Change search
Refine search result
12 1 - 50 of 88
CiteExportLink to result list
Permanent link
Cite
Citation style
  • apa
  • ieee
  • modern-language-association-8th-edition
  • vancouver
  • Other style
More styles
Language
  • de-DE
  • en-GB
  • en-US
  • fi-FI
  • nn-NO
  • nn-NB
  • sv-SE
  • Other locale
More languages
Output format
  • html
  • text
  • asciidoc
  • rtf
Rows per page
  • 5
  • 10
  • 20
  • 50
  • 100
  • 250
Sort
  • Standard (Relevance)
  • Author A-Ö
  • Author Ö-A
  • Title A-Ö
  • Title Ö-A
  • Publication type A-Ö
  • Publication type Ö-A
  • Issued (Oldest first)
  • Issued (Newest first)
  • Created (Oldest first)
  • Created (Newest first)
  • Last updated (Oldest first)
  • Last updated (Newest first)
  • Disputation date (earliest first)
  • Disputation date (latest first)
  • Standard (Relevance)
  • Author A-Ö
  • Author Ö-A
  • Title A-Ö
  • Title Ö-A
  • Publication type A-Ö
  • Publication type Ö-A
  • Issued (Oldest first)
  • Issued (Newest first)
  • Created (Oldest first)
  • Created (Newest first)
  • Last updated (Oldest first)
  • Last updated (Newest first)
  • Disputation date (earliest first)
  • Disputation date (latest first)
Select
The maximal number of hits you can export is 250. When you want to export more records please use the Create feeds function.
  • 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, Population Genetics.
    Karlsson, Sten
    Ryman, Nils
    Stockholm University, Faculty of Science, Department of Zoology, Population Genetics.
    Laikre, Linda
    Stockholm University, Faculty of Science, Department of Zoology, Population Genetics.
    Mapping and monitoring genetic diversity in brown trout population systems in alpine lakes by applying newly proposed indicatorsManuscript (preprint) (Other academic)
  • 4.
    Andersson, Anastasia
    et al.
    Stockholm University, Faculty of Science, Department of Zoology, Population Genetics.
    Karlsson, Sten
    Ryman, Nils
    Stockholm University, Faculty of Science, Department of Zoology, Population Genetics.
    Laikre, Linda
    Stockholm University, Faculty of Science, Department of Zoology, Population Genetics.
    Monitoring genetic diversity with new indicators applied to an alpine freshwater top predator2022In: Molecular Ecology, ISSN 0962-1083, E-ISSN 1365-294X, Vol. 31, no 24, p. 6422-6439Article in journal (Refereed)
    Abstract [en]

    Genetic diversity is the basis for population adaptation and long-term survival, yet rarely considered in biodiversity monitoring. One key issue is the need for useful and straightforward indicators of genetic diversity. We monitored genetic diversity over 40 years (1970–2010) in metapopulations of brown trout (Salmo trutta) inhabiting 27 small mountain lakes representing 10 lake systems in central Sweden using >1200 fish per time point. We tested six newly proposed indicators; three were designed for broad, international use in the UN Convention on Biological Diversity (CBD) and are currently applied in several countries. The other three were recently elaborated for national use by a Swedish science-management effort and applied for the first time here. The Swedish indicators use molecular genetic data to monitor genetic diversity within and between populations (indicators ΔH and ΔFST, respectively) and assess the effective population size (Ne-indicator). We identified 29 genetically distinct populations, all retained over time. Twelve of the 27 lakes harboured more than one population indicating that brown trout biodiversity hidden as cryptic, sympatric populations are more common than recognized. The Ne indicator showed values below the threshold (Ne ≤ 500) in 20 populations with five showing Ne < 100. Statistically significant genetic diversity reductions occurred in several populations. Metapopulation structure appears to buffer against diversity loss; applying the indicators to metapopulations suggest mostly acceptable rates of change in all but one system. The CBD indicators agreed with the Swedish ones but provided less detail. All these indicators are appropriate for managers to initiate monitoring of genetic biodiversity. 

  • 5.
    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.

  • 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. 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.

  • 8. 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.

  • 9. Bertola, Laura D.
    et al.
    Brueniche-Olsen, Anna
    Kershaw, Francine
    Russo, Isa-Rita M.
    Macdonald, Anna J.
    Sunnucks, Paul
    Bruford, Michael W.
    Cadena, Carlos Daniel
    Ewart, Kyle M.
    de Bruyn, Mark
    Eldridge, Mark D. B.
    Frankham, Richard
    Guayasamin, Juan M.
    Grueber, Catherine E.
    Hoareau, Thierry B.
    Hoban, Sean
    Hohenlohe, Paul A.
    Hunter, Margaret E.
    Kotze, Antoinette
    Kuja, Josiah
    Lacy, Robert C.
    Laikre, Linda
    Stockholm University, Faculty of Science, Department of Zoology, Population Genetics.
    Lo, Nathan
    Meek, Mariah H.
    Mergeay, Joachim
    Mittan-Moreau, Cinnamon
    Neaves, Linda E.
    O'Brien, David
    Ochieng, Joel W.
    Ogden, Rob
    Orozco-terWengel, Pablo
    Paez-Vacas, Monica
    Pierson, Jennifer
    Ralls, Katherine
    Shaw, Robyn E.
    Sogbohossou, Etotepe A.
    Stow, Adam
    Steeves, Tammy
    Vernesi, Cristiano
    Watsa, Mrinalini
    Segelbacher, Gernot
    A pragmatic approach for integrating molecular tools into biodiversity conservation2024In: Conservation science and practice, ISSN 2578-4854, Vol. 6, no 1, article id e13053Article in journal (Refereed)
    Abstract [en]

    Molecular tools are increasingly applied for assessing and monitoring biodiversity and informing conservation action. While recent developments in genetic and genomic methods provide greater sensitivity in analysis and the capacity to address new questions, they are not equally available to all practitioners: There is considerable bias across institutions and countries in access to technologies, funding, and training. Consequently, in many cases, more accessible traditional genetic data (e.g., microsatellites) are still utilized for making conservation decisions. Conservation approaches need to be pragmatic by tackling clearly defined management questions and using the most appropriate methods available, while maximizing the use of limited resources. Here we present some key questions to consider when applying the molecular toolbox for accessible and actionable conservation management. Finally, we highlight a number of important steps to be addressed in a collaborative way, which can facilitate the broad integration of molecular data into conservation. Molecular tools are increasingly applied in conservation management; however, they are not equally available to all practitioners. We here provide key questions when establishing a conservation genetic study and highlight important steps which need to be addressed when these tools are globally applied.image

  • 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 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.

  • 11.
    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.

  • 12.
    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

  • 13.
    Dussex, Nicolas
    et al.
    Stockholm University, Faculty of Science, Department of Zoology. Centre for Palaeogenetics, Sweden; Swedish Museum of Natural History, Sweden.
    Alberti, Federica
    Heino, Matti T.
    Olsen, Remi-André
    Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics. Stockholm University, Science for Life Laboratory (SciLifeLab).
    van der Valk, Tom
    Ryman, Nils
    Stockholm University, Faculty of Science, Department of Zoology.
    Laikre, Linda
    Stockholm University, Faculty of Science, Department of Zoology.
    Ahlgren, Hans
    Stockholm University, Faculty of Humanities, Department of Archaeology and Classical Studies.
    Askeyev, Igor
    Askeyev, Oleg
    Shaymuratova, Dilyara N.
    Askeyev, Arthur O.
    Döppes, Doris
    Friedrich, Ronny
    Lindauer, Susanne
    Rosendahl, Wilfried
    Aspi, Jouni
    Hofreiter, Michael
    Lidén, Kerstin
    Stockholm University, Faculty of Humanities, Department of Archaeology and Classical Studies.
    Dalén, Love
    Díez-del-Molino, David
    Stockholm University, Faculty of Science, Department of Zoology. Centre for Palaeogenetics, Sweden; Swedish Museum of Natural History, Sweden.
    Moose genomes reveal past glacial demography and the origin of modern lineages2020In: BMC Genomics, E-ISSN 1471-2164, Vol. 21, no 1, article id 854Article in journal (Refereed)
    Abstract [en]

    Background: Numerous megafauna species from northern latitudes went extinct during the Pleistocene/Holocene transition as a result of climate-induced habitat changes. However, several ungulate species managed to successfully track their habitats during this period to eventually flourish and recolonise the holarctic regions. So far, the genomic impacts of these climate fluctuations on ungulates from high latitudes have been little explored. Here, we assemble a de-novo genome for the European moose (Alces alces) and analyse it together with re-sequenced nuclear genomes and ancient and modern mitogenomes from across the moose range in Eurasia and North America.

    Results: We found that moose demographic history was greatly influenced by glacial cycles, with demographic responses to the Pleistocene/Holocene transition similar to other temperate ungulates. Our results further support that modern moose lineages trace their origin back to populations that inhabited distinct glacial refugia during the Last Glacial Maximum (LGM). Finally, we found that present day moose in Europe and North America show low to moderate inbreeding levels resulting from post-glacial bottlenecks and founder effects, but no evidence for recent inbreeding resulting from human-induced population declines.

    Conclusions: Taken together, our results highlight the dynamic recent evolutionary history of the moose and provide an important resource for further genomic studies.

  • 14.
    Dussex, Nicolas
    et al.
    Stockholm University, Faculty of Science, Department of Zoology, Population Genetics. Centre for Palaeogenetics, Sweden; Swedish Museum of Natural History, Sweden; Norwegian University of Science and Technology, Sweden.
    Kurland, Sara
    Stockholm University, Faculty of Science, Department of Zoology, Population Genetics. Stockholm Univ, Dept Zool, Div Populat Genet, SE-10691 Stockholm, Sweden.
    Olsen, Remi-André
    Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics. Stockholm University, Science for Life Laboratory (SciLifeLab).
    Spong, Göran
    Ericsson, Göran
    Ekblom, Robert
    Ryman, Nils
    Stockholm University, Faculty of Science, Department of Zoology, Population Genetics.
    Dalén, Love
    Stockholm University, Faculty of Science, Department of Zoology, Population Genetics. Centre for Palaeogenetics, Sweden; Swedish Museum of Natural History, Sweden.
    Laikre, Linda
    Stockholm University, Faculty of Science, Department of Zoology, Population Genetics.
    Range-wide and temporal genomic analyses reveal the consequences of near-extinction in Swedish moose2023In: Communications Biology, E-ISSN 2399-3642, Vol. 6, no 1, article id 1035Article in journal (Refereed)
    Abstract [en]

    Ungulate species have experienced severe declines over the past centuries through overharvesting and habitat loss. Even if many game species have recovered thanks to strict hunting regulation, the genome-wide impacts of overharvesting are still unclear. Here, we examine the temporal and geographical differences in genome-wide diversity in moose (Alces alces) over its whole range in Sweden by sequencing 87 modern and historical genomes. We found limited impact of the 1900s near-extinction event but local variation in inbreeding and load in modern populations, as well as suggestion of a risk of future reduction in genetic diversity and gene flow. Furthermore, we found candidate genes for local adaptation, and rapid temporal allele frequency shifts involving coding genes since the 1980s, possibly due to selective harvesting. Our results highlight that genomic changes potentially impacting fitness can occur over short time scales and underline the need to track both deleterious and selectively advantageous genomic variation.

  • 15.
    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.

  • 16. Hill, Jason
    et al.
    Enbody, Erik D.
    Pettersson, Mats E.
    Sprehn, C. Grace
    Bekkevold, Dorte
    Folkvord, Arild
    Laikre, Linda
    Stockholm University, Faculty of Science, Department of Zoology.
    Kleinau, Gunnar
    Scheerer, Patrick
    Andersson, Leif
    Recurrent convergent evolution at amino acid residue 261 in fish rhodopsin2019In: Proceedings of the National Academy of Sciences of the United States of America, ISSN 0027-8424, E-ISSN 1091-6490, Vol. 116, no 37, p. 18473-18478Article in journal (Refereed)
    Abstract [en]

    The evolutionary process that occurs when a species colonizes a new environment provides an opportunity to explore the mechanisms underlying genetic adaptation, which is essential knowledge for understanding evolution and the maintenance of biodiversity. Atlantic herring has an estimated total breeding stock of about 1 trillion (10(12)) and has colonized the brackish Baltic Sea within the last 10,000 y. Minute genetic differentiation between Atlantic and Baltic herring populations at selectively neutral loci combined with this rapid adaptation to a new environment facilitated the identification of hundreds of loci underlying ecological adaptation. A major question in the field of evolutionary biology is to what extent such an adaptive process involves selection of novel mutations with large effects or genetic changes at many loci, each with a small effect on phenotype (i.e., selection on standing genetic variation). Here we show that a missense mutation in rhodopsin (Phe261Tyr) is an adaptation to the red-shifted Baltic Sea light environment. The transition from phenylalanine to tyrosine differs only by the presence of a hydroxyl moiety in the latter, but this results in an up to 10-nm red-shifted light absorbance of the receptor. Remarkably, an examination of the rhodopsin sequences from 2,056 species of fish revealed that the same missense mutation has occurred independently and been selected for during at least 20 transitions between light environments across all fish. Our results provide a spectacular example of convergent evolution and how a single amino acid change can have a major effect on ecological adaptation.

  • 17. Hoban, Sean
    et al.
    Bruford, Michael
    D'Urban Jackson, Josephine
    Lopes-Fernandes, Margarida
    Heuertz, Myriam
    Hohenlohe, Paul A.
    Paz-Vinas, Ivan
    Sjögren-Gulve, Per
    Segelbacher, Gernot
    Vernesi, Cristiano
    Aitken, Sally
    Bertola, Laura D.
    Bloomer, Paulette
    Breed, Martin
    Rodríguez-Correa, Hernando
    Funk, W. Chris
    Grueber, Catherine E.
    Hunter, Margaret E.
    Jaffe, Rodolfo
    Liggins, Libby
    Mergeay, Joachim
    Moharrek, Farideh
    O'Brien, David
    Ogden, Rob
    Palma-Silva, Clarisse
    Pierson, Jennifer
    Ramakrishnan, Uma
    Simo-Droissart, Murielle
    Tani, Naoki
    Waits, Lisette
    Laikre, Linda
    Stockholm University, Faculty of Science, Department of Zoology.
    Genetic diversity targets and indicators in the CBD post-2020 Global Biodiversity Framework must be improved2020In: Biological Conservation, ISSN 0006-3207, E-ISSN 1873-2917, Vol. 248, article id 108654Article in journal (Refereed)
    Abstract [en]

    The 196 parties to the Convention on Biological Diversity (CBD) will soon agree to a post-2020 global framework for conserving the three elements of biodiversity (genetic, species, and ecosystem diversity) while ensuring sustainable development and benefit sharing. As the most significant global conservation policy mechanism, the new CBD framework has far-reaching consequences- it will guide conservation actions and reporting for each member country until 2050. In previous CBD strategies, as well as other major conservation policy mechanisms, targets and indicators for genetic diversity (variation at the DNA level within species, which facilitates species adaptation and ecosystem function) were undeveloped and focused on species of agricultural relevance. We assert that, to meet global conservation goals, genetic diversity within all species, not just domesticated species and their wild relatives, must be conserved and monitored using appropriate metrics. Building on suggestions in a recent Letter in Science (Laikre et al., 2020) we expand argumentation for three new, pragmatic genetic indicators and modifications to two current indicators for maintaining genetic diversity and adaptive capacity of all species, and provide guidance on their practical use. The indicators are: 1) the number of populations with effective population size above versus below 500, 2) the proportion of populations maintained within species, 3) the number of species and populations in which genetic diversity is monitored using DNA-based methods. We also present and discuss Goals and Action Targets for post-2020 biodiversity conservation which are connected to these indicators and underlying data. These pragmatic indicators and goals have utility beyond the CBD; they should benefit conservation and monitoring of genetic diversity via national and global policy for decades to come.

  • 18. Hoban, Sean
    et al.
    Bruford, Michael W.
    da Silva, Jessica M.
    Funk, W. Chris
    Frankham, Richard
    Gill, Michael J.
    Grueber, Catherine E.
    Heuertz, Myriam
    Hunter, Margaret E.
    Kershaw, Francine
    Lacy, Robert C.
    Lees, Caroline
    Lopes-Fernandes, Margarida
    MacDonald, Anna J.
    Mastretta-Yanes, Alicia
    McGowan, Philip J. K.
    Meek, Mariah H.
    Mergeay, Joachim
    Millette, Katie L.
    Mittan-Moreau, Cinnamon S.
    Navarro, Laetitia M.
    O'Brien, David
    Ogden, Rob
    Segelbacher, Gernot
    Paz-Vinas, Ivan
    Vernesi, Cristiano
    Laikre, Linda
    Stockholm University, Faculty of Science, Department of Zoology.
    Genetic diversity goals and targets have improved, but remain insufficient for clear implementation of the post-2020 global biodiversity framework2023In: Conservation Genetics, ISSN 1566-0621, E-ISSN 1572-9737, Vol. 24, no 2, p. 181-191Article in journal (Refereed)
    Abstract [en]

    Genetic diversity among and within populations of all species is necessary for people and nature to survive and thrive in a changing world. Over the past three years, commitments for conserving genetic diversity have become more ambitious and specific under the Convention on Biological Diversity’s (CBD) draft post-2020 global biodiversity framework (GBF). This Perspective article comments on how goals and targets of the GBF have evolved, the improvements that are still needed, lessons learned from this process, and connections between goals and targets and the actions and reporting that will be needed to maintain, protect, manage and monitor genetic diversity. It is possible and necessary that the GBF strives to maintain genetic diversity within and among populations of all species, to restore genetic connectivity, and to develop national genetic conservation strategies, and to report on these using proposed, feasible indicators.

  • 19. Hoban, Sean
    et al.
    Bruford, Michael W.
    Funk, W. Chris
    Galbusera, Peter
    Griffith, M. Patrick
    Grueber, Catherine E.
    Heuertz, Myriam
    Hunter, Margaret E.
    Hvilsom, Christina
    Kalamujic Stroil, Belma
    Kershaw, Francine
    Khoury, Colin K.
    Laikre, Linda
    Stockholm University, Faculty of Science, Department of Zoology, Population Genetics.
    Lopes-Fernandes, Margarida
    MacDonald, Anna J.
    Mergeay, Joachim
    Meek, Mariah
    Mittan, Cinnamon
    Mukassabi, Tarek A.
    O'Brien, David
    Ogden, Rob
    Palma-Silva, Clarisse
    Ramakrishnan, Uma
    Segelbacher, Gernot
    Shaw, Robyn E.
    Sjögren-Gulve, Per
    Veličković, Nevena
    Vernesi, Cristiano
    Global Commitments to Conserving and Monitoring Genetic Diversity Are Now Necessary and Feasible2021In: BioScience, ISSN 0006-3568, E-ISSN 1525-3244, Vol. 71, no 9, p. 964-976Article in journal (Refereed)
    Abstract [en]

    Global conservation policy and action have largely neglected protecting and monitoring genetic diversity-one of the three main pillars of biodiversity. Genetic diversity (diversity within species) underlies species' adaptation and survival, ecosystem resilience, and societal innovation. The low priority given to genetic diversity has largely been due to knowledge gaps in key areas, including the importance of genetic diversity and the trends in genetic diversity change; the perceived high expense and low availability and the scattered nature of genetic data; and complicated concepts and information that are inaccessible to policymakers. However, numerous recent advances in knowledge, technology, databases, practice, and capacity have now set the stage for better integration of genetic diversity in policy instruments and conservation efforts. We review these developments and explore how they can support improved consideration of genetic diversity in global conservation policy commitments and enable countries to monitor, report on, and take action to maintain or restore genetic diversity.

  • 20. Hoban, Sean
    et al.
    da Silva, Jessica M.
    Mastretta-Yanes, Alicia
    Grueber, Catherine E.
    Heuertz, Myriam
    Hunter, Margaret E.
    Mergeay, Joachim
    Paz-Vinas, Ivan
    Fukaya, Keiichi
    Ishihama, Fumiko
    Jordan, Rebecca
    Köppä, Viktoria
    Stockholm University, Faculty of Science, Department of Zoology, Population Genetics.
    Latorre-Cárdenas, María Camilla
    MacDonald, Anna J.
    Rincon-Parra, Victor
    Sjögren-Gulve, Per
    Tani, Naoki
    Thurfjell, Henrik
    Laikre, Linda
    Stockholm University, Faculty of Science, Department of Zoology, Population Genetics.
    Monitoring status and trends in genetic diversity for the Convention on Biological Diversity: An ongoing assessment of genetic indicators in nine countries2023In: Conservation Letters, ISSN 1755-263X, E-ISSN 1755-263X, Vol. 16, no 3, article id e12953Article in journal (Refereed)
    Abstract [en]

    Recent scientific evidence shows that genetic diversity must be maintained, managed, and monitored to protect biodiversity and nature's contributions to people. Three genetic diversity indicators, two of which do not require DNA-based assessment, have been proposed for reporting to the Convention on Biological Diversity and other conservation and policy initiatives. These indicators allow an approximation of the status and trends of genetic diversity to inform policy, using existing demographic and geographic information. Application of these indicators has been initiated and here we describe ongoing efforts in calculating these indicators with examples. We specifically describe a project underway to apply these indicators in nine countries, provide example calculations, address concerns of policy makers and implementation challenges, and describe a roadmap for further development and deployment, incorporating feedback from the broader community. We also present guidance documents and data collection tools for calculating indicators. We demonstrate that Parties can successfully and cost-effectively report these genetic diversity indicators with existing biodiversity observation data, and, in doing so, better conserve the Earth's biodiversity. 

  • 21.
    Hössjer, Ola
    et al.
    Stockholm University, Faculty of Science, Department of Mathematics.
    Laikre, Linda
    Stockholm University, Faculty of Science, Department of Zoology, Population Genetics.
    Ryman, Nils
    Stockholm University, Faculty of Science, Department of Zoology, Population Genetics.
    Assessment of the Global Variance Effective Size of Subdivided Populations, and Its Relation to Other Effective Sizes2023In: Acta Biotheoretica, ISSN 0001-5342, E-ISSN 1572-8358, Vol. 71, no 3, article id 19Article in journal (Refereed)
    Abstract [en]

    The variance effective population size (N-eV) is frequently used to quantify the expected rate at which a population's allele frequencies change over time. The purpose of this paper is to find expressions for the global N-eV of a spatially structured population that are of interest for conservation of species. Since N-eV depends on allele frequency change, we start by dividing the cause of allele frequency change into genetic drift within subpopulations (I) and a second component mainly due to migration between subpopulations (II). We investigate in detail how these two components depend on the way in which subpopulations are weighted as well as their dependence on parameters of the model such a migration rates, and local effective and census sizes. It is shown that under certain conditions the impact of II is eliminated, and N-eV of the metapopulation is maximized, when subpopulations are weighted proportionally to their long term reproductive contributions. This maximal N-eV is the sought for global effective size, since it approximates the gene diversity effective size N-eGD, a quantifier of the rate of loss of genetic diversity that is relevant for conservation of species and populations. We also propose two novel versions of N-eV, one of which (the backward version of N-eV) is most stable, exists for most populations, and is closer to N-eGD than the classical notion of N-eV. Expressions for the optimal length of the time interval for measuring genetic change are developed, that make it possible to estimate any version of N-eV with maximal accuracy.

  • 22.
    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.

  • 23.
    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.

  • 24.
    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.

  • 25. 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, review/survey (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.

  • 26.
    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.

  • 27.
    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.

  • 28.
    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.

  • 29.
    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, 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.

  • 30.
    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 rates of inbreeding, extensive loss of genetic diversity and lack of correlation 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.

    Download full text (pdf)
    Jansson_etal
  • 31.
    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

    Download full text (pdf)
    fulltext
  • 32. 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.

  • 33. Kershaw, Francine
    et al.
    Bruford, Michael W.
    Funk, W. Chris
    Grueber, Catherine E.
    Hoban, Sean
    Hunter, Margaret E.
    Laikre, Linda
    Stockholm University, Faculty of Science, Department of Zoology, Population Genetics.
    MacDonald, Anna J.
    Meek, Mariah H.
    Mittan, Cinnamon
    O'Brien, David
    Ogden, Rob
    Shaw, Robyn E.
    Vernesi, Cristiano
    Segelbacher, Gernot
    The Coalition for Conservation Genetics: Working across organizations to build capacity and achieve change in policy and practice2022In: Conservation Science and Practice, E-ISSN 2578-4854, Vol. 4, no 4, article id e12635Article in journal (Refereed)
    Abstract [en]

    The Coalition for Conservation Genetics (CCG) brings together four eminent organizations with the shared goal of improving the integration of genetic information into conservation policy and practice. We provide a historical context of conservation genetics as a field and reflect on current barriers to conserving genetic diversity, highlighting the need for collaboration across traditional divides, international partnerships, and coordinated advocacy. We then introduce the CCG and illustrate through examples how a coalition approach can leverage complementary expertise and improve the organizational impact at multiple levels. The CCG has proven particularly successful at implementing large synthesis-type projects, training early-career scientists, and advising policy makers. Achievements to date highlight the potential for the CCG to make effective contributions to practical conservation policy and management that no one “parent” organization could achieve on its own. Finally, we reflect on the lessons learned through forming the CCG, and our vision for the future.

  • 34.
    Kurland, Sara
    et al.
    Stockholm University, Faculty of Science, Department of Zoology, Population Genetics.
    Nils, Ryman
    Ola, Hössjer
    Linda, Laikre
    Effects of subpopulation extinction on effective size (Ne) of metapopulationsManuscript (preprint) (Other academic)
  • 35.
    Kurland, Sara
    et al.
    Stockholm University, Faculty of Science, Department of Zoology, Population Genetics.
    Rafati, Nima
    Nils, Ryman
    Linda, Laikre
    Genomic dynamics of brown trout (Salmo trutta) populations released to a novel environmentManuscript (preprint) (Other academic)
    Abstract [en]

    Population translocations occur for a variety of reasons, from displacement due to climate change, to human-induced transfers. Such actions have adverse effects on genetic variation and understanding their microevolutionary consequences requires monitoring. Here, we return to an experimental release of brown trout (Salmo trutta) in order to monitor genomic effects of population translocations. In 1979, fish from each of two genetically and ecologically separate populations were released at one point in time to the same lake system. Whole-genome sequencing data is used to characterize diversity within and divergence between introduced fish from different source populations and fish inhabiting two lakes down-stream of the release sites, sampled 30 years later (c. 5 generations). Diversity and divergence among introduced populations and fish sampled in the wild c. 5 generations later suggest extensive hybridization. Introduced fish are unequally represented in the lakes down-stream of the release sites, with fish from one population mainly contributing to the lake closest to the release site, and the fish from the other dominating the lake further downstream. We also identify genomic regions putatively under directional selection in the new lake system, where genes from one of the introduced populations, regulating metabolism, appear advantageous. Our results demonstrate that genetic effects of population translocations e.g., establishment, hybridization, and adaptation can be rapid after release into novel environments – even for a species with relatively small local effective population sizes and a large, complex genome. This is an important contribution to understanding the microevolutionary effects population translocations have on intraspecific diversity.  

  • 36.
    Kurland, Sara
    et al.
    Stockholm University, Faculty of Science, Department of Zoology, Population Genetics.
    Rafati, Nima
    Ryman, Nils
    Stockholm University, Faculty of Science, Department of Zoology, Population Genetics.
    Laikre, Linda
    Stockholm University, Faculty of Science, Department of Zoology, Population Genetics.
    Genomic dynamics of brown trout populations released to a novel environment2022In: Ecology and Evolution, E-ISSN 2045-7758, Vol. 12, no 7, article id e9050Article in journal (Refereed)
    Abstract [en]

    Population translocations occur for a variety of reasons, from displacement due to climate change to human-induced transfers. Such actions have adverse effects on genetic variation and understanding their microevolutionary consequences requires monitoring. Here, we return to an experimental release of brown trout (Salmo trutta) in order to monitor the genomic effects of population translocations. In 1979, fish from each of two genetically (FST = 0.16) and ecologically separate populations were simultaneously released, at one point in time, to a lake system previously void of brown trout. Here, whole-genome sequencing of pooled DNA (Pool-seq) is used to characterize diversity within and divergence between the introduced populations and fish inhabiting two lakes downstream of the release sites, sampled 30 years later (c. 5 generations). Present results suggest that while extensive hybridization has occurred, the two introduced populations are unequally represented in the lakes downstream of the release sites. One population, which is ecologically resident in its original habitat, mainly contributes to the lake closest to the release site. The other population, migratory in its natal habitat, is genetically more represented in the lake further downstream. Genomic regions putatively under directional selection in the new habitat are identified, where allele frequencies in both established populations are more similar to the introduced population stemming from a resident population than the migratory one. Results suggest that the microevolutionary consequences of population translocations, for example, hybridization and adaptation, can be rapid and that Pool-seq can be used as an initial tool to monitor genome-wide effects.

  • 37.
    Kurland, Sara
    et al.
    Stockholm University, Faculty of Science, Department of Zoology, Population Genetics.
    Ryman, Nils
    Stockholm University, Faculty of Science, Department of Zoology, Population Genetics.
    Hössjer, Ola
    Stockholm University, Faculty of Science, Department of Mathematics.
    Laikre, Linda
    Stockholm University, Faculty of Science, Department of Zoology, Population Genetics.
    Effects of subpopulation extinction on effective size (Ne) of metapopulations2023In: Conservation Genetics, ISSN 1566-0621, E-ISSN 1572-9737, Vol. 24, no 4, p. 417-433Article in journal (Refereed)
    Abstract [en]

    Population extinction is ubiquitous in all taxa. Such extirpations can reduce intraspecific diversity, but the extent to which genetic diversity of surviving populations are affected remains largely unclear. A key concept in this context is the effective population size (Ne), which quantifies the rate at which genetic diversity within populations is lost. Ne was developed for single, isolated populations while many natural populations are instead connected to other populations via gene flow. Recent analytical approaches and software permit modelling of Ne of interconnected populations (metapopulations). Here, we apply such tools to investigate how extinction of subpopulations affects Ne of the metapopulation (NeMeta) and of separate surviving subpopulations (NeRx) under different rates and patterns of genetic exchange between subpopulations. We assess extinction effects before and at migration-drift equilibrium. We find that the effect of extinction on NeMeta increases with reduced connectivity, suggesting that stepping stone models of migration are more impacted than island-migration models when the same number of subpopulations are lost. Furthermore, in stepping stone models, after extinction and before a new equilibrium has been reached, NeRx can vary drastically among surviving subpopulations and depends on their initial spatial position relative to extinct ones. Our results demonstrate that extinctions can have far more complex effects on the retention of intraspecific diversity than typically recognized. Metapopulation dynamics need heightened consideration in sustainable management and conservation, e.g., in monitoring genetic diversity, and are relevant to a wide range of species in the ongoing extinction crisis. 

  • 38.
    Kurland, Sara
    et al.
    Stockholm University, Faculty of Science, Department of Zoology, Population Genetics.
    Saha, Atal
    Keehnen, Naomi
    de la Paz Celorio Mancera, Maria
    Díez del Molino, David
    Nils, Ryman
    Linda, Laikre
    Conservation genetic monitoring of natural brown trout (Salmo trutta) populations using whole genome resequencing dataManuscript (preprint) (Other academic)
  • 39.
    Kurland, Sara
    et al.
    Stockholm University, Faculty of Science, Department of Zoology, Population Genetics. Uppsala University, Sweden.
    Saha, Atal
    Stockholm University, Faculty of Science, Department of Zoology, Population Genetics. University of Agder, Kristiansand, Norway.
    P. Keehnen, Naomi L.
    Stockholm University, Faculty of Science, Department of Zoology, Population Genetics. SLU, Sweden.
    Celorio-Mancera, Maria de la Paz
    Stockholm University, Faculty of Science, Department of Zoology, Population Genetics. Stockholm University, Faculty of Science, Department of Zoology, Animal Ecology.
    Diez-del-Molino, David
    Stockholm University, Faculty of Science, Department of Zoology. Swedish Museum of Natural History, Sweden.
    Ryman, Nils
    Stockholm University, Faculty of Science, Department of Zoology, Population Genetics.
    Laikre, Linda
    Stockholm University, Faculty of Science, Department of Zoology, Population Genetics.
    New indicators for monitoring genetic diversity applied to alpine brown trout populations using whole genome sequence data2023In: Molecular Ecology, ISSN 0962-1083, E-ISSN 1365-294XArticle in journal (Refereed)
    Abstract [en]

    International policy recently adopted commitments to maintain genetic diversity in wild populations to secure their adaptive potential, including metrics to monitor temporal trends in genetic diversity - so-called indicators. A national programme for assessing trends in genetic diversity was recently initiated in Sweden. Relating to this effort, we systematically assess contemporary genome-wide temporal trends (40 years) in wild populations using the newly adopted indicators and whole genome sequencing (WGS). We use pooled and individual WGS data from brown trout (Salmo trutta) in eight alpine lakes in protected areas. Observed temporal trends in diversity metrics (nucleotide diversity, Watterson's. and heterozygosity) lie within proposed acceptable threshold values for six of the lakes, but with consistently low values in lakes above the tree line and declines observed in these northern-most lakes. Local effective population size is low in all lakes, highlighting the importance of continued protection of interconnected systems to allow genetic connectivity for long-term viability of these populations. Inbreeding (FROH) spans 10%-30% and is mostly represented by ancient (<1 Mb) runs of homozygosity, with observations of little change in mutational load. We also investigate adaptive dynamics over evolutionarily short time frames (a few generations); identifying putative parallel selection across all lakes within a gene pertaining to skin pigmentation as well as candidates of selection unique to specific lakes and lake systems involved in reproduction and immunity. We demonstrate the utility of WGS for systematic monitoring of natural populations, a priority concern if genetic diversity is to be protected.

  • 40.
    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, 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.

  • 41.
    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.

  • 42. 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)
  • 43.
    Laikre, Linda
    et al.
    Stockholm University, Faculty of Science, Department of Zoology, Population Genetics.
    Allendorf, Fred W.
    Aspi, Jouni
    Carroll, Carlos
    Dalén, Love
    Stockholm University, Faculty of Science, Department of Zoology, Animal Ecology.
    Fredrickson, Richard
    Hansen Wheat, Christina
    Hedrick, Philip
    Johannesson, Kerstin
    Kardos, Marty
    Peterson, Rolf O.
    Phillips, Mike
    Ryman, Nils
    Stockholm University, Faculty of Science, Department of Zoology, Population Genetics.
    Räikkönen, Jannikke
    Vilà, Carles
    Wheat, Christopher W.
    Stockholm University, Faculty of Science, Department of Zoology, Population Genetics. Stockholm University, Faculty of Science, Department of Zoology, Systematic Zoology.
    Vernesi, Cristiano
    Vucetich, John A.
    Planned cull endangers Swedish wolf population2022In: Science, ISSN 0036-8075, E-ISSN 1095-9203, Vol. 377, no 6602Article in journal (Refereed)
    Abstract [en]

    In May, the Swedish Parliament announced a goal to reduce the Swedish wolf population from about 400 to about 200 individuals (1). This action further threatens this highly endangered population, which is genetically isolated and inbred. Scientific advice for improvements has not been implemented (2, 3).

    The Swedish Parliament proposed this drastic cull at a time when biodiversity is a global focus. The 50-year anniversary of the first UN conference on the environment was celebrated in June, and the UN Convention on Biological Diversity (CBD) will soon finalize its global biodiversity framework for 2020 to 2050. Sweden’s actions are inconsistent with the country’s obligations under the CBD and European Union law.

    Few wild populations are as well studied as the Scandinavian wolf. Genetic monitoring has provided a full pedigree since the population was reestablished in the 1980s after extinction, and the data confirm persisting genetic isolation (4–6). Hunting, conducted both legally and illegally, has prevented population expansion and the influx of genetic variation.

    Three founders comprised the population’s genetic origin until 2007, and only three more wolves have subsequently contributed genetically to the present population (6). The genetic base is thus extremely narrow, and genomic erosion has been confirmed (7, 8). The average level of inbreeding is similar to the level found in the offspring of two full siblings (6). Inbreeding in this population has been shown to reduce litter size (4). Also, high frequencies of anatomical defects (9) and male reproductive disorders (10) have been observed.

    To make this population viable, population size and immigration must increase. So far, the population has been too small, and limited immigration followed by inbreeding could lead to extinction, similar to the Isle Royale wolf population (11). The goal should be to recreate a well-connected metapopulation spanning Scandinavia and Finland with a genetically effective population size of over 500, in line with the proposed CBD indicator (12). Considerably more genetic exchange than the current one-migrant-per-generation aim is needed (3).

  • 44.
    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.

  • 45.
    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)
  • 46.
    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.

  • 47.
    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.

  • 48.
    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.

  • 49.
    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.

  • 50.
    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.

12 1 - 50 of 88
CiteExportLink to result list
Permanent link
Cite
Citation style
  • apa
  • ieee
  • modern-language-association-8th-edition
  • vancouver
  • Other style
More styles
Language
  • de-DE
  • en-GB
  • en-US
  • fi-FI
  • nn-NO
  • nn-NB
  • sv-SE
  • Other locale
More languages
Output format
  • html
  • text
  • asciidoc
  • rtf