1,721,149 research outputs found
Environmental DNA metabarcoding of water samples as a tool for monitoring Iberian freshwater fish composition
No full textEnvironmental DNA (eDNA) metabarcoding has been increasingly used to monitor the community assemblages of a wide variety of organisms. Here, we test the efficacy of eDNA metabarcoding to assess the composition of Iberian freshwater fishes, one of the most endangered groups of vertebrates in Spain. For this purpose, we sampled 12 sampling sites throughout one of Spain’s largest basins, the Duero, which is home to approximately 70% of the genera and 30%oftheprimary freshwater fish in Spain. We sampled these sampling sites in the summer by using electrofishing, a traditional sampling method, and eDNA metabarcoding of river water samples using the mitochondrial 12S rRNA gene (12S) as a marker. Wealsoresampled four of these sampling sites in autumn by eDNA. We compared the results obtained through eDNA metabarcoding with those of electrofishing surveys (ones conducted for the present study and past ones) and assessed the suitability of 12S as an eDNAmetabarcoding marker forthis group of freshwater fishes. We found that the 12S fragment, analysed for 25 Iberian species, showed sufficient taxonomic resolution to be useful for eDNAapproaches, and evenshowed population-level differences in the studied populations across the tissue samples for Achondrostoma arcasii. In most cases, a greater number of species was detected through eDNA metabarcoding than through electrofishing. Based on our results, eDNA metabarcoding is a powerful tool to study the freshwater fish composition in the Iberian Peninsula and to unmask cryptic diversity. However, we highlight the need to generate a local genetic database for 12S gene for such studies and to interpret the results with caution when studying only mitochondrial DNA. Finally, our survey shows that the high detection sensitivity of eDNA metabarcoding and the non-invasiveness of this method allows it to act as a detection system for species of low abundance, such as early invasive species or species in population decline, two key aspects of conservation management of Spanish freshwater fishes.Peer reviewe
FIGURE 2 in Garra roseae, a new species from the Makran region in southern Iran (Teleostei: Cyprinidae)
No full textFIGURE 2. Phylogenetic tree of mitochondrial COI barcode region rendered by Bayesian inference (BI). Numbers on branches indicate posterior probability values for BI and Maximum Likelihood (ML) bootstrap. Model of rate heterogeneity: Gamma with 4 categories Gamma shape alpha: 0.1905. Black solid bars right to the specimen labels indicate species delimitation results from mPTP followed by the results of the PTP approach as gray solid bars. The tree is drawn to scale with branch lengths depicting number of substitutions per site.Published as part of Mousavi-Sabet, Hamed, Saemi-Komsari, Maryam, Doadrio, Ignacio & Freyhof, Jörg, 2019, Garra roseae, a new species from the Makran region in southern Iran (Teleostei: Cyprinidae), pp. 223-239 in Zootaxa 4671 (2) on page 225, DOI: 10.11646/zootaxa.4671.2.3, http://zenodo.org/record/344236
Descripción de tres nuevas especies del género Cobitis L., 1758 (Actinopterygii, Cobitidae) en la península Ibérica
No full textThree new species, Cobitis almadae sp. nov., Cobitis atlantica sp. nov., and Cobitis mellaria sp. nov. are described on the basis of morphological and genetic traits. Cobitis almadae sp. nov. is restricted to the Sizandro Drainage in Portugal and can be distinguished from other Cobitis species through a combination of morphometric and genetic traits including large and low peduncle depth, lateral ethmoid (suborbital spine) well developed with long narrow mediocaudal, laterocaudal and mediorostral processes, an elongated and narrow frontoparietal fontanel and a wide third Gambetta’s zone sprinkled with numerous black spots. Furthermore, two autapomorphies are found within its mitochondrial cytochrome b gene. Cobitis atlantica sp. nov. inhabits the northern Atlantic rivers of the Iberian Peninsula from the Minho Drainage to the Alcoa Drainage and can be differentiated from other Cobitis species through a set of morphometric and genetic traits including short and high peduncle depth, a well-developed lateral ethmoid (suborbital spine) with short and wide mediocaudal, laterocaudal and mediorostral processes, wide frontoparietal fontanel, and developed ventral pigmentation in adult individuals. In females, the Gambetta’s fourth row has 10-16 blotches reaching the ventral pigmentation in the caudal region and the third Gambetta’s zone is narrow with black spots. Cobitis mellaria sp. nov inhabits the Valle Drainage in southern Spain and is distinguished from other Cobitis species through the following morphometric and genetic traits: low peduncle depth, lamina circularis with convex outer edge, lateral ethmoid (suborbital spine) with short laterocaudal process and large mediorostral process, elongated frontoparietal fontanel, no ventral pigmentation in adults. In females, Gambetta’s fourth row has 10-15 blotches. One autapomorphy is found within the mitochondrial cytochrome b gene of Cobitis mellaria sp. nov.Se describen tres nuevas especies del género Cobitis: Cobitis almadae sp. nov., Cobitis atlantica sp. nov., y Cobitis mellaria sp. nov. mediante caracteres morfológicos y genéticos. Cobitis almadae sp. nov. está restringida a la cuenca del Sizandro en Portugal y se puede diferenciar de otras especies del género Cobitis a través de una combinación de caracteres morfométricos y genéticos que incluyen un pedúnculo largo y estrecho, etmoides lateral (espina suborbitaria) bien desarrollado con apófisis mediocaudales, laterocaudales y mediorostrales largas y estrechas, fontanela frontoparietal alargada y estrecha, la tercera zona de Gambetta es ancha y se encuentra salpicada de numerosas manchas negras. Además, tiene dos autapomorfias en su citocromo b. Cobitis atlantica sp. nov. vive en los ríos que vierten al Atlántico norte de la Península Ibérica, desde la cuenca del Miño hasta la cuenca del río Alcoa y se puede diferenciar de otras especies del género Cobitis a través de un conjunto de caracteres morfométricos y genéticos que incluyen un pedúnculo corto y alto, etmoides lateral (espina suborbitaria) bien desarrollada con apófisis mediocaudales, laterocaudales y mediorostrales cortas y anchas, fontanela frontoparietal ancha, pigmentación ventral presente en los individuos adultos. En las hembras, la cuarta fila de Gambetta tiene 10-16 manchas que alcanzan la pigmentación ventral en la región caudal y la tercera zona de Gambetta es estrecha con algunas manchas negras. Cobitis mellaria sp. nov. vive en la cuenca del río Valle en el sur de España y se puede distinguir de otras especies del género Cobitis a través de una combinación de caracteres morfométricos y genéticos: pedúnculo caudal bajo, lámina circular con su borde exterior convexo, etmoides lateral (espina suborbital) con apófisis laterocaudal corta y apófisis mediorostral muy larga, fontanela frontoparietal alargada, sin pigmentación ventral en los adultos, en las hembras la cuarta fila de Gambetta tiene 10-15 manchas. Cobitis mellaria sp. nov. presenta una autapomorfía en el citocromo b.Peer reviewe
Description of two new species of the genus Squalius Bonaparte, 1837 (Actinopterygii, Leuciscidae) in the Iberian Peninsula
No full textTwo new species, Squalius gaditanus sp. nov. and Squalius tartessicus sp. nov. are described on the basis of morphological and genetic traits. Squalius gaditanus is restricted to the Barbate, Jara and Miel drainages in the province of Cádiz (Southern Spain). Squalius gaditanus sp. nov. can be distinguished from other Squalius species from the Iberian Peninsula through a combination of morphometric, meristic and genetic characters: 3640 (χ = 38) pored scales on the lateral line; 6-7 (χ = 6.7) scales above the lateral line; 2-3 (χ = 2.8) scales below the lateral line; vertebrae 37-39 (χ = 38); second infraorbital bone narrower than the third in adults; maxilla with reduced pointed anterior process; posterior process of the maxilla long and thin; lower branch of the pharyngeal bone short and robust; pharyngeal plate of basioccipital rounded and two autapomorphies in the mitochondrial cytochrome b gene. Squalius tartessicus sp. nov. inhabits the Almargem, Gilão, Odiel, Guadiana, Guadalquivir, Guadalete, Guadalhorce, Velez, Guadalfeo and Segura drainages in the southern part of the Iberian Peninsula. Squalius tartessicus sp. nov. can be differentiated from other Squalius species from the Iberian Peninsula through a set of morphometric, meristic and genetic traits: 37-41(χ = 38.8) pored scales on the lateral line; 6-7 (χ = 7) scales above the lateral line; 2-3 (χ = 2.9) scales below the lateral line; 37-39 (χ = 38) number of vertebrae; infraorbital bones unusually wide in adults; maxilla with discernable pointed anterior process; posterior process of the maxilla long and thin; lower branch of the pharyngeal bone short and robust; pharyngeal plate of basioccipital triangular in shape; posterior lamina of cleithrum expanding posteriorly.Peer reviewe
Cytochrome b Mitochondrial Gene Revealed a Strong Genetic Differentiation between Two Populations of the Endemic Freshwater Fish Moroccan Loach Cobitis maroccana Pellegrin, 1929
No full textCobitis maroccana, also known as the Moroccan loach, is an endemic freshwater fish found in the rivers of the Loukkos and Sebou basins in Morocco. In order to gain a better understanding of the genetic differentiation within C. maroccana from the Loukkos and Sebou populations, a comprehensive study was conducted, focusing on the mitochondrial cytochrome b gene. A total of 30 sequences of the complete cytochrome b (1140 bp) were obtained from C. maroccana specimens. Through a combination of phylogenetic analysis, phylogeographic assessments, as well as the estimation of the Fst index, the research outcomes revealed significant genetic differentiation between the two juxtaposed basin populations. Notably, each of these basins displayed unique and distinct haplotype groups within the C. maroccana specimens. These intriguing findings strongly suppose that the populations in the Loukkos and Sebou basins have become reproductively isolated from each other over time, indicating limited or no interbreeding between them.Funding for this study was provided by The Moroccan MENFPESRS and CNRST to Ahmed Yahyaoui (PPR/2015/1) for the project “Impact of Climate Changes on the Genetic Diversity of Moroccan Freshwater Fish”.Peer reviewe
Multiple ancestries and shared gene flow among modern livestock guarding dogs
Full text linkLivestock guarding dogs (LGDs) have been used to protect livestock for millennia. While previous works suggested a single origin of modern LGDs, the degree and source of shared ancestry have not been tested. To address this, we generated genome-wide SNP data from 304 LGDs and combined it with public genomic data from 2,183 modern and 22 ancient dogs. Our findings reveal shared ancestry and extensive gene flow among modern LGD breeds which we attribute to historical livestock migrations. Additionally, admixture between LGDs and free-ranging dogs argues against reproductive isolation as a core mechanism for maintaining the specialized skills of LGDs. Finally, we identify two lineages within modern LGDs and uncover multiple ancestries tracing back to distinct Eurasian ancient dogs, concordant with the absence of a single ancestor. Overall, our work explores the complex evolutionary history of LGDs, offering valuable insights into how human and livestock co-migrations shaped this functional group
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
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