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  • 1. Allendorf, Fred
    et al.
    Ryman, Nils
    Stockholm University, Faculty of Science, Department of Zoology.
    The role of genetics in population viability analysis2002In: Population Viability Analysis / [ed] Beissinger,S.R. and McCullough,D.R., Chicago: University of Chicago Press , 2002, p. 50-85Chapter in book (Other academic)
  • 2. Allendorf, Fred W.
    et al.
    Berry, Oliver
    Ryman, Nils
    Stockholm University, Faculty of Science, Department of Zoology.
    So long to genetic diversity, and thanks for all the fish2014In: Molecular Ecology, ISSN 0962-1083, E-ISSN 1365-294X, Vol. 23, no 1, p. 23-25Article in journal (Refereed)
    Abstract [en]

    The world faces a global fishing crisis. Wild marine fisheries comprise nearly 15% of all animal protein in the human diet, but, according to the U.N. Food and Agriculture Organization, nearly 60% of all commercially important marine fish stocks are overexploited, recovering, or depleted (FAO 2012; Fig. 1). Some authors have suggested that the large population sizes of harvested marine fish make even collapsed populations resistant to the loss of genetic variation by genetic drift (e. g. Beverton 1990). In contrast, others have argued that the loss of alleles because of overfishing may actually be more dramatic in large populations than in small ones (Ryman et al. 1995). In this issue, Pinsky & Palumbi (2014) report that overfished populations have approximately 2% lower heterozygosity and 12% lower allelic richness than populations that are not overfished. They also performed simulations which suggest that their estimates likely underestimate the actual loss of rare alleles by a factor of three or four. This important paper shows that the harvesting of marine fish can have genetic effects that threaten the long-term sustainability of this valuable resource.

  • 3. Allendorf, Fred W
    et al.
    England, Phillip R
    Luikart, Gordon
    Ritchie, Peter A
    Ryman, Nils
    Stockholm University, Faculty of Science, Department of Zoology.
    Genetic effects of harvest on wild animal populations.2008In: Trends Ecol Evol, ISSN 0169-5347, Vol. 23, no 6, p. 327-37Article in journal (Refereed)
    Abstract [en]

    Human harvest of animals in the wild occurs in terrestrial and aquatic habitats throughout the world and is often intense. Harvest has the potential to cause three types of genetic change: alteration of population subdivision, loss of genetic variation, and selective genetic changes. To sustain the productivity of harvested populations, it is crucial to incorporate genetic considerations into management. Nevertheless, it is not necessary to disentangle genetic and environmental causes of phenotypic changes to develop management plans for individual species. We recommend recognizing that some genetic change due to harvest is inevitable. Management plans should be developed by applying basic genetic principles combined with molecular genetic monitoring to minimize harmful genetic change.

  • 4.
    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.

  • 5.
    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.

  • 6. 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.

  • 7. 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.

  • 8. Bekkevold, D.
    et al.
    Clausen, L. A. W
    Mariani, S.
    Andre, C.
    Hatfield, E. M. C.
    Torstensen, E.
    Ryman, Nils
    Stockholm University, Faculty of Science, Department of Zoology, Population Genetics.
    Carvalho, G. R
    Ruzzante, D. E.
    Genetic mixed-stock analysis of Atlantic herring populations in a mixed feeding area2011In: Marine Ecology Progress Series, ISSN 0171-8630, E-ISSN 1616-1599, Vol. 442, p. 187-199Article in journal (Refereed)
    Abstract [en]

     Determining spatio-temporal distributions of fish populations is of interest to marine ecology, in general, and to fisheries science in particular. Genetic mixed-stock analysis is routinely applied in several anadromous fishes for determining migratory routes and timing but has rarely been used for marine fishes, for which population differentiation is commonly weak and the method presumably less powerful. We used microsatellite information for Northeast Atlantic herring Clupea harengus L. populations and mixed stocks to address 2 questions. We used simulated mixture samples and 3 different statistical approaches to determine whether mixed stock composition could be determined with accuracy. Simulations showed that the applied approaches and mixture samples of 100 individuals enabled detailed composition analyses on a regional level, with resolution for tracing the ecologically dominant Rügen (Greifswalder Bodden) herring population. We then estimated spatio-temporal variation in herring migratory behaviour in the Skagerrak from 17 mixed samples collected over 2 seasons and 2 yr, and identified hitherto undescribed differences in distributions among populations that feed and winter in the area.

  • 9.
    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.

  • 10.
    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.

  • 11.
    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

  • 12.
    Hössjer, Ola
    et al.
    Stockholm University, Faculty of Science, Department of Mathematics.
    Jorde, Per Erik
    Ryman, Nils
    Stockholm University, Faculty of Science, Department of Zoology.
    Quasi equilibrium approximations of the fixation index under neutrality: The finite and infinite island models2013In: Theoretical Population Biology, ISSN 0040-5809, E-ISSN 1096-0325, Vol. 84, p. 9-24Article in journal (Refereed)
    Abstract [en]

    The fixation index FST and the coefficient of gene differentiation GST are analyzed for the finite island model under short time spans, ignoring mutations. Dividing the reproduction cycle into the three steps–gamete formation, fertilization, and migration–we develop a new approach for computing quasi equilibrium formulas for FST (and GST). Our formulas generalize earlier ones and reveal that the equilibrium value of FST is influenced not only by the migration rate and local effective population size, Ne, but also by the local census size N, particularly so when the migration rate is high. The order of migration and fertilization is found to have a smaller effect on FST. A major advantage compared to previous approaches is that stochastic allele frequency of migrants is easily accommodated, thereby avoiding underestimation of FST for large migration rates.

  • 13.
    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.

  • 14.
    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.

  • 15.
    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.

  • 16.
    Hössjer, Ola
    et al.
    Stockholm University, Faculty of Science, Department of Mathematics.
    Ryman, Nils
    Stockholm University, Faculty of Science, Department of Genetics, Microbiology and Toxicology.
    Quasi equilibrium, variance effective population size and fixation index for models with spatial structure2012Report (Other academic)
  • 17.
    Hössjer, Ola
    et al.
    Stockholm University, Faculty of Science, Department of Mathematics.
    Ryman, Nils
    Stockholm University, Faculty of Science, Department of Zoology.
    Quasi equilibrium, variance effective size and fixation index for populations with substructure2014In: Journal of Mathematical Biology, ISSN 0303-6812, E-ISSN 1432-1416, Vol. 69, no 5, p. 1057-1128Article in journal (Refereed)
    Abstract [en]

    In this paper, we develop a method for computing the variance effective size , the fixation index and the coefficient of gene differentiation of a structured population under equilibrium conditions. The subpopulation sizes are constant in time, with migration and reproduction schemes that can be chosen with great flexibility. Our quasi equilibrium approach is conditional on non-fixation of alleles. This is of relevance when migration rates are of a larger order of magnitude than the mutation rates, so that new mutations can be ignored before equilibrium balance between genetic drift and migration is obtained. The vector valued time series of subpopulation allele frequencies is divided into two parts; one corresponding to genetic drift of the whole population and one corresponding to differences in allele frequencies among subpopulations. We give conditions under which the first two moments of the latter, after a simple standardization, are well approximated by quantities that can be explicitly calculated. This enables us to compute approximations of the quasi equilibrium values of , and . Our findings are illustrated for several reproduction and migration scenarios, including the island model, stepping stone models and a model where one subpopulation acts as a demographic reservoir. We also make detailed comparisons with a backward approach based on coalescence probabilities.

  • 18. 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.

  • 19. Jorde, Per Erik
    et al.
    Ryman, Nils
    Stockholm University, Faculty of Science, Department of Zoology. Populationsgenetik.
    Unbiased estimator for genetic drift and effective population size2007In: Genetics, Vol. 177, p. 927-935Article in journal (Refereed)
  • 20. Karlsson, Sten
    et al.
    Hagen, Merethe
    Eriksen, Line
    Hindar, Kjetil
    Jensen, Arne J.
    de Leaniz, Carlos Garcia
    Cotter, Deirdre
    Guðbergsson, Guðni
    Kahilainen, Kimmo
    Guðjónsson, Sigurður
    Romakkaniemi, Atso
    Ryman, Nils
    Stockholm University, Faculty of Science, Department of Zoology.
    A genetic marker for the maternal identification of Atlantic salmon x brown trout hybrids2013In: Conservation Genetics Resources, ISSN 1877-7252, E-ISSN 1877-7260, Vol. 5, no 1, p. 47-49Article in journal (Refereed)
    Abstract [en]

    Interspecific hybridization between Atlantic salmon and brown trout is well documented, but why it should vary so much among populations is not clear. Determining the maternal origin of hybrids can provide insights into the mechanisms underlying interspecific hybridization, but this information is lacking in many studies. Here we present a species-specific mitochondrial DNA marker for the identification of the maternal origin of hybrids. This marker involves only one PCR step followed by fragment analysis, can be integrated within PCR multiplexing for existing nuclear markers for hybrid identification, and is therefore faster and more cost-effective than previous methods.

  • 21.
    Kurland, Sara
    et al.
    Stockholm University, Faculty of Science, Department of Zoology.
    Wheat, Christopher W.
    Stockholm University, Faculty of Science, Department of Zoology.
    Celorio Mancera, Maria de la Paz
    Stockholm University, Faculty of Science, Department of Zoology.
    Kutschera, Verena E.
    Stockholm University, Science for Life Laboratory (SciLifeLab). Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics.
    Hill, Jason
    Stockholm University, Faculty of Science, Department of Zoology.
    Andersson, Anastasia
    Stockholm University, Faculty of Science, Department of Zoology.
    Rubin, Carl-Johan
    Andersson, Leif
    Ryman, Nils
    Stockholm University, Faculty of Science, Department of Zoology.
    Laikre, Linda
    Stockholm University, Faculty of Science, Department of Zoology.
    Exploring a Pool-seq-only approach for gaining population genomic insights in nonmodel species2019In: Ecology and Evolution, ISSN 2045-7758, E-ISSN 2045-7758, Vol. 9, p. 11448-11463Article in journal (Refereed)
    Abstract [en]

    Developing genomic insights is challenging in nonmodel species for which resources are often scarce and prohibitively costly. Here, we explore the potential of a recently established approach using Pool-seq data to generate a de novo genome assembly for mining exons, upon which Pool-seq data are used to estimate population divergence and diversity. We do this for two pairs of sympatric populations of brown trout (Salmo trutta): one naturally sympatric set of populations and another pair of populations introduced to a common environment. We validate our approach by comparing the results to those from markers previously used to describe the populations (allozymes and individual-based single nucleotide polymorphisms [SNPs]) and from mapping the Pool-seq data to a reference genome of the closely related Atlantic salmon (Salmo salar). We find that genomic differentiation (F-ST) between the two introduced populations exceeds that of the naturally sympatric populations (F-ST = 0.13 and 0.03 between the introduced and the naturally sympatric populations, respectively), in concordance with estimates from the previously used SNPs. The same level of population divergence is found for the two genome assemblies, but estimates of average nucleotide diversity differ (pi over bar approximate to 0.002 and pi over bar approximate to 0.001 when mapping to S. trutta and S. salar, respectively), although the relationships between population values are largely consistent. This discrepancy might be attributed to biases when mapping to a haploid condensed assembly made of highly fragmented read data compared to using a high-quality reference assembly from a divergent species. We conclude that the Pool-seq-only approach can be suitable for detecting and quantifying genome-wide population differentiation, and for comparing genomic diversity in populations of nonmodel species where reference genomes are lacking.

  • 22. 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)
  • 23.
    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.

  • 24.
    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.

  • 25.
    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.

  • 26.
    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.

  • 27.
    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.

  • 28.
    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.

  • 29.
    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)
  • 30.
    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.

  • 31. 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.

  • 32. Lamichhaney, Sangeet
    et al.
    Fuentes-Pardo, Angela P.
    Rafati, Nima
    Ryman, Nils
    Stockholm University, Faculty of Science, Department of Zoology.
    McCracken, Gregory R.
    Bourne, Christina
    Singh, Rabindra
    Ruzzante, Daniel E.
    Andersson, Leif
    Parallel adaptive evolution of geographically distant herring populations on both sides of the North Atlantic Ocean2017In: Proceedings of the National Academy of Sciences of the United States of America, ISSN 0027-8424, E-ISSN 1091-6490, Vol. 114, no 17, p. E3452-E3461Article in journal (Refereed)
    Abstract [en]

    Atlantic herring is an excellent species for studying the genetic basis of adaptation in geographically distant populations because of its characteristically large population sizes and low genetic drift. In this study we compared whole-genome resequencing data of Atlantic herring populations from both sides of the Atlantic Ocean. An important finding was the very low degree of genetic differentiation among geographically distant populations (fixation index = 0.026), suggesting lack of reproductive isolation across the ocean. This feature of the Atlantic herring facilitates the detection of genetic factors affecting adaptation because of the sharp contrast between loci showing genetic differentiation resulting from natural selection and the low background noise resulting from genetic drift. We show that genetic factors associated with timing of reproduction are shared between genetically distinct and geographically distant populations. The genes for thyroid-stimulating hormone receptor (TSHR), the SOX11 transcription factor (SOX11), calmodulin (CALM), and estrogen receptor 2 (ESR2A), all with a significant role in reproductive biology, were among the loci that showed the most consistent association with spawning time throughout the species range. In fact, the same two SNPs located at the 5' end of TSHR showed the most significant association with spawning time in both the east and west Atlantic. We also identified unexpected haplotype sharing between spring-spawning oceanic herring and autumn-spawning populations across the Atlantic Ocean and the Baltic Sea. The genomic regions showing this pattern are unlikely to control spawning time but may be involved in adaptation to ecological factor(s) shared among these populations.

  • 33.
    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.

  • 34.
    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.

  • 35.
    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

  • 36.
    Luikart, Gordon
    et al.
    University of Montana.
    Ryman, Nils
    Stockholm University, Faculty of Science, Department of Zoology. Stockholm University, Faculty of Science, Department of Zoology, Population Genetics.
    Tallmon, David A.
    University of Alaska.
    Schwartz, Michael K.
    USDA Forest Service.
    Allendorf, Fred W.
    7.Victoria University of Wellington School of Biological Sciences.
    Estimation of census and effective population sizes  : the increasing usefulness of DNA-based approaches2010In: Conservation Genetics, ISSN 1566-0621, E-ISSN 1572-9737, Vol. 11, p. 355-373Article in journal (Refereed)
    Abstract [en]

    Population census size (N C) and effective population sizes (N e) are two crucial parameters that influence population viability, wildlife management decisions, and conservation planning. Genetic estimators of both N C and N e are increasingly widely used because molecular markers are increasingly available, statistical methods are improving rapidly, and genetic estimators complement or improve upon traditional demographic estimators. We review the kinds and applications of estimators of both N C and N e, and the often undervalued and misunderstood ratio of effective-to-census size (N e /N C). We focus on recently improved and well evaluated methods that are most likely to facilitate conservation. Finally, we outline areas of future research to improve N e and N C estimation in wild populations

  • 37. Neel, M. C.
    et al.
    McKelvey, K.
    Ryman, Nils
    Stockholm University, Faculty of Science, Department of Zoology.
    Lloyd, M. W.
    Bull, R. Short
    Allendorf, F. W.
    Schwartz, M. K.
    Waples, R. S.
    Estimation of effective population size in continuously distributed populations: there goes the neighborhood2013In: Heredity, ISSN 0018-067X, E-ISSN 1365-2540, Vol. 111, no 3, p. 189-199Article in journal (Refereed)
    Abstract [en]

    Use of genetic methods to estimate effective population size (N-e) is rapidly increasing, but all approaches make simplifying assumptions unlikely to be met in real populations. In particular, all assume a single, unstructured population, and none has been evaluated for use with continuously distributed species. We simulated continuous populations with local mating structure, as envisioned by Wright's concept of neighborhood size (NS), and evaluated performance of a single-sample estimator based on linkage disequilibrium (LD), which provides an estimate of the effective number of parents that produced the sample (N-b). Results illustrate the interacting effects of two phenomena, drift and mixture, that contribute to LD. Samples from areas equal to or smaller than a breeding window produced estimates close to the NS. As the sampling window increased in size to encompass multiple genetic neighborhoods, mixture LD from a two-locus Wahlund effect overwhelmed the reduction in drift LD from incorporating offspring from more parents. As a consequence, (N) over cap (b) never approached the global N-e, even when the geographic scale of sampling was large. Results indicate that caution is needed in applying standard methods for estimating effective size to continuously distributed populations.

  • 38.
    Nyström, Veronica
    et al.
    Stockholm University, Faculty of Science, Department of Zoology.
    Dalén, Love
    Stockholm University, Faculty of Science, Department of Zoology.
    Vartanyan, Sergey
    Department of Geography, Herzen University, nab. Moyki, 48, St Petersburg.
    Lidén, Kerstin
    Stockholm University, Faculty of Humanities, Department of Archaeology and Classical Studies.
    Ryman, Nils
    Stockholm University, Faculty of Science, Department of Zoology.
    Angerbjörn, Anders
    Stockholm University, Faculty of Science, Department of Zoology.
    Temporal genetic change in the last remaining population of woolly mammoth2010In: Proceedings of the Royal Society of London. Biological Sciences, ISSN 0962-8452, E-ISSN 1471-2954, Vol. 277, no 1692, p. 2331-2337Article in journal (Refereed)
    Abstract [en]

    During the Late Pleistocene, the woolly mammoth (Mammuthus primigenius) experienced a series of local extinctions generally attributed to human predation or environmental change. Some small and isolated populations did however survive far into the Holocene. Here, we investigated the genetic consequences of the isolation of the last remaining mammoth population on Wrangel Island. We analysed 741 bp of the mitochondrial DNA and found a loss of genetic variation in relation to the isolation event, probably caused by a demographic bottleneck or a founder event. However, in spite of ca 5000 years of isolation, we did not detect any further loss of genetic variation. Together with the relatively high number of mitochondrial haplotypes on Wrangel Island near the final disappearance, this suggests a sudden extinction of a rather stable population.

  • 39.
    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.

  • 40.
    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.

  • 41.
    Olsson, Jens
    et al.
    Stockholm University, Faculty of Science, Department of Zoology. Swedish University of Agricultural Sciences, Sweden.
    Florin, A. B.
    Mo, K.
    Aho, T.
    Ryman, Nils
    Stockholm University, Faculty of Science, Department of Zoology.
    Genetic structure of whitefish (Coregonus maraena) in the Baltic Sea2012In: Eustarine, Coastal and Shelf Science, ISSN 0272-7714, Vol. 97, p. 104-113Article in journal (Refereed)
    Abstract [en]

    Stocks of whitefish (Coregonus maraena) in the northern part of the Baltic Sea have in many areas declined drastically during recent years. Causes for the decline are yet not fully understood, but knowledge on the genetic population structure of the species is pivotal for future conservation measures. In this study we analyse the genetic variation at seven microsatellite loci for whitefish from 18 different sites along the Swedish coast of the Baltic Sea. We found a strong dependence of isolation by distance (R = 0.73), and a week but rather fine scaled genetic structure. In addition, there were differences between more northern and southern sites in the population genetic structure, where the degree of differentiation appears to be stronger in the north compared to the south. The results suggest that whitefish is a species suitable for local management with a regional context of the management strategy. In addition, the findings corroborate what is previously known for other coastal fish species in the Baltic Sea, such as perch and pike, suggesting that the majority of gene flow occurs between adjacent areas. Finally, our results highlight the potential for genetic subdivision even when the dependence of isolation by distance is strong.

  • 42.
    Olsson, Jens
    et al.
    Stockholm University, Faculty of Science, Department of Zoology, Population Genetics.
    Mo, K.
    Florin, A. B.
    Aho, T.
    Ryman, Nils
    Stockholm University, Faculty of Science, Department of Zoology.
    Genetic population structure of perch Perca fluviatilis along the Swedish coast of the Baltic Sea2011In: Journal of Fish Biology, ISSN 0022-1112, E-ISSN 1095-8649, Vol. 79, no 1, p. 122-137Article in journal (Refereed)
    Abstract [en]

    In this study, the genetic variation of perch Perca fluviatilis from 18 different sites along the Swedish coast of the Baltic Sea was assessed. There was a relative strong support for isolation by distance and the results suggest an overall departure from panmixia. The level of genetic divergence was moderate (global FST = 0·04) and indications of differences in the population genetic structure between the two major basins (central Baltic Sea and Gulf of Bothnia) in the Baltic Sea were found. There was a higher level of differentiation in the central Baltic Sea compared to the Gulf of Bothnia, and the results suggest that stretches of deep water might act as barriers to gene flow in the species. On the basis of the estimation of genetic patch size, the results corroborate previous mark–recapture studies and suggest that this is a species suitable for local management. In all, the findings of this study emphasize the importance of considering regional differences even when strong isolation by distance characterize the genetic population structure of species.

  • 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, 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.

  • 45.
    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)
  • 46.
    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.

  • 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.
    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)
  • 48.
    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)
  • 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
    Ryman, Nils
    Stockholm University, Faculty of Science, Department of Zoology, Population Genetics.
    Laikre, Linda
    Stockholm University, Faculty of Science, Department of Zoology, Population Genetics.
    Conclusions on conservation genetic risks associated with compensatory releases of salmon in the Baltic Sea.: A brief summary of a synthesis report to the Swedish Agency for Marine and Water Management.2012Report (Other academic)
  • 50.
    Ryman, Nils
    et al.
    Stockholm University, Faculty of Science, Department of Zoology.
    Laikre, Linda
    Stockholm University, Faculty of Science, Department of Zoology.
    Hössjer, Ola
    Stockholm University, Faculty of Science, Department of Mathematics.
    Do estimates of contemporary effective population size tell us what we want to know?2019In: Molecular Ecology, ISSN 0962-1083, E-ISSN 1365-294X, Vol. 28, no 8, p. 1904-1918Article in journal (Refereed)
    Abstract [en]

    Estimation of effective population size (N-e) from genetic marker data is a major focus for biodiversity conservation because it is essential to know at what rates inbreeding is increasing and additive genetic variation is lost. But are these the rates assessed when applying commonly used N-e estimation techniques? Here we use recently developed analytical tools and demonstrate that in the case of substructured populations the answer is no. This is because the following: Genetic change can be quantified in several ways reflecting different types of N-e such as inbreeding (N-eI), variance (N-eV), additive genetic variance (N-eAV), linkage disequilibrium equilibrium (N-eLD), eigenvalue (N-eE) and coalescence (N-eCo) effective size. They are all the same for an isolated population of constant size, but the realized values of these effective sizes can differ dramatically in populations under migration. Commonly applied N-e-estimators target N-eV or N(eLD )of individual subpopulations. While such estimates are safe proxies for the rates of inbreeding and loss of additive genetic variation under isolation, we show that they are poor indicators of these rates in populations affected by migration. In fact, both the local and global inbreeding (N-eI) and additive genetic variance (N-eAV) effective sizes are consistently underestimated in a subdivided population. This is serious because these are the effective sizes that are relevant to the widely accepted 50/500 rule for short and long term genetic conservation. The bias can be infinitely large and is due to inappropriate parameters being estimated when applying theory for isolated populations to subdivided ones.

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