Ferran Palero | CEAB_CSIC - Academia.edu (original) (raw)
Papers by Ferran Palero
Helgoland Marine Research, 2014
Arthropod Structure & Development, 2015
A new fossil lobster from the Cretaceous of Lebanon, Charbelicaris maronites gen. et sp. nov., is... more A new fossil lobster from the Cretaceous of Lebanon, Charbelicaris maronites gen. et sp. nov., is presented here, while the former species 'Cancrinos' libanensis is re-described as Paracancrinos libanensis comb. nov. P. libanensis is shown to be closer related to the contemporary slipper lobsters than to Cancrinos claviger (lithographic limestones, Jurassic, southern Germany). A finely-graded evolutionary scenario for the slipper-lobster morphotype is reconstructed based on these fossil species and extant forms. The evolutionary changes that gave rise to the current plate-like antennae of Scyllaridae, a key apomorphy of this group, are traced back through time. The antenna of what is considered the oldest slipper lobster became petaloid and consisted of about 20 fully articulated elements. For this group the name Scyllarida sensu lato tax. nov. is introduced. In a next evolutionary step, the proximal articles became conjoined and a lateral extension appeared on peduncle element 3. The entire distal petaloid region is conjoined already at the node of Verscyllarida tax. nov. In modern slipper lobsters, Neoscyllarida tax nov., the distal region is no longer petaloid in shape but asymmetrical. The study also emphasizes that exceptionally preserved fossils need to be documented with optimal documentation techniques to obtain all available information.
Applied and Environmental Microbiology, 2015
Legionella pneumophila is an accidental human pathogen associated with aerosol formation in water... more Legionella pneumophila is an accidental human pathogen associated with aerosol formation in water-related sources. High recombination rates make Legionella populations genetically diverse, and near two thousand different sequence types (STs) have been described to date for this environmental pathogen. The spatial distribution of STs is extremely heterogeneous, with some variants being present worldwide while others are detected only at a local scale. Similarly, some STs have been associated with disease outbreaks, such as ST578 or ST23.Spain is among the European countries with highest incidence rates of reported Legionellosis cases and, specifically, Comunitat Valenciana (CV) is the second most affected area in the country. In this work, we aimed at studying the overall diversity of Legionella pneumophila populations found in the period 1998-2013 in 79 localities encompassing 23 regions within CV. To do so, we performed Sequence-Based Typed (SBT) on 1,088 L. pneumophila strains detected in the area from both environmental and clinical sources. A comparison with the genetic structuring detected in a global dataset that included 20 European and 7 non-European countries was performed. Our results reveal a level of diversity in CV that can be considered representative of the diversity found in other countries worldwide.
We review phylogenetic inference methods with a special emphasis on inference from molecular data... more We review phylogenetic inference methods with a special emphasis on inference from molecular data. We begin with a general comment on phylogenetic inference using DNA sequences, followed by a clear statement of the relevance of a good alignment of sequences. Then we provide a general description of models of sequence evolution, including evolutionary models that account for rate heterogeneity along the DNA sequences or complex secondary structure (i.e., ribosomal genes). We then present an overall description of the most relevant inference methods, focusing on key concepts of general interest. We point out the most relevant traits of methods such as maximum parsimony (MP), distance methods, maximum likelihood (ML) and Bayesian inference (BI). Finally, we discuss different measures of support for the estimated phylogeny and discuss how this relates to confidence in particular nodes of a phylogeny reconstruction.
The Science of the total environment, Jan 25, 2015
We assessed the role of euryhalinity and life-history traits on the population genetic structure ... more We assessed the role of euryhalinity and life-history traits on the population genetic structure of the four main caridean shrimp species from the Iberian Peninsula (Atyaephyra desmarestii, Dugastella valentina, Palaemon varians and Palaemon zariquieyi) able to complete their life cycle in freshwater/oligohaline habitats. Seawater exposure experiments indicated that A. desmarestii, D. valentina and P. zariquieyi are more sensitive to high salinity waters than P. varians and confirm the relationship between osmolality regulation and spatial distribution of species. The limited or no survival in seawater could explain the restricted distributions observed in D. valentina and P. zariquieyi, whereas the current A. desmarestii distribution could be due to either past river dynamics and/or human-mediated water transfers. Conversely, the high tolerance of P. varians to a large salinity range (euryhalinity) could explain its capacity to colonize geographically distant estuaries. In agreemen...
The growing convergence of computing, electronics and communications has led in recent years to a... more The growing convergence of computing, electronics and communications has led in recent years to a global Information Society. Nowadays, there is a clear consensus on the importance of Information and Communication Technologies (ICT) to facilitate the economic and social progress of a country. Importantly, the use of ICT does not only enhance learning, but allows to transform the teaching and increases the number of teaching courses available in parallel with the more traditional education. At present, we can relax the contents and structure of our courses through new educational platforms provided by multiple web sites. A phenomenon that has received a significant boost in recent years is the development of MOOCs (Massive Online Open Courses). The MOOCs integrate the social network connectivity, the availability of an expert in the field of study of recognized prestige, and a collection of open access resources from the internet. The most important of a MOOC is that it relies on the active participation of a large number of students (up to the thousands) who organize their own participation depending on their own learning goals, their prior knowledge and skills, or the existence of common interests with other students. This paper starts from the premise that key factors such as the increasing complexity of ICT and its role as a tool for education and training involve the need to expand the boundaries of the traditional university, fostering cooperation between teachers of different schools. Thus, we present an updated report on the current situation (regarding the contents and teaching methods) in different Spanish and Latin American universities for the specific case of the teaching of Genetics and Evolution. In addition, we will discuss the possibilities of establishing a transnational teaching group for the development of an 'online' course with shared materials and using a new platform called 'MiriadaX'.
Systematic biology, 2014
Lobsters are a ubiquitous and economically important group of decapod crustaceans that include th... more Lobsters are a ubiquitous and economically important group of decapod crustaceans that include the infraorders Polychelida, Glypheidea, Astacidea and Achelata. They include familiar forms such as the spiny, slipper, clawed lobsters and crayfish and unfamiliar forms such as the deep-sea and "living fossil" species. The high degree of morphological diversity among these infraorders has led to a dynamic classification and conflicting hypotheses of evolutionary relationships. In this study, we estimated phylogenetic relationships among the major groups of all lobster families and 94% of the genera using six genes (mitochondrial and nuclear) and 195 morphological characters across 173 species of lobsters for the most comprehensive sampling to date. Lobsters were recovered as a non-monophyletic assemblage in the combined (molecular + morphology) analysis. All families were monophyletic, with the exception of Cambaridae, and 7 of 79 genera were recovered as poly- or paraphyletic....
Invertebrate Systematics, 2014
Early reports on larval distributions are frustratingly obscure due to ambiguous identification o... more Early reports on larval distributions are frustratingly obscure due to ambiguous identification of plankton samples. A particularly striking case is posed by the so-called 'giant phyllosoma' which attain 80 mm in total length and are among the largest larvae known in marine invertebrates. Based on the supposition that these giant larvae are produced by local species, Philip Robertson (1968) assigned them to Parribacus. In the present study, 12 phyllosoma larvae collected in the Coral Sea and corresponding to intermediate stages VI to IX are described in detail. The identity of these freshly caught specimens was confirmed as belonging to Parribacus antarcticus (Lund, 1793) by using DNA barcoding methods. This new collection further allowed us to complete the larval series for the genus. The intermediate stage VI, which was missing in previous accounts, is described here for the first time. Besides the Coral Sea larvae, another five phyllosoma specimens previously deposited in UK and German museum collections are also described. Given that no useful DNA could be obtained from the old collection specimens, these larvae were identified as Parribacus sp. based on morphology only. Furthermore, a complete morphometric analysis of Parribacus larvae was undertaken including information from literature dating back to 1830. The first detailed description of all dactyli from a complete phyllosoma of the genus Parribacus is presented, with further comparison with those from other genera of Scyllaridae.
Crustacean Issues, 2009
We review phylogenetic inference methods with a special emphasis on inference from molecular data... more We review phylogenetic inference methods with a special emphasis on inference from molecular data. We begin with a general comment on phylogenetic inference using DNA sequences, followed by a clear statement of the relevance of a good alignment of sequences. Then we provide a general description of models of sequence evolution, including evolutionary models that account for rate heterogeneity along the DNA sequences or complex secondary structure (i.e., ribosomal genes). We then present an overall description of the most relevant inference methods, focusing on key concepts of general interest. We point out the most relevant traits of methods such as maximum parsimony (MP), distance methods, maximum likelihood (ML) and Bayesian inference (BI). Finally, we discuss different measures of support for the estimated phylogeny and discuss how this relates to confidence in particular nodes of a phylogeny reconstruction.
Helgoland Marine Research, 2014
Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases, 2015
Recombination is a pervasive process generating diversity in most viruses. It joins variants that... more Recombination is a pervasive process generating diversity in most viruses. It joins variants that arise independently within the same molecule, creating new opportunities for viruses to overcome selective pressures and to adapt to new environments and hosts. Consequently, the analysis of viral recombination attracts the interest of clinicians, epidemiologists, molecular biologists and evolutionary biologists. In this review we present an overview of three major areas related to viral recombination: (i) the molecular mechanisms that underlie recombination in model viruses, including DNA-viruses (Herpesvirus) and RNA-viruses (Human Influenza Virus and Human Immunodeficiency Virus), (ii) the analytical procedures to detect recombination in viral sequences and to determine the recombination breakpoints, along with the conceptual and methodological tools currently used and a brief overview of the impact of new sequencing technologies on the detection of recombination, and (iii) the major...
![Research paper thumbnail of [Molecular epidemiology studies on the immigrant population in Spain]](https://attachments.academia-assets.com/42302952/thumbnails/1.jpg)
](Revista española de salud pública
Molecular epidemiology is a new scientific discipline which allows to integrate information on th... more Molecular epidemiology is a new scientific discipline which allows to integrate information on the genetic variation of infectious pathogens with their diffusion in a population and its subgroups including, for instance, resistance mutations to antibiotics and antiretrovirals. We present the results of an analysis of scientific publications that analyze the health status of the immigrant population in Spain from a molecular epidemiology perspective. We reviewed original articles published in 1998-2014 with the keywords "molecular epidemiology", "molecular…
Helgoland Marine Research, 2014
Arthropod Structure & Development, 2015
A new fossil lobster from the Cretaceous of Lebanon, Charbelicaris maronites gen. et sp. nov., is... more A new fossil lobster from the Cretaceous of Lebanon, Charbelicaris maronites gen. et sp. nov., is presented here, while the former species 'Cancrinos' libanensis is re-described as Paracancrinos libanensis comb. nov. P. libanensis is shown to be closer related to the contemporary slipper lobsters than to Cancrinos claviger (lithographic limestones, Jurassic, southern Germany). A finely-graded evolutionary scenario for the slipper-lobster morphotype is reconstructed based on these fossil species and extant forms. The evolutionary changes that gave rise to the current plate-like antennae of Scyllaridae, a key apomorphy of this group, are traced back through time. The antenna of what is considered the oldest slipper lobster became petaloid and consisted of about 20 fully articulated elements. For this group the name Scyllarida sensu lato tax. nov. is introduced. In a next evolutionary step, the proximal articles became conjoined and a lateral extension appeared on peduncle element 3. The entire distal petaloid region is conjoined already at the node of Verscyllarida tax. nov. In modern slipper lobsters, Neoscyllarida tax nov., the distal region is no longer petaloid in shape but asymmetrical. The study also emphasizes that exceptionally preserved fossils need to be documented with optimal documentation techniques to obtain all available information.
Applied and Environmental Microbiology, 2015
Legionella pneumophila is an accidental human pathogen associated with aerosol formation in water... more Legionella pneumophila is an accidental human pathogen associated with aerosol formation in water-related sources. High recombination rates make Legionella populations genetically diverse, and near two thousand different sequence types (STs) have been described to date for this environmental pathogen. The spatial distribution of STs is extremely heterogeneous, with some variants being present worldwide while others are detected only at a local scale. Similarly, some STs have been associated with disease outbreaks, such as ST578 or ST23.Spain is among the European countries with highest incidence rates of reported Legionellosis cases and, specifically, Comunitat Valenciana (CV) is the second most affected area in the country. In this work, we aimed at studying the overall diversity of Legionella pneumophila populations found in the period 1998-2013 in 79 localities encompassing 23 regions within CV. To do so, we performed Sequence-Based Typed (SBT) on 1,088 L. pneumophila strains detected in the area from both environmental and clinical sources. A comparison with the genetic structuring detected in a global dataset that included 20 European and 7 non-European countries was performed. Our results reveal a level of diversity in CV that can be considered representative of the diversity found in other countries worldwide.
We review phylogenetic inference methods with a special emphasis on inference from molecular data... more We review phylogenetic inference methods with a special emphasis on inference from molecular data. We begin with a general comment on phylogenetic inference using DNA sequences, followed by a clear statement of the relevance of a good alignment of sequences. Then we provide a general description of models of sequence evolution, including evolutionary models that account for rate heterogeneity along the DNA sequences or complex secondary structure (i.e., ribosomal genes). We then present an overall description of the most relevant inference methods, focusing on key concepts of general interest. We point out the most relevant traits of methods such as maximum parsimony (MP), distance methods, maximum likelihood (ML) and Bayesian inference (BI). Finally, we discuss different measures of support for the estimated phylogeny and discuss how this relates to confidence in particular nodes of a phylogeny reconstruction.
The Science of the total environment, Jan 25, 2015
We assessed the role of euryhalinity and life-history traits on the population genetic structure ... more We assessed the role of euryhalinity and life-history traits on the population genetic structure of the four main caridean shrimp species from the Iberian Peninsula (Atyaephyra desmarestii, Dugastella valentina, Palaemon varians and Palaemon zariquieyi) able to complete their life cycle in freshwater/oligohaline habitats. Seawater exposure experiments indicated that A. desmarestii, D. valentina and P. zariquieyi are more sensitive to high salinity waters than P. varians and confirm the relationship between osmolality regulation and spatial distribution of species. The limited or no survival in seawater could explain the restricted distributions observed in D. valentina and P. zariquieyi, whereas the current A. desmarestii distribution could be due to either past river dynamics and/or human-mediated water transfers. Conversely, the high tolerance of P. varians to a large salinity range (euryhalinity) could explain its capacity to colonize geographically distant estuaries. In agreemen...
The growing convergence of computing, electronics and communications has led in recent years to a... more The growing convergence of computing, electronics and communications has led in recent years to a global Information Society. Nowadays, there is a clear consensus on the importance of Information and Communication Technologies (ICT) to facilitate the economic and social progress of a country. Importantly, the use of ICT does not only enhance learning, but allows to transform the teaching and increases the number of teaching courses available in parallel with the more traditional education. At present, we can relax the contents and structure of our courses through new educational platforms provided by multiple web sites. A phenomenon that has received a significant boost in recent years is the development of MOOCs (Massive Online Open Courses). The MOOCs integrate the social network connectivity, the availability of an expert in the field of study of recognized prestige, and a collection of open access resources from the internet. The most important of a MOOC is that it relies on the active participation of a large number of students (up to the thousands) who organize their own participation depending on their own learning goals, their prior knowledge and skills, or the existence of common interests with other students. This paper starts from the premise that key factors such as the increasing complexity of ICT and its role as a tool for education and training involve the need to expand the boundaries of the traditional university, fostering cooperation between teachers of different schools. Thus, we present an updated report on the current situation (regarding the contents and teaching methods) in different Spanish and Latin American universities for the specific case of the teaching of Genetics and Evolution. In addition, we will discuss the possibilities of establishing a transnational teaching group for the development of an 'online' course with shared materials and using a new platform called 'MiriadaX'.
Systematic biology, 2014
Lobsters are a ubiquitous and economically important group of decapod crustaceans that include th... more Lobsters are a ubiquitous and economically important group of decapod crustaceans that include the infraorders Polychelida, Glypheidea, Astacidea and Achelata. They include familiar forms such as the spiny, slipper, clawed lobsters and crayfish and unfamiliar forms such as the deep-sea and "living fossil" species. The high degree of morphological diversity among these infraorders has led to a dynamic classification and conflicting hypotheses of evolutionary relationships. In this study, we estimated phylogenetic relationships among the major groups of all lobster families and 94% of the genera using six genes (mitochondrial and nuclear) and 195 morphological characters across 173 species of lobsters for the most comprehensive sampling to date. Lobsters were recovered as a non-monophyletic assemblage in the combined (molecular + morphology) analysis. All families were monophyletic, with the exception of Cambaridae, and 7 of 79 genera were recovered as poly- or paraphyletic....
Invertebrate Systematics, 2014
Early reports on larval distributions are frustratingly obscure due to ambiguous identification o... more Early reports on larval distributions are frustratingly obscure due to ambiguous identification of plankton samples. A particularly striking case is posed by the so-called 'giant phyllosoma' which attain 80 mm in total length and are among the largest larvae known in marine invertebrates. Based on the supposition that these giant larvae are produced by local species, Philip Robertson (1968) assigned them to Parribacus. In the present study, 12 phyllosoma larvae collected in the Coral Sea and corresponding to intermediate stages VI to IX are described in detail. The identity of these freshly caught specimens was confirmed as belonging to Parribacus antarcticus (Lund, 1793) by using DNA barcoding methods. This new collection further allowed us to complete the larval series for the genus. The intermediate stage VI, which was missing in previous accounts, is described here for the first time. Besides the Coral Sea larvae, another five phyllosoma specimens previously deposited in UK and German museum collections are also described. Given that no useful DNA could be obtained from the old collection specimens, these larvae were identified as Parribacus sp. based on morphology only. Furthermore, a complete morphometric analysis of Parribacus larvae was undertaken including information from literature dating back to 1830. The first detailed description of all dactyli from a complete phyllosoma of the genus Parribacus is presented, with further comparison with those from other genera of Scyllaridae.
Crustacean Issues, 2009
We review phylogenetic inference methods with a special emphasis on inference from molecular data... more We review phylogenetic inference methods with a special emphasis on inference from molecular data. We begin with a general comment on phylogenetic inference using DNA sequences, followed by a clear statement of the relevance of a good alignment of sequences. Then we provide a general description of models of sequence evolution, including evolutionary models that account for rate heterogeneity along the DNA sequences or complex secondary structure (i.e., ribosomal genes). We then present an overall description of the most relevant inference methods, focusing on key concepts of general interest. We point out the most relevant traits of methods such as maximum parsimony (MP), distance methods, maximum likelihood (ML) and Bayesian inference (BI). Finally, we discuss different measures of support for the estimated phylogeny and discuss how this relates to confidence in particular nodes of a phylogeny reconstruction.
Helgoland Marine Research, 2014
Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases, 2015
Recombination is a pervasive process generating diversity in most viruses. It joins variants that... more Recombination is a pervasive process generating diversity in most viruses. It joins variants that arise independently within the same molecule, creating new opportunities for viruses to overcome selective pressures and to adapt to new environments and hosts. Consequently, the analysis of viral recombination attracts the interest of clinicians, epidemiologists, molecular biologists and evolutionary biologists. In this review we present an overview of three major areas related to viral recombination: (i) the molecular mechanisms that underlie recombination in model viruses, including DNA-viruses (Herpesvirus) and RNA-viruses (Human Influenza Virus and Human Immunodeficiency Virus), (ii) the analytical procedures to detect recombination in viral sequences and to determine the recombination breakpoints, along with the conceptual and methodological tools currently used and a brief overview of the impact of new sequencing technologies on the detection of recombination, and (iii) the major...
Revista española de salud pública
Molecular epidemiology is a new scientific discipline which allows to integrate information on th... more Molecular epidemiology is a new scientific discipline which allows to integrate information on the genetic variation of infectious pathogens with their diffusion in a population and its subgroups including, for instance, resistance mutations to antibiotics and antiretrovirals. We present the results of an analysis of scientific publications that analyze the health status of the immigrant population in Spain from a molecular epidemiology perspective. We reviewed original articles published in 1998-2014 with the keywords "molecular epidemiology", "molecular…