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  • 1.
    Andersson, Anastasia
    et al.
    Stockholm University, Faculty of Science, Department of Zoology.
    Jansson, Eeva
    Stockholm University, Faculty of Science, Department of Zoology. Institute of Marine Research, Norway.
    Wennerström, Lovisa
    Stockholm University, Faculty of Science, Department of Zoology.
    Chiriboga, Fidel
    Stockholm University, Faculty of Science, Department of Zoology.
    Arnyasi, Mariann
    Kent, Matthew P.
    Ryman, Nils
    Stockholm University, Faculty of Science, Department of Zoology.
    Laikre, Linda
    Stockholm University, Faculty of Science, Department of Zoology.
    Complex genetic diversity patterns of cryptic, sympatric brown trout (Salmo trutta) populations in tiny mountain lakes2017In: Conservation Genetics, ISSN 1566-0621, E-ISSN 1572-9737, Vol. 18, no 5, p. 1213-1227Article in journal (Refereed)
    Abstract [en]

    Intraspecific genetic variation can have similar effects as species diversity on ecosystem function; understanding such variation is important, particularly for ecological key species. The brown trout plays central roles in many northern freshwater ecosystems, and several cases of sympatric brown trout populations have been detected in freshwater lakes based on apparent morphological differences. In some rare cases, sympatric, genetically distinct populations lacking visible phenotypic differences have been detected based on genetic data alone. Detecting such cryptic sympatric populations without prior grouping of individuals based on phenotypic characteristics is more difficult statistically, though. The aim of the present study is to delineate the spatial connectivity of two cryptic, sympatric genetic clusters of brown trout discovered in two interconnected, tiny subarctic Swedish lakes. The structures were detected using allozyme markers, and have been monitored over time. Here, we confirm their existence for almost three decades and report that these cryptic, sympatric populations exhibit very different connectivity patterns to brown trout of nearby lakes. One of the clusters is relatively isolated while the other one shows high genetic similarity to downstream populations. There are indications of different spawning sites as reflected in genetic structuring among parr from different creeks. We used > 3000 SNPs on a subsample and find that the SNPs largely confirm the allozyme pattern but give considerably lower F (ST) values, and potentially indicate further structuring within populations. This type of complex genetic substructuring over microgeographical scales might be more common than anticipated and needs to be considered in conservation management.

  • 2.
    Andersson, Anastasia
    et al.
    Stockholm University, Faculty of Science, Department of Zoology.
    Johansson, Frank
    Sundbom, Marcus
    Stockholm University, Faculty of Science, Department of Environmental Science and Analytical Chemistry.
    Ryman, Nils
    Stockholm University, Faculty of Science, Department of Zoology.
    Laikre, Linda
    Stockholm University, Faculty of Science, Department of Zoology.
    Lack of trophic polymorphism despite substantial genetic differentiation in sympatric brown trout (Salmo trutta) populations2017In: Ecology of Freshwater Fish, ISSN 0906-6691, E-ISSN 1600-0633, Vol. 26, no 4, p. 643-652Article in journal (Refereed)
    Abstract [en]

    Sympatric populations occur in many freshwater fish species; such populations are typically detected through morphological distinctions that are often coupled to food niche and genetic separations. In salmonids, trophic and genetically separate sympatric populations have been reported in landlocked Arctic char, whitefish and brown trout. In Arctic char and brown trout rare cases of sympatric, genetically distinct populations have been detected based on genetic data alone, with no apparent morphological differences, that is cryptic structuring. It remains unknown whether such cryptic, sympatric structuring can be coupled to food niche separation. Here, we perform an extensive screening for trophic divergence of two genetically divergent, seemingly cryptic, sympatric brown trout populations documented to remain in stable sympatry over several decades in two interconnected, tiny mountain lakes in a nature reserve in central Sweden. We investigate body shape, body length, gill raker metrics, breeding status and diet (stomach content analysis and stable isotopes) in these populations. We find small significant differences for body shape, body size and breeding status, and no evidence of food niche separation between these two populations. In contrast, fish in the two lakes differed in body shape, diet, and nitrogen and carbon isotope signatures despite no genetic difference between lakes. These genetically divergent populations apparently coexist using the same food resources and showing the same adaptive plasticity to the local food niches of the two separate lakes. Such observations have not been reported previously but may be more common than recognised as genetic screenings are necessary to detect the structures.

  • 3.
    Andersson, Anastasia
    et al.
    Stockholm University, Faculty of Science, Department of Zoology.
    Laikre, Linda
    Stockholm University, Faculty of Science, Department of Zoology.
    Bergvall, Ulrika A.
    Stockholm University, Faculty of Science, Department of Zoology. Swedish University of Agricultural Sciences, Sweden.
    Two shades of boldness: novel object and anti-predator behavior reflect different personality dimensions in domestic rabbits2014In: Journal of ethology, ISSN 0289-0771, E-ISSN 1439-5444, Vol. 32, no 3, p. 123-136Article in journal (Refereed)
    Abstract [en]

    It is increasingly common to quantify and describe behavioral variation in domestic and wild animals in terms of personality. Correlating behavioral traits are referred to as personality dimensions or factors and different dimensions have been reported in different species. Boldness is a well-described personality dimension in several species, although some issues remain unclear. Previous models of boldness include both novelty and risk taking, but recent studies indicate that these types of behaviors may reflect separate personality dimensions. In this study, we developed a behavioral test battery for domestic rabbits, and recorded behaviors of 61 individuals in four different situations (novel object, novel arena, social, and predator interactions). We used domestic rabbits as a model because behavioral variation in rabbits has rarely been quantified in terms of personality dimensions, although rabbit behavior is described. We also wanted to investigate behavioral variation in a Swedish rabbit breed of conservation concern - the Gotland rabbit. Factor analysis of the behavioral test measures suggested three personality dimensions: exploration, boldness, and anxiety. Novel object scores clustered in the exploration and boldness factors, whereas scores associated with predator interactions were explained by anxiety, indicating that novel object and anti-predator behavior reflect different personality dimensions in rabbits.

  • 4. André, Carl
    et al.
    Larsson, Lena C
    Stockholm University, Faculty of Science, Department of Zoology.
    Laikre, Linda
    Stockholm University, Faculty of Science, Department of Zoology.
    Bekkevold, D
    Brigham, J
    Carvalho, GR
    Dahlgren, TG
    Hutchinson, WF
    Mariani, S
    Mudde, K
    Ruzzante, DE
    Ryman, Nils
    Stockholm University, Faculty of Science, Department of Zoology.
    Detecting population structure in a high gene-flow species, Atlantic herring (Clupea harengus): direct, simultaneous evaluation of neutral vs putatively selected loci2011In: Heredity, ISSN 0018-067X, E-ISSN 1365-2540, Vol. 106, no 2, p. 270-280Article in journal (Refereed)
    Abstract [en]

    In many marine fish species, genetic population structure is typically weak because populations are large, evolutionarily young and have a high potential for gene flow. We tested whether genetic markers influenced by natural selection are more efficient than the presumed neutral genetic markers to detect population structure in Atlantic herring (Clupea harengus), a migratory pelagic species with large effective population sizes. We compared the spatial and temporal patterns of divergence and statistical power of three traditional genetic marker types, microsatellites, allozymes and mitochondrial DNA, with one microsatellite locus, Cpa112, previously shown to be influenced by divergent selection associated with salinity, and one locus located in the major histocompatibility complex class IIA (MHC-IIA) gene, using the same individuals across analyses. Samples were collected in 2002 and 2003 at two locations in the North Sea, one location in the Skagerrak and one location in the low-saline Baltic Sea. Levels of divergence for putatively neutral markers were generally low, with the exception of single outlier locus/sample combinations; microsatellites were the most statistically powerful markers under neutral expectations. We found no evidence of selection acting on the MHC locus. Cpa112, however, was highly divergent in the Baltic samples. Simulations addressing the statistical power for detecting population divergence showed that when using Cpa112 alone, compared with using eight presumed neutral microsatellite loci, sample sizes could be reduced by up to a tenth while still retaining high statistical power. Our results show that the loci influenced by selection can serve as powerful markers for detecting population structure in high gene-flow marine fish species.

  • 5. Anrup, Roland
    et al.
    Fareld, Victoria
    Stockholm University, Faculty of Humanities, Department of Literature and History of Ideas, History of Ideas.
    Fornäs, Johan
    Frisk, Syliva
    Fur, Gunlög
    Ganetz, Hillevi
    Stockholm University, Faculty of Humanities, Department of Ethnology, History of Religions and Gender Studies, Gender Studies.
    Gardell, Mattias
    Hedman Hvitfeldt, Maria
    Höghede, Erika
    Iordanoglou, Dimitrios
    Jalmert, Lars
    Stockholm University, Faculty of Social Sciences, Department of Education.
    Johansen, Maria
    Jonsson, Stefan
    Josephson, Peter
    Karlsohn, Thomas
    Laikre, Linda
    Stockholm University, Faculty of Science, Department of Zoology.
    Larsson, Åsa Bharathi
    Lorenzoni, Patricia
    Liedman, Sven-Eric
    Madison, Guy
    Manga, Edda
    Munthe, Christian
    Nilsson, Ulrika
    Nylin, Sören
    Stockholm University, Faculty of Science, Department of Zoology.
    Olsson, Erik J.
    Peralta, Julia
    Persson, Mats
    Priebe, Gunilla
    Rider, Sharon
    Rooke, Tetz
    Rådström, Niklas
    Söderblom, Staffan
    Sörensen, Jens
    Tydén, Mattias
    Stockholm University, Faculty of Humanities, Department of History.
    Zetterholm, Magnus
    Öberg, Johan
    Centrala universitetsvärden hotas av bolagiseringsidén2013In: Dagens nyheter, ISSN 1101-2447Article in journal (Other (popular science, discussion, etc.))
    Abstract [sv]

    Högskolestiftelser. Förslaget att driva svenska universitet i stiftelseform ­öppnar för bolagisering. Men det är ingen riktig utredning, utan en politisk pamflett utan ­eftertanke. Privatisering av universitet hotar både oberoendet, forskningskvaliteten och samhällsnyttan, skriver 36 forskare vid svenska högskolor och universitet.

  • 6. Barrio, Alvaro Martinez
    et al.
    Lamichhaney, Sangeet
    Fan, Guangyi
    Rafati, Nima
    Pettersson, Mats
    Zhang, He
    Dainat, Jacques
    Ekman, Diana
    Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics. Stockholm University, Science for Life Laboratory (SciLifeLab).
    Hoppner, Marc
    Jern, Patric
    Martin, Marcel
    Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics. Stockholm University, Science for Life Laboratory (SciLifeLab).
    Nystedt, Björn
    Liu, Xin
    Chen, Wenbin
    Liang, Xinming
    Shi, Chengcheng
    Fu, Yuanyuan
    Ma, Kailong
    Zhan, Xiao
    Feng, Chungang
    Gustafson, Ulla
    Rubin, Carl-Johan
    Almen, Markus Sallman
    Blass, Martina
    Casini, Michele
    Folkvord, Arild
    Laikre, Linda
    Stockholm University, Faculty of Science, Department of Zoology.
    Ryman, Nils
    Stockholm University, Faculty of Science, Department of Zoology.
    Lee, Simon Ming-Yuen
    Xu, Xun
    Andersson, Leif
    The genetic basis for ecological adaptation of the Atlantic herring revealed by genome sequencing2016In: eLIFE, E-ISSN 2050-084X, Vol. 5, article id e12081Article in journal (Refereed)
    Abstract [en]

    Ecological adaptation is of major relevance to speciation and sustainable population management, but the underlying genetic factors are typically hard to study in natural populations due to genetic differentiation caused by natural selection being confounded with genetic drift in subdivided populations. Here, we use whole genome population sequencing of Atlantic and Baltic herring to reveal the underlying genetic architecture at an unprecedented detailed resolution for both adaptation to a new niche environment and timing of reproduction. We identify almost 500 independent loci associated with a recent niche expansion from marine (Atlantic Ocean) to brackish waters (Baltic Sea), and more than 100 independent loci showing genetic differentiation between spring- and autumn-spawning populations irrespective of geographic origin. Our results show that both coding and non-coding changes contribute to adaptation. Haplotype blocks, often spanning multiple genes and maintained by selection, are associated with genetic differentiation.

  • 7.
    Charlier, Johan
    et al.
    Stockholm University, Faculty of Science, Department of Zoology.
    Laikre, Linda
    Stockholm University, Faculty of Science, Department of Zoology.
    Ryman, Nils
    Stockholm University, Faculty of Science, Department of Zoology.
    Genetic monitoring reveals temporal stability over 30 years in a small, lake-resident brown trout population2012In: Heredity, ISSN 0018-067X, E-ISSN 1365-2540, Vol. 109, no 4, p. 246-253Article in journal (Refereed)
    Abstract [en]

    Knowledge of the degree of temporal stability of population genetic structure and composition is important for understanding microevolutionary processes and addressing issues of human impact of natural populations. We know little about how representative single samples in time are to reflect population genetic constitution, and we explore the temporal genetic variability patterns over a 30-year period of annual sampling of a lake-resident brown trout (Salmo trutta) population, covering 37 consecutive cohorts and five generations. Levels of variation remain largely stable over this period, with no indication of substructuring within the lake. We detect genetic drift, however, and the genetically effective population size (Ne) was assessed from allele-frequency shifts between consecutive cohorts using an unbiased estimator that accounts for the effect of overlapping generation. The overall mean Ne is estimated as 74. We find indications that Ne varies over time, but there is no obvious temporal trend. We also estimated Ne using a one-sample approach based on linkage disequilibrium (LD) that does not account for the effect of overlapping generations. Combining one-sample estimates for all years gives an Ne estimate of 76. This similarity between estimates may be coincidental or reflecting a general robustness of the LD approach to violations of the discrete generations assumption. In contrast to the observed genetic stability, body size and catch per effort have increased over the study period. Estimates of annual effective number of breeders (Nb) correlated with catch per effort, suggesting that genetic monitoring can be used for detecting fluctuations in abundance.

  • 8.
    Charlier, Johan
    et al.
    Stockholm University, Faculty of Science, Department of Zoology.
    Laikre, Linda
    Stockholm University, Faculty of Science, Department of Zoology.
    Ryman, Nils
    Stockholm University, Faculty of Science, Department of Zoology.
    Genetic structure and evidence of a local bottleneck in moose in Sweden2008In: Journal of Wildlife Management, ISSN 0022-541X, E-ISSN 1937-2817, Vol. 72, no 2, p. 411-415Article in journal (Refereed)
    Abstract [en]

    The moose (Alces alces) is the most intensely managed game species in Sweden. Despite the biological and socioeconomical importance of moose, little is known of its population genetic structure. We analyzed 132 individuals from 4 geographically separate regions in Sweden for genetic variability at 6 microsatellite loci. We found evidence of strong substructuring and restricted levels of gene flow in this potentially mobile mammal. FST values were around 10%, and assignment tests indicated 3 genetically distinct populations over the study area. Spatial autocorrelation analysis provided a genetic patch size of approximately 420 km, implying that moose less than this distance apart are genetically more similar than 2 random individuals. Allele and genotype frequency distributions suggested a recent bottleneck in southern Sweden. Results indicate that moose may be more genetically divergent than currently anticipated, and therefore, the strong hunting pressure that is maintained over all of Sweden may have considerable local effects on genetic diversity. Sustainable moose hunting requires identification of spatial genetic structure to ensure that separate, genetically distinct subpopulations are not overharvested.

  • 9.
    Charlier, Johan
    et al.
    Stockholm University, Faculty of Science, Department of Zoology, Population Genetics.
    Palmé, Anna
    Stockholm University, Faculty of Science, Department of Zoology, Population Genetics.
    Laikre, Linda
    Stockholm University, Faculty of Science, Department of Zoology, Population Genetics.
    Andersson, Jens
    Ryman, Nils
    Stockholm University, Faculty of Science, Department of Zoology, Population Genetics.
    Census (NC) and genetically effective (Ne) population size in a lake-resident population of brown trout Salmo trutta2011In: Journal of Fish Biology, ISSN 0022-1112, E-ISSN 1095-8649, Vol. 79, no 7, p. 2074-2082Article in journal (Refereed)
    Abstract [en]

    Census (NC) and effective population size (Ne) were estimated for a lake-resident population of brown trout Salmo trutta as 576 and 63, respectively. The point estimate of the ratio of effective to census population size (Ne:NC) for this population is 0·11 with a range of 0·06–0·26, suggesting that Ne:NC ratio for lake-resident populations agree more with estimates for fishes with anadromous life histories than the small ratios observed in many marine fishes

  • 10.
    Guban, Peter
    et al.
    Stockholm University, Faculty of Science, Department of Zoology.
    Wennerström, Lovisa
    Stockholm University, Faculty of Science, Department of Zoology.
    Elfvving, Tina
    Stockholm University, Faculty of Science, Stockholm University Baltic Sea Centre.
    Sundelin, Brita
    Stockholm University, Faculty of Science, Department of Environmental Science and Analytical Chemistry.
    Laikre, Linda
    Stockholm University, Faculty of Science, Department of Zoology.
    Genetic diversity in Monoporeia affinis at polluted and reference sites of the Baltic Bothnian Bay2015In: Marine Pollution Bulletin, ISSN 0025-326X, E-ISSN 1879-3363, Vol. 93, no 1-2, p. 245-249Article in journal (Refereed)
    Abstract [en]

    The amphipod Monoporeia affinis plays an important role in the Baltic Sea ecosystem as prey and as detritivore. The species is monitored for contaminant effects, but almost nothing is known about its genetics in this region. A pilot screening for genetic variation at the mitochondrial COI gene was performed in 113 individuals collected at six sites in the northern Baltic. Three coastal sites were polluted by pulp mill effluents, PAHs, and trace metals, and two coastal reference sites were without obvious connection to pollution sources. An off-coastal reference site was also included. Contaminated sites showed lower levels of genetic diversity than the coastal reference ones although the difference was not statistically significant. Divergence patterns measured as Phi(ST) showed no significant differentiation within reference and polluted groups, but there was significant genetic divergence between them. The off-coastal sample differed significantly from all coastal sites and also showed lower genetic variation.

  • 11.
    Hössjer, Ola
    et al.
    Stockholm University, Faculty of Science, Department of Mathematics.
    Laikre, Linda
    Stockholm University, Faculty of Science, Department of Zoology.
    Ryman, Nils
    Stockholm University, Faculty of Science, Department of Zoology.
    Effective sizes and time to migration-drift equilibrium in geographically subdivided populations2016In: Theoretical Population Biology, ISSN 0040-5809, E-ISSN 1096-0325, Vol. 112, p. 139-156Article in journal (Refereed)
    Abstract [en]

    Many versions of the effective population size (N-e) exist, and they are important in population genetics in order to quantify rates of change of various characteristics, such as inbreeding, heterozygosity, or allele frequencies. Traditionally, N-e was defined for single, isolated populations, but we have recently presented a mathematical framework for subdivided populations. In this paper we focus on diploid populations with geographic subdivision, and present new theoretical results. We compare the haploid and diploid versions of the inbreeding effective size (N-ei) with novel expression for the variance effective size (N-ev), and conclude that for local populations N-ev is often much smaller than both versions of Nei, whenever they exist. Global N(ev)of the metapopulation, on the other hand, is close to the haploid Net and much larger than the diploid Nei. We introduce a new effective size, the additive genetic variance effective size Neill', which is of particular interest for long term protection of species. It quantifies the rate at which additive genetic variance is lost and we show that this effective size is closely related to the haploid version of Nei. Finally, we introduce a new measure of a population's deviation from migration-drift equilibrium, and apply it to quantify the time it takes to reach this equilibrium. Our findings are of importance for understanding the concept of effective population size in substructured populations and many of the results have applications in conservation biology.

  • 12.
    Hössjer, Ola
    et al.
    Stockholm University, Faculty of Science, Department of Mathematics.
    Olsson, Fredrik
    Stockholm University, Faculty of Science, Department of Mathematics.
    Laikre, Linda
    Stockholm University, Faculty of Science, Department of Zoology.
    Ryman, Nils
    Stockholm University, Faculty of Science, Department of Zoology.
    A new general analytical approach for modeling patterns of genetic differentiation and effective size of subdivided populations over time2014In: Mathematical Biosciences, ISSN 0025-5564, E-ISSN 1879-3134, Vol. 258, p. 113-133Article in journal (Refereed)
    Abstract [en]

    The main purpose of this paper is to develop a theoretical framework for assessing effective population size and genetic divergence in situations with structured populations that consist of various numbers of more or less interconnected subpopulations. We introduce a general infinite allele model for a diploid, monoecious and subdivided population, with subpopulation sizes varying overtime, including local subpopulation extinction and recolonization, bottlenecks, cyclic census size changes or exponential growth. Exact matrix analytic formulas are derived for recursions of predicted (expected) gene identities and gene diversities, identity by descent and coalescence probabilities, and standardized variances of allele frequency change. This enables us to compute and put into a general framework a number of different types of genetically effective population sizes (N-e) including variance, inbreeding, nucleotide diversity, and eigenvalue effective size. General expressions for predictions (g(ST)) of the coefficient of gene differentiation G(ST) are also derived. We suggest that in order to adequately describe important properties of a subdivided population with respect to allele frequency change and maintenance of genetic variation over time, single values of g(ST) and N-e are not enough. Rather, the temporal dynamic patterns of these properties are important to consider. We introduce several schemes for weighting subpopulations that enable effective size and expected genetic divergence to be calculated and described as functions of time, globally for the whole population and locally for any group of subpopulations. The traditional concept of effective size is generalized to situations where genetic drift is confounded by external sources, such as immigration and mutation. Finally, we introduce a general methodology for state space reduction, which greatly decreases the computational complexity of the matrix analytic formulas.

  • 13.
    Hössjer, Ola
    et al.
    Stockholm University, Faculty of Science, Department of Mathematics.
    Olsson, Fredrik
    Stockholm University, Faculty of Science, Department of Mathematics.
    Laikre, Linda
    Stockholm University, Faculty of Science, Department of Zoology.
    Ryman, Nils
    Stockholm University, Faculty of Science, Department of Zoology.
    Metapopulation inbreeding dynamics, effective size and subpopulation differentiation-A general analytical approach for diploid organisms2015In: Theoretical Population Biology, ISSN 0040-5809, E-ISSN 1096-0325, Vol. 102, p. 40-59Article in journal (Refereed)
    Abstract [en]

    Motivated by problems in conservation biology we study genetic dynamics in structured populations of diploid organisms (monoecious or dioecious). Our analysis provides an analytical framework that unifies substantial parts of previous work in terms of exact identity by descent (IBD) and identity by state (IBS) recursions. We provide exact conditions under which two structured haploid and diploid populations are equivalent, and some sufficient conditions under which a dioecious diploid population can be treated as a monoecious diploid one. The IBD recursions are used for computing local and metapopulation inbreeding and coancestry effective population sizes and for predictions of several types of fixation indices over different time horizons.

  • 14. Jackson, Jennifer A.
    et al.
    Laikre, Linda
    Stockholm University, Faculty of Science, Department of Zoology, Population Genetics.
    Baker, C. Scott
    Kendall, Katherine C.
    Guidelines for collecting and maintaining archives for genetic monitoring2012In: Conservation Genetics Resources, ISSN 1877-7252, E-ISSN 1877-7260, Vol. 4, no 2, p. 527-536Article in journal (Refereed)
    Abstract [en]

    Rapid advances in molecular genetic techniques and the statistical analysis of genetic data have revolutionized the way that populations of animals, plants and microorganisms can be monitored. Genetic monitoring is the practice of using molecular genetic markers to track changes in the abundance, diversity or distribution of populations, species or ecosystems over time, and to follow adaptive and non-adaptive genetic responses to changing external conditions. In recent years, genetic monitoring has become a valuable tool in conservation management of biological diversity and ecological analysis, helping to illuminate and define cryptic and poorly understood species and populations. Many of the detected biodiversity declines, changes in distribution and hybridization events have helped to drive changes in policy and management. Because a time series of samples is necessary to detect trends of change in genetic diversity and species composition, archiving is a critical component of genetic monitoring. Here we discuss the collection, development, maintenance, and use of archives for genetic monitoring. This includes an overview of the genetic markers that facilitate effective monitoring, describes how tissue and DNA can be stored, and provides guidelines for proper practice.

  • 15.
    Jansson, Mija
    et al.
    Stockholm University, Faculty of Science, Department of Zoology.
    Amundin, Mats
    Laikre, Linda
    Stockholm University, Faculty of Science, Department of Zoology.
    Genetic contribution from a zoo population can increase genetic variation in the highly inbred wild Swedish wolf population2015In: Conservation Genetics, ISSN 1566-0621, E-ISSN 1572-9737, Vol. 16, no 6, p. 1501-1505Article in journal (Refereed)
    Abstract [en]

    The Swedish wolf population (Canis lupus) descends from five individuals and is isolated and highly inbred with an average inbreeding coefficient of 0.27. In addition, inbreeding depression has led to reduced litter size and a high frequency of spinal disorders. To achieve the management goal of reducing the mean level of inbreeding, introductions into the wild population from a zoo conservation breeding program have been proposed by authorities. We used pedigree data of the wild and zoo populations to evaluate the extent to which the captive population can contribute genetic variation to the wild one. We measure genetic variation as founder alleles and founder genome equivalents. The two populations have three founders in common, but in spite of this common ancestry, our results show a potential to almost double genetic variation from 11.2 to 21.1 founder alleles. Similarly, the number of founder genome equivalents in the wild population can increase from the present 1.8 to 3.2, but this requires that almost 50 % of the wild gene pool consists of genes from the zoo population. Average kinship in the joint zoo and wild population is 0.15, which is above the management target of 0.1. Genetic contribution from the zoo has the potential to improve, but not solve, the genetically precarious situation of the wild population.

  • 16.
    Jansson, Mija
    et al.
    Stockholm University, Faculty of Science, Department of Zoology, Population Genetics.
    Amundin, Mats
    Linköpings Universitet.
    Laikre, Linda
    Stockholm University, Faculty of Science, Department of Zoology, Population Genetics.
    Supportive release from a zoo population by cross-fostering can significantly increase genetic variation in the highly inbred wild Swedish wolf populationManuscript (preprint) (Other academic)
    Abstract [en]

    The wild wolf population (Canis lupus) in Sweden is classified as Endangered and descends from only five individuals. The population is isolated and highly inbred; individuals are on average more related to each other than siblings. Inbreeding depression expressed as reduced litter size and a high frequency of spinal disorders have been reported. Management goals include reducing levels of inbreeding, and one suggestion to achieve this is through crossfostering release of pups from a zoo conservation breeding program into wild dens. We used pedigree data of the wild and zoo populations, respectively, to evaluate to what extent the zoo population can support the wild one with respect to increased genetic variation and reduction of inbreeding. The results show a potential to almost double genetic variation measured as founder alleles from 11.2 to 21.1, despite the fact that the two populations have three common founders. Potentially, the number of founder genome equivalents can be increased from present 1.8 to around 3.2. However, to achieve maximum genetic support, almost 50 percent of the wild population gene pool must consist of genes from the zoo population. Average kinship in the joint population of zoo and wild wolves is 0.15, thus release of zoo wolves cannot in itself be expected to reduce average inbreeding below the management target of 0.1. We conclude that releases from the zoo can support but not resolve the genetically precarious situation of the wild Swedish wolf population.

  • 17.
    Jansson, Mija
    et al.
    Stockholm University, Faculty of Science, Department of Zoology, Population Genetics.
    Laikre, Linda
    Stockholm University, Faculty of Science, Department of Zoology, Population Genetics.
    Monitoring rate of inbreeding and loss of genetic variation in traditional Swedish dog breeds of conservation concern using pedigree dataManuscript (preprint) (Other academic)
    Abstract [en]

    Increasing conservation genetic focus is directed towards domestic animal populations because: 1) domestic animals are of direct socio-economic importance to humans, and 2) strong selective breeding for a single or a few traits are considered to rapidly deplete the genetic variability of many domestic animal populations. International policy work within the Convention on Biological Diversity identifies strategies for minimizing genetic erosion of domesticated animals as one of the key biodiversity targets for 2010-2020. We investigated recent rate of inbreeding and loss of genetic variation in 12 traditional Swedish dog breeds, 10 of which have been identified as of conservation concern by the Swedish Board of Agriculture. We used studbook data provided by the Swedish Kennel Club with pedigrees dating back to the mid 20th century and comprising 5-10 generations with 350-60,000 individuals per pedigree. We assessed levels of inbreeding and loss of genetic variation measured in relation to the number of founding animals (founder alleles) among live animals at five points in time (1980, 1990, 2000, 2006, and 2012). We found average inbreeding coefficients among breeds to double over our period of monitoring, from an average of 0.03 over breeds in 1980 to 0.07 in 2012. This is in spite of the majority of breeds being large with pedigrees comprising thousands of individuals. The loss of genetic variation is extensive with an average of 70 percent loss of founder alleles over the study period, and the proportion of founder genome equivalents in relation to the number of founders is on average only 0.09. This is comparable to previously published rates of genetic variability loss in dog breeds, indicating that the explicit conservation goals for these traditional Swedish breeds is not yet reflected in conservation genetic status. One of the breeds is particularly threatened - the Gotland hound with less than 150 living individuals, but this breed also shows comparably larger retention of genetic variation.

  • 18.
    Jansson, Mija
    et al.
    Stockholm University, Faculty of Science, Department of Zoology.
    Laikre, Linda
    Stockholm University, Faculty of Science, Department of Zoology.
    Pedigree data indicate rapid inbreeding and loss of genetic diversity within populations of native, traditional dog breeds of conservation concern2018In: PLoS ONE, ISSN 1932-6203, E-ISSN 1932-6203, Vol. 13, no 9, article id e0202849Article in journal (Refereed)
    Abstract [en]

    Increasing concern is directed towards genetic diversity of domestic animal populations because strong selective breeding can rapidly deplete genetic diversity of socio-economically valuable animals. International conservation policy identifies minimizing genetic erosion of domesticated animals as a key biodiversity target. We used breeding records to assess potential indications of inbreeding and loss of founder allelic diversity in 12 native Swedish dog breeds, traditional to the country, ten of which have been identified by authorities as of conservation concern. The pedigrees dated back to the mid-1900, comprising 5-11 generations and 350-66,500 individuals per pedigree. We assessed rates of inbreeding and potential indications of loss of genetic variation by measuring inbreeding coefficients and remaining number of founder alleles at five points in time during 1980-2012. We found average inbreeding coefficients among breeds to double-from an average of 0.03 in 1980 to 0.07 in 2012 -in spite of the majority of breeds being numerically large with pedigrees comprising thousands of individuals indicating that such rapid increase of inbreeding should have been possible to avoid. We also found indications of extensive loss of intra-breed variation; on average 70 percent of founder alleles are lost during 1980-2012. Explicit conservation goals for these breeds were not reflected in pedigree based conservation genetic measures; breeding needs to focus more on retaining genetic variation, and supplementary genomic analyses of these breeds are highly warranted in order to find out the extent to which the trends indicated here are reflected over the genomes of these breeds.

  • 19.
    Jansson, Mija
    et al.
    Stockholm University, Faculty of Science, Department of Zoology, Population Genetics.
    Laikre, Linda
    Stockholm University, Faculty of Science, Department of Zoology, Population Genetics.
    Recent breeding history of dog breeds in Sweden: modest ratesof inbreeding, extensive loss of genetic diversity and lack ofcorrelation between inbreeding and health2014In: Journal of Animal Breeding and Genetics, ISSN 0931-2668, E-ISSN 1439-0388, Vol. 131, no 2, p. 153-162Article in journal (Refereed)
    Abstract [en]

    One problem in modern dogs is a high occurrence of physical diseases,defects and disorders. Many breeds exhibit physical problems that affectindividual dogs throughout life. A potential cause of these problems isinbreeding that is known to reduce the viability of individuals. We investigatedthe possible correlation between recent inbreeding and health problemsin dogs and used studbook data from 26 breeds provided by theSwedish Kennel Club for this purpose. The pedigrees date back to themid-20th century and comprise 5–10 generations and 1 000–50 000 individualsper pedigree over our study period of 1980–2010. We comparedlevels of inbreeding and loss of genetic variation measured in relation tothe number of founding animals during this period in the investigated dogbreeds that we classified as ‘healthy’ (11 breeds) or ‘unhealthy’ (15) basedon statistics on the extent of veterinary care obtained from Sweden’sfour largest insurance companies for pets. We found extensive loss ofgenetic variation and moderate levels of recent inbreeding in all breedsexamined, but no strong indication of a difference in these parametersbetween healthy versus unhealthy breeds over this period. Thus, recentbreeding history with respect to rate of inbreeding does not appear to be amain cause of poor health in the investigated dog breeds in Sweden. Weidentified both strengths and weaknesses of the dog pedigree data importantto consider in future work of monitoring and conserving geneticdiversity of dog breeds.

  • 20.
    Jansson, Mija
    et al.
    Stockholm University, Faculty of Science, Department of Zoology, Population Genetics.
    Ståhl, Ingvar
    Laikre, Linda
    Stockholm University, Faculty of Science, Department of Zoology, Population Genetics.
    mPed: a computer program for converting pedigree data to a format used by the PMx-software for conservation genetic analysis2013In: Conservation Genetics Resources, ISSN 1877-7252, E-ISSN 1877-7260, Vol. 5, no 3, p. 651-653Article in journal (Refereed)
    Abstract [en]

    There is a growing need for conservation genetic management of animal populations when individual relatedness data (pedigrees) are available. Such data can be used to monitor rates of inbreeding and loss of genetic diversity. Traditionally, pedigree analysis for conservationmanagement has focused on zoo populations of threatened wild animals; available software has been developed in that context. Population Management x (PMx) is a free software for estimating genetic parameters including inbreeding, kinship, founder allele contribution and survival. PMx is an accessory program to the zoo studbook platform Single Population Analysis and Records Keeping System (SPARKS) and is not easily applied outside this platform, but such use is of interest for various domestic breeds or wild populations. We developed a converter program (mPed) for making pedigrees of any studbook format fitting the input requirements of PMx. mPed can be downloaded free at www.popgen.su.se/mped.php

  • 21. Jorde, Per Erik
    et al.
    Andersson, Anastasia
    Stockholm University, Faculty of Science, Department of Zoology.
    Ryman, Nils
    Stockholm University, Faculty of Science, Department of Zoology.
    Laikre, Linda
    Stockholm University, Faculty of Science, Department of Zoology.
    Are we underestimating the occurrence of sympatric populations?2018In: Molecular Ecology, ISSN 0962-1083, E-ISSN 1365-294X, Vol. 27, no 20, p. 4011-4025Article in journal (Refereed)
    Abstract [en]

    Sympatric populations are conspecific populations that coexist spatially. They are of interest in evolutionary biology by representing the potential first steps of sympatric speciation and are important to identify and monitor in conservation management. Reviewing the literature pertaining to sympatric populations, we find that most cases of sympatry appear coupled to phenotypic divergence, implying ease of detection. In comparison, phenotypically cryptic, sympatric populations seem rarely documented. We explore the statistical power for detecting population mixtures from genetic marker data, using commonly applied tests for heterozygote deficiency (i.e., Wahlund effect) and the structure software, through computer simulations. We find that both tests are efficient at detecting population mixture only when genetic differentiation is high, sample size and number of genetic markers are reasonable and the sympatric populations happen to occur in similar proportions in the sample. We present an approximate expression based on these experimental factors for the lower limit of F-ST, beyond which power for structure collapses and only the heterozygote-deficiency tests retain some, although low, power. The findings suggest that cases of cryptic sympatry may have passed unnoticed in population genetic screenings using number of loci typical of the pre-genomics era. Hence, cryptic sympatric populations may be more common than hitherto thought, and we urge more attention being diverted to their detection and characterization.

  • 22.
    Laikre, Linda
    Stockholm University, Faculty of Science, Department of Zoology.
    Genetic diversity is overlooked in international conservation policy implementation.2010In: Conservation Genetics, ISSN 1566-0621, E-ISSN 1572-9737, Conservation Genetics, Vol. 11, p. 349-354Article in journal (Refereed)
    Abstract [en]

    The importance of genetic variation for maintaining biological diversity and evolutionary processes has been recognized by researchers for decades. This realization has prompted agreements by world leaders toconserve genetic diversity, and this is an explicit goal of the Convention on Biological Diversity (CBD). Nevertheless, very limited action has been taken to protect genetic diversity on a global scale. International conservation efforts to halt biodiversity loss focus on habitats and species,whereas little or no attention is paid to gene level variation. By this year, 2010, world leaders have agreed that a significant reduction of the rate of biodiversity loss should have been achieved. However, gene level diversity is still not monitored, indicators that can help identify threats to genetic variation are missing, and there is no strategy for how genetic aspects can be included in biodiversity targets beyond 2010. Important findings and conclusions from decades of conservation genetic research are not translated into concrete conservation action in the arena of international policy development. There is an urgent need for conservation geneticists worldwide to become involved in policy and practical conservation work beyond the universities and research institutions.

  • 23. Laikre, Linda
    et al.
    Allendorf, F. W.
    Aroner, L. C.
    Baker, C. S.
    Gregovich, D. P.
    Hansen, M. M.
    Jackson, J. A.
    Kendall, K. C.
    McKelvey, K.
    Neel, M. C.
    Ryman, Nils
    Stockholm University, Faculty of Science, Department of Zoology.
    Schwartz, M. K.
    Shortbull, R.
    Stetz, J. B.
    Tallmon, D. A.
    Taylor, B. L.
    Vojta, C. D.
    Waller, D. M.
    Waples, R. S.
    Neglect of genetic diversity in implementation of the Convention on Biological Diversity2010In: Conservation Biology, Vol. 24, p. 86-88Article in journal (Refereed)
  • 24.
    Laikre, Linda
    et al.
    Stockholm University, Faculty of Science, Department of Zoology, Population Genetics.
    Jansson, Mija
    Stockholm University, Faculty of Science, Department of Zoology, Population Genetics.
    Allendorf, Fred W.
    Jakobsson, Sven
    Stockholm University, Faculty of Science, Department of Zoology, Ethology.
    Ryman, Nils
    Stockholm University, Faculty of Science, Department of Zoology, Population Genetics.
    Hunting Effects on Favourable Conservation Status of Highly Inbred Swedish Wolves2013In: Conservation Biology, ISSN 0888-8892, E-ISSN 1523-1739, Vol. 27, no 2, p. 248-253Article in journal (Refereed)
    Abstract [en]

    The wolf (Canis lupus) is classified as endangered in Sweden by the Swedish Species Information Centre, which is the official authority for threat classification. The present population, which was founded in the early 1980s, descends from 5 individuals. It is isolated and highly inbred, and on average individuals are more related than siblings. Hunts have been used by Swedish authorities during 2010 and 2011 to reduce the population size to its upper tolerable level of 210 wolves. European Union (EU) biodiversity legislation requires all member states to promote a concept called “favourable conservation status” (FCS) for a series of species including the wolf. Swedish national policy stipulates maintenance of viable populations with sufficient levels of genetic variation of all naturally occurring species. Hunting to reduce wolf numbers in Sweden is currently not in line with national and EU policy agreements and will make genetically based FCS criteria less achievable for this species. We suggest that to reach FCS for the wolf in Sweden the following criteria need to be met: (1) a well-connected, large, subdivided wolf population over Scandinavia, Finland, and the Russian Karelia-Kola region should be reestablished, (2) genetically effective size (Ne) of this population is in the minimum range of Ne = 500–1000, (3) Sweden harbors a part of this total population that substantially contributes to the total Ne and that is large enough to not be classified as threatened genetically or according to IUCN criteria, and (4) average inbreeding levels in the Swedish population are <0.1.

  • 25.
    Laikre, Linda
    et al.
    Stockholm University, Faculty of Science, Department of Zoology.
    Jonsson, Bengt-Gunnar
    Ihse, Margareta
    Stockholm University, Faculty of Science, Department of Physical Geography and Quaternary Geology.
    Marissink, Mark
    Dock Gustavsson, Ann-Marie
    Ebenhard, Torbjörn
    Hagberg, Lovisa
    Stål, Pär-Olof
    von Walter, Susanne
    Wramner, Per
    Wanted: Scientists in the CBD process2008In: Conservation Biology, ISSN 0888-8892, E-ISSN 1523-1739, Vol. 22, no 4, p. 814-815Article in journal (Other academic)
  • 26.
    Laikre, Linda
    et al.
    Stockholm University, Faculty of Science, Department of Zoology.
    Larsson, Lena C.
    Stockholm University, Faculty of Science, Department of Zoology.
    Palmé, Anna
    Stockholm University, Faculty of Science, Department of Zoology.
    Charlier, Johan
    Stockholm University, Faculty of Science, Department of Zoology.
    Josefsson, Melanie
    Ryman, Nils
    Stockholm University, Faculty of Science, Department of Zoology.
    Potentials for monitoring gene level biodiversity: using Sweden as an example2008In: Biodiversity and Conservation, ISSN 0960-3115, E-ISSN 1572-9710, Vol. 17, no 4, p. 893-910Article in journal (Refereed)
    Abstract [en]

    Programs for monitoring biological diversity over time are needed to detect changes that can constitute threats to biological resources. The convention on biological diversity regards effective monitoring as necessary to halt the ongoing erosion of biological variation, and such programs at the ecosystem and species levels are enforced in several countries. However, at the level of genetic biodiversity, little has been accomplished, and monitoring programs need to be developed. We define “conservation genetic monitoring” to imply the systematic, temporal study of genetic variation within particular species/populations with the aim to detect changes that indicate compromise or loss of such diversity. We also (i) identify basic starting points for conservation genetic monitoring, (ii) review the availability of such information using Sweden as an example, (iii) suggest categories of species for pilot monitoring programs, and (iv) identify some scientific and logistic issues that need to be addressed in the context of conservation genetic monitoring. We suggest that such programs are particularly warranted for species subject to large scale enhancement and harvest—operations that are known to potentially alter the genetic composition and reduce the variability of populations.

  • 27.
    Laikre, Linda
    et al.
    Stockholm University, Faculty of Science, Department of Zoology.
    Lundmark, Carina
    Jansson, Eeva
    Wennerström, Lovisa
    Stockholm University, Faculty of Science, Department of Zoology.
    Edman, Mari
    Stockholm University, Faculty of Science, Department of Zoology.
    Sandström, Annica
    Lack of recognition of genetic biodiversity: International policy and its implementation in Baltic Sea marine protected areas2016In: Ambio, ISSN 0044-7447, E-ISSN 1654-7209, Vol. 45, no 6, p. 661-680Article in journal (Refereed)
    Abstract [en]

    Genetic diversity is needed for species' adaptation to changing selective pressures and is particularly important in regions with rapid environmental change such as the Baltic Sea. Conservation measures should consider maintaining large gene pools to maximize species' adaptive potential for long-term survival. In this study, we explored concerns regarding genetic variation in international and national policies that governs biodiversity and evaluated if and how such policy is put into practice in management plans governing Baltic Sea Marine Protected Areas (MPAs) in Sweden, Finland, Estonia, and Germany. We performed qualitative and quantitative textual analysis of 240 documents and found that agreed international and national policies on genetic biodiversity are not reflected in management plans for Baltic Sea MPAs. Management plans in all countries are largely void of goals and strategies for genetic biodiversity, which can partly be explained by a general lack of conservation genetics in policies directed toward aquatic environments.

  • 28.
    Laikre, Linda
    et al.
    Stockholm University, Faculty of Science, Department of Zoology, Population Genetics.
    Miller, Loren M.
    University of Minnesota.
    Palmé, Anna
    Stockholm University, Faculty of Science, Department of Zoology, Population Genetics.
    Palm, Stefan
    Stockholm University, Faculty of Science, Department of Zoology, Population Genetics.
    Kapuscinski, Anne R.
    University of Minnesota.
    Thoresson, Gunnar
    National Board of Fisheries.
    Ryman, Nils
    Stockholm University, Faculty of Science, Department of Zoology, Population Genetics.
    Spatial genetic structure of northern pike (Esox lucius) in the Baltic Sea2005In: Molecular Ecology, ISSN 0962-1083, E-ISSN 1365-294X, Vol. 14, no 7, p. 1955-1964Article in journal (Refereed)
    Abstract [en]

    The genetic relationships among 337 northern pike (Esox lucius) collected from the coastal zone of the central Baltic region and the Finnish islands of Åland were analysed using five microsatellite loci. Spatial structure was delineated using both traditional F-statistics and individually based approaches including spatial autocorrelation analysis. Our results indicate that the observed genotypic distribution is incompatible with that of a single, panmictic population. Isolation by distance appears important for shaping the genetic structure of pike in this region resulting in a largely continuous genetic change over the study area. Spatial autocorrelation analysis (Moran’s I) of individual pairwise genotypic data show significant positive genetic correlation among pike collected within geographical distances of less than c. 100–150 km (genetic patch size). We suggest that the genetic patch size may be used as a preliminary basis for identifying management units for pike in the Baltic Sea.

  • 29.
    Laikre, Linda
    et al.
    Stockholm University, Faculty of Science, Department of Zoology.
    Nilsson, T
    Länsstyrelsen Värmland.
    Primmer, CR
    University of Turku, Finland.
    Ryman, Nils
    Stockholm University, Faculty of Science, Department of Zoology.
    Allendorf, FW
    University of Montana, USA.
    Importance of Genetics in the Interpretation of Favourable Conservation Status2009In: Conservation Biology, ISSN 0888-8892, E-ISSN 1523-1739, Vol. 23, p. 1378-1381Article in journal (Refereed)
    Abstract [en]

    “Favourable Conservation Status” (FCS) is a central concept in the biodiversity conservation legislation of the European Union (EU). Here, we highlight the importance of incorporating aspects of conservation genetics in interpretation of this concept. Recent documents from the EU Commission indicate that knowledge of conservation genetics has so far been lacking among those who have tried to employ the concept. We think it is crucial that aspects of conservation genetics be incorporated in discussion of this concept and that this be done before the EU Court of Justice takes a position on the legal interpretation of FCS.

  • 30.
    Laikre, Linda
    et al.
    Stockholm University, Faculty of Science, Department of Zoology.
    Olsson, Fredrik
    Stockholm University, Faculty of Science, Department of Mathematics.
    Jansson, Eeva
    Stockholm University, Faculty of Science, Department of Zoology.
    Hössjer, Ola
    Stockholm University, Faculty of Science, Department of Mathematics.
    Ryman, Nils
    Stockholm University, Faculty of Science, Department of Zoology.
    Metapopulation effective size and conservation genetic goals for the Fennoscandian wolf (Canis lupus) population2016In: Heredity, ISSN 0018-067X, E-ISSN 1365-2540, Vol. 117, no 4, p. 279-289Article in journal (Refereed)
    Abstract [en]

    The Scandinavian wolf population descends from only five individuals, is isolated, highly inbred and exhibits inbreeding depression. To meet international conservation goals, suggestions include managing subdivided wolf populations over Fennoscandia as a metapopulation; a genetically effective population size of N-e >= 500, in line with the widely accepted long-term genetic viability target, might be attainable with gene flow among subpopulations of Scandinavia, Finland and Russian parts of Fennoscandia. Analytical means for modeling N-e of subdivided populations under such non-idealized situations have been missing, but we recently developed new mathematical methods for exploring inbreeding dynamics and effective population size of complex metapopulations. We apply this theory to the Fennoscandian wolves using empirical estimates of demographic parameters. We suggest that the long-term conservation genetic target for metapopulations should imply that inbreeding rates in the total system and in the separate subpopulations should not exceed Delta f = 0.001. This implies a meta-Ne of N-eMeta >= 500 and a realized effective size of each subpopulation of N-eRx >= 500. With current local effective population sizes and one migrant per generation, as recommended by management guidelines, the meta-Ne that can be reached is similar to 250. Unidirectional gene flow from Finland to Scandinavia reduces meta-N-e to similar to 130. Our results indicate that both local subpopulation effective sizes and migration among subpopulations must increase substantially from current levels to meet the conservation target. Alternatively, immigration from a large (N-e >= 500) population in northwestern Russia could support the Fennoscandian metapopulation, but immigration must be substantial (5-10 effective immigrants per generation) and migration among Fennoscandian subpopulations must nevertheless increase.

  • 31.
    Laikre, Linda
    et al.
    Stockholm University, Faculty of Science, Department of Zoology.
    Palmé, Anna
    Stockholm University, Faculty of Science, Department of Zoology.
    Internationellt fokus på laxgener2012In: HavsUtsikt, ISSN 1104-0513, no 1Article in journal (Other (popular science, discussion, etc.))
  • 32.
    Laikre, Linda
    et al.
    Stockholm University, Faculty of Science, Department of Zoology, Population Genetics.
    Palmé, Anna
    Stockholm University, Faculty of Science, Department of Zoology, Population Genetics.
    Josefsson, Melanie
    Department of Environmental Monitoring and Assessment, Swedish Environmental Protection Agency.
    Utter, Fred
    School of Aquatic and Fisheries Sciences, University of Washington .
    Ryman, Nils
    Stockholm University, Faculty of Science, Department of Zoology, Population Genetics.
    Release of alien populations in Sweden2006In: Ambio, ISSN 0044-7447, E-ISSN 1654-7209, Vol. 35, no 5, p. 255-261Article in journal (Refereed)
    Abstract [en]

    Introduction of alien species is a major threat to biological diversity. Although public attention typically focuses on the species level, guidelines from the Convention of Biological Diversity define alien species to include entities below species level. This inclusion recognizes that release of nonlocal populations of native species may also result in negative effects on biodiversity. In practice, little is known about the extent, degree of establishment, or the effects on natural gene pools of such releases. Existing information on the releases in Sweden shows that alien populations are spread to a great extent. The most commonly released species include brown trout, Atlantic salmon, Arctic char, common whitefish, Scots pine, Norway spruce, mallard duck, gray partridge, and pheasant. Although millions of forest trees, fish, and birds are released annually, poor documentation makes the geographic and genetic origin of these populations, as well as the sites where they have been released, largely unclear. We provide recommendations for urgently needed first steps relating to the risks and problems associated with release of alien populations.

  • 33.
    Laikre, Linda
    et al.
    Stockholm University, Faculty of Science, Department of Zoology.
    Palmé, Anna
    Stockholm University, Faculty of Science, Department of Zoology.
    Larsson, Lena C
    Stockholm University, Faculty of Science, Department of Zoology.
    Charlier, Johan
    Stockholm University, Faculty of Science, Department of Zoology.
    Ryman, Nils
    Stockholm University, Faculty of Science, Department of Zoology.
    Effekter av spridning av genetiskt främmande populationer: en kartläggning av förutsättningarna för uppföljande studier av utsättningar av djur och växter i Sverige2008Report (Other academic)
  • 34.
    Laikre, Linda
    et al.
    Stockholm University, Faculty of Science, Department of Zoology.
    Schwartz, Michael K.
    Waples, Robin S.
    Ryman, Nils
    Stockholm University, Faculty of Science, Department of Zoology.
    Compromising genetic diversity in the wild: unmonitored large-scale release of plants and animals2010In: Trends in Ecology & Evolution, ISSN 0169-5347, E-ISSN 1872-8383, Vol. 25, no 9, p. 520-529Article in journal (Refereed)
    Abstract [en]

    Large-scale exploitation of wild animals and plants through fishing, hunting and logging often depends on augmentation through releases of translocated or captively raised individuals. Such releases are performed worldwide in vast numbers. Augmentation can be demographically and economically beneficial but can also cause four types of adverse genetic change to wild populations: (1) loss of genetic variation, (2) loss of adaptations, (3) change of population composition, and (4) change of population structure. While adverse genetic impacts are recognized and documented in fisheries, little effort is devoted to actually monitoring them. In forestry and wildlife management, genetic risks associated with releases are largely neglected. We outline key features of programs to effectively monitor consequences of such releases on natural populations.

  • 35. Lamichhaney, Sangeet
    et al.
    Barrio, Alvaro Martinez
    Rafati, Nima
    Sundström, Görel
    Rubin, Carl-Johan
    Gilbert, Elizabeth R.
    Berglund, Jonas
    Wetterbom, Anna
    Laikre, Linda
    Stockholm University, Faculty of Science, Department of Zoology.
    Webster, Matthew T.
    Grabherr, Manfred
    Ryman, Nils
    Stockholm University, Faculty of Science, Department of Zoology.
    Andersson, Leif
    Population-scale sequencing reveals genetic differentiation due to local adaptation in Atlantic herring2012In: Proceedings of the National Academy of Sciences of the United States of America, ISSN 0027-8424, E-ISSN 1091-6490, Vol. 109, no 47, p. 19345-19350Article in journal (Refereed)
    Abstract [en]

    The Atlantic herring (Clupea harengus), one of the most abundant marine fishes in the world, has historically been a critical food source in Northern Europe. It is one of the few marine pecies that can reproduce throughout the brackish salinity gradient of the Baltic Sea. Previous studies based on few genetic markers have revealed a conspicuous lack of genetic differentiation between geographic regions, consistent with huge population sizes and minute genetic drift. Here, we present a cost-effective genome-wide study in a species that lacks a genome sequence. We first assembled a muscle transcriptome and then aligned genomic reads to the transcripts, creating an “exome assembly,” capturing both exons and flanking sequences. We then resequenced pools of fish from a wide geographic range, including the Northeast Atlantic, as well as different regions in the Baltic Sea, aligned the reads to the exome assembly, and identified 440,817 SNPs. The great majority of SNPs showed no appreciable differences in allele frequency among populations; however, several thousand SNPs showed striking differences, some approaching fixation for different alleles. The contrast between low genetic differentiation at most loci and striking differences at others implies that the latter category primarily reflects natural selection. A simulation study confirmed that the distribution of the fixation index FST deviated significantly from expectation for selectively neutral loci. This study provides insights concerning the population  structure of an important marine fish and establishes the Atlantic herring as a model for population genetic studies of adaptation and natural selection.

  • 36.
    Larsson, Lena C.
    et al.
    Stockholm University, Faculty of Science, Department of Zoology.
    Charlier, Johan
    Stockholm University, Faculty of Science, Department of Zoology.
    Laikre, Linda
    Stockholm University, Faculty of Science, Department of Zoology.
    Ryman, Nils
    Stockholm University, Faculty of Science, Department of Zoology.
    Statistical power for detecting genetic divergence–organelle versus nuclear markers2009In: Conservation Genetics, ISSN 1566-0621, E-ISSN 1572-9737, Vol. 10, no 5, p. 1255-1264Article in journal (Refereed)
    Abstract [en]

    Statistical power is critical in conservation for detecting genetic differences in space or time from allele frequency data. Organelle and nuclear genetic markers have fundamentally different transmission dynamics; the potential effect of these differences on power to detect divergence have been speculated on but not investigated. We examine, analytically and with computer simulations, the relative performance of organelle and nuclear markers under basic, ideal situations. We conclude that claims of a generally higher resolving power of either marker type are not correct. The ratio R = FST,organelle/FST,nuclear varies between 1 and 4 during differentiation and this greatly affects the power relationship. When nuclear FST is associated with organelle differentiation four times higher, the power of the organelle marker is similar to two nuclear loci with the same allele frequency distribution. With large sample sizes (n C 50) and several populations or many alleles per locus (C5), the power difference may typically be disregarded when nuclear FST[0.05. To correctly interpret observed patterns of genetic differentiation in practical situations, the expected FSTs and the statistical properties (i.e., power analysis) of the genetic markers used should be evaluated, taking the observed allele frequency distributions into consideration.

  • 37.
    Larsson, Lena C.
    et al.
    Stockholm University, Faculty of Science, Department of Zoology, Population Genetics.
    Laikre, Linda
    Stockholm University, Faculty of Science, Department of Zoology, Population Genetics.
    André, Carl
    Tjärnö marinbiologiska laboratorium, Göteborgs universitet.
    Dahlgren, Thomas G.
    Göteborgs universitet.
    Ryman, Nils
    Stockholm University, Faculty of Science, Department of Zoology, Population Genetics.
    Temporally stable genetic structure of heavily exploited Atlantic herring (Clupea harengus) in Swedish waters2010In: Heredity, ISSN 0018-067X, E-ISSN 1365-2540, Vol. 104, no 1, p. 40-51Article in journal (Refereed)
    Abstract [en]

    Information on the temporal stability of genetic structures is important to permit detection of changes that can constitute threats to biological resources. Large scale harvesting operations are known to potentially alter the composition and reduce the variability of populations, and Atlantic herring (Clupea harengus) has a long history of heavy exploitation. In the Baltic Sea and Skagerrak waters the census population sizes have declined by 35-50% over the last three decades. We compared the genetic structure of Atlantic herring in these waters sampled at least two different times between 1979 and 2003 by assaying eleven allozyme and nine microsatellite loci. We cannot detect any changes in the amount of genetic variation or spatial structure, and differentiation is weak with overall FST=0.003 among localities for the older samples and FST=0.002 for the newer ones. There are indications of temporal allele frequency changes, particularly in one of five sampling localities that is reflected in a relatively small local Ne estimate of c. 400. The previously identified influence of selection at the microsatellite locus Cpa112 remains stable over the 24-year period studied here. In spite of little genetic differentiation, migration among localities appears small enough to permit demographic independence between populations.

  • 38.
    Larsson, Lena
    et al.
    Stockholm University, Faculty of Science, Department of Zoology. Populationsgenetik.
    Laikre, Linda
    Stockholm University, Faculty of Science, Department of Zoology. Populationsgenetik.
    Palm, Stefan
    Stockholm University, Faculty of Science, Department of Zoology. Populationsgenetik.
    André, Carl
    Carvalho, Gary R.
    Ryman, Nils
    Stockholm University, Faculty of Science, Department of Zoology. Populationsgenetik.
    Concordance of allozyme and microsatellite differentiation in a marine fish, but evidence of selection at a microsatellite locus2007In: Molecular Ecology, Vol. 16, p. 1135-1147Article in journal (Refereed)
    Abstract [en]

    Previous studies have reported higher levels of divergence for microsatellites than for allozymes in several species, suggested to reflect stabilizing selection on the allozymes. We compared the differentiation patterns of 11 allozyme and nine microsatellite loci using 679 spawning Atlantic herring (Clupea harengus) collected in the Baltic and North Seas to test for differential natural selection on these markers. Observed distributions of F statistics for the two types of markers are conspicuously dissimilar, but we show that these differences can largely be explained by sampling phenomena caused by different allele frequency distributions and degrees of variability. The results show consistently low levels of differentiation for both marker types, with the exception of one outlier microsatellite locus with a notably high FST. The aberrant pattern at this locus is primarily due to two alleles occurring at markedly high frequencies in the Baltic, suggesting selection at this locus, or a closely linked one. When excluding this locus, the two marker types show similar, weak differentiation patterns with FST values between the Baltic and the North Seas of 0.001 and 0.002 for allozymes and microsatellites, respectively. This small heterogeneity, and weak isolation by distance, is easier to distinguish statistically with microsatellites than with allozymes that have fewer alleles and skewed frequency distributions. The allozymes, however, also detect surprisingly low levels of divergence. Our results support suggestions that previously described differences between marker types are primarily caused by a small number of outlier loci

  • 39. Lundmark, Carina
    et al.
    Andersson, Klas
    Sandström, Annica
    Laikre, Linda
    Stockholm University, Faculty of Science, Department of Zoology.
    Effectiveness of short-term knowledge communication on Baltic Sea marine genetic biodiversity to public managers2017In: Regional Environmental Change, ISSN 1436-3798, E-ISSN 1436-378X, Vol. 17, no 3, p. 841-849Article in journal (Refereed)
    Abstract [en]

    The aim of this study is to assess the impact of two forms of short-term knowledge communication-lectures and group deliberations-on public managers' policy beliefs regarding genetic biodiversity in the Baltic Sea. Genetic biodiversity is a key component of biological variation, but despite scientific knowledge and far-reaching political goals, genetic biodiversity remains neglected in marine management. Previous research highlights lack of knowledge among managers as one explanation to the implementation deficit. This multidisciplinary study builds on the identified need for an improved knowledge transfer between science and ongoing management. A basic knowledge package on genetic biodiversity in the Baltic Sea was presented as either a lecture or a deliberative group discussion to two separate samples of public managers who are involved in Baltic Sea and other biodiversity management at the regional level in Sweden. The empirical findings show that the communicated information has an impact on the public managers' beliefs on genetic biodiversity of the Baltic Sea. Lectures seem more efficient to transfer knowledge on this theme. Those who received information through a lecture strengthen their confidence in area protection as a management tool to conserve genetic diversity. They were also more convinced of the obligation of authorities at national and regional level to take on larger responsibility for genetic conservation than those managers who participated in a deliberative discussion.

  • 40. Lundmark, Carina
    et al.
    Sandström, Annica
    Andersson, Klas
    Laikre, Linda
    Stockholm University, Faculty of Science, Department of Zoology.
    Monitoring the effects of knowledge communication on conservation managers' perception of genetic biodiversity - A case study from the Baltic Sea2019In: Marine Policy, ISSN 0308-597X, E-ISSN 1872-9460, Vol. 99, p. 223-229Article in journal (Refereed)
    Abstract [en]

    Despite the attention given to genetic biodiversity in international agreements such as the Convention on Biological Diversity (CBD) Strategic Plan and the Aichi Targets, previous research points at a conservation genetics gap, indicating that scientific insights into genetic biodiversity are poorly integrated into practical management. Both researchers and managers call for platforms for knowledge exchange between science and practice. However, few scientific studies on the potential effects of such knowledge transfer have been conducted. The present study is a follow-up to Lundmark et al. (2017), which identified significant effects of two forms of knowledge communication on conservation managers' concerns and beliefs in regard to Baltic Sea genetic biodiversity. This study departs from Landmark et al. (2017) and explores (a) whether the identified alterations in knowledge and beliefs persist over time, and (b) whether potential stability differs between different types of policy beliefs as well as between two types of knowledge communication (lecture and group deliberation). The results of this follow-up study show that the positive impacts on managers' self-assessed knowledge remained, while the effects on policy beliefs largely had vanished a few months after the knowledge communication. Thus, changes in beliefs seem perishable, suggesting that continuity is more important than the form of educational efforts.

  • 41.
    Olsson, Fredrik
    et al.
    Stockholm University, Faculty of Science, Department of Mathematics.
    Hössjer, Ola
    Stockholm University, Faculty of Science, Department of Mathematics.
    Laikre, Linda
    Stockholm University, Faculty of Science, Department of Zoology.
    Ryman, Nils
    Stockholm University, Faculty of Science, Department of Zoology.
    Characteristics of the variance effective population size over time using an age structured model with variable size2013In: Theoretical Population Biology, ISSN 0040-5809, E-ISSN 1096-0325, Vol. 90, p. 91-103Article in journal (Refereed)
    Abstract [en]

    The variance effective population size (N-ev) is a key concept in population biology, because it quantifies the microevolutionary process of random genetic drift, and understanding the characteristics of N-ev is thus of central importance. Current formulas for Nev for populations with overlapping generations weight age classes according to their reproductive values (i.e. reflecting the contribution of genes from separate age classes to the population growth) to obtain a correct measure of genetic drift when computing the variance of the allele frequency change over time. In this paper, we examine the effect of applying different weights to the age classes using a novel analytical approach for exploring N-ev. We consider a haploid organism with overlapping generations and populations of increasing, declining, or constant expected size and stochastic variation with respect to the number of individuals in the separate age classes. We define Nov, as a function of how the age classes are weighted, and of the span between the two points in time, when measuring allele frequency change. With this model, time profiles for N-ev can be calculated for populations with various life histories and with fluctuations in life history composition, using different weighting schemes. We examine analytically and by simulations when Nei, using a weighting scheme with respect to reproductive contribution of separate age classes, accurately reflect the variance of the allele frequency change due to genetic drift over time. We show that the discrepancy of N-ev, calculated with reproductive values as weights, compared to when individuals are weighted equally, tends to a constant when the time span between the two measurements increases. This constant is zero only for a population with a constant expected population size. Our results confirm that the effect of ignoring overlapping generations, when empirically assessing Nell from allele frequency shifts, gets smaller as the time interval between samples increases. Our model has empirical applications including assessment of (i) time intervals necessary to permit ignoring the effect of overlapping generations for N-ev estimation by means of the temporal method, and (ii) effects of life table manipulation on N-ev over varying time periods.

  • 42.
    Olsson, Fredrik
    et al.
    Stockholm University, Faculty of Science, Department of Mathematics.
    Laikre, Linda
    Stockholm University, Faculty of Science, Department of Zoology.
    Hössjer, Ola
    Stockholm University, Faculty of Science, Department of Mathematics.
    Ryman, Nils
    Stockholm University, Faculty of Science, Department of Zoology.
    GESP: A computer program for modelling genetic effective population size, inbreeding and divergence in substructured populations2017In: Molecular Ecology Resources, ISSN 1755-098X, E-ISSN 1755-0998, Vol. 17, no 6, p. 1378-1384Article in journal (Refereed)
    Abstract [en]

    The genetically effective population size (N-e) is of key importance for quantifying rates of inbreeding and genetic drift and is often used in conservation management to set targets for genetic viability. The concept was developed for single, isolated populations and the mathematical means for analysing the expected N-e in complex, subdivided populations have previously not been available. We recently developed such analytical theory and central parts of that work have now been incorporated into a freely available software tool presented here. gesp (Genetic Effective population size, inbreeding and divergence in Substructured Populations) is R-based and designed to model short- and long-term patterns of genetic differentiation and effective population size of subdivided populations. The algorithms performed by gesp allow exact computation of global and local inbreeding and eigenvalue effective population size, predictions of genetic divergence among populations (G(ST)) as well as departures from random mating (F-IS, F-IT) while varying (i) subpopulation census and effective size, separately or including trend of the global population size, (ii) rate and direction of migration between all pairs of subpopulations, (iii) degree of relatedness and divergence among subpopulations, (iv) ploidy (haploid or diploid) and (v) degree of selfing. Here, we describe gesp and exemplify its use in conservation genetics modelling.

  • 43.
    Palme, Anna
    et al.
    Stockholm University, Faculty of Science, Department of Zoology, Population Genetics.
    Laikre, Linda
    Stockholm University, Faculty of Science, Department of Zoology, Population Genetics.
    Ryman, Nils
    Stockholm University, Faculty of Science, Department of Zoology, Population Genetics.
    Monitoring reveals two genetically distinct brown trout populations remaining in stable sympatry over 20 years in tiny mountain lakes2013In: Conservation Genetics, ISSN 1566-0621, E-ISSN 1572-9737, Vol. 14, no 4, p. 795-808Article in journal (Refereed)
    Abstract [en]

    Detecting population subdivision when apparent barriers to gene flow are lacking is important in evolutionary and conservation biology. Recent research indicates that intraspecific population complexity can be crucial for maintaining a species' evolutionary potential, productivity, and ecological role. We monitored the genetic relationships at 14 allozyme loci among similar to 4,000 brown trout (Salmo trutta) collected during 19 years from two small interconnected mountain lakes (0.10 and 0.17 km(2), respectively) in central Sweden. There were no allele frequency differences between the lakes. However, heterozygote deficiencies within lakes became obvious after a few years of monitoring. Detailed analyses were then carried out without a priori grouping of samples, revealing unexpected differentiation patterns: (i) the same two genetically distinct (F (ST) a parts per thousand yen 0.10) populations occur sympatrically at about equal frequencies within both lakes, (ii) the genetic subdivision is not coupled with apparent phenotypical dichotomies, (iii) this cryptic structure remains stable over the two decades monitored, and (iv) the point estimates of effective population size are c. 120 and 190, respectively, indicating that genetic drift is important in this system. A subsample of 382 fish was also analyzed for seven microsatellites. The genetic pattern does not follow that of the allozymes, and in this subsample the presence of multiple populations would have gone undetected if only scoring microsatellites. Sympatric populations may be more common than anticipated, but difficult to detect when individuals cannot be grouped appropriately, or when markers or sample sizes are insufficient to provide adequate statistical power with approaches not requiring prior grouping.

  • 44.
    Palmé, Anna
    et al.
    Stockholm University, Faculty of Science, Department of Zoology.
    Laikre, Linda
    Stockholm University, Faculty of Science, Department of Zoology.
    Spridning av främmande populationer i Sverige2005Report (Other academic)
  • 45.
    Palmé, Anna
    et al.
    Stockholm University, Faculty of Science, Department of Zoology, Population Genetics.
    Laikre, Linda
    Stockholm University, Faculty of Science, Department of Zoology, Population Genetics.
    Ryman, Nils
    Stockholm University, Faculty of Science, Department of Zoology, Population Genetics.
    Genetic monitoring reveals two sympatric brown trout populations in a small mountain lakeManuscript (preprint) (Other academic)
    Abstract [en]

    It is contentious to what extent sympatric speciation represents a general and taxonomically widespread phenomenon. Documenting the occurrence of multiple, genetically distinct populations within areas lacking barriers to gene flow can increase our understanding of this type of speciation, because such populations are expected to represent the first steps of sympatric speciation. We analyzed the genetic relationships among over 4000 brown trout (Salmo trutta) collected during 19 sampling years from a series of small mountain lakes in northern Scandinavia. Our results clearly indicate the presence of two sympatric populations within these lakes. The populations are characterized by a high degree of genetic divergence coupled with a lack of apparent phenotypic dichotomy. The differentiation pattern appears stable over the two decades monitored, and the exchange of individuals between the two populations appears small. The existence of sympatric populations characterized by substantial genetic divergence may be a much more common phenomenon than anticipated, but difficult to detect in situations where morphological or ecological differentiation is missing. Larger samples than typically collected in a single sampling effort may be needed for revealing situations of sympatry, and for reliable estimation of the number of populations.

  • 46.
    Palmé, Anna
    et al.
    Stockholm University, Faculty of Science, Department of Zoology.
    Laikre, Linda
    Stockholm University, Faculty of Science, Department of Zoology.
    Ryman, Nils
    Stockholm University, Faculty of Science, Department of Zoology.
    Population genetics of harbour porpoise in Swedish waters - a literature review2004Report (Other academic)
  • 47.
    Palmé, Anna
    et al.
    Stockholm University, Faculty of Science, Department of Zoology.
    Laikre, Linda
    Stockholm University, Faculty of Science, Department of Zoology.
    Utter, Fred
    Ryman, Nils
    Stockholm University, Faculty of Science, Department of Zoology.
    Conservation genetics without knowing what to conserve: the case of the Baltic harbour porpoise Phocoena phocoena2008In: Oryx, ISSN 0030-6053, E-ISSN 1365-3008, Vol. 42, no 2, p. 305-308Article in journal (Refereed)
    Abstract [en]

    Effective conservation requires that arguments for identifying units for preservation and management are based on scientifically sound information. There is a strong conservation concern for the harbour porpoise Phocoena phocoena of the Baltic Sea. This concern rests on the assumption that these porpoises represent a genetically distinct population reproductively separated from adjacent populations to the west. We argue that current scientific support for this claim is weak and to a large degree speculative. Current management of Baltic harbour porpoises as a genetically separate conservation unit is premature and we urge that high priority be given towards resolving this issue.

  • 48.
    Palmé, Anna
    et al.
    Stockholm University, Faculty of Science, Department of Zoology.
    Laikre, Linda
    Stockholm University, Faculty of Science, Department of Zoology.
    Utter, Fred
    Ryman, Nils
    Stockholm University, Faculty of Science, Department of Zoology.
    The genetic structure of harbour porpoise in the Baltic Sea relative to adjacent waters remains to be clarified: a reply to Berggren & Wang2008In: Oryx, ISSN 0030-6053, E-ISSN 1365-3008, Vol. 42, no 4, p. 490-490Article in journal (Refereed)
  • 49.
    Palmé, Anna
    et al.
    Stockholm University, Faculty of Science, Department of Zoology, Population Genetics.
    Wennerström, Lovisa
    Stockholm University, Faculty of Science, Department of Zoology, Population Genetics.
    Guban, Peter
    Laikre, Linda
    Stockholm University, Faculty of Science, Department of Zoology, Population Genetics.
    Stopping compensatory releases of salmon in the Baltic Sea. Good or bad for Baltic salmon gene pools?: Report from the Baltic Salmon 2012 symposium and workshop, Stockholm university February 9-102012Report (Other academic)
  • 50.
    Palmé, Anna
    et al.
    Stockholm University, Faculty of Science, Department of Zoology, Population Genetics.
    Wennerström, Lovisa
    Stockholm University, Faculty of Science, Department of Zoology, Population Genetics.
    Guban, Peter
    Ryman, Nils
    Stockholm University, Faculty of Science, Department of Zoology, Population Genetics.
    Laikre, Linda
    Stockholm University, Faculty of Science, Department of Zoology, Population Genetics.
    Compromising Baltic salmon genetic diversity: Conservation genetic risks associated with compensatory releases of salmon in the Baltic Sea2012Report (Other academic)
12 1 - 50 of 61
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