Morten Limborg | University of Washington (original) (raw)

Papers by Morten Limborg

Ecology and Evolution, 2011

Recent advances in molecular interrogation techniques now allow unprecedented genomic inference a... more Recent advances in molecular interrogation techniques now allow unprecedented genomic inference about the role of adaptive genetic divergence in wild populations. We used high-throughput genotyping to screen a genome-wide panel of 276 single nucleotide polymorphisms (SNPs) for the economically and culturally important salmonid Oncorhynchus mykiss. Samples included 805 individuals from 11 anadromous and resident populations from the northwestern United States and British Columbia, and represented two major lineages including paired populations of each life history within single drainages of each lineage. Overall patterns of variation affirmed clear distinctions between lineages and in most instances, isolation by distance within them. Evidence for divergent selection at eight candidate loci included significant landscape correlations, particularly with temperature. High diversity of two nonsynonymous mutations within the peptide-binding region of the major histocompatibility complex (MHC) class II (DAB) gene provided signatures of balancing selection. Weak signals for potential selection between sympatric resident and anadromous populations were revealed from genome scans and allele frequency comparisons. Our results suggest an important adaptive role for immune-related functions and present a large genomic resource for future studies

ABSTRACT The importance of marine organisms for both economical and ecological reasons is enormou... more ABSTRACT The importance of marine organisms for both economical and ecological reasons is enormous; and knowledge of population structure and connectivity is crucial for the sustainable utilisation and conservation of exploited fish stocks. However in most cases our understanding of these spatial patterns of natural variation, both neutral and adaptive, is limited. For marine fish, the maintenance of local stocks containing adaptive diversity is associated with the sustainability and resilience of marine fisheries in the face of climatic and anthropogenic threats. However, many previous studies with genetic markers such as microsatellites have observed weak genetic structure in marine fish and combined with a pelagic larval stage, this has supported the hypothesis that gene flow is extensive and that there is little opportunity for differentiation on local scales. A consequence of the limited opportunity for divergence is the associated assumption that local adaptation would be similarly restricted, except perhaps at macrogeographic levels. However, the application of Single Nucleotide Polymorphisms (SNPs) has the potential to demonstrate previously undetected spatial and temporal population structuring and signatures of adaptive variation. Additionally, SNPs are uniquely applicable for the identification and monitoring of wild fish populations and the traceability of products throughout the food supply chain, allowing effective enforcement of fisheries regulations. Here we demonstrate the utility of SNP panels developed in a European Commission-funded consortium, FishPopTrace, to scenarios that are relevant for the identification of potential illegal fishing and/or mislabeling for two commercially important Atlantic species; cod (Gadus morhua) and herring (Clupea harengus). Markers under selection are typically inappropriate for assessing demographic processes such as gene flow. However, the broad distribution of SNP loci throughout the genome, together with the potential to score large numbers using high throughout approaches, allows for the additional flexibility in traceability studies to establish marker panels with loci that vary in their evolutionary dynamics. Strategies for optimizing population assignment in relation to SNP characteristics and target species biology across various spatial scales will be discussed.

Technical University of …

Abstract Geographic distributions of most temperate marine fishes are affected by post-glacial re... more Abstract Geographic distributions of most temperate marine fishes are affected by post-glacial recolonisation events which have left complex genetic imprints on populations of marine species. This study investigated population structure and demographic history of ...

Report of the Working …, Jan 1, 2009

ICES Journal of …, Jan 1, 2011

Molecular …, Jan 1, 2012

High gene flow is considered the norm for most marine organisms and is expected to limit their ab... more High gene flow is considered the norm for most marine organisms and is expected to limit their ability to adapt to local environments. Few studies have directly compared the patterns of differentiation at neutral and selected gene loci in marine organisms. We analysed a transcriptome-derived panel of 281 SNPs in Atlantic herring (Clupea harengus), a highly migratory small pelagic fish, for elucidating neutral and selected genetic variation among populations and to identify candidate genes for environmental adaptation. We analysed 607 individuals from 18 spawning locations in the northeast Atlantic, including two temperature clines (5-12°C) and two salinity clines (5-35&). By combining genome scan and landscape genetic analyses, four genetically distinct groups of herring were identified: Baltic Sea, Baltic-North Sea transition area, North Sea ⁄ British Isles and North Atlantic; notably, samples exhibited divergent clustering patterns for neutral and selected loci. We found statistically strong evidence for divergent selection at 16 outlier loci on a global scale, and significant correlations with temperature and salinity at nine loci. On regional scales, we identified two outlier loci with parallel patterns across temperature clines and five loci associated with temperature in the North Sea ⁄ North Atlantic. Likewise, we found seven replicated outliers, of which five were significantly associated with low salinity across both salinity clines. Our results reveal a complex pattern of varying spatial genetic variation among outlier loci, likely reflecting adaptations to local environments. In addition to disclosing the fine scale of local adaptation in a highly vagile species, our data emphasize the need to preserve functionally important biodiversity.

PloS one, Jan 1, 2012

The introduction of Next Generation Sequencing (NGS) has revolutionised population genetics, prov... more The introduction of Next Generation Sequencing (NGS) has revolutionised population genetics, providing studies of nonmodel species with unprecedented genomic coverage, allowing evolutionary biologists to address questions previously far beyond the reach of available resources. Furthermore, the simple mutation model of Single Nucleotide Polymorphisms (SNPs) permits cost-effective high-throughput genotyping in thousands of individuals simultaneously. Genomic resources are scarce for the Atlantic herring (Clupea harengus), a small pelagic species that sustains high revenue fisheries. This paper details the development of 578 SNPs using a combined NGS and high-throughput genotyping approach. Eight individuals covering the species distribution in the eastern Atlantic were bar-coded and multiplexed into a single cDNA library and sequenced using the 454 GS FLX platform. SNP discovery was performed by de novo sequence clustering and contig assembly, followed by the mapping of reads against consensus contig sequences. Selection of candidate SNPs for genotyping was conducted using an in silico approach. SNP validation and genotyping were performed simultaneously using an Illumina 1,536 GoldenGate assay. Although the conversion rate of candidate SNPs in the genotyping assay cannot be predicted in advance, this approach has the potential to maximise cost and time efficiencies by avoiding expensive and time-consuming laboratory stages of SNP validation. Additionally, the in silico approach leads to lower ascertainment bias in the resulting SNP panel as marker selection is based only on the ability to design primers and the predicted presence of intron-exon boundaries. Consequently SNPs with a wider spectrum of minor allele frequencies (MAFs) will be genotyped in the final panel. The genomic resources presented here represent a valuable multi-purpose resource for developing informative marker panels for population discrimination, microarray development and for population genomic studies in the wild.

Nature …, Jan 1, 2012

Illegal, unreported and unregulated fishing has had a major role in the overexploitation of globa... more Illegal, unreported and unregulated fishing has had a major role in the overexploitation of global fish populations. In response, international regulations have been imposed and many fisheries have been 'eco-certified' by consumer organizations, but methods for independent control of catch certificates and eco-labels are urgently needed. Here we show that, by using geneassociated single nucleotide polymorphisms, individual marine fish can be assigned back to population of origin with unprecedented high levels of precision. By applying high differentiation single nucleotide polymorphism assays, in four commercial marine fish, on a pan-European scale, we find 93-100% of individuals could be correctly assigned to origin in policy-driven case studies. We show how case-targeted single nucleotide polymorphism assays can be created and forensically validated, using a centrally maintained and publicly available database. our results demonstrate how application of gene-associated markers will likely revolutionize origin assignment and become highly valuable tools for fighting illegal fishing and mislabelling worldwide.

Ecology and …, Jan 1, 2012

Recent advances in molecular interrogation techniques now allow unprecedented genomic inference a... more Recent advances in molecular interrogation techniques now allow unprecedented genomic inference about the role of adaptive genetic divergence in wild populations. We used high-throughput genotyping to screen a genome-wide panel of 276 single nucleotide polymorphisms (SNPs) for the economically and culturally important salmonid Oncorhynchus mykiss. Samples included 805 individuals from 11 anadromous and resident populations from the northwestern United States and British Columbia, and represented two major lineages including paired populations of each life history within single drainages of each lineage. Overall patterns of variation affirmed clear distinctions between lineages and in most instances, isolation by distance within them. Evidence for divergent selection at eight candidate loci included significant landscape correlations, particularly with temperature. High diversity of two nonsynonymous mutations within the peptide-binding region of the major histocompatibility complex (MHC) class II (DAB) gene provided signatures of balancing selection. Weak signals for potential selection between sympatric resident and anadromous populations were revealed from genome scans and allele frequency comparisons. Our results suggest an important adaptive role for immune-related functions and present a large genomic resource for future studies

World Fishing & Aquaculture, Jan 1, 2009

Molecular Ecology …, Jan 1, 2008

Nine microsatellite markers were characterized in the fungus Botrytis cinerea . Genomic DNA seque... more Nine microsatellite markers were characterized in the fungus Botrytis cinerea . Genomic DNA sequences from the partial sequencing of 12 000 bacterial artificial chromosome (BAC) clones, were screened by BLAST for various microsatellite motives, and primer pairs were designed. Cross-amplification and polymorphism were assessed on 49 isolates from B. cinerea and two related species, collected from natural populations on several plants and locations.

Mar Ecol Prog Ser, Jan 1, 2009

ABSTRACT The importance of marine organisms for both economical and ecological reasons is enormou... more ABSTRACT The importance of marine organisms for both economical and ecological reasons is enormous; and knowledge of population structure and connectivity is crucial for the sustainable utilisation and conservation of exploited fish stocks. However in most cases our understanding of these spatial patterns of natural variation, both neutral and adaptive, is limited. For marine fish, the maintenance of local stocks containing adaptive diversity is associated with the sustainability and resilience of marine fisheries in the face of climatic and anthropogenic threats. However, many previous studies with genetic markers such as microsatellites have observed weak genetic structure in marine fish and combined with a pelagic larval stage, this has supported the hypothesis that gene flow is extensive and that there is little opportunity for differentiation on local scales. A consequence of the limited opportunity for divergence is the associated assumption that local adaptation would be similarly restricted, except perhaps at macrogeographic levels. However, the application of Single Nucleotide Polymorphisms (SNPs) has the potential to demonstrate previously undetected spatial and temporal population structuring and signatures of adaptive variation. Additionally, SNPs are uniquely applicable for the identification and monitoring of wild fish populations and the traceability of products throughout the food supply chain, allowing effective enforcement of fisheries regulations. Here we demonstrate the utility of SNP panels developed in a European Commission-funded consortium, FishPopTrace, to scenarios that are relevant for the identification of potential illegal fishing and/or mislabeling for two commercially important Atlantic species; cod (Gadus morhua) and herring (Clupea harengus). Markers under selection are typically inappropriate for assessing demographic processes such as gene flow. However, the broad distribution of SNP loci throughout the genome, together with the potential to score large numbers using high throughout approaches, allows for the additional flexibility in traceability studies to establish marker panels with loci that vary in their evolutionary dynamics. Strategies for optimizing population assignment in relation to SNP characteristics and target species biology across various spatial scales will be discussed.

Technical University of …

Abstract Geographic distributions of most temperate marine fishes are affected by post-glacial re... more Abstract Geographic distributions of most temperate marine fishes are affected by post-glacial recolonisation events which have left complex genetic imprints on populations of marine species. This study investigated population structure and demographic history of ...

Report of the Working …, Jan 1, 2009

Ecology and Evolution, 2011

Recent advances in molecular interrogation techniques now allow unprecedented genomic inference a... more Recent advances in molecular interrogation techniques now allow unprecedented genomic inference about the role of adaptive genetic divergence in wild populations. We used high-throughput genotyping to screen a genome-wide panel of 276 single nucleotide polymorphisms (SNPs) for the economically and culturally important salmonid Oncorhynchus mykiss. Samples included 805 individuals from 11 anadromous and resident populations from the northwestern United States and British Columbia, and represented two major lineages including paired populations of each life history within single drainages of each lineage. Overall patterns of variation affirmed clear distinctions between lineages and in most instances, isolation by distance within them. Evidence for divergent selection at eight candidate loci included significant landscape correlations, particularly with temperature. High diversity of two nonsynonymous mutations within the peptide-binding region of the major histocompatibility complex (MHC) class II (DAB) gene provided signatures of balancing selection. Weak signals for potential selection between sympatric resident and anadromous populations were revealed from genome scans and allele frequency comparisons. Our results suggest an important adaptive role for immune-related functions and present a large genomic resource for future studies

ABSTRACT The importance of marine organisms for both economical and ecological reasons is enormou... more ABSTRACT The importance of marine organisms for both economical and ecological reasons is enormous; and knowledge of population structure and connectivity is crucial for the sustainable utilisation and conservation of exploited fish stocks. However in most cases our understanding of these spatial patterns of natural variation, both neutral and adaptive, is limited. For marine fish, the maintenance of local stocks containing adaptive diversity is associated with the sustainability and resilience of marine fisheries in the face of climatic and anthropogenic threats. However, many previous studies with genetic markers such as microsatellites have observed weak genetic structure in marine fish and combined with a pelagic larval stage, this has supported the hypothesis that gene flow is extensive and that there is little opportunity for differentiation on local scales. A consequence of the limited opportunity for divergence is the associated assumption that local adaptation would be similarly restricted, except perhaps at macrogeographic levels. However, the application of Single Nucleotide Polymorphisms (SNPs) has the potential to demonstrate previously undetected spatial and temporal population structuring and signatures of adaptive variation. Additionally, SNPs are uniquely applicable for the identification and monitoring of wild fish populations and the traceability of products throughout the food supply chain, allowing effective enforcement of fisheries regulations. Here we demonstrate the utility of SNP panels developed in a European Commission-funded consortium, FishPopTrace, to scenarios that are relevant for the identification of potential illegal fishing and/or mislabeling for two commercially important Atlantic species; cod (Gadus morhua) and herring (Clupea harengus). Markers under selection are typically inappropriate for assessing demographic processes such as gene flow. However, the broad distribution of SNP loci throughout the genome, together with the potential to score large numbers using high throughout approaches, allows for the additional flexibility in traceability studies to establish marker panels with loci that vary in their evolutionary dynamics. Strategies for optimizing population assignment in relation to SNP characteristics and target species biology across various spatial scales will be discussed.

Technical University of …

Abstract Geographic distributions of most temperate marine fishes are affected by post-glacial re... more Abstract Geographic distributions of most temperate marine fishes are affected by post-glacial recolonisation events which have left complex genetic imprints on populations of marine species. This study investigated population structure and demographic history of ...

Report of the Working …, Jan 1, 2009

ICES Journal of …, Jan 1, 2011

Molecular …, Jan 1, 2012

High gene flow is considered the norm for most marine organisms and is expected to limit their ab... more High gene flow is considered the norm for most marine organisms and is expected to limit their ability to adapt to local environments. Few studies have directly compared the patterns of differentiation at neutral and selected gene loci in marine organisms. We analysed a transcriptome-derived panel of 281 SNPs in Atlantic herring (Clupea harengus), a highly migratory small pelagic fish, for elucidating neutral and selected genetic variation among populations and to identify candidate genes for environmental adaptation. We analysed 607 individuals from 18 spawning locations in the northeast Atlantic, including two temperature clines (5-12°C) and two salinity clines (5-35&). By combining genome scan and landscape genetic analyses, four genetically distinct groups of herring were identified: Baltic Sea, Baltic-North Sea transition area, North Sea ⁄ British Isles and North Atlantic; notably, samples exhibited divergent clustering patterns for neutral and selected loci. We found statistically strong evidence for divergent selection at 16 outlier loci on a global scale, and significant correlations with temperature and salinity at nine loci. On regional scales, we identified two outlier loci with parallel patterns across temperature clines and five loci associated with temperature in the North Sea ⁄ North Atlantic. Likewise, we found seven replicated outliers, of which five were significantly associated with low salinity across both salinity clines. Our results reveal a complex pattern of varying spatial genetic variation among outlier loci, likely reflecting adaptations to local environments. In addition to disclosing the fine scale of local adaptation in a highly vagile species, our data emphasize the need to preserve functionally important biodiversity.

PloS one, Jan 1, 2012

The introduction of Next Generation Sequencing (NGS) has revolutionised population genetics, prov... more The introduction of Next Generation Sequencing (NGS) has revolutionised population genetics, providing studies of nonmodel species with unprecedented genomic coverage, allowing evolutionary biologists to address questions previously far beyond the reach of available resources. Furthermore, the simple mutation model of Single Nucleotide Polymorphisms (SNPs) permits cost-effective high-throughput genotyping in thousands of individuals simultaneously. Genomic resources are scarce for the Atlantic herring (Clupea harengus), a small pelagic species that sustains high revenue fisheries. This paper details the development of 578 SNPs using a combined NGS and high-throughput genotyping approach. Eight individuals covering the species distribution in the eastern Atlantic were bar-coded and multiplexed into a single cDNA library and sequenced using the 454 GS FLX platform. SNP discovery was performed by de novo sequence clustering and contig assembly, followed by the mapping of reads against consensus contig sequences. Selection of candidate SNPs for genotyping was conducted using an in silico approach. SNP validation and genotyping were performed simultaneously using an Illumina 1,536 GoldenGate assay. Although the conversion rate of candidate SNPs in the genotyping assay cannot be predicted in advance, this approach has the potential to maximise cost and time efficiencies by avoiding expensive and time-consuming laboratory stages of SNP validation. Additionally, the in silico approach leads to lower ascertainment bias in the resulting SNP panel as marker selection is based only on the ability to design primers and the predicted presence of intron-exon boundaries. Consequently SNPs with a wider spectrum of minor allele frequencies (MAFs) will be genotyped in the final panel. The genomic resources presented here represent a valuable multi-purpose resource for developing informative marker panels for population discrimination, microarray development and for population genomic studies in the wild.

Nature …, Jan 1, 2012

Illegal, unreported and unregulated fishing has had a major role in the overexploitation of globa... more Illegal, unreported and unregulated fishing has had a major role in the overexploitation of global fish populations. In response, international regulations have been imposed and many fisheries have been 'eco-certified' by consumer organizations, but methods for independent control of catch certificates and eco-labels are urgently needed. Here we show that, by using geneassociated single nucleotide polymorphisms, individual marine fish can be assigned back to population of origin with unprecedented high levels of precision. By applying high differentiation single nucleotide polymorphism assays, in four commercial marine fish, on a pan-European scale, we find 93-100% of individuals could be correctly assigned to origin in policy-driven case studies. We show how case-targeted single nucleotide polymorphism assays can be created and forensically validated, using a centrally maintained and publicly available database. our results demonstrate how application of gene-associated markers will likely revolutionize origin assignment and become highly valuable tools for fighting illegal fishing and mislabelling worldwide.

Ecology and …, Jan 1, 2012

Recent advances in molecular interrogation techniques now allow unprecedented genomic inference a... more Recent advances in molecular interrogation techniques now allow unprecedented genomic inference about the role of adaptive genetic divergence in wild populations. We used high-throughput genotyping to screen a genome-wide panel of 276 single nucleotide polymorphisms (SNPs) for the economically and culturally important salmonid Oncorhynchus mykiss. Samples included 805 individuals from 11 anadromous and resident populations from the northwestern United States and British Columbia, and represented two major lineages including paired populations of each life history within single drainages of each lineage. Overall patterns of variation affirmed clear distinctions between lineages and in most instances, isolation by distance within them. Evidence for divergent selection at eight candidate loci included significant landscape correlations, particularly with temperature. High diversity of two nonsynonymous mutations within the peptide-binding region of the major histocompatibility complex (MHC) class II (DAB) gene provided signatures of balancing selection. Weak signals for potential selection between sympatric resident and anadromous populations were revealed from genome scans and allele frequency comparisons. Our results suggest an important adaptive role for immune-related functions and present a large genomic resource for future studies

World Fishing & Aquaculture, Jan 1, 2009

Molecular Ecology …, Jan 1, 2008

Nine microsatellite markers were characterized in the fungus Botrytis cinerea . Genomic DNA seque... more Nine microsatellite markers were characterized in the fungus Botrytis cinerea . Genomic DNA sequences from the partial sequencing of 12 000 bacterial artificial chromosome (BAC) clones, were screened by BLAST for various microsatellite motives, and primer pairs were designed. Cross-amplification and polymorphism were assessed on 49 isolates from B. cinerea and two related species, collected from natural populations on several plants and locations.

Mar Ecol Prog Ser, Jan 1, 2009

ABSTRACT The importance of marine organisms for both economical and ecological reasons is enormou... more ABSTRACT The importance of marine organisms for both economical and ecological reasons is enormous; and knowledge of population structure and connectivity is crucial for the sustainable utilisation and conservation of exploited fish stocks. However in most cases our understanding of these spatial patterns of natural variation, both neutral and adaptive, is limited. For marine fish, the maintenance of local stocks containing adaptive diversity is associated with the sustainability and resilience of marine fisheries in the face of climatic and anthropogenic threats. However, many previous studies with genetic markers such as microsatellites have observed weak genetic structure in marine fish and combined with a pelagic larval stage, this has supported the hypothesis that gene flow is extensive and that there is little opportunity for differentiation on local scales. A consequence of the limited opportunity for divergence is the associated assumption that local adaptation would be similarly restricted, except perhaps at macrogeographic levels. However, the application of Single Nucleotide Polymorphisms (SNPs) has the potential to demonstrate previously undetected spatial and temporal population structuring and signatures of adaptive variation. Additionally, SNPs are uniquely applicable for the identification and monitoring of wild fish populations and the traceability of products throughout the food supply chain, allowing effective enforcement of fisheries regulations. Here we demonstrate the utility of SNP panels developed in a European Commission-funded consortium, FishPopTrace, to scenarios that are relevant for the identification of potential illegal fishing and/or mislabeling for two commercially important Atlantic species; cod (Gadus morhua) and herring (Clupea harengus). Markers under selection are typically inappropriate for assessing demographic processes such as gene flow. However, the broad distribution of SNP loci throughout the genome, together with the potential to score large numbers using high throughout approaches, allows for the additional flexibility in traceability studies to establish marker panels with loci that vary in their evolutionary dynamics. Strategies for optimizing population assignment in relation to SNP characteristics and target species biology across various spatial scales will be discussed.

Technical University of …

Abstract Geographic distributions of most temperate marine fishes are affected by post-glacial re... more Abstract Geographic distributions of most temperate marine fishes are affected by post-glacial recolonisation events which have left complex genetic imprints on populations of marine species. This study investigated population structure and demographic history of ...

Report of the Working …, Jan 1, 2009