1,720,966 research outputs found
An evaluation of the taxonomic status of Musa viridis and Musa splendida using high-throughput sequencing data
No full textThe delimitation of species based on morphological traits can be challenging due to overlapping trait variation. The taxonomic identity of closely related sympatric species with individuals displaying intermediate phenotypes is particularly questionable. However, thorough morphological assessments or traditional molecular analyses often lack resolution to clarify if two species are truly separate taxonomic entities or should be merged. Interestingly, advances in high-throughput sequencing methods and data processing during the last decades enable the use of high-resolution data to tackle taxonomic problems. Several species with an unclear taxonomic status are found in the banana family (Musaceae). In Vietnam, the Musa species M. viridis and M. splendida have very similar morphological trait characteristics. The main difference between the two species is the colour of the male flower bud: M. splendida has red flower buds, whereas M. viridis has pink flower buds. Both species occur sympatrically, and individuals with red and pink male flower buds are found together in some populations. In this study, we used high-throughput (DArT) sequencing data from plants of nine populations to investigate the taxonomic status of these Musa species. Maximum likelihood phylogenetic trees were reconstructed for over 12,000 loci (< 120 base pairs) and one ASTRAL consensus tree was created from all locus trees. The individuals in the ASTRAL phylogenetic tree did not cluster by species identity, but by population, having individuals from different species in the same cluster. Consequently, we propose to merge the species M. viridis and M. splendida into one species named M. splendida according to nomenclatural conventions
A genetic assessment of Musa viridis and Musa splendida indicates that they are conspecific
No full textSpecies delimitation based on morphological trait characteristics can be challenging due to overlapping trait variation. This is especially true for closely related sympatric species with individuals exhibiting intermediate phenotypes. However, traditional morphological and molecular analyses often lack resolution to determine whether two taxa are distinct species or are conspecific. Recent advances in generating and processing high-throughput sequencing data enable the use of high-resolution data to address such taxonomic problems. Within the banana family (Musaceae), several species have an ambiguous taxonomic status. Musa viridis and M. splendida are two wild Vietnamese banana species that are locally used as ornamentals or added to rice wine as flavor enhancers. Their fruits are not favored for consumption, mainly because they have seeded bananas. Both species have very similar morphological trait characteristics. The main difference between these species is the colour of the male flower bud: M. splendida has red flower buds, whereas M. viridis has pink flower buds. Both species also occur sympatrically with some populations comprising individuals with red and pink male flower bracts. In this study, we applied a high-throughput (DArT) sequencing approach to investigate the taxonomic status of M. viridis and M. splendida based on 121 plants from nine different populations. Maximum likelihood phylogenetic trees were reconstructed for over 12,000 loci (< 120 base pairs) and one ASTRAL consensus tree was generated from all locus trees. The ASTRAL phylogenetic tree showed that individuals did not cluster by species but by population, with individuals from different species appearing in the same clade. Consequently, we propose to treat M. viridis as a synonym of M. splendida. Our work clarified the taxonomic status of two wild relatives of cultivated bananas, potentially facilitating their use in crop breeding programs in the future
An evaluation of the taxonomic status of Musa viridis and Musa splendida using high-throughput sequencing data
No full textThe delimitation of species based on morphological traits can be challenging due to overlapping trait variation. The taxonomic identity of closely related sympatric species with individuals displaying intermediate phenotypes is particularly questionable. However, thorough morphological assessments or traditional molecular analyses often lack resolution to clarify if two species are truly separate taxonomic entities or should be merged. Interestingly, advances in high-throughput sequencing methods and data processing during the last decades enable the use of high-resolution data to tackle taxonomic problems. Several species with an unclear taxonomic status are found in the banana family (Musaceae). In Vietnam, the Musa species M. viridis and M. splendida have very similar morphological trait characteristics. The main difference between the two species is the colour of the male flower bud: M. splendida has red flower buds, whereas M. viridis has pink flower buds. Both species occur sympatrically, and individuals with red and pink male flower buds are found together in some populations. In this study, we used high-throughput (DArT) sequencing data from plants of nine populations to investigate the taxonomic status of these Musa species. Maximum likelihood phylogenetic trees were reconstructed for over 12,000 loci (< 120 base pairs) and one ASTRAL consensus tree was created from all locus trees. The individuals in the ASTRAL phylogenetic tree did not cluster by species identity, but by population, having individuals from different species in the same cluster. Consequently, we propose to merge the species M. viridis and M. splendida into one species named M. splendida according to nomenclatural conventions
A genetic assessment of Musa viridis and Musa splendida indicates that they are conspecific
No full textSpecies delimitation based on morphological trait characteristics can be challenging due to overlapping trait variation. This is especially true for closely related sympatric species with individuals exhibiting intermediate phenotypes. However, traditional morphological and molecular analyses often lack resolution to determine whether two taxa are distinct species or are conspecific. Recent advances in generating and processing high-throughput sequencing data enable the use of high-resolution data to address such taxonomic problems. Within the banana family (Musaceae), several species have an ambiguous taxonomic status. Musa viridis and M. splendida are two wild Vietnamese banana species that are locally used as ornamentals or added to rice wine as flavor enhancers. Their fruits are not favored for consumption, mainly because they have seeded bananas. Both species have very similar morphological trait characteristics. The main difference between these species is the colour of the male flower bud: M. splendida has red flower buds, whereas M. viridis has pink flower buds. Both species also occur sympatrically with some populations comprising individuals with red and pink male flower bracts. In this study, we applied a high-throughput (DArT) sequencing approach to investigate the taxonomic status of M. viridis and M. splendida based on 121 plants from nine different populations. Maximum likelihood phylogenetic trees were reconstructed for over 12,000 loci (< 120 base pairs) and one ASTRAL consensus tree was generated from all locus trees. The ASTRAL phylogenetic tree showed that individuals did not cluster by species but by population, with individuals from different species appearing in the same clade. Consequently, we propose to treat M. viridis as a synonym of M. splendida. Our work clarified the taxonomic status of two wild relatives of cultivated bananas, potentially facilitating their use in crop breeding programs in the future
Identifying coffee: development of a low-cost and robust barcoding assay for wild African Coffea species
No full textWith an estimated consumption of more than two billion cups a day, coffee is one of the most popular beverages in the world. Nearly all coffee is produced from the seeds of two species: Coffea arabica (Arabica coffee) and Coffea canephora (Robusta coffee). Both Arabica and Robusta coffee production is threatened by climate fluctuations and disease outbreaks, reducing yields and ravaging coffee plantations. To overcome these challenges, the potential of other wild Coffea species for the improvement of existing coffee varieties or for the development of new varieties has been studied. The Coffea genus consists of circa 130 described species that are mainly found in sub-Saharan Africa and Madagascar. Coffea species on the African continent are more closely related to Arabica and Robusta coffee. Nevertheless, the identification of African Coffea species at species level based on morphological traits can be challenging as several species seem to have overlapping trait characteristics. In this study, we developed a molecular barcoding assay consisting of eight nuclear markers between ca. 200 and 800 base pairs long that can be sequenced using Sanger sequencing. Marker regions were selected based on the output of publicly available genotyping-by-sequencing data, ensuring that each Coffea species included in this dataset had a unique allele for at least two out of eight markers. The resulting barcoding assay is a cost-efficient and accessible tool for the molecular identification of wild African Coffea species, facilitating their conservation and their application for the improvement of coffee cultivation
Identifying coffee: development of a low-cost and robust barcoding assay for wild African Coffea species
No full textWith an estimated consumption of more than two billion cups a day, coffee is one of the most popular beverages in the world. Nearly all coffee is produced from the seeds of two species: Coffea arabica (Arabica coffee) and Coffea canephora (Robusta coffee). Both Arabica and Robusta coffee production is threatened by climate fluctuations and disease outbreaks, reducing yields and ravaging coffee plantations. To overcome these challenges, the potential of other wild Coffea species for the improvement of existing coffee varieties or for the development of new varieties has been studied. The Coffea genus consists of circa 130 described species that are mainly found in sub-Saharan Africa and Madagascar. Coffea species on the African continent are more closely related to Arabica and Robusta coffee. Nevertheless, the identification of African Coffea species at species level based on morphological traits can be challenging as several species seem to have overlapping trait characteristics. In this study, we developed a molecular barcoding assay consisting of eight nuclear markers between ca. 200 and 800 base pairs long that can be sequenced using Sanger sequencing. Marker regions were selected based on the output of publicly available genotyping-by-sequencing data, ensuring that each Coffea species included in this dataset had a unique allele for at least two out of eight markers. The resulting barcoding assay is a cost-efficient and accessible tool for the molecular identification of wild African Coffea species, facilitating their conservation and their application for the improvement of coffee cultivation
Going Beyond Counting First Authors in Author Co-citation Analysis
Full text linkThe present study examines one of the fundamental aspects of author co-citation analysis (ACA) - the way co-citation
counts are defined. Co-citation counting provides the data on which all subsequent statistical analyses and mappings
are based, and we compare ACA results based on two different types of co-citation counting - the traditional type that
only counts the first one among a cited work's authors on the one hand and a non-traditional type that takes into
account the first 5 authors of a cited work on the other hand. Results indicate that the picture produced through this non-traditional author co-citation counting contains more coherent author groups and is therefore considerably clearer. However, this picture represents fewer specialties in the research field being studied than that produced through the traditional first-author co-citation counting when the same number of top-ranked authors is selected and analyzed. Reasons for these effects are discussed
Variations on the Author
Full text link“Variations on the Author” discusses two of Eduardo Coutinho’s recent films (Um Dia na Vida, from 2010, and Últimas Conversas, posthumously released in 2015) and their contribution to the general question of documentary authorship. The director’s filmography is characterized by a consistent yet self-effacing form of authorial self-inscription: Coutinho often features as an interviewer that rather than express opinions propels discourses; an interviewer that is good at listening. This mode of self-inscription characterizes him as an author who is not expressive but who is nonetheless markedly present on the screen. In Um Dia na Vida, however, Coutinho is completely absent form the image, while Últimas Conversas, on the contrary, includes a confessional prologue that moves the director from the margins to the center of his films. This article examines the ways in which these works stand out in the filmography of a director who offers new insights into the notion of cinematic authorship
Appropriate Similarity Measures for Author Cocitation Analysis
Full text linkWe provide a number of new insights into the methodological discussion about author cocitation analysis. We first argue that the use of the Pearson correlation for measuring the similarity between authors’ cocitation profiles is not very satisfactory. We then discuss what kind of similarity measures may be used as an alternative to the Pearson correlation. We consider three similarity measures in particular. One is the well-known cosine. The other two similarity measures have not been used before in the bibliometric literature. Finally, we show by means of an example that our findings have a high practical relevance.information science;Pearson correlation;cosine;similarity measure;author cocitation analysis
- …
