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Pre-prints

Mäkinen H, Sävilammi T, Papakostas S, Leder E, Vollestad A, Primmer CR (2017) Modularity Facilitates Flexible Tuning Of Plastic And Evolutionary Gene Expression Responses During Early Divergence. BioRxiv

Barson NJ, Aykanat T, Hindar K, Baranski M, Bolstad GH, Fiske P, Jacq C, Jensen AJ, Johnston SE, Karlsson S, Kent M, Niemelä E, Nome T, Næsje TF, Orell P, Romakkaniemi A, Sægrov H, Urdal K, Erkinaro J, Lien S, Primmer CR Sex-dependent dominance at a single locus maintains variation in age at maturity in Atlantic salmon. BioRxiv (Now published in Nature (see below))

Aykanat T, Johnston S, Orell P, Kent M, Lien S, Niemela E, Erkinaro J, Primmer CR Low but significant genetic differentiation underlies biologically meaningful phenotypic divergence in a large Atlantic salmon population. BioRxiv (Now published in Molecular Ecology (see below))

Publications

156) Bernatchez L, Wellenreuther N & 13 alphabetically listed co-authors including Primmer CR (2017) Harnessing the Power of Genomics to Secure the Future of Seafood. Trends in Ecology and Evolution 32: 665-680.

155) MacQueen DM, Primmer CR, Houston RD, Nowak RF and the FAASG consortium (2017) Functional Annotation of All Salmonid Genomes (FAASG): an international initiative supporting future salmonid research, conservation and aquaculture. BMC Genomics 18: 484.

154) Uusi-Heikkilä S, T Sävilammi, E Leder, R Arlinghaus, CR Primmer (2017) Rapid, broad-scale gene expression evolution in experimentally harvested fish populations. Molecular Ecology 26: 3954–3967.

153) Pritchard VL, Viitaniemi HM, McCairns RJS, Merilä J, Nikinmaa M, Primmer CR, and Leder E (2017) Rapid, broad-scale gene expression evolution in experimentally harvested fish populations. Animal Genetics 48: 237-241.

152) Kijas J, Elliot N, Kube P, Evans B, Botwright N, King H, Primmer CR, and Verbyla K (2017) Rapid, broad-scale gene expression evolution in experimentally harvested fish populations. Animal Genetics 48: 237-241.

151) Aykanat T, Pritchard VL, Lindqvist M, Primmer CR (2016) From population genomics to conservation and management: a workflow for targeted analysis of markers identified using genome-wide approaches in Atlantic salmon. Journal of Fish Biology 89: 2658-2679.

150) Pritchard VL, Viitaniemi HM, McCairns RJS, Nikinmaa M, Merilä J, Primmer CR, Leder EH (2016) Regulatory architecture of gene expression variation in the threespine stickleback. Genes, Genomes, Genetics 7: 165-178

149) Pritchard VL, Erkinaro J, Kent MP, Niemelä E, Orell P, Lien S, Primmer CR (2016) SNPs to discriminate different classes of hybrid between wild Atlantic salmon and aquaculture escapees Evolutionary Applications 9: 1017-1031.

148) Shafer A and 30 co-authors in alphabetical order including Primmer CR (2016) Genomics in conservation: case studies and bridging the gap between data and application: Reply. Trends in Ecology and Evolution 31:83-84.

147) Mäkinen H, Papakostas S, Vollestad A, Leder E, Primmer CR (2016) Plastic and Evolutionary Gene Expression Responses Are Correlated in European Grayling (Thymallus thymallus) Subpopulations Adapted to Different Thermal Environments Journal of Heredity 107: 82-89.

146) Barson NJ*, Aykanat T*, Hindar K, Baranski M, Bolstad GH, Fiske P, Jacq C, Jensen AJ, Johnston SE, Karlsson S, Kent M, Moen T, Niemelä E, Nome T, Næsje TF, Orell P, Romakkaniemi A, Sægrov H, Urdal K, Erkinaro J, Lien S, Primmer CR Sex-dependent dominance at a single locus maintains variation in age at maturity in salmon. Nature 528: 405-408.

145) Lumme J, Ozerov M, Veselov A, Primmer CR (2015) The formation of landlocked populations of Atlantic salmon. In: Evolutionary Biology of the Atlantic Salmon (Eds: Vladic T, Petersson E) CSC Press.

144) Aykanat T, Johnston S, Orell P, Kent M, Lien S, Niemela E, Erkinaro J, Primmer CR (2015) Low but significant genetic differentiation underlies biologically meaningful phenotypic divergence in a large Atlantic salmon population Molecular Ecology 24: 5158-5174.

143) Mäkinen H, Vasemägi A, McGinnity P, Cross TF, Primmer CR (2015) Population genomic analyses of the early phases of domestication in the Atlantic salmon (Salmo salar) Evolutionary Applications 8: 93-107.

142) Shafer A, Wolf J and 39 co-authors in alphabetical order including Primmer CR (2015) Conservation Genomics: academic exercise or transition with real-world implications? Trends in Ecology and Evolution 30:78-87.

141) Leder EH, McCairns RJS, Leinonen T, Cano JM, Viitaniemi HM, Nikinmaa M, Primmer CR, Merilä J (2015) The evolution and adaptive potential of transcriptional variation in sticklebacks - signatures of selection and widespread heritability Molecular Biology and Evolution 32: 674-689.

140) Uusi-Heikkilä S, Whiteley A, Kuparinen A, Matsumura S, Venturelli PA, Wolter C, Slate J, Primmer CR, Meinelt T, Killen S, Bierbach D, Polverino G, Ludwig A, Arlinghaus R (2015) The evolutionary legacy of size-selective harvest extends from genes to populations Evolutionary Applications 8: 597-620.

139) Mäkinen H, Niva T, Koljonen M-L, Swatdipong A, Primmer CR (2015) Temporal variation in lake-run brown trout (Salmo trutta) mixed-stock fishery catch in a large Fennoscandian lake Boreal Environment Research (in press).

138) Laaksonen T and 25 co-authors including Primmer CR (2015) Sympatric divergence and clinal variation in multiple colouration traits of Ficedula flycatchers. Journal of Evolutionary Biology 28:779-790.

137) Ozerov M Himberg M, Aykanat T, Sendek DS, Hägerstrand H, Verliin A, Krause T, Olsson J, Primmer CR & Vasemägi A (2015) Generation of a neutral FST baseline for testing local adaptation on gill raker number within and between European whitefish ecotypes in the Baltic Sea basin Journal of Evolutionary Biology 28:1170-1183.

136) Papakostas S, Vollestad A, Bruneaux M, Vanoverbeke J, Mei N, Aykanat T, Primmer CR*, Leder E* (2014) Gene pleiotropy constrains gene expression changes in fish adapted to different thermal conditions Nature Communications 5: 4071.

135) Johnston S, Orell P, Pritchard V, Kent M, Lien S, Niemela E, Erkinaro J, Primmer CR (2014) Genome-wide SNP analysis reveals a genetic basis for sea-age variation in a wild population of Atlantic salmon (Salmo salar). Molecular Ecology 23: 3452-3468.

134) Aykanat T, Johnston SE, Cotter D, Cross TF, Poole R, Prodohl PA, Reed T, Rogan G, McGinnity P*, Primmer CR* (2014) Molecular pedigree reconstruction and estimation of evolutionary parameters in a wild Atlantic salmon river system with incomplete sampling: a power analysis. BMC Evolutionary Biology 14:68.

133) Bruneaux M, Nikinmaa M, Laine VN, Lindström K, Primmer CR, Vasemägi A (2014) Differences in the metabolic response to temperature acclimation in nine-spined stickleback (Pungitius pungitius) populations from contrasting thermal environments. Journal of Experimental Zoology 321: 550-565.

132) Zueva KJ, Lumme J, Veselov AE, Kent MP, Lien S, Primmer CR (2014). Footprints of directional selection in wild Atlantic salmon populations: evidence for parasite-driven evolution? PLoS One 9: e91672.

131) Lumme J, Ozerov M, Veselov A, Primmer CR (2014) The formation of landlocked populations of Atlantic salmon. In: Evolutionary Biology of the Atlantic Salmon (Eds: Vladi? T, Petersson E, Ucan-Marin F) CSC Press.

130) Papakostas S, Vasemägi A, Himberg M, Primmer CR (2014) Proteome variance differences within populations of European whitefish (Coregonus lavaretus) originating from contrasting salinity environments. Journal of Proteomics 105: 144-150.

129) Johnston SE, Lindqvist M, Niemelä E, Orell P, Erkinaro J, Kent MP, Lien S, Vähä J-P, Vasemägi A, Primmer CR (2013) Fish scales and SNP chips: SNP genotyping and allele frequency estimation in individual and pooled DNA from historical samples of Atlantic salmon (Salmo salar). BMC Genomics 14:439.

128) Hoban SM and 21 co-authors including Primmer CR (2013) Conservation Genetic Resources for Effective Species Survival (ConGRESS): Bridging the divide between conservation research and practice. Journal for Nature Conservation 21: 433-437.

127) Wennerström L, Laikre L, Ryman N, Utter FM, Ghani NIA, André C, DeFaveri J, Kautsky L, Merilä J, Mikhailova N, Johansson D, Pereyra R, Teacher A, Wenne R, Vasemägi A, Zbavicka M, Johannesson K, Primmer CR (2013) Genetic biodiversity in the Baltic Sea: species-specific patterns challenge management. Biodiversity and Conservation 22: 3045-3065.

126) Primmer CR, Papakostas S, Leder EH, Davis M, Ragan M (2013) Annotated genes and non-annotated genomes: cross-species use of Gene Ontology in ecology and evolution research. Invited review in Molecular Ecology 22: 3216-3241

125) Bourret V, Kent M, Primmer CR, Vasemägi A, Karlsson S, Hindar K, McGinnity P, Verspoor E, Bernatchez L, Lien S (2013) SNP-array reveals genome wide patterns of geographical and potential adaptive divergence across the natural range of Atlantic salmon (Salmo salar) Molecular Ecology 22: 532-551.

124) Bruneaux M, Johnston S, Herczeg G, Merilä J, Primmer CR, Vasemägi A (2013) Molecular evolutionary and population genomic analysis of the nine-spined stickleback using a modified RAD tag approach Molecular Ecology 22: 565-582.

123) Swatdipong A, Vasemägi A Niva T, Koljonen M-L, Primmer CR (2013) Genetic mixed-stock analysis of lake-run brown trout Salmo trutta L. fisheries catches in the Inari basin, northern Finland: implications for conservation and management. Journal of Fish Biology 83: 598-617

122) Nikinmaa M, McCairns RJS, Nikinmaa MW Vuori KA, Kanerva M, Leinonen T, Primmer CR, Merilä J, Leder EH (2013) Transcription and redox enzyme activities: comparison of equilibrium and disequilibrium levels in the three-spined stickleback Proceedings of the Royal Society: B, Biological Sciences 280: 20122974

121) Hoban SM, Hauffe HC, Pérez-Espona S, Arntzen JW, Bertorelle G, Bryja J, Frith K, Gaggiotti OE, Galbusera P, Godoy JA., Hoelzel AR, Nichols RA, Primmer CR, Russo I-R, Segelbacher G, Siegismund HR, Sihvonen M, Vernesi C, Vilà C, Bruford MW (2013) Sample Planning Optimization Tool for conservation and population Genetics (SPOTG): a software for choosing the appropriate number of markers and samples. Methods in Ecology and Evolution 4:299–303

120) Hoban SM, Hauffe HC, Pérez-Espona S, Arntzen JW, Bertorelle G, Bryja J, Frith K, Gaggiotti OE, Galbusera P, Godoy JA., Hoelzel AR, Nichols RA, Primmer CR, Russo I-R, Segelbacher G, Siegismund HR, Sihvonen M, Vernesi C, Vilà C, Bruford MW (2013) Bringing genetic diversity to the forefront of conservation policy and management. Conservation Genetics Resources 5: 593-598

119) Laine VN, Lilley T, Norrdahl K, Primmer CR (2013) Population genetics of Daubenton’s bat (Myotis daubentonii) in the Archipelago Sea, southwest Finland. Annales Zoologici Fennica 50: 303-315

118) Leskinen P, Piironen J & Primmer CR (2013) Population genetic characterization of newly discovered Finnish Arctic charr (Salvelinus alpinus) population: stocked or natural? Journal of Ichthyology 53: 183-190

117) Vasemägi A, Nilsson J, McGinnity P, Cross T, O’Reilly P, Glebe B, Peng B, Berg P, Primmer CR (2012) Screen for Footprints of Selection during Domestication/Captive Breeding of Atlantic Salmon. Comparative and Functional Genomics 2012: Article ID 628204

116) Leskinen P, Laaksonen T, Ruuskanen S, Primmer CR, Leder E (2012). The proteomics of feather development in pied flycatchers (Ficedula hypoleuca) with different plumage coloration. Molecular Ecology 21: 5762-5777

115) Ozerov M, Veselov A, Lumme J, Primmer CR (2012) 'Riverscape' genetics: river characteristics influence the genetic structure and diversity of anadromous and freshwater Atlantic salmon (Salmo salar) populations in northwest Russia. Canadian Journal of Fisheries and Aquatic Sciences 69: 1947-1958

114) Hashemzadeh Segherloo I, Farahmand H, Abdoli A, Bernatchez L, Primmer CR, Swatdipong A, Karami M, Khalili B (2012). Phylogenetic status of brown trout Salmo trutta populations in five rivers from the southern Caspian Sea and two inland lake basins, Iran: a morphogenetic approach. Journal of Fish Biology 81: 1479-1500

113) Hashemzadeh Segherloo I, Bernatchez L, Golzarianpour K, Abdoli A, Primmer CR, Bakhtiary M (2012) Genetic differentiation between two sympatric morphs of the blind Iran cave barb Iranocypris typhlops. Journal of Fish Biology 81: 1747-1753

112) Xia, X. and Primmer CR (2012) Genotypic Frequency In: S Maloy, K Hughes, editors. Encyclopedia of Genetics, 2nd edition: Elsevier.

111) Laine VN, Herczeg G, Shikano T & Primmer CR (2012) Heterozygosity-behaviour correlations in nine-spined stickleback (Pungitius pungitius) populations: contrasting effects at random and functional loci. Molecular Ecology 21: 4872-4884.

110) Papakostas S, Vasemägi A, Vähä J-P, Himberg M, Peil L & Primmer CR (2012) A proteomics approach reveals divergent molecular responses to salinity in populations of European whitefish (Coregonus lavaretus). Molecular Ecology 21: 3516-3530.

109) Laine VN, Primmer CR, Herczeg G, Merilä J & Shikano T (2012) Isolation and characterization of 13 new nine-spined stickleback, Pungitius pungitius, microsatellites located nearby candidate genes for behavioural variation Annales Zoologici Fennici 49: 123-128.

108) Lehtonen PK, Laaksonen T, Artemyev AV, Belskii E, Berg PR, Both C, Buggiotti L, Bureš S, Burgess MD, Bushuev AV, Krams I, Moreno J, Mägi M, Nord A, Potti J, Ravussin P-A, Sirkiä PM, Sætre G-P, Winkel W, Primmer CR. (2012) Candidate genes for colour and vision exhibit signals of selection across the pied flycatcher (Ficedula hypoleuca) breeding range. Heredity 108: 431-440.

107) Rytkönen, KT, Williams, TA, Renshaw, GM, Primmer, CR, Nikinmaa, M (2011) Molecular Evolution of the Metazoan PHD-HIF Oxygen-Sensing System. Molecular Biology and Evolution 28: 1913-1926.

106) Ellis JS, (and 29 co-authors including Primmer CR) (2011) Microsatellite standardization and evaluation of genotyping error in a large multi-partner research programme for conservation of Atlantic salmon (Salmo salar L.) . Genetica 139: 353-367.

105) Janhunen M, Peuhkuri N, Primmer CR, Kolari I, Piironen J (2011) Does Breeding Ornamentation Signal Genetic Quality in Arctic charr, Salvelinus alpinus? Evolutionary Biology 38: 68-78.

104) Primmer C.R (2011) Genetics of local adaptation in salmonid fishes. Heredity 106: 401-403.

103) Junge C, Vollestad LA, Barson NJ, Haugen TO, Otero J, Saetre GP, Leder EH, Primmer CR (2011) Strong gene flow and lack of stable population structure in the face of rapid adaptation to local temperature in a spring-spawning salmonid, the European grayling (Thymallus thymallus) Heredity 106:460-471.

102) Vähä JP, Erkinaro J, Niemela E, Primmer CR, Saloniemi I, Johansen M, Svenning M, Brors S (2011) Temporally stable population-specific differences in run timing of one-sea-winter Atlantic salmon returning to a large river system. Evolutionary Applications 4:39-53.

101) Papakostas S, Vollestad LA, Primmer CR, Leder EH (2010) Proteomic Profiling of Early Life Stages of European Grayling (Thymallus thymallus) Journal of Proteome Research 9: 4790-4800.

100) Swatdipong A, Vasemägi A Niva T, Koljonen M-L, Primmer CR. High level of population genetic structuring in lake-run brown trout, Salmo trutta L., of the Inari basin, northern Finland. Journal of Fish Biology 77: 2048-2071.

99) Tonteri A, Vasemägi A, Lumme J & Primmer CR (2010) Beyond MHC: signals of elevated selection pressure in Atlantic salmon (Salmo salar) immune relevant loci. Molecular Ecology ‘from the cover’ 19: 1273-1282.

98) Ozerov MY, Veselov AJ, Lumme J, Primmer CR. (2010) Genetic structure of freshwater Atlantic salmon (Salmo salar L.) populations from the lakes Onega and Ladoga of northwest Russia and implications for conservation. Conservation Genetics 11: 1711-1724.

97) Leder EH, JM Cano, T Leinonen, RB O’Hara, M Nikinmaa, CR Primmer, and J Merilä. (2010) Concentration of female-biased expression on the X chromosome as an intermediate step in the evolution of sex chromosomes. Molecular Biology and Evolution 27: 1495-1503.

96) Ozerov MY, Lumme J, Päkk P, Rintamäki, P, Zietara MS, Barskaya Y, Lebedeva D, Saadre E, Gross R, Primmer CR & Vasemägi A (2010) Elevated susceptibility of triploid Atlantic salmon (Salmo salar L.) to monogenean parasite Gyrodactylus salaris. Diseases of Aquatic Organisms 91: 129-136.

95) Vasemägi A, Gross R, Palm D, Paaver T and Primmer CR (2010) Discovery and application of insertion-deletion (INDEL) polymorphisms for QTL mapping of early life-history traits in Atlantic salmon. BMC Genomics 11: 156.

94) Junge C, Primmer CR, Vøllestad LA & Leder EH. (2010) Isolation and characterization of 19 new microsatellites for European grayling, Thymallus thymallus (Linnaeus, 1758), and their cross-amplification in four other salmonid species Conservation Genetics Resources.

93) Erkinaro J, Niemelä E, Vähä J-PK, Primmer CR, Brørs S, Hassinen E, Orell P & Länsman M (2010) Distribution and biological characteristics of escaped farmed salmon in a major subarctic wild salmon river: implications for monitoring. Canadian Journal of Fisheries & Aquatic Sciences 67: 130-142.

92) Swatdipong A, Primmer CR & Vasemägi A. (2010) Historical and contemporary genetic bottlenecks in European grayling, Thymallus thymallus. Conservation Genetics 11: 279-292.

91) Holmen J, Vøllestad LA, Jakobsen KS, Primmer CR. (2009) Cross-species amplification of 36 cyprinid microsatellite loci in Phoxinus phoxinus (L.) and Scardinius erythrophthalmus (L.) BMC Research Notes 2: 248.

90) Laikre L, Nilsson T, Primmer CR, Ryman N, Allendorf FW (2009) Genetics is crucial in the interpretation of Favourable Conservation Status Conservation Biology 6: 1378-1381.

89) Lehtonen PK, Laaksonen T, Artemyev AV, Belskii E, Both C, Bureš S, Bushuev AV, Krams I, Moreno J, Mägi M, Nord A, Potti J, Ravussin P-A, Sirkiä PM, Sætre G-P, Primmer CR. Geographic patterns of genetic differentiation and plumage colour variation are different in the pied flycatcher (Ficedula hypoleuca). Molecular Ecology 18: 4463-4476.

88) Leder EH, Merilä J, & Primmer CR. A flexible whole-genome microarray for transcriptomics in threespine sticklebacks. BMC Genomics 10: 426.

87) Kekäläinen J, Vallunen JA, Rätty S, Primmer CR & Taskinen J (2009) Major Histocompatibility Complex overdominance in a wild salmonid population. Proceedings of the Royal Society of London: Series B. 276: 3133-3140.

86) Primmer CR (2009) From conservation genetics to conservation genomics. Annals of the New York Academy of Sciences 1162: 357-368.

85) Lehtonen PK, Primmer CR, Laaksonen T (2009). Different traits affect gain of extrapair paternity and loss of paternity in the pied flycatcher (Ficedula hypoleuca) Animal Behaviour 77: 1103-1110.

84) Tiira K & Primmer CR (2009) Genetic diversity and fitness related traits in endangered salmonids.Population Genetics for Animal Conservation eds. G Bertorelle, MW Bruford, HC Hauffe, A Rizzoli and C Vernesi, pp. 235-262.

83) Swatdipong A, Koskinen MT, Piironen J, Vasemägi A & Primmer CR (2009) Unanticipated population structure of European grayling in its northern distribution: implications for conservation prioritization. Frontiers in Zoology 6:6.

82) Barson NJ, Haugen TO, Vøllestad LA & Primmer CR (2009) Contemporary isolation-by-distance, but not isolation-by-time, among demes of European grayling (Thymallus Thymallus, Linnaeus) with recent common ancestors. Evolution 63: 549-556.

81) Tonteri A, Veselov AJ, Zubchenko AV, Lumme J & Primmer CR (2009) Microsatellites reveal clear genetic boundaries among Atlantic salmon (Salmo salar) populations from the Barents and White Seas, northwest Russia. Canadian Journal of Fisheries and Aquatic Sciences 66: 717-735.

80) Kuusela J, Holopainen R, Meinilä M, Anttila P, Koski P, Zietara MS, Veselov A, Primmer CR & Lumme J (2009) Clonal structure of salmon parasite Gyrodactylus salaris on a co-evolutionary gradient on Fennoscandian salmon (Salmo salar) Annales Zoologici Feinnici 46: 21-33.

79) Lehtonen PK, Tonteri A, Sendek D, Titov S & Primmer CR (2009) Spatio-temporal genetic structuring of brown trout (Salmo trutta L.) populations within in the River Luga, northwest Russia. Conservation Genetics 10: 281-289.

78) Tonteri A, Vasemägi A, Lumme J & Primmer CR (2008) Use of differential expression data for identification of novel immune relevant expressed sequence tag-linked microsatellite markers in Atlantic salmon (Salmo salar L.) Molecular Ecology Resources 6: 1486-1490.

77) Backstrom N, Karaiskou N, Leder EH, Gustafsson L, Primmer CR, Qvarnstrom A & Ellegren H (2008) A gene-based genetic linkage map of the collared flycatcher (Ficedula albicollis) reveals extensive synteny and gene-order conservation during 100 million years of avian evolution. Genetics 179: 1479-1495

76) Rytkönen KT, Ryynänen HJ, Nikinmaa M & Primmer CR (2008) Variable patterns in the molecular evolution of the hypoxia-inducible factor-1 alpha (HIF-1a) gene in teleost fishes and mammals. Gene 420: 1-10.

75) Karaiskou N, Buggiotti L, Leder E & Primmer CR (2008) High degree of transferability of 86 newly developed zebra finch EST-linked microsatellite markers in 8 bird species. Journal of Heredity 6: 688-693.

74) Buggiotti L, Kouvonen P, Corthals GR, Primmer CR and Leder E (2008) Identification of differentially expressed proteins in Ficedula flycatchers. Proteomics 10: 2150-2153 Supporting information

73) Karaiskou N and Primmer CR (2008) PCR-multiplexing for maximising genetic analyses with limited DNA: an example in the collared flycatcher, Ficedula albicollis Annales Zoologici Fennici 45: 478-482.

72) Vähä J-PK, Erkinaro J, Niemelä E and Primmer CR (2008) Retrospective genetic monitoring of Atlantic salmon populations within a river system over two decades –implications for management. Evolutionary Applications 1: 137-154

71) Leder EH, Karaiskou N and Primmer CR (2008) 70 new microsatellites for the pied flycatcher Ficedula hypoleuca and amplification in other passerine birds. Molecular Ecology Resources 8: 874- 880.

70) Ryynänen HJ, Tonteri A, Vasemägi A and Primmer CR A (2007) comparison of bi-allelic markers and microsatellites for the estimation of population and conservation genetic parameters in Atlantic salmon (Salmo salar). Journal of Heredity 98: 692-704

69) Johansson M, Primmer CR & Merilä J. (2007) Does habitat fragmentation reduce fitness and adaptability? A case study of the common frog (Rana temporaria). Molecular Ecology 16: 2693 -2700.

68) Tonteri A, Veselov A, Titov S, Lumme J and Primmer CR (2007) The effect of migratory behavior on genetic diversity and population divergence: a comparison of anadromous and freshwater Atlantic salmon (Salmo salar L.) Journal of Fish Biology 70C: 381-398.

67) Rytkönen KT, Vuori KAM, Primmer CR & Nikinmaa M (2007) Comparison of hypoxia-inducible factor 1 alpha (HIF-1a) in hypoxia-sensitive and hypoxia-tolerant fishes. Comparative Biochemistry and Physiology Part D: Genomics & Proteomics 2: 177-186.

66) Lesbarrères D, Schmeller D, Primmer CR, Merilä J (2007) Genetic variability predicts common frog (Rana temporaria) size at metamorphosis in the wild. Heredity 99: 41-46.

65) Vähä J-PK, Erkinaro J, Niemelä E, and Primmer CR (2007) Life-history and habitat features influence the within-river genetic structure of Atlantic salmon. Molecular Ecology 16: 2638-2654.

64) Tiira K, Piironen J and Primmer CR (2006) Evidence for reduced genetic variation in severely deformed juvenile salmonids. Canadian Journal of Fisheries and Aquatic Sciences 63: 2700-2707.

63) Buggiotti L, Hellström M and Primmer CR (2006) Characterization of the first growth hormone gene sequence for a passerine bird - the pied flycatcher (Ficedula hypoleuca). DNA Sequence 17:401-406.

62) Lesbarrères D, Primmer CR, Lodé T and Merilä J (2006) The effects of 20 years of highway presence on the genetic structure of Rana dalmatina populations. Ecoscience13: 531-538.

61) Buggiotti L and Primmer CR (2006) Molecular evolution of the avian growth hormone gene and comparison with its mammalian counterpart. Journal of Evolutionary Biology 19: 844-854.

60) Ryynänen HJ and Primmer CR (2006) Single nucleotide polymorphism (SNP) discovery in duplicated genomes: intron-primed exon-crossing (IPEC) as a strategy for avoiding amplification of duplicated loci in Atlantic salmon (Salmo salar) and other salmonid fishes. BMC Genomics 7: 192

59) Johansson M, Primmer CR and Merilä J. (2006) History vs. current demography: Explaining the genetic population structure of the common frog (Rana temporaria). Molecular Ecology 15: 975-983.

58) Primmer CR, Veselov AJ, Zubchenko A, Poututkin A, Bakhmet I & Koskinen MT (2006) Isolation by distance within a river system: genetic population structuring of Atlantic salmon, Salmo salar, in tributaries of the Varzuga River in northwest Russia. Molecular Ecology 15: 653-666.

57) Vähä J-PK and Primmer CR (2006) Detecting hybridization between individuals of closely related populations - a simulation study to assess the efficiency of model-based Bayesian methods to detect hybrid individuals. Molecular Ecology 15: 63-72.

56) Ryynänen H and Primmer CR. (2006) Varying signals of the effects of natural selection during teleost growth hormone gene evolution. Genome 49: 42-53.

55) Tiira K, Laurila A, Enberg K, Piironen J, Aikio S, Ranta E and Primmer CR (2006) Do dominants have higher heterozygosity? Social status and genetic variation in brown trout, Salmo trutta. Behavioral Ecology and Sociobiology 59: 657-665.

54) Vasemägi A and Primmer CR (2005) Challenges for identifying functionally important genetic variation: the promise of combining complementary research strategies. Invited Review in Molecular Ecology 14: 3623-3642.
Full document (pdf)

53) Johansson M. Primmer CR, Sahlsten J and Merilä J (2005) The influence of landscape structure on occurrence, abundance and genetic diversity of the common frog, Rana temporaria. Global Change Biology 11: 1664-1679.

52) Holmen J, Vøllestad LA, Jakobsen KS and Primmer CR (2005) Cross-species amplification of zebrafish and central stoneroller microsatellite loci in six other cyprinids. Journal of Fish Biology 66: 851-859.

51) Vasemägi A, Nilsson J and Primmer CR (2005) Expressed sequence tag (EST) linked microsatellites as a source of gene associated polymorphisms for detecting signatures of divergent selection in Atlantic salmon (Salmo salar L.). Molecular Biology and Evolution 22: 1067-1076
Full document (pdf)

50) Primmer CR, Painter JN, Koskinen MT, Palo JU and Merilä J (2005) Factors affecting avian cross-species microsatellite amplification. Journal of Avian Biology 36: 348-360.
Full document (pdf)

49) Tonteri A, Titov S, Veselov A, Zubchenko A, Koskinen MT, Lesbarrères D, Kaluzhin S, Bakhmet I, Lumme J & Primmer CR (2005) Phylogeography of anadromous and non-anadromous Atlantic salmon (Salmo salar) from northern Europe Annales Zoologici Fennici 42: 1-22.
Full document (pdf)

48) Vasemägi A, Nilsson J and Primmer CR (2005) Seventy five EST-linked Atlantic salmon (Salmo salar L.) microsatellite markers and their cross-species amplification in salmonids. Molecular Ecology Notes 5: 282-288.
Supplementary appendix with primer sequences and electropherograms
Supplementary appendix with cross-species amplification information

47) Ryynänen HJ and Primmer CR (2004) Distribution of genetic variation in the growth hormone 1 gene in Atlantic salmon (Salmo salar) populations from Europe and North America. Molecular Ecology 13: 3857-3869.
Full document (pdf)

46) Ryynänen HJ and Primmer CR (2004) PCR-based molecular markers for detecting genetic variation in the Atlantic salmon (Salmo salar) growth hormone 1-gene. Molecular Ecology Notes 4: 664-667.

45)Lesbarreres D, Primmer CR, Laurila A & Merilä J (2005) Environmental and population dependency of heterozygosity-fitness correlations in Rana temporaria populations. Molecular Ecology 14: 311-323.

44) Koskinen MT, Hirvonen H, Landry P-A and Primmer CR (2004) The benefits of increasing the number of microsatellites utilized in genetic population studies: an empirical perspective from analyses of grayling (Thymallus thymallus) evolutionary relationships. Hereditas 141: 61-67.
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43) Palo JU, Lesbarreres D, Schmeller DS, Primmer CR & Merilä J (2004) Microsatellite marker data suggest sex-biased dispersal in the common frog Rana temporaria. Molecular Ecology 13: 2865-2869. Full document (pdf)

42) Palo JU, Schmeller DS, Laurila A, Primmer CR, Kumzin SL & Merilä J (2004) High degree of population subdivision in a wide-spread amphibian. Molecular Ecology 13: 2631-2644.
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41) Asplund T, Veselov A, Primmer CR, Bakhmet I, Potutkin A, Titov S, Zubchenko A, Studenov I, Kaluzchin S and Lumme J (2004) Origin of maternal lineages of anadromous Atlantic salmon (Salmo salarL.) in the Barents Sea and White Sea rivers. Annales Zoologici Fennici 41: 465-475.
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40) Tiira K, Laurila A, Peuhkuri N, Piironen J, Ranta E and Primmer CR. (2003) Aggressiveness is associated with genetic diversity in landlocked salmon, Salmo salar. Molecular Ecology 12: 2399-2407.
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39) Brommer JE, Karell P, Pihlaja T, Painter JN, Primmer CR and Pietiäinen H. (2003) Ural owl sex allocation and parental investment in poor food conditions. Oikos 137: 140-147.

38) Primmer CR, Landry P-A, Ranta E, Merilä J, Piironen J, Tiira K, Peuhkuri N, Pakkasmaa S and Eskelinen P.(2003) Prediction of offspring fitness based on parental genetic diversity in endangered salmonid populations. Journal of Fish Biology 63: 909-927.
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37) Froufe E, Knizhin I, Koskinen MT, Primmer CR and Weiss S. (2003) Phenotypic and genetic variation of Amur grayling Thymallus grubii Dybowski 1869, reflect both allopatric and sympatric origins, secondary contact, and reproductive isolation of at least three distinct lineages. Molecular Ecology 12: 2345-2355.
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36) Palo JU, O’Hara RB, Laugen AT, Laurila A, Primmer CR & Merilä J. (2003) Latitudinal divergence of common frog (Rana temporaria) life history traits by natural selection: evidence from a comparison of molecular and quantitative genetic data. Molecular Ecology 12: 1963-1978.

35) Møller A-P, Brohede J, Cuervo JJ, de Lope F, Primmer CR and Ellegren H. (2003) Extrapair paternity in relation to sexual ornamentation, arrival date and condition in a migratory bird. Animal 14: 707-712.

34) Sætre G-P, Borge T, Lindroos K, Haavie J, Sheldon BC, Primmer CR, and Syvänen A-C. (2003) Sex chromosome evolution and speciation in Ficedula flycatchers. Proceedings of the Royal Society of London. Series B. 270: 53-59.
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33) Koskinen MT, Knizhin I, Primmer CR, Schlötterer C and Weiss S. (2002) Mitochondrial and nuclear DNA phylogeography of Thymallus spp. (grayling) provides evidence of ice-age mediated environmental perturbations in the world's oldest body of fresh water, Lake Baikal. Molecular Ecology 11: 2599-2611.
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32) Koskinen MT, Haugen TO and Primmer CR. (2002) Contemporary fisherian life-history evolution in small salmonid populations. Nature 419: 826-830.
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Corrigendum to Table 1 & Fig 2 (pdf)
Supplementary information (pdf)

31) Landry P-A, Koskinen MT and Primmer CR. (2002) Deriving evolutionary relationships among populations using microsatellites and (delta-Mu)2: all loci are equal, but some are more equal than others. Genetics 161: 1339-1347.
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30) Brohede J, Primmer CR, Møller A-P and Ellegren H. (2002) Heterogeneity in the rate and pattern of germline mutation at individual microsatellite loci. Nucleic Acids Research 30: 1997- 2003.
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29) Koskinen MT, Ranta E, Piironen J, Veselov A, Nilsson J and Primmer CR. (2002) Microsatellite data detect low levels of intrapopulation genetic diversity and resolve phylogeographic patterns in European grayling, Thymallus thymallus, Salmonidae.Heredity 88: 391-401.
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28) Primmer CR, Borge T, Haavie J, and Sætre G-P. (2002) Single-nucleotide polymorphism (SNP) characterization in species with limited available sequence information: high nucleotide diversity revealed in the avian genome. Molecular Ecology 11: 603-612.
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27) Koskinen MT, Piironen J, Sundell P and Primmer CR. (2002) Spatiotemporal evolutionary relationships and genetic assessment of stocking effects in grayling (Thymallus thymallus, Salmonidae) Ecology Letters 5: 193-205.
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26) Primmer CR and Merilä J. (2002) A low rate of cross-species microsatellite amplification success in ranid frogs. Conservation Genetics 3: 445-449.
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25) Koskinen MT, Piironen J and Primmer CR (2001) Deep inter-population divergence in European grayling (Thymallus thymallus, Salmonidae) at a microgeographic scale: implications for conservation. Conservation Genetics 2: 133-143.

24) Koskinen MT and Primmer CR, (2001) High throughput analysis of 17 microsatellite loci in grayling (Thymallus spp. Salmonidae). Conservation Genetics 2: 173-177.

23) Sætre G-P, Borge T, Lindell J, Moum T, Haavie J, Primmer CR, Sheldon B, Johnsen A and Ellegren H. (2001) Speciation, introgressive hybridization and non-linear rate of molecular evolution in flycatchers. Molecular Ecology 10: 737-749.
Abstract
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22) Nilsson J, Gross R, Dove O, Jansson H, Kohlmann K, Löytynoja A, Nielsen EE, Paaver T, Penttilä H, Primmer CR, Vasemägi A, Veselov A, Öst T and Lumme J. (2001) Matrilinear phylogeography of Atlantic salmon (Salmo salar L.) in Europe and postglacial colonization of the Baltic Sea area. Molecular Ecology 10: 89-102.

21) Primmer CR, Koskinen MT and Piironen J. (2000) The one that did not get away: individual assignment using microsatellite data detects a case of fishing competition fraud. Proceedings of the Royal Society of London. Series B. 267: 1699-1704.
Abstract
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Report on article in Current Biology (pdf)

20) Koskinen MT, Ranta E, Piironen J, Veselov A, Titov S, Haugen TO, Nilsson J, Carlstein M and Primmer CR. (2000) Genetic lineages and postglacial colonization of the grayling (Thymallus thymallus, Salmonidae) in Europe, as revealed by mitochondrial DNA analyses. Molecular Ecology 9: 1609-1624.
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19) Koskinen MT and Primmer CR. (1999) Cross-species amplification of salmonid microsatellites which reveal polymorphism in European and Arctic grayling, Salmonidae: Thymallus spp. Hereditas 131: 171-176.

18) Primmer CR, Aho T, Piironen J and Ranta E. (1999) Examination of microsatellite variability in Nordic land-locked arctic charr, Salvelinus alpinus populations: implications for conservation. Hereditas 130: 277-289.
Abstract

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17) Saino N, Primmer CR, Ellegren H and Møller AP. (1999) Breeding synchrony and paternity in the barn swallow, Hirundo rustica. Behavioral Ecology and Sociobiology 45: 211-218.

16) McPartlan HC, Matthews ME, Primmer CR, McCauley L, Thompson C, Robinson NA. (1999) A dog microsatellite at the VIAS-D21 locus with demonstrated linkage to the marker CXX20. Animal Genetics 30:75

15) Primmer CR and Ellegren H. (1998) Patterns of molecular evolution in avian microsatellites. Molecular Biology and Evolution 15: 997-1008.
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14) Primmer CR, Saino N, Møller AP and Ellegren H. (1998) Unravelling the processes of microsatellite evolution through analysis of germline mutations in barn swallows Hirundo rustica. Molecular Biology and Evolution 15: 1047-1054.
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13) Johnsen A, Lifjeld JT, Rohde PA, Primmer CR and Ellegren H. (1998) Sexual conflict over fertilizations: female bluethroats escape male paternity guards. Behavioral Ecology and Sociobiology 43: 401-408.

12) Ellegren H, Lindgren G, Primmer CR and Møller, AP. (1997) Fitness loss and germline mutations in barn swallows breeding in Chernobyl. Nature 389: 593-596.

11) Primmer CR, Raudsepp T, Chowdhary BP, Møller AP and Ellegren H. (1997) Low frequency of microsatellites in the avian genome. Genome Research 7: 471-482.
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10) Saino N, Primmer CR, Møller AP and Ellegren H. (1997) An experimental study of paternity and tail ornamentation in the barn swallow, Hirundo rustica. Evolution 51: 562-570.

9) Primmer CR, Saino N, Møller AP and Ellegren H. (1996) Directional evolution in germline microsatellite mutations. Nature Genetics 13: 391-393.

8) Primmer CR, Møller AP and Ellegren H. (1996) A wide-range survey of cross-species microsatellite amplification in birds. Molecular Ecology 5: 365-378. See also erratum to FhU primer sequences (Appendix 1) published in Mol. Ecol. 6: 101.
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7) Primmer CR, Møller AP and Ellegren H. (1996) New microsatellites from the pied flycatcher Ficedula hypoleuca and the swallow Hirundo rustica genomes. Hereditas 124:281- 283.
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6) Ellegren H, Primmer CR and Sheldon BC. (1995) Microsatellite 'evolution': directionality or bias? Nature Genetics 11:360-362.

5) Ellegren H, Lifjeld JT, Slagsvold T and Primmer CR. (1995) Handicapped males and extrapair paternity in pied flycatchers: an experiment using microsatellite markers. Molecular Ecology 4:739 -744.

4) Primmer CR, Møller AP and Ellegren H. (1995) Resolving genetic relationships with microsatellite markers: a parentage testing system for the swallow Hirundo rustica. Molecular Ecology 4:493-498.

3) Primmer CR, Robinson N and Matthews ME. (1994) Canine dinucleotide repeat polymorphism at the VIAS-D23 locus. Animal Genetics 25:197.

2) Primmer CR and Matthews ME. (1993) Canine tetranucleotide repeat polymorphism at the VIAS -D10 locus. Animal Genetics 24:332.

1) Primmer CR and Matthews ME. (1993) Ovine dinucleotide repeat polymorphism at the VIAS-S5 locus. Animal Genetics 24:146.

Laboratory of Genetics, Department of Biology, FI-20014 UNIVERSITY OF TURKU, FINLAND