[Show abstract][Hide abstract] ABSTRACT: Unravelling the factors shaping the genetic structure of mobile marine species is challenging due to the high potential for gene flow. However, genetic inference can be greatly enhanced by increasing the genomic, geographic or environmental resolution of population genetic studies. Here we investigated the population structure of turbot (Scophthalmus maximus) by screening 17 random and gene-linked markers in 999 individuals at 290 geographical locations throughout the Northeast Atlantic Ocean. A seascape genetics approach with the inclusion of high resolution oceanographic data was used to quantify the association of genetic variation with spatial, temporal and environmental parameters. Neutral loci identified three subgroups: an Atlantic group, a Baltic Sea group and one on the Irish Shelf. The inclusion of loci putatively under selection suggested an additional break in the North Sea, subdividing southern from northern Atlantic individuals. Environmental and spatial seascape variables correlated marginally with neutral genetic variation, but explained significant proportions (respectively 8.7 % and 10.3 %) of adaptive genetic variation. Environmental variables associated with outlier allele frequencies included salinity, temperature, bottom shear stress, dissolved oxygen concentration and depth of the pycnocline. Furthermore, levels of explained adaptive genetic variation differed markedly among basins (3% vs 12% in the North and Baltic Sea, respectively). We suggest that stable environmental selection pressure contributes to relatively strong local adaptation in the Baltic Sea. Our seascape genetic approach using a large number of sampling locations and associated oceanographic data proved useful for the identification of population units as the basis of management decisions. This article is protected by copyright. All rights reserved.
[Show abstract][Hide abstract] ABSTRACT: Fasciola hepatica is a parasitic trematode that infects wild and domesticated mammals, particularly cattle and sheep, and causes significant economic losses to global livestock production. In the present study, we used codominant genetic markers to define and build, for the first time, complex genotype networks for F. hepatica isolated from cattle and sheep in NW Spain. We generated three types of random networks with a number of nodes and edges as close as possible to the observed networks, and we then calculated 14 node centrality measures for both observed and random networks. Finally, using Linear Discriminant Analysis (LDA) and these measures as inputs, we constructed a Quantitative Structure-Property Relationship (QSPR)-like model able to predict the propensity of a specific genotype of F. hepatica to infect different infrapopulations, farms and/or host species. The accuracy, sensitivity and specificity of the model were>90% for both training and cross-validation series. We also assessed the applicability domain of the model. This type of QSPR model is a potentially powerful tool for epidemiological studies and could be used to manage and prevent the spread of fasciolosis.
Journal of Theoretical Biology 11/2013; · 2.35 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: The turbot (Scophthalmus maximus) is a commercially valuable flatfish and one of the most promising aquaculture species in Europe. Two transcriptome 454-pyrosequencing runs were used in order to detect Single Nucleotide Polymorphisms (SNPs) in genes related to immune response and gonad differentiation. A total of 866 true SNPs were detected in 140 different contigs representing 262,093 bp as a whole. Only one true SNP was analyzed in each contig. One hundred and thirteen SNPs out of the 140 analyzed were feasible (genotyped), while Ш were polymorphic in a wild population. Transition/transversion ratio (1.354) was similar to that observed in other fish studies. Unbiased gene diversity (He) estimates ranged from 0.060 to 0.510 (mean = 0.351), minimum allele frequency (MAF) from 0.030 to 0.500 (mean = 0.259) and all loci were in Hardy-Weinberg equilibrium after Bonferroni correction. A large number of SNPs (49) were located in the coding region, 33 representing synonymous and 16 non-synonymous changes. Most SNP-containing genes were related to immune response and gonad differentiation processes, and could be candidates for functional changes leading to phenotypic changes. These markers will be useful for population screening to look for adaptive variation in wild and domestic turbot.
International journal of molecular sciences. 01/2013; 14(3):5694-711.
[Show abstract][Hide abstract] ABSTRACT: Twelve polymorphic genetic markers, eight allozymic loci and four microsatellites, were used to characterize 20 infrapopulations of Fasciola hepatica (all flukes from 10 individual cattle and 10 sheep) from 11 farms in Northwest Spain. Results suggest different patterns of population genetic structure depending on the host species. Individuals identified as clones were much more frequent in sheep. The common presence of clones and its nonrandom occurrence among individual hosts suggests clumped transmission of liver flukes in sheep. After reducing significant repeated multilocus genotypes to one unique copy within infrapopulations, results show relatively high levels of gene diversity within infrapopulations from cattle and sheep (0.411 and 0.360 on average, respectively). However, parasites of sheep appear to show significantly more structured variation at the infrapopulation level (Standardized F(ST)=0.087 and 0.170 for parasites of cattle and sheep, respectively). Compared to the parasites from cattle, results suggest that populations from sheep show lower levels of gene flow, higher degree of aggregate transmission, higher probability of mating within clones, and lower parasitic load. These differences have implications for the evolution of anthelmintic resistance because they affect the effective population size and the degree of inbreeding. The development and rapid spread of resistance seems likely in the parasites of cattle because populations from the study area are characterized by high gene flow. However, results also suggest that the efficient selection of a new recessive advantageous mutation would be favored in parasites of sheep due to a greater potential for inbreeding.
Infection, genetics and evolution: journal of molecular epidemiology and evolutionary genetics in infectious diseases 01/2012; 12(1):45-52. · 3.22 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: Nonrandom recruitment of parasites among hosts can lead to genetic differentiation among hosts and mating dynamics that promote inbreeding. It has been hypothesized that strictly aquatic parasites with intermediate hosts will behave as panmictic populations among hosts because ample opportunity exists for random mixing of unrelated individuals during transmission to the definitive host. A previous allozyme study on the marine trematode Lecithochirium fusiforme did not support this hypothesis; in that, there was genetic differentiation among, and significant heterozygote deficiencies within, definitive hosts. We revisit this system and use microsatellites to obtain multilocus genotypes. Our goal was to determine whether cryptic subgroups and/or the presence of clones could account for the apparent deviation from 'panmixia'. We find strong evidence for cryptic subdivision (three genetic clusters) that causes the Wahlund effect and differentiation among definitive hosts. After accounting for these cryptic groups, we see panmictic genetic structure among definitive hosts that is consistent with the 'high mixing in aquatic habitats' hypothesis. We see evidence for cotransmission of clones in all three clusters, but this level of clonal structure did not have a major impact in causing deviations from Hardy-Weinberg equilibrium, and only affected genetic differentiation among hosts in one cluster. A cursory examination of the data may have led to incorrect conclusions about nonrandom transmission. However, it is obvious in this system that there is more than meets the eye in relation to the actual make-up of parasite populations. In general, the methods we employ will be useful for elucidating hidden patterns in other organisms where cryptic structure may be common (e.g. those with limited morphology or complex life histories).
[Show abstract][Hide abstract] ABSTRACT: The analysis of an enriched partial genomic library and of public expressed sequence tag (EST) resources allowed the characterization of the first microsatellite loci in the protozoan parasite Perkinsus olseni. Clonal cultures from laboratory isolates derived from infected clams Ruditapes decussatus (from Spain), R. philippinarum (from Spain and Japan), and Austrovenus stutchburyi (from New Zealand) were used for the characterization of 12 microsatellites. Low variation was detected at most loci, with the number of alleles at polymorphic loci ranging from 2 to 7 (average 3.20 +/- 0.51) and gene diversity from 0.11 to 0.79 (average 0.40 +/- 0.07). Preliminary results show that (1) isolates of P. olseni are diploid cells, and (2) multiple infections can occur within a single host. Eight of the loci analyzed successfully cross-amplified in the congeneric species P. mediterraneus. These microsatellite markers will be useful to analyze in detail the population genetic structure of P. olseni, crucial for the efficient management of this parasitic disease.
Diseases of Aquatic Organisms 04/2011; 94(2):161-5. · 1.73 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: Twelve microsatellite markers were used to characterize 130 clonal cultures of Perkinsus olseni derived from 30 clams from six different geographic locations. Only two loci were polymorphic in the four populations studied from Spanish coast (mean sample size = 31.2), and a third locus was variable in only two populations. In contrast, five parasites isolated from five clams from Japan and New Zealand showed variation at nine loci. Low genetic variation (2.08 ± 0.64 alleles per locus; mean genetic diversity: 0.101 ± 0.022), and very high F(IS) values (0.857 on average) were observed in Spanish populations. A total of 39 multilocus genotypes (MLGs) were identified in the whole sample (121 clonal isolates after excluding incomplete MLGs due to missing data). A three-level hierarchical analysis of molecular variance found significant levels of genetic variation within infrapopulations (all the parasites in a single host; Φ(IS) = 0.679) and among infrapopulations within the component population (all the parasites among a host population; Φ(SC) = 0.579). Differences among the component population from different geographic locations were not significant (Φ(CT) = 0.057). These results suggest that an important fraction of F(IS) is explained by the Wahlund effect, but also strong inbreeding within infrapopulations. Another explanation for the high F(IS) within infrapopulations is the presence of haploid and diploid stages in the clam. Although fully aquatic system provides many opportunities for mixing of parasites from different clams, results are consistent with the consideration of all P. olseni in a clam as a cohesive genetic unit (i.e., deme). If the parasite was introduced into the Spanish coast with the importation of infected clams from Asia and Oceania, the low microsatellite polymorphism could be reflecting founder effects in the recent evolutionary history of P. olseni. The loss of alleles would be intensified in a scenario structured in numerous demes because of recurrent founder effects at microgeographic level.
Infection, genetics and evolution: journal of molecular epidemiology and evolutionary genetics in infectious diseases 03/2011; 11(5):904-11. · 3.22 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: Protein electrophoresis was used to study allozyme variation in Fasciola hepatica collected from three locations in Galicia (NW Spain), an area where fascioliasis is endemic. Eleven of 16 loci showed variation in at least one population and 7 loci were polymorphic in all populations studied. Five of these markers showed expected heterozygosities ranging from 0.137 to 0.569. The Nei's unbiased genetic diversity within populations ranged from 0.146 to 0.168. Genotypic frequencies were consistent with panmixia in 25 of 28 cases. Only 2 loci showed a significant deficit of heterozygotes. Genetic distances between populations were small (D(a)=0.003-0.010). These results suggest high levels of genetic variability and low population structure. This study shows that several of the markers developed are useful for study the population genetic structure of the parasite, which is essential to investigate the evolution of drug resistance that has recently emerged in populations of the study area.
[Show abstract][Hide abstract] ABSTRACT: Population genetic structure approaches offer the possibility of defining management units in conservation activities of species.
The genetic structure of the brown trout Salmo trutta in Galicia (NW Spain) was investigated by using microsatellites. We determined genetic variation across 10 microsatellite
loci of 901 individuals from 30 geographical populations representing 18 river basins. The analysis of the spatial distribution
of the genetic variation by using different methods clearly revealed strong genetic differentiation among two groups of populations
living in the studied area. This result is concordant with previous work using allozymes and mtDNA markers, and confirms a
secondary contact among two highly differentiated evolutionary lineages in Miño Basin. Although both lineages might be locally
adapted, results suggest that they hybridize at the middle course of the river. The brown trout from the Upper Miño Basin
belongs to the previously described Duero lineage, an Iberian endemism threatened by introgression with other Atlantic forms.
The results support the recognition of the Upper Miño Basin as a particular biotic region in Galicia. This study illustrates
how a multidisciplinary approach in spatial genetic analysis contributes to the delineation of conservation units as conspecific
KeywordsGenetic structure-Microsatellites-Brown trout-Conservation genetics-Management units
[Show abstract][Hide abstract] ABSTRACT: Sex determination in fish is a labile character in evolutionary terms. The sex-determining (SD) master gene can differ even between closely related fish species. This group is an interesting model for studying the evolution of the SD region and the gonadal differentiation pathway. The turbot (Scophthalmus maximus) is a flatfish of great commercial value, where a strong sexual dimorphism exists for growth rate. Following a QTL and marker association approach in five families and a natural population, we identified the main SD region of turbot at the proximal end of linkage group (LG) 5, close to the SmaUSC-E30 marker. The refined map of this region suggested that this marker would be 2.6 cM and 1.4 Mb from the putative SD gene. This region appeared mostly undifferentiated between males and females, and no relevant recombination frequency differences were detected between sexes. Comparative genomics of LG5 marker sequences against five model species showed no similarity of this chromosome to the sex chromosomes of medaka, stickleback, and fugu, but suggested a similarity to a sex-associated QTL from Oreochromis spp. The segregation analysis of the closest markers to the SD region demonstrated a ZW/ZZ model of sex determination in turbot. A small proportion of families did not fit perfectly with this model, which suggests that other minor genetic and/or environmental factors are involved in sex determination in this species.
[Show abstract][Hide abstract] ABSTRACT: Several graph representations have been introduced for different data in theoretical biology. For instance, complex networks based on Graph theory are used to represent the structure and/or dynamics of different large biological systems such as protein-protein interaction networks. In addition, Randic, Liao, Nandy, Basak, and many others developed some special types of graph-based representations. This special type of graph includes geometrical constrains to node positioning in space and adopts final geometrical shapes that resemble lattice-like patterns. Lattice networks have been used to visually depict DNA and protein sequences but they are very flexible. However, despite the proved efficacy of new lattice-like graph/networks to represent diverse systems, most works focus on only one specific type of biological data. This work proposes a generalized type of lattice and illustrates how to use it in order to represent and compare biological data from different sources. We exemplify the following cases: protein sequence; mass spectra (MS) of protein peptide mass fingerprints (PMF); molecular dynamic trajectory (MDTs) from structural studies; mRNA microarray data; single nucleotide polymorphisms (SNPs); 1D or 2D-Electrophoresis study of protein polymorphisms and protein-research patent and/or copyright information. We used data available from public sources for some examples but for other, we used experimental results reported herein for the first time. This work may break new ground for the application of Graph theory in theoretical biology and other areas of biomedical sciences.
Journal of Theoretical Biology 08/2009; 261(1):136-47. · 2.35 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: Between the spring of 1999 and the spring of 2002, 196 conger eels, Conger conger, were collected from the Ría de Arousa, Galicia, Spain, and examined for hemiurid flukes. Five trematode species belonging to the family Hemiuridae were found: Hemiurus communis, Lecithochirium fusiforme, Lecithochirium rufoviride, Lecithochirium furcolabiatum, and Lecithochirium musculus. The 2 most common species were L. fusiforme and L. rufoviride, each with a prevalence of more than 80%. Furthermore, both species occurred simultaneously in 145 conger eels (74%). In contrast to the population of L. rufoviride, the mean intensity and abundance of L. fusiforme revealed a clear seasonal pattern, with peak values coinciding with each of the 3 winters studied. However, the prevalence of L. fusiforme did not increase significantly during winter. These differences may be related to an aggregated distribution of the parasite. The results show that infrapopulations of this species fluctuate greatly in the host with time and suggest that this parasite matures relatively quickly but does not survive for much longer than 3 mo in conger eels.
[Show abstract][Hide abstract] ABSTRACT: The analysis of nucleolar organizer regions (NORs) using silver (Ag-) staining and in situ hybridization (ISH) in brown trout (Salmo trutta) from various river basins in the Iberian Peninsula revealed high variation in the number and location of NORs. A total of 17 different Ag-NOR sites were revealed in 10 different chromosome pairs. Three different Ag-NOR patterns clustered by river basins and strongly associated to the internal transcribed spacer 1 (ITS1) variation were detected. The main variability in NOR-sites was found in a secondary contact between two divergent lineages of brown trouts at Duero basin. Our results confirmed the abrupt break in the spatial distribution of genetic variation of brown trout populations previously reported at Duero basin. We hypothesize that NOR-site variation might be a consequence of hybridization between divergent lineages of brown trouts and that NORs could play a major role in the maintenance of a hybrid zone in Duero basin via post-zygotic isolation mechanisms.
[Show abstract][Hide abstract] ABSTRACT: The detection of microsatellite sequences within expressed sequence tags (ESTs) connects potential markers with specific genes, generating type I markers. We have developed and mapped by linkage analysis a set of EST-derived microsatellites in the turbot, Scophthalmus maximus. One hundred and ninety-one microsatellites were identified from 9256 turbot ESTs. Primer design was possible with 98 microsatellites. After genotyping 25 wild turbot and the parents of two reference families for linkage analysis, 43 EST-derived microsatellites were selected because they met technical and polymorphism criteria. A final set of 31 EST-derived microsatellites could be mapped to 17 linkage groups of the turbot consensus map based on 242 anonymous microsatellites. Twenty-four microsatellite-containing ESTs were functionally annotated, confirming them as type I markers. Nineteen were mapped in the turbot consensus map. These EST-derived microsatellites constitute useful tools for genome scanning of turbot populations, marker-assisted selection programmes and comparative mapping.
[Show abstract][Hide abstract] ABSTRACT: Previous studies using mitochondrial markers and microsatellites revealed a new highly differentiated Atlantic lineage of
brown trout in the Iberian Peninsula mainly confined to the Upper Duero Basin. Data suggest that Duero lineage (DU) hybridizes
with previously described Atlantic (AT) lineages in that basin. However, nuclear and cytogenetic data suggest another hybrid
zone between divergent lineages might be present in the Miño Basin, another Atlantic drainage located to the north. Here,
we extend those studies by analyzing the mitochondrial haplotype variability of brown trout populations from northwestern
Spain, a poorly studied area, to obtain an accurate picture of the distribution of DU. Results show that the DU haplotype
is fixed in several isolated populations from the upper course of the Miño River and its main tributary the Sil River. DU
haplotype co-occurs with two related AT haplotypes in the Miño Basin revealing a new secondary contact zone. The identification
of both longtime stable populations of DU and several other populations showing introgression with widespread AT lineages
will be useful for the management and conservation of such an endemic lineage.
[Show abstract][Hide abstract] ABSTRACT: Seven polymorphic loci containing dinucleotide repeats and one trinucleotide microsatellite were developed for the hemiurid fluke Lecithochirium fusiforme, a parasite of the European conger eel Conger conger. All parasites that were collected from a single individual host (a total of 54 specimens) were genotyped. The number of alleles ranged from two to eight. The observed and expected heterozygosities ranged from 0.057 to 0.736 and from 0.091 to 0.794, respectively. Hardy–Weinberg deviations were statistically significant for two loci. These markers will be useful for study of parasite transmission patterns and population genetic structure.
[Show abstract][Hide abstract] ABSTRACT: We examined the relative merits of mitochondrial DNA loci and ribosomal DNA internal transcribed spacers for their use in prospecting for cryptic species of platyhelminth parasites. Sequence divergence at ITS1 and ITS2 was compared with divergence at 2 mtDNA loci (NADH dehydrogenase-1 and cytochrome c oxidase I) between closely related species of trematodes and cestodes. Both spacers accumulated substitutions substantially more slowly than mtDNA, which clearly shows a higher level of divergence among species relative to intra-specific variation. Besides a slow rate of substitution, other caveats that may be encountered when using ITS sequences as a prospecting marker are discussed. In particular, we note recent studies that suggest the existence of substantial levels of intra-individual variation in ITS sequences of flatworms. Because it is likely that closely related species share this phenomenon, it may confound the detection of cryptic species, especially if small sample sizes are studied. Although potential limitations of mtDNA are also recognized, the higher rate of evolution and smaller effective population size of this marker increases the probability of detecting diagnostic characters between cryptic species.