Revalidation of the Argentinian pouched lamprey Geotria macrostoma (Burmeister, 1868) with molecular and morphological evidence

Background The Argentinian pouched lamprey, classified as Petromyzon macrostomus Burmeister, 1868 was first described in 1867 in De La Plata River, in Buenos Aires, Argentina, and subsequently recorded in several rivers from Patagonia. Since its original description, the validity of P. macrostomus was questioned by several ichthyologists and 36 years after its original discovery it was considered a junior synonym of Geotria australis Gray, 1851. For a long time, the taxonomic status of G. australis has been uncertain, largely due to the misinterpretations of the morphological alterations that occur during sexual maturation, including the arrangement of teeth, size and position of fins and cloaca, and the development of an exceptionally large gular pouch in males. In this study, the taxonomic status of Geotria from across the "species" range was evaluated using both molecular analysis and examination of morphological characteristics. Methodology/principal findings Phylogenetic and species delimitation analyses based on mitochondrial DNA sequences of Cytochrome b (Cyt b) and Cytochrome C Oxidase Subunit 1 (COI) genes, along with morphological analysis of diagnostic characters reported in the original descriptions of the species were used to assess genetic and morphological variation within Geotria and to determine the specific status of the Argentinian lamprey. These analyses revealed that Geotria from Argentina constitutes a well differentiated lineage from Chilean and Australasian populations. The position of the cloaca and the distance between the second dorsal and caudal fins in sub-adult individuals, and at previous life stages, can be used to distinguish between the two species. In addition, the genetic distance between G. macrostoma and G. australis for the COI and Cyt b mitochondrial genes is higher than both intra-and inter-specific distances reported for other Petromyzontiformes. Conclusions/significance Our results indicate that the Argentinian pouched lamprey, found along a broad latitudinal gradient on the south-west Atlantic coast of South America, should be named as Geotria macrostoma (Burmeister, 1868) and not as G. australis Gray 1851, returning to its earliest valid designation in Argentina. Geotria macrostoma can now be considered as the single lamprey species inhabiting Argentinian Patagonia, with distinct local adaptations and evolutionary potential. It is essential that this distinctiveness is recognized in order to guide future conservation and management actions against imminent threats posed by human actions in the major basins of Patagonia.Fil: Riva Rossi, Carla Marcela. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Centro Nacional Patagónico. Instituto de Diversidad y Evolución Austral; ArgentinaFil: Barrasso, Diego Andrés. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Centro Nacional Patagónico. Instituto de Diversidad y Evolución Austral; Argentina. Universidad Nacional de La Plata. Facultad de Ciencias Naturales y Museo. Departamento Científico Zoología Vertebrados; ArgentinaFil: Baker, Cindy. National Institute Of Water And Atmospheric Research; Nueva ZelandaFil: Quiroga, Analía Pamela. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Centro Nacional Patagónico. Instituto de Diversidad y Evolución Austral; ArgentinaFil: Baigún, Claudio Rafael M.. Universidad Nacional de San Martín. Instituto de Investigación e Ingeniería Ambiental. - Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Parque Centenario. Instituto de Investigación e Ingeniería Ambiental; ArgentinaFil: Basso, Nestor Guillermo. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Centro Nacional Patagónico. Instituto de Diversidad y Evolución Austral; Argentin

Twist exome capture allows for lower average sequence coverage in clinical exome sequencing

Background Exome and genome sequencing are the predominant techniques in the diagnosis and research of genetic disorders. Sufficient, uniform and reproducible/consistent sequence coverage is a main determinant for the sensitivity to detect single-nucleotide (SNVs) and copy number variants (CNVs). Here we compared the ability to obtain comprehensive exome coverage for recent exome capture kits and genome sequencing techniques. Results We compared three different widely used enrichment kits (Agilent SureSelect Human All Exon V5, Agilent SureSelect Human All Exon V7 and Twist Bioscience) as well as short-read and long-read WGS. We show that the Twist exome capture significantly improves complete coverage and coverage uniformity across coding regions compared to other exome capture kits. Twist performance is comparable to that of both short- and long-read whole genome sequencing. Additionally, we show that even at a reduced average coverage of 70× there is only minimal loss in sensitivity for SNV and CNV detection. Conclusion We conclude that exome sequencing with Twist represents a significant improvement and could be performed at lower sequence coverage compared to other exome capture techniques

A Solve-RD ClinVar-based reanalysis of 1522 index cases from ERN-ITHACA reveals common pitfalls and misinterpretations in exome sequencing

Purpose Within the Solve-RD project (https://solve-rd.eu/), the European Reference Network for Intellectual disability, TeleHealth, Autism and Congenital Anomalies aimed to investigate whether a reanalysis of exomes from unsolved cases based on ClinVar annotations could establish additional diagnoses. We present the results of the “ClinVar low-hanging fruit” reanalysis, reasons for the failure of previous analyses, and lessons learned. Methods Data from the first 3576 exomes (1522 probands and 2054 relatives) collected from European Reference Network for Intellectual disability, TeleHealth, Autism and Congenital Anomalies was reanalyzed by the Solve-RD consortium by evaluating for the presence of single-nucleotide variant, and small insertions and deletions already reported as (likely) pathogenic in ClinVar. Variants were filtered according to frequency, genotype, and mode of inheritance and reinterpreted. Results We identified causal variants in 59 cases (3.9%), 50 of them also raised by other approaches and 9 leading to new diagnoses, highlighting interpretation challenges: variants in genes not known to be involved in human disease at the time of the first analysis, misleading genotypes, or variants undetected by local pipelines (variants in off-target regions, low quality filters, low allelic balance, or high frequency). Conclusion The “ClinVar low-hanging fruit” analysis represents an effective, fast, and easy approach to recover causal variants from exome sequencing data, herewith contributing to the reduction of the diagnostic deadlock

Distribution and abundance of the Patagonian lamprey (Geotria macrostoma) in the largest unfragmented river of southern Patagonia, Argentina

The distribution, relative abundance, and rearing habitat of larvae of the Patagonian lamprey (Geotria macrostoma) were investigated in the Santa Cruz River basin, Patagonia, Argentina, usingelectrofishing and bile acid (petromyzonol sulfate) concentration. Both techniques revealed that larvae are widely distributed along the basin, aggregated at habitats of fine substrates and slow waters. Both, density and pheromone concentrations were consistent in detecting the presence of larvae and for gauging their abundance. Throughout the basin, length distribution of larvae ranged from 10 to 122 mm; larvae of the smaller length classes were present at both, upper sections and at the lower course of the main stem river, suggesting that these sites contained 0+recruits fromthe previous spawning season. Currently construction of two hydroelectric dams in the main courseof the Santa Cruz River will interrupt the migratory corridor of adult lamprey in search of their spawning grounds and will flood critical habitats for larvae rearing. The information generated in this study may be used as guidance for developing sampling surveys for the purpose of monitoring changes in populations trends for Patagonian lamprey in this river and other Patagonian drainages altered by human activities.Fil: Quiroga, Analía Pamela. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Centro Nacional Patagónico. Instituto de Diversidad y Evolución Austral; ArgentinaFil: Baker, Cindy F.. National Institute of Water and Atmospheric Research Ltd; Nueva ZelandaFil: Baigún, Claudio Rafael M.. Universidad Nacional de San Martín. Instituto de Investigación e Ingeniería Ambiental. - Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Parque Centenario. Instituto de Investigación e Ingeniería Ambiental; ArgentinaFil: Stewart, Michael. Streamlined Environmental Ltd; Nueva ZelandaFil: Lancelotti, Julio Lucio. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Centro Nacional Patagónico. Instituto Patagónico para el Estudio de los Ecosistemas Continentales; ArgentinaFil: Riva Rossi, Carla Marcela. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Centro Nacional Patagónico. Instituto de Diversidad y Evolución Austral; Argentin

Stable isotope profiles of partially migratory salmonid populations in Atlantic rivers of Patagonia

In the present study, profiles of stable isotope composition were characterized for two species with partially migratory populations in rivers along the latitudinal gradient of Patagonia, brown trout Salmo trutta and rainbow trout Oncorhynchus mykiss. The effects of factors (e.g. ontogeny of fishes, location, species and fasting) that may influence the stable isotope analysis (SIA) were evaluated, as was SIA evaluated as a tool to assign individual fish to their corresponding ecotype. Anadromous fishes exhibited enriched δ15N (15·2 ± 1·0‰; mean ±s.d.) and δ13C (−19·2 ± 1·3‰) relative to resident fishes’δ15N (8·8 ± 1·1‰) and δ13C (−23·2 ± 2·5‰). For both species, the difference in δ15N was larger between resident (range 6·8–10·7‰) and anadromous (range 14·3–17·8‰) fishes than that in δ13C. Values of δ13C, while not as dramatically contrasting in rainbow trout, provided a powerful anadromy marker for brown trout in the region. Increases were found in both δ15N and δ13C during the spawning migration of anadromous rainbow trout, most likely due to fasting. Differences in stable isotopes between location, size and species were found, suggesting different stable isotopes base levels in freshwater environments and different trophic levels and feeding location of anadromous populations. The SIA was demonstrated as a powerful tool for ecotype discrimination in Patagonian Rivers, overriding any effect of sampling location, size or species.Fil: Ciancio Blanc, Javier Ernesto. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Centro Nacional Patagónico; ArgentinaFil: Pascual, Miguel Alberto. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Centro Nacional Patagónico; Argentina. Universidad Nacional de la Patagonia "San Juan Bosco"; ArgentinaFil: Botto, Florencia. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina. Universidad Nacional de Mar del Plata. Facultad de Cs.exactas y Naturales. Departamento de Biología. Laboratorio de Ecología; ArgentinaFil: Amaya Santi, M.. Subsecretaria de Pesca y Actividades Portuarias de Santa Cruz; ArgentinaFil: O'Neal, S.. University of Montana; Estados UnidosFil: Riva Rossi, Carla Marcela. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Centro Nacional Patagónico; ArgentinaFil: Iribarne, Oscar Osvaldo. Universidad Nacional de Mar del Plata. Facultad de Cs.exactas y Naturales. Departamento de Biología. Laboratorio de Ecología; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentin

On the invalid resurrection of the lamprey genus Exomegas Gill, 1883

The lamprey genus Exomegas Gill, 1883, was erected on the assumption that it was distinguishable from Geotria Gray, 1851, by possessing three rather than two cusps on the transverse lingual lamina (TLL). Based on literature review and examination of holotypes and new data, the authors reaffirm that the TLL of Geotria possesses two or three cusps in the adult stage. The reduction or disappearance of the middle cusp at the beginning or during the spawning run constitutes a key feature of Geotria. The resurrection of Exomegas by Firpo Lacoste, Fernández and Scioscia, Journal of Fish Biology, 2021, 1-6, 1507-1512, is therefore unjustified and not supported.Fil: Riva Rossi, Carla Marcela. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Centro Nacional Patagónico. Instituto de Diversidad y Evolución Austral; ArgentinaFil: Renaud, Claude B.. Canadian Museum of Nature; CanadáFil: Neira, Francisco J.. Neira Marine Sciences Consulting (Marscco); AustraliaFil: Baigún, Claudio Rafael M.. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina. Universidad Nacional de San Martín; ArgentinaFil: Baker, Cindy F.. National Institute Of Water And Atmospheric Research; Nueva ZelandaFil: Quiroga, Analía Pamela. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Centro Nacional Patagónico. Instituto de Diversidad y Evolución Austral; ArgentinaFil: Potter, Ian. Murdoch University; Australi

Freshwater fishes of Patagonia: conservation and fisheries

The absence of much literature on the Patagonian fish fauna in comparison with that of the neotropics, has previously been blamed on its poor species diversity. Knowledge of the fishes of Patagonia, however, rose sharply at the beginning of the present century, allowing for an understanding of the complex biogeographical history that has led to the present diversity and distribution patterns. There are several new and potential threats to biodiversity and conservation of Patagonian fishes, such as the introduction of exotic species, damming, climate change and changes geared to safeguard economic interests, often acting synergistically. A great amount of new information is now available and the aim of the present review is to articulate this knowledge in a comprehensive way in order to aid in the development of tools to face the increasing challenges posed by environmental change and human activity. Knowledge about fishes of Patagonia has grown at the same time as human actions, and presence.Fil: Cussac, Victor Enrique. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Patagonia Norte. Instituto de Investigaciones en Biodiversidad y Medioambiente. Universidad Nacional del Comahue. Centro Regional Universidad Bariloche. Instituto de Investigaciones en Biodiversidad y Medioambiente; ArgentinaFil: Habit, E.. Universidad de Concepción; ChileFil: Ciancio Blanc, Javier Ernesto. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Nacional Patagónico; ArgentinaFil: Battini, Miguel Ángel. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Patagonia Norte. Instituto de Investigaciones en Biodiversidad y Medioambiente. Universidad Nacional del Comahue. Centro Regional Universidad Bariloche. Instituto de Investigaciones en Biodiversidad y Medioambiente; ArgentinaFil: Riva Rossi, Carla Marcela. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Nacional Patagónico; ArgentinaFil: Barriga, Juan Pablo. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Patagonia Norte. Instituto de Investigaciones en Biodiversidad y Medioambiente. Universidad Nacional del Comahue. Centro Regional Universidad Bariloche. Instituto de Investigaciones en Biodiversidad y Medioambiente; ArgentinaFil: Baigún, Claudio Rafael M.. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata. Instituto de Investigaciones Biotecnológicas. Instituto de Investigaciones Biotecnológicas "Dr. Raúl Alfonsín" (sede Chascomús). Universidad Nacional de San Martín. Instituto de Investigaciones Biotecnológicas. Instituto de Investigaciones Biotecnológicas "Dr. Raúl Alfonsín" (sede Chascomús); ArgentinaFil: Crichigno, Sonia Alejandra. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Patagonia Norte. Instituto de Investigaciones en Biodiversidad y Medioambiente. Universidad Nacional del Comahue. Centro Regional Universidad Bariloche. Instituto de Investigaciones en Biodiversidad y Medioambiente; Argentin

Fish and Fisheries of the Patagonian Steppe

The Patagonian steppe is a vast territory with a diverse array of aquatic environments with low fish richness, including several exotic species which are mostly salmonids. Unlike the Andean region, knowledge of the ichthyofauna and fisheries of the Patagonian plateau is comparatively scarce. The characteristics of the ichthyofauna and their assemblages and fisheries vary greatly in the large basins that cross the steppe. Fish assemblages of north Patagonia include elements of the Patagonian, Andean Cuyean, and Pampean ichthyological provinces, where Austral and Brazilic subregion species overlap. Salmonid richness increases from northern to southern latitudes, as do anadromous species. The steppe also presents some endorheic basins inhabited by species of high conservation value and restricted distribution. Threats and impacts that have been identified include land and water use, damming, pollution, climate change, and exotic species introduction. Historical and current management policies have permitted uncontrolled stocking of exotic species due to their high fishing value, thus favoring a reduction in the distribution and abundance of native fishes, including endangered species with an extreme degree of endemism.Fil: Baigún, Claudio Rafael M.. Universidad Nacional de San Martín. Instituto de Investigación e Ingeniería Ambiental. - Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Parque Centenario. Instituto de Investigación e Ingeniería Ambiental; ArgentinaFil: Casalinuovo, Miguel Angel. Consejo Nacional de Investigaciones Científicas y Técnicas; ArgentinaFil: Quiroga, Analía Pamela. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Centro Nacional Patagónico. Instituto de Diversidad y Evolución Austral; ArgentinaFil: Riva Rossi, Carla Marcela. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Centro Nacional Patagónico. Instituto de Diversidad y Evolución Austral; ArgentinaFil: Colautti, Dario César. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata. Instituto de Limnología "Dr. Raúl A. Ringuelet". Universidad Nacional de La Plata. Facultad de Ciencias Naturales y Museo. Instituto de Limnología; ArgentinaFil: Solimano, Patricio José. Consejo Nacional de Investigaciones Cientificas y Tecnicas. Centro de Investigaciones y Transferencia de Rio Negro. Sede Choele Choel del Centro de Investigaciones y Transferencia de Rio Negro | Universidad Nacional de Rio Negro. Centro de Investigaciones y Transferencia de Rio Negro. Sede Choele Choel del Centro de Investigaciones y Transferencia de Rio Negro.; ArgentinaFil: Bovcon, Nelson Darío. Universidad Nacional de la Patagonia "San Juan Bosco". Facultad de Ciencias Naturales y Ciencias de la Salud - Sede Esquel. Departamento de Química; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; ArgentinaFil: Maiztegui, Tomás. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata. Instituto de Limnología "Dr. Raúl A. Ringuelet". Universidad Nacional de La Plata. Facultad de Ciencias Naturales y Museo. Instituto de Limnología; ArgentinaFil: Llompart, Facundo Manuel. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Austral de Investigaciones Científicas; Argentina. Universidad Nacional de Tierra del Fuego, Antártida e Islas del Atlántico Sur. Instituto de Ciencias Polares, Ambientales y Recursos Naturales; Argentin

Morphometric and physical characteristics distinguishing adult Patagonian lamprey, Geotria macrostoma from the pouched lamprey, Geotria australis

The pouched lamprey, Geotria australis Gray, 1851, has long been considered monotypic in the Geotriidae family with a wide southern temperate distribution across Australasia and South America. Recent studies have provided molecular and morphological evidence for a second Geotria species in South America; Geotria macrostoma (Burmeister, 1868). The aim of this study was to determine morphometric and physical characteristics of adult G. macrostoma that further differentiate this re-instated species of Geotriidae from G. australis. The diagnostic features discriminating immature adult G. macrostoma from G. australis when entering fresh water, are distinct differences in dentition, oral papillae and fimbriae counts and differences in coloration. In addition, G. macrostoma display greater growth of the prebranchial region and oral disc and has a deeper body depth and higher condition fac tor. All current ecological knowledge of the genus Geotria is based on Australasian popula tions, which may not be applicable to G. macrostoma. To ensure the conservation and protection of the Patagonian lamprey as a re-identified species, further investigations are needed to understand its life history, biology and ecology throughout its range.Fil: Baker, Cindy F.. National Institute of Water and Atmospheric Research; Nueva ZelandaFil: Riva Rossi, Carla Marcela. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Centro Nacional Patagónico. Instituto de Diversidad y Evolución Austral; ArgentinaFil: Quiroga, Analía Pamela. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Centro Nacional Patagónico. Instituto de Diversidad y Evolución Austral; ArgentinaFil: White, Emily. National Institute of Water and Atmospheric Research; Nueva ZelandaFil: Williams, Peter. National Institute of Water and Atmospheric Research; Nueva ZelandaFil: Kitson, Jane. Kitson Consulting; Nueva ZelandaFil: Bice, Christopher M.. South Australian Research And Development Institute; Australia. University of Adelaide; AustraliaFil: Renaud, Claude B.. Canadian Museum Of Nature; CanadáFil: Potter, Ian. Murdoch University; AustraliaFil: Neira, Francisco J.. Neira Marine Sciences Consulting; AustraliaFil: Baigún, Claudio. Universidad Nacional de San Martín. Instituto de Investigación en Ingeniería Ambiental; Argentin