program.

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Holden, Clare Janaki. "Bantu language trees reflect the spread of farming across sub-Saharan Africa: a maximum-parsimony analysis." Proceedings of the Royal Society of London. Series B: Biological Sciences 269, no. 1493 (April 22, 2002): 793–99. http://dx.doi.org/10.1098/rspb.2002.1955.

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Ali, Mohammad Ajmal, M. Oliur Rahman, Joongku Lee, Fahad Al Hemaid, Sidanand V. Kambhar, Meena Elangbam, and Arun Bahadur Gurung. "Dissecting molecular evolutionary relationship of Krameriaceae inferred from phylotranscriptomic analysis." Bangladesh Journal of Plant Taxonomy 27, no. 2 (December 11, 2020): 427–33. http://dx.doi.org/10.3329/bjpt.v27i2.50677.

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The systematic relationships of Krameriaceae have changed considerably. The phylotranscriptomic data sets provide highly informative data for resolving deeper‐level phylogenetic relationships. The phylotranscriptomic analyses to infer evolutionary relationships of Krameriaceae in the order Zygophyllales using the Minimum Evolution, Maximum Parsimony and Maximum Likelihood methods recovered similar topology and taxon proximity. Under the Zygophyllales clade, Krameria lanceolata Torr. of the family Krameriaceae nested with Tribulus eichlerianus K.L. Wilson and Larrea tridentata (Sessé & Moc. ex DC.) Coville belonging to the family Zygophyllaceae with strong nodal support. The phylotranscriptomic analyses suggest that the family Krameriaceae is sister to Zygophyllaceae. Bangladesh J. Plant Taxon. 27(2): 427-433, 2020 (December)

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LI, MING-HE, GUO-QIANG ZHANG, ZHONG-JIAN LIU, and SI-REN LAN. "Revision of Hygrochilus (Orchidaceae: Epidendroideae: Aeridinae) and a molecular phylogenetic analysis." Phytotaxa 159, no. 4 (February 18, 2014): 256. http://dx.doi.org/10.11646/phytotaxa.159.4.2.

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Hygrochilus and Sedirea are genera of orchids with only three species endemic to Asia. An analysis of ITS and five plastid regions using parsimony, maximum likelihood, and Bayesian methods obtain clear evidence that Sedirea is nested within and should be considered synonymous with Hygrochilus. We adopt a broadly defined Hygrochilus characterized by possession of four pollinia. A new combination, namely, Hygrochilus japonica, and a new species, namely, Hygrochilus tsii (Orchidaceae: Epidedroideae: Aeridinae), are proposed.

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Kasalicky, Thomas, Heidi Döring, Gerhard Rambold, and Mats Wedin. "A comparison of ITS and LSU nrDNA phylogenies of Fulgensia (Teloschistaceae, Lecanorales), a genus of lichenised ascomycetes." Canadian Journal of Botany 78, no. 12 (December 1, 2000): 1580–89. http://dx.doi.org/10.1139/b00-126.

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The phylogeny of the lichen genus Fulgensia Massal. & De Not. (Teloschistaceae, Lecanorales) is analysed using maximum parsimony and neighbor joining analyses of nuclear ITS and partial large subunit nuclear ribosomal DNA (nrDNA) sequences. Three matrices were analysed with maximum parsimony; an internal transcribed spacer nrDNA matrix, a large subunit nrDNA matrix, and a combined data set. The internal transcribed spacer region contributes 70% of the informative sites to the combined data set. The topology of the trees resulting from the analysis of the internal transcribed spacer region is identical to the tree topology resulting from the combined analysis, but it shows less resolution at basal parts of the tree. Two sites for putative spliceosomal introns in the large subunit nrDNA, at position 808 and 914 (relative to Saccharomyces cerevisiae) are reported. Fulgensia, as currently understood, is polyphyletic and some species have to be excluded. The molecular analyses identified groups of species within the genus that are also supported by anatomical and morphological characters. The results of the analyses are compared with existing classification concepts based on morphological and anatomical data.Key words: LSU, ITS, nrDNA, introns, Fulgensia, phylogeny.

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Guo, Peng, Ermi Zhao, Yaping Zhang, and Junfeng Pang. "A Re-analysis of the phylogeny of the genus Protobothrops (Reptilia: Viperidae), with particular reference to the systematic position of P. xiangchengensis." Amphibia-Reptilia 27, no. 3 (2006): 433–39. http://dx.doi.org/10.1163/156853806778189954.

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AbstractBased on three mitochondrial gene fragments (12S rRNA, 16S rRNA, cytochrome b), the phylogeny of Protobothrops is re-analyzed using Maximum-parsimony (MP), Maximum-likelihood (ML), and Bayesian (BI) approaches. All phylogenetic analyses indicate that all putative Protobothrops species examined formed a monophyletic group; however, the intrageneric relationships are still unresolved. The phylogenetic relationships further confirm that P. xiangchengensis is a valid species distinct from P. mucrosquamatus and that it is closely related to P. jerdonii.

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Guillemaud, Thomas, Maria L. Cancela, Pedro Afonso, Telmo Morato, Ricardo S. Santos, and Peter Wirtz. "Molecular insights into the taxonomic status of Coris atlantica (Pisces: Labridae)." Journal of the Marine Biological Association of the United Kingdom 80, no. 5 (October 2000): 929–33. http://dx.doi.org/10.1017/s0025315400002915.

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A molecular genetic analysis of Coris julis from different sites in the Mediterranean and the Atlantic and C. atlantica from the Cabo Verde Islands was applied to infer phylogenetic relationships between the taxa. More precisely, partial 12S mitochondrial rDNA sequence data were used in maximum parsimony, neighbour-joining, and maximum likelihood analysis to generate phylogenetic trees. The polymorphism observed indicated an important differentiation between the C. atlantica and C. julis specimens and supported the existence of two different species.

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Peng, Yu-lan, Yu Zhang, Xin-fen Gao, Lin-jing Tong, Liang Li, Ren-Yuan Li, Zhang-Ming Zhu, and Jun-ren Xian. "A phylogenetic analysis and new delimitation of Crepidiastrum (Asteraceae, tribe Cichorieae)." Phytotaxa 159, no. 4 (February 18, 2014): 241. http://dx.doi.org/10.11646/phytotaxa.159.4.1.

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The systematic position of Paraixeris humifusa (Asteraceae) is hard to define, because the circumscription of Paraixeris, Youngia and Crepidiastrum, three closely related genera in subtribe Crepidinae (Cichorieae), is not clear. This paper reports on the relationships between 30 species in subtribe Crepidinae, based on an analysis of nucleotides from one nuclear (ITS) and three chloroplast DNA regions ( trnL-F, rps16 and atpB-rbcL). The phylogenetic analyses used maximum parsimony with maximum likelihood inference. The monophyly of Crepidiastrum in the most recent generic classification of Shih & Kilian (2011) is explored. The results show that 12 species in Crepidiastrum constitute a monophyletic group, and that Paraixeris humifusa should be treated as Youngia humifusa.

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Downie, Stephen R., Deborah S. Katz-Downie, Feng-Jie Sun, and Chang-Shook Lee. "Phylogeny and biogeography of Apiaceae tribe Oenantheae inferred from nuclear rDNA ITS and cpDNA psbI–5′trnK(UUU) sequences, with emphasis on the North American Endemics clade." Botany 86, no. 9 (September 2008): 1039–64. http://dx.doi.org/10.1139/b08-055.

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Intergeneric phylogenetic relationships within Apiaceae tribe Oenantheae were investigated using sequence data from the chloroplast DNA psbI–5′trnK(UUU) and nuclear ribosomal DNA internal transcribed spacer regions. One hundred and thirty-one accessions were examined, representing all 17 genera of the tribe and approximately one-half of its species. The cpDNA region includes four intergenic spacers and the rps16 intron and these noncoding loci were analyzed separately to assess their relative utility for resolving relationships. Separate maximum parsimony analyses of the entire psbI–5′trnK(UUU) and ITS regions, each with and without scored indels, yielded concordant trees. Phylogenies derived from maximum parsimony, Bayesian, or maximum likelihood analyses of combined chloroplast and nuclear DNA sequences for 82 accessions were highly resolved, well supported, and consistent. Among the five noncoding loci examined, the trnQ(UUG)–5′rps16 and 3′rps16–5′trnK(UUU) intergenic spacers are the most variable, with the latter contributing the greatest total number of parsimony informative characters relative to its size. The North American genera Atrema , Cynosciadium , Daucosma , Limnosciadium , Neogoezia , Oxypolis , Ptilimnium , and Trepocarpus ally with the western hemispheric and Australasian genus Lilaeopsis in a strongly supported North American Endemics clade that is a sister group to a clade composed primarily of Old World taxa ( Berula sensu lato, Cryptotaenia , Helosciadium , and Sium ). Oxypolis and Ptilimnium are not monophyletic, with the rachis-leaved members of each comprising a clade separate from their compound-leaved congeners. Dispersal-vicariance analysis suggests that the ancestors of the North American Endemics clade probably originated in Canada and the USA or in a broader ancestral area including Mexico and South America.

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Giribet, Gonzalo, Salvador Carranza, Marta Riutort, Jaume Baguñà, and Carles Ribera. "Internal phylogeny of the Chilopoda (Myriapoda, Arthropoda) using complete 18S rDNA and partial 28S rDNA sequences." Philosophical Transactions of the Royal Society of London. Series B: Biological Sciences 354, no. 1380 (January 29, 1999): 215–22. http://dx.doi.org/10.1098/rstb.1999.0373.

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The internal phylogeny of the ‘myriapod’ class Chilopoda is evaluated for 12 species belonging to the five extant centipede orders, using 18S rDNA complete gene sequence and 28S rDNA partial gene sequence data. Equally and differentially weighted parsimony, neighbour–joining and maximum–likelihood were used for phylogenetic reconstruction, and bootstrapping and branch support analyses were performed to evaluate tree topology stability. The results show that the Chilopoda constitute a monophyletic group that is divided into two lines, Notostigmophora (= Scutigeromorpha) and Pleurostigmophora, as found in previous morphological analyses. The Notostigmophora are markedly modified for their epigenic mode of life. The first offshoot of the Pleurostigmophora are the Lithobiomorpha, followed by the Craterostigmomorpha and by the Epimorpha s. str. (= Scolopendromorpha + Geophilomorpha), although strong support for the monophyly of the Epimorpha s. lat. (= Craterostigmomorpha + Epimorpha s. str.) is only found in the differentially weighted parsimony analysis.

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Yang, Z., S. Kumar, and M. Nei. "A new method of inference of ancestral nucleotide and amino acid sequences." Genetics 141, no. 4 (December 1, 1995): 1641–50. http://dx.doi.org/10.1093/genetics/141.4.1641.

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Abstract A statistical method was developed for reconstructing the nucleotide or amino acid sequences of extinct ancestors, given the phylogeny and sequences of the extant species. A model of nucleotide or amino acid substitution was employed to analyze data of the present-day sequences, and maximum likelihood estimates of parameters such as branch lengths were used to compare the posterior probabilities of assignments of character states (nucleotides or amino acids) to interior nodes of the tree; the assignment having the highest probability was the best reconstruction at the site. The lysozyme c sequences of six mammals were analyzed by using the likelihood and parsimony methods. The new likelihood-based method was found to be superior to the parsimony method. The probability that the amino acids for all interior nodes at a site reconstructed by the new method are correct was calculated to be 0.91, 0.86, and 0.73 for all, variable, and parsimony-informative sites, respectively, whereas the corresponding probabilities for the parsimony method were 0.84, 0.76, and 0.51, respectively. The probability that an amino acid in an ancestral sequence is correctly reconstructed by the likelihood analysis ranged from 91.3 to 98.7% for the four ancestral sequences.

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Michu, E. "A short guide to phylogeny reconstruction." Plant, Soil and Environment 53, No. 10 (January 7, 2008): 442–46. http://dx.doi.org/10.17221/2194-pse.

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This review is a short introduction to phylogenetic analysis. Phylogenetic analysis allows comprehensive understanding of the origin and evolution of species. Generally, it is possible to construct the phylogenetic trees according to different features and characters (e.g. morphological and anatomical characters, RAPD patterns, FISH patterns, sequences of DNA/RNA and amino acid sequences). The DNA sequences are preferable for phylogenetic analyses of closely related species. On the other hand, the amino acid sequences are used for phylogenetic analyses of more distant relationships. The sequences can be analysed using many computer programs. The methods most often used for phylogenetic analyses are neighbor-joining (NJ), maximum parsimony (MP), maximum likelihood (ML) and Bayesian inference.

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TENNAKOON, DANUSHKA S., RUNGTIWA PHOOKAMSAK, DHANUSHKA N. WANASINGHE, JUN-BO YANG, SAISAMORN LUMYONG, and KEVIN D. HYDE. "Morphological and phylogenetic insights resolve Plenodomus sinensis (Leptosphaeriaceae) as a new species." Phytotaxa 324, no. 1 (October 6, 2017): 73. http://dx.doi.org/10.11646/phytotaxa.324.1.5.

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Plenodomus species were collected from Tamarindus indica L. (Fabaceae) and Plukenetia volubilis L. (Euphorbiaceae) in Yunnan Province, China and subjected to morphological and molecular analysis. Morphologically novel collections comprise unique characters in having mucilaginous globoid-shaped apical and basal appendages (1.5–1.8 μm) and wider third cell from the apex in ascospores. Phylogenetic analysis (Maximum-likelihood, maximum-parsimony and Bayesian analyses) of combined LSU, SSU and ITS sequence data reveal that these collections differ from all other species in the genus. Therefore, a novel species, Plenodomus sinensis is introduced in this study. The new species is compared with other Plenodomus species and a comprehensive description and micrographs are provided.

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Koenemann, Stefan, and Frederick R. Schram. "The limitations of ontogenetic data in phylogenetic analyses." Contributions to Zoology 71, no. 1-3 (2002): 47–65. http://dx.doi.org/10.1163/18759866-0710103005.

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The analysis of consecutive ontogenetic stages, or events, introduces a new class of data to phylogenetic systematics that are distinctly different from traditional morphological characters and molecular sequence data. Ontogenetic event sequences are distinguished by varying degrees of both a collective and linear type of dependence and, therefore, violate the criterion of character independence. We applied different methods of phylogenetic reconstruction to ontogenetic data including maximum parsimony and distance (cluster) analyses. Two different data sets were investigated: (1) four simulated ontogenies with defined phylogenies of six hypothetical taxa, and (2) a set of “real” data comprising sequences of 29 ontogenetic events from 11 vertebrate taxa. We confirm that heterochronic event sequences do contain a phylogenetic signal. However, based on our results we argue that maximum parsimony is a biased method to analyze such developmental sequence data. Ontogenetic events require a special analytical algorithm that would not neglect instances of chronological (horizontal) dependence of this type of data. One coding method, “event-pairing”, appeared to fulfill this requirement in the vertebrate analyses. However, to accurately analyze ontogenetic sequence data, a more sophisticated coding method and algorithm are needed, for example, measuring distances of dependent events.

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Achurra, Ainara, M. Arantzazu Elejalde, and Pilar Rodriguez. "Phylogenetic analysis of oligochaete Tubificinae (Annelida:Clitellata) based on mitochondrial sequence data." Invertebrate Systematics 25, no. 3 (2011): 208. http://dx.doi.org/10.1071/is10040.

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Partial sequences of the mitochondrial genes 16S rRNA and cytochrome c oxidase subunit I (COI) were used (1) to resolve the internal relationships of the subfamily Tubificinae (Annelida : Clitellata) and (2) to test the existence of cryptic species within the stygobiont oligochaete Troglodrilus galarzai (Giani & Rodriguez, 1988). Phylogenies were estimated using maximum likelihood, Bayesian inference and parsimony. Although trees were incompletely resolved at intergeneric level, a close relationship between Heterochaeta Claparède, 1863 and Troglodrilus Juget, des Châtelliers & Rodriguez was revealed, and the separation of Lophochaeta ignota Štolc, 1886 and Heterochaeta costata Claparède, 1863 from Tubifex Lamarck, 1816 was corroborated by mitochondrial molecular data. Maximum genetic divergence between allopatric populations of T. galarzai was 18% for COI (uncorrected pairwise distance), suggesting cryptic speciation within this nominal species.

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WANG, RUN-ZHI, ZHI-YONG YUAN, CHANG-ZHI HAN, and CHANG-LIN ZHAO. "Morphological and molecular identification of a new species of Cinereomyces (Polyporales, Basidiomycota) in southern China." Phytotaxa 459, no. 1 (September 9, 2020): 51–60. http://dx.doi.org/10.11646/phytotaxa.459.1.5.

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A new poroid wood-inhabiting fungal species, Cinereomyces fimbriatus sp. nov., is proposed based on morphological and molecular characteristics. The species is characterized by resupinate, brittle basidiomata with cream pore surface, a dimitic hyphal system with clamped generative hyphae, broad allantoid, hyaline, thin-walled, smooth basidiospores (3.6–4.6 × 0.8–1.1 µm). The internal transcribed spacer (ITS) region of nuclear ribosomal RNA gene sequences of the studied samples were generated, and phylogenetic analyses were performed with maximum likelihood, maximum parsimony and bayesian inference methods. The phylogenetic analysis based on ITS sequences showed that C. fimbriatus formed a monophyletic lineage with strong supports (100% BS, 100% BT, 1.00 BPP) sister to C. lindbladii.

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Ascarrunz, Eduardo, Julien Claude, and Walter G. Joyce. "Estimating the phylogeny of geoemydid turtles (Cryptodira) from landmark data: an assessment of different methods." PeerJ 7 (August 22, 2019): e7476. http://dx.doi.org/10.7717/peerj.7476.

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Background In the last 20 years, a general picture of the evolutionary relationships between geoemydid turtles (ca. 70 species distributed over the Northern hemisphere) has emerged from the analysis of molecular data. However, there is a paucity of good traditional morphological characters that correlate with the phylogeny, which are essential for the robust integration of fossil and molecular data. Part of this problem might be due to intrinsic limitations of traditional discrete characters. Here, we explore the use of continuous data in the form of 3D coordinates of homologous landmarks on the turtle shell for phylogenetic inference and the phylogenetic placement of single species on a scaffold molecular tree. We focus on the performance yielded by sampling the carapace and/or plastral lobes and using various phylogenetic methods. Methods We digitised the landmark coordinates of the carapace and plastron of 42 and 46 extant geoemydid species, respectively. The configurations were superimposed and we estimated the phylogenetic tree of geoemydids with landmark analysis under parsimony, traditional Farris parsimony, unweighted squared-change parsimony, maximum likelihood with a Brownian motion model, and neighbour-joining on a matrix of pairwise Procrustes distances. We assessed the performance of those analyses by comparing the trees against a reference phylogeny obtained from seven molecular markers. For comparisons between trees we used difference measures based on quartets and splits. We used the same reference tree to evaluate phylogenetic placement performance by a leave-one-out validation procedure. Results Whatever method we used, similarity to the reference phylogeny was low. The carapace alone gave slightly better results than the plastron or the complete shell. Assessment of the potential for placement of single species on the reference tree with landmark data gave much better results, with similar accuracy and higher precision compared to the performance of discrete characters with parsimony.

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Castagnone-Sereno, Philippe, Flavie Vanlerberghe-Masutti, and Frederic Leroy. "Genetic polymorphism between and within Meloidogyne species detected with RAPD markers." Genome 37, no. 6 (December 1, 1994): 904–9. http://dx.doi.org/10.1139/g94-129.

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Genetic analyses were conducted on root-knot nematode populations belonging to the four major species of the genus Meloidogyne and originating from many countries throughout the world. Discrete genetic markers used in this study were random genomic DNA sequences amplified by the polymerase chain reaction (RAPD). Primers of 17–30 nucleotides with 30–55% G + C content were tested. Five of them generated a total of 74 scorable markers that provided reliable polymorphisms both between and within species. Using RAPD patterns alone or in combination, all the Meloidogyne species and populations studied could be unambiguously discriminated. Based on the presence or absence of bands, maximum-parsimony analysis of the data resulted in clustering of species and populations congruent with previous isoenzymatic and molecular data. The resulting tree confirmed the early divergence of M. hapla from the other species and also that M. arenaria is closer to M. javanica than it is to M. incognita. The bootstrap analysis significantly supported most of the specific branching observed in the topology but did not identify the three M. arenaria populations as a monophyletic group.Key words: Meloidogyne spp., parsimony, phylogenetic analysis, RAPD.

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Lee, Michael S. Y., and Trevor H. Worthy. "Likelihood reinstates Archaeopteryx as a primitive bird." Biology Letters 8, no. 2 (October 26, 2011): 299–303. http://dx.doi.org/10.1098/rsbl.2011.0884.

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The widespread view that Archaeopteryx was a primitive (basal) bird has been recently challenged by a comprehensive phylogenetic analysis that placed Archaeopteryx with deinonychosaurian theropods. The new phylogeny suggested that typical bird flight (powered by the front limbs only) either evolved at least twice, or was lost/modified in some deinonychosaurs. However, this parsimony-based result was acknowledged to be weakly supported. Maximum-likelihood and related Bayesian methods applied to the same dataset yield a different and more orthodox result: Archaeopteryx is restored as a basal bird with bootstrap frequency of 73 per cent and posterior probability of 1. These results are consistent with a single origin of typical (forelimb-powered) bird flight. The Archaeopteryx –deinonychosaur clade retrieved by parsimony is supported by more characters (which are on average more homoplasious), whereas the Archaeopteryx –bird clade retrieved by likelihood-based methods is supported by fewer characters (but on average less homoplasious). Both positions for Archaeopteryx remain plausible, highlighting the hazy boundary between birds and advanced theropods. These results also suggest that likelihood-based methods (in addition to parsimony) can be useful in morphological phylogenetics.

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WHITTINGTON, I. D., M. R. DEVENEY, J. A. T. MORGAN, L. A. CHISHOLM, and R. D. ADLARD. "A preliminary phylogenetic analysis of the Capsalidae (Platyhelminthes: Monogenea: Monopisthocotylea) inferred from large subunit rDNA sequences." Parasitology 128, no. 5 (May 2004): 511–19. http://dx.doi.org/10.1017/s0031182004004901.

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Phylogenetic relationships within the Capsalidae (Monogenea) were examined using large subunit ribosomal DNA sequences from 17 capsalid species (representing 7 genera, 5 subfamilies), 2 outgroup taxa (Monocotylidae) plusUdonella caligorum(Udonellidae). Trees were constructed using maximum likelihood, minimum evolution and maximum parsimony algorithms. An initial tree, generated from sequences 315 bases long, suggests that Capsalinae, Encotyllabinae, Entobdellinae and Trochopodinae are monophyletic, but that Benedeniinae is paraphyletic. Analyses indicate thatNeobenedenia, currently in the Benedeniinae, should perhaps be placed in a separate subfamily. An additional analysis was made which omitted 3 capsalid taxa (for which only short sequences were available) and all outgroup taxa because of alignment difficulties. Sequence length increased to 693 bases and good branch support was achieved. The Benedeniinae was again paraphyletic. Higher-level classification of the Capsalidae, evolution of the Entobdellinae and issues of species identity inNeobenedeniaare discussed.

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Lavery, S. "Electrophoretic analysis of Phylogenetic relationships among Australian Carcharhinid Sharks." Marine and Freshwater Research 43, no. 1 (1992): 97. http://dx.doi.org/10.1071/mf9920097.

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The phylogenetic relationships of 17 species of carcharhinid sharks and four other closely related species were examined by allozyme electrophoresis. Genetic data from 38 loci were used in three different techniques of phylogeny reconstruction (including both phenetic and cladistic methods). The two most instructive trees were produced by using maximum parsimony (PAUP) and Distance Wagner procedures. There was evidence that both the genus Carcharhinus and the family Carcharhinidae may actually comprise paraphyletic groups. A number of proposed morphological species groups were shown to also be closely related genetically. These included C. limbatus/C. tilstoni/C. amblyrhynchoides, C. melanopterus/C. cautus, and C. amblyrhynchos/C. albimarginatus. There appears to be a distinct lineage within the Carcharhinidae that may be characterized by the absence of the interdorsal ridge.

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Kelch, Dean G. "Phylogenetic assessment of the monotypic genera Sundacarpus and Manoao (Coniferales: Podocarpaceae) utilising evidence from 18S rDNA sequences." Australian Systematic Botany 15, no. 1 (2002): 29. http://dx.doi.org/10.1071/sb01002.

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The Podocarpaceae are the most morphologically diverse of conifer families. A taxonomic trend has resulted in recognising this diversity via smaller generic groupings, including several monotypes. A phylogenetic assessment of the monotypic genera Sundacarpus and Manoao was conducted employing maximum parsimony the analysis of sequence data from 18S-ribosomal DNA from 34 gymnosperm taxa, including 29 Podocarpaceae. In resulting trees, there is high bootstrap support for Podocarpaceae, including Phyllocladus, but the order of deep branches within the family is equivocal. Prumnopitys (Sundacarpus) amara (Blume) de Laub. and four other Prumnopitys spp. comprise a clade with a bootstrap value of 100%, supporting the retention of Sundacarpus as a section of Prumnopitys. Lagarostrobos franklinii (Hook.f.) Quinn and L. (Manoao) colensoi (Hook.) Quinn comprise a clade with equivocal bootstrap support, echoing previous results from parsimony analysis of morphological data. A conservative approach (i.e. one avoiding unnecessary monotypes) favours the retention of L. colensoi in Lagarostrobos, pending further evidence of relationships within the group.

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Smith, James F. "A Phylogenetic Analysis of Tribes Beslerieae and Napeantheae (Gesneriaceae) and Evolution of Fruit Types: Parsimony and Maximum Likelihood Analyses of ndhF Sequences." Systematic Botany 25, no. 1 (January 2000): 72. http://dx.doi.org/10.2307/2666674.

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Hardig, T. M., C. K. Anttila, and S. J. Brunsfeld. "A Phylogenetic Analysis of Salix (Salicaceae) Based on matK and Ribosomal DNA Sequence Data." Journal of Botany 2010 (December 28, 2010): 1–12. http://dx.doi.org/10.1155/2010/197696.

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The genus Salix has proven a fertile taxon for a host of evolutionary and ecological studies, yet much work remains in the development of a definitive phylogenetic context for those studies. We performed phylogenetic analyses, using both maximum likelihood and maximum parsimony techniques, of chloroplast-encoded matK and nuclear-encoded ribosomal DNA (rDNA) gene sequences, gathered from specimens deemed representative of the existing subgeneric classification, with the objective of identifying and elaborating the phylogenetic relationships within Salix. Comparisons between the two phylogenetic hypotheses indicate a high degree of polyphyly in the matK-based phylogeny. This we attribute to the effects of hybridization, introgression, and lineage sorting. Comparisons with previous molecule-based phylogenetic hypotheses indicate a fair degree of congruence and all are unanimous in placing Chosenia arbutifolia within the genus Salix. The phylogenetic analysis of our ITS data set has produced results that generally support the most-recent infrageneric classification.

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Christy, Buti Y., and Dewi I. Roesma Dahelmi. "Phylogenetic Analysis of Tetragonula Minangkabau and Other Species Using Cytochrome B Gene." Journal of Apicultural Science 63, no. 1 (June 1, 2019): 117–24. http://dx.doi.org/10.2478/jas-2019-0008.

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AbstractTetragonula a genus in the Meliponini tribe (Apidae), is difficult to identify due to the many cryptic species. As technology develops, molecular taxonomic studies are used to help identify species with limited morphological characteristics. This study presents an analysis of the phylogenetic relationship between several species in the Tetragonula genus based on the sequences of the cytochrome b gene. Maximum parsimony, neighbor joining, maximum likelihood and minimum evolution methods were used to construct phylogenetic trees. The sequence divergence between T. minangkabau collected from Limau Manis and Ulu Gadut is 0.8%, while between T. minangkabau with T. minangkabau forma darek 5.5%. The low sequence divergence indicated that T. minangkabau and T. minangkabau forma darek have a close phylogenetic relationship. The analysis showed that Tetragonula (T. minangkabau, T. minangkabau forma darek, T. laeviceps, T. drescheri and T. fuscobalteata) is monophyletic. A sequence divergence of 5.5% supports the separation of Tetragonula minangkabau and T. minangkabau forma darek.

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Belchior de Andrade, Ana Flávia, and Cibele Rodrigues Bonvicino. "A new karyological variant of Oecomys (Rodentia: Sigmodontinae) and its phylogenetic relationship based on molecular data." Genome 46, no. 2 (April 1, 2003): 195–203. http://dx.doi.org/10.1139/g02-123.

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A new karyological variant of the Sigmodontinae genus Oecomys was detected in specimens from Brazilian Pantanal. Karyologic analyses showed 2n = 72 and FN = 90, which differs from all known chromosomal complements of the genus. This new karyomorph showed distinctive morphological attributes and could not be attributed to any described Oecomys species. Molecular analysis using cytochrome-b sequence data suggested the monophyly of Oecomys. Maximum-likelihood analyses placed the Oecomys sp. haplotype clade as the sister branch to Oecomys bicolor, whereas maximum-parsimony analyses did not resolve its relationship with the other Oecomys species. Kimura's two parameters distance estimates between this and other Oecomys species are high, and active gene flow has been found not to coexist with these divergence estimates.Key words: Oecomys sp., rodent, Sigmodontinae, karyotype, molecular phylogeny.

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VILLALOBOS, FEDERICO, and FERNANDO CERVANTES-REZA. "Phylogenetic relationships of Mesoamerican species of the genus Sciurus (Rodentia: Sciuridae)." Zootaxa 1525, no. 1 (July 12, 2007): 31–40. http://dx.doi.org/10.11646/zootaxa.1525.1.3.

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The phylogenetic relationships of Sciurus species present in Mesoamerica are addressed using a morphological analysis under Maximum Parsimony. Our results recovered the existence of two clades: one comprising S. aureogaster, S. colliaei, S. variegatoides and Syntheosciurus brochus and the other clade composed by S. richmondi, S. granatensis, S. deppei, S. yucatanensis and Microsciurus alfari. The taxonomic status of the genera Microsciurus and Syntheosciurus is discussed as well the biogeographic implications of these findings.

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HUNTER, REBECCA L. "Morphological cladistic analysis of Ophiurolepis Matsumoto, 1915 (Ophiurida: Ophiuridae) from the Southern Ocean." Zootaxa 1401, no. 1 (February 1, 2007): 33. http://dx.doi.org/10.11646/zootaxa.1401.1.2.

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A phylogenetic analysis using morphological characters was done on the Antarctic ophiuroid genus Ophiurolepis Matsumoto, 1915. This genus is one of the more abundant and ecologically dominant ophiuroid genera in the Antarctic and surrounding Southern Ocean. Maximum parsimony was used to infer phylogenetic relationships. Although strongly supported nodes were not recovered for most groupings within Ophiurolepis, this first attempt at a phylogeny revealed the presence of three tentative clades. Two of the three Ophiurolepis clades included species currently assigned to other genera, but closely allied with Ophiurolepis in the taxonomic literature. This indicates that Ophiurolepis as currently defined is not a monophyletic group. Additional forms of data, namely molecular, are needed to more definitively resolve relationships within this group.

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HUNTER, REBECCA L. "Morphological cladistic analysis of Ophiurolepis Matsumoto, 1915 (Ophiurida: Ophiuridae) from the Southern Ocean." Zootaxa 1401, no. 1 (February 1, 2007): 33. http://dx.doi.org/10.11646/zootaxa.1401.2.

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A phylogenetic analysis using morphological characters was done on the Antarctic ophiuroid genus Ophiurolepis Matsumoto, 1915. This genus is one of the more abundant and ecologically dominant ophiuroid genera in the Antarctic and surrounding Southern Ocean. Maximum parsimony was used to infer phylogenetic relationships. Although strongly supported nodes were not recovered for most groupings within Ophiurolepis, this first attempt at a phylogeny revealed the presence of three tentative clades. Two of the three Ophiurolepis clades included species currently assigned to other genera, but closely allied with Ophiurolepis in the taxonomic literature. This indicates that Ophiurolepis as currently defined is not a monophyletic group. Additional forms of data, namely molecular, are needed to more definitively resolve relationships within this group.

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AL-QURAISHY, S., A. S. ABDEL-BAKI, H. AL-QAHTANI, M. DKHIL, G. CASAL, and C. AZEVEDO. "A new microsporidian parasite, Heterosporis saurida n. sp. (Microsporidia) infecting the lizardfish, Saurida undosquamis from the Arabian Gulf, Saudi Arabia: ultrastructure and phylogeny." Parasitology 139, no. 4 (February 8, 2012): 454–62. http://dx.doi.org/10.1017/s0031182011001971.

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SUMMARYA new microsporidian that infects the lizardfish Saurida undosquamis (Richardson, 1848) that are caught in the Arabian Gulf in Saudi Arabia is described here. This parasite invades the skeletal muscle of the abdominal cavity forming white, cyst-like structures containing numerous spores. The prevalence of the infection was 32·1% (135/420). The spores were oval to pyriform in shape and measured approximately 3·3 μm×2·0 μm. The developing spores were found within parasitophorous vacuoles. In mature spores, the polar filament was arranged into 5 coils in a row. Molecular analysis of the rRNA genes, including the ITS region, and phylogenetic analyses using maximum parsimony, maximum likelihood, and Bayesian inference were performed. The ultrastructural characteristics and phylogenetic analyses support the recognition of a new species, herein named Heterosporis saurida n. sp.

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Hailegeorgis, Teklu T., and Knut Alfredsen. "Multi-basin and regional calibration based identification of distributed precipitation–runoff models for hourly runoff simulation: calibration and transfer of full and partial parameters." Hydrology Research 47, no. 2 (July 17, 2015): 239–59. http://dx.doi.org/10.2166/nh.2015.174.

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Identification of distributed precipitation–runoff models for hourly runoff simulation based on transfer of full parameters (FP) and partial parameters (PP) are lacking for boreal mid-Norway. We evaluated storage–discharge relationships based model (Kirchmod), the Basic-Grid-Model (BGM) and a simplified Hydrologiska Byråns Vattenbalansavdelning (HBV) model for multi-basins (26 catchments). A regional calibration objective function, which uses all streamflow records in the region, was used to optimize local calibration parameters for each catchment and regional parameters yielding maximum regional weighted average (MRWA) performance measures (PM). Based on regional median Nash–Sutcliffe efficiency (NSE) and NSEln (for log-transformed series) for the calibration and validation periods, the Kirchmod model performed better than the others. Parsimony of the Kirchmod model provided less parameter uncertainty for the FP case but did not guarantee parameter identifiability. Tradeoffs between parsimony and performance were observed despite advantages of parsimony to reduce parameter correlations for the PP, which requires preliminary sensitivity analysis to identify which parameters to transfer. There are potential advantages of using the MRWA method for parameter transfer in space. However, temporal validation indicated marked deterioration of the PM. The tradeoffs between parameter transfers in space and time substantiate both spatial and temporal validation of the regional calibration methodology.

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Ivanova, Natalia V., Paula T. Depriest, Vera K. Bobrova, and Alexey V. Troitsky. "Phylogenetic Analysis of the Lichen Family Umbilicariaceae based on nuclear ITS1 and ITS2 rDNA Sequences." Lichenologist 31, no. 5 (September 1999): 477–89. http://dx.doi.org/10.1006/lich.1999.0223.

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AbstractThe lichen family Umbilicariaceae is accepted by most lichenologists as consisting of two genera, Lasallia and Umbilicaria. The monophyly of these two genera was examined by phylogenetic analyses of nucleotide sequences of ITS 1 and ITS2 rDNA. Sequences of these regions from three Lasallia and 17 Umbilicaria species were aligned to those of seven representatives of the outgroup taxa including Eurotiales, Onygenales and Caliciales (Mycocaliciaceae) and subjected to maximum parsimony, maximum likelihood and neighbour-joining analyses. The resulting phylogenetic hypotheses supported the monophyly of the representative species of Lasallia. However, the species of Umbilicaria did not form a monophyletic sistergroup to Lasallia due to the basal placement of other Umbilicaria species in some analyses. Based on these analyses, if Lasallia is recognized as a separate genus then Umbilicaria appears to be paraphyletic. Although further taxon sampling is required to resolve the monophyly of Umbilicaria, for the present we recommend retaining the current treatment of Lasallia as separate from Umbilicaria.

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Journal articles on the topic 'Maximum Parsimony Analysis'

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