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Bertola, L. D., Brueniche-Olsen, A., Kershaw, F., Russo, I.-R. M., Macdonald, A. J., Sunnucks, P., . . . Segelbacher, G. (2024). A pragmatic approach for integrating molecular tools into biodiversity conservation. Conservation science and practice, 6(1), Article ID e13053.
Open this publication in new window or tab >>A pragmatic approach for integrating molecular tools into biodiversity conservation
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2024 (English)In: Conservation science and practice, ISSN 2578-4854, Vol. 6, no 1, article id e13053Article in journal (Refereed) Published
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

Keywords
conservation, management, molecular tools
National Category
Biochemistry and Molecular Biology
Identifiers
urn:nbn:se:su:diva-225825 (URN)10.1111/csp2.13053 (DOI)001138192500001 ()2-s2.0-85180826226 (Scopus ID)
Available from: 2024-01-23 Created: 2024-01-23 Last updated: 2024-01-23Bibliographically approved
Saha, A., Kurland, S., Kutschera, V. E., Díez-del-Molino, D., Ekman, D., Ryman, N. & Laikre, L. (2024). Monitoring genome-wide diversity over contemporary time with new indicators applied to Arctic charr populations. Conservation Genetics
Open this publication in new window or tab >>Monitoring genome-wide diversity over contemporary time with new indicators applied to Arctic charr populations
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2024 (English)In: Conservation Genetics, ISSN 1566-0621, E-ISSN 1572-9737Article in journal (Refereed) Epub ahead of print
Abstract [en]

Genetic diversity is fundamental to the adaptive potential and survival of species. Although its importance has long been recognized in science, it has a history of neglect within policy, until now. The new Global Biodiversity Framework recently adopted by the Convention on Biological Diversity, states that genetic diversity must be maintained at levels assuring adaptive potential of populations, and includes metrics for systematic monitoring of genetic diversity in so called indicators. Similarly, indicators for genetic diversity are being developed at national levels. Here, we apply new indicators for Swedish national use to one of the northernmost salmonid fishes, the Arctic charr (Salvelinus alpinus). We sequence whole genomes to monitor genetic diversity over four decades in three landlocked populations inhabiting protected alpine lakes in central Sweden. We find levels of genetic diversity, inbreeding and load to differ among lakes but remain stable over time. Effective population sizes are generally small (< 500), suggesting a limited ability to maintain adaptive variability if genetic exchange with nearby populations became eliminated. We identify genomic regions potentially shaped by selection; SNPs exhibiting population divergence exceeding expectations under drift and a putative selective sweep acting within one lake to which the competitive brown trout (Salmo trutta) was introduced during the sampling period. Identified genes appear involved in immunity and salinity tolerance. Present results suggest that genetically vulnerable populations of Arctic charr have maintained neutral and putatively adaptive genetic diversity despite small effective sizes, attesting the importance of continued protection and assurance of gene flow among populations.

Keywords
Adaptive potential, Genetic monitoring, CBD, WGS, Genetic indicators, EBVs, Salmonid
National Category
Zoology Genetics
Identifiers
urn:nbn:se:su:diva-226065 (URN)10.1007/s10592-023-01586-3 (DOI)001145706500001 ()2-s2.0-85182671789 (Scopus ID)
Available from: 2024-02-12 Created: 2024-02-12 Last updated: 2024-02-12
Pearman, P. B., Laikre, L., Posledovich, D. & Bruford, M. (2024). Monitoring of species' genetic diversity in Europe varies greatly and overlooks potential climate change impacts. Nature Ecology & Evolution, 8, 267-281
Open this publication in new window or tab >>Monitoring of species' genetic diversity in Europe varies greatly and overlooks potential climate change impacts
2024 (English)In: Nature Ecology & Evolution, E-ISSN 2397-334X, Vol. 8, p. 267-281Article in journal (Refereed) Published
Abstract [en]

Genetic monitoring of populations currently attracts interest in the context of the Convention on Biological Diversity but needs long-term planning and investments. However, genetic diversity has been largely neglected in biodiversity monitoring, and when addressed, it is treated separately, detached from other conservation issues, such as habitat alteration due to climate change. We report an accounting of efforts to monitor population genetic diversity in Europe (genetic monitoring effort, GME), the evaluation of which can help guide future capacity building and collaboration towards areas most in need of expanded monitoring. Overlaying GME with areas where the ranges of selected species of conservation interest approach current and future climate niche limits helps identify whether GME coincides with anticipated climate change effects on biodiversity. Our analysis suggests that country area, financial resources and conservation policy influence GME, high values of which only partially match species' joint patterns of limits to suitable climatic conditions. Populations at trailing climatic niche margins probably hold genetic diversity that is important for adaptation to changing climate. Our results illuminate the need in Europe for expanded investment in genetic monitoring across climate gradients occupied by focal species, a need arguably greatest in southeastern European countries. This need could be met in part by expanding the European Union's Birds and Habitats Directives to fully address the conservation and monitoring of genetic diversity. Comparing data on genetic monitoring efforts across Europe with the distributions of areas at species' climatic niche margins, the authors show that monitoring efforts should be expanded to populations at trailing niche margins to include genetic variation that may prove important for adaptation to ongoing climate warming.

National Category
Biological Sciences
Identifiers
urn:nbn:se:su:diva-226344 (URN)10.1038/s41559-023-02260-0 (DOI)001143466500003 ()38225425 (PubMedID)2-s2.0-85182481927 (Scopus ID)
Available from: 2024-02-07 Created: 2024-02-07 Last updated: 2024-02-07Bibliographically approved
Hössjer, O., Laikre, L. & Ryman, N. (2023). Assessment of the Global Variance Effective Size of Subdivided Populations, and Its Relation to Other Effective Sizes. Acta Biotheoretica, 71(3), Article ID 19.
Open this publication in new window or tab >>Assessment of the Global Variance Effective Size of Subdivided Populations, and Its Relation to Other Effective Sizes
2023 (English)In: Acta Biotheoretica, ISSN 0001-5342, E-ISSN 1572-8358, Vol. 71, no 3, article id 19Article in journal (Refereed) Published
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.

Keywords
Genetic diversity, Length of time interval, Matrix analytic recursions, Metapopulation, Migration-drift equilibrium, Perturbation theory of matrices, Variance effective size
National Category
Evolutionary Biology
Identifiers
urn:nbn:se:su:diva-221119 (URN)10.1007/s10441-023-09470-w (DOI)001032489500001 ()37458852 (PubMedID)2-s2.0-85158004417 (Scopus ID)
Available from: 2023-09-19 Created: 2023-09-19 Last updated: 2023-09-19Bibliographically approved
Robuchon, M., da Silva, J., Dubois, G., Gumbs, R., Hoban, S., Laikre, L., . . . Perino, A. (2023). Conserving species' evolutionary potential and history: Opportunities under the Kunming–Montreal Global Biodiversity Framework. Conservation Science and Practice, 5(6), Article ID e12929.
Open this publication in new window or tab >>Conserving species' evolutionary potential and history: Opportunities under the Kunming–Montreal Global Biodiversity Framework
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2023 (English)In: Conservation Science and Practice, E-ISSN 2578-4854, Vol. 5, no 6, article id e12929Article in journal (Refereed) Published
Abstract [en]

Genetic diversity (GD) and phylogenetic diversity (PD) respectively represent species' evolutionary potential and history, and support most of the biodiversity benefits to humanity. Yet, these two biodiversity facets have been overlooked in previous biodiversity policies. As the Parties to the Convention on Biological Diversity (CBD) adopted the Kunming–Montreal Global Biodiversity Framework (GBF) in December 2022, we analyze how GD and PD are considered in this new framework and discuss how their incorporation in the GBF could strengthen their conservation. Although the inclusion of certain indicators could be elevated, both GD and PD are an integral part of the recently adopted GBF. This represents a significant improvement compared to the CBD strategic plan 2011–2020 and an unprecedented opportunity to bring species' evolutionary potential and history to the core of public biodiversity policies. We urge the scientific community to leverage this opportunity to actually improve the conservation of species' evolutionary potential and history. 

Keywords
biodiversity policies, genetic diversity, multilateral environmental agreements, phylogenetic diversity, science-policy interface
National Category
Other Biological Topics Evolutionary Biology Social Sciences Interdisciplinary
Identifiers
urn:nbn:se:su:diva-216980 (URN)10.1111/csp2.12929 (DOI)000969267100001 ()2-s2.0-85152774462 (Scopus ID)
Available from: 2023-05-09 Created: 2023-05-09 Last updated: 2023-09-26Bibliographically approved
Kurland, S., Ryman, N., Hössjer, O. & Laikre, L. (2023). Effects of subpopulation extinction on effective size (Ne) of metapopulations. Conservation Genetics, 24(4), 417-433
Open this publication in new window or tab >>Effects of subpopulation extinction on effective size (Ne) of metapopulations
2023 (English)In: Conservation Genetics, ISSN 1566-0621, E-ISSN 1572-9737, Vol. 24, no 4, p. 417-433Article in journal (Refereed) Published
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. 

Keywords
Inbreeding effective population size, Eigenvalue effective size, Realized effective size, Substructured populations, Conservation genetics
National Category
Genetics Ecology
Identifiers
urn:nbn:se:su:diva-216315 (URN)10.1007/s10592-023-01510-9 (DOI)000953077900002 ()2-s2.0-85150289396 (Scopus ID)
Available from: 2023-04-12 Created: 2023-04-12 Last updated: 2023-10-04Bibliographically approved
Hoban, S., Bruford, M. W., da Silva, J. M., Funk, W. C., Frankham, R., Gill, M. J., . . . Laikre, L. (2023). Genetic diversity goals and targets have improved, but remain insufficient for clear implementation of the post-2020 global biodiversity framework. Conservation Genetics, 24(2), 181-191
Open this publication in new window or tab >>Genetic diversity goals and targets have improved, but remain insufficient for clear implementation of the post-2020 global biodiversity framework
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2023 (English)In: Conservation Genetics, ISSN 1566-0621, E-ISSN 1572-9737, Vol. 24, no 2, p. 181-191Article in journal (Refereed) Published
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.

Keywords
Adaptive capacity, Gene flow, Global conservation policy, Effective population size, Indicators
National Category
Biological Sciences
Identifiers
urn:nbn:se:su:diva-214868 (URN)10.1007/s10592-022-01492-0 (DOI)000914363000001 ()36683963 (PubMedID)2-s2.0-85146290176 (Scopus ID)
Available from: 2023-02-21 Created: 2023-02-21 Last updated: 2023-04-20Bibliographically approved
Hoban, S., da Silva, J. M., Mastretta-Yanes, A., Grueber, C. E., Heuertz, M., Hunter, M. E., . . . Laikre, L. (2023). Monitoring status and trends in genetic diversity for the Convention on Biological Diversity: An ongoing assessment of genetic indicators in nine countries. Conservation Letters, 16(3), Article ID e12953.
Open this publication in new window or tab >>Monitoring status and trends in genetic diversity for the Convention on Biological Diversity: An ongoing assessment of genetic indicators in nine countries
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2023 (English)In: Conservation Letters, ISSN 1755-263X, E-ISSN 1755-263X, Vol. 16, no 3, article id e12953Article in journal (Refereed) Published
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. 

Keywords
adaptive capacity, conservation genetics, indicators, monitoring, policy, resilience
National Category
Genetics Environmental Sciences Social Sciences Interdisciplinary
Identifiers
urn:nbn:se:su:diva-220231 (URN)10.1111/conl.12953 (DOI)000979327700001 ()2-s2.0-85158056742 (Scopus ID)
Available from: 2023-08-23 Created: 2023-08-23 Last updated: 2023-08-23Bibliographically approved
Kurland, S., Saha, A., P. Keehnen, N. L., Celorio-Mancera, M. d., Diez-del-Molino, D., Ryman, N. & Laikre, L. (2023). New indicators for monitoring genetic diversity applied to alpine brown trout populations using whole genome sequence data. Molecular Ecology
Open this publication in new window or tab >>New indicators for monitoring genetic diversity applied to alpine brown trout populations using whole genome sequence data
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2023 (English)In: Molecular Ecology, ISSN 0962-1083, E-ISSN 1365-294XArticle in journal (Refereed) Epub ahead of print
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.

Keywords
biodiversity, EBVs, indicators of genetic diversity, microevolution, population genomics, temporal genetic variation
National Category
Ecology
Identifiers
urn:nbn:se:su:diva-224675 (URN)10.1111/mec.17213 (DOI)001114869500001 ()38014725 (PubMedID)2-s2.0-85178076867 (Scopus ID)
Available from: 2023-12-19 Created: 2023-12-19 Last updated: 2023-12-19
Dussex, N., Kurland, S., Olsen, R.-A., Spong, G., Ericsson, G., Ekblom, R., . . . Laikre, L. (2023). Range-wide and temporal genomic analyses reveal the consequences of near-extinction in Swedish moose. Communications Biology, 6(1), Article ID 1035.
Open this publication in new window or tab >>Range-wide and temporal genomic analyses reveal the consequences of near-extinction in Swedish moose
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2023 (English)In: Communications Biology, E-ISSN 2399-3642, Vol. 6, no 1, article id 1035Article in journal (Refereed) Published
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.

National Category
Genetics Ecology
Identifiers
urn:nbn:se:su:diva-224297 (URN)10.1038/s42003-023-05385-x (DOI)001097463800001 ()37848497 (PubMedID)2-s2.0-85174459749 (Scopus ID)
Available from: 2023-12-07 Created: 2023-12-07 Last updated: 2023-12-07Bibliographically approved
Organisations
Identifiers
ORCID iD: ORCID iD iconorcid.org/0000-0001-9286-3361

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