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1. A continuous genome assembly of the corkwing wrasse (Symphodus melops)

Author:
Hansen, Michael M.,   et al.   ; Mattingsdal, Morten; Jentoft, Sissel; Tørresen, Ole K.; Knutsen, Halvor; Robalo, Joana I.; Zagrodzka, Zuzanna; André, Carl; Gonzalez, Enrique Blanco;     Show all 9 Authors
Source:
Genomics 2018 v.110 no.6 pp. 399-403
ISSN:
0888-7543
Subject:
Caligidae; Labrus; Symphodus melops; cleaning; drugs; fish culture; genes; genetic analysis; genome assembly; genomics; glycosylation; lice infestations; nucleotide sequences; phosphotransferases (kinases); salmon; stress response
Abstract:
... The wrasses (Labridae) are one of the most successful and species-rich families of the Perciformes order of teleost fish. Its members display great morphological diversity, and occupy distinct trophic levels in coastal waters and coral reefs. The cleaning behaviour displayed by some wrasses, such as corkwing wrasse (Symphodus melops), is of particular interest for the salmon aquaculture industry t ...
DOI:
10.1016/j.ygeno.2018.04.009

2. All roads lead to home: panmixia of European eel in the Sargasso Sea

Author:
Hansen, Michael M.,   et al.   ; Als, Thomas D.; Maes, Gregory E.; Castonguay, Martin; Riemann, Lasse; Aarestrup, Kim; Munk, Peter; Sparholt, Henrik; Hanel, Reinhold; Bernatchez, Louis;     Show all 10 Authors
Source:
Molecular ecology 2011 v.20 no.7 pp. 1333-1346
ISSN:
0962-1083
Subject:
Anguilla anguilla; Anguilla rostrata; coasts; eel; genetic techniques and protocols; genetic variation; hybridization; hybrids; juveniles; larvae; microsatellite repeats; spawning; sympatry; Iceland; Sargasso Sea
Abstract:
... European eels (Anguilla anguilla) spawn in the remote Sargasso Sea in partial sympatry with American eels (Anguilla rostrata), and juveniles are transported more than 5000 km back to the European and North African coasts. The two species have been regarded as classic textbook examples of panmixia, each comprising a single, randomly mating population. However, several recent studies based on contin ...
DOI:
10.1111/j.1365-294X.2011.05011.x
PubMed:
21299662

3. Brown trout (salmo trutta) stocking impact assessment using microsatellite dna markers

Author:
Hansen, Michael M.,   et al.   ; Ruzzante, Daniel E.; Nielsen, Einar E.; Mensberg, Karen-Lise D.;     Show all 4 Authors
Source:
Ecological applications 2001 v.11 no.1 pp. 148-160
ISSN:
1051-0761
Subject:
Salmo trutta; age structure; alleles; extinction; fish communities; gene pool; genetic markers; genetic relationships; genetic stability; genetic variation; hatcheries; introgression; loci; microsatellite repeats; monitoring; rivers; trout
Abstract:
... The genetic integrity of many salmonid fish populations is threatened by stocking of domesticated conspecifics. The purpose of this study was to assess the utility of microsatellite DNA markers for detecting loss of genetic diversity in hatchery strains, for estimating their genetic relationships, and for monitoring the genetic impact of stocking activity on wild populations of salmonid fishes. Br ...

4. Comparative analysis of complete mitochondrial genomes suggests that relaxed purifying selection is driving high nonsynonymous evolutionary rate of the NADH2 gene in whitefish (Coregonus ssp.)

Author:
Hansen, Michael M.,   et al.   ; Jacobsen, Magnus W.; da Fonseca, Rute R.; Bernatchez, Louis;     Show all 4 Authors
Source:
Molecular phylogenetics and evolution 2016 v.95 pp. 161-170
ISSN:
1055-7903
Subject:
Anguillidae; Coregonus; NADH dehydrogenase; Percidae; Scombridae; adaptive radiation; amino acids; fish; genes; genetic drift; mitochondria; mitochondrial genome
Abstract:
... Several studies have recently reported evidence for positive selection acting on the mitochondrial genome (mitogenome), emphasizing its potential role in adaptive divergence and speciation. In this study we searched 107 full mitogenomes of recently diverged species and lineages of whitefish (Coregonus ssp.) for signals of positive selection. These salmonids show several distinct morphological and ...
DOI:
10.1016/j.ympev.2015.11.008

5. Comparative estimation of effective population sizes and temporal gene flow in two contrasting population systems

Author:
HANSEN, MICHAEL M.,   et al.   ; FRASER, DYLAN J.; ØSTERGAARD, SIRI; TESSIER, NATHALIE; LEGAULT, MICHEL; BERNATCHEZ, LOUIS;     Show all 6 Authors
Source:
Molecular ecology 2007 v.16 no.18 pp. 3866-3889
ISSN:
0962-1083
Subject:
Salmo salar; Salmo trutta; founder effect; gene flow; genetic variation; linkage disequilibrium; models; population size; population structure; salmon; trout; wildlife management
Abstract:
... Estimation of effective population sizes (Ne) and temporal gene flow (Nem, m) has many implications for understanding population structure in evolutionary and conservation biology. However, comparative studies that gauge the relative performance of Ne, Nem or m methods are few. Using temporal genetic data from two salmonid fish population systems with disparate population structure, we (i) evaluat ...
DOI:
10.1111/j.1365-294X.2007.03453.x
PubMed:
17850551

6. Evidence of microsatellite hitch-hiking selection in Atlantic cod (Gadus morhua L.): implications for inferring population structure in nonmodel organisms

Author:
HANSEN, MICHAEL M.,   et al.   ; NIELSEN, EINAR E.; MELDRUP, DORTE;     Show all 3 Authors
Source:
Molecular ecology 2006 v.15 no.11 pp. 3219-3229
ISSN:
0962-1083
Subject:
Gadus morhua; biogeography; genetic variation; loci; marine fish; microsatellite repeats; population size; population structure; selection methods; taxonomy; variance; Baltic Sea; Barents Sea; Newfoundland and Labrador; North Sea
Abstract:
... Microsatellites have gained wide application for elucidating population structure in nonmodel organisms. Since they are generally noncoding, neutrality is assumed but rarely tested. In Atlantic cod (Gadus morhua L.), microsatellite studies have revealed highly heterogeneous estimates of genetic differentiation among loci. In particular one locus, Gmo 132, has demonstrated elevated genetic differen ...
DOI:
10.1111/j.1365-294X.2006.03025.x
PubMed:
16968266

7. Expression of interest: transcriptomics and the designation of conservation units

Author:
Hansen, Michael M.
Source:
Molecular ecology 2010 v.19 no.9 pp. 1757-1759
ISSN:
0962-1083
Subject:
Salmo salar; adaptive radiation; gene expression; genetic markers; genetic variation; population structure; transcriptomics
Abstract:
... An important task within conservation genetics consists in defining intraspecific conservation units. Most conceptual frameworks involve two steps: (i) identifying demographically independent units, and (ii) evaluating their degree of adaptive divergence. Whereas a plethora of methods are available for delineating genetic population structure, assessment of functional genetic divergence remains a ...
DOI:
10.1111/j.1365-294X.2010.04597.x
PubMed:
20529066

8. Gene flow, effective population size and selection at major histocompatibility complex genes: brown trout in the Hardanger Fjord, Norway

Author:
HANSEN, MICHAEL M.,   et al.   ; SKAALA, ØYSTEIN; JENSEN, LASSE FAST; BEKKEVOLD, DORTE; MENSBERG, KAREN-LISE D.;     Show all 5 Authors
Source:
Molecular ecology 2007 v.16 no.7 pp. 1413-1425
ISSN:
0962-1083
Subject:
Lepeophtheirus salmonis; Salmo trutta; Ursidae; alleles; aquaculture; gene flow; history; immune system; loci; major histocompatibility complex; microsatellite repeats; population dynamics; population size; prediction; Norway
Abstract:
... Brown trout populations in the Hardanger Fjord, Norway, have declined drastically due to increased exposure to salmon lice from salmonid aquaculture. We studied contemporary samples from seven populations and historical samples (1972 and 1983) from the two largest populations, one of which has declined drastically whereas the other remains stable. We analysed 11 microsatellite loci, including one ...
DOI:
10.1111/j.1365-294X.2007.03255.x
PubMed:
17391266

9. Genetic population structure and variation at phenology‐related loci in anadromous Arctic char (Salvelinus alpinus)

Author:
Hansen, Michael M.,   et al.   ; Madsen, Rikke P. A.; Jacobsen, Magnus W.; O'Malley, Kathleen G.; Nygaard, Rasmus; Præbel, Kim; Jónsson, Bjarni; Pujolar, Jose M.; Fraser, Dylan J.; Bernatchez, Louis;     Show all 10 Authors
Source:
Ecology of freshwater fish 2020 v.29 no.1 pp. 170-183
ISSN:
0906-6691
Subject:
Salvelinus alpinus; alleles; anadromous fish; autocorrelation; climate change; foraging; gene flow; latitude; loci; population structure; single nucleotide polymorphism; spawning; surface water temperature; Arctic region; Greenland
Abstract:
... The Arctic will be especially affected by climate change, resulting in altered seasonal timing. Anadromous Arctic char (Salvelinus alpinus) is strongly influenced by sea surface temperature (SST) delimiting time periods available for foraging in the sea. Recent studies of salmonid species have shown variation at phenology‐related loci associated with timing of migration and spawning. We contrasted ...
DOI:
10.1111/eff.12504

10. Genetic structure and demographic history of brown trout (Salmo trutta) populations from the southern Balkans

Author:
HANSEN, MICHAEL M.,   et al.   ; APOSTOLIDIS, APOSTOLOS P.; MADEIRA, MARIA-JOSE; MACHORDOM, ANNIE;     Show all 4 Authors
Source:
Freshwater biology 2008 v.53 no.8 pp. 1555-1566
ISSN:
0046-5070
Subject:
Salmo trutta; biodiversity; gene pool; genetic variation; hybrids; immigration; introgression; microsatellite repeats; mitochondrial DNA; rivers; trout; Balkans
Abstract:
... 1. The present study was designed to characterize the genetic structure of brown trout (Salmo trutta) populations from the southern Balkans and to assess the spread of non-native strains and their introgression into native trout gene pools. We analysed polymorphism at nine microsatellite loci in seven supposedly non-admixed and three stocked brown trout populations. 2. The analyses confirmed the a ...
DOI:
10.1111/j.1365-2427.2008.01988.x

11. Genomic footprints of speciation in Atlantic eels (Anguilla anguilla and A. rostrata)

Author:
Hansen, Michael M.,   et al.   ; Jacobsen, Magnus W.; Pujolar, Jose Martin; Bernatchez, Louis; Munch, Kasper; Jian, Jianbo; Niu, Yongchao;     Show all 7 Authors
Source:
Molecular ecology 2014 v.23 no.19 pp. 4785-4798
ISSN:
0962-1083
Subject:
Anguilla anguilla; Anguilla rostrata; DNA; eel; gene flow; genes; genetic drift; genomics; larvae; linkage disequilibrium; migratory behavior; phosphorylation; population size; spawning
Abstract:
... The importance of speciation‐with‐geneflow scenarios is increasingly appreciated. However, the specific processes and the resulting genomic footprints of selection are subject to much discussion. We studied the genomics of speciation between the two panmictic, sympatrically spawning sister species; European (Anguilla anguilla) and American eel (A. rostrata). Divergence is assumed to have initiated ...
DOI:
10.1111/mec.12896
PubMed:
25155907

12. Genomic parallelism and lack thereof in contrasting systems of three‐spined sticklebacks

Author:
Hansen, Michael M.,   et al.   ; Liu, Shenglin; Ferchaud, Anne‐Laure; Grønkjær, Peter; Nygaard, Rasmus;     Show all 5 Authors
Source:
Molecular ecology 2018 v.27 no.23 pp. 4725-4743
ISSN:
0962-1083
Subject:
DNA; Gasterosteus aculeatus; chromosome inversions; empirical research; freshwater; genes; genomics; parallel evolution; phenotype; single nucleotide polymorphism; Denmark; Greenland
Abstract:
... Parallel evolution and the extent to which it involves gene reuse have attracted much interest. Whereas it has theoretically been predicted under which circumstances gene reuse is expected, empirical studies that directly compare systems showing high and low parallelism are rare. Three‐spined stickleback (Gasterosteus aculeatus), where freshwater populations have been independently founded by ance ...
DOI:
10.1111/mec.14782

13. Half a century of genetic interaction between farmed and wild Atlantic salmon: Status of knowledge and unanswered questions

Author:
Hansen, Michael M,   et al.   ; Glover, Kevin A; Solberg, Monica F; McGinnity, Phil; Hindar, Kjetil; Verspoor, Eric; Coulson, Mark W; Araki, Hitoshi; Skaala, Øystein; Svåsand, Terje;     Show all 10 Authors
Source:
Fish and fisheries 2017 v.18 no.5 pp. 890-927
ISSN:
1467-2960
Subject:
Salmo salar; aquaculture; domestication; farmed fish; field experimentation; fish production; introgression; life history; progeny; salmon; transcription (genetics); Norway
Abstract:
... Atlantic salmon (Salmo salar) is one of the best researched fishes, and its aquaculture plays a global role in the blue revolution. However, since the 1970s, tens of millions of farmed salmon have escaped into the wild. We review current knowledge of genetic interactions and identify the unanswered questions. Native salmon populations are typically genetically distinct from each other and potentia ...
DOI:
10.1111/faf.12214

14. Heat tolerance and gene expression responses to heat stress in threespine sticklebacks from ecologically divergent environments

Author:
Hansen, Michael M.,   et al.   ; Dammark, Karin Brydsø; Ferchaud, Anne-Laure; Sørensen, Jesper G.;     Show all 4 Authors
Source:
Journal of thermal biology 2018 v.75 pp. 88-96
ISSN:
0306-4565
Subject:
Gasterosteus aculeatus; ectothermy; energy; fish; gene expression; genes; heat stress; heat tolerance; lakes; phenotypic plasticity; surface water; temperature; Denmark
Abstract:
... Ectothermic animals like fishes are extremely dependent on temperature, as they are not able to change body temperature physiologically. When populations are found in isolated water bodies such as small lakes they will have to respond to stressful high temperatures by behavioral avoidance, phenotypic plasticity or microevolutionary change. We analyzed threespine sticklebacks from two large and two ...
DOI:
10.1016/j.jtherbio.2018.06.003

15. Human effects on ecological connectivity in aquatic ecosystems: Integrating scientific approaches to support management and mitigation

Author:
Hansen, Michael M.,   et al.   ; Crook, David A.; Lowe, Winsor H.; Allendorf, Frederick W.; Erős, Tibor; Finn, Debra S.; Gillanders, Bronwyn M.; Hadwen, Wade L.; Harrod, Chris; Hermoso, Virgilio; Jennings, Simon; Kilada, Raouf W.; Nagelkerken, Ivan; Page, Timothy J.; Riginos, Cynthia; Fry, Brian; Hughes, Jane M.;     Show all 17 Authors
Source:
The Science of the total environment 2015 v.534 pp. 52-64
ISSN:
0048-9697
Subject:
analytical methods; anthropogenic activities; aquatic ecosystems; aquatic organisms; biodiversity; case studies; climate change; dams (hydrology); environmental impact; habitat destruction; humans; models; phenotypic plasticity; population structure; rivers
Abstract:
... Understanding the drivers and implications of anthropogenic disturbance of ecological connectivity is a key concern for the conservation of biodiversity and ecosystem processes. Here, we review human activities that affect the movements and dispersal of aquatic organisms, including damming of rivers, river regulation, habitat loss and alteration, human-assisted dispersal of organisms and climate c ...
DOI:
10.1016/j.scitotenv.2015.04.034

16. Identifying footprints of selection in stocked brown trout populations: a spatio-temporal approach

Author:
Hansen, Michael M.,   et al.   ; Meier, Kristian; Mensberg, Karen-Lise D.;     Show all 3 Authors
Source:
Molecular ecology 2010 v.19 no.9 pp. 1787-1800
ISSN:
0962-1083
Subject:
Salmo trutta; alleles; expressed sequence tags; farmed fish; hatcheries; loci; microsatellite repeats; natural selection; quantitative trait loci; trout; wild fish; Denmark
Abstract:
... Studies of interactions between farmed and wild salmonid fishes have suggested reduced fitness of farmed strains in the wild, but evidence for selection at the genic level is lacking. We studied three brown trout populations in Denmark which have been significantly admixed with stocked hatchery trout (19-64%), along with two hatchery strains used for stocking. The wild populations were represented ...
DOI:
10.1111/j.1365-294X.2010.04615.x
PubMed:
20345684

17. Landscape genetics, historical isolation and cross-Andean gene flow in the wax palm, Ceroxylon echinulatum (Arecaceae)

Author:
HANSEN, MICHAEL M.,   et al.   ; TRÉNEL, PHILIPP; NORMAND, SIGNE; BORCHSENIUS, FINN;     Show all 4 Authors
Source:
Molecular ecology 2008 v.17 no.15 pp. 3528-3540
ISSN:
0962-1083
Subject:
Ceroxylon; biodiversity; crossing; founder effect; friction; gene flow; landscapes; models; montane forests; phylogeography; Andes region; Ecuador; Peru
Abstract:
... Knowledge of the role of landscapes in shaping genetic connectivity and divergence is essential for understanding patterns of biogeography and diversity. This is particularly relevant for the Andes region, a major biodiversity hotspot of relatively recent origin. We examined the phylogeography and landscape genetics of the Andean wax palm Ceroxylon echinulatum (Arecaceae) that occurs in two narrow ...
DOI:
10.1111/j.1365-294X.2008.03853.x
PubMed:
19160480

18. Long‐term effective population sizes, temporal stability of genetic composition and potential for local adaptation in anadromous brown trout (Salmo trutta) populations

Author:
Hansen, Michael M.,   et al.   ; Ruzzante, Daniel E.; Nielsen, Einar E.; Bekkevold, Dorte; Mensberg, Karen‐Lise D.;     Show all 5 Authors
Source:
Molecular ecology 2002 v.11 no.12 pp. 2523-2535
ISSN:
0962-1083
Subject:
microsatellite repeats; Salmo trutta; rivers; analysis of variance; genetic distance; models; gene flow; genetic stability; genetic drift; genetic techniques and protocols; genetic variation; population size; genetic relationships; Denmark
Abstract:
... We examined the long‐term temporal (1910s to 1990s) genetic variation at eight microsatellite DNA loci in brown trout (Salmo trutta L) collected from five anadromous populations in Denmark to assess the long‐term stability of genetic composition and to estimate effective population sizes (Ne). Contemporary and historical samples consisted of tissue and archived scales, respectively. Pairwise θST e ...
DOI:
10.1046/j.1365-294X.2002.01634.x

19. Microsatellite DNA analysis of northern pike (Esox lucius L.) populations: insights into the genetic structure and demographic history of a genetically depauperate species

Author:
Hansen, Michael M.,   et al.   ; Jacobsen, Birgitte H.; Loeschcke, Volker;     Show all 3 Authors
Source:
Biological journal of the Linnean Society 2005 v.84 no.1 pp. 91-101
ISSN:
0024-4066
Subject:
Bayesian theory; DNA; Esox lucius; alleles; effective population size; founder effect; freshwater fish; genetic distance; genetic variation; loci; microsatellite repeats; multidimensional scaling; mutation; phylogeography; population dynamics; surface water; variance; Ireland; North America; Northern European region
Abstract:
... The northern pike Esox lucius L. is a freshwater fish exhibiting pronounced population subdivision and low genetic variability. However, there is limited knowledge on phylogeographical patterns within the species, and it is not known whether the low genetic variability reflects primarily current low effective population sizes or historical bottlenecks. We analysed six microsatellite loci in ten ...
DOI:
10.1111/j.1095-8312.2005.00416.x

20. Mitogenome sequencing reveals shallow evolutionary histories and recent divergence time between morphologically and ecologically distinct European whitefish (Coregonus spp.)

Author:
HANSEN, MICHAEL M.,   et al.   ; JACOBSEN, MAGNUS W.; ORLANDO, LUDOVIC; BEKKEVOLD, DORTE; BERNATCHEZ, LOUIS; WILLERSLEV, ESKE; GILBERT, M. THOMAS P.;     Show all 7 Authors
Source:
Molecular ecology 2012 v.21 no.11 pp. 2727-2742
ISSN:
0962-1083
Subject:
Coregonus clupeaformis; genome; haplotypes; introgression; microsatellite repeats; mutation; reproductive isolation; Denmark; North America; North Sea
Abstract:
... The advent of second‐generation sequencing has made it possible to quickly and economically generate whole mitochondrial genome (mitogenome) sequences. To date, mitogenome studies of nonmodel organisms have demonstrated increased power for resolving interspecies relationships. We explored an alternate use of such data to recover relationships and population history of closely related lineages with ...
DOI:
10.1111/j.1365-294X.2012.05561.x
PubMed:
22509795

21. Monitoring adaptive genetic responses to environmental change

Author:
HANSEN, MICHAEL M.,   et al.   ; OLIVIERI, ISABELLE; WALLER, DONALD M.; NIELSEN, EINAR E.; ,;     Show all 5 Authors
Source:
Molecular ecology 2012 v.21 no.6 pp. 1311-1329
ISSN:
0962-1083
Subject:
Daphnia; Drosophila; animals; climate change; eggs; evolution; experimental design; harvesting; landscapes; molecular genetics; monitoring; phenotypic variation
Abstract:
... Widespread environmental changes including climate change, selective harvesting and landscape alterations now greatly affect selection regimes for most organisms. How animals and plants can adapt to these altered environments via contemporary evolution is thus of strong interest. We discuss how to use genetic monitoring to study adaptive responses via repeated analysis of the same populations over ...
DOI:
10.1111/j.1365-294X.2011.05463.x
PubMed:
22269082

22. Oceanic Spawning Migration of the European Eel (Anguilla anguilla)

Author:
Hansen, Michael M.,   et al.   ; Aarestrup, Kim; Økland, Finn; Righton, David; Gargan, Patrik; Castonguay, Martin; Bernatchez, Louis; Howey, Paul; Sparholt, Henrik; Pedersen, Michael I.; McKinley, Robert S.;     Show all 11 Authors
Source:
Science 2009 v.325 no.5948 pp. 1660
ISSN:
0036-8075
Subject:
Anguilla anguilla; Gulf Stream; eel; larvae; migratory behavior; satellites; spawning; swimming; Atlantic Ocean; Europe; Sargasso Sea
Abstract:
... European eels (Anguilla anguilla) undertake a approximately 5000-kilometer (km) spawning migration from Europe to the Sargasso Sea. The larvae are transported back to European waters by the Gulf Stream and North Atlantic Drift. However, details of the spawning migration remain unknown because tracking eels in the Atlantic Ocean has, so far, eluded study. Recent advances in satellite tracking enabl ...
DOI:
10.1126/science.1178120

23. Performance of farmed, hybrid, and wild Atlantic salmon (Salmo salar) families in a natural river environment

Author:
Hansen, Michael M.,   et al.   ; Skaala, Øystein; Glover, Kevin A.; Barlaup, Bjørn T.; Svåsand, Terje; Besnier, Francois; Borgstrøm, Reidar;     Show all 7 Authors
Source:
Canadian journal of fisheries and aquatic sciences 2012 v.69 no.12 pp. 1994-2006
ISSN:
1205-7533
Subject:
Salmo salar; crossing; diet; eggs; farmed fish; farms; genetic markers; hybrids; parents; progeny; rivers; salmon; smolts; wild fish; Norway
Abstract:
... Survival, growth, and diet were compared for farmed, hybrid, and wild Atlantic salmon (Salmo salar) families from the eyed egg to the smolt stage in River Guddalselva, Hardangerfjord, Norway. All individuals that survived until the smolt stage were captured in a Wolf trap and identified to one of the 69 experimental families using microsatellite markers. Survival of farmed salmon progeny was signi ...
DOI:
10.1139/f2012-118

24. Population and family structure of brown trout, Salmo trutta, in a Mediterranean stream

Author:
Hansen, Michael M.,   et al.   ; Vera, Manuel; Sanz, Nuria; Almodóvar, Ana; García-Marín, José-Luis;     Show all 5 Authors
Source:
Marine & freshwater research 2010 v.61 no.6 pp. 676-685
ISSN:
1323-1650
Subject:
Salmo trutta; adults; basins; family structure; genetic variation; microsatellite repeats; population structure; rivers; spawning; streams; trout
Abstract:
... The physical arrangement of closely related individuals is expected to significantly influence the pattern of population genetic structure. For example, if related individuals are non-randomly distributed and included in samples, this may lead to exaggerated conclusions about genetic differentiation. In the present study, we compared population structure v. family relationships of brown trout (Sal ...
DOI:
10.1071/MF09098

25. Population transcriptomics of life-history variation in the genus Salmo

Author:
HANSEN, MICHAEL M.,   et al.   ; GIGER, THOMAS; EXCOFFIER, LAURENT; AMSTUTZ, URSULA; DAY, PHILIP J.R.; CHAMPIGNEULLE, ALEXIS; KELSO, JANET; LARGIADÈR, CARLO R.;     Show all 8 Authors
Source:
Molecular ecology 2008 v.17 no.13 pp. 3095-3108
ISSN:
0962-1083
Subject:
Salmo salar; Salmo trutta; complementary DNA; discriminant analysis; experimental design; gene expression; gene expression regulation; genes; heat shock proteins; life history; loci; microarray technology; migratory behavior; phenotype; respiratory system; seawater; transaldolase; transcriptomics
Abstract:
... In this study, we demonstrate the power of applying complementary DNA (cDNA) microarray technology to identifying candidate loci that exhibit subtle differences in expression levels associated with a complex trait in natural populations of a nonmodel organism. Using a highly replicated experimental design involving 180 cDNA microarray experiments, we measured gene-expression levels from 1098 trans ...
DOI:
10.1111/j.1365-294X.2008.03820.x
PubMed:
18522696

26. PSMC (pairwise sequentially Markovian coalescent) analysis of RAD (restriction site associated DNA) sequencing data

Author:
Hansen, Michael M.,   et al.   ; Liu, Shenglin;     Show all 2 Author
Source:
Molecular ecology resources 2017 v.17 no.4 pp. 631-641
ISSN:
1755-098X
Subject:
DNA; Gasterosteus aculeatus; genome; lakes; loci; mutation; nucleotide sequences; Greenland
Abstract:
... The pairwise sequentially Markovian coalescent (PSMC) method uses the genome sequence of a single individual to estimate demographic history covering a time span of thousands of generations. Although originally designed for whole‐genome data, we here use simulations to investigate its applicability to reference genome‐aligned restriction site associated DNA (RAD) data. We find that RAD data can po ...
DOI:
10.1111/1755-0998.12606

27. Region‐wide and ecotype‐specific differences in demographic histories of threespine stickleback populations, estimated from whole genome sequences

Author:
Hansen, Michael M.,   et al.   ; Liu, Shenglin; Jacobsen, Magnus W.;     Show all 3 Authors
Source:
Molecular ecology 2016 v.25 no.20 pp. 5187-5202
ISSN:
0962-1083
Subject:
Gasterosteus aculeatus; ancestry; freshwater; freshwater fish; mitochondrial genome; parallel evolution; phylogeography; population growth; principal component analysis; single nucleotide polymorphism; Greenland; North America; Northern European region
Abstract:
... We analysed 81 whole genome sequences of threespine sticklebacks from Pacific North America, Greenland and Northern Europe, representing 16 populations. Principal component analysis of nuclear SNPs grouped populations according to geographical location, with Pacific populations being more divergent from each other relative to European and Greenlandic populations. Analysis of mitogenome sequences s ...
DOI:
10.1111/mec.13827

28. Single nucleotide polymorphism markers for analysis of historical and contemporary samples of Arctic char (Salvelinus alpinus)

Author:
Hansen, Michael M.,   et al.   ; Jacobsen, Magnus W.; Christensen, Camilla; Madsen, Rikke; Nygaard, Rasmus; Jónsson, Bjarni; Præbel, Kim;     Show all 7 Authors
Source:
Conservation genetics resources 2017 v.9 no.4 pp. 587-589
ISSN:
1877-7252
Subject:
Salvelinus alpinus; fisheries; freshwater; habitats; monitoring; single nucleotide polymorphism; temperature; Arctic region
Abstract:
... Arctic regions are predicted to experience drastic temperature increases in the future, which may impact species negatively by changing their environments and habitats. One such species is the Arctic Char (Salvelinus alpinus), which is an important target for local fisheries and the top predator in many freshwater systems. Here we present 53 SNPs for population genetic inferences in the species. T ...
DOI:
10.1007/s12686-017-0728-y

29. Single nucleotide polymorphism markers for assessing potential maternal population structure in European eel (Anguilla anguilla)

Author:
Hansen, Michael M.,   et al.   ; Jacobsen, Magnus W.; Pujolar, José Martin; Pedersen, Lisette;     Show all 4 Authors
Source:
Conservation genetics resources 2018 v.10 no.4 pp. 907-909
ISSN:
1877-7252
Subject:
Anguilla anguilla; females; genotyping; inheritance (genetics); leptocephalus larvae; mitochondria; mitochondrial DNA; philopatry; population structure; single nucleotide polymorphism; spawning; Sargasso Sea
Abstract:
... The European eel is considered to be panmictic. However, this view has been challenged by results based on maternally inherited mitochondrial DNA that suggest female philopatric behavior. Resolving this issue is of high importance, as it is the prerequisite for efficient conservation efforts. We developed a total of 91 SNPs adequate for re-testing panmixia in European eel (Anguilla anguilla), incl ...
DOI:
10.1007/s12686-017-0917-8

30. Sixty years of anthropogenic pressure: a spatio-temporal genetic analysis of brown trout populations subject to stocking and population declines

Author:
Hansen, Michael M.,   et al.   ; Fraser, Dylan J.; Meier, Kristian; Mensberg, Karen-Lise D.;     Show all 4 Authors
Source:
Molecular ecology 2009 v.18 no.12 pp. 2549-2562
ISSN:
0962-1083
Subject:
Salmo trutta; adverse effects; genetic techniques and protocols; habitats; hatcheries; humans; introgression; microsatellite repeats; population dynamics; population size; rivers; trout; Denmark
Abstract:
... Analyses of historical samples can provide invaluable information on changes to the genetic composition of natural populations resulting from human activities. Here, we analyse 21 microsatellite loci in historical (archived scales from 1927 to 1956) and contemporary samples of brown trout (Salmo trutta) from six neighbouring rivers in Denmark, to compare the genetic structure of wild populations b ...
DOI:
10.1111/j.1365-294X.2009.04198.x
PubMed:
19457206

31. Spatial and temporal genetic differentiation and effective population size of brown trout (Salmo trutta, L.) in small Danish rivers

Author:
Hansen, Michael M.,   et al.   ; Jensen, Lasse F.; Carlsson, Jens; Loeschcke, Volker; Mensberg, Karen-Lise D.;     Show all 5 Authors
Source:
Conservation genetics 2005 v.6 no.4 pp. 615-621
ISSN:
1566-0621
Subject:
Salmo trutta; gene flow; genetic variation; immigration; lakes; microsatellite repeats; models; pollution; population size; rivers; trout; variance; Denmark
Abstract:
... The spatial and temporal genetic structure of brown trout populations from three small tributaries of Lake Hald, Denmark, was studied using analysis of variation at eight microsatellite loci. From two of the populations temporal samples were available, separated by up to 13 years (3.7 generations). Significant genetic differentiation was observed among all samples, however, hierarchical analysis o ...
DOI:
10.1007/s10592-005-9014-8

32. The impact of selection, gene flow and demographic history on heterogeneous genomic divergence: three‐spine sticklebacks in divergent environments

Author:
Hansen, Michael M.,   et al.   ; Ferchaud, Anne‐Laure;     Show all 2 Author
Source:
Molecular ecology 2016 v.25 no.1 pp. 238-259
ISSN:
0962-1083
Subject:
Gasterosteus aculeatus; coasts; fish; freshwater; gene flow; gene frequency; genes; lakes; morphs; parallel evolution; population dynamics; predators; rivers; single nucleotide polymorphism; Baltic Sea; Denmark; North Sea
Abstract:
... Heterogeneous genomic divergence between populations may reflect selection, but should also be seen in conjunction with gene flow and drift, particularly population bottlenecks. Marine and freshwater three‐spine stickleback (Gasterosteus aculeatus) populations often exhibit different lateral armour plate morphs. Moreover, strikingly parallel genomic footprints across different marine–freshwater po ...
DOI:
10.1111/mec.13399