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William A Parker - One of the best experts on this subject based on the ideXlab platform.
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genomics of sablefish anoplopoma fimbria expressed genes mitochondrial phylogeny linkage map and identification of a putative sex gene
BMC Genomics, 2013Co-Authors: Eric Rondeau, Amber M Messmer, Dan S Sanderson, Stuart G Jantzen, Kristian R Von Schalburg, David R Minkley, Jong S Leong, Graham M Macdonald, Amanda E Davidsen, William A ParkerAbstract:The sablefish (order: Scorpaeniformes) is an economically important species in commercial fisheries of the North Pacific and an emerging species in aquaculture. Aside from a handful of sequences in NCBI and a few published microsatellite markers, little is known about the genetics of this species. The development of genetic tools, including polymorphic markers and a linkage map will allow for the successful development of future broodstock and mapping of phenotypes of interest. The significant sexual dimorphism between females and males makes a genetic test for early identification of sex desirable. A full mitochondrial genome is presented and the resulting phylogenetic analysis verifies the placement of the sablefish within the Scorpaeniformes. Nearly 35,000 assembled transcript sequences are used to identify genes and obtain polymorphic SNP and microsatellite markers. 360 transcribed polymorphic loci from two sablefish families produce a map of 24 linkage groups. The sex phenotype maps to sablefish LG14 of the male map. We show significant conserved synteny and conservation of gene-order between the threespine stickleback Gasterosteus aculeatus and sablefish. An additional 1843 polymorphic SNP markers are identified through next-generation sequencing techniques. Sex-specific markers and sequence insertions are identified immediately upstream of the gene gonadal-soma derived factor (gsdf), the master sex determinant locus in the medaka species Oryzias luzonensis. The first genomic resources for sablefish provide a foundation for further studies. Over 35,000 transcripts are presented, and the genetic map represents, as far as we can determine, the first linkage map for a member of the Scorpaeniformes. The observed level of conserved synteny and comparative mapping will allow the use of the stickleback genome in future genetic studies on sablefish and other related fish, particularly as a guide to whole-genome assembly. The identification of sex-specific insertions immediately upstream of a known master sex determinant implicates gsdf as an excellent candidate for the master sex determinant for sablefish.
Eric Rondeau - One of the best experts on this subject based on the ideXlab platform.
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genomics of sablefish anoplopoma fimbria expressed genes mitochondrial phylogeny linkage map and identification of a putative sex gene
BMC Genomics, 2013Co-Authors: Eric Rondeau, Amber M Messmer, Dan S Sanderson, Stuart G Jantzen, Kristian R Von Schalburg, David R Minkley, Jong S Leong, Graham M Macdonald, Amanda E Davidsen, William A ParkerAbstract:The sablefish (order: Scorpaeniformes) is an economically important species in commercial fisheries of the North Pacific and an emerging species in aquaculture. Aside from a handful of sequences in NCBI and a few published microsatellite markers, little is known about the genetics of this species. The development of genetic tools, including polymorphic markers and a linkage map will allow for the successful development of future broodstock and mapping of phenotypes of interest. The significant sexual dimorphism between females and males makes a genetic test for early identification of sex desirable. A full mitochondrial genome is presented and the resulting phylogenetic analysis verifies the placement of the sablefish within the Scorpaeniformes. Nearly 35,000 assembled transcript sequences are used to identify genes and obtain polymorphic SNP and microsatellite markers. 360 transcribed polymorphic loci from two sablefish families produce a map of 24 linkage groups. The sex phenotype maps to sablefish LG14 of the male map. We show significant conserved synteny and conservation of gene-order between the threespine stickleback Gasterosteus aculeatus and sablefish. An additional 1843 polymorphic SNP markers are identified through next-generation sequencing techniques. Sex-specific markers and sequence insertions are identified immediately upstream of the gene gonadal-soma derived factor (gsdf), the master sex determinant locus in the medaka species Oryzias luzonensis. The first genomic resources for sablefish provide a foundation for further studies. Over 35,000 transcripts are presented, and the genetic map represents, as far as we can determine, the first linkage map for a member of the Scorpaeniformes. The observed level of conserved synteny and comparative mapping will allow the use of the stickleback genome in future genetic studies on sablefish and other related fish, particularly as a guide to whole-genome assembly. The identification of sex-specific insertions immediately upstream of a known master sex determinant implicates gsdf as an excellent candidate for the master sex determinant for sablefish.
Cerro Ramon, Lluís I Del - One of the best experts on this subject based on the ideXlab platform.
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Revisió taxonòmica mundial de la família Triglidae (Pisces, Scorpaeniformes)
'Edicions de la Universitat de Barcelona', 2013Co-Authors: Cerro Ramon, Lluís I DelAbstract:[cat]El present treball parteix de la base d'estudi dels exemplars de la Família Triglidae capturats dintre del Programa de Recerca anomenat Fundaments for the Restructuration of the Demersal Fisheries in the Pacific Mexican Coast finançat per la Comunitat Europea. En el seu inici, i a manca de més informació, hom considerà seriosament la possibilitat de l'estudi taxonòmic de les espècies d'aquesta família com a matèria interessant d'anàlisi. Amb aquesta decisió, donàvem per fet que la sistemàtica del grup a nivell supra-específic era clara i, a més, que el grup, és a dir, la família Triglidae, estava clarament assentada dins l'organització del Regne Animal. Amb aquesta idea inicial, hom començà a triar i conservar mostres de lluernes per a llur estudi posterior a terra. Amb aquest material obtingut en aigües del Pacífic oriental, afegit a les mostres conservades a les Col•leccions Biològiques de Referència (CBR) de l'Institut de Ciències del Mar (ICM), creguérem disposar d'un bon punt de sortida per a un treball d'aquestes característiques. La revisió inicial dels exemplars conservats a les nostres col•leccions i dels que amablement rebérem en préstec d'algunes institucions de tot el món, juntament amb l'estudi i anàlisi bibliogràfics, no feu altre cosa que aprofundir la sensació que teníem de confusió general a l'hora de classificar els peixos de la família. Sorprenentment, fins i tot els treballs publicats recentment palesaven aquest fet i alguns dels autors llegits demanaven explícitament una revisió global de certs taxa supra-específics, fins i tot a nivell de la família. Per altra banda, ens adonàrem que quasi tota la bibliografia utilitzada per a la identificació de les mostres tenia un fort biaix geogràfic, fent necessari conèixer l'àrea de captura dels individus per tal de poder utilitzar la clau escaient. A més a més, els caràcters utilitzats per a la descripció de grups eren sovint incomparables (com si dues parts del món s'ignoressin), no tant sols entre diferents autors ans també entre dues espècies descrites en el mateix treball. Segons això, no ens va caldre gaire temps ni llegir gaires treballs per veure que la nostra concepció inicial d'harmonia i estabilitat sistemàtica de la família era força equivocada i, com més informació rebíem, més difícil se'ns feia esbrinar què podia donar-se per bo i on calia aprofundir per mirar de clarificar. Totes aquestes circumstàncies preliminars podran donar una idea d'un sentiment més o menys estès entre els investigadors embrancats en la família: la situació taxonòmica i sistemàtica és caòtica. Aquesta crua sentència, amb paraules diferents segons l'autor, es fa palesa llegint alguns dels treballs generals sobre la família i taxa superiors. També ens adonàrem dels diversos parers sobre quins taxa havien d'assignar-se a la família Triglidae, depenent de l'ictiòleg que opinava, i que tampoc la imatge inicial que ens havíem fet d’aquesta família, definida de la manera que hom veurà més endavant, podia considerar-se vàlida. Alguns d'aquells investigadors pensaven que la família Triglidae és clarament diferent de l’anomenada família Peristediidae, mentre d'altres escrigueren que ambdós taxa havien de considerar-se una única família Triglidae, en qualsevol cas subdividit en dues subfamílies: Triglinae i Peristediinae. Hi havia qui, fins i tot (alguns dels antics), hi feia entrar espècies que pertanyen a famílies absolutament diferents com, per exemple, Cottidae. Per recomanació d'autors amb més base filogenètica de la que nosaltres disposàvem, prenguérem la decisió de considerar el que per alguns eren les famílies Triglidae i Peristediidae com a una unitat englobada en la família Triglidae. Fou aleshores quan decidirem modificar el rumb inicial de la recerca per tal d'enfocar-lo vers una revisió supra-específica, al nostre albir molt més necessària que l’específica per tal de sistematitzar globalment la família: des de la definició d'aquesta fins el nivell de subgènere, deixant per més endavant la clarificació de la situació de les espècies un cop creguéssim organitzada aquella. Amb aquesta fita final i la idea de trobar descripcions curtes però clares dels diferents taxa amb trets vàlids per a qualsevol espècie en qualsevol lloc del món, endegàrem la tasca que hom ara presenta. Enguany, creiem haver arribat al moment de fer una proposta d'organització a nivell supra-específic de la família Triglidae, que no pretén altra cosa que intentar acostar-se subjectivament a la classificació natural del grup. En el capítol ANTECEDENTS, per una banda, hom fa un repàs de les diverses situacions que poden trobar-se en la bibliografia de caire taxonòmic de la família. Hom palesa, de forma molt resumida, algunes de les incongruències que poden trobar s'hi i que, pel lector no avesat en el tema, poden dur a confusió i a una necessitat de revisió amb detall per tal d'esbrinar la part correcta dels treballs. Per altra banda, en el mateix capítol, hom fa una exposició sobre la posició sistemàtica de la família Triglidae en base a una sèrie de treballs seleccionats des de la publicació de la desena edició del treball de Linné (1758). Amb aquestes revisions hom palesa la situació, esmentada més amunt, de que fins i tot no està clara la sistemàtica de l'Ordre Scorpaeniformes al que pertany la família estudiada. Finalment, en els ANTECEDENTS i dintre de l'apartat anomenat CRONOLOGIA DE LES DESCRIPCIONS, hom descriu i comenta els diferents taxa de rang comprés entre el familiar i el subgenèric descrits tanmateix des del treball de Linné (1758). Amb això hom pretén informar al lector de la confusió intra-familiar pel que fa a la definició de taxa i al diferent ús que de cadascun d'ells s'ha anat fent al llarg de la història de la ictiologia moderna. En el capítol dedicat a la METODOLOGIA, hom cita les espècies estudiades i llur procedència geogràfica, per tal de donar al lector una indicació de l'abast de la informació que hom disposa per a la realització de l'estudi. La part més extensa, però, del conjunt d'aquest capítol es dedica a la descripció de les variables morfomètriques i merístiques utilitzades al llarg dels anys de realització del treball. Amb això es fa la proposta d'estandardització de les esmentades variables amb la finalitat d'assolir la uniformització de la presa de dades per part dels investigadors dedicats a l'estudi de la família. Finalment, i dins del mateix capítol, es defineixen les bases d'utilització dels mètodes de taxonomia numèrica emprats com a eina complementària per a la definició dels diferents grups tractats en aquest estudi. En qualsevol cas, cal tenir en compte que, malgrat la potència d'algunes tècniques de taxonomia numèrica, aquesta metodologia no s'ha emprat en cap moment com a mètode definitori de les característiques dels diferents taxa tractats amb més detall en el capítol de RESULTATS, ans sempre ha estat prioritària, en cas de divergències clares, la visió humana del problema. El capítol 5 fa referència als RESULTATS tot i que bona part de l'anomenat ANTECEDENTS conté dades que podrien incloure's en el primer i que no s'ha fet per tal de mantenir un fil conductor que facilités la comprensió cronològica de la situació i ajudés a veure els resultats. En aquest capítol, i partint de la base d’una única família sense divisions preestablertes, hom va fent separacions en base a caràcters bàsicament merístics partint del nivell de família fins arribar al nivell subgenèric. Un cop clarificada la separació en dos o més grups del conjunt de partida, hom en dóna els trets diferenciadors i s'hi inclouen, finalment, les diverses espècies que compleixen les característiques citades. A partir d'ací, tot i que es mantenen per raons d'estabilitat de la nomenclatura els noms de la immensa majoria de taxa, aquests són redefinits en base als caràcters definitoris emprats per a la separació. Per necessitats ineludibles, al nostre parer, només un taxon de nivell subgenèric ha estat anomenat com a nou. Amb tot això, hom arriba a la conclusió que la Família Triglidae està estructurada com una unitat sistemàtica i que inclou dues Subfamílies (Peristedioninae i Triglinae), cinc Tribus (Gargariscini, Peristedionini, Prionotini, Pterygotriglini i Triglini), nou Gèneres (Gargariscus, Heminodus, Peristedion, Satyrichthys, Prionotus, Pterygotrigla, Uradia, Lepidotrigla i Trigla) i setze Subgèneres (Heminodus, Paraheminodus, Bellator, Prionotus, Bovitrigla, Dixiphichthys, Otohime, Pterygotrigla, Lepidotrigla, Pectorisquamis subgen. nov., Paratrigla Aspitrigla, Chelidonichthys, Eutrigla, Trigla i Trigloporus). Part important d'aquest treball consisteix en la INTRODUCCIÓ A LA BIOGEOGRAFIA DE LA FAMÍLIA TRIGLIDAE. Certament, aquesta és la primera aproximació a nivell mundial que hom fa de la distribució geogràfica de la família arreu del món. Aquest capítol s'il•lustra amb la inclusió de mapes, partint de la base de les àrees de pesca de FAO, per a cadascun dels taxa tractats en el capítol de RESULTATS, de tal manera que pot veure's la localització d'aquells en els diferents mars i oceans del planeta. Aquesta introducció biogeogràfica intenta explicar-se mitjançant una HIPÒTESI DE RADIACIÓ a partir de l'hipotètic punt d'origen en el Pangea i durant el període Triàsic. Aquest capítol es complementa amb un llistat de les diferents espècies que hom pot trobar en cadascuna de les àrees geogràfiques del món. Deixant de banda les CONCLUSIONS, part de les quals s'han inclòs de forma implícita en aquest RESUM, el capítol de BIBLIOGRAFIA clou la present memòria de Tesi Doctoral. En aquest s'han inclòs, a banda dels treballs citats en el text, tota una sèrie de treballs de caire taxonòmic sobre la família Triglidae i que, malgrat no ésser exhaustiu, sí que representa la major part del que s'ha publicat en temps de la ictiologia moderna.[eng]This work arises from the study of the specimens of the Family Triglidae collected during the research program named Fundaments for the Restructuration of the Demersal Fisheries in the Pacific Mexican Coast which was financed by the European Commission. Initially, and with the information available at that time, we seriously considered the possibility of the taxonomic study of the species of this family as an interesting subject for analysis. By making this decision we were accepting beforehand that the systematics of this group at a supraspecific level was clear and that of the group itself, the family Triglidae, was also precisely defined and settled within the organisation of the Animal Kingdom. Having this initial idea in mind, we began to choose and preserve many samples of gurnards for their later study on land. With these specimens collected in waters of the Eastern Pacific ocean plus those preserved in the Biological Reference Collections (CBR) of the Institut de Ciències del Mar (ICM) at Barcelona, we believed to have a good starting point to face the work in mind. The initial revision of the specimens preserved in our collections and those kindly loaned by research institutions from all around the world combined with the study and analysis of the literature rapidly increased our feeling of a general confusion on the classification of the species of the family. Surprisingly, even recent papers shared this feeling of ours and some of the authors explicitly claimed for a global revision of several supraspecific taxa, even at a family level. On the other side, we realised that almost all literature used for the identification of the samples had a noticeable geographical bias, making thus necessary to know the capture area to use the proper key. Additionally, the characters used in the description of taxonomic groups were often incomparable (as two parts of the world were ignoring each other), not only between different authors but also between two different species described in the same article. After that, we did not need too much time and read too many papers to realise that our initial concept of systematic harmony and stability of this family was quite wrong and the more information we gathered more difficult was to choose what could be considered as valid and where should we focus in an intent to clarify the situation. All these preliminary circumstances afford evidences of a rather common feeling among the taxonomists engaged in the study of this family: the taxonomic and systematic situation is chaotic. This crude sentence, differently worded depending on the author, is understood when reading some of the general works on this family and higher taxa. We could also read and receive the different opinions, depending on the ichthyologist, on which taxa should be assigned to the family Triglidae and that neither the initial picture we made of it, defined as is explained in this memoir, could be considered as valid. Some of these researchers thought that the family Triglidae is clearly distinguished from the family Peristediidae, while others wrote that both taxa should be considered as a single family Triglidae eventually splitted into two subfamilies: Triglinae and Peristediinae. Even some of the older authors included species in Triglidae which actually belong to families absolutely different as Cottidae. Following the recommendation of authors with a deeper phylogenetic background that ours we made the decision of considering the (for some authors) families Triglidae and Peristediidae as a single family Triglidae. It was at that time when we decided to modify the original objective of our research to focus it on a supraspecific revision which, in our opinion, seemed to be much more necessary than the specific with the aim of globally systematize the family Triglidae: from its definition down to the subgeneric level, leaving the species clarification for later works once the systematics of the family is clarified. With this new final goal in mind and the commitment of giving short but clear descriptions of the supraspecific taxa by using valid common characters for any species anywhere in the world, we began the task now delivered. Today, we believe to have reached the point to make a proposal on the organisation of the family Triglidae at a supraspecific level which pretends to contribute with a subjective approach to the natural classification of this group. In the chapter ANTECEDENTS (BACKGROUND) a revision of the different situations found in the taxonomic literature of the family is done. In a very brief way, some of the inconsistencies are presented. Those inconsistencies may confuse the student and thus make necessary a more detailed reading to find out the correct part of the works for those not familiar with the matter. On the other side and in the same chapter, it is presented the systematic position of the family based on the revision of the major works since Linnaeus (1758). The situation above mentioned can be clearly seen when discussing those revisions where even is uncertain the systematics of the Order Scorpaeniformes to which the family Triglidae is assigned. Finally, in the chapter BACKGROUND and under the section named CRONOLOGIA DE LES DESCRIPCIONS (CHRONOLOGY OF DESCRIPTIONS) the different taxa between the family and the subgenera described up-to-date since Linnaeus (1758) are explained and commented. This intends to reveal the intra-familiar confusion regarding the taxa definition and the different usage throughout the years in modern ichthyology. In the chapter devoted to METODOLOGIA (METHODOLOGY) the species studied and their geographical origin are listed to make a picture of the amount of information used in the present study. The largest part, however, of this chapter is devoted to the description of the morphological and meristic variables used in this work. This is also a proposal on the standardization of those variables with the aim of its use by as many ichthyologists of this family as possible. In this chapter too, the use of the methods of numerical taxonomy are described which are used as a complementary tool for the definition of the different groups treated in this study. In any case, besides the power of some of these techniques of numerical taxonomy, this methodology has never been used as the final argument to define the characters of the different taxa treated in detail in the chapter RESULTATS (RESULTS) as the human point of view has always been considered as the primary when clear diverging conclusions have been reached by any of those two means. Chapter 5 deals with the RESULTS although part of the content of the BACKGROUND could be also included in the former. The information has been structured into chapters in such a way that the reader can follow a chronological path of the overall situation and thus the results of the study be easier understood. In this fifth chapter, and starting from the concept of a single family without predefined divisions, this taxon is splitted into groups mostly using meristic characters beginning at the family level and going down until the subgenus. Once a starting group is separated into two or more units, its differentiating features are given and the species accomplishing them are assigned to it. For stability reasons most taxa names are maintained although these are redefined based on the differentiating features found and used in the separation of groups. Due to unavoidable reasons, only a new taxon of subgenus rank has been described. After the completion of the study we reach the conclusion that the Family Triglidae is structured as a systematic unit including two Subfamilies (Peristedioninae and Triglinae), five Tribes (Gargariscini, Peristedionini, Prionotini, Pterygotriglini and Triglini), nine Genera (Gargariscus, Heminodus, Peristedion, Satyrichthys, Prionotus, Pterygotrigla, Uradia, Lepidotrigla and Trigla) and sixteen Subgenera (Heminodus, Paraheminodus, Bellator, Prionotus, Bovitrigla, Dixiphichthys, Otohime, Pterygotrigla, Lepidotrigla, Pectorisquamis subgen. nov., Paratrigla Aspitrigla, Chelidonichthys, Eutrigla, Trigla and Trigloporus). An important part of this work is the INTRODUCCIÓ A LA BIOGEOGRAFIA DE LA FAMÍLIA TRIGLIDAE (INTRODUCTION TO THE BIOGEOGRAPHY OF THE FAMILY TRIGLIDAE). Indeed this is the first world-wide approach to the geographical distribution of the family. This chapter is built by maps of the FAO fishing areas for each of the taxa given in the RESULTS in such a way that the reader can graphically see the distribution of any group in the oceans and seas of the Earth. We try to explain this introduction to the biogeographic distribution by means of a radiation hypothesis located in the Pangea of the Triassic period. This chapter is complemented with a list of the different species that can be found in each of the geographical areas of the world. Besides the CONCLUSIONS which implicitly have been cited in this abstract, this Ph.D. manuscript is finished with a chapter on the LITERATURE. In it not only the works cited in the body of the text have been listed but also a series of taxonomic papers on the family Triglidae that, although not exhaustive, are the majority of the papers published by modern ichthyologist
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Revisió taxonòmica mundial de la família Triglidae (Pisces, Scorpaeniformes)
'Edicions de la Universitat de Barcelona', 1997Co-Authors: Cerro Ramon, Lluís I DelAbstract:El present treball parteix de la base d'estudi dels exemplars de la Família Triglidae capturats dintre del Programa de Recerca anomenat Fundaments for the Restructuration of the Demersal Fisheries in the Pacific Mexican Coast finançat per la Comunitat Europea. En el seu inici, i a manca de més informació, hom considerà seriosament la possibilitat de l'estudi taxonòmic de les espècies d'aquesta família com a matèria interessant d'anàlisi. Amb aquesta decisió, donàvem per fet que la sistemàtica del grup a nivell supra-específic era clara i, a més, que el grup, és a dir, la família Triglidae, estava clarament assentada dins l'organització del Regne Animal. Amb aquesta idea inicial, hom començà a triar i conservar mostres de lluernes per a llur estudi posterior a terra. Amb aquest material obtingut en aigües del Pacífic oriental, afegit a les mostres conservades a les Col•leccions Biològiques de Referència (CBR) de l'Institut de Ciències del Mar (ICM), creguérem disposar d'un bon punt de sortida per a un treball d'aquestes característiques. La revisió inicial dels exemplars conservats a les nostres col•leccions i dels que amablement rebérem en préstec d'algunes institucions de tot el món, juntament amb l'estudi i anàlisi bibliogràfics, no feu altre cosa que aprofundir la sensació que teníem de confusió general a l'hora de classificar els peixos de la família. Sorprenentment, fins i tot els treballs publicats recentment palesaven aquest fet i alguns dels autors llegits demanaven explícitament una revisió global de certs taxa supra-específics, fins i tot a nivell de la família. Per altra banda, ens adonàrem que quasi tota la bibliografia utilitzada per a la identificació de les mostres tenia un fort biaix geogràfic, fent necessari conèixer l'àrea de captura dels individus per tal de poder utilitzar la clau escaient. A més a més, els caràcters utilitzats per a la descripció de grups eren sovint incomparables (com si dues parts del món s'ignoressin), no tant sols entre diferents autors ans també entre dues espècies descrites en el mateix treball. Segons això, no ens va caldre gaire temps ni llegir gaires treballs per veure que la nostra concepció inicial d'harmonia i estabilitat sistemàtica de la família era força equivocada i, com més informació rebíem, més difícil se'ns feia esbrinar què podia donar-se per bo i on calia aprofundir per mirar de clarificar. Totes aquestes circumstàncies preliminars podran donar una idea d'un sentiment més o menys estès entre els investigadors embrancats en la família: la situació taxonòmica i sistemàtica és caòtica. Aquesta crua sentència, amb paraules diferents segons l'autor, es fa palesa llegint alguns dels treballs generals sobre la família i taxa superiors. També ens adonàrem dels diversos parers sobre quins taxa havien d'assignar-se a la família Triglidae, depenent de l'ictiòleg que opinava, i que tampoc la imatge inicial que ens havíem fet d’aquesta família, definida de la manera que hom veurà més endavant, podia considerar-se vàlida. Alguns d'aquells investigadors pensaven que la família Triglidae és clarament diferent de l’anomenada família Peristediidae, mentre d'altres escrigueren que ambdós taxa havien de considerar-se una única família Triglidae, en qualsevol cas subdividit en dues subfamílies: Triglinae i Peristediinae. Hi havia qui, fins i tot (alguns dels antics), hi feia entrar espècies que pertanyen a famílies absolutament diferents com, per exemple, Cottidae. Per recomanació d'autors amb més base filogenètica de la que nosaltres disposàvem, prenguérem la decisió de considerar el que per alguns eren les famílies Triglidae i Peristediidae com a una unitat englobada en la família Triglidae. Fou aleshores quan decidirem modificar el rumb inicial de la recerca per tal d'enfocar-lo vers una revisió supra-específica, al nostre albir molt més necessària que l’específica per tal de sistematitzar globalment la família: des de la definició d'aquesta fins el nivell de subgènere, deixant per més endavant la clarificació de la situació de les espècies un cop creguéssim organitzada aquella. Amb aquesta fita final i la idea de trobar descripcions curtes però clares dels diferents taxa amb trets vàlids per a qualsevol espècie en qualsevol lloc del món, endegàrem la tasca que hom ara presenta. Enguany, creiem haver arribat al moment de fer una proposta d'organització a nivell supra-específic de la família Triglidae, que no pretén altra cosa que intentar acostar-se subjectivament a la classificació natural del grup. En el capítol ANTECEDENTS, per una banda, hom fa un repàs de les diverses situacions que poden trobar-se en la bibliografia de caire taxonòmic de la família. Hom palesa, de forma molt resumida, algunes de les incongruències que poden trobar s'hi i que, pel lector no avesat en el tema, poden dur a confusió i a una necessitat de revisió amb detall per tal d'esbrinar la part correcta dels treballs. Per altra banda, en el mateix capítol, hom fa una exposició sobre la posició sistemàtica de la família Triglidae en base a una sèrie de treballs seleccionats des de la publicació de la desena edició del treball de Linné (1758). Amb aquestes revisions hom palesa la situació, esmentada més amunt, de que fins i tot no està clara la sistemàtica de l'Ordre Scorpaeniformes al que pertany la família estudiada. Finalment, en els ANTECEDENTS i dintre de l'apartat anomenat CRONOLOGIA DE LES DESCRIPCIONS, hom descriu i comenta els diferents taxa de rang comprés entre el familiar i el subgenèric descrits tanmateix des del treball de Linné (1758). Amb això hom pretén informar al lector de la confusió intra-familiar pel que fa a la definició de taxa i al diferent ús que de cadascun d'ells s'ha anat fent al llarg de la història de la ictiologia moderna. En el capítol dedicat a la METODOLOGIA, hom cita les espècies estudiades i llur procedència geogràfica, per tal de donar al lector una indicació de l'abast de la informació que hom disposa per a la realització de l'estudi. La part més extensa, però, del conjunt d'aquest capítol es dedica a la descripció de les variables morfomètriques i merístiques utilitzades al llarg dels anys de realització del treball. Amb això es fa la proposta d'estandardització de les esmentades variables amb la finalitat d'assolir la uniformització de la presa de dades per part dels investigadors dedicats a l'estudi de la família. Finalment, i dins del mateix capítol, es defineixen les bases d'utilització dels mètodes de taxonomia numèrica emprats com a eina complementària per a la definició dels diferents grups tractats en aquest estudi. En qualsevol cas, cal tenir en compte que, malgrat la potència d'algunes tècniques de taxonomia numèrica, aquesta metodologia no s'ha emprat en cap moment com a mètode definitori de les característiques dels diferents taxa tractats amb més detall en el capítol de RESULTATS, ans sempre ha estat prioritària, en cas de divergències clares, la visió humana del problema. El capítol 5 fa referència als RESULTATS tot i que bona part de l'anomenat ANTECEDENTS conté dades que podrien incloure's en el primer i que no s'ha fet per tal de mantenir un fil conductor que facilités la comprensió cronològica de la situació i ajudés a veure els resultats. En aquest capítol, i partint de la base d’una única família sense divisions preestablertes, hom va fent separacions en base a caràcters bàsicament merístics partint del nivell de família fins arribar al nivell subgenèric. Un cop clarificada la separació en dos o més grups del conjunt de partida, hom en dóna els trets diferenciadors i s'hi inclouen, finalment, les diverses espècies que compleixen les característiques citades. A partir d'ací, tot i que es mantenen per raons d'estabilitat de la nomenclatura els noms de la immensa majoria de taxa, aquests són redefinits en base als caràcters definitoris emprats per a la separació. Per necessitats ineludibles, al nostre parer, només un taxon de nivell subgenèric ha estat anomenat com a nou. Amb tot això, hom arriba a la conclusió que la Família Triglidae està estructurada com una unitat sistemàtica i que inclou dues Subfamílies (Peristedioninae i Triglinae), cinc Tribus (Gargariscini, Peristedionini, Prionotini, Pterygotriglini i Triglini), nou Gèneres (Gargariscus, Heminodus, Peristedion, Satyrichthys, Prionotus, Pterygotrigla, Uradia, Lepidotrigla i Trigla) i setze Subgèneres (Heminodus, Paraheminodus, Bellator, Prionotus, Bovitrigla, Dixiphichthys, Otohime, Pterygotrigla, Lepidotrigla, Pectorisquamis subgen. nov., Paratrigla Aspitrigla, Chelidonichthys, Eutrigla, Trigla i Trigloporus). Part important d'aquest treball consisteix en la INTRODUCCIÓ A LA BIOGEOGRAFIA DE LA FAMÍLIA TRIGLIDAE. Certament, aquesta és la primera aproximació a nivell mundial que hom fa de la distribució geogràfica de la família arreu del món. Aquest capítol s'il•lustra amb la inclusió de mapes, partint de la base de les àrees de pesca de FAO, per a cadascun dels taxa tractats en el capítol de RESULTATS, de tal manera que pot veure's la localització d'aquells en els diferents mars i oceans del planeta. Aquesta introducció biogeogràfica intenta explicar-se mitjançant una HIPÒTESI DE RADIACIÓ a partir de l'hipotètic punt d'origen en el Pangea i durant el període Triàsic. Aquest capítol es complementa amb un llistat de les diferents espècies que hom pot trobar en cadascuna de les àrees geogràfiques del món. Deixant de banda les CONCLUSIONS, part de les quals s'han inclòs de forma implícita en aquest RESUM, el capítol de BIBLIOGRAFIA clou la present memòria de Tesi Doctoral. En aquest s'han inclòs, a banda dels treballs citats en el text, tota una sèrie de treballs de caire taxonòmic sobre la família Triglidae i que, malgrat no ésser exhaustiu, sí que representa la major part del que s'ha publicat en temps de la ictiologia moderna.This work arises from the study of the specimens of the Family Triglidae collected during the research program named Fundaments for the Restructuration of the Demersal Fisheries in the Pacific Mexican Coast which was financed by the European Commission. Initially, and with the information available at that time, we seriously considered the possibility of the taxonomic study of the species of this family as an interesting subject for analysis. By making this decision we were accepting beforehand that the systematics of this group at a supraspecific level was clear and that of the group itself, the family Triglidae, was also precisely defined and settled within the organisation of the Animal Kingdom. Having this initial idea in mind, we began to choose and preserve many samples of gurnards for their later study on land. With these specimens collected in waters of the Eastern Pacific ocean plus those preserved in the Biological Reference Collections (CBR) of the Institut de Ciències del Mar (ICM) at Barcelona, we believed to have a good starting point to face the work in mind. The initial revision of the specimens preserved in our collections and those kindly loaned by research institutions from all around the world combined with the study and analysis of the literature rapidly increased our feeling of a general confusion on the classification of the species of the family. Surprisingly, even recent papers shared this feeling of ours and some of the authors explicitly claimed for a global revision of several supraspecific taxa, even at a family level. On the other side, we realised that almost all literature used for the identification of the samples had a noticeable geographical bias, making thus necessary to know the capture area to use the proper key. Additionally, the characters used in the description of taxonomic groups were often incomparable (as two parts of the world were ignoring each other), not only between different authors but also between two different species described in the same article. After that, we did not need too much time and read too many papers to realise that our initial concept of systematic harmony and stability of this family was quite wrong and the more information we gathered more difficult was to choose what could be considered as valid and where should we focus in an intent to clarify the situation. All these preliminary circumstances afford evidences of a rather common feeling among the taxonomists engaged in the study of this family: the taxonomic and systematic situation is chaotic. This crude sentence, differently worded depending on the author, is understood when reading some of the general works on this family and higher taxa. We could also read and receive the different opinions, depending on the ichthyologist, on which taxa should be assigned to the family Triglidae and that neither the initial picture we made of it, defined as is explained in this memoir, could be considered as valid. Some of these researchers thought that the family Triglidae is clearly distinguished from the family Peristediidae, while others wrote that both taxa should be considered as a single family Triglidae eventually splitted into two subfamilies: Triglinae and Peristediinae. Even some of the older authors included species in Triglidae which actually belong to families absolutely different as Cottidae. Following the recommendation of authors with a deeper phylogenetic background that ours we made the decision of considering the (for some authors) families Triglidae and Peristediidae as a single family Triglidae. It was at that time when we decided to modify the original objective of our research to focus it on a supraspecific revision which, in our opinion, seemed to be much more necessary than the specific with the aim of globally systematize the family Triglidae: from its definition down to the subgeneric level, leaving the species clarification for later works once the systematics of the family is clarified. With this new final goal in mind and the commitment of giving short but clear descriptions of the supraspecific taxa by using valid common characters for any species anywhere in the world, we began the task now delivered. Today, we believe to have reached the point to make a proposal on the organisation of the family Triglidae at a supraspecific level which pretends to contribute with a subjective approach to the natural classification of this group. In the chapter ANTECEDENTS (BACKGROUND) a revision of the different situations found in the taxonomic literature of the family is done. In a very brief way, some of the inconsistencies are presented. Those inconsistencies may confuse the student and thus make necessary a more detailed reading to find out the correct part of the works for those not familiar with the matter. On the other side and in the same chapter, it is presented the systematic position of the family based on the revision of the major works since Linnaeus (1758). The situation above mentioned can be clearly seen when discussing those revisions where even is uncertain the systematics of the Order Scorpaeniformes to which the family Triglidae is assigned. Finally, in the chapter BACKGROUND and under the section named CRONOLOGIA DE LES DESCRIPCIONS (CHRONOLOGY OF DESCRIPTIONS) the different taxa between the family and the subgenera described up-to-date since Linnaeus (1758) are explained and commented. This intends to reveal the intra-familiar confusion regarding the taxa definition and the different usage throughout the years in modern ichthyology. In the chapter devoted to METODOLOGIA (METHODOLOGY) the species studied and their geographical origin are listed to make a picture of the amount of information used in the present study. The largest part, however, of this chapter is devoted to the description of the morphological and meristic variables used in this work. This is also a proposal on the standardization of those variables with the aim of its use by as many ichthyologists of this family as possible. In this chapter too, the use of the methods of numerical taxonomy are described which are used as a complementary tool for the definition of the different groups treated in this study. In any case, besides the power of some of these techniques of numerical taxonomy, this methodology has never been used as the final argument to define the characters of the different taxa treated in detail in the chapter RESULTATS (RESULTS) as the human point of view has always been considered as the primary when clear diverging conclusions have been reached by any of those two means. Chapter 5 deals with the RESULTS although part of the content of the BACKGROUND could be also included in the former. The information has been structured into chapters in such a way that the reader can follow a chronological path of the overall situation and thus the results of the study be easier understood. In this fifth chapter, and starting from the concept of a single family without predefined divisions, this taxon is splitted into groups mostly using meristic characters beginning at the family level and going down until the subgenus. Once a starting group is separated into two or more units, its differentiating features are given and the species accomplishing them are assigned to it. For stability reasons most taxa names are maintained although these are redefined based on the differentiating features found and used in the separation of groups. Due to unavoidable reasons, only a new taxon of subgenus rank has been described. After the completion of the study we reach the conclusion that the Family Triglidae is structured as a systematic unit including two Subfamilies (Peristedioninae and Triglinae), five Tribes (Gargariscini, Peristedionini, Prionotini, Pterygotriglini and Triglini), nine Genera (Gargariscus, Heminodus, Peristedion, Satyrichthys, Prionotus, Pterygotrigla, Uradia, Lepidotrigla and Trigla) and sixteen Subgenera (Heminodus, Paraheminodus, Bellator, Prionotus, Bovitrigla, Dixiphichthys, Otohime, Pterygotrigla, Lepidotrigla, Pectorisquamis subgen. nov., Paratrigla Aspitrigla, Chelidonichthys, Eutrigla, Trigla and Trigloporus). An important part of this work is the INTRODUCCIÓ A LA BIOGEOGRAFIA DE LA FAMÍLIA TRIGLIDAE (INTRODUCTION TO THE BIOGEOGRAPHY OF THE FAMILY TRIGLIDAE). Indeed this is the first world-wide approach to the geographical distribution of the family. This chapter is built by maps of the FAO fishing areas for each of the taxa given in the RESULTS in such a way that the reader can graphically see the distribution of any group in the oceans and seas of the Earth. We try to explain this introduction to the biogeographic distribution by means of a radiation hypothesis located in the Pangea of the Triassic period. This chapter is complemented with a list of the different species that can be found in each of the geographical areas of the world. Besides the CONCLUSIONS which implicitly have been cited in this abstract, this Ph.D. manuscript is finished with a chapter on the LITERATURE. In it not only the works cited in the body of the text have been listed but also a series of taxonomic papers on the family Triglidae that, although not exhaustive, are the majority of the papers published by modern ichthyologist
Tetsuji Nakabo - One of the best experts on this subject based on the ideXlab platform.
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first record of albinism in the rockfish sebastes pachycephalus complex Scorpaeniformes scorpaenidae
Ichthyological Research, 2013Co-Authors: Nozomu Muto, Yoshiaki Kai, Tsutomu Noda, Tetsuji NakaboAbstract:Albinism, a condition resulting from a group of genetically determined disorders of the melanin pigmentary system (Kinnear et al. 1985), occurs in two forms: (1) complete albinism, which is phenotypically expressed as a lack of integumentary and retinal melanin, indicating defects in the integumentary and retinal melanophores, and (2) partial albinism or leucism. The latter describes an individual with reduced or absent integumentary pigment, but with pigmented retinas, resulting in diminished or no body coloration and darkly pigmented eyes. Primarily used in herpetological literature, the term leucism has recently been suggested as appropriate for ichthyology (Clark 2002). Complete albinism and leucism have been reported in numerous teleost species (e.g., Follett and Dempster 1966; Huzita and Nishino 1966; Dawson 1967; Shinohara and Amaoka 1993; Delgado et al. 2009; Mansur 2011; Pillai and Somvanshi 2011), as well as among chondrichthyans (e.g., Talent 1973; Ishihara et al. 2001; Bottaro et al. 2005; Sandoval-Castillo et al. 2006; Reum et al. 2008; Veena et al. 2011). However, in rockfishes of the genus Sebastes Cuvier 1829, only one record of albinism has been documented to date [Follet and Dempster 1966, as Sebastodes melanostomus (Eigenmann and Eigenmann 1890)], an unusual example of leucism, termed ‘‘melanalbinism’’ by the authors. On 28 February 2012, a single leucistic individual of Sebastes pachycephalus complex was captured alive in a basket trap in Kamaishi Bay, Iwate Prefecture, Japan (Fig. 1). A brief description of the specimen is given below. Morphological characters were examined following Muto et al. (2011) except for the lower jaw length, which was taken as the distance between the symphysis and the posteriormost point of the dentary, after fixation in 10 % formalin and preservation in 70 % ethanol. Terminology of the head spines follows Randall and Eschmeyer (2001). Counts and measurements were taken from the right side of the body, the left side having been damaged. The specimen was deposited in the Kyoto University Fish Collection (FAKU). Description (based on FAKU 134960, 245.3 mm in standard length). The following measurements are expressed as percentage of standard length: head length 41.3; snout length 10.5; orbital length 8.6; postorbital length 22.6; upper jaw length 18.3; lower jaw length 16.6; body width 25.6; caudal peduncle depth 12.1; preanal length 68.2; predorsal length 32.7; prepelvic length 46.9; longest dorsal-fin spine (both fourth and fifth) length 15.3; longest dorsal-fin soft ray (fourth) length 16.4; first anal-fin This article was registered to the Official Register of Zoological Nomenclature (ZooBank) as DE8B323D-8BC9-4B36-90D5-6F3EC46CACE5. This article was published as an Online First article on the online publication date shown on this page. The article should be cited by using the doi number.
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taxonomic review of the sebastes pachycephalus complex Scorpaeniformes scorpaenidae
Zootaxa, 2013Co-Authors: Yoshiaki Kai, Tetsuji NakaboAbstract:A taxonomic review of the Sebastes pachycephalus complex established the existence of two valid species, S. pachyceph-alus and S. nudus . Similarities between them include: cranium armed dorsally with robust preocular, supraocular, postoc-ular, and parietal spines; interorbital space concave; lower jaw lacking scales, shorter than upper jaw; thickened rays in ventral half of pectoral fin; dorsal fin usually with 13 spines and 12 soft-rays; pored lateral line scales 27–35 (usually 29– 33). However, S. pachycephalus is distinguishable from the latter in having minute scales below the entire dorsal-fin spine base (vs. lacking minute scales below first to fifth or variously to the posteriormost spine in the latter), dark spots scattered on the dorsal, anal and caudal fins (vs. no distinct dark spots), and lacking distinct colored markings on the dorsum (vs. yellow or reddish-brown markings present). Although both species occur off the southern Korean Peninsula and in the Bohai and Yellow Seas, in Japanese waters, the former is distributed from northern Honshu Is. southward to southern Ky-ushu Is., whereas the latter extends from southern Hokkaido southward along the Pacific coast of Japan to Kanagawa, and along the Sea of Japan coast to northern Kyushu Is., including the Seto Inland Sea. Sebastes nigricaus , S. nigricans , and S. latus are confirmed as junior synonyms of S. pachycephalus , and S. chalcogrammus as junior synonym of S. nudus , based on the examination of type specimens.
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genetic and morphological divergence within the sebastes pachycephalus complex Scorpaeniformes scorpaenidae
Ichthyological Research, 2011Co-Authors: Yoshiaki Kai, Kouji Nakayama, Tetsuji NakaboAbstract:Genetic and morphological divergence among the four subspecies in the Sebastes pachycephalus complex (S. pachycephalus pachycephalus, S. p. nigricans, S. p.nudus and S. p. chalcogrammus) was clarified. Principal coordinate analysis (PCoA) based on AFLP clearly divided 55 specimens of the complex into two groups, the S. p. pachycephalus–S. p. nigricans group (P-Ni group) and the S. p. nudus–S. p. chalcogrammus group (Nu-C group), although three specimens occupied intermediate positions. The minimum spanning network (MSN) based on partial sequences of the mitochondrial control region (mtCR) failed to separate either the P-Ni and Nu-C groups or the four subspecies into distinct clades, although restricted gene flow and genetic differentiation between the former were indicated by the FST estimation. Differences in morphological characters, including counts of pectoral fin rays and counts of dorsal fin spines lacking basal scales, were also evident between the two groups. However, little or no genetic or morphological difference was found between the two subspecies within each group. It was concluded that the P-Ni and Nu-C groups of the S. pachycephalus complex actually represent two different species, which is further supported by their sympatric distribution. Differences in dorsal body coloration and the presence or absence of brown spots on the ventral surface, which were formerly used to discriminate between four “subspecies,” may simply represent intraspecific variation. The three specimens occupying intermediate positions in the AFLP PCoA also occupied equivocal positions between the two species in the principal component analysis (PCA) based on morphometric characters, suggesting that they were hybrids between the two species. The star-shaped MSN of mtCR, which lacks distinct clades representing the two species, may be due to not only interspecific hybridization but also the sharing of ancestral haplotypes.
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genetic and morphological differences between sebastes vulpes and s zonatus teleostei Scorpaeniformes scorpaenidae
2011Co-Authors: Nozomu Muto, Yoshiaki Kai, Tetsuji NakaboAbstract:The taxonomic status of Sebastes vulpes and S. zonatus were clarified by comprehensive genetic (amplif ied fragment length polymorphisms [AFLP] and mitochondrial DNA [mtDNA] variation) and morphological analyses on a total of 65 specimens collected from a single locality. A principal coordinate analysis based on 364 AFLP loci separated the specimens completely into two genetically distinct groups that corresponded to S. vulpes and S. zonatus according to body coloration and that indicated that they are reproductively isolated species. Significant morphological differences were also evident between the two groups; 1) separation by principal component analysis based on 31 measurements, and 2)separation according to differences in counts of gill rakers and dorsal-fin spines without basal scales, and in the frequencies of specimens with small scales on the lower jaw. Restriction of gene flow between the two groups was also indicated by the pairwise ΦST values estimated from variations in partial sequences from the mtDNA control region, although the minimum spanning network did not result in separation into distinct clades. The latter was likely due to incomplete lineage sorting between S. vulpes and S. zonatus owing to their recent speciation.
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Taxonomic review of the Sebastes inermis species complex (Scorpaeniformes: Scorpaenidae)
Ichthyological Research, 2008Co-Authors: Tetsuji NakaboAbstract:A taxonomic review of three color morphotypes of the Sebastes inermis species complex established the existence of three valid species, viz. S. inermis , S. ventricosus , and S. cheni . The complex is defined by having two sharp lachrymal spines, the head weakly armed with nasal, preocular, supraocular and parietal spines, and the caudal fin not distinctly emarginated. Sebastes inermis , known from southern Hokkaido southward to Kyushu, Japan, and the southern part of the Korean Peninsula, is characterized as follows: body dark red or light brown dorsally and laterally when fresh, pectoral fin extending beyond level of anus when depressed, pectoral-fin rays 15, anal-fin rays 7, pored lateral line scales 36–44 and gill rakers 31–37. Sebastes ventricosus , known from Iwate and Ishikawa Prefecture southward to Kyushu, Japan, and the southern part of the Korean Peninsula, is characterized as follows: body somewhat greenish-black dorsally and dark silver ventrally when fresh, pectoral-fin rays 16, anal-fin rays 7–8, pored lateral line scales 43–49, and gill rakers 35–39. Sebastes cheni , known from Iwate and Akita Pref. southward to Kyushu, Japan, and the southern part of the Korean Peninsula, is characterized as follows: body dark golden-brown dorsally and laterally when fresh, pelvic fin extending beyond anus when depressed, pectoral-fin rays 17, anal-fin rays 8, pored lateral line scales 37–46 and gill rakers 32–37. In the genetic analysis, the presence or absence of two AFLP fragments was completely fixed among the three species. Sebastes tokionis and S. guentheri are regarded as junior synonyms of S. inermis and S. ventricosus , respectively. A lectotype is designated for S. cheni , and a key to the three species of the S. inermis species complex provided.
Kristian R Von Schalburg - One of the best experts on this subject based on the ideXlab platform.
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genomics of sablefish anoplopoma fimbria expressed genes mitochondrial phylogeny linkage map and identification of a putative sex gene
BMC Genomics, 2013Co-Authors: Eric Rondeau, Amber M Messmer, Dan S Sanderson, Stuart G Jantzen, Kristian R Von Schalburg, David R Minkley, Jong S Leong, Graham M Macdonald, Amanda E Davidsen, William A ParkerAbstract:The sablefish (order: Scorpaeniformes) is an economically important species in commercial fisheries of the North Pacific and an emerging species in aquaculture. Aside from a handful of sequences in NCBI and a few published microsatellite markers, little is known about the genetics of this species. The development of genetic tools, including polymorphic markers and a linkage map will allow for the successful development of future broodstock and mapping of phenotypes of interest. The significant sexual dimorphism between females and males makes a genetic test for early identification of sex desirable. A full mitochondrial genome is presented and the resulting phylogenetic analysis verifies the placement of the sablefish within the Scorpaeniformes. Nearly 35,000 assembled transcript sequences are used to identify genes and obtain polymorphic SNP and microsatellite markers. 360 transcribed polymorphic loci from two sablefish families produce a map of 24 linkage groups. The sex phenotype maps to sablefish LG14 of the male map. We show significant conserved synteny and conservation of gene-order between the threespine stickleback Gasterosteus aculeatus and sablefish. An additional 1843 polymorphic SNP markers are identified through next-generation sequencing techniques. Sex-specific markers and sequence insertions are identified immediately upstream of the gene gonadal-soma derived factor (gsdf), the master sex determinant locus in the medaka species Oryzias luzonensis. The first genomic resources for sablefish provide a foundation for further studies. Over 35,000 transcripts are presented, and the genetic map represents, as far as we can determine, the first linkage map for a member of the Scorpaeniformes. The observed level of conserved synteny and comparative mapping will allow the use of the stickleback genome in future genetic studies on sablefish and other related fish, particularly as a guide to whole-genome assembly. The identification of sex-specific insertions immediately upstream of a known master sex determinant implicates gsdf as an excellent candidate for the master sex determinant for sablefish.
