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Kyriazis CC, Serieys LE, Bishop JM, Drouilly M, Viljoen S, Wayne RK, Lohmueller KE. The influence of gene flow on population viability in an isolated urban caracal population. Mol Ecol 2024; 33:e17346. [PMID: 38581173 PMCID: PMC11035096 DOI: 10.1111/mec.17346] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Revised: 01/23/2024] [Accepted: 03/26/2024] [Indexed: 04/08/2024]
Abstract
Wildlife populations are becoming increasingly fragmented by anthropogenic development. Small and isolated populations often face an elevated risk of extinction, in part due to inbreeding depression. Here, we examine the genomic consequences of urbanization in a caracal (Caracal caracal) population that has become isolated in the Cape Peninsula region of the City of Cape Town, South Africa, and is thought to number ~50 individuals. We document low levels of migration into the population over the past ~75 years, with an estimated rate of 1.3 effective migrants per generation. As a consequence of this isolation and small population size, levels of inbreeding are elevated in the contemporary Cape Peninsula population (mean FROH = 0.20). Inbreeding primarily manifests as long runs of homozygosity >10 Mb, consistent with the effects of isolation due to the rapid recent growth of Cape Town. To explore how reduced migration and elevated inbreeding may impact future population dynamics, we parameterized an eco-evolutionary simulation model. We find that if migration rates do not change in the future, the population is expected to decline, though with a low projected risk of extinction. However, if migration rates decline or anthropogenic mortality rates increase, the potential risk of extinction is greatly elevated. To avert a population decline, we suggest that translocating migrants into the Cape Peninsula to initiate a genetic rescue may be warranted in the near future. Our analysis highlights the utility of genomic datasets coupled with computational simulation models for investigating the influence of gene flow on population viability.
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Affiliation(s)
- Christopher C. Kyriazis
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA 90095, USA
| | - Laurel E.K. Serieys
- Panthera, 8 W 40th St, 18th Floor, New York, NY 10018, USA
- Institute for Communities and Wildlife in Africa, Department of Biological Sciences, University of Cape Town, Rondebosch, 7701, South Africa
| | - Jacqueline M. Bishop
- Institute for Communities and Wildlife in Africa, Department of Biological Sciences, University of Cape Town, Rondebosch, 7701, South Africa
| | - Marine Drouilly
- Panthera, 8 W 40th St, 18th Floor, New York, NY 10018, USA
- Institute for Communities and Wildlife in Africa, Department of Biological Sciences, University of Cape Town, Rondebosch, 7701, South Africa
- Centre for Social Science Research, University of Cape Town, Rondebosch, 7701, South Africa
| | - Storme Viljoen
- Institute for Communities and Wildlife in Africa, Department of Biological Sciences, University of Cape Town, Rondebosch, 7701, South Africa
| | - Robert K. Wayne
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA 90095, USA
| | - Kirk E. Lohmueller
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA 90095, USA
- Interdepartmental Program in Bioinformatics, University of California, Los Angeles, CA 90095, USA
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, CA 90095, USA
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2
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Smeds L, Huson LSA, Ellegren H. Structural genomic variation in the inbred Scandinavian wolf population contributes to the realized genetic load but is positively affected by immigration. Evol Appl 2024; 17:e13652. [PMID: 38333557 PMCID: PMC10848878 DOI: 10.1111/eva.13652] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Revised: 01/08/2024] [Accepted: 01/16/2024] [Indexed: 02/10/2024] Open
Abstract
When populations decrease in size and may become isolated, genomic erosion by loss of diversity from genetic drift and accumulation of deleterious mutations is likely an inevitable consequence. In such cases, immigration (genetic rescue) is necessary to restore levels of genetic diversity and counteract inbreeding depression. Recent work in conservation genomics has studied these processes focusing on the genetic diversity of single nucleotide polymorphisms. In contrast, our knowledge about structural genomic variation (insertions, deletions, duplications and inversions) in endangered species is limited. We analysed whole-genome, short-read sequences from 212 wolves from the inbred Scandinavian population and from neighbouring populations in Finland and Russia, and detected >35,000 structural variants (SVs) after stringent quality and genotype frequency filtering; >26,000 high-confidence variants remained after manual curation. The majority of variants were shorter than 1 kb, with a distinct peak in the length distribution of deletions at 190 bp, corresponding to insertion events of SINE/tRNA-Lys elements. The site frequency spectrum of SVs in protein-coding regions was significantly shifted towards rare alleles compared to putatively neutral variants, consistent with purifying selection. The realized genetic load of SVs in protein-coding regions increased with inbreeding levels in the Scandinavian population, but immigration provided a genetic rescue effect by lowering the load and reintroducing ancestral alleles at loci fixed for derived SVs. Our study shows that structural variation comprises a common type of in part deleterious mutations in endangered species and that establishing gene flow is necessary to mitigate the negative consequences of loss of diversity.
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Affiliation(s)
- Linnéa Smeds
- Department of Ecology and Genetics, Evolutionary BiologyUppsala UniversityUppsalaSweden
| | - Lars S. A. Huson
- Department of Ecology and Genetics, Evolutionary BiologyUppsala UniversityUppsalaSweden
| | - Hans Ellegren
- Department of Ecology and Genetics, Evolutionary BiologyUppsala UniversityUppsalaSweden
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3
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Robinson J, Kyriazis CC, Yuan SC, Lohmueller KE. Deleterious Variation in Natural Populations and Implications for Conservation Genetics. Annu Rev Anim Biosci 2023; 11:93-114. [PMID: 36332644 PMCID: PMC9933137 DOI: 10.1146/annurev-animal-080522-093311] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Deleterious mutations decrease reproductive fitness and are ubiquitous in genomes. Given that many organisms face ongoing threats of extinction, there is interest in elucidating the impact of deleterious variation on extinction risk and optimizing management strategies accounting for such mutations. Quantifying deleterious variation and understanding the effects of population history on deleterious variation are complex endeavors because we do not know the strength of selection acting on each mutation. Further, the effect of demographic history on deleterious mutations depends on the strength of selection against the mutation and the degree of dominance. Here we clarify how deleterious variation can be quantified and studied in natural populations. We then discuss how different demographic factors, such as small population size, nonequilibrium population size changes, inbreeding, and gene flow, affect deleterious variation. Lastly, we provide guidance on studying deleterious variation in nonmodel populations of conservation concern.
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Affiliation(s)
- Jacqueline Robinson
- Institute for Human Genetics, University of California, San Francisco, California, USA;
| | - Christopher C Kyriazis
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, California, USA; , ,
| | - Stella C Yuan
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, California, USA; , ,
| | - Kirk E Lohmueller
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, California, USA; , , .,Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, California, USA
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4
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Muller-Girard M, Fowles G, Duchamp J, Kouneski S, Mollohan C, Smyser TJ, Turner GG, Westrich B, Doyle JM. A novel SNP assay reveals increased genetic variability and abundance following translocations to a remnant Allegheny woodrat population. BMC Ecol Evol 2022; 22:137. [PMID: 36418951 PMCID: PMC9686018 DOI: 10.1186/s12862-022-02083-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Accepted: 10/19/2022] [Indexed: 11/26/2022] Open
Abstract
BACKGROUND Allegheny woodrats (Neotoma magister) are found in metapopulations distributed throughout the Interior Highlands and Appalachia. Historically these metapopulations persisted as relatively fluid networks, enabling gene flow between subpopulations and recolonization of formerly extirpated regions. However, over the past 45 years, the abundance of Allegheny woodrats has declined throughout the species' range due to a combination of habitat destruction, declining hard mast availability, and roundworm parasitism. In an effort to initiate genetic rescue of a small, genetically depauperate subpopulation in New Jersey, woodrats were translocated from a genetically robust population in Pennsylvania (PA) in 2015, 2016 and 2017. Herein, we assess the efficacy of these translocations to restore genetic diversity within the recipient population. RESULTS We designed a novel 134 single nucleotide polymorphism panel, which was used to genotype the six woodrats translocated from PA and 82 individuals from the NJ population captured before and after the translocation events. These data indicated that a minimum of two translocated individuals successfully produced at least 13 offspring, who reproduced as well. Further, population-wide observed heterozygosity rose substantially following the first set of translocations, reached levels comparable to that of populations in Indiana and Ohio, and remained elevated over the subsequent years. Abundance also increased during the monitoring period, suggesting Pennsylvania translocations initiated genetic rescue of the New Jersey population. CONCLUSIONS Our results indicate, encouragingly, that very small numbers of translocated individuals can successfully restore the genetic diversity of a threatened population. Our work also highlights the challenges of managing very small populations, such as when translocated individuals have greater reproductive success relative to residents. Finally, we note that ongoing work with Allegheny woodrats may broadly shape our understanding of genetic rescue within metapopulations and across heterogeneous landscapes.
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Affiliation(s)
- Megan Muller-Girard
- grid.265122.00000 0001 0719 7561Department of Environmental Science and Studies, Towson University, 8000 York Rd, Baltimore, MD 21252 USA
| | - Gretchen Fowles
- Endangered and Nongame Species Program, New Jersey DEP Fish and Wildlife, 1255 County Rd 629, Lebanon, NJ 08833 USA
| | - Joseph Duchamp
- grid.257427.10000000088740847Department of Biology, Indiana University of Pennsylvania, 975 Oakland Avenue, Indiana, PA 15705-1081 USA
| | - Samantha Kouneski
- grid.265122.00000 0001 0719 7561Department of Biological Sciences, Towson University, 8000 York Rd, Baltimore, MD 21252 USA
| | | | - Timothy J. Smyser
- grid.413759.d0000 0001 0725 8379USDA-APHIS-WS National Wildlife Research Center, Fort Collins, CO USA
| | - Gregory G. Turner
- Pennsylvania Game Commission, 2001 Elmerton Avenue, Harrisburg, PA 17110 USA
| | - Bradford Westrich
- grid.448453.a0000 0004 1130 5264Indiana Department of Natural Resources, 5596 East State Road 46, Bloomington, IN 47401 USA
| | - Jacqueline M. Doyle
- grid.265122.00000 0001 0719 7561Department of Biological Sciences, Towson University, 8000 York Rd, Baltimore, MD 21252 USA
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5
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Wallén J, Norén K, Angerbjörn A, Eide NE, Landa A, Flagstad Ø. Context‐dependent demographic and genetic effects of translocation from a captive breeding project. Anim Conserv 2022. [DOI: 10.1111/acv.12831] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Affiliation(s)
- J. Wallén
- Department of Zoology Stockholm University Stockholm Sweden
| | - K. Norén
- Department of Zoology Stockholm University Stockholm Sweden
| | - A. Angerbjörn
- Department of Zoology Stockholm University Stockholm Sweden
| | - N. E. Eide
- Norwegian Institute for Nature Research Trondheim Norway
| | - A. Landa
- Norwegian Institute for Nature Research Bergen Norway
| | - Ø. Flagstad
- Norwegian Institute for Nature Research Trondheim Norway
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6
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Ochoa A, Onorato DP, Roelke-Parker ME, Culver M, Fitak RR. Give and Take: Effects of Genetic Admixture on Mutation Load in Endangered Florida Panthers. J Hered 2022; 113:491-499. [PMID: 35930593 DOI: 10.1093/jhered/esac037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Accepted: 08/02/2022] [Indexed: 11/14/2022] Open
Abstract
Genetic admixture is a biological event inherent to genetic rescue programs aimed at the long-term conservation of endangered wildlife. Although the success of such programs can be measured by the increase in genetic diversity and fitness of subsequent admixed individuals, predictions supporting admixture costs to fitness due to the introduction of novel deleterious alleles are necessary. Here, we analyzed nonsynonymous variation from conserved genes to quantify and compare levels of mutation load (i.e., proportion of deleterious alleles and genotypes carrying these alleles) among endangered Florida panthers and non-endangered Texas pumas. Specifically, we used canonical (i.e., non-admixed) Florida panthers, Texas pumas, and F1 (canonical Florida x Texas) panthers dating from a genetic rescue program and Everglades National Park panthers with Central American ancestry resulting from an earlier admixture event. We found neither genetic drift nor selection significantly reduced overall proportions of deleterious alleles in the severely bottlenecked canonical Florida panthers. Nevertheless, the deleterious alleles identified were distributed into a disproportionately high number of homozygous genotypes due to close inbreeding in this group. Conversely, admixed Florida panthers (either with Texas or Central American ancestry) presented reduced levels of homozygous genotypes carrying deleterious alleles but increased levels of heterozygous genotypes carrying these variants relative to canonical Florida panthers. Although admixture is likely to alleviate the load of standing deleterious variation present in homozygous genotypes, our results suggest introduced novel deleterious alleles (temporarily present in heterozygous state) in genetically rescued populations could potentially be expressed in subsequent generations if their effective sizes remain small.
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Affiliation(s)
- Alexander Ochoa
- Department of Biology and Genomics and Bioinformatics Cluster, University of Central Florida, Orlando, FL
| | - David P Onorato
- Fish and Wildlife Research Institute, Florida Fish and Wildlife Conservation Commission, Naples, FL
| | - Melody E Roelke-Parker
- Frederick National Laboratory of Cancer Research, Leidos Biomedical Research, Inc., Bethesda, MD
| | - Melanie Culver
- U.S. Geological Survey, Arizona Cooperative Fish and Wildlife Research Unit, and School of Natural Resources and the Environment, University of Arizona, Tucson, AZ
| | - Robert R Fitak
- Department of Biology and Genomics and Bioinformatics Cluster, University of Central Florida, Orlando, FL
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7
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Jackson HA, Percival‐Alwyn L, Ryan C, Albeshr MF, Venturi L, Morales HE, Mathers TC, Cocker J, Speak SA, Accinelli GG, Barker T, Heavens D, Willman F, Dawson D, Ward L, Tatayah V, Zuël N, Young R, Concannon L, Whitford H, Clavijo B, Bunbury N, Tyler KM, Ruhomaun K, Grace MK, Bruford MW, Jones CG, Tollington S, Bell DJ, Groombridge JJ, Clark M, Van Oosterhout C. Genomic erosion in a demographically recovered bird species during conservation rescue. CONSERVATION BIOLOGY : THE JOURNAL OF THE SOCIETY FOR CONSERVATION BIOLOGY 2022; 36:e13918. [PMID: 35554972 PMCID: PMC9546124 DOI: 10.1111/cobi.13918] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Revised: 01/07/2022] [Accepted: 01/13/2022] [Indexed: 06/15/2023]
Abstract
The pink pigeon (Nesoenas mayeri) is an endemic species of Mauritius that has made a remarkable recovery after a severe population bottleneck in the 1970s to early 1990s. Prior to this bottleneck, an ex situ population was established from which captive-bred individuals were released into free-living subpopulations to increase population size and genetic variation. This conservation rescue led to rapid population recovery to 400-480 individuals, and the species was twice downlisted on the International Union for the Conservation of Nature (IUCN) Red List. We analyzed the impacts of the bottleneck and genetic rescue on neutral genetic variation during and after population recovery (1993-2008) with restriction site-associated sequencing, microsatellite analyses, and quantitative genetic analysis of studbook data of 1112 birds from zoos in Europe and the United States. We used computer simulations to study the predicted changes in genetic variation and population viability from the past into the future. Genetic variation declined rapidly, despite the population rebound, and the effective population size was approximately an order of magnitude smaller than census size. The species carried a high genetic load of circa 15 lethal equivalents for longevity. Our computer simulations predicted continued inbreeding will likely result in increased expression of deleterious mutations (i.e., a high realized load) and severe inbreeding depression. Without continued conservation actions, it is likely that the pink pigeon will go extinct in the wild within 100 years. Conservation rescue of the pink pigeon has been instrumental in the recovery of the free-living population. However, further genetic rescue with captive-bred birds from zoos is required to recover lost variation, reduce expression of harmful deleterious variation, and prevent extinction. The use of genomics and modeling data can inform IUCN assessments of the viability and extinction risk of species, and it helps in assessments of the conservation dependency of populations.
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Affiliation(s)
- Hazel A. Jackson
- Durrell Institute of Conservation and Ecology, School of Anthropology and ConservationUniversity of KentCanterburyUK
| | | | - Camilla Ryan
- School of Environmental SciencesUniversity of East AngliaNorwichUK
- The Earlham InstituteNorwichUK
| | - Mohammed F. Albeshr
- School of Biological SciencesUniversity of East AngliaNorwichUK
- Department of Zoology, Faculty of ScienceKing Saud UniversityRiyadhSaudi Arabia
| | - Luca Venturi
- Department of Life SciencesThe Natural History MuseumLondonUK
| | | | | | - Jonathan Cocker
- The Earlham InstituteNorwichUK
- School of Biological SciencesUniversity of East AngliaNorwichUK
| | - Samuel A. Speak
- School of Environmental SciencesUniversity of East AngliaNorwichUK
| | | | | | | | - Faye Willman
- Durrell Institute of Conservation and Ecology, School of Anthropology and ConservationUniversity of KentCanterburyUK
- Institute of ZoologyZoological Society of LondonLondonUK
| | - Deborah Dawson
- NERC Biomolecular Analysis Facility, Department of Animal and Plant SciencesUniversity of SheffieldSheffieldUK
| | - Lauren Ward
- Durrell Institute of Conservation and Ecology, School of Anthropology and ConservationUniversity of KentCanterburyUK
- NERC Biomolecular Analysis Facility, Department of Animal and Plant SciencesUniversity of SheffieldSheffieldUK
| | | | - Nicholas Zuël
- Mauritian Wildlife FoundationVacoas‐PhoenixMauritius
| | - Richard Young
- Durrell Wildlife Conservation TrustJerseyChannel Islands
| | | | | | | | - Nancy Bunbury
- Seychelles Islands FoundationVictoriaSeychelles
- Centre for Ecology and ConservationUniversity of ExeterPenrynUK
| | - Kevin M. Tyler
- Norwich Medical SchoolUniversity of East AngliaNorwichUK
| | - Kevin Ruhomaun
- National Parks and Conservation Service, Ministry of EnvironmentGovernment of MauritiusRéduitMauritius
| | - Molly K. Grace
- Molly K. Grace, Department of ZoologyUniversity of OxfordOxfordUK
| | | | - Carl G. Jones
- Mauritian Wildlife FoundationVacoas‐PhoenixMauritius
- Durrell Wildlife Conservation TrustJerseyChannel Islands
| | - Simon Tollington
- Durrell Institute of Conservation and Ecology, School of Anthropology and ConservationUniversity of KentCanterburyUK
- NERC Biomolecular Analysis Facility, Department of Animal and Plant SciencesUniversity of SheffieldSheffieldUK
- North of England Zoological SocietyChester ZooChesterUK
| | - Diana J. Bell
- School of Biological SciencesUniversity of East AngliaNorwichUK
| | - Jim J. Groombridge
- Durrell Institute of Conservation and Ecology, School of Anthropology and ConservationUniversity of KentCanterburyUK
| | - Matt Clark
- The Earlham InstituteNorwichUK
- Department of Life SciencesThe Natural History MuseumLondonUK
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8
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Hasselgren M, Dussex N, von Seth J, Angerbjörn A, Olsen RA, Dalén L, Norén K. Genomic and fitness consequences of inbreeding in an endangered carnivore. Mol Ecol 2021; 30:2790-2799. [PMID: 33955096 DOI: 10.1111/mec.15943] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Revised: 03/31/2021] [Accepted: 04/14/2021] [Indexed: 12/28/2022]
Abstract
Reduced fitness through genetic drift and inbreeding is a major threat to small and isolated populations. Although previous studies have generally used genetically verified pedigrees to document effects of inbreeding and gene flow, these often fail to capture the whole inbreeding history of the species. By assembling a draft arctic fox (Vulpes lagopus) genome and resequencing complete genomes of 23 additional foxes born before and after a well-documented immigration event in Scandinavia, we here look into the genomic consequences of inbreeding and genetic rescue. We found a difference in genome-wide diversity, with 18% higher heterozygosity and 81% lower FROH in immigrant F1 compared to native individuals. However, more distant descendants of immigrants (F2, F3) did not show the same pattern. We also found that foxes with lower inbreeding had higher probability to survive their first year of life. Our results demonstrate the important link between genetic variation and fitness as well as the transient nature of genetic rescue. Moreover, our results have implications in conservation biology as they demonstrate that inbreeding depression can effectively be detected in the wild by a genomic approach.
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Affiliation(s)
| | - Nicolas Dussex
- Department of Zoology, Stockholm University, Stockholm, Sweden.,Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden
| | - Johanna von Seth
- Department of Zoology, Stockholm University, Stockholm, Sweden.,Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden
| | | | - Remi-André Olsen
- Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, Solna, Sweden
| | - Love Dalén
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden
| | - Karin Norén
- Department of Zoology, Stockholm University, Stockholm, Sweden
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