Deutsche Zeitschrift für die Gesamte Gerichtliche Medizin
The genetic polymorphism of inter-alpha-trypsin inhibitor (ITI) was analyzed in 2 samples of 554 ... more The genetic polymorphism of inter-alpha-trypsin inhibitor (ITI) was analyzed in 2 samples of 554 residents and 303 autochthonous healthy unrelated individuals from the Basque Country (northern Spain), by isoelectric focusing on miniaturized polyacrylamide gels followed by immunoblotting. The allele frequencies were ITI*1 = 0.586, ITI*2 = 0.402 and ITI*3 = 0.012 in residents and ITI*1 = 0.548, ITI*2 = 0.449 and ITI*3 = 0.003 in the autochthonous population. These allele frequencies were compared with those reported in other European populations.
Illegal, Unreported and Unregulated (IUU) fishing has played a major role in the overexploitation... more Illegal, Unreported and Unregulated (IUU) fishing has played a major role in the overexploitation of global fish populations. The European anchovy (Engraulis encrasicolus) and the albacore tuna (Thunnus alalunga) fisheries have great economical and cultural importance in the Bay of Biscay. The high commercial value of these species makes them highly vulnerable to fishing impacts and commercial frauds. Genetic traceability tools can result in a positive impact on marine ecosystems through conservation of fish stocks, because the designation of origin maintains the sustainability of the population combining the economic productivity. After the collapse of the European anchovy fishery in the Bay of Biscay last decade, a protection of the eco-label of origin for this anchovy (“Anchoa del Cantábrico”) has become necessary. A previous patent designed by our research group of the University of the Basque Country (UPV/EHU) and AZTI-Tecnalia (patent ES 2 392 610 B1), assigned -using 16 SNPs-...
European anchovy is a small teleost with major socio-economic importance that fuels research effo... more European anchovy is a small teleost with major socio-economic importance that fuels research efforts. The population genetic structure of this species has been much studied and previous studies, using molecular markers and otolith microstructure and chemistry, have suggested genetic heterogeneity for the Bay of Biscay anchovy; however, the extent of differentiation and mechanisms producing and maintaining it are still not understood. This study has assessed the population genetic structure of European anchovy with a particular focus on the fine-spatial scale structure of the Bay of Biscay analyzing 482 transcriptome-derived SNPs. Two populations with differentiated ecological properties and distributions were identified in the Bay of Biscay, which are in concordance with the two anchovy ecotypes previously proposed for the species: a large wide-shelf population associated with oceanic waters, and a small narrow-shelf population that inhabits in Abra and Gironde estuary plumes; the l...
One of the most common problems in fisheries is the definition of management units. Albacore (Thu... more One of the most common problems in fisheries is the definition of management units. Albacore (Thunnus alalunga) is an important species for commercial fisheries. Its population structure is still partially unknown; however, on the basis of fisheries data, tagging experiments and morpho-ecological studies, six management units are currently accepted for this species. The main objective of the present study was to define genetic entities within T. alalunga and, based on it, discuss the appropriateness of current management units. With this purpose, 13 microsatellite loci were applied to 551 albacore samples worldwide and the population genetic structure was assessed. Most relevant mismatches depict (1) Atlantic and Indian Ocean samples genetically indistinguishablility, (2) slight differentiation within the Pacific Ocean, and (3) two genetically differentiated populations in the Mediterranean Sea. Thus, this study provides genetic information to clarify albacore population delimitatio...
Ninety novel SNPs (75 nuclear and 15 mitochondrial) were discovered in European anchovy 22 (Engra... more Ninety novel SNPs (75 nuclear and 15 mitochondrial) were discovered in European anchovy 22 (Engraulis encrasicolus) by applying four different approaches: 1) the construction of a 23 partial genomic library by random cloning, 2) the Exon-Primed Intron Crossing strategy 24 (EPIC), 3) the alignment of publicly available sequences, and 4) by targeting five mtDNA 25 genes/fragments. These SNPs were considered polymorphic and reliably scored after 797 26 individuals covering the entire distributional range of the species had been genotyped. These 27 markers are currently being used in studies aiming to determine the European anchovy stock 28 structure and to trace its fishery's products. 29 30 31 Page 2 of 40 Molecular Ecology Resources 3 32 The European anchovy (Engraulis encrasicolus) is a species of high economic interest. In 33 particular, the Bay of Biscay anchovy has a high commercial value and a high socio-34 economic value for the local community. The recent collapse of the Biscayan fishery in 2005 35 (ICES 2010) made it clear that a reliable molecular tool for determining the origin of the 36 species' products was necessary. Moreover, the population structure of this species has not 37 yet been fully determined, and thus management does not take genetic structure into account 38 in its decisions. Apart from one study that genotyped seven microsatellites, in which a 39 relatively high rate of null alleles made a fine assessment of the anchovy population structure 40 impossible (Zarraonaindia et al. 2009), the genetic studies on this species to date have used 41 markers with relatively low discriminatory power, mostly allozymes and mitochondrial RFLP 42
In the present study we have investigated the population genetic structure of albacore (Thunnus a... more In the present study we have investigated the population genetic structure of albacore (Thunnus alalunga, Bonnaterre 1788) and assessed the loss of genetic diversity, likely due to overfishing, of albacore population in the North Atlantic Ocean. For this purpose, 1,331 individuals from 26 worldwide locations were analyzed by genotyping 75 novel nuclear SNPs. Our results indicated the existence of four genetically homogeneous populations delimited within the Mediterranean Sea, the Atlantic Ocean, the Indian Ocean and the Pacific Ocean. Current definition of stocks allows the sustainable management of albacore since no stock includes more than one genetic entity. In addition, short-and long-term effective population sizes were estimated for the North Atlantic Ocean albacore population, and results showed no historical decline for this population. Therefore, the genetic diversity and, consequently, the adaptive potential of this population have not been significantly affected by overfishing.
We present a population genetic study focused on the two subspecies of the M evolutionary lineage... more We present a population genetic study focused on the two subspecies of the M evolutionary lineage, A. m. mellifera and A. m. iberiensis. Nuclear and mtDNA variation was analysed in 27 bee populations from the Iberian Peninsula, France and Belgium. Microsatellite data provides compelling evidence of a barrier to neutral gene flow at the Pyrenees. In addition, they suggest isolation by distance between populations of the M lineage. Mitochondrial data support the hypothesis that the Iberian Peninsula served as glacial refugia for the honeybees of western Europe. They show two paths of post-glacial re-colonization in the extremes of the Pyrenees and suggest that the western path was more significant in the post-glacial re-colonization process. Thus, we report here on three main factors for mellifera and iberiensis subspecies differentiation: the Pyrenean barrier, isolation by distance and the post-glacial re-colonization process.
one of the analyzed populations renders it necessary to carry out this study in other independent... more one of the analyzed populations renders it necessary to carry out this study in other independent populations, with the aim of substantiating the repeatability of the present results. Nevertheless, the present results deepen our understanding of the genetic basis of susceptibility and resistance mechanisms related to MAP infection in cattle and, in turn, constitute a step forward toward the implementation of marker-assisted selection in breeding programs aimed at controlling paratuberculosis.
Toll-like receptors (TLR) are membrane proteins that play a key role in innate immunity, by recog... more Toll-like receptors (TLR) are membrane proteins that play a key role in innate immunity, by recognizing pathogens and subsequently activating appropriate responses. Mutations in TLR genes are associated with susceptibility to inflammatory and infectious diseases in humans. In cattle, 3 members of the TLR family, TLR1, TLR2, and TLR4, are associated with Mycobacterium avium ssp. paratuberculosis infection, although the extent of this association for the TLR1 and TLR4 receptors has not yet been determined. Moreover, the causal variant in the TLR2 gene has not yet been unequivocally established. In this study, 24 single nucleotide polymorphisms (SNP) in the bovine TLR1, TLR2, and TLR4 genes were selected from the literature, databases, and in silico searches, for a population-based genetic association study of a Spanish Holstein-Friesian sample. Whereas previous results regarding the TLR1 gene were not corroborated, a risk haplotype was detected in TLR2; however, its low frequency indicates that this detected association should be interpreted with caution. In the case of the TLR4 gene, 3 tightly linked SNP were found to be associated with susceptibility to M. avium ssp. paratuberculosis infection. Moreover, one of these SNP, the SNP c.-226G > C, which is localized in the 5 UTR region of the TLR4 gene, has been reported to be able to alter TLR4 expression, raising the possibility that this mutation may contribute to the response of the individual to infection.
A genetic susceptibility to Mycobacterium avium subsp. paratuberculosis (MAP) infections in rumin... more A genetic susceptibility to Mycobacterium avium subsp. paratuberculosis (MAP) infections in ruminants has been longtime suspected to exist. Recently, natural infections in cattle have been reclassified into latent and patent forms based on histopathological findings and their associations with immunological and microbiological variables. This study aims to explore whether these newly defined phenotypes are associated with twenty-four single-nucleotide polymorphisms (SNPs) in six bovine candidate genes: nucleotide-binding oligomerization domain 2 (NOD2), solute carrier family 11 member A1 (SLC11A1), nuclear body protein SP110 (SP110), toll-like receptors (TLRs) 2 and 4, and CD209 (also known as DC-SIGN, dendritic cell-specific ICAM3-grabbing nonintegrin). SNPs were genotyped for 772 Holstein-Friesian animals (52.6% apparently free; 38.1% latent; 9.3% patent) by TaqMan OpenArray technology. Genotypic-phenotypic associations were assessed by logistic regression analysis adjusted for age at slaughter, under five models (codominant, dominant, recessive, overdominant, and log-additive), and corrected for multiple testing. The rs208222804 C allele (CD209 gene) was found to be associated with latent paratuberculosis (log-additive model: < 0.0034 after permutation procedure; OR = 0.64, 95% CI = 0.48-0.86). No significant association was detected between any SNP and the patent phenotype. Consequently, CD209 gene may play a key role in the pathogenesis of bovine paratuberculosis.
Geographic surveys of allozymes, microsatellites, nuclear DNA (nDNA) and mitochondrial DNA (mtDNA... more Geographic surveys of allozymes, microsatellites, nuclear DNA (nDNA) and mitochondrial DNA (mtDNA) have detected several genetic subdivisions among European anchovy populations. However, these studies have been limited in their power to detect some aspects of population structure by the use of a single or a few molecular markers, or by limited geographic sampling. We use a multi-marker approach, 47 nDNA and 15 mtDNA single nucleotide polymorphisms (SNPs), to analyze 626 European anchovies from the whole range of the species to resolve shallow and deep levels of population structure. Nuclear SNPs define 10 genetic entities within two larger genetically distinctive groups associated with oceanic variables and different life-history traits. MtDNA SNPs define two deep phylogroups that reflect ancient dispersals and colonizations. These markers define two ecological groups. One major group of Iberian-Atlantic populations is associated with upwelling areas on narrow continental shelves and includes populations spawning and overwintering in coastal areas. A second major group includes northern populations in the North East (NE) Atlantic (including the Bay of Biscay) and the Mediterranean and is associated with wide continental shelves with local larval retention currents. This group tends to spawn and overwinter in oceanic areas. These two groups encompass ten populations that differ from previously defined management stocks in the Alboran Sea, Iberian-Atlantic and Bay of Biscay regions. In addition, a new North Sea-English Channel stock is defined. SNPs indicate that some populations in the Bay of Biscay are genetically closer to North Western (NW) Mediterranean populations than to other populations in the NE Atlantic, likely due to colonizations of the Bay of Biscay and NW Mediterranean by migrants from a common ancestral population. Northern NE Atlantic populations were subsequently established by migrants from the Bay of Biscay. Populations along the Iberian-Atlantic coast appear to have been founded by secondary waves of migrants from a southern refuge. Citation: Zarraonaindia I, Iriondo M, Albaina A, Pardo MA, Manzano C, et al. (2012) Multiple SNP Markers Reveal Fine-Scale Population and Deep Phylogeographic Structure in European Anchovy (Engraulis encrasicolus L.). PLoS ONE 7(7): e42201.
A total of 250 autochthonous Basque individuals were tested in the HLA-DQA1 system, and the allel... more A total of 250 autochthonous Basque individuals were tested in the HLA-DQA1 system, and the allele frequency distribution found was significantly different from that of any other European population. The differences centre mainly on the alleles DQAI*0201 and DQAl*0501: for the former the Basques have the highest frequency described anywhere in the world (f = 0.210) and for the latter they have the lowest frequency in Europe (f = 0.204). For the allele DQAI*0201 a genocline is also described in Europe with the Basques and Finno-Ugric populations basically at the extremes. The genocline reflects the isolation of the Basque population since prehistoric times, and supports existing linguistic, archaeological and genetic data.
2009. Microsatellite variability in European anchovy (Engraulis encrasicolus) calls for further i... more 2009. Microsatellite variability in European anchovy (Engraulis encrasicolus) calls for further investigation of its genetic structure and biogeography. -ICES Journal of Marine Science, 66: 000-000.
Group-specific component (GC), transferrin (TF) and alpha-1-antitrypsin (PI) polymorphisms have b... more Group-specific component (GC), transferrin (TF) and alpha-1-antitrypsin (PI) polymorphisms have been studied in the Basque population of Alava. The following gene frequencies were found: GC*1S = 0.525, GC*1F = 0.109, GC*2 = 0.366; TF*C1 = 0.793, TFC*2 = 0.171, TF*C3 = 0.032, TF*B = 0.003; PI*M1 = 0.611, PI*M2 = 0.164, PI*M3 = 0.101, PI*M4 = 0.019, PI*S = 0.101, PI*T = 0.003, PI*Z = 0.002. These results show that there is heterogeneity within the Basque population. In comparison with other populations from the Iberian Peninsula, the Basques from Alava show significant differences only for the PI system.
Population data studies for six short-tandem repeat loci (HUMCSF1P0, HUMTPOX, HUMTH01, HUMHPRTB, ... more Population data studies for six short-tandem repeat loci (HUMCSF1P0, HUMTPOX, HUMTH01, HUMHPRTB, HUMFES/FPS, and HUMvWF) were carried out on a sample of 326 autochthonous Basques. Comparing with other European samples, we found the highest frequencies known so far for allele 11 of the HUMCSF1P0 locus (0.380), allele 10 of the HUMFES/FPS locus (0.384), and allele 17 of the HUMvWF locus (0.329). On the other hand, we found the lowest frequencies recorded in Europe for allele 12 of the HUMCSF1P0 locus (0.291), allele 7 of the HUMTH01 locus (0.128), and allele 11 of the HUMFES/FPS system (0.317). These results support the hypothesis that the Basque population is a remnant of early European settlers.
Deutsche Zeitschrift für die Gesamte Gerichtliche Medizin
The genetic polymorphism of inter-alpha-trypsin inhibitor (ITI) was analyzed in 2 samples of 554 ... more The genetic polymorphism of inter-alpha-trypsin inhibitor (ITI) was analyzed in 2 samples of 554 residents and 303 autochthonous healthy unrelated individuals from the Basque Country (northern Spain), by isoelectric focusing on miniaturized polyacrylamide gels followed by immunoblotting. The allele frequencies were ITI*1 = 0.586, ITI*2 = 0.402 and ITI*3 = 0.012 in residents and ITI*1 = 0.548, ITI*2 = 0.449 and ITI*3 = 0.003 in the autochthonous population. These allele frequencies were compared with those reported in other European populations.
Illegal, Unreported and Unregulated (IUU) fishing has played a major role in the overexploitation... more Illegal, Unreported and Unregulated (IUU) fishing has played a major role in the overexploitation of global fish populations. The European anchovy (Engraulis encrasicolus) and the albacore tuna (Thunnus alalunga) fisheries have great economical and cultural importance in the Bay of Biscay. The high commercial value of these species makes them highly vulnerable to fishing impacts and commercial frauds. Genetic traceability tools can result in a positive impact on marine ecosystems through conservation of fish stocks, because the designation of origin maintains the sustainability of the population combining the economic productivity. After the collapse of the European anchovy fishery in the Bay of Biscay last decade, a protection of the eco-label of origin for this anchovy (“Anchoa del Cantábrico”) has become necessary. A previous patent designed by our research group of the University of the Basque Country (UPV/EHU) and AZTI-Tecnalia (patent ES 2 392 610 B1), assigned -using 16 SNPs-...
European anchovy is a small teleost with major socio-economic importance that fuels research effo... more European anchovy is a small teleost with major socio-economic importance that fuels research efforts. The population genetic structure of this species has been much studied and previous studies, using molecular markers and otolith microstructure and chemistry, have suggested genetic heterogeneity for the Bay of Biscay anchovy; however, the extent of differentiation and mechanisms producing and maintaining it are still not understood. This study has assessed the population genetic structure of European anchovy with a particular focus on the fine-spatial scale structure of the Bay of Biscay analyzing 482 transcriptome-derived SNPs. Two populations with differentiated ecological properties and distributions were identified in the Bay of Biscay, which are in concordance with the two anchovy ecotypes previously proposed for the species: a large wide-shelf population associated with oceanic waters, and a small narrow-shelf population that inhabits in Abra and Gironde estuary plumes; the l...
One of the most common problems in fisheries is the definition of management units. Albacore (Thu... more One of the most common problems in fisheries is the definition of management units. Albacore (Thunnus alalunga) is an important species for commercial fisheries. Its population structure is still partially unknown; however, on the basis of fisheries data, tagging experiments and morpho-ecological studies, six management units are currently accepted for this species. The main objective of the present study was to define genetic entities within T. alalunga and, based on it, discuss the appropriateness of current management units. With this purpose, 13 microsatellite loci were applied to 551 albacore samples worldwide and the population genetic structure was assessed. Most relevant mismatches depict (1) Atlantic and Indian Ocean samples genetically indistinguishablility, (2) slight differentiation within the Pacific Ocean, and (3) two genetically differentiated populations in the Mediterranean Sea. Thus, this study provides genetic information to clarify albacore population delimitatio...
Ninety novel SNPs (75 nuclear and 15 mitochondrial) were discovered in European anchovy 22 (Engra... more Ninety novel SNPs (75 nuclear and 15 mitochondrial) were discovered in European anchovy 22 (Engraulis encrasicolus) by applying four different approaches: 1) the construction of a 23 partial genomic library by random cloning, 2) the Exon-Primed Intron Crossing strategy 24 (EPIC), 3) the alignment of publicly available sequences, and 4) by targeting five mtDNA 25 genes/fragments. These SNPs were considered polymorphic and reliably scored after 797 26 individuals covering the entire distributional range of the species had been genotyped. These 27 markers are currently being used in studies aiming to determine the European anchovy stock 28 structure and to trace its fishery's products. 29 30 31 Page 2 of 40 Molecular Ecology Resources 3 32 The European anchovy (Engraulis encrasicolus) is a species of high economic interest. In 33 particular, the Bay of Biscay anchovy has a high commercial value and a high socio-34 economic value for the local community. The recent collapse of the Biscayan fishery in 2005 35 (ICES 2010) made it clear that a reliable molecular tool for determining the origin of the 36 species' products was necessary. Moreover, the population structure of this species has not 37 yet been fully determined, and thus management does not take genetic structure into account 38 in its decisions. Apart from one study that genotyped seven microsatellites, in which a 39 relatively high rate of null alleles made a fine assessment of the anchovy population structure 40 impossible (Zarraonaindia et al. 2009), the genetic studies on this species to date have used 41 markers with relatively low discriminatory power, mostly allozymes and mitochondrial RFLP 42
In the present study we have investigated the population genetic structure of albacore (Thunnus a... more In the present study we have investigated the population genetic structure of albacore (Thunnus alalunga, Bonnaterre 1788) and assessed the loss of genetic diversity, likely due to overfishing, of albacore population in the North Atlantic Ocean. For this purpose, 1,331 individuals from 26 worldwide locations were analyzed by genotyping 75 novel nuclear SNPs. Our results indicated the existence of four genetically homogeneous populations delimited within the Mediterranean Sea, the Atlantic Ocean, the Indian Ocean and the Pacific Ocean. Current definition of stocks allows the sustainable management of albacore since no stock includes more than one genetic entity. In addition, short-and long-term effective population sizes were estimated for the North Atlantic Ocean albacore population, and results showed no historical decline for this population. Therefore, the genetic diversity and, consequently, the adaptive potential of this population have not been significantly affected by overfishing.
We present a population genetic study focused on the two subspecies of the M evolutionary lineage... more We present a population genetic study focused on the two subspecies of the M evolutionary lineage, A. m. mellifera and A. m. iberiensis. Nuclear and mtDNA variation was analysed in 27 bee populations from the Iberian Peninsula, France and Belgium. Microsatellite data provides compelling evidence of a barrier to neutral gene flow at the Pyrenees. In addition, they suggest isolation by distance between populations of the M lineage. Mitochondrial data support the hypothesis that the Iberian Peninsula served as glacial refugia for the honeybees of western Europe. They show two paths of post-glacial re-colonization in the extremes of the Pyrenees and suggest that the western path was more significant in the post-glacial re-colonization process. Thus, we report here on three main factors for mellifera and iberiensis subspecies differentiation: the Pyrenean barrier, isolation by distance and the post-glacial re-colonization process.
one of the analyzed populations renders it necessary to carry out this study in other independent... more one of the analyzed populations renders it necessary to carry out this study in other independent populations, with the aim of substantiating the repeatability of the present results. Nevertheless, the present results deepen our understanding of the genetic basis of susceptibility and resistance mechanisms related to MAP infection in cattle and, in turn, constitute a step forward toward the implementation of marker-assisted selection in breeding programs aimed at controlling paratuberculosis.
Toll-like receptors (TLR) are membrane proteins that play a key role in innate immunity, by recog... more Toll-like receptors (TLR) are membrane proteins that play a key role in innate immunity, by recognizing pathogens and subsequently activating appropriate responses. Mutations in TLR genes are associated with susceptibility to inflammatory and infectious diseases in humans. In cattle, 3 members of the TLR family, TLR1, TLR2, and TLR4, are associated with Mycobacterium avium ssp. paratuberculosis infection, although the extent of this association for the TLR1 and TLR4 receptors has not yet been determined. Moreover, the causal variant in the TLR2 gene has not yet been unequivocally established. In this study, 24 single nucleotide polymorphisms (SNP) in the bovine TLR1, TLR2, and TLR4 genes were selected from the literature, databases, and in silico searches, for a population-based genetic association study of a Spanish Holstein-Friesian sample. Whereas previous results regarding the TLR1 gene were not corroborated, a risk haplotype was detected in TLR2; however, its low frequency indicates that this detected association should be interpreted with caution. In the case of the TLR4 gene, 3 tightly linked SNP were found to be associated with susceptibility to M. avium ssp. paratuberculosis infection. Moreover, one of these SNP, the SNP c.-226G > C, which is localized in the 5 UTR region of the TLR4 gene, has been reported to be able to alter TLR4 expression, raising the possibility that this mutation may contribute to the response of the individual to infection.
A genetic susceptibility to Mycobacterium avium subsp. paratuberculosis (MAP) infections in rumin... more A genetic susceptibility to Mycobacterium avium subsp. paratuberculosis (MAP) infections in ruminants has been longtime suspected to exist. Recently, natural infections in cattle have been reclassified into latent and patent forms based on histopathological findings and their associations with immunological and microbiological variables. This study aims to explore whether these newly defined phenotypes are associated with twenty-four single-nucleotide polymorphisms (SNPs) in six bovine candidate genes: nucleotide-binding oligomerization domain 2 (NOD2), solute carrier family 11 member A1 (SLC11A1), nuclear body protein SP110 (SP110), toll-like receptors (TLRs) 2 and 4, and CD209 (also known as DC-SIGN, dendritic cell-specific ICAM3-grabbing nonintegrin). SNPs were genotyped for 772 Holstein-Friesian animals (52.6% apparently free; 38.1% latent; 9.3% patent) by TaqMan OpenArray technology. Genotypic-phenotypic associations were assessed by logistic regression analysis adjusted for age at slaughter, under five models (codominant, dominant, recessive, overdominant, and log-additive), and corrected for multiple testing. The rs208222804 C allele (CD209 gene) was found to be associated with latent paratuberculosis (log-additive model: < 0.0034 after permutation procedure; OR = 0.64, 95% CI = 0.48-0.86). No significant association was detected between any SNP and the patent phenotype. Consequently, CD209 gene may play a key role in the pathogenesis of bovine paratuberculosis.
Geographic surveys of allozymes, microsatellites, nuclear DNA (nDNA) and mitochondrial DNA (mtDNA... more Geographic surveys of allozymes, microsatellites, nuclear DNA (nDNA) and mitochondrial DNA (mtDNA) have detected several genetic subdivisions among European anchovy populations. However, these studies have been limited in their power to detect some aspects of population structure by the use of a single or a few molecular markers, or by limited geographic sampling. We use a multi-marker approach, 47 nDNA and 15 mtDNA single nucleotide polymorphisms (SNPs), to analyze 626 European anchovies from the whole range of the species to resolve shallow and deep levels of population structure. Nuclear SNPs define 10 genetic entities within two larger genetically distinctive groups associated with oceanic variables and different life-history traits. MtDNA SNPs define two deep phylogroups that reflect ancient dispersals and colonizations. These markers define two ecological groups. One major group of Iberian-Atlantic populations is associated with upwelling areas on narrow continental shelves and includes populations spawning and overwintering in coastal areas. A second major group includes northern populations in the North East (NE) Atlantic (including the Bay of Biscay) and the Mediterranean and is associated with wide continental shelves with local larval retention currents. This group tends to spawn and overwinter in oceanic areas. These two groups encompass ten populations that differ from previously defined management stocks in the Alboran Sea, Iberian-Atlantic and Bay of Biscay regions. In addition, a new North Sea-English Channel stock is defined. SNPs indicate that some populations in the Bay of Biscay are genetically closer to North Western (NW) Mediterranean populations than to other populations in the NE Atlantic, likely due to colonizations of the Bay of Biscay and NW Mediterranean by migrants from a common ancestral population. Northern NE Atlantic populations were subsequently established by migrants from the Bay of Biscay. Populations along the Iberian-Atlantic coast appear to have been founded by secondary waves of migrants from a southern refuge. Citation: Zarraonaindia I, Iriondo M, Albaina A, Pardo MA, Manzano C, et al. (2012) Multiple SNP Markers Reveal Fine-Scale Population and Deep Phylogeographic Structure in European Anchovy (Engraulis encrasicolus L.). PLoS ONE 7(7): e42201.
A total of 250 autochthonous Basque individuals were tested in the HLA-DQA1 system, and the allel... more A total of 250 autochthonous Basque individuals were tested in the HLA-DQA1 system, and the allele frequency distribution found was significantly different from that of any other European population. The differences centre mainly on the alleles DQAI*0201 and DQAl*0501: for the former the Basques have the highest frequency described anywhere in the world (f = 0.210) and for the latter they have the lowest frequency in Europe (f = 0.204). For the allele DQAI*0201 a genocline is also described in Europe with the Basques and Finno-Ugric populations basically at the extremes. The genocline reflects the isolation of the Basque population since prehistoric times, and supports existing linguistic, archaeological and genetic data.
2009. Microsatellite variability in European anchovy (Engraulis encrasicolus) calls for further i... more 2009. Microsatellite variability in European anchovy (Engraulis encrasicolus) calls for further investigation of its genetic structure and biogeography. -ICES Journal of Marine Science, 66: 000-000.
Group-specific component (GC), transferrin (TF) and alpha-1-antitrypsin (PI) polymorphisms have b... more Group-specific component (GC), transferrin (TF) and alpha-1-antitrypsin (PI) polymorphisms have been studied in the Basque population of Alava. The following gene frequencies were found: GC*1S = 0.525, GC*1F = 0.109, GC*2 = 0.366; TF*C1 = 0.793, TFC*2 = 0.171, TF*C3 = 0.032, TF*B = 0.003; PI*M1 = 0.611, PI*M2 = 0.164, PI*M3 = 0.101, PI*M4 = 0.019, PI*S = 0.101, PI*T = 0.003, PI*Z = 0.002. These results show that there is heterogeneity within the Basque population. In comparison with other populations from the Iberian Peninsula, the Basques from Alava show significant differences only for the PI system.
Population data studies for six short-tandem repeat loci (HUMCSF1P0, HUMTPOX, HUMTH01, HUMHPRTB, ... more Population data studies for six short-tandem repeat loci (HUMCSF1P0, HUMTPOX, HUMTH01, HUMHPRTB, HUMFES/FPS, and HUMvWF) were carried out on a sample of 326 autochthonous Basques. Comparing with other European samples, we found the highest frequencies known so far for allele 11 of the HUMCSF1P0 locus (0.380), allele 10 of the HUMFES/FPS locus (0.384), and allele 17 of the HUMvWF locus (0.329). On the other hand, we found the lowest frequencies recorded in Europe for allele 12 of the HUMCSF1P0 locus (0.291), allele 7 of the HUMTH01 locus (0.128), and allele 11 of the HUMFES/FPS system (0.317). These results support the hypothesis that the Basque population is a remnant of early European settlers.
Uploads
Papers by Carmen Manzano