Miguel Hermida

University of Santiago de Compostela | USC · Department of Genetics

Sex determination (SD) shows huge variation among fish and a high evolutionary rate, as illustrated by the Pleuronectiformes (flatfishes). This order is characterized by its adaptation to demersal life, compact genomes and diversity of SD mechanisms. Here, we assembled the Solea senegalensis genome, a flatfish of great commercial value, into 82 con...

Shell color shows broad variation within mollusc species and despite information on the genetic pathways involved in shell construction and color has recently increased, more studies are needed to understand its genetic architecture. The common cockle (Cerastoderma edule) is a valuable species from ecological and commercial perspectives which shows...

The development of genetic markers for genomic screening is essential for addressing more accurate breeding programs in aquaculture and to ascertain the genetic architecture of productive traits, particularly the mechanisms underlying sex determination in fish. Sex determination systems display huge variation in fish, ranging from those strictly de...

Shell colour pattern shows broad diversity in molluscs, and both genetic and environmental factors seem to interact to some extent on the final phenotype. Despite information on the genetic component and pathways involved in shell construction and colour has increased in the last decade, more data are needed particularly to understand colour variat...

Sex determination (SD) mechanisms are exceptionally diverse and show high evolutionary rates in fish. Pleuronectiformes is an emblematic fish group characterized by its adaptation to demersal life and its compact genomes. Here, we present a chromosome-level genome assembly of Senegalese sole, a promising European aquaculture species. We combined lo...

Abstract Knowledge on correlations between environmental factors and genome divergence between populations of marine species is crucial for sustainable management of fisheries and wild populations. The edible cockle (Cerastoderma edule) is a marine bivalve distributed along the Northeast Atlantic coast of Europe and is an important resource from bo...

The breeding scheme in the Rubia Gallega cattle population is based upon traits measured in farms and slaughterhouses. In recent years, genomic evaluation has been implemented by using a ssGBLUP (single-step Genomic Best Linear Unbiased Prediction). This procedure can reparameterized to perform ssGWAS (single-step Genome Wide Association Studies) b...

Background Understanding sex determination (SD) across taxa is a major challenge for evolutionary biology. The new genomic tools are paving the way to identify genomic features underlying SD in fish, a group frequently showing limited sex chromosome differentiation and high SD evolutionary turnover. Turbot (Scophthalmus maximus) is a commercially i...

Background The irruption of Next-generation sequencing (NGS) and restriction site-associated DNA sequencing (RAD-seq) in the last decade has led to the identification of thousands of molecular markers and their genotyping for refined genomic screening. This approach has been especially useful for non-model organisms with limited genomic resources....

Knowledge on how environmental factors shape the genome of marine species is crucial for sustainable management of fisheries and wild populations. The edible cockle (Cerastoderma edule) is a marine bivalve distributed along the Northeast Atlantic coast of Europe and is an important resource from both commercial and ecological perspectives. We perfo...

Tasas de crecimiento en dos poblaciones naturales de Gasterosteus aculeatus en el noroeste de España: relación con otros parámetros vitales Se analizaron las tasas de crecimiento de dos poblaciones naturales de Galicia (noroeste de España) del pez espinoso Gasterosteus aculeatus, cuyo ciclo biológico es estrictamente anual. Para ello, se utilizó un...

Background The irruption of Next-generation sequencing (NGS) and restriction site-associated DNA sequencing (RAD-seq) in the last decade has led to the identification of thousands of molecular markers and their genotyping for refined genomic screening. This approach has been especially useful for non-model organisms with limited genomic resources....

Background: The irruption of Next-generation sequencing (NGS) and restriction site-associated DNA sequencing (RAD-seq) in the last decade has led to the identification of thousands of molecular markers and their genotyping for refined genomic screening. This approach has been especially useful for non-model organisms with limited genomic resources....

Rhamdia quelen, a Neotropical fish with hybridization between highly divergent mitochondrial DNA (mtDNA) lineages, represents an interesting evolutionary model. Previous studies suggested that there might be demographic differences between coastal lagoons and riverine environments, as well as divergent populations that could be reproductively isola...

Selective breeding for improving host responses to infectious pathogens is a promising option for disease control. In fact, disease resilience, the ability of a host to survive or cope with infectious challenge, has become a highly desirable breeding goal. However, resilience is a complex trait composed of two different host defence mechanisms, nam...

The impact of escapees from aquaculture is of general concern for the sustainability of natural resources. Turbot Scophthalmus maximus is a marine flatfish of great commercial value whose land-based aquaculture started approx. 40 yr ago; hence, a low impact of escapees is expected on wild populations. However, enhancement of wild stocks using farme...

• Application of genomics tools for conservation purposes (i.e. conservation genomics) allows looking deep into the genetic structure and adaptations of populations and species in order to define management units, trace exploited stocks, and identification of species. • In this work, a double‐digestion restriction‐site‐associated DNA sequencing (dd...

Highly dense linkage maps enable positioning thousands of landmarks useful for anchoring the whole genome and for analysing genome properties. Turbot is the most important cultured flatfish worldwide and breeding programs in the fifth generation of selection are targeted to improve growth rate, obtain disease resistant broodstock and understand sex...

Turbot (Scophthalmus maximus) is a valuable flatfish with current selection programs to increase growth rate in the fifth generation. Disentangling the genetic architecture of growth traits has biological and productive relevance. Growth-related quantitative trait loci (QTL) and associated markers have been previously reported in turbot. Here, we t...

Unraveling adaptive genetic variation represents, in addition to the estimate of population demographic parameters, a cornerstone for the management of aquatic natural living resources, which in turn, represent the raw material for breeding programs. The turbot (Scophthalmus maximus) is a marine flatfish of high commercial value living on the Europ...

The development of Genotyping-By-Sequencing (GBS) technologies enables cost-effective analysis of large numbers of Single Nucleotide Polymorphisms (SNPs), especially in "non-model" species. Nevertheless, as such technologies enter a mature phase, biases and errors inherent to GBS are becoming evident. Here, we evaluated the performance of double di...

Fluorescent in situ hybridisation (FISH) of Characidium gomesi mitotic plates with female-specific RAD locus probes.

Fish species exhibit substantial variation in the degree of genetic differentiation between sex chromosome pairs, and therefore offer the opportunity to study the full range of sex chromosome evolution. We used restriction-site associated DNA sequencing (RAD-seq) to study the sex chromosomes of Characidium gomesi, a species with conspicuous heterom...

Genetic isolation and drift may imperil peripheral populations of wide-ranging species more than central ones. Therefore, information about species genetic variability and population structure is invaluable for conservation managers. The Iberian populations of three-spined stickleback lie at the southwestern periphery of the European distribution o...

Basic descriptors of the 18 polymorphic microsatellite loci selected to assess the genetic diversity and differentiation of G. aculeatus. k, number of alleles; AR, allelic richness overall populations (based on sample size of 16 diploid individuals); HO, observed heterozygosity; HE, expected heterozygosity. Significance of FIS was obtained after 1,...

Details about the samples used in the present study. (PDF)

95% statistical parsimony network obtained for 172 mitochondrial haplotypes (755 bp) of G. aculeatus. Our cytb data were aligned and collapsed with the homologous fragments reported in Europe by prior literature [17, 20, 24, 49–54]. The basal haplotype/s were inferred using the homologous fragment of a Japanese specimen of G. aculeatus (Accession n...

Geographic distances (km) between sampling localities. Above diagonal: straight line distances. Below diagonal: shortest pairwise water distances among sampling sites using Google Earth. Note that samples from S14 (Valencia) were geographically coded as located at river Orlina (42°23’6.09”N, 3°1’59.29”E), the source of individuals for the transloca...

Geographic and frequency distribution of the 48 mitochondrial haplotypes (cytochrome b (cytb) and control region (cr)) of G. aculeatus (rows) obtained by the present study. (DOCX)

Proportional contribution to allelic and mitochondrial diversity of each of the 15 extant sites using data from nuclear microsatellites and haplotype sequences (cytb+cr), respectively. (PDF)

Identification of the most likely number of G. aculeatus populations by the analysis of microsatellite data with STRUCTURE 2.3.4. Up: estimated log probability of data for the different number of inferred clusters (K); bars correspond to standard deviation, after 20 independent runs. Down: rate of change in the log probability of data between succe...

Proportion of null alleles in loci initially used to genotype the 17 sites where G. aculeatus was sampled for the present study. Loci stn3, stn12 and stn174 excluded from this calculation due to presence of intermediate (1 bp difference) alleles. (DOCX)

Original code, frequency and geographic origin of the 172 mitochondrial haplotypes (cytb) of G. aculeatus used in the present work. (XLSX)

Output of CLUMPAK [41]. (PDF)

The turbot (Scophthalmus maximus) is a flatfish with an increasing aquaculture value. It shows one of the highest growth rates and sexual growth dimorphism among the cultured marine species. An important investment has been done on genomic research in this species for boosting breeding programs, currently in their fifth generation of selection. Rec...

Flatfish have a high market acceptance thus representing a profitable aquaculture production. The main farmed species is the turbot (Scophthalmus maximus) followed by Japanese flounder (Paralichthys olivaceous) and tongue sole (Cynoglossus semilaevis), but other species like Atlantic halibut (Hippoglossus hippoglossus), Senegalese sole (Solea seneg...

The turbot is a flatfish (Pleuronectiformes) with increasing commercial value, which has prompted active genomic research aimed at more efficient selection. Here we present the sequence and annotation of the turbot genome, which represents a milestone for both boosting breeding programmes and ascertaining the origin and diversification of flatfish....

Growth traits represent a main goal in aquaculture breeding programs and may be related to adaptive variation in wild fisheries. Integrating quantitative trait loci (QTL) mapping and next generation sequencing can greatly help to identify variation in candidate genes, which can result in marker-assisted selection and better genetic structure inform...

Variability at 20 microsatellite loci was examined to assess the population genetic structure, gene flow, and effective population size (N e) in three populations of three-spined stickleback (Gasterosteus aculeatus) from the upper basin of the Miño River in Galicia, NW Spain, where this species is threatened. The three populations showed similar le...

The Senegalese sole (Solea senegalensis, Kaup 1858) is a flatfish species of great value for aquaculture. In this study, we develop the first linkage map in this species based on microsatellite markers characterized from genomic DNA libraries and EST databases of Senegalese sole and from other flatfish species. Three reference gynogenetic families...

Fish sex determination (SD) systems are varied, suggesting evolutionary changes including either multiple evolution origins of genetic SD from non-genetic systems (such as environmental SD), and/or turnover events replacing one genetic system by another. When genetic SD is found, cytological differentiation between the two members of the sex chromo...

Abstract Genetic maps constitute valuable tools to detect genomic regions associated with complex traits and to go forward to understand their genetic basis. Flatfish include several species of great commercial value for which increasing genomic resources are available including genetic maps and EST databases. Application of comparative mapping str...

The turbot (Scophthalmusmaximus) is a species of great relevance to European aquaculture and hence might benefit from enhanced genomic resources. The aim of this study was to integrate all previous turbot mapping resources to obtain a dense consensus genetic map. A total of 514 single nucleotide polymorphisms (SNP) and microsatellite markers from r...

One of the main objectives of genetic breeding programs in turbot industry is to reduce disease-related mortality. In the present study, a genome scan to detect quantitative trait loci (QTL) affecting resistance and survival to viral haemorrhagic septicaemia (VHS) was carried out. Three full-sib families with approximately 90 individuals each were...

The turbot (Scophthalmus maximus) is a relevant species in European aquaculture. The small turbot genome provides a source for genomics strategies to use in order to understand the genetic basis of productive traits, particularly those related to sex, growth and pathogen resistance. Genetic maps represent essential genomic screening tools allowing...

Table S3. Number of markers and map length for each linkage group (LG) of turbot.