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  • 1.
    Ament-Velásquez, Sandra Lorena
    et al.
    Stockholm University, Faculty of Science, Department of Zoology, Population Genetics.
    Gilchrist, Ciaran
    Stockholm University, Faculty of Science, Department of Zoology, Population Genetics.
    Rêgo, Alexandre
    Stockholm University, Faculty of Science, Department of Zoology, Population Genetics.
    Bendixsen, Devin P.
    Stockholm University, Faculty of Science, Department of Zoology, Population Genetics.
    Brice, Claire
    Stockholm University, Faculty of Science, Department of Zoology, Population Genetics.
    Grosse-Sommer, Julie Michelle
    Stockholm University, Faculty of Science, Department of Zoology, Population Genetics. Maastricht University, The Netherlands.
    Rafati, Nima
    Stelkens, Rike
    Stockholm University, Faculty of Science, Department of Zoology, Population Genetics.
    The Dynamics of Adaptation to Stress from Standing Genetic Variation and de novo Mutations 2022In: Molecular biology and evolution, ISSN 0737-4038, E-ISSN 1537-1719, Vol. 39, no 11, article id msac242Article in journal (Refereed)
    Abstract [en]

    Adaptation from standing genetic variation is an important process underlying evolution in natural populations, but we rarely get the opportunity to observe the dynamics of fitness and genomic changes in real time. Here, we used experimental evolution and Pool-Seq to track the phenotypic and genomic changes of genetically diverse asexual populations of the yeast Saccharomyces cerevisiae in four environments with different fitness costs. We found that populations rapidly and in parallel increased in fitness in stressful environments. In contrast, allele frequencies showed a range of trajectories, with some populations fixing all their ancestral variation in <30 generations and others maintaining diversity across hundreds of generations. We detected parallelism at the genomic level (involving genes, pathways, and aneuploidies) within and between environments, with idiosyncratic changes recurring in the environments with higher stress. In particular, we observed a tendency of becoming haploid-like in one environment, whereas the populations of another environment showed low overall parallelism driven by standing genetic variation despite high selective pressure. This work highlights the interplay between standing genetic variation and the influx of de novo mutations in populations adapting to a range of selective pressures with different underlying trait architectures, advancing our understanding of the constraints and drivers of adaptation. 

  • 2.
    Ament-Velásquez, Sandra Lorena
    et al.
    Stockholm University, Faculty of Science, Department of Zoology, Population Genetics.
    Vogan, Aaron A.
    Podospora anserina2022In: Trends in Microbiology, ISSN 0966-842X, E-ISSN 1878-4380, Vol. 30, no 12, p. 1243-1244Article in journal (Refereed)
  • 3.
    Ament-Velásquez, Sandra Lorena
    et al.
    Stockholm University, Faculty of Science, Department of Zoology, Population Genetics.
    Vogan, Aaron A.
    Wallerman, Ola
    Hartmann, Fanny E.
    Gautier, Valerie
    Silar, Philippe
    Giraud, Tatiana
    Johannesson, Hanna
    Stockholm University, Faculty of Science, Department of Ecology, Environment and Plant Sciences.
    High-Quality Genome Assemblies of 4 Members of the Podospora anserina Species Complex2024In: Genome Biology and Evolution, E-ISSN 1759-6653, Vol. 16, no 3, article id evae034Article in journal (Refereed)
    Abstract [en]

    The filamentous fungus Podospora anserina is a model organism used extensively in the study of molecular biology, senescence, prion biology, meiotic drive, mating-type chromosome evolution, and plant biomass degradation. It has recently been established that P. anserina is a member of a complex of 7 closely related species. In addition to P. anserina, high-quality genomic resources are available for 2 of these taxa. Here, we provide chromosome-level annotated assemblies of the 4 remaining species of the complex, as well as a comprehensive data set of annotated assemblies from a total of 28 Podospora genomes. We find that all 7 species have genomes of around 35 Mb arranged in 7 chromosomes that are mostly collinear and less than 2% divergent from each other at genic regions. We further attempt to resolve their phylogenetic relationships, finding significant levels of phylogenetic conflict as expected from a rapid and recent diversification.

  • 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.
    Mapping and monitoring genetic diversity in brown trout population systems in alpine lakes by applying newly proposed indicatorsManuscript (preprint) (Other academic)
  • 5.
    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. 

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

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

  • 7.
    Bendixsen, Devin P.
    et al.
    Stockholm University, Faculty of Science, Department of Zoology, Population Genetics.
    Frazão, João G.
    Stockholm University, Faculty of Science, Department of Zoology, Population Genetics.
    Stelkens, Rike
    Stockholm University, Faculty of Science, Department of Zoology, Population Genetics.
    Saccharomyces yeast hybrids on the rise2022In: Yeast, ISSN 0749-503X, E-ISSN 1097-0061, Vol. 39, no 1-2, p. 40-54Article, review/survey (Refereed)
    Abstract [en]

    Saccharomyces hybrid yeasts are receiving increasing attention as a powerful model system to understand adaptation to environmental stress and speciation mechanisms, using experimental evolution and omics techniques. We compiled all genomic resources available from public repositories of the eight recognized Saccharomyces species and their interspecific hybrids. We present the newest numbers on genomes sequenced, assemblies, annotations, and sequencing runs, and an updated species phylogeny using orthogroup inference. While genomic resources are highly skewed towards Saccharomyces cerevisiae, there is a noticeable movement to use wild, recently discovered yeast species in recent years. To illustrate the degree and potential causes of reproductive isolation, we reanalyzed published data on hybrid spore viabilities across the entire genus and tested for the role of genetic, geographic, and ecological divergence within and between species (28 cross types and 371 independent crosses). Hybrid viability generally decreased with parental genetic distance likely due to antirecombination and negative epistasis, but notable exceptions emphasize the importance of strain-specific structural variation and ploidy differences. Surprisingly, the viability of crosses within species varied widely, from near reproductive isolation to near-perfect viability. Geographic and ecological origins of the parents predicted cross viability to an extent, but with certain caveats. Finally, we highlight publication trends in the field and point out areas of special interest, where hybrid yeasts are particularly promising for innovation through research and development, and experimental evolution and fermentation.

  • 8.
    Bendixsen, Devin P.
    et al.
    Stockholm University, Faculty of Science, Department of Zoology, Population Genetics.
    Peris, David
    Stelkens, Rike
    Stockholm University, Faculty of Science, Department of Zoology, Population Genetics.
    Patterns of Genomic Instability in Interspecific Yeast Hybrids With Diverse Ancestries2021In: Frontiers in Fungal Biology, E-ISSN 2673-6128, Vol. 2, article id 742894Article in journal (Refereed)
    Abstract [en]

    The genomes of hybrids often show substantial deviations from the features of the parent genomes, including genomic instabilities characterized by chromosomal rearrangements, gains, and losses. This plastic genomic architecture generates phenotypic diversity, potentially giving hybrids access to new ecological niches. It is however unclear if there are any generalizable patterns and predictability in the type and prevalence of genomic variation and instability across hybrids with different genetic and ecological backgrounds. Here, we analyzed the genomic architecture of 204 interspecific Saccharomyces yeast hybrids isolated from natural, industrial fermentation, clinical, and laboratory environments. Synchronous mapping to all eight putative parental species showed significant variation in read depth indicating frequent aneuploidy, affecting 44% of all hybrid genomes and particularly smaller chromosomes. Early generation hybrids with largely equal genomic content from both parent species were more likely to contain aneuploidies than introgressed genomes with an older hybridization history, which presumably stabilized the genome. Shared k-mer analysis showed that the degree of genomic diversity and variability varied among hybrids with different parent species. Interestingly, more genetically distant crosses produced more similar hybrid genomes, which may be a result of stronger negative epistasis at larger genomic divergence, putting constraints on hybridization outcomes. Mitochondrial genomes were typically inherited from the species also contributing the majority nuclear genome, but there were clear exceptions to this rule. Together, we find reliable genomic predictors of instability in hybrids, but also report interesting cross- and environment-specific idiosyncrasies. Our results are an important step in understanding the factors shaping divergent hybrid genomes and their role in adaptive evolution.

     

  • 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.
    Celorio-Mancera, Maria de la Paz
    et al.
    Stockholm University, Faculty of Science, Department of Zoology, Population Genetics. Stockholm University, Faculty of Science, Department of Zoology, Animal Ecology.
    Steward, Rachel A.
    Stockholm University, Faculty of Science, Department of Zoology.
    Pruisscher, Peter
    Smialowska, Agata
    Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics. Stockholm University, Science for Life Laboratory (SciLifeLab).
    Braga, Mariana Pires
    Janz, Niklas
    Stockholm University, Faculty of Science, Department of Zoology, Animal Ecology.
    Wheat, Christopher W.
    Stockholm University, Faculty of Science, Department of Zoology, Population Genetics. Stockholm University, Faculty of Science, Department of Zoology, Systematic Zoology.
    Nylin, Sören
    Stockholm University, Faculty of Science, Department of Zoology, Animal Ecology. Stockholm University, Faculty of Science, Department of Zoology, Population Genetics.
    Larval transcriptomes reflect the evolutionary history of plant-insect associations2023In: Evolution, ISSN 0014-3820, E-ISSN 1558-5646, Vol. 77, no 2, p. 519-533Article in journal (Refereed)
    Abstract [en]

    In this study, we investigated whether patterns of gene expression in larvae feeding on different plants can explain important aspects of the evolution of insect-plant associations, such as phylogenetic conservatism of host use and re-colonization of ancestral hosts that have been lost from the host repertoire. To this end, we performed a phylogenetically informed study comparing the transcriptomes of 4 nymphalid butterfly species in Polygonia and the closely related genus Nymphalis. Larvae were reared on Urtica dioica, Salix spp., and Ribes spp. Plant-specific gene expression was found to be similar across butterfly species, even in the case of host plants that are no longer used by two of the butterfly species. These results suggest that plant-specific transcriptomes can be robust over evolutionary time. We propose that adaptations to particular larval food plants can profitably be understood as an evolved set of modules of co-expressed genes, promoting conservatism in host use and facilitating re-colonization. Moreover, we speculate that the degree of overlap between plant-specific transcriptomes may correlate with the strength of trade-offs between plants as resources and hence to the probability of colonizing hosts and complete host shifts.

  • 11.
    Celorio-Mancera, Maria de la Paz
    et al.
    Stockholm University, Faculty of Science, Department of Zoology, Animal Ecology.
    Wheat, Christopher W.
    Stockholm University, Faculty of Science, Department of Zoology, Population Genetics.
    Vogel, Heiko
    Söderlind, Lina
    Stockholm University, Faculty of Science, Department of Zoology, Animal Ecology.
    Janz, Niklas
    Stockholm University, Faculty of Science, Department of Zoology, Animal Ecology.
    Nylin, Sören
    Stockholm University, Faculty of Science, Department of Zoology, Animal Ecology.
    Mechanisms of macroevolution: polyphagous plasticity in butterfly larvae revealed by RNA-Seq2013In: Molecular Ecology, ISSN 0962-1083, E-ISSN 1365-294X, Vol. 22, no 19, p. 4884-4895Article in journal (Refereed)
    Abstract [en]

    Transcriptome studies of insect herbivory are still rare, yet studies in model systems have uncovered patterns of transcript regulation that appear to provide insights into how insect herbivores attain polyphagy, such as a general increase in expression breadth and regulation of ribosomal, digestion- and detoxification-related genes. We investigated the potential generality of these emerging patterns, in the Swedish comma, Polygonia c-album, which is a polyphagous, widely-distributed butterfly. Urtica dioica and Ribes uva-crispa are hosts of P. c-album, but Ribes represents a recent evolutionary shift onto a very divergent host. Utilizing the assembled transcriptome for read mapping, we assessed gene expression finding that caterpillar life-history (i.e. 2nd vs. 4th-instar regulation) had a limited influence on gene expression plasticity. In contrast, differential expression in response to host-plant identified genes encoding serine-type endopeptidases, membrane-associated proteins and transporters. Differential regulation of genes involved in nucleic acid binding was also observed suggesting that polyphagy involves large scale transcriptional changes. Additionally, transcripts coding for structural constituents of the cuticle were differentially expressed in caterpillars in response to their diet indicating that the insect cuticle may be a target for plant defence. Our results state that emerging patterns of transcript regulation from model species appear relevant in species when placed in an evolutionary context.

  • 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. Clavé, Corinne
    et al.
    Dheur, Sonia
    Ament-Velásquez, Sandra Lorena
    Stockholm University, Faculty of Science, Department of Zoology, Population Genetics.
    Granger-Farbos, Alexandra
    Saupe, Sven J.
    het-B allorecognition in Podospora anserina is determined by pseudo-allelic interaction of genes encoding a HET and lectin fold domain protein and a PII-like protein2024In: PLOS Genetics, ISSN 1553-7390, E-ISSN 1553-7404, Vol. 20, no 2, article id e1011114Article in journal (Refereed)
    Abstract [en]

    Filamentous fungi display allorecognition genes that trigger regulated cell death (RCD) when strains of unlike genotype fuse. Podospora anserina is one of several model species for the study of this allorecognition process termed heterokaryon or vegetative incompatibility. Incompatibility restricts transmission of mycoviruses between isolates. In Panserina, genetic analyses have identified nine incompatibility loci, termed het loci. Here we set out to clone the genes controlling het-B incompatibility. het-B displays two incompatible alleles, het-B1 and het-B2. We find that the het-B locus encompasses two adjacent genes, Bh and Bp that exist as highly divergent allelic variants (Bh1/Bh2 and Bp1/Bp2) in the incompatible haplotypes. Bh encodes a protein with an N-terminal HET domain, a cell death inducing domain bearing homology to Toll/interleukin-1 receptor (TIR) domains and a C-terminal domain with a predicted lectin fold. The Bp product is homologous to PII-like proteins, a family of small trimeric proteins acting as sensors of adenine nucleotides in bacteria. We show that although the het-B system appears genetically allelic, incompatibility is in fact determined by the non-allelic Bh1/Bp2 interaction while the reciprocal Bh2/Bp1 interaction plays no role in incompatibility. The highly divergent C-terminal lectin fold domain of BH determines recognition specificity. Population studies and genome analyses indicate that het-B is under balancing selection with trans-species polymorphism, highlighting the evolutionary significance of the two incompatible haplotypes. In addition to emphasizing anew the central role of TIR-like HET domains in fungal RCD, this study identifies novel players in fungal allorecognition and completes the characterization of the entire het gene set in that species.

  • 14.
    de la Paz Celorio-Mancera, Maria
    et al.
    Stockholm University, Faculty of Science, Department of Zoology, Population Genetics.
    Wheat, Christopher W.
    Stockholm University, Faculty of Science, Department of Zoology, Population Genetics.
    Huss, Mikael
    Vezzi, Francesco
    Neethiraj, Ramprasad
    Stockholm University, Faculty of Science, Department of Zoology, Population Genetics.
    Reimegård, Johan
    Nylin, Sören
    Stockholm University, Faculty of Science, Department of Zoology, Animal Ecology.
    Janz, Niklas
    Stockholm University, Faculty of Science, Department of Zoology, Animal Ecology.
    Evolutionary history of host use, rather than plant phylogeny, determines gene expression in a generalist butterfly2016In: BMC Evolutionary Biology, E-ISSN 1471-2148, Vol. 16, article id 59Article in journal (Refereed)
    Abstract [en]

    Background: Although most insect species are specialized on one or few groups of plants, there are phytophagous insects that seem to use virtually any kind of plant as food. Understanding the nature of this ability to feed on a wide repertoire of plants is crucial for the control of pest species and for the elucidation of the macroevolutionary mechanisms of speciation and diversification of insect herbivores. Here we studied Vanessa cardui, the species with the widest diet breadth among butterflies and a potential insect pest, by comparing tissue-specific transcriptomes from caterpillars that were reared on different host plants. We tested whether the similarities of gene-expression response reflect the evolutionary history of adaptation to these plants in the Vanessa and related genera, against the null hypothesis of transcriptional profiles reflecting plant phylogenetic relatedness. Result: Using both unsupervised and supervised methods of data analysis, we found that the tissue-specific patterns of caterpillar gene expression are better explained by the evolutionary history of adaptation of the insects to the plants than by plant phylogeny. Conclusion: Our findings suggest that V. cardui may use two sets of expressed genes to achieve polyphagy, one associated with the ancestral capability to consume Rosids and Asterids, and another allowing the caterpillar to incorporate a wide range of novel host-plants.

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  • 15. Delmore, Kira
    et al.
    Justen, Hannah
    Kay, Kathleen M.
    Kitano, Jun
    Moyle, Leonie C.
    Stelkens, Rike
    Stockholm University, Faculty of Science, Department of Zoology, Population Genetics.
    Streisfeld, Matthew A.
    Yamasaki, Yo Y.
    Ross, Joseph
    Genomic Approaches Are Improving Taxonomic Representation in Genetic Studies of Speciation2024In: Cold Spring Harbor Perspectives in Biology, E-ISSN 1943-0264, Vol. 16, no 2, article id a041438Article, review/survey (Refereed)
    Abstract [en]

    Until recently, our understanding of the genetics of speciation was limited to a narrow group of model species with a specific set of characteristics that made genetic analysis feasible. Rapidly advancing genomic technologies are eliminating many of the distinctions between laboratory and natural systems. In light of these genomic developments, we review the history of speciation genetics, advances that have been gleaned from model and non-model organisms, the current state of the field, and prospects for broadening the diversity of taxa included in future studies. Responses to a survey of speciation scientists across the world reveal the ongoing division between the types of questions that are addressed in model and non-model organisms. To bridge this gap, we suggest integrating genetic studies from model systems that can be reared in the laboratory or greenhouse with genomic studies in related non-models where extensive ecological knowledge exists.

  • 16.
    Dort, Hanna
    et al.
    Stockholm University, Faculty of Science, Department of Zoology, Population Genetics.
    Okamura, Yu
    Wahlberg, Niklas
    Vogel, Heiko
    Wheat, Christopher W.
    Stockholm University, Faculty of Science, Department of Zoology, Population Genetics. Stockholm University, Faculty of Science, Department of Zoology, Systematic Zoology.
    The Great Pieridae Project: Associating gene-birth death dynamics with dietary shifts in crucifer-feeding butterflies and their relativesManuscript (preprint) (Other academic)
  • 17.
    Dort, Hanna
    et al.
    Stockholm University, Faculty of Science, Department of Zoology, Population Genetics.
    van der Bijl, Wouter
    Stockholm University, Faculty of Science, Department of Zoology.
    Wahlberg, Niklas
    Nylin, Sören
    Stockholm University, Faculty of Science, Department of Zoology, Animal Ecology. Stockholm University, Faculty of Science, Department of Zoology, Population Genetics.
    Wheat, Christopher W.
    Stockholm University, Faculty of Science, Department of Zoology, Population Genetics. Stockholm University, Faculty of Science, Department of Zoology, Systematic Zoology.
    Genome-wide gene birth-death dynamics are associated with diet breadth variation in LepidopteraManuscript (preprint) (Other academic)
  • 18.
    Dort, Hanna
    et al.
    Stockholm University, Faculty of Science, Department of Zoology, Population Genetics.
    Wheat, Christopher W.
    Stockholm University, Faculty of Science, Department of Zoology, Population Genetics. Stockholm University, Faculty of Science, Department of Zoology, Systematic Zoology.
    Steward, Rachel A.
    Removing specialized detoxification mechanisms reveals generalized responses in a host plant feeding specialistManuscript (preprint) (Other academic)
    Abstract [en]

    Coevolutionary innovations are thought to be a large driver of insect and plant biodiversity. Several such innovations have arisen from gene duplication events and subsequent divergence between gene copies, including many adaptations that allow insects to overcome defensive host plant chemistry. However, the role adaptive gene duplicates play in a wider transcriptional framework is still poorly understood. Here, we use short-term feeding assays and CRISPR-Cas9 modified lines of cabbage white (Pieris brassicae) caterpillars to explore how non-functionalization of different members of a family of specialized detoxification genes affects the larval transcriptome at large. We find that the transcriptional response to host plant changes is strongest when all genes in the detoxification family are functional, suggesting that the gene family is part of a larger regulatory response to host plant defences. Further, among individuals lacking specialized detoxification genes, we find that certain general detoxification genes are uniquely upregulated in response to stressful host plant switches. Our results shed light on the importance of transcriptional plasticity in plant-insect interactions and lead to new hypotheses about the initial colonization of mustards by early pierid butterflies.

  • 19.
    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.

  • 20.
    Díez-del-Molino, David
    et al.
    Stockholm University, Faculty of Humanities, Department of Archaeology and Classical Studies, Archaeology. Stockholm University, Faculty of Science, Department of Zoology, Population Genetics. Centre for Palaeogenetics, Sweden; Swedish Museum of Natural History, Sweden.
    Dehasque, Marianne
    Stockholm University, Faculty of Science, Department of Zoology. Centre for Palaeogenetics, Sweden; Swedish Museum of Natural History, Sweden.
    Chacón-Duque, J. Camilo
    Stockholm University, Faculty of Humanities, Department of Archaeology and Classical Studies. Centre for Palaeogenetics, Sweden.
    Pecnerova, Patricia
    Tikhonov, Alexei
    Protopopov, Albert
    Plotnikov, Valeri
    Kanellidou, Foteini
    Nikolskiy, Pavel
    Mortensen, Peter
    Danilov, Gleb K.
    Vartanyan, Sergey
    Gilbert, M. Thomas P.
    Lister, Adrian M.
    Heintzman, Peter
    Stockholm University, Faculty of Science, Department of Geological Sciences. Centre for Palaeogenetics, Sweden.
    van der Valk, Tom
    Dalén, Love
    Stockholm University, Faculty of Science, Department of Ecology, Environment and Plant Sciences. Stockholm University, Faculty of Science, Department of Zoology, Animal Ecology. Centre for Palaeogenetics, Sweden; Swedish Museum of Natural History, Sweden.
    Genomics of adaptive evolution in the woolly mammoth2023In: Current Biology, ISSN 0960-9822, E-ISSN 1879-0445, Vol. 33, no 9, p. 1753-1764Article in journal (Refereed)
    Abstract [en]

    Ancient genomes provide a tool to investigate the genetic basis of adaptations in extinct organisms. However, the identification of species-specific fixed genetic variants requires the analysis of genomes from multiple individuals. Moreover, the long-term scale of adaptive evolution coupled with the short-term nature of tradi-tional time series data has made it difficult to assess when different adaptations evolved. Here, we analyze 23 woolly mammoth genomes, including one of the oldest known specimens at 700,000 years old, to identify fixed derived non-synonymous mutations unique to the species and to obtain estimates of when these mutations evolved. We find that at the time of its origin, the woolly mammoth had already acquired a broad spectrum of positively selected genes, including ones associated with hair and skin development, fat storage and metabolism, and immune system function. Our results also suggest that these phenotypes continued to evolve during the last 700,000 years, but through positive selection on different sets of genes. Finally, we also identify additional genes that underwent comparatively recent positive selection, including multiple genes related to skeletal morphology and body size, as well as one gene that may have contributed to the small ear size in Late Quaternary woolly mammoths.

  • 21.
    Gilchrist, Ciaran
    et al.
    Stockholm University, Faculty of Science, Department of Zoology, Population Genetics.
    Cerorio Mancera, Maria de le Paz
    Stockholm University, Faculty of Science, Department of Zoology, Population Genetics.
    Stelkens, Rike
    Stockholm University, Faculty of Science, Department of Zoology, Population Genetics.
    Hybridisation between laboratory-evolved populations prolongs survival in a deteriorating environmentManuscript (preprint) (Other academic)
  • 22.
    Gilchrist, Ciaran
    et al.
    Stockholm University, Faculty of Science, Department of Zoology, Population Genetics.
    Stenberg, Simon
    Warringer, Jonas
    Stelkens, Rike
    Stockholm University, Faculty of Science, Department of Zoology, Population Genetics.
    Hybridisation along a lab-evolved parental divergence gradient increases resilience to a large range of novel environmental stressManuscript (preprint) (Other academic)
  • 23.
    Gobbo, Erik
    et al.
    Stockholm University, Faculty of Science, Department of Zoology. Naturhistoriska Riksmuseet.
    Wheat, Christopher W.
    Stockholm University, Faculty of Science, Department of Zoology, Population Genetics. Stockholm University, Faculty of Science, Department of Zoology, Systematic Zoology.
    Ronquist, Fredrik
    Stockholm University, Faculty of Science, Department of Zoology.
    Shotgun sequencing of hymenopteran inhabitants of rose galls reveals a surprising lack of bacteriaManuscript (preprint) (Other academic)
    Abstract [en]

    In recent years, our knowledge of the microbiomes associated with insects has increased rapidly thanks to new sequencing methods, but the taxonomic and biological diversity of the studied insect species is still limited. Insects inhabiting galls represent a particularly interesting ecological guild that has not yet had its microbiome fully characterized, although it is well known that many gall insects are infected by Wolbachia. Here, we use shotgun sequencing to characterize the microbiome of the larvae of four hymenopteran species inhabiting bedeguar galls on roses: the gall inducer (Diplolepis rosae, Cynipidae), a phytophagous inquiline (Periclistus brandtii, Cynipidae), and two parasitoids (Torymus bedeguaris, Torymidae, and Orthopelma mediator, Ichneumonidae). Analyses with Metaphlan2 detected the presence of Wolbachia in two of the larvae (one of three Diplolepis larvae, and one of two Torymus larvae); three other bacteria detected by Metaphlan2 in high abundance could be shown to be false positives. An annotation screen of the assembled genomes gave similar results. Almost all contigs that were likely to be of bacterial origin matched Wolbachia; the few remaining ones were likely false positives. Matching the assemblies to proteomes of candidate symbionts showed that the two infected larvae contained a substantial portion of the Wolbachia genome while the other Diplolepis and Torymus larvae only contained small sections of it. Our results suggest that the bedeguar gall is largely devoid of bacteria except for Wolbachia. This could potentially be related to previous reports that galls induced by cynipids produce antibiotics. Our results fail to support the much-discussed hypothesis that symbiotic bacteria are involved in gall induction in cynipids.

  • 24. Gudmunds, Erik
    et al.
    Wheat, Christopher W.
    Stockholm University, Faculty of Science, Department of Zoology, Population Genetics.
    Khila, Abderrahman
    Husby, Arild
    Functional genomic tools for emerging model species2022In: Trends in Ecology & Evolution, ISSN 0169-5347, E-ISSN 1872-8383, Vol. 37, no 12, p. 1104-1115Article in journal (Refereed)
    Abstract [en]

    Most studies in the field of ecology and evolution aiming to connect genotype to phenotype rarely validate identified loci using functional tools. Recent developments in RNA interference (RNAi) and clustered regularly interspaced palindromic repeats (CRISPR)-Cas genome editing have dramatically increased the feasibility of functional validation. However, these methods come with specific challenges when applied to emerging model organisms, including limited spatial control of gene silencing, low knock-in efficiencies, and low throughput of functional validation. Moreover, many functional studies to date do not recapitulate ecologically relevant variation, and this limits their scope for deeper insights into evolutionary processes. We therefore argue that increased use of gene editing by allelic replacement through homology-directed repair (HDR) would greatly benefit the field of ecology and evolution. 

  • 25.
    Hill, Jason
    et al.
    Stockholm University, Faculty of Science, Department of Zoology, Population Genetics. Uppsala University, Sweden.
    Rastas, Pasi
    Hornett, Emily A.
    Neethiraj, Ramprasad
    Stockholm University, Faculty of Science, Department of Zoology, Population Genetics.
    Clark, Nathan
    Morehouse, Nathan
    de la Paz Celorio-Mancera, Maria
    Stockholm University, Faculty of Science, Department of Zoology, Population Genetics.
    Carnicer Cols, Jofre
    Dircksen, Heinrich
    Stockholm University, Faculty of Science, Department of Zoology, Functional Morphology.
    Meslin, Camille
    Keehnen, Naomi
    Stockholm University, Faculty of Science, Department of Zoology, Population Genetics.
    Pruisscher, Peter
    Stockholm University, Faculty of Science, Department of Zoology, Population Genetics.
    Sikkink, Kristin
    Vives, Maria
    Vogel, Heiko
    Wiklund, Christer
    Stockholm University, Faculty of Science, Department of Zoology, Population Genetics.
    Woronik, Alyssa
    Stockholm University, Faculty of Science, Department of Zoology, Population Genetics. New York University, USA.
    Boggs, Carol L.
    Nylin, Sören
    Stockholm University, Faculty of Science, Department of Zoology, Population Genetics.
    Wheat, Christopher W.
    Stockholm University, Faculty of Science, Department of Zoology, Population Genetics.
    Unprecedented reorganization of holocentric chromosomes provides insights into the enigma of lepidopteran chromosome evolution2019In: Science Advances, E-ISSN 2375-2548, Vol. 5, no 6, article id eaau3648Article in journal (Refereed)
    Abstract [en]

    Chromosome evolution presents an enigma in the mega-diverse Lepidoptera. Most species exhibit constrained chromosome evolution with nearly identical haploid chromosome counts and chromosome-level gene collinearity among species more than 140 million years divergent. However, a few species possess radically inflated chromosomal counts due to extensive fission and fusion events. To address this enigma of constraint in the face of an exceptional ability to change, we investigated an unprecedented reorganization of the standard lepidopteran chromosome structure in the green-veined white butterfly (Pieris napi). We find that gene content in P. napi has been extensively rearranged in large collinear blocks, which until now have been masked by a haploid chromosome number close to the lepidopteran average. We observe that ancient chromosome ends have been maintained and collinear blocks are enriched for functionally related genes suggesting both a mechanism and a possible role for selection in determining the boundaries of these genome-wide rearrangements.

  • 26. Hiltunen, Markus
    et al.
    Ament-Velásquez, Sandra Lorena
    Stockholm University, Faculty of Science, Department of Zoology, Population Genetics. Uppsala University, Sweden.
    Ryberg, Martin
    Johannesson, Hanna
    Stockholm University, Faculty of Science, Department of Ecology, Environment and Plant Sciences. Uppsala University, Sweden.
    Stage-specific transposon activity in the life cycle of the fairy-ring mushroom Marasmius oreades2022In: Proceedings of the National Academy of Sciences of the United States of America, ISSN 0027-8424, E-ISSN 1091-6490, Vol. 119, no 46, article id e2208575119Article in journal (Refereed)
    Abstract [en]

    Genetic variability can be generated by different mechanisms, and across the life cycle. Many basidiomycete fungi have an extended somatic stage, during which each cell carries two genetically distinct haploid nuclei (dikaryosis), resulting from fusion of two compatible monokaryotic individuals. Recent findings have revealed remarkable genome stability at the nucleotide level during dikaryotic growth in these organisms, but whether this pattern extends to mutations affecting large genomic regions remains unknown. Furthermore, despite high genome integrity during dikaryosis, basidiomycete populations are not devoid of genetic diversity, begging the question of when this diversity is introduced. Here, we used a Marasmius oreades fairy ring to investigate the rise of large-scale variants during mono- and dikaryosis. By separating the two nuclear genotypes from four fruiting bodies and generating complete genome assemblies, we gained access to investigate genomic changes of any size. We found that during dikaryotic growth in nature the genome stayed intact, but after separating the nucleotypes into monokaryons, a considerable amount of structural variation started to accumulate, driven to large extent by transposons. Transposon insertions were also found in monokaryotic single-meiospore isolates. Hence, we show that genome integrity in basidiomycetes can be interrupted during monokaryosis, leading to genomic rearrangements and increased activity of transposable elements. We suggest that genetic diversification is disproportionate between life cycle stages in mushroom-forming fungi, so that the short-lived monokaryotic growth stage is more prone to genetic changes than the dikaryotic stage.

  • 27. 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.

  • 28. Hoban, Sean
    et al.
    da Silva, Jessica M.
    Hughes, Alice
    Hunter, Margaret E.
    Stroil, Belma Kalamujić
    Laikre, Linda
    Stockholm University, Faculty of Science, Department of Zoology, Population Genetics.
    Mastretta-Yanes, Alicia
    Millette, Katie
    Paz-Vinas, Ivan
    Bustos, Lucia Ruiz
    Shaw, Robyn E.
    Vernesi, Cristiano
    Funk, Chris
    Grueber, Catherine
    Kershaw, Francine
    Macdonald, Anna
    Meek, Mariah
    Mittan, Cinnamon
    O'Brien, David
    Ogden, Rob
    Segelbacher, Gernot
    Too simple, too complex, or just right? Advantages, challenges, and guidance for indicators of genetic diversity2024In: BioScience, ISSN 0006-3568, E-ISSN 1525-3244, Vol. 74, no 4, p. 269-280Article in journal (Refereed)
    Abstract [en]

    Measuring genetic diversity of wild species using DNA-based data remains resource intensive and time consuming for nearly all species. However, genetic assessments are needed for global conservation commitments, including the Convention on Biological Diversity, and for governments and managers to evaluate conservation progress, as well as prioritizing species and populations to preserve and recover genetic diversity (e.g., via genetic rescue). Recently, indicators were developed for tracking and reporting genetic diversity status and trends for hundreds of species. The indicators quantify two simple proxies of within-population and among-population genetic diversity and adaptive potential: small effective population size (Ne < 500) and the loss of genetically distinct populations. The indicators must balance scientific credibility, practicality, and simplicity. In the present article, we summarize the advantages of these pragmatic indicators, address critiques by scientists for simplifying assumptions and by policymakers for complexity, and propose potential solutions and next steps. We aim to support practitioners putting indicators into policy, action, legislation, and reporting.

  • 29. 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, 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. 

  • 30.
    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.

  • 31.
    Ittonen, Mats
    et al.
    Stockholm University, Faculty of Science, Department of Zoology. Stockholm University, Faculty of Science, The Bolin Centre for Climate Research (together with KTH & SMHI).
    Wheat, Christopher W.
    Stockholm University, Faculty of Science, The Bolin Centre for Climate Research (together with KTH & SMHI). Stockholm University, Faculty of Science, Department of Zoology, Population Genetics. Stockholm University, Faculty of Science, Department of Zoology, Systematic Zoology.
    Gotthard, Carl
    Stockholm University, Faculty of Science, The Bolin Centre for Climate Research (together with KTH & SMHI). Stockholm University, Faculty of Science, Department of Physics. Stockholm University, Faculty of Science, Department of Zoology, Animal Ecology.
    Repeated evolution of seasonal plasticity during a climate-driven butterfly range expansion is not associated with parallel genomic signatures of selectionManuscript (preprint) (Other academic)
  • 32. 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.

  • 33.
    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.

  • 34.
    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.

  • 35.
    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.

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  • 36.
    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

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  • 37.
    Jorde, Per Erik
    Stockholm University, Faculty of Science, Department of Zoology, Population Genetics.
    Temporal allele frequency change in populations with overlapping generations: estimation of effective size of natural populations as exemplified using brown trout (Salmo trutta)1995Doctoral thesis, comprehensive summary (Other academic)
  • 38.
    Keehnen, Naomi
    et al.
    Stockholm University, Faculty of Science, Department of Zoology, Population Genetics.
    Fors, Lisa
    Stockholm University, Faculty of Science, Department of Zoology, Population Genetics.
    Integrating immune cell expression with signatures of selection suggests novel targets in melanin trafficking for geographic differences in melanin-related immune performanceManuscript (preprint) (Other academic)
  • 39.
    Keehnen, Naomi
    et al.
    Stockholm University, Faculty of Science, Department of Zoology, Population Genetics.
    Fors, Lisa
    Stockholm University, Faculty of Science, Department of Zoology, Population Genetics.
    Järver, Peter
    Stockholm University, Faculty of Science, Department of Molecular Biosciences, The Wenner-Gren Institute.
    Spetz, Anna-Lena
    Stockholm University, Faculty of Science, Department of Molecular Biosciences, The Wenner-Gren Institute.
    Nylin, Sören
    Stockholm University, Faculty of Science, Department of Zoology, Animal Ecology.
    Theopold, Ulrich
    Stockholm University, Faculty of Science, Department of Molecular Biosciences, The Wenner-Gren Institute.
    Wheat, Christopher
    Stockholm University, Faculty of Science, Department of Zoology, Population Genetics.
    Geographic variation in hemocyte diversity and phagocytic propensity shows a diffuse genomic signature in the green veined white butterflyManuscript (preprint) (Other academic)
    Abstract [en]

    Insects rely on their innate immune system to successfully mediate complex interactions with their internal microbiota, as well as the microbes present in the environment. Given the variation in microbes across habitats, the challenges to respond to them is likely to result in local adaptation in the immune system. Here we focus upon phagocytosis, a mechanism by which pathogens and foreign particles are engulfed in order to be contained, killed and processed for antigen presentation. We investigated the phenotypic and genetic variation related to phagocytosis, in two allopatric populations of the butterfly Pieris napi. We found that the populations differ in their hemocyte composition, and overall phagocytic capability, driven by the increased phagocytic propensity of each cell type. However, no evidence for divergence in phagocytosis-related genes was observed, though an enrichment of genes involved in glutamine metabolism was found, which have recently been linked to immune cell differentiation in mammals.

  • 40.
    Keehnen, Naomi L. P.
    et al.
    Stockholm University, Faculty of Science, Department of Zoology, Population Genetics.
    Kučerova, Lucie
    Stockholm University, Faculty of Science, Department of Molecular Biosciences, The Wenner-Gren Institute. Biology Centre CAS, Czech Republic.
    Nylin, Sören
    Stockholm University, Faculty of Science, Department of Zoology, Animal Ecology.
    Theopold, Ulrich
    Stockholm University, Faculty of Science, Department of Molecular Biosciences, The Wenner-Gren Institute.
    Wheat, Christopher W.
    Stockholm University, Faculty of Science, Department of Zoology, Population Genetics.
    The consequences of surviving infection across the metamorphic boundary: tradeoff insights from RNAseq and life history measuresManuscript (preprint) (Other academic)
    Abstract [en]

    The broad diversity of insect life has been shaped, in part, by pathogen pressure, yet the influence of injury and infection during critical periods of development is understudied. During development, insects undergo metamorphosis, wherein the organism experiences a dramatic shift in their overall morphology, and physiology. In temperate zones, metamorphosis is often directly followed by a developmental arrest called diapause, for which the insect needs to acquire enough energy reserves before the onset of winter. We investigated the long-term effects of injury and infection using two bacteria in the butterfly Pieris napi, revealing that the negative consequences of bacterial infection carry across the metamorphic boundary. Initial direct effects of infection were weight loss and slower development, as well as an increased mortality at higher infection levels. The detrimental effects were stronger in the gram-positive Micrococcus luteus compared to gram-negative Escherichia coli. Transcriptome-wide differences between the two bacteria were already observed in the gene expression profile of the first 24 hours after infection. Larvae infected with M. luteus showed a strong suppression of all non-immunity related processes, with several types of immune responses being activated. The impact of these transcriptomic changes, a tradeoff between homeostasis and immune response, were visible in the life history data, wherein individuals infected with M. luteus had the highest mortality rate, along with the lowest pupal weight, developmental rate and adult weight of all the treatments. Overall, we find that the cost of infection and wounding in the final larval instar carries over the metamorphic boundary, and is expected to negatively affect their lifetime fitness.

  • 41. 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.

  • 42.
    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)
  • 43.
    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.  

  • 44.
    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.

  • 45.
    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. 

  • 46.
    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)
  • 47.
    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.
    Díez-del-Molino, David
    Stockholm University, Faculty of Science, Department of Zoology, Population Genetics. Centre for Palaeogenetics, Sweden; 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 data2024In: Molecular Ecology, ISSN 0962-1083, E-ISSN 1365-294X, Vol. 33, no 2, article id e17213Article 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 ϴ 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.

  • 48.
    Lagercrantz, Ulf
    Stockholm University, Faculty of Science, Department of Zoology, Population Genetics.
    Genetic structure of natural populations: aspects of the association between genetical and morphological variability patterns1992Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    Most species comprise a number of more or less reproductively isolated subpopulations. These subpopulations may exhibit striking differences in morphology and ecology, and on the basis of those differences they are often given the rank of subspecies, race, stock, variety, etc. Morphological and ecological traits most often are quantitatively inherited, and to a large extent, are affected by environmental factors. Phenotypic differences, therefore, may give little or no information on genotypic differences. As a consequence, the amount of genetic divergence between populations in many cases is poorly known.

    The need for such information from an evolutionary and management perspective provided the impetus for this study, which describes the genetical and morphological variability patterns revealed by protein polymorphism and morphological characters. Four species were chosen from three diverse taxonomic groups: Atlantic herring (Clupea harengus), Norway spruce (Picea abies), and Palaemon prawn (P. adspersus and P. squilla). Associations between variability patterns for the two sets of characters were also analyzed to provide information on the causes of morphological variability in natural populations.

    In Atlantic herring, the amount of genetic differentiation observed was conspicuously small: more than 99% of the total gene diversity was found within populations. This contrasts with previous conclusions that were based on morphological data. The present study indicates that environmental factors have an important influence on the morphological differentiation pattern; they suggest, also, that herring stocks either diverged rather recently or that the amount of gene flow is large enough to prevent genetic differentiation.

    The patterns for distribution of genetical and morphological variability in Norway spruce, on the other hand, are very similar, indicating that the same evolutionary forces have acted on both sets of characters. A clear geographic component of variation was also observed. Data suggest that historical events during the last glaciation have affected not only the pattern of distribution of allozymic variation in the Norway spruce but probably also the pattern of its morphological traits.

    The analysis of data collected from progeny of wind-pollinated Norway spruce grown under experimental conditions suggests that inbreeding and inbreeding depression are common phenomena in trials of this species. A significant positive relationship found between allozyme heterozygosity and growth performance (apparent allozyme heterosis) in one population appears to be due to dominance rather than overdominance.

    Members of nontidal populations of the prawn Palaemon squilla are known to be much smaller than their tidal relatives, and to produce fewer offspring. Using estimates of genetic divergence based on allozyme data, we tested the hypothesis that these deficiencies are an effect of continuous gene flow resulting in poor adaptation. Genetic data did not support this hypothesis: P. squilla ought to have the possibility to adapt to local conditions.

    The results from the present study modify some previous conceptions about genetical and morphological variability patterns in all species that were investigated.

    In combination these findings demonstrate the importance of true genetic data for clarifying genetic population structure, understanding the forces that underlie current population structure, and for interpreting ecological and morphological variability patterns among natural populations.

  • 49.
    Laikre, Linda
    Stockholm University, Faculty of Science, Department of Zoology, Population Genetics.
    Genetic processes in small populations: conservation and management considerations with particular focus on inbreeding and its effects1996Doctoral thesis, comprehensive summary (Other academic)
  • 50.
    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).

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