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4. Notulae to the Italian native vascular flora: 8

Author

Gianluigi Bacchetta, Goffredo Filibeck, Bruno Petriglia, L. Gubellini, Corrado Tietto, Giovanni Maiorca, Francesco Roma-Marzio, Sara Magrini, Federica Bonini, Vito Buono, Daniele Viciani, G. Gestri, Pier Luigi Nimis, Giovanni Spampinato, Lina Podda, Serafino Cannavò, Fabrizio Bartolucci, Claudia Turcato, Simonetta Peccenini, Livia Lunardi, Nicole Hofmann, Sara Mossini, Gianmaria Bonari, Assunta Esposito, Sergio Buono, Robert P. Wagensommer, Daniela Gigante, Leonardo Beccarisi, Andrea Mainetti, Liliana Bernardo, Richard Lorenz, Günter Gottschlich, Luigi Forte, G. Barberis, Giacomo Calvia, Valeria Tomaselli, Chiara Nepi, Gianniantonio Domina, Rita T. Messa Ballarin, Giuliano Mereu, Salvatore Brullo, Simone Ravetto Enri, Luigi Minuto, Nicodemo G. Passalacqua, Manuel Tiburtini, Graziana Fiorini, Enrico Banfi, Michele Lonati, Franco Ballarin, Giovanni Bacaro, Lorenzo Lastrucci, Nicola M. G. Ardenghi, Leonardo Rosati, Franco Caldararo, Gabriele Galasso, Alessandro Ruggero, Mario Calbi, Adriano Stinca, Simonetta Fascetti, Laura Cancellieri, Giovanna Potenza, Davide Dagnino, Carmelo Maria Musarella, Bartolucci F., Domina G., Ardenghi N.M.G., Bacaro G., Bacchetta G., Ballarin F., Banfi E., Barberis G., Beccarisi L., Bernardo L., Bonari G., Bonini F., Brullo S., Buono S., Buono V., Calbi M., Caldararo F., Calvia G., Cancellieri L., Cannavo S., Dagnino D., Esposito A., Fascetti S., Filibeck G., Fiorini G., Forte L., Galasso G., Gestri G., Gigante D., Gottschlich G., Gubellini L., Hofmann N., Lastrucci L., Lonati M., Lorenz R., Lunardi L., Magrini S., Mainetti A., Maiorca G., Mereu G., Ballarin R.T.M., Minuto L., Mossini S., Musarella C.M., Nimis P.L., Passalacqua N.G., Peccenini S., Petriglia B., Podda L., Potenza G., Enri S.R., Roma-Marzio F., Rosati L., Ruggero A., Spampinato G., Stinca A., Tiburtini M., Tietto C., Tomaselli V., Turcato C., Viciani D., Wagensommer R.P., Nepi C., Bartolucci, F., Domina, G., Ardenghi, N. M. G., Bacaro, G., Bacchetta, G., Ballarin, F., Banfi, E., Barberis, G., Beccarisi, L., Bernardo, L., Bonari, G., Bonini, F., Brullo, S., Buono, S., Buono, V., Calbi, M., Caldararo, F., Calvia, G., Cancellieri, L., Cannavo, S., Dagnino, D., Esposito, A., Fascetti, S., Filibeck, G., Fiorini, G., Forte, L., Galasso, G., Gestri, G., Gigante, D., Gottschlich, G., Gubellini, L., Hofmann, N., Lastrucci, L., Lonati, M., Lorenz, R., Lunardi, L., Magrini, S., Mainetti, A., Maiorca, G., Mereu, G., Ballarin, R. T. M., Minuto, L., Mossini, S., Musarella, C. M., Nimis, P. L., Passalacqua, N. G., Peccenini, S., Petriglia, B., Podda, L., Potenza, G., Enri, S. R., Roma-Marzio, F., Rosati, L., Ruggero, A., Spampinato, G., Stinca, A., Tiburtini, M., Tietto, C., Tomaselli, V., Turcato, C., Viciani, D., Wagensommer, R. P., Nepi, C., Bartolucci, F, Domina, G, Ardenghi, Nmg, Bacaro, G, Bacchetta, G, Ballarin, F, Banfi, E, Barberis, G, Beccarisi, L, Bernardo, L, Bonari, G, Bonini, F, Brullo, S, Buono, S, Buono, V, Calbi, M, Caldararo, F, Calvia, G, Cancellieri, L, Cannavò, S, Dagnino, D, Esposito, A, Fascetti, S, Filibeck, G, Fiorini, G, Forte, L, Galasso, G, Gestri, G, Gigante, D, Gottschlich, G, Gubellini, L, Hofmann, N, Lastrucci, L, Lonati, M, Lorenz, R, Lunardi, L, Magrini, S, Mainetti, A, Maiorca, G, Mereu, G, Messa Ballarin, Rt, Minuto, L, Mossini, S, Musarella, Cm, Nimis, Pl, Passalacqua, Ng, Peccenini, S, Petriglia, B, Podda, L, Potenza, G, Ravetto Enri, S, Roma-Marzio, F, Rosati, L, Ruggero, A, Spampinato, G, Stinca, A, Tiburtini, M, Tietto, C, Tomaselli, V, Turcato, C, Viciani, D, Wagensommer, Rp, and Nepi, C

Subjects
0106 biological sciences, Endemic, Floristic data, Italy, Nomenclature, Flora, Nomenclature, Zoology, Floristic data, Plant Science, Biology, 010603 evolutionary biology, 01 natural sciences, lcsh:QK1-989, Endemic, Italy, lcsh:Botany, Settore BIO/03 - Botanica Ambientale E Applicata, Ecology, Evolution, Behavior and Systematics, 010606 plant biology & botany
Abstract

In this contribution, new data concerning the distribution of native vascular flora in Italy are presented. It includes new records, confirmations, exclusions, and status changes to the Italian administrative regions for taxa in the genera Ajuga, Chamaemelum, Clematis, Convolvulus, Cytisus, Deschampsia, Eleocharis, Epipactis, Euphorbia, Groenlandia, Hedera, Hieracium, Hydrocharis, Jacobaea, Juncus, Klasea, Lagurus, Leersia, Linum, Nerium, Onopordum, Persicaria, Phlomis, Polypogon, Potamogeton, Securigera, Sedum, Soleirolia, Stachys, Umbilicus, Valerianella, and Vinca. Nomenclatural and distribution updates, published elsewhere, and corrigenda are provided as Suppl. material 1.

Published
2019
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5. Notulae to the Italian alien vascular flora: 6

Author

Chiara Steffanini, Gaetano Pazienza, A. Sani, Lorenzo Peruzzi, Adriano Stinca, Francesco Saverio D’Amico, Luigi Forte, Alessandro Ruggero, Giuliano Mereu, Maurizio Trenchi, Giacomo Mei, Gianluigi Bacchetta, Francesca Carruggio, Pietro Medagli, Lorenzo Lazzaro, Liliana Bernardo, Giovanni Maiorca, Domenico Gargano, Franco Caldararo, Gabriele Galasso, Giancarlo Tondi, Domenico Saulle, Sara Magrini, Massimiliano Rempicci, Günter Gottschlich, Francesco Di Carlo, Massimo Terzi, Daniele Viciani, Filippo Prosser, Chiara Nepi, Gianniantonio Domina, Nicola Olivieri, Danio Miserocchi, Alessandro Cavagna, Francesco Festi, Fabrizio Bartolucci, Robert P. Wagensommer, Flavio Mennini, Giovanni Buccomino, Nicodemo G. Passalacqua, Nicola M. G. Ardenghi, Sergio Buono, Giacomo Calvia, Francesco Roma-Marzio, Galasso G., Domina G., Alessandrini A., Ardenghi N.M.G., Bacchetta G., Ballelli S., Bartolucci F., Brundu G., Buono S., Busnardo G., Calvia G., Capece P., D'Antraccoli M., Di Nuzzo L.D., Fanfarillo E., Ferretti G., Guarino R., Iamonico D., Iberite M., Latini M., Lazzaro L., Lonati M., Lozano V., Magrini S., Mei G., Mereu G., Moro A., Mugnai M., Nicolella G., Nimis P.L., Olivieri N., Pennesi R., Peruzzi L., Podda L., Probo M., Prosser F., Enri S.R., Roma-Marzio F., Ruggero A., Scafidi F., Stinca A., Nepi C., Ardenghi N.M., Bernardo L., Buccomino G., Caldararo F., Carruggio F., Cavagna A., D'Amico F.S., Di Carlo F., Festi F., Forte L., Gargano D., Gottschlich G., Maiorca G., Medagli P., Mennini F., Miserocchi D., Passalacqua N.G., Pazienza G., Rempicci M., Sani A., Saulle D., Steffanini C., Terzi M., Tondi G., Trenchi M., Viciani D., Wagensommer R.P., Galasso, Gabriele, Domina, Gianniantonio, Alessandrini, Alessandro, Ardenghi, Nicola M. G., Bacchetta, Gianluigi, Ballelli, Sandro, Bartolucci, Fabrizio, Brundu, Giuseppe, Buono, Sergio, Busnardo, Giuseppe, Calvia, Giacomo, Capece, Paolo, D’Antraccoli, Marco, Di Nuzzo, Luca, Fanfarillo, Emanuele, Ferretti, Giulio, Guarino, Riccardo, Iamonico, Duilio, Iberite, Mauro, Latini, Marta, Lazzaro, Lorenzo, Lonati, Michele, Lozano, Vanessa, Magrini, Sara, Mei, Giacomo, Mereu, Giuliano, Moro, Andrea, Mugnai, Michele, Nicolella, Gianluca, Nimis, Pierluigi, Olivieri, Nicola, Pennesi, Riccardo, Peruzzi, Lorenzo, Podda, Lina, Probo, Massimiliano, Prosser, Filippo, Ravetto Enri, Simone, Roma-Marzio, Francesco, Ruggero, Alessandro, Scafidi, Filippo, Stinca, Adriano, and Nepi, Chiara

Subjects
0106 biological sciences, Flora, alien specie, Alien species, Plant Science, Alien, Biology, 010603 evolutionary biology, 01 natural sciences, Plant science, floristic data, italian flora, lcsh:Botany, Botany, Nomenclature, Ecology, Evolution, Behavior and Systematics, Alien specie, alien species, Italy, Ecology, Floristic data, lcsh:QK1-989, Geography, Alien species, floristic data, Italy, Settore BIO/03 - Botanica Ambientale E Applicata, Floristic data, Italy, nomenclature, 010606 plant biology & botany
Abstract

In this contribution, new data concerning the distribution of vascular flora alien to Italy are presented. It includes new records, confirmations, exclusions, and status changes for Italy or for Italian administrative regions of taxa in the generaAcalypha,Acer,Canna,Cardamine,Cedrus,Chlorophytum,Citrus,Cyperus,Epilobium,Eucalyptus,Euphorbia,Gamochaeta,Hesperocyparis,Heteranthera,Lemna,Ligustrum,Lycium,Nassella,Nothoscordum,Oenothera,Osteospermum,Paspalum,Pontederia,Romulea,Rudbeckia,Salvia,Sesbania,Setaria,Sicyos,Styphnolobium,Symphyotrichum, andTradescantia. Nomenclature and distribution updates, published elsewhere, and corrigenda are provided as supplementary material.

Published
2018
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6. The genetic code is very close to a global optimum in a model of its origin taking into account both the partition energy of amino acids and their biosynthetic relationships.

Author

Caldararo F and Di Giulio M

Subjects
Codon genetics, Evolution, Molecular, Genetic Code genetics, Amino Acids chemistry, Amino Acids genetics, Models, Genetic
Abstract

We used the Moran's I index of global spatial autocorrelation with the aim of studying the distribution of the physicochemical or biological properties of amino acids within the genetic code table. First, using this index we are able to identify the amino acid property - among the 530 analyzed - that best correlates with the organization of the genetic code in the set of amino acid permutation codes. Considering, then, a model suggested by the coevolution theory of the genetic code origin - which in addition to the biosynthetic relationships between amino acids took into account also their physicochemical properties - we investigated the level of optimization achieved by these properties either on the entire genetic code table, or only on its columns or only on its rows. Specifically, we estimated the optimization achieved in the restricted set of amino acid permutation codes subject to the constraints derived from the biosynthetic classes of amino acids, in which we identify the most optimized amino acid property among all those present in the database. Unlike what has been claimed in the literature, it would appear that it was not the polarity of amino acids that structured the genetic code, but that it could have been their partition energy instead. In actual fact, it would seem to reach an optimization level of about 96% on the whole table of the genetic code and 98% on its columns. Given that this result has been obtained for amino acid permutation codes subject to biosynthetic constraints, that is to say, for a model of the genetic code consistent with the coevolution theory, we should consider the following conclusions reasonable. (i) The coevolution theory might be corroborated by these observations because the model used referred to the biosynthetic relationships between amino acids, which are suggested by this theory as having been fundamental in structuring the genetic code. (ii) The very high optimization on the columns of the genetic code would not only be compatible but would further corroborate the coevolution theory because this suggests that, as the genetic code was structured along its rows by the biosynthetic relationships of amino acids, on its columns strong selective pressure might have been put in place to minimize, for example, the deleterious effects of translation errors. (iii) The finding that partition energy could be the most optimized property of amino acids in the genetic code would in turn be consistent with one of the main predictions of the coevolution theory. Since the partition energy is reflective of the protein structure and therefore of the enzymatic catalysis, the latter might really have been the main selective pressure that would have promoted the origin of the genetic code. Indeed, we observe that the β-strands show an optimization percentage of 95.45%; so it is possible to hypothesize that they might have become the object of selection during the origin of the genetic code, conditioning the choice of biosynthetic relationships between amino acids. (iv) The finding that the polarity of amino acids is less optimized than their partition energy in the genetic code table might be interpreted against the physicochemical theories of the origin of the genetic code because these would suggest, for example, that a very high optimization of the polarity of amino acids in the code could be an expression of interactions between amino acids and codons or anticodons, which would have promoted its origin. This might now become less sustainable, given the very high optimization that is instead observed in favor of the partition energy but not polarity. Finally, (v) the very high optimization of the partition energy of amino acids would seem to make a neutral origin of error minimization, i.e. of the ability of the genetic code to buffer, for example, the deleterious effects of translation errors, very unlikely. Indeed, an optimization of about 100% would seem that it might not have been achieved by a simple neutral process, but this ability should probably have been generated instead by the intervention of natural selection. In actual fact, we show that the neutral theory of the origin of error minimization has been falsified for the model analyzed here. Therefore, we will discuss our observations within the theories proposed to explain the origin of the organization of the genetic code, reaching the conclusion that the coevolution theory is the most strongly corroborated theory., (Copyright © 2022. Published by Elsevier B.V.)

Published
2022
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7. Absorbent Markov chains as a model for the study of the evolution of proteins.

Author

Di Giulio M and Caldararo F

Subjects
Amino Acid Sequence, Amino Acids genetics, Mutation, Biological Evolution, Markov Chains, Models, Genetic, Probability, Proteins genetics
Abstract

The formalism of absorbent Markov chains, previously developed by Kemeny & Snell (1960) is used as a model for the study of the evolution of proteins. Within the limits of statistical analysis used, the amino acid substitution frequencies of McLachlan (1972) are explained by the numerical values derived from the model used. In addition, the amino acid composition of proteins is partially explained and the relative mutability of amino acids receives a new interpretation in the light of the above mentioned stochastic model. The results show that some basic aspect of protein evolution can be predicted by a stochastic model and therefore a significant component of protein evolution is driven by a random element.

Published
1987
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