Simone Cardoni
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View article: Pruning the Tree: Comparing <scp>OTUs</scp> and <scp>ASVs</scp> in High‐Throughput Sequencing of <scp>5S</scp> ‐ <scp>IGS</scp> Nuclear Ribosomal <scp>DNA</scp> in Phylogenetic Studies
Pruning the Tree: Comparing <span>OTUs</span> and <span>ASVs</span> in High‐Throughput Sequencing of <span>5S</span> ‐ <span>IGS</span> Nuclear Ribosomal <span>DNA</span> in Phylogenetic Studies Open
Amplicon sequencing of the nuclear ribosomal 5S RNA gene arrays is highly promising for genotaxonomy, to delineate genetic resources of species and trace their evolution. However, the huge amount of data retrieved with this approach is dif…
View article: A subgeneric classification of Fagus (Fagaceae) and revised taxonomy of western Eurasian beeches
A subgeneric classification of Fagus (Fagaceae) and revised taxonomy of western Eurasian beeches Open
We propose a long-overdue subgeneric classification of Fagus and revision of its western Eurasian taxa based on population-level sampling of morphological and molecular data. The molecular sequence data bolstering this classification deriv…
View article: Enhanced precipitation events and forests stability: a case study in Emilia-Romagna and Tuscany (Italy).
Enhanced precipitation events and forests stability: a case study in Emilia-Romagna and Tuscany (Italy). Open
Climate change is endangering natural and anthropogenic ecosystems, as pointed out by the recent IPCC Reports and the COPs' statements. The impacts of climate change on natural ecosystems can affect their production capacity, particularly …
View article: High-Throughput Sequencing of 5S-IGS rDNA in Fagus L. (Fagaceae) reveals complex evolutionary patterns and hybrid origin of modern species
High-Throughput Sequencing of 5S-IGS rDNA in Fagus L. (Fagaceae) reveals complex evolutionary patterns and hybrid origin of modern species Open
Standard models of speciation assume strictly dichotomous genealogies in which a species, the ancestor, is replaced by two offspring species. The reality is more complex: plant species can evolve from other species via isolation when genet…
View article: Variability of airborne microbiome at different urban sites across seasons: a case study in Rome
Variability of airborne microbiome at different urban sites across seasons: a case study in Rome Open
Introduction: Biogenic fraction of airborne PM 10 dominated by bacteria and fungi, has been recognized as serious environmental and human health issues in cities. Methods: In the present study, we combined a high-throughput amplicon sequen…
View article: Complex Scenarios of Reticulation, Polyploidization, and Species Diversity within Annual Pansies of Subsect. Bracteolatae (Viola Sect. Melanium, Violaceae) in Italy: Insights from 5S-IGS High-Throughput Sequencing and Plastid DNA Variation
Complex Scenarios of Reticulation, Polyploidization, and Species Diversity within Annual Pansies of Subsect. Bracteolatae (Viola Sect. Melanium, Violaceae) in Italy: Insights from 5S-IGS High-Throughput Sequencing and Plastid DNA Variation Open
Viola sect. Melanium, the so-called pansy, is an allopolyploid morphologically well-defined lineage of ca. 110 perennial and annual species in the northern hemisphere, characterized by markedly complex genomic configurations. Five annual p…
View article: High-Throughput Sequencing of the 5S-IGS nuclear DNA in Viola sect- Melanium (Violaceae)
High-Throughput Sequencing of the 5S-IGS nuclear DNA in Viola sect- Melanium (Violaceae) Open
This fileset reports intra-genomic, intra- and inter-individual variation of the multycopy, nuclear encoded 5S rDNA region in four Viola (V. tricolor, V. arvensis, V. kitaibeliana, V. hymettia) and outgroup species of section Melanium. The…
View article: 5S‐IGS rDNA in wind‐pollinated trees ( <i>Fagus</i> L.) encapsulates 55 million years of reticulate evolution and hybrid origins of modern species
5S‐IGS rDNA in wind‐pollinated trees ( <i>Fagus</i> L.) encapsulates 55 million years of reticulate evolution and hybrid origins of modern species Open
SUMMARY Standard models of plant speciation assume strictly dichotomous genealogies in which a species, the ancestor, is replaced by two offspring species. The reality in wind‐pollinated trees with long evolutionary histories is more compl…
View article: 5S-IGS rDNA in wind-pollinated trees (<i>Fagus</i>L.) encapsulates 55 million years of reticulate evolution and hybrid origins of modern species
5S-IGS rDNA in wind-pollinated trees (<i>Fagus</i>L.) encapsulates 55 million years of reticulate evolution and hybrid origins of modern species Open
Summary Standard models of plant speciation assume strictly dichotomous genealogies in which a species, the ancestor, is replaced by two offspring species. The reality in wind-pollinated trees with long evolutionary histories is more compl…
View article: High-Throughput Sequencing of the 5S-IGS nuclear DNA in Viola sect- Melanium (Violaceae)
High-Throughput Sequencing of the 5S-IGS nuclear DNA in Viola sect- Melanium (Violaceae) Open
This fileset reports intra-genomic, intra- and inter-individual variation of the multycopy, nuclear encoded 5S rDNA region in four Viola (V. tricolor, V. arvensis, V. kitaibeliana, V. hymettia) and outgroup species of section Melanium. The…
View article: Data for Cardoni et al. (2021): High-Throughput Sequencing of 5S-IGS rDNA in Fagus L.
Data for Cardoni et al. (2021): High-Throughput Sequencing of 5S-IGS rDNA in Fagus L. Open
Data dump of and supplement to Cardoni et al. (2021) High-Throughput Sequencing of 5S-IGS rDNA in Fagus L. (Fagaceae) reveals complex evolutionary patterns and hybrid origin of modern species. bioRxiv. https://doi.org/10.1101/2021.02.26.43…
View article: Tracking diversity and evolutionary pathways of Lebanese oak taxa through plastome analyses
Tracking diversity and evolutionary pathways of Lebanese oak taxa through plastome analyses Open
The aim of this study is to better understand the phylogeography and evolution of the Lebanese oaks and to assess the convergence between their morpho-ecological and molecular characteristics. We investigated DNA sequence variation in four…
View article: Phylogenetic relationships and taxonomic issues in <i>Gastridium</i> (Poaceae) inferred from plastid and nuclear DNA sequence analysis
Phylogenetic relationships and taxonomic issues in <i>Gastridium</i> (Poaceae) inferred from plastid and nuclear DNA sequence analysis Open
Gastridium P. Beauv. is a Mediterranean-Paleotropical member of the Poaceae family, whose species number and diversity are still imperfectly known. We examined patterns of DNA diversity at two plastid (trnH-psbA, trnL-F) and one nuclear (I…
View article: Tracking diversity and evolutionary pathways of Lebanese oak taxa through plastome analyses
Tracking diversity and evolutionary pathways of Lebanese oak taxa through plastome analyses Open
The aim of this study is to better understand the phylogeography and evolution of the Lebanese oaks and to assess the convergence between their morpho-ecological and molecular characteristics. We investigated DNA sequence variation in four…
View article: Genetic diversity and taxonomic issues in<i>Gastridium</i>P.Beauv (Poaceae) inferred from plastid and nuclear DNA sequence analysis
Genetic diversity and taxonomic issues in<i>Gastridium</i>P.Beauv (Poaceae) inferred from plastid and nuclear DNA sequence analysis Open
Incomplete taxonomic knowledge may seriously hamper biodiversity conservation efforts that are crucial in a context of global change. Gastridium P.Beauv. is a Mediterranean-Paleotropical member of the Poaceae family, inhabiting ephemeral g…
View article: Peer Review #2 of "Comparative systematics and phylogeography of Quercus Section Cerris in western Eurasia: inferences from plastid and nuclear DNA variation (v0.1)"
Peer Review #2 of "Comparative systematics and phylogeography of Quercus Section Cerris in western Eurasia: inferences from plastid and nuclear DNA variation (v0.1)" Open
Oaks (Quercus) comprise more than 400 species worldwide and centres of diversity for most sections lie in the Americas and East/Southeast Asia.The only exception is the Eurasian sect.Cerris that comprises about 15 species, most of which ar…
View article: Comparative systematics and phylogeography of <i>Quercus</i> Section <i>Cerris</i> in western Eurasia: inferences from plastid and nuclear DNA variation
Comparative systematics and phylogeography of <i>Quercus</i> Section <i>Cerris</i> in western Eurasia: inferences from plastid and nuclear DNA variation Open
Oaks ( Quercus ) comprise more than 400 species worldwide and centres of diversity for most sections lie in the Americas and East/Southeast Asia. The only exception is the Eurasian sect. Cerris that comprises about 15 species, most of whic…
View article: Peer Review #1 of "Comparative systematics and phylogeography of Quercus Section Cerris in western Eurasia: inferences from plastid and nuclear DNA variation (v0.1)"
Peer Review #1 of "Comparative systematics and phylogeography of Quercus Section Cerris in western Eurasia: inferences from plastid and nuclear DNA variation (v0.1)" Open
Oaks (Quercus) comprise more than 400 species worldwide and centres of diversity for most sections lie in the Americas and East/Southeast Asia.The only exception is the Eurasian sect.Cerris that comprises about 15 species, most of which ar…
View article: Comparative systematics and phylogeography of <i>Quercus</i> Section <i>Cerris</i> in western Eurasia: inferences from plastid and nuclear DNA variation
Comparative systematics and phylogeography of <i>Quercus</i> Section <i>Cerris</i> in western Eurasia: inferences from plastid and nuclear DNA variation Open
Oaks ( Quercus ) comprise more than 400 species worldwide and centres of diversity for most sections lie in the Americas and East/Southeast Asia. The only exception is the Eurasian Sect. Cerris that comprises 15 species, a dozen of which a…
View article: Comparative systematics and phylogeography of <i>Quercus</i> Section <i>Cerris</i> in western Eurasia: inferences from plastid and nuclear DNA variation
Comparative systematics and phylogeography of <i>Quercus</i> Section <i>Cerris</i> in western Eurasia: inferences from plastid and nuclear DNA variation Open
Oaks ( Quercus ) comprise more than 400 species worldwide and centres of diversity for most sections lie in the Americas and East/Southeast Asia. The only exception is the Eurasian Sect. Cerris that comprises 15 species, a dozen of which a…
View article: DNA barcoding and faunistic criteria for a revised taxonomy of Italian Ephemeroptera
DNA barcoding and faunistic criteria for a revised taxonomy of Italian Ephemeroptera Open
Mayfly (Ephemeroptera) systematics has considerably changed over the years, but many questions have yet to be answered. The synergistic connection between traditional knowledge and new data sources, producing increasingly complex informati…
View article: DNA barcoding and faunistic criteria for a revised taxonomy of Italian Ephemeroptera
DNA barcoding and faunistic criteria for a revised taxonomy of Italian Ephemeroptera Open
Mayfly (Ephemeroptera) systematics has considerably changed over the years, but many questions have yet to be answered. The synergistic connection between traditional knowledge and new data sources, producing increasingly complex informati…
View article: Plastome data reveal multiple geographic origins of <i>Quercus</i> Group Ilex
Plastome data reveal multiple geographic origins of <i>Quercus</i> Group Ilex Open
Nucleotide sequences from the plastome are currently the main source for assessing taxonomic and phylogenetic relationships in flowering plants and their historical biogeography at all hierarchical levels. One major exception is the large …
View article: Plastome data reveal multiple geographic origins of <i>Quercus</i> Group Ilex
Plastome data reveal multiple geographic origins of <i>Quercus</i> Group Ilex Open
Nucleotide sequences from the plastome are currently the main source for assessing taxonomic and phylogenetic relationships in flowering plants and their historical biogeography at all hierarchical levels. One exception is the large and ec…
View article: Plastome data reveal multiple geographic origins of <i>Quercus </i>Group Ilex
Plastome data reveal multiple geographic origins of <i>Quercus </i>Group Ilex Open
Nucleotide sequences from the plastome are currently the main source for assessing taxonomic and phylogenetic relationships in flowering plants and their historical biogeography at all hierarchical levels. One exception is the large and ec…