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  • 1.
    Corrales, Carolina
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Population and Conservation Biology.
    Höglund, Jacob
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Population and Conservation Biology.
    Maintenance of gene flow by female-biased dispersal of black grouse, Tetrao tetrix in northern Sweden2012In: Journal of Ornithology = Journal fur Ornithologie, ISSN 0021-8375, E-ISSN 1439-0361, Vol. 153, no 4, p. 1127-1139Article in journal (Refereed)
    Abstract [en]

    Sex-biased dispersal is a common phenomenon in most birds. In general, males breed at or near their site of birth while most of the females disperse. We investigated the dispersal patterns and genetic structure of lekking Black Grouse Tetrao tetrix based on ten microsatellite loci. Data for 469 individuals from 25 localities spaced from 45 to 558 km apart revealed low levels of genetic differentiation and high connectivity among studied sites due to female-biased dispersal. The spatial distribution of the genetic variation did not follow an isolation by distance pattern neither for females nor for males. STRUCTURE identified three clusters of male individuals but without any geographical pattern. Only one cluster was identified for females. Several tests of sex-biased dispersal were executed. Most of them showed no difference between sexes, but the mean assignment index and F IS showed a statistically significant female-biased dispersal. Therefore, we consider that the northern Swedish Black Grouse population is a panmictic population. The amount of gene flow throughout time has been consistent with dispersal and with no strong effect of forest fragmentation in the region.

  • 2.
    Corrales, Carolina
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Population and Conservation Biology.
    Pavlovska, Mariia
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Population and Conservation Biology.
    Hoglund, Jacob
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Population and Conservation Biology.
    Phylogeography and subspecies status of Black Grouse2014In: Journal of Ornithology = Journal fur Ornithologie, ISSN 0021-8375, E-ISSN 1439-0361, Vol. 155, no 1, p. 13-25Article in journal (Refereed)
    Abstract [en]

    The cold periods of the Pleistocene have had a striking impact on the diversification of most organisms in temperate regions. Phylogeographic patterns and postglacial expansion are poorly understood in the Black Grouse (Tetrao tetrix). This species is widely distributed across Eurasia, and has been divided into a number of subspecies on the basis of morphological differences and geographic isolation. To investigate the evolutionary history of the species, 143 samples from different regions were examined for a mtDNA control region fragment. Overall, analyses of mtDNA gave support for the divergence between Tetrao tetrix tetrix, T. t. ussuriensis and T. t. mongolicus. The analyses reveal the effects of colonisation out of glacial refugia on the genetic diversity and genetic structure of Black Grouse. The phylogeographical results are consistent with a demographic population expansion following a bell-shaped mismatch distribution, a star-shaped phylogeny and low nucleotide diversity. Patterns of postglacial dispersal imply that Black Grouse from southern Europe have been restricted to this area, and did not contribute to the genetic diversity of northern Europe. Instead, Black Grouse spread out to northern Europe from a refugium in the east and a possible one in western Europe, following the retreat of glacial ice sheets, although both refugia remain unidentified. We suggest that T. t. britannicus and T. t. viridanus correspond to northern T. t. tetrix, and that this lineage has diverged from the other subspecies. This division is tentative due to limited sampling, but it will facilitate the management of different evolutionary significant units of the species.

  • 3.
    Cortazar-Chinarro, Maria
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology.
    Lattenkamp, Ella Z.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology. Max Planck Inst Psycholinguist, Dept Neurogenet Vocal Commun, Box 310, NL-6500 Nijmegen, Netherlands..
    Meyer-Lucht, Yvonne
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology.
    Luquet, Emilien
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology. Univ Claude Bernard Lyon I, CNRS, UMR 5023, LEHNA, 3-6 Rue Raphael Dubois,Batiments Darwin C & Forel, F-69622 Villeurbanne 43, France..
    Laurila, Anssi
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology.
    Höglund, Jacob
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology.
    Drift, selection, or migration?: Processes affecting genetic differentiation and variation along a latitudinal gradient in an amphibian2017In: BMC Evolutionary Biology, ISSN 1471-2148, E-ISSN 1471-2148, Vol. 17, article id 189Article in journal (Refereed)
    Abstract [en]

    Background: Past events like fluctuations in population size and post-glacial colonization processes may influence the relative importance of genetic drift, migration and selection when determining the present day patterns of genetic variation. We disentangle how drift, selection and migration shape neutral and adaptive genetic variation in 12 moor frog populations along a 1700 km latitudinal gradient. We studied genetic differentiation and variation at a MHC exon II locus and a set of 18 microsatellites. Results: Using outlier analyses, we identified the MHC II exon 2 (corresponding to the beta-2 domain) locus and one microsatellite locus (RCO8640) to be subject to diversifying selection, while five microsatellite loci showed signals of stabilizing selection among populations. STRUCTURE and DAPC analyses on the neutral microsatellites assigned populations to a northern and a southern cluster, reflecting two different post-glacial colonization routes found in previous studies. Genetic variation overall was lower in the northern cluster. The signature of selection on MHC exon II was weaker in the northern cluster, possibly as a consequence of smaller and more fragmented populations. Conclusion: Our results show that historical demographic processes combined with selection and drift have led to a complex pattern of differentiation along the gradient where some loci are more divergent among populations than predicted from drift expectations due to diversifying selection, while other loci are more uniform among populations due to stabilizing selection. Importantly, both overall and MHC genetic variation are lower at northern latitudes. Due to lower evolutionary potential, the low genetic variation in northern populations may increase the risk of extinction when confronted with emerging pathogens and climate change.

  • 4.
    Cortazar-Chinarro, Maria
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology. Uppsala University.
    Meyer-Lucht, Yvonne
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology.
    Laurila, Anssi
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology.
    Höglund, Jacob
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology.
    Signatures of historical selection on MHC reveal different selection patterns in the moor frog (Rana arvalis)2018In: Immunogenetics, ISSN 0093-7711, E-ISSN 1432-1211, Vol. 70, no 7, p. 477-484Article in journal (Refereed)
    Abstract [en]

    MHC genes are key components in disease resistance and an excellent system for studying selection acting on genetic variation in natural populations. Current patterns of variation in MHC genes are likely to be influenced by past and ongoing selection as well as demographic fluctuations in population size such as those imposed by post-glacial recolonization processes. Here, we investigated signatures of historical selection and demography on an MHC class II gene in 12 moor frog populations along a 1700-km latitudinal gradient. Sequences were obtained from 207 individuals and consecutively assigned into two different clusters (northern and southern clusters, respectively) in concordance with a previously described dual post-glacial colonization route. Selection analyses comparing the relative rates of non-synonymous to synonymous substitutions (dN/dS) suggested evidence of different selection patterns in the northern and the southern clusters, with divergent selection prevailing in the south but uniform positive selection predominating in the north. Also, models of codon evolution revealed considerable differences in the strength of selection: The southern cluster appeared to be under strong selection while the northern cluster showed moderate signs of selection. Our results indicate that the MHC alleles in the north diverged from southern MHC alleles as a result of differential selection patterns.

  • 5.
    Ekblom, Robert
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolutionary Biology, Population Biology.
    Sæther, Stein Are
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolutionary Biology, Population Biology. Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolutionary Biology, Evolutionary Biology.
    Grahn, Mats
    Fiske, Peder
    Kålås, John Atle
    Höglund, Jacob
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolutionary Biology, Population Biology.
    Major histocompatibility complex variation and mate choice in a lekking bird, the great snipe (Gallinago media)2004In: Molecular Ecology, ISSN 0962-1083, E-ISSN 1365-294X, Vol. 13, no 12, p. 3821-3828Article in journal (Refereed)
    Abstract [en]

    Genes of the major histocompatibility complex (MHC) play a major part in the activation of the vertebrate immune system. In addition, they also appear to function as cues for mate choice. In mammals especially, several kinds of MHC-dependent mate choice have been hypothesized and observed. These include choice of mates that share no or few alleles with the choosing individual, choice of mates with alleles that differ as much as possible from the choosing individual, choice of heterozygous mates, choice of certain genotypes and choice of rare alleles. We investigated these different aspects of mate choice in relation to MHC in a lekking bird species, the great snipe (Gallinago media). We found no evidence for MHC disassortative mating, no preference for males with many MHC alleles and no preference for rare alleles. However, we did find that some allelic lineages were more often found in males with mating success than in males without mating success. Females do not seem to use themselves as references for the MHC-dependent mate choice, rather they seem to prefer males with certain allele types. We speculate that these alleles may be linked to resistance to common parasites.

  • 6.
    Ekblom, Robert
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Evolution, Population Biology.
    Sæther, Stein Are
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolutionary Biology, Population Biology. Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolutionary Biology, Evolutionary Biology.
    Hasselquist, Dennis
    Hannersjö, David
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolutionary Biology, Population Biology.
    Fiske, Peder
    Kålås, John Atle
    Höglund, Jacob
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolutionary Biology, Population Biology.
    Female choice and male humoral immune response in the lekking great snipe (Gallinago media)2005In: Behavioral Ecology, ISSN 1045-2249, E-ISSN 1465-7279, Vol. 16, no 2, p. 346-351Article in journal (Refereed)
    Abstract [en]

    Parasites and diseases constitute major evolutionary forces in many natural populations, and thus having an efficient immune defense to resist infections is crucial for many organisms. Properties of the immune response may also influence mate choice decisions in many animals. Theory predicts several advantages for females when choosing males with superior immune systems. These benefits can be both direct (e.g. increased paternal care and reduced disease transmission) and indirect (good genes). We have investigated female choice with respect to antibody response to two novel antigens in males of a lekking bird, the great snipe (Gallinago media). Because of the lek mating system, female choice probably mainly incurs indirect (genetic) rather than direct benefits. Males responded to vaccination with diphtheria and tetanus toxoids by producing specific antibodies to both antigens. Triggering the immune system had no negative impact on display activities or survival. Males that were chosen by females as mates had on average higher antibody response to the tetanus antigen than their neighbors. We did not, however, find any covariance between the strength of the antibody response and male mating success.

  • 7.
    Ekblom, Robert
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Evolution, Population and Conservation Biology.
    Sæther, Stein Are
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Evolution, Population and Conservation Biology.
    Jacobsson, Pär
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Evolution, Population and Conservation Biology.
    Fiske, Peder
    Sahlman, Tobias
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Evolution, Population and Conservation Biology.
    Grahn, Mats
    Kålås, John Atle
    Höglund, Jacob
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Evolution, Population and Conservation Biology.
    Spatial pattern of MHC class II variation in the great snipe (Gallinago media)2007In: Molecular Ecology, ISSN 0962-1083, E-ISSN 1365-294X, Vol. 16, no 7, p. 1439-1451Article in journal (Refereed)
    Abstract [en]

    The genes of the major histocompatibility complex (MHC) code for proteins involved in antigen recognition and triggering of the adaptive immune response, and are therefore likely to be under selection from parasites. These selection regimes may vary in space and time. Here we report a strong geographical structure in MHC class II B genes of a migrating bird, the great snipe (Gallinago media). Genetic differentiation in the MHC between two ecologically distinct distributional regions (Scandinavian mountain populations vs. East European lowland populations) was still present after statistically controlling for the effect of selectively neutral variation (microsatellites) using partial Mantel tests. This suggests a role for selection in generating this spatial structure and that it represents local adaptation to different environments. Differentiation between populations within the two regions was negligible. Overall, we found a high number of MHC alleles (50, from 175 individuals). This, together with a tendency for a higher rate of nonsynonymous than synonymous substitutions in the peptide binding sites, and high Tajima's D in certain regions of the gene, suggests a history of balancing selection. MHC variation is often thought to be maintained by some form of balancing selection, but the nature of this selection remains unclear. Our results support the hypothesis that spatial variation in selection regimes contributes to the high polymorphism.

  • 8.
    Fisher, Matthew C.
    et al.
    Imperial Coll London, Sch Publ Hlth, Fac Med, Dept Infect Dis Epidemiol, St Marys Campus, London W2 1PG, England.
    Ghosh, Pria
    Imperial Coll London, Sch Publ Hlth, Fac Med, Dept Infect Dis Epidemiol, St Marys Campus, London W2 1PG, England;North West Univ, Unit Environm Sci & Management, Private Bag x6001, ZA-2520 Potchefstroom, South Africa.
    Shelton, Jennifer M. G.
    Imperial Coll London, Sch Publ Hlth, Fac Med, Dept Infect Dis Epidemiol, St Marys Campus, London W2 1PG, England.
    Bates, Kieran
    Imperial Coll London, Sch Publ Hlth, Fac Med, Dept Infect Dis Epidemiol, St Marys Campus, London W2 1PG, England.
    Brookes, Lola
    Inst Zool, Regents Pk, London NW1 4RY, England.
    Wierzbicki, Claudia
    Imperial Coll London, Sch Publ Hlth, Fac Med, Dept Infect Dis Epidemiol, St Marys Campus, London W2 1PG, England.
    Rosa, Goncalo M.
    Inst Zool, Regents Pk, London NW1 4RY, England;Univ Lisbon, Fac Ciencias, Ctr Ecol Evolut & Environm Changes CE3C, Lisbon, Portugal.
    Farrer, Rhys A.
    Imperial Coll London, Sch Publ Hlth, Fac Med, Dept Infect Dis Epidemiol, St Marys Campus, London W2 1PG, England.
    Aanensen, David M.
    Imperial Coll London, Sch Publ Hlth, Fac Med, Dept Infect Dis Epidemiol, St Marys Campus, London W2 1PG, England;Ctr Genom Pathogen Surveillance, Wellcome Genome Campus, Hinxton, Cambs, England.
    Alvarado-Rybak, Mario
    Univ Andres Bello, Fac Ecol & Recursos Nat, Ctr Invest Sustentabilidad, Republ 440, Santiago, Chile.
    Bataille, Arnaud
    Seoul Natl Univ, Sch Biol Sci, Lab Behav & Populat Ecol, Seoul 08826, South Korea;CIRAD, UMR ASTRE, F-34398 Montpellier, France;Univ Montpellier, ASTRE, CIRAD, INRA, Montpellier, France.
    Berger, Lee
    James Cook Univ, Coll Publ Hlth Med & Vet Sci, Hlth Res Grp 1, Townsville, Qld 4811, Australia.
    Böll, Susanne
    Agcy Populat Ecol & Nat Conservancy, Gerbrunn, Germany.
    Bosch, Jaime
    CSIC, Museo Nacl Ciencias Nat, C Jose Gutierrez Abascal 2, E-28006 Madrid, Spain.
    Clare, Frances C.
    Imperial Coll London, Sch Publ Hlth, Fac Med, Dept Infect Dis Epidemiol, St Marys Campus, London W2 1PG, England.
    Courtois, Elodie A.
    Univ Guyane, CNRS, IFREMER, LEEISA, Cayenne 97300, French Guiana.
    Crottini, Angelica
    Univ Porto, InBIO, CIBIO Ctr Invest Biodiversidade & Recursos Genet, P-4485661 Vairao, Portugal.
    Cunningham, Andrew A.
    Inst Zool, Regents Pk, London NW1 4RY, England.
    Doherty-Bone, Thomas M.
    Royal Zool Soc Scotland, Conservat Programmes, Edinburgh, Midlothian, Scotland.
    Gebresenbet, Fikirte
    Oklahoma State Univ, Dept Integrat Biol, Life Sci West 113, Stillwater, OK 74078 USA.
    Gower, David J.
    Nat Hist Museum, Life Sci, London SW7 5BD, England.
    Höglund, Jacob
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology.
    James, Timothy Y.
    Univ Michigan, Dept Ecol & Evolutionary Biol, Ann Arbor, MI 48109 USA.
    Jenkinson, Thomas S.
    Univ Michigan, Dept Ecol & Evolutionary Biol, Ann Arbor, MI 48109 USA.
    Kosch, Tiffany A.
    Seoul Natl Univ, Sch Biol Sci, Lab Behav & Populat Ecol, Seoul 08826, South Korea;James Cook Univ, Coll Publ Hlth Med & Vet Sci, Hlth Res Grp 1, Townsville, Qld 4811, Australia.
    Lambertini, Carolina
    Univ Estadual Campinas, Inst Biol, Dept Biol Anim, Lab Hist Nat Anfibios Brasileiros, BR-13083862 Campinas, SP, Brazil.
    Laurila, Anssi
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology.
    Lin, Chun-Fu
    Endem Species Res Inst, Zool Div, 1 Ming Shen East Rd, Nantou 552, Taiwan.
    Loyau, Adeline
    UFZ Helmholtz Ctr Environm Res, Dept Conservat Biol, Permoserstr 15, D-04318 Leipzig, Germany;Univ Toulouse, CNRS, ECOLAB, INPT,UPS, Toulouse, France.
    Martel, An
    Univ Ghent, Dept Pathol Bacteriol & Avian Dis, Fac Vet Med, Salisburylaan 133, B-9820 Merelbeke, Belgium.
    Meurling, Sara
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology.
    Miaud, Claude
    Univ Paul Valery Montpellier, Univ Montpellier, PSL Res Univ, CEFE,UMR 5175,CNRS,EPHE,Biogeog & Ecol Vertebres, Montpellier, France.
    Minting, Pete
    Amphibian & Reptile Conservat ARC Trust, 655A Christchurch Rd, Bournemouth BH1 4AP, Dorset, England.
    Ndriantsoa, Serge
    Durrell Wildlife Conservat Trust, Madagascar Programme, Antananarivo, Madagascar.
    O'Hanlon, Simon J.
    Imperial Coll London, Sch Publ Hlth, Fac Med, Dept Infect Dis Epidemiol, St Marys Campus, London W2 1PG, England;Inst Zool, Regents Pk, London NW1 4RY, England.
    Pasmans, Frank
    Univ Ghent, Dept Pathol Bacteriol & Avian Dis, Fac Vet Med, Salisburylaan 133, B-9820 Merelbeke, Belgium.
    Rakotonanahary, Tsanta
    Durrell Wildlife Conservat Trust, Madagascar Programme, Antananarivo, Madagascar.
    Rabemananjara, Falitiana C. E.
    Durrell Wildlife Conservat Trust, Madagascar Programme, Antananarivo, Madagascar;IUCN SSC Amphibian Specialist Grp Madagascar, Antananarivo 101, Madagascar.
    Ribeiro, Luisa P.
    Univ Estadual Campinas, Inst Biol, Dept Biol Anim, Lab Hist Nat Anfibios Brasileiros, BR-13083862 Campinas, SP, Brazil.
    Schmeller, Dirk S.
    UFZ Helmholtz Ctr Environm Res, Dept Conservat Biol, Permoserstr 15, D-04318 Leipzig, Germany;Univ Toulouse, CNRS, ECOLAB, INPT,UPS, Toulouse, France.
    Schmidt, Benedikt R.
    Univ Zurich, Dept Evolutionary Biol & Environm Studies, Winterthurerstr 190, CH-8057 Zurich, Switzerland;Univ Neuchatel, Info Fauna Karch, Bellevaux 51,UniMail Batiment 6, CH-2000 Neuchatel, Switzerland.
    Skerratt, Lee
    James Cook Univ, Coll Publ Hlth Med & Vet Sci, Hlth Res Grp 1, Townsville, Qld 4811, Australia.
    Smith, Freya
    APHA, Natl Wildlife Management Ctr, Woodchester Pk GL10 3UJ, Glos, England.
    Soto-Azat, Claudio
    Univ Andres Bello, Fac Ecol & Recursos Nat, Ctr Invest Sustentabilidad, Republ 440, Santiago, Chile.
    Tessa, Giulia
    Nonprofit Assoc Zirichiltaggi Sardinia Wildlife C, Str Vicinale Filigheddu 62-C, I-07100 Sassari, Italy.
    Toledo, Luis Felipe
    Univ Estadual Campinas, Inst Biol, Dept Biol Anim, Lab Hist Nat Anfibios Brasileiros, BR-13083862 Campinas, SP, Brazil.
    Valenzuela-Sanchez, Andres
    Univ Andres Bello, Fac Ecol & Recursos Nat, Ctr Invest Sustentabilidad, Republ 440, Santiago, Chile;ONG Ranita Darwin, Nataniel Cox 152, Santiago, Chile.
    Verster, Ruhan
    North West Univ, Unit Environm Sci & Management, Private Bag x6001, ZA-2520 Potchefstroom, South Africa.
    Vörös, Judit
    Hungarian Nat Hist Museum, Dept Zool, Collect Amphibians & Reptiles, Baross U 13, H-1088 Budapest, Hungary.
    Waldman, Bruce
    Seoul Natl Univ, Sch Biol Sci, Lab Behav & Populat Ecol, Seoul 08826, South Korea.
    Webb, Rebecca J.
    James Cook Univ, Coll Publ Hlth Med & Vet Sci, Hlth Res Grp 1, Townsville, Qld 4811, Australia.
    Weldon, Che
    North West Univ, Unit Environm Sci & Management, Private Bag x6001, ZA-2520 Potchefstroom, South Africa.
    Wombwell, Emma
    Inst Zool, Regents Pk, London NW1 4RY, England.
    Zamudio, Kelly R.
    Cornell Univ, Dept Ecol & Evolutionary Biol, Ithaca, NY 14853 USA.
    Longcore, Joyce E.
    Univ Maine, Sch Biol & Ecol, Orono, ME 04469 USA.
    Garner, Trenton W. J.
    Inst Zool, Regents Pk, London NW1 4RY, England;Nonprofit Assoc Zirichiltaggi Sardinia Wildlife C, Str Vicinale Filigheddu 62-C, I-07100 Sassari, Italy;North West Univ, Unit Environm Sci & Management, Private Bag x6001, ZA-2520 Potchefstroom, South Africa.
    Development and worldwide use of non-lethal, and minimal population-level impact, protocols for the isolation of amphibian chytrid fungi2018In: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 8, article id 7772Article in journal (Refereed)
    Abstract [en]

    Parasitic chytrid fungi have emerged as a significant threat to amphibian species worldwide, necessitating the development of techniques to isolate these pathogens into culture for research purposes. However, early methods of isolating chytrids from their hosts relied on killing amphibians. We modified a pre-existing protocol for isolating chytrids from infected animals to use toe clips and biopsies from toe webbing rather than euthanizing hosts, and distributed the protocol to researchers as part of the BiodivERsA project RACE; here called the RML protocol. In tandem, we developed a lethal procedure for isolating chytrids from tadpole mouthparts. Reviewing a database of use a decade after their inception, we find that these methods have been applied across 5 continents, 23 countries and in 62 amphibian species. Isolation of chytrids by the non-lethal RML protocol occured in 18% of attempts with 207 fungal isolates and three species of chytrid being recovered. Isolation of chytrids from tadpoles occured in 43% of attempts with 334 fungal isolates of one species (Batrachochytrium dendrobatidis) being recovered. Together, these methods have resulted in a significant reduction and refinement of our use of threatened amphibian species and have improved our ability to work with this group of emerging pathogens.

  • 9. Florin, Ann-Britt
    et al.
    Höglund, Jacob
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Evolution, Population and Conservation Biology.
    Absence of population structure of turbot (Psetta maxima) in the Baltic Sea2007In: Molecular Ecology, ISSN 0962-1083, E-ISSN 1365-294X, Vol. 16, no 1, p. 115-126Article in journal (Refereed)
    Abstract [en]

    We found low, albeit significant, genetic differentiation among turbot (Psetta maxima) in the Baltic Sea but in contrast to earlier findings we found no evidence of isolation by distance. In fact temporal variation among years in one locality exceeded spatial variation among localities. This is an unexpected result since adult turbot are sedentary and eggs are demersal at the salinities occurring in the Baltic. Our findings are most likely explained by the fact that we sampled fish that were born after/during a large influx of water to the Baltic Sea, which may have had the consequence that previously locally and relatively sedentary populations became admixed. These results suggest that populations that colonize relatively variable habitats, like the Baltic, face problems. Any adaptations to local conditions that may build up during stable periods may quickly become eroded when conditions change and/or when populations become admixed. Our results indicate that the ability of turbot to survive and reproduce at the low salinity in the Baltic is more likely due to phenotypic plasticity than a strict genetic adaptation to low salinity.

  • 10.
    Graham, Stuart
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology. Department of Ecology, Evolution and Marine Biology, University of California, Santa Barbara, CA 93106, USA..
    Kozma, Radoslav
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology.
    Höglund, Jacob
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology.
    The utility of effective population size in population management 1:estimating contemporary effective size2016In: Conservation Genetics, ISSN 1566-0621, E-ISSN 1572-9737Article in journal (Refereed)
    Abstract [en]

    Estimates of effective population size (Ne) are highly desirable in managed populations because they are informative of the rate at which genetic variation is being lost through the processes of genetic drift or inbreeding. Due to the notorious difficulty of accurate Ne estimation in natural populations, myriad estimation methods have been developed over the last 50 years. Conservation practitioners and researchers who are unfamiliar with the Ne estimation literature are now faced with an overwhelming amount of choice when selecting an estimation method and, unfortunately, the resources available to help them make this decision rarely consider the practicalities of implementing these methods. This review aims to alleviate this problem by explicitly considering these practicalities while describing and comparing the most popular estimation methods available. We begin by clearly describing how estimates of Ne can be used in population management. We then go on to describe the most popular methods available for Ne estimation, stating the assumptions that are made and the data that are required. The review concludes with recommendations of the most appropriate estimation methods given specific motivations for estimating Ne and the types of data that are practical to collect.

  • 11.
    Halvarsson, Peter
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology.
    Kålås, John Atle
    Norsk institutt for naturforskning.
    Höglund, Jacob
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology.
    Avian Malaria Prevalence Affects Survival in Great Snipe (Gallinago media)Manuscript (preprint) (Other academic)
  • 12.
    Halvarsson, Peter
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology.
    Meyer-Lucht, Yvonne
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology.
    Miller, Andrea
    Muralidhar, Pavitra
    Höglund, Johan
    Höglund, Jacob
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology.
    Relationship between helminth infections and MHC class II supertype diversity in natural water voles (Arvicola amphibius) populationsManuscript (preprint) (Other academic)
  • 13. Hartman, Goran
    et al.
    Kolzsch, Andrea
    Larsson, Karl
    Nordberg, Marcus
    Höglund, Jacob
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Population and Conservation Biology.
    Trends and population dynamics of a Velvet Scoter (Melanitta fusca) population: influence of density dependence and winter climate2013In: Journal of Ornithology = Journal fur Ornithologie, ISSN 0021-8375, E-ISSN 1439-0361, Vol. 154, no 3, p. 837-847Article in journal (Refereed)
    Abstract [en]

    As many seaduck populations around the world have been reported to be in decline, there is an increasing demand for knowledge about intrinsic and extrinsic factors determining population dynamics of these species. In this study, we analyzed long-term dynamics of the summer population of Velvet Scoters (Melanitta fusca) breeding in the Aland archipelago in the Baltic Sea; in particular, we examined the influence of winter weather and density dependence on population change. The studied population exhibited substantial fluctuations but only a weak negative trend during the total period of 58 years (1949-2007), and no significant trend at all during the latter three decades of the study (1977-2007). We tested for density dependence and incorporated the winter North Atlantic Oscillation index into the model to test for effects of winter conditions. Our final model explained 56.3 % of the variance of population growth of the studied population. Delayed density dependence explained 29.7 %, pre-breeding climate 8.3 %, and post-breeding climate 18.3 % of the variance. That breeding success is density dependent in a delayed manner is in accordance with the apprehension that Velvet Scoters breed at the age of 2 years. We conclude that density dependence and winter conditions must be taken into consideration when discussing population changes in seaducks in general and the Velvet Scoter in particular.

  • 14.
    Hoglund, Jacob
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology.
    Saether, Stein Are
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics.
    Fiske, Peder
    Wheatcroft, David
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology.
    Kalas, John Atle
    A hybrid snipe Gallinago gallinago x G-media found in the wild2015In: Journal of Ornithology = Journal fur Ornithologie, ISSN 0021-8375, E-ISSN 1439-0361, Vol. 156, no 3, p. 819-827Article in journal (Refereed)
    Abstract [en]

    A hybrid snipe male was observed and caught in 2009 in the Norwegian mountains. We report behaviour, vocalizations, morphology, and genetic data for this bird. Mitochondrial and nuclear DNA sequences revealed that the hybrid had a great snipe mother and a common snipe father. The hybrid was intermediate in most measured morphometric traits and showed some intermediate plumage characteristics. The behaviour was similar to that of a great snipe-it displayed and vocalised at a great snipe lek for more than a week. The song was somewhat reminiscent of a great snipe's, but lacked the frequency-modulated whistles that are part of the great snipe song, consisting of more rapid click notes of a narrower frequency spectrum. This is the only putative hybrid that we have found among the more than 4,400 adult individuals we have examined between 1986 and 2014 at great snipe leks in Norway, Sweden, Poland, and Estonia. Common snipes invariably occur near these sites. Reports on putative hybrids among snipe species are very rare, and we question the validity of previous claims. This is the first where the parental origins-and, indeed, the hybrid status-have been unequivocally determined. We speculate on how a great snipe female, known for being extremely choosy about mating, came to mate with a common snipe male. We also note that, although perhaps behaviourally more likely, physical constraints on chick development (caused by the smaller egg size of the common snipe and larger body size of the great snipe) might prevent any successful male great snipe x female common snipe hybridisation-a possible example of an unidirectional post-zygotic barrier.

  • 15.
    Höglund, J
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Biology, Department of Evolutionary Biology. POPULATION BIOLOGY.
    Lek-kin in birds - provoking theory and surprising new results2003In: Annales Zoologici Fennici, Vol. 40, p. 249-253Article in journal (Refereed)
  • 16.
    Höglund, J
    et al.
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Biology, Department of Evolutionary Biology. POPULATION BIOLOGY.
    Shorey, L
    Local genetic structure in a white-bearded manakin population2003In: Molecular Ecology, Vol. 12, p. 2457-2463Article in journal (Refereed)
  • 17.
    Höglund, Jacob
    et al.
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Biology, Department of Ecology and Evolution. Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Biology, Department of Ecology and Evolution, Population Biology. populationsbiologi.
    Baines, D
    Larsson, Karl
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Biology, Department of Ecology and Evolution. Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Biology, Department of Ecology and Evolution, Population Biology. populationsbiologi.
    Segelbacher, Gernot
    Population fragmentation and genetic variability in European Black Grouse: a progress report2004In: Sylvia: supplement, Vol. 39, p. 17-23Article in journal (Refereed)
  • 18.
    Höglund, Jacob
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Population and Conservation Biology.
    Cortazar-Chinarro, Maria
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Population and Conservation Biology.
    Jarnemo, Anders
    Thulin, Carl-Gustaf
    Genetic variation and structure in Scandinavian red deer (Cervus elaphus): influence of ancestry, past hunting, and restoration management2013In: Biological Journal of the Linnean Society, ISSN 0024-4066, E-ISSN 1095-8312, Vol. 109, no 1, p. 43-53Article in journal (Refereed)
    Abstract [en]

    In the 19th century, the red deer (Cervus elaphus) population in Sweden experienced a rapid decline in numbers and distribution. A small population was, however, remnant in the southernmost province (Skane) of the country, presumably corresponding to the nominate form of red deer (Cervus elaphus elaphusLinnaeus, 1758). After management, reintroductions, and supplementary release during the 20th century the Swedish C.elaphus population recovered. The recovery was partially uncontrolled, and included introductions of C.elaphus of continental origin. In northern central Sweden (Jamtland) the current C.elaphus population may stem from natural colonization from Norway and/or from specimens of Swedish origin that have escaped from enclosures. To evaluate the status of the current, partially separated populations, we investigated variation at microsatellite markers in 157 C.elaphus specimens from ten locations in Sweden and Norway. Analyses suggest that the highest-likelihood phylogenetic structure among the individuals sampled is described four distinct genetic clusters: (1) animals from the province of Vastergotland in south-western Sweden; (2) deer from the southernmost province of Skane; (3) deer from the provinces Jamtland, Blekinge, and Vastmanland; and (4) Norwegian deer. Cervus elaphus from a captive herd at the Skane Zoo cluster with deer from Skane or deer from Vastergotland, depending on the method of analysis. A number of populations in Sweden may genetically match the nominate form of red deer (C.e.elaphus). The recently established C.elaphus population in Jamtland seems to stem mainly from escapees from enclosures, with a mixed ancestry from the wild remnant population in Skane and continental deer, whereas the influx from Norway is minor, if any. Our results show the need for a detailed assessment of genetic differentiation, and emphasize the value of local management plans when planning and managing introductions.

  • 19.
    Höglund, Jacob
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Population and Conservation Biology.
    Larsson, Jobs Karl
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Population and Conservation Biology.
    Corrales, Carolina
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Population and Conservation Biology.
    Santafé, Guzman
    Baines, David
    Segelbacher, Gernot
    Genetic structure among black grouse in Britain: implications for designing conservation units2011In: Animal Conservation, ISSN 1367-9430, E-ISSN 1469-1795, Vol. 14, no 4, p. 400-408Article in journal (Refereed)
    Abstract [en]

    Black grouse in Britain have faced contraction of their range and have declined in numbers during the recent decades. As such, the species is a conservation concern in the UK. In order to aid conservation decisions, the terms Evolutionary Significant Unit (ESU) and Management Unit (MU) have been proposed. An ESU is an independently evolving evolutionary lineage defined by being reciprocally monophyletic for mitochondrial alleles, and which is significantly different from other lineages with regard to nuclear alleles, whereas an MU is operationally defined by only the latter criterion. Using mitochondrial sequences and nuclear microsatellite loci, we failed to find evidence that British black grouse is an ESU. However, British black grouse are sufficiently different from continental black grouse both with respect to mitochondrial and nuclear data to regard them as a separate MU. Furthermore, we present genetic data which suggest that British black grouse presently occur in what are probably three demographically independent units (roughly corresponding to Wales, northern England/southern Scotland and northern Scotland), which are genetically differentiated. The two southern units (Wales and northern England/southern Scotland) have lower genetic diversity and show signs of having lost genetic variability

  • 20.
    Höglund, Jacob
    et al.
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Biology, Department of Ecology and Evolution. Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Biology, Department of Ecology and Evolution, Population Biology. populationsbiologi.
    Shorey, Lisa
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Biology, Department of Ecology and Evolution. Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Biology, Department of Ecology and Evolution, Population Biology. populationsbiologi.
    Genetic divergence in the superspecies Manacus2004In: Biological Journal of the Linnean Socitey, Vol. 81, p. 439-447Article in journal (Refereed)
  • 21.
    Höglund, Jacob
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics. Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolutionary Biology, Population Biology.
    Wang, Biao
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics. Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolutionary Biology, Population Biology.
    Axelsson, Thomas
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Sciences, Molecular Medicine.
    Quintela, Maria
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics. Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolutionary Biology, Population Biology.
    Phylogeography of willow grouse (Lagopus lagopus) in the Arctic: taxonomic discordance as inferred from molecular data2013In: Biological Journal of the Linnean Society, ISSN 0024-4066, E-ISSN 1095-8312, Vol. 110, no 1, p. 77-90Article in journal (Refereed)
    Abstract [en]

    Using independently segregating nuclear single nucleotide polymorphisms (SNPs) and mitochondrial control region sequences, we found an east-west division among sampled willow grouse Lagopus lagopus subspecies. This division cut across the range of the subspecies with the largest distribution (lagopus) and thus contradicted existing taxonomic classifications. Russian Lagopus lagopus lagopus tended to cluster with North American willow grouse partly classified as other subspecies. Scandinavian willow grouse (L.l. lagopus) clustered with red grouse from Britain and Ireland (Lagopus lagopus scoticus and Lagopus lagopus hibernicus) but substructuring confirmed the monophyly of the latter. In North America, we could not detect any major genetic divisions apart from two birds described as alexandrae from the Heceta Island (Alaska) when using mitochondrial sequences. Other samples from North America were intermingled regardless of whether they were described as muriei, alexandrae or lagopus. A specimen described as alexandrae was to some extent distinct when analysing the SNP data. The genetic analyses indicated some concordance between genetics and taxonomy but not complete congruence. This is particularly evident for mitochondrial DNA network analyses. We suggest that the taxonomy of this species would benefit by a careful re-examination of the available evidence for subspecies. It appears as if subspecies status is a poor proxy for assigning evolutionary significant units and management units in this species.

  • 22.
    Höglund, Jacob
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology.
    Wang, Biao
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics.
    Sæther, Stein Are
    Norwegian Inst Nat Res NINA, Trondheim, Norway.
    Blom, Mozes Pil Kyu
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics. Australian Natl Univ, Res Sch Biol, Div Evolut Ecol & Genet, Canberra, ACT, Australia.
    Fiske, Peder
    Norwegian Inst Nat Res NINA, Trondheim, Norway.
    Halvarsson, Peter
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology.
    Horsburgh, Gavin J.
    Univ Sheffield, Dept Anim & Plant Sci, Sheffield, S Yorkshire, England.
    Burke, Terry
    Univ Sheffield, Dept Anim & Plant Sci, Sheffield, S Yorkshire, England.
    Kålås, John Atle
    Norwegian Inst Nat Res NINA, Trondheim, Norway.
    Ekblom, Robert
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology. Univ Sheffield, Dept Anim & Plant Sci, Sheffield, S Yorkshire, England.
    Blood transcriptomes and de novo identification of candidate loci for mating success in lekking great snipe (Gallinago media)2017In: Molecular Ecology, ISSN 0962-1083, E-ISSN 1365-294X, Vol. 26, no 13, p. 3458-3471Article in journal (Refereed)
    Abstract [en]

    We assembled the great snipe blood transcriptome using data from fourteen lekking males, in order to de novo identify candidate genes related to sexual selection, and determined the expression profiles in relation to mating success. The three most highly transcribed genes were encoding different haemoglobin subunits. All tended to be overexpressed in males with high mating success. We also called single nucleotide polymorphisms (SNPs) from the transcriptome data and found considerable genetic variation for many genes expressed during lekking. Among these, we identified 14 polymorphic candidate SNPs that had a significant genotypic association with mating success (number of females mated with) and/or mating status (mated or not). Four of the candidate SNPs were found in HBAA (encoding the haemoglobin a-chain). Heterozygotes for one of these and one SNP in the gene PABPC1 appeared to enjoy higher mating success compared to males homozygous for either of the alleles. In a larger data set of individuals, we genotyped 38 of the identified SNPs but found low support for consistent selection as only one of the zygosities of previously identified candidate SNPs and none of their genotypes were associated with mating status. However, candidate SNPs generally showed lower levels of spatial genetic structure compared to noncandidate markers. We also scored the prevalence of avian malaria in a subsample of birds. Males infected with avian malaria parasites had lower mating success in the year of sampling than noninfected males. Parasite infection and its interaction with specific genes may thus affect performance on the lek.

  • 23.
    Höglund, Jacob
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology.
    Wengström, Åsa
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology.
    Rogell, Björn
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology.
    Meyer-Lucht, Yvonne
    Low MHC variation in isolated island populations of the Natterjack toad (Bufo calamita)2015In: Conservation Genetics, ISSN 1566-0621, E-ISSN 1572-9737, Vol. 16, no 4, p. 1007-1010Article in journal (Refereed)
    Abstract [en]

    We studied variation at the class II gene of the major histocompatibility complex (MHC) in Natterjack toad populations (Bufo [Epidalea] calamita) on islands off the west coast of Sweden. These isolated populations have previously been shown to exhibit low levels of neutral genetic variation. On seven investigated islands we found only two different MHC alleles, indicating that the genetic variation at this locus is also low. The two alleles were found in all populations, although in one population there was only a single heterozygous individual. The Swedish toads showed similar low levels of MHC variation as revealed by previously published data from populations in northern Europe. We did not find a correlation between MHC and neutral genetic variation (as determined by AFLP). However, our findings show that reduced genetic variation in the Swedish Natterjack toads is not restricted to neutral markers, but is likewise reflected at the MHC.

  • 24.
    Johansson, Frank
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology.
    Halvarsson, Peter
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology.
    Mikolajewski, D. J.
    Free Univ Berlin, Inst Biol, Konigin Luise Str 1-3, D-14195 Berlin, Germany..
    Höglund, Jacob
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology.
    Genetic differentiation in the boreal dragonfly Leucorrhinia dubia in the Palearctic region2017In: Biological Journal of the Linnean Society, ISSN 0024-4066, E-ISSN 1095-8312, Vol. 121, no 2, p. 294-304Article in journal (Refereed)
    Abstract [en]

    The last glacial period had a strong influence on the population genetic structure of boreal species in southern and central Europe. In addition, recent and current human impact on the boreal environment has led to habitat loss, which also has a large influence on population genetic structure of species. Here we present the spatial genetic structure of the boreal dragonfly Leucorrhinia dubia using ddRAD sequencing. We sampled individuals from nine locations in Europe, three in Asia (Russia and Japan) and one location of L. intermedia in Japan. Results showed three distinct genetic clusters in Europe. One genetic cluster consisted of individuals sampled from the locations in the Swiss Alps, a second consisted of individuals sampled in the United Kingdom, and a third cluster consisted of individuals from the rest of the seven sampled locations in Europe covering a latitudinal gradient from the French Pyrenees to the north of Finland. There was also a week support that the French Pyrenees and Austrian Alps samples differentiated from the cluster of the five samples from central and north Europe. We suggest that these clusters reflect historical recolonization patterns since the last glaciation. The L. dubia individuals sampled from locations in Asia formed one cluster referring to L. dubia orientalis separated from the individuals sampled in European and from the L. intermedia locality sampled. Our result suggests that aquatic insects in the fragmented boreal landscape in south central Europe and United Kingdom need conservation consideration.

  • 25.
    Johansson, Frank
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology.
    Halvarsson, Peter
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology.
    Mikolajewski, Dirk J.
    Free Univ Berlin, Inst Biol, Berlin, Germany..
    Höglund, Jacob
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology.
    Phylogeography and larval spine length of the dragonfly Leucorhinia dubia in Europe2017In: PLoS ONE, ISSN 1932-6203, E-ISSN 1932-6203, Vol. 12, no 9, article id e0184596Article in journal (Refereed)
    Abstract [en]

    Presence or absence of predators selects for different kind of morphologies. Hence, we expect variation in traits that protect against predators to vary over geographical areas where predators vary in past and present abundance. Abdominal larval spines in dragonfly larvae provide protection against fish predators. We studied geographical variation in larval spine length of the dragonfly Leucorrhinia dubia across Western Europe using a phylogenetic approach. Larvae were raised in a common garden laboratory experiment in the absence of fish predators. Results show that larvae from northern Europe (Sweden and Finland) had significantly longer larval spines compared to larvae from western and central Europe. A phylogeny based on SNP data suggests that short larval spines is the ancestral stage in the localities sampled in this study, and that long spines have evolved in the Fenno-Scandian clade. The role of predators in shaping the morphological differences among the sampled localities is discussed.

  • 26.
    Johansson, Magnus P.
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Population and Conservation Biology.
    Mcmahon, Barry J.
    Höglund, Jacob
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Population and Conservation Biology.
    Segelbacher, Gernot
    Amplification success of multilocus genotypes from feathers found in the field compared with feathers obtained from shot birds2012In: Ibis, ISSN 0019-1019, E-ISSN 1474-919X, Vol. 154, no 1, p. 15-20Article in journal (Refereed)
    Abstract [en]

    Effective DNA extraction methods from bird feathers have facilitated non-invasive sampling, leading to the suggestion that feathers are a great source for genetic studies. However, few studies have assessed whether all feathers can be used or provide equal numbers of useful templates. In this study, feathers collected in various ways from Red Grouse Lagopus lagopus were examined to establish the quality of DNA extracted. Individual samples were classified into two categories according to whether they were collected from shot birds or found in the field. DNA was extracted from all samples and genotyped at 19 microsatellite loci. PCR products were analysed on a MegaBACE 1000. A total of 93% of the shot category produced a genotype that was considered successful (i.e. 15 of 18 loci) and 23% of the collected category produced successful genotypes under the same criteria. There was a significant difference between shot and collected samples in genotyping success and the observed number of missing loci. Recommendations and best practices are discussed along with the utility of bird feathers as a source of DNA for population and conservation biology.

  • 27.
    Klinga, Peter
    et al.
    Tech Univ, Fac Forestry, SK-96053 Zvolen, Slovakia..
    Mikolas, Martin
    Czech Univ Life Sci, Fac Forestry & Wood Sci, Prague 16521 6, Suchdol, Czech Republic.;PRALES, SK-01322 Rosina, Slovakia..
    Zhelev, Petar
    Univ Forestry, Fac Forestry, BG-17456 Sofia, Bulgaria..
    Höglund, Jacob
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology.
    Paule, Ladislav
    Tech Univ, Fac Forestry, SK-96053 Zvolen, Slovakia..
    Genetic differentiation of western capercaillie in the Carpathian Mountains: the importance of post glacial expansions and habitat connectivity2015In: Biological Journal of the Linnean Society, ISSN 0024-4066, E-ISSN 1095-8312, Vol. 116, no 4, p. 873-889Article in journal (Refereed)
    Abstract [en]

    Population structure and barriers to gene flow are important components for understanding the evolutionary history of a species. Here we study population structure and differentiation in the western capercaillie (Aves: Phasianidae) along the Carpathian Mountains. Further, we compared the levels of population differentiation among capercaillie from the Carpathian Mountains, Balkans (Bulgaria) and the boreal forest (Russia and Sweden) in order to reveal past and current processes which may influence population structure. Tissue samples, non-invasive faeces and feathers and toe pads from museum specimens were used for genetic analyses of mitochondrial (mtDNA) sequences and allelic variation at nine nuclear DNA (nDNA) microsatellite loci. Analyses of mtDNA sequences revealed a southern subclade within the northern clade. Within the northern clade, microsatellite data distinguished two groups: (1) Western Carpathian populations; and (2) Eastern Carpathian and boreal forest populations. Bulgarian populations constituted a third cluster corresponding to the southern phylogenetic subclade. The Western Carpathian populations showed a heterozygote deficiency. The analyses indicate that the abundant Eastern Carpathian populations share alleles with populations from the boreal forest suggesting a common origin of these populations since the last glacial period. On the other hand, the Western Carpathian populations have been isolated over a long period with only a few migrants from the east, thereby becoming differentiated from the eastern and northern populations. The southern populations have been isolated from the northern populations since the last glacial maximum. The molecular analyses did not support the currently recognised taxonomy at the subspecies level.

  • 28.
    Klinga, Peter
    et al.
    Tech Univ Zvolen, Fac Forestry, Zvolen, Slovakia.
    Mikoláš, Martin
    Czech Univ Life Sci, Fac Forestry & Wood Sci, Prague, Czech Republic; PRALES, Rosina, Slovakia.
    Smolko, Peter
    DIANA, Banska Bystrica, Slovakia; Univ Alberta, Dept Biol Sci, Edmonton, AB T6G 2E9, Canada.
    Tejkal, Martin
    Czech Univ Life Sci, Fac Forestry & Wood Sci, Prague, Czech Republic.
    Höglund, Jacob
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology.
    Paule, Ladislav
    Tech Univ Zvolen, Fac Forestry, Zvolen, Slovakia.
    Considering landscape connectivity and gene flow in the Anthropocene using complementary landscape genetics and habitat modelling approaches2019In: Landscape Ecology, ISSN 0921-2973, E-ISSN 1572-9761, Vol. 34, no 3, p. 521-536Article in journal (Refereed)
    Abstract [en]

    Context: A comprehensive understanding of how rapidly changing environments affect species gene flow is critical for mitigating future biodiversity losses. While recent methodological developments in landscape ecology and genetics have greatly advanced our understanding of biodiversity conservation, they are rarely combined and applied in studies.

    Objectives: We merged multifaceted landscape habitat modelling with genetics to detect and design biological corridors, and we evaluated the importance of habitat patches to test corridor efficacy for gene flow in a fragmented landscape. We examined an isolated population of an endangered umbrella species, the capercaillie (Tetrao urogallus), in the Western Carpathians; they have experienced habitat deterioration and accompanying population declines in recent decades.

    Methods: To detect spatial patterns of genetic distances, we combined and optimized resistance surfaces using species distribution modelling, structural and functional connectivity analyses, multivariate regression approaches, and Moran’s eigenvector maps at hierarchical scales.

    Results: Larger habitat patches had better gene flow among them, and we confirmed a broken metapopulation network characterised by a pattern of isolation by the environment. Distance to human settlements explained landscape genetic patterns better than other environmental and landscape features, MaxEnt resistance, Conefor resistance surfaces, and the pairwise Euclidean distances among individuals. The closer individuals were to settlements, the more pronounced were the effects of logging and other negative factors on their connectivity.

    Conclusions: Merging multifaceted landscape habitat modelling with genetics can effectively test corridor efficacy for gene flow, and it represents a powerful tool for conservation of endangered species.

  • 29.
    Kozma, Radoslav
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology.
    Graham, Stuart
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology. Department of Ecology, Evolution and Marine Biology, University of California, Santa Barbara, CA 93106, USA.
    Höglund, Jacob
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology.
    The utility of effective population size in population management 2:estimating demographic history2016In: Conservation Genetics, ISSN 1566-0621, E-ISSN 1572-9737Article in journal (Refereed)
    Abstract [en]

    Elucidating demographic history by tracking the fluctuations of effective population size (Ne) through time has helped uncover interesting insight into the ecology and evolutionary history of a wide array of populations and species. This field of research has seen many exciting methods put forth that together can retrieve the demographic history across many time scales and as such, it is becoming a very useful tool available for conservation practitioners. However, due to the inherent difficulties associated with estimating Ne, the literature can be very technical it is often unclear how methods differ in their assumptions and data requirements. Thus, the choice of which method to use for what purpose can be an extremely difficult one. With this review, we aim to first describe the major methods used to estimate demographic history and clarify their underlying requirements and assumptions. We then highlight some of the overarching motives to understand past Ne fluctuations and we conclude with advice about which methods to use to address these specific motives with a particular focus on the temporal resolution required.

  • 30.
    Kozma, Radoslav
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology.
    Höglund, Jacob
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology.
    Insight into speciation and adaptation in grouse as revealed by whole genome sequencingManuscript (preprint) (Other academic)
    Abstract [en]

    Understanding the molecular basis of adaption is one of the central goals in evolutionary biology and when investigated across sister species it can provide detailed insight into the mechanisms of speciation. The grouse (subfamily Tetraoninae) constitute an avian lineage whose members inhabit a wide variety of habitats and possess diverse plumage traits and as such offer an interesting case study. Here, we sequence the genomes of 34 individuals comprising three grouse taxa; the willow grouse (Lagopus lagopus lagopus), the red grouse (Lagopus lagopus scoticus) and the rock ptarmigan (Lagopus muta) in order to uncover the genomic architecture of speciation and the genes involved in adaptation. We identify 6 regions, containing 7 genes that show consistent signs of differential selection across the species. These genes are highly involved in a variety of cell processes ranging from stress response to neural, gut, olfactory and limb development. Genome wide neutrality test statistics also reveal a strong signal of population expansion acting across the genomes, which is in line with previous demographic studies in these systems. Additionally, we uncover a 3.5Mb region on chromosome 20 that shows considerably lower levels of differentiation across the three grouse lineages, indicating the action of uniform selection. The Agouti gene, which is integral in the pigmentation pathway, lies at the 5' start of this region hinting at the conserved development of brown plumage across the three taxa. Together, our results provide a key step in the exploration of grouse speciation and adaptation. 

  • 31.
    Kozma, Radoslav
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology.
    Lillie, Mette
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology. Univ Gothenburg, Dept Biol & Environm Sci, Gothenburg, Sweden.
    Benito, Blas M.
    Department of Bioscience, Section for Ecoinformatics and Biodiversity, University of Aarhus, Ny Munkegade, building 1540, DK-8000 Aarhus C, Denmark.
    Svenning, Jens-Christian
    Department of Bioscience, Section for Ecoinformatics and Biodiversity, University of Aarhus, Ny Munkegade, building 1540, DK-8000 Aarhus C, Denmark.
    Höglund, Jacob
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology.
    Past and potential future population dynamics of three grouse species using ecological and whole genome coalescent modeling2018In: Ecology and Evolution, ISSN 2045-7758, E-ISSN 2045-7758, Vol. 8, no 13, p. 6671-6681Article in journal (Other academic)
    Abstract [en]

    Studying demographic history of species provides insight into how the past has shaped the current levels of overall biodiversity and genetic composition of species, but also how these species may react to future perturbations. Here we investigated the demographic history of the willow grouse (Lagopus lagopus), rock ptarmigan (Lagopus muta), and black grouse (Tetrao tetrix) through the Late Pleistocene using two complementary methods and whole genome data. Species distribution modeling (SDM) allowed us to estimate the total range size during the Last Interglacial (LIG) and Last Glacial Maximum (LGM) as well as to indicate potential population subdivisions. Pairwise Sequentially Markovian Coalescent (PSMC) allowed us to assess fluctuations in effective population size across the same period. Additionally, we used SDM to forecast the effect of future climate change on the three species over the next 50years. We found that SDM predicts the largest range size for the cold-adapted willow grouse and rock ptarmigan during the LGM. PSMC captured intraspecific population dynamics within the last glacial period, such that the willow grouse and rock ptarmigan showed multiple bottlenecks signifying recolonization events following the termination of the LGM. We also see signals of population subdivision during the last glacial period in the black grouse, but more data are needed to strengthen this hypothesis. All three species are likely to experience range contractions under future warming, with the strongest effect on willow grouse and rock ptarmigan due to their limited potential for northward expansion. Overall, by combining these two modeling approaches, we have provided a multifaceted examination of the biogeography of these species and how they have responded to climate change in the past. These results help us understand how cold-adapted species may respond to future climate changes.

  • 32.
    Kozma, Radoslav
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology.
    Melsted, Páll
    Faculty of Industrial Engineering, Mechanical Engineering and Computer Science, University of Iceland, Reykjavik, Iceland & deCODE Genetics/Amgen, Reykjavik, Iceland.
    Magnússon, Kristinn, P.
    The Icelandic Institute of Natural History, Borgir v. Nordurslod, Akureyri 600, Iceland & Department of Natural Resource Sciences, University of Akureyri, Borgir vid Nordurslod, Akureyri 600, Iceland & Biomedical Center, University of Iceland, Vatnsmyrarvegur 16, Reykjavik 101, Iceland.
    Höglund, Jacob
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology.
    Looking into the past: the reaction of three grouse species to climate change over the last million years using whole genome sequences2016In: Molecular Ecology, ISSN 0962-1083, E-ISSN 1365-294X, Vol. 25, no 2, p. 570-580Article in journal (Refereed)
    Abstract [en]

    Tracking past population fluctuations can give insight into current levels of genetic variation present within species. Analysing population dynamics over larger timescales can be aligned to known climatic changes to determine the response of species to varying environments. Here, we applied the Pairwise Sequentially Markovian Coalescent (PSMC) model to infer past population dynamics of three widespread grouse species; black grouse, willow grouse and rock ptarmigan. This allowed the tracking of the effective population size (Ne) of all three species beyond 1 Mya, revealing that (i) early Pleistocene cooling (~2.5 Mya) caused an increase in the willow grouse and rock ptarmigan populations, (ii) the mid-Brunhes event (~430 kya) and following climatic oscillations decreased the Ne of willow grouse and rock ptarmigan, but increased the Ne of black grouse and (iii) all three species reacted differently to the last glacial maximum (LGM) – black grouse increased prior to it, rock ptarmigan experienced a severe bottleneck and willow grouse was maintained at large population size. We postulate that the varying PSMC signal throughout the LGM depicts only the local history of the species. Nevertheless, the large population fluctuations in willow grouse and rock ptarmigan indicate that both species are opportunistic breeders while black grouse tracks the climatic changes more slowly and is maintained at lower Ne. Our results highlight the usefulness of the PSMC approach in investigating species’ reaction to climate change in the deep past, but also that caution should be taken in drawing general conclusions about the recent past.

  • 33.
    Kozma, Radoslav
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology.
    Mörch, Patrik Rödin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology.
    Höglund, Jacob
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology.
    Genomic regions of speciation and adaptation among three species of grouse2019In: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 9, article id 812Article in journal (Refereed)
    Abstract [en]

    Understanding the molecular basis of adaption is one of the central goals in evolutionary biology and when investigated across sister species it can provide detailed insight into the mechanisms of speciation. Here, we sequence the genomes of 34 individuals from three closely related grouse species in order to uncover the genomic architecture of speciation and the genes involved in adaptation. We identify 6 regions, containing 7 genes that show lineage specific signs of differential selection across the species. These genes are involved in a variety of cell processes ranging from stress response to neural, gut, olfactory and limb development. Genome wide neutrality test statistics reveal a strong signal of population expansion acting across the genomes. Additionally, we uncover a 3.5 Mb region on chromosome 20 that shows considerably lower levels of differentiation across the three grouse lineages, indicating possible action of uniform selection in this region.

  • 34.
    Kärvemo, Simon
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology. Swedish Univ Agr Sci, Dept Ecol, S-75007 Uppsala, Sweden.
    Laurila, Anssi
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology.
    Höglund, Jacob
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology.
    Urban environment and reservoir host species are associated with Batrachochytrium dendrobatidis infection prevalence in the common toad2019In: Diseases of Aquatic Organisms, ISSN 0177-5103, E-ISSN 1616-1580, Vol. 134, no 1, p. 33-42Article in journal (Refereed)
    Abstract [en]

    Human-induced changes of the environment, including landscape alteration and habitat loss, may affect wildlife disease dynamics and have important ramifications for wildlife conservation. Amphibians are among the vertebrate taxa most threatened by anthropogenic habitat change. The emerging fungal pathogen Batrachochytrium dendrobatidis (Bd) has caused extinctions and population declines in hundreds of anuran species globally. We studied how the urban landscape is associated with the prevalence of Bd infections by sampling 655 anurans of 3 species (mainly the common toad Bufo bufo) in 42 ponds surrounded by different amounts of urban habitat (defined as towns, cities or villages). We also examined the association between Bd infections and a potential reservoir host species (the moor frog Rana arvalis). We found that 38% of the sites were positive for Bd with an infection prevalence of 4.4%. The extent of urban landscape was negatively correlated with Bd infection prevalence. However, the positive association of Bd with the presence of the possible reservoir species was substantially stronger than the urban effects. The body condition index of B. bufo was negatively associated with Bd infection. This Bd effect was stronger than the negative effect of urban landscape on body condition. Our results suggest that urban environments in Sweden have a negative impact on Bd infections, while the presence of the reservoir species has a positive impact on Bd prevalence. Our study also highlights the potential importance of Bd infection on host fitness, especially in rural landscapes.

    The full text will be freely available from 2024-05-01 13:44
  • 35.
    Kärvemo, Simon
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics.
    Meurling, Sara
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology.
    Berger, David
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology.
    Höglund, Jacob
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology.
    Laurila, Anssi
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology.
    Effects of host species and environmental factors on the prevalence of Batrachochytrium dendrobatidis in northern Europe2018In: PLoS ONE, ISSN 1932-6203, E-ISSN 1932-6203, Vol. 13, no 10, article id e0199852Article in journal (Refereed)
    Abstract [en]

    The fungal pathogen Batrachochytrium dendrobatidis (Bd) poses a major threat to amphibian populations. To assist efforts to address such threats, we examined differences in Bd host infection prevalence among amphibian species and its relations to both local environmental factors in breeding habitats and landscape variables measured at three scales (500, 2000 and 5000 m radii) around breeding sites in southernmost Sweden. We sampled 947 anurans of six species in 31 ponds and assessed their infection status. We then examined correlations of infection prevalence with canopy cover, pond perimeter and pH (treated as local-scale pond characteristics), and the number of ponds, area of arable land, area of mature forest, number of resident people and presence of sea within the three radii (treated as landscape variables). The Bd infection prevalence was very low, 0.5-1.0%, in two of the six anuran species (Bufo bufo and Rana temporaria), and substantially higher (13-64%) in the other four (Bombina bombina, Bufotes variabilis, Epidalea calamita, Rana arvalis). In the latter four species Bd infection prevalence was positively associated with ponds' pH (site range: 5.3-8.1), and negatively associated with areas of mature forest and/or wetlands in the surroundings. Our results show that the infection dynamics of Bd are complex and associated with host species, local pond characteristics and several landscape variables at larger spatial scales. Knowledge of environmental factors associated with Bd infections and differences in species' susceptibility may help to counter further spread of the disease and guide conservation action plans, especially for the most threatened species.

  • 36.
    Kölzsch, Andrea
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Evolution, Population and Conservation Biology.
    Saether, Stein Are
    Gustafsson, Henrik
    Fiske, Peder
    Höglund, Jacob
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Evolution, Population and Conservation Biology.
    Kålås, John Atle
    Population fluctuations and regulation in great snipe: a time-series analysis2007In: Journal of Animal Ecology, ISSN 0021-8790, E-ISSN 1365-2656, Vol. 76, no 4, p. 740-749Article in journal (Refereed)
    Abstract [en]

    1. During the last centuries, the breeding range of the great snipe Gallinago media has declined dramatically in the western part of its distribution. To examine present population dynamics in the Scandinavian mountains, we collected and analysed a 19-year time series of counts of great snipe males at leks in central Norway, 1987-2005. 2. The population showed large annual fluctuations in the number of males displaying at lek sites (range 45-90 males at the peak of the mating season), but no overall trend. 3. We detected presence of direct density-dependent mechanisms regulating this population. Inclusion of the density-dependent term in a Ricker-type model significantly improved the fit with observed data (evaluated with Parametric Bootstrap Likelihood Ratio tests and Akaike's Information Criterion for small sample size). 4. An analysis of (a number of a priori likely) environmental covariates suggests that the population dynamics were affected by conditions influencing reproduction and survival of offspring during the summer, but not by conditions influencing survival at the wintering grounds in Africa. This is in contrast to many altricial birds breeding in the northern hemisphere, and supports the idea that population dynamics of migratory nidifugous birds are more influenced by conditions during reproduction. 5. Inclusion of these external factors into our model improved the detectability of density dependence. This illustrates that allowing for external effects may increase statistical power of density dependence tests and thus be of particular importance in relatively short time series. 6. In our best model of the population dynamics, two likely density-independent offspring survival covariates explained 47·3% of the variance in great snipe numbers (predation pressure estimated by willow grouse reproductive success and food availability estimated by the amount of precipitation in June), whereas density dependence explained 35·5%. Demographic stochasticity and unidentified environmental stochasticity may account for the remaining 17·2%.

  • 37.
    Lagerholm, Vendela K.
    et al.
    Swedish Museum Nat Hist, Dept Bioinformat & Genet, Stockholm, Sweden.;Stockholm Univ, Dept Zool, Stockholm, Sweden..
    Sandoval-Castellanos, Edson
    Swedish Museum Nat Hist, Dept Bioinformat & Genet, Stockholm, Sweden.;Stockholm Univ, Dept Zool, Stockholm, Sweden.;Univ Nacl Autonoma Mexico, Ctr Ciencias Complejidad, Ciudad De Mexico, Mexico..
    Vaniscotte, Amelie
    UiT Arctic Univ Norway, Dept Arctic & Marine Biol, Tromso, Norway..
    Potapova, Olga R.
    SD Inc, Mammoth Site Hot Springs, Hot Springs, NC USA..
    Tomek, Teresa
    Polish Acad Sci, Inst Systemat & Evolut Anim, Krakow, Poland..
    Bochenski, Zbigniew M.
    Polish Acad Sci, Inst Systemat & Evolut Anim, Krakow, Poland..
    Shepherd, Paul
    British Geol Survey, Nottingham, England..
    Barton, Nick
    Univ Oxford, Inst Archaeol, Oxford, England..
    Van Dyck, Marie-Claire
    Catholic Univ Louvain, Inst Anal Change Contemporary & Hist Soc, Louvain La Neuve, Belgium..
    Miller, Rebecca
    Univ Liege, Serv Prehist, Liege, Belgium..
    Höglund, Jacob
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology.
    Yoccoz, Nigel G.
    UiT Arctic Univ Norway, Dept Arctic & Marine Biol, Tromso, Norway..
    Dalen, Love
    Swedish Museum Nat Hist, Dept Bioinformat & Genet, Stockholm, Sweden..
    Stewart, John R.
    Bournemouth Univ, Sch Appl Sci, Dorset House,Talbot Campus, Poole, Dorset, England..
    Range shifts or extinction?: Ancient DNA and distribution modelling reveal past and future responses to climate warming in cold-adapted birds2017In: Global Change Biology, ISSN 1354-1013, E-ISSN 1365-2486, Vol. 23, no 4, p. 1425-1435Article in journal (Refereed)
    Abstract [en]

    Global warming is predicted to cause substantial habitat rearrangements, with the most severe effects expected to occur in high-latitude biomes. However, one major uncertainty is whether species will be able to shift their ranges to keep pace with climate-driven environmental changes. Many recent studies on mammals have shown that past range contractions have been associated with local extinctions rather than survival by habitat tracking. Here, we have used an interdisciplinary approach that combines ancient DNA techniques, coalescent simulations and species distribution modelling, to investigate how two common cold-adapted bird species, willow and rock ptarmigan (Lagopus lagopus and Lagopus muta), respond to long-term climate warming. Contrary to previous findings in mammals, we demonstrate a genetic continuity in Europe over the last 20 millennia. Results from back-casted species distribution models suggest that this continuity may have been facilitated by uninterrupted habitat availability and potentially also the greater dispersal ability of birds. However, our predictions show that in the near future, some isolated regions will have little suitable habitat left, implying a future decrease in local populations at a scale unprecedented since the last glacial maximum.

  • 38.
    Lamichhaney, Sangeet
    et al.
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology.
    Fan, Guangyi
    BGI Shenzhen, Shenzhen, Peoples R China.;Univ Macau, Inst Chinese Med Sci, State Key Lab Qual Res Chinese Med, Taipa, Peoples R China..
    Widemo, Fredrik
    Swedish Univ Agr Sci, Dept Wildlife Fish & Environm Studies, S-90183 Umea, Sweden..
    Gunnarsson, Ulrika
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology.
    Thalmann, Doreen Schwochow
    Swedish Univ Agr Sci, Dept Anim Breeding & Genet, Uppsala, Sweden.;AgroParisTech, Inst Natl Rech Agron, Genet Anim & Biol Integrat, Jouy En Josas, France..
    Höppner, Marc P.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Computational and Systems Biology.
    Kerje, Susanne
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology.
    Gustafson, Ulla
    Swedish Univ Agr Sci, Dept Anim Breeding & Genet, Uppsala, Sweden..
    Shi, Chengcheng
    BGI Shenzhen, Shenzhen, Peoples R China..
    Zhang, He
    BGI Shenzhen, Shenzhen, Peoples R China..
    Chen, Wenbin
    BGI Shenzhen, Shenzhen, Peoples R China..
    Liang, Xinming
    BGI Shenzhen, Shenzhen, Peoples R China..
    Huang, Leihuan
    BGI Shenzhen, Shenzhen, Peoples R China..
    Wang, Jiahao
    BGI Shenzhen, Shenzhen, Peoples R China..
    Liang, Enjing
    BGI Shenzhen, Shenzhen, Peoples R China..
    Wu, Qiong
    BGI Shenzhen, Shenzhen, Peoples R China..
    Lee, Simon Ming-Yuen
    Univ Macau, Inst Chinese Med Sci, State Key Lab Qual Res Chinese Med, Taipa, Peoples R China..
    Xu, Xun
    BGI Shenzhen, Shenzhen, Peoples R China..
    Höglund, Jacob
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology.
    Liu, Xin
    BGI Shenzhen, Shenzhen, Peoples R China..
    Andersson, Leif
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology. Swedish Univ Agr Sci, Dept Anim Breeding & Genet, Uppsala, Sweden.;Texas A&M Univ, Dept Vet Integrat Biosci, College Stn, TX USA..
    Structural genomic changes underlie alternative reproductive strategies in the ruff (Philomachus pugnax)2016In: Nature Genetics, ISSN 1061-4036, E-ISSN 1546-1718, Vol. 48, no 1, p. 84-+Article in journal (Refereed)
    Abstract [en]

    The ruff is a Palearctic wader with a spectacular lekking behavior where highly ornamented males compete for females(1-4). This bird has one of the most remarkable mating systems in the animal kingdom, comprising three different male morphs (independents, satellites and faeders) that differ in behavior, plumage color and body size. Remarkably, the satellite and faeder morphs are controlled by dominant alleles(5,6). Here we have used whole-genome sequencing and resolved the enigma of how such complex phenotypic differences can have a simple genetic basis. The Satellite and Faeder alleles are both associated with a 4.5-Mb inversion that occurred about 3.8 million years ago. We propose an evolutionary scenario where the Satellite chromosome arose by a rare recombination event about 500,000 years ago. The ruff mating system is the result of an evolutionary process in which multiple genetic changes contributing to phenotypic differences between morphs have accumulated within the inverted region.

  • 39.
    Larsson, Jobs Karl
    et al.
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Biology, Department of Evolutionary Biology. Department of Ecology and Evolution, Population Biology. Populationsbiologi.
    Sun, Y-H
    Fang, Y
    Segelbacher, G
    Höglund, J
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Biology, Department of Evolutionary Biology. Department of Ecology and Evolution, Population Biology. Populationsbiologi.
    Microsatellite variation in a Chinese grouse Bonaza sewerzovi population: signs of genetic impoverishment?2003In: Wildlife Biology, Vol. 9, p. 261-266Article in journal (Refereed)
  • 40. Lebigre, Christophe
    et al.
    Alatalo, Rauno V.
    Soulsbury, Carl D.
    Höglund, Jacob
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology.
    Siitari, Heli
    Limited indirect fitness benefits of male group membership in a lekking species2014In: Molecular Ecology, ISSN 0962-1083, E-ISSN 1365-294X, Vol. 23, no 21, p. 5356-5365Article in journal (Refereed)
    Abstract [en]

    In group living species, individuals may gain the indirect fitness benefits characterizing kin selection when groups contain close relatives. However, tests of kin selection have primarily focused on cooperatively breeding and eusocial species, whereas its importance in other forms of group living remains to be fully understood. Lekking is a form of grouping where males display on small aggregated territories, which females then visit to mate. As females prefer larger aggregations, territorial males might gain indirect fitness benefits if their presence increases the fitness of close relatives. Previous studies have tested specific predictions of kin selection models using measures such as group-level relatedness. However, a full understanding of the contribution of kin selection in the evolution of group living requires estimating individuals' indirect fitness benefits across multiple sites and years. Using behavioural and genetic data from the black grouse (Tetrao tetrix), we show that the indirect fitness benefits of group membership were very small because newcomers joined leks containing few close relatives who had limited mating success. Males' indirect fitness benefits were higher in yearlings during increasing population density but marginally changed the variation in male mating success. Kin selection acting through increasing group size is therefore unlikely to contribute substantially to the evolution and maintenance of lekking in this black grouse population.

  • 41.
    Lindsay, Willow R.
    et al.
    Univ Gothenburg, Dept Biol & Environm Sci, Gothenburg, Sweden.
    Andersson, Staffan
    Univ Gothenburg, Dept Biol & Environm Sci, Gothenburg, Sweden.
    Bererhi, Badreddine
    Univ Gothenburg, Dept Biol & Environm Sci, Gothenburg, Sweden.
    Höglund, Jacob
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology.
    Johnsen, Arild
    Univ Oslo, Nat Hist Museum, Oslo, Norway.
    Kvarnemo, Charlotta
    Univ Gothenburg, Dept Biol & Environm Sci, Gothenburg, Sweden.
    Leder, Erica H.
    Univ Oslo, Nat Hist Museum, Oslo, Norway.
    Lifjeld, Jan T.
    Univ Oslo, Nat Hist Museum, Oslo, Norway.
    Ninnes, Calum E.
    Univ Gothenburg, Dept Biol & Environm Sci, Gothenburg, Sweden; Univ Florida, Dept Entomol & Nematol, Gainesville, FL USA.
    Olsson, Mats
    Univ Gothenburg, Dept Biol & Environm Sci, Gothenburg, Sweden.
    Parker, Geoff A.
    Univ Liverpool, Inst Integrat Biol, Liverpool, Merseyside, England.
    Pizzari, Tommaso
    Univ Oxford, Edward Grey Inst, Dept Zool, Oxford, England.
    Qvarnström, Anna
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology.
    Safran, Rebecca J.
    Univ Colorado, Dept Ecol & Evolutionary Biol, Boulder, CO USA.
    Svensson, Ola
    Södertörn Univ, Sch Nat Sci Technol & Environm Studies, Huddinge, Sweden.
    Edwards, Scott, V
    Harvard Univ, Dept Organism & Evolutionary Biol, Cambridge, MA USA; Harvard Univ, Museum Comparat Zool, Cambridge, MA USA; Chalmers Univ Technol, Gothenburg Ctr Adv Studies Sci & Technol, Gothenburg, Sweden.
    Endless forms of sexual selection2019In: PeerJ, ISSN 2167-8359, E-ISSN 2167-8359, Vol. 7, article id e7988Article in journal (Refereed)
    Abstract [en]

    In recent years, the field of sexual selection has exploded, with advances in theoretical and empirical research complementing each other in exciting ways. This perspective piece is the product of a "stock-taking'' workshop on sexual selection and sexual conflict. Our aim is to identify and deliberate on outstanding questions and to stimulate discussion rather than provide a comprehensive overview of the entire field. These questions are organized into four thematic sections we deem essential to the field. First we focus on the evolution of mate choice and mating systems. Variation in mate quality can generate both competition and choice in the opposite sex, with implications for the evolution of mating systems. Limitations on mate choice may dictate the importance of direct vs. indirect benefits in mating decisions and consequently, mating systems, especially with regard to polyandry. Second, we focus on how sender and receiver mechanisms shape signal design. Mediation of honest signal content likely depends on integration of temporally variable social and physiological costs that are challenging to measure. We view the neuroethology of sensory and cognitive receiver biases as the main key to signal form and the 'aesthetic sense' proposed by Darwin. Since a receiver bias is sufficient to both initiate and drive ornament or armament exaggeration, without a genetically correlated or even coevolving receiver, this may be the appropriate 'null model' of sexual selection. Thirdly, we focus on the genetic architecture of sexually selected traits. Despite advances in modern molecular techniques, the number and identity of genes underlying performance, display and secondary sexual traits remains largely unknown. In-depth investigations into the genetic basis of sexual dimorphism in the context of long-term field studies will reveal constraints and trajectories of sexually selected trait evolution. Finally, we focus on sexual selection and conflict as drivers of speciation. Population divergence and speciation are often influenced by an interplay between sexual and natural selection. The extent to which sexual selection promotes or counteracts population divergence may vary depending on the genetic architecture of traits as well as the covariance between mating competition and local adaptation. Additionally, post-copulatory processes, such as selection against heterospecific sperm, may influence the importance of sexual selection in speciation. We propose that efforts to resolve these four themes can catalyze conceptual progress in the field of sexual selection, and we offer potential avenues of research to advance this progress.

  • 42.
    Luquet, Emilien
    et al.
    Univ Claude Bernard Lyon 1, Univ Lyon, CNRS, ENTPE,LEHNA UMR5023, Villeurbanne, France.
    Mörch, Patrik Rödin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology.
    Cortazar-Chinarro, Maria
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology.
    Meyer-Lucht, Yvonne
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology.
    Höglund, Jacob
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology.
    Laurila, Anssi
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology.
    Post-glacial colonization routes coincide with a life-history breakpoint along a latitudinal gradient2019In: Journal of Evolutionary Biology, ISSN 1010-061X, E-ISSN 1420-9101, Vol. 32, no 4, p. 356-368Article in journal (Refereed)
    Abstract [en]

    Although adaptive divergence along environmental gradients has repeatedly been demonstrated, the role of post‐glacial colonization routes in determining phenotypic variation along gradients has received little attention. Here, we used a hierarchical QSTFST approach to separate the roles of adaptive and neutral processes in shaping phenotypic variation in moor frog (Rana arvalis) larval life histories along a 1,700 km latitudinal gradient across northern Europe. This species has colonized Scandinavia via two routes with a contact zone in northern Sweden. By using neutral SNP and common garden phenotypic data from 13 populations at two temperatures, we showed that most of the variation along the gradient occurred between the two colonizing lineages. We found little phenotypic divergence within the lineages; however, all phenotypic traits were strongly diverged between the southern and northern colonization routes, with higher growth and development rates and larger body size in the north. The QST estimates between the colonization routes were four times higher than FST, indicating a prominent role for natural selection. QST within the colonization routes did not generally differ from FST, but we found temperature‐dependent adaptive divergence close to the contact zone. These results indicate that lineage‐specific variation can account for much of the adaptive divergence along a latitudinal gradient.

  • 43. McMahon, Barry J.
    et al.
    Johansson, Magnus P.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Population and Conservation Biology.
    Piertney, Stuart B.
    Buckley, Kieran
    Höglund, Jacob
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Population and Conservation Biology.
    Genetic variation among endangered Irish red grouse (Lagopus lagopus hibernicus) populations: implications for conservation and management2012In: Conservation Genetics, ISSN 1566-0621, E-ISSN 1572-9737, Vol. 13, no 3, p. 639-647Article in journal (Refereed)
    Abstract [en]

    Extant populations of Irish red grouse (Lagopus lagopus hibernicus) are both small and fragmented, and as such may have an increased risk of extinction through the effects of inbreeding depression and compromised adaptive potential. Here we used 19 microsatellite markers to assay genetic diversity across 89 georeferenced samples from putatively semi-isolated areas throughout the Republic of Ireland and we also genotyped 27 red grouse from Scotland using the same markers. The genetic variation within Ireland was low in comparison to previously published data from Britain and the sample of Scottish red grouse, and comparable to threatened European grouse populations of related species. Irish and Scottish grouse were significantly genetically differentiated (F-ST = 0.07, 95% CI = 0.04-0.10). There was evidence for weak population structure within Ireland with indications of four distinct genetic clusters. These correspond approximately to grouse populations inhabiting suitable habitat patches in the North West, Wicklow Mountains, Munster and Cork, respectively, although some admixture was detected. Pair-wise F-ST values among these populations ranged from 0.02 to 0.04 and the overall mean allelic richness was 5.5. Effective population size in the Munster area was estimated to be 62 individuals (95% CI = 33.6-248.8). Wicklow was the most variable population with an AR value of 5.4 alleles/locus. Local (Munster) neighbourhood size was estimated to 31 individuals corresponding to an average dispersal distance of 31 km. In order to manage and preserve Irish grouse we recommend that further fragmentation and destruction of habitats need to be prevented in conjunction with population management, including protection of the integrity of the existing population by refraining from augmenting it with individuals from mainland Britain to maximise population size.

  • 44. McMahon, Barry J.
    et al.
    Teeling, Emma C.
    Höglund, Jacob
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology.
    How and why should we implement genomics into conservation?2014In: Evolutionary Applications, ISSN 1752-4571, E-ISSN 1752-4571, Vol. 7, no 9, p. 999-1007Article, review/survey (Refereed)
    Abstract [en]

    Conservation genetics has provided important information into the dynamics of endangered populations. The rapid development of genomic methods has posed an important question, namely where do genetics and genomics sit in relation to their application in the conservation of species? Although genetics can answer a number of relevant questions related to conservation, the argument for the application of genomics is not yet fully exploited. Here, we explore the transition and rationale for the move from genetic to genomic research in conservation biology and the utility of such research. We explore the idea of a conservation prior' and how this can be determined by genomic data and used in the management of populations. We depict three different conservation scenarios and describe how genomic data can drive management action in each situation. We conclude that the most effective applications of genomics will be to inform stakeholders with the aim of avoiding emergency room conservation'.

  • 45.
    Meurling, Sara
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology.
    Cortazar-Chinarro, Maria
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology.
    Siljestam, Mattias
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology.
    Åhlén, David
    Ågren, Erik
    Höglund, Jacob
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology.
    Laurila, Anssi
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology.
    Body size mediates latitudinal population differences in response to Bd infection in two amphibian speciesManuscript (preprint) (Other academic)
    Abstract [en]

    The chytrid fungus Batrachochytrium dendrobatidis (Bd), is a generalist pathogen which has caused amphibian population declines worldwide. In many species Bd infection causes the disease chytridiomycosis, leading to high mortality. However, infection may cause sub-lethal fitness effects even in species that are resistant or tolerant to Bd. Moreover, populations of the same species may differ in their sensitivity to Bd, but the factors behind this variation are poorly understood. Here we exposed two common North European amphibians (moor frog Rana arvalis, common toad Bufo bufo) from two latitudinally divergent regions to two different BdGPL strains in a laboratory experiment. We found that Bd exposure lowered survival in both species, but this effect was much stronger in B. bufo.  Moreover, survival was lower in the northern region in both species, this difference again being much stronger in B. bufo. Northern individuals were smaller in both species and the survival difference between regions was size mediated with smaller individuals being more sensitive to Bd. We discuss potential additional factors contributing to this result. Bd exposure also led to sub-lethal effects in terms of reduced growth in both species suggesting that even individuals surviving the infection may have reduced fitness mediated by reduction if body size. However, we did not detect any differences in amphibian responses to the two Bd strains.

  • 46. Meurling, Sara
    et al.
    Kärvemo, Simon
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology.
    Cortazar-Chinarro, Maria
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology.
    Åhlén, David
    Brookes, Lola
    Nyström, Per
    Stenberg, Marika
    Garner, Trenton W.J.
    Höglund, Jacob
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology.
    Laurila, Anssi
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology.
    Occurrence of Batrachochytrium dendrobatidis in Sweden: higher infection prevalence in southern speciesManuscript (preprint) (Other academic)
    Abstract [en]

    The chytrid fungus Batrachochytrium dendrobatidis (Bd) has caused worldwide declines in amphibian populations. While Bd is widespread in southern and central Europe, its occurrence and distribution in northernmost Europe is mostly unknown. We surveyed for Bd in breeding anurans in Sweden by sampling 1917 amphibians from 101 localities and three regions in Sweden (Southern, Northern and Central). We found that Bd was widespread in southern and central Sweden, occurring in all nine investigated species and in 45.5 % of the 101 localities with an overall prevalence of 13.8%. No infected individuals were found in the four northern sites sampled. The records from central Sweden represent the northernmost records of Bd in Europe. While the proportion of sites positive for Bd was similar between the southern and central areas, prevalence was much higher in the southern area. This was due to southern species with a distribution mainly restricted to southernmost Sweden having higher prevalence than widespread generalist species. The nationally red-listed green toad Bufotes variabilis and fire bellied toad Bombina bombina had the highest prevalence (61.4% and 48.9% respectively). Across species, Bd prevalence was strongly positively correlated with water temperature at the start of egg-laying. However, no individuals showing visual signs of chytridiomycosis were found in the field. These results indicate that Bd is widespread and common in southern and central Sweden with southern species breeding in higher temperatures and with longer breeding periods having higher prevalence. However, the impact of Bd on amphibian populations in northernmost Europe remains unknown.

  • 47.
    Meyer-Lucht, Yvonne
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology.
    Luquet, Emilien
    Univ Lyon 1, Lab Ecol Hydrosyst Nat & Anthropises, Villeurbanne, France.
    Johannesdottir, Frida
    Cornell Univ, Dept Ecol & Evolutionary Biol, Ithaca, NY USA;Univ Oulu, Ecol & Genet Res Unit, Oulu, Finland.
    Mörch, Patrik Rödin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology.
    Quintela, Maria
    Inst Marine Res, Dept Populat Genet, Bergen, Norway.
    Richter Boix, Alex
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology.
    Höglund, Jacob
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology.
    Laurila, Anssi
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology.
    Genetic basis of amphibian larval development along a latitudinal gradient: Gene diversity, selection and links with phenotypic variation in transcription factor C/EBP-12019In: Molecular Ecology, ISSN 0962-1083, E-ISSN 1365-294X, Vol. 28, no 11, p. 2786-2801Article in journal (Refereed)
    Abstract [en]

    Ectotherm development rates often show adaptive divergence along climatic gradients, but the genetic basis for this variation is rarely studied. Here, we investigated the genetic basis for phenotypic variation in larval development in the moor frog Rana arvalis from five regions along a latitudinal gradient from Germany to northern Sweden. We focused on the C/EBP-1 gene, a transcription factor associated with larval development time. Allele frequencies at C/EBP-1 varied strongly among geographical regions. Overall, the distribution of alleles along the gradient was in concordance with the dual post-glacial colonization routes into Scandinavia, with a large number of alleles exclusively present along the southern colonization route. Only three of 38 alleles were shared between the routes. Analysis of contemporary selection on C/EBP-1 showed divergent selection among the regions, probably reflecting adaptation to the local environmental conditions, although this was especially strong between southern and northern regions coinciding also with lineages from different colonization routes. Overall, the C/EBP-1 gene has historically been under purifying selection, but two specific amino acid positions showed significant signals of positive selection. These positions showed divergence between southern and northern regions, and we suggest that they are functionally involved in the climatic adaptation of larval development. Using phenotypic data from a common garden experiment, we found evidence for specific C/EBP-1 alleles being correlated with larval development time, suggesting a functional role in adaptation of larval development to large-scale climatic variation.

  • 48.
    Morandin, C.
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics.
    Loveridge, A. J.
    Segelbacher, G.
    Elliot, N.
    Madzikanda, H.
    Macdonald, D. W.
    Höglund, Jacob
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology.
    Gene flow and immigration: genetic diversity and population structure of lions (Panthera leo) in Hwange National Park, Zimbabwe2014In: Conservation Genetics, ISSN 1566-0621, E-ISSN 1572-9737, Vol. 15, no 3, p. 697-706Article in journal (Refereed)
    Abstract [en]

    The genetic diversity and population structure of a population of African lions in Hwange National Park, Zimbabwe, was studied using 17 microsatellite loci. Spatial genetic analysis using Bayesian methods suggested a weak genetic structure within the population and high levels of gene flow across the study area. We were able to identify a few individuals with aberrant or admixed ancestry, which we interpreted as either immigrants or as descendants thereof. This, together with relatively high genetic diversity, suggests that immigrants from beyond the study area have influenced the genetic structure within the park. We suggest that the levels of genetic diversity and the observed weak structure are indicative of the large and viable Okavango-Hwange population of which our study population is a part. Genetic patterns can also be attributed to still existing high levels of habitat connectivity between protected areas. Given expected increases in human populations and anthropogenic impacts, efforts to identify and maintain existing movement corridors between regional lion populations will be important in retaining the high genetic diversity status of this population. Our results show that understanding existing levels of genetic diversity and genetic connectivity has implications, not only for this lion population, but also for managing large wild populations of carnivores.

  • 49.
    Mörch, Patrik Rödin
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology.
    Luquet, Emilien
    CNRS, ENTPE, UMR5023 LEHNA, Univ Lyon, Université Claude Bernard Lyon 1, Villeurbanne, France.
    Meyer-Lucht, Yvonne
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology.
    Richter Boix, Alex
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology.
    Höglund, Jacob
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology.
    Laurila, Anssi
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology.
    Latitudinal divergence in a widespread amphibian: Contrasting patterns of neutral and adaptive genomic variation2019In: Molecular Ecology, ISSN 0962-1083, E-ISSN 1365-294X, Vol. 28, no 12, p. 2996-3011Article in journal (Refereed)
    Abstract [en]

    Stochastic effects from demographic processes and selection are expected to shape the distribution of genetic variation in spatially heterogeneous environments. As the amount of genetic variation is central for long‐term persistence of populations, understanding how these processes affect variation over large‐scale geographical gradients is pivotal. We investigated the distribution of neutral and putatively adaptive genetic variation, and reconstructed demographic history in the moor frog (Rana arvalis) using 136 individuals from 15 populations along a 1,700‐km latitudinal gradient from northern Germany to northern Sweden. Using double digest restriction‐site associated DNA sequencing we obtained 27,590 single nucleotide polymorphisms (SNPs), and identified differentiation outliers and SNPs associated with growing season length. The populations grouped into a southern and a northern cluster, representing two phylogeographical lineages from different post‐glacial colonization routes. Hybrid index estimation and demographic model selection showed strong support for a southern and northern lineage and evidence of gene flow between regions located on each side of a contact zone. However, patterns of past gene flow over the contact zone differed between neutral and putatively adaptive SNPs. While neutral nucleotide diversity was higher along the southern than the northern part of the gradient, nucleotide diversity in differentiation outliers showed the opposite pattern, suggesting differences in the relative strength of selection and drift along the gradient. Variation associated with growing season length decreased with latitude along the southern part of the gradient, but not along the northern part where variation was lower, suggesting stronger climate‐mediated selection in the north. Outlier SNPs included loci involved in immunity and developmental processes.

  • 50.
    O'Hanlon, Simon J.
    et al.
    Imperial Coll London, Sch Publ Hlth, Dept Infect Dis Epidemiol, London W2 1PG, England;Imperial Coll London, Sch Publ Hlth, MRC Ctr Global Infect Dis Anal, London W2 1PG, England;Inst Zool, Regents Pk, London NW1 4RY, England.
    Rieux, Adrien
    CIRAD, St Pierre 97410, Reunion, France.
    Farrer, Rhys A.
    Imperial Coll London, Sch Publ Hlth, Dept Infect Dis Epidemiol, London W2 1PG, England;Imperial Coll London, Sch Publ Hlth, MRC Ctr Global Infect Dis Anal, London W2 1PG, England.
    Rosa, Goncalo M.
    Inst Zool, Regents Pk, London NW1 4RY, England;Univ Nevada, Dept Biol, Reno, NV 89557 USA;Univ Lisbon, Fac Ciencias, CE3C, Lisbon, Portugal.
    Waldman, Bruce
    Seoul Natl Univ, Sch Biol Sci, Lab Behav & Populat Ecol, Seoul 08826, South Korea.
    Bataille, Arnaud
    Seoul Natl Univ, Sch Biol Sci, Lab Behav & Populat Ecol, Seoul 08826, South Korea;CIRAD, UMR ASTRE, F-34398 Montpellier, France.
    Kosch, Tiffany A.
    Seoul Natl Univ, Sch Biol Sci, Lab Behav & Populat Ecol, Seoul 08826, South Korea;James Cook Univ, Coll Publ Hlth Med & Vet Sci, Hlth Res Grp 1, Townsville, Qld 4811, Australia.
    Murray, Kris A.
    Imperial Coll London, Sch Publ Hlth, Dept Infect Dis Epidemiol, London W2 1PG, England;Imperial Coll London, Sch Publ Hlth, MRC Ctr Global Infect Dis Anal, London W2 1PG, England.
    Brankovics, Balazs
    Westerdijk Fungal Biodivers Inst, Uppsalalaan 8, NL-3584 CT Utrecht, Netherlands;Univ Amsterdam, Inst Biodivers & Ecosyst Dynam, Sci Pk 904, NL-1098 XH Amsterdam, Netherlands.
    Fumagalli, Matteo
    Imperial Coll London, Dept Life Sci, Silwood Pk Campus, Ascot, Berks, England;UCL, Genet Inst, London WC1E 6BT, England.
    Martin, Michael D.
    Norwegian Univ Sci & Technol NTNU, NTNU Univ Museum, Dept Nat Hist, Erling Skakkes Gate 49, NO-7012 Trondheim, Norway;Univ Copenhagen, Nat Hist Museum Denmark, Ctr GeoGenet, Oster Voldgade 5-7, DK-1350 Copenhagen, Denmark.
    Wales, Nathan
    Univ Copenhagen, Nat Hist Museum Denmark, Ctr GeoGenet, Oster Voldgade 5-7, DK-1350 Copenhagen, Denmark.
    Alvarado-Rybak, Mario
    Univ Andres Bello, Fac Ecol & Recursos Nat, Ctr Invest Sustentabilidad, Republ 440, Santiago, Chile.
    Bates, Kieran A.
    Imperial Coll London, Sch Publ Hlth, Dept Infect Dis Epidemiol, London W2 1PG, England;Imperial Coll London, Sch Publ Hlth, MRC Ctr Global Infect Dis Anal, London W2 1PG, England;Inst Zool, Regents Pk, London NW1 4RY, England.
    Berger, Lee
    James Cook Univ, Coll Publ Hlth Med & Vet Sci, Hlth Res Grp 1, Townsville, Qld 4811, Australia.
    Boell, Susanne
    Agcy Populat Ecol & Nat Conservancy, Gerbrunn, Germany.
    Brookes, Lola
    Inst Zool, Regents Pk, London NW1 4RY, England.
    Clare, Frances
    Imperial Coll London, Sch Publ Hlth, Dept Infect Dis Epidemiol, London W2 1PG, England;Imperial Coll London, Sch Publ Hlth, MRC Ctr Global Infect Dis Anal, London W2 1PG, England;Inst Zool, Regents Pk, London NW1 4RY, England.
    Courtois, Elodie A.
    Univ Guyane, CNRS, IFREMER, LEEISA, Cayenne 97300, French Guiana.
    Cunningham, Andrew A.
    Inst Zool, Regents Pk, London NW1 4RY, England.
    Doherty-Bone, Thomas M.
    Royal Zool Soc Scotland, Conservat Programmes, Edinburgh, Midlothian, Scotland.
    Ghosh, Pria
    Imperial Coll London, Sch Publ Hlth, Dept Infect Dis Epidemiol, London W2 1PG, England;Imperial Coll London, Sch Publ Hlth, MRC Ctr Global Infect Dis Anal, London W2 1PG, England;North West Univ, Unit Environm Sci & Management, Private Bag X6001, ZA-2520 Potchefstroom, South Africa.
    Gower, David J.
    Nat Hist Museum, Life Sci, London SW7 5BD, England.
    Hintz, William E.
    Univ Victoria, Dept Biol, Victoria, BC V8W 3N5, Canada.
    Höglund, Jacob
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology.
    Jenkinson, Thomas S.
    Univ Michigan, Dept Ecol & Evolutionary Biol, Ann Arbor, MI 48109 USA.
    Lin, Chun-Fu
    Endem Species Res Inst, Div Zool, 1 Ming Shen East Rd, Nantou 552, Taiwan.
    Laurila, Anssi
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology.
    Loyau, Adeline
    UFZ Helmholtz Ctr Environm Res, Dept Conservat Biol, D-04318 Leipzig, Germany;Univ Toulouse, UPS, CNRS, EcoLab,INPT, Toulouse, France.
    Martel, An
    Univ Ghent, Fac Vet Med, Dept Pathol Bacteriol & Avian Dis, B-9820 Merelbeke, Belgium.
    Meurling, Sara
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology.
    Miaud, Claude
    Univ Paul Valery Montpellier, Univ Montpellier, PSL Res Univ, CEFE UMR 5175,CNRS,EPHE, Montpellier, France.
    Minting, Pete
    Amphibian & Reptile Conservat ARC Trust, Bournemouth BH1 4AP, Dorset, England.
    Pasmans, Frank
    Univ Ghent, Fac Vet Med, Dept Pathol Bacteriol & Avian Dis, B-9820 Merelbeke, Belgium.
    Schmeller, Dirk S.
    UFZ Helmholtz Ctr Environm Res, Dept Conservat Biol, D-04318 Leipzig, Germany;Univ Toulouse, UPS, CNRS, EcoLab,INPT, Toulouse, France.
    Schmidt, Benedikt R.
    Univ Zurich, Dept Evolutionary Biol & Environm Studies, CH-8057 Zurich, Switzerland;Info Fauna Karch, UniMail Batiment G,Bellevaux 51, CH-2000 Neuchatel, Switzerland.
    Shelton, Jennifer M. G.
    Imperial Coll London, Sch Publ Hlth, Dept Infect Dis Epidemiol, London W2 1PG, England;Imperial Coll London, Sch Publ Hlth, MRC Ctr Global Infect Dis Anal, London W2 1PG, England.
    Skerratt, Lee F.
    James Cook Univ, Coll Publ Hlth Med & Vet Sci, Hlth Res Grp 1, Townsville, Qld 4811, Australia.
    Smith, Freya
    Inst Zool, Regents Pk, London NW1 4RY, England;APHA, Natl Wildlife Management Ctr, Woodchester Pk GL10 3UJ, Glos, England.
    Soto-Azat, Claudio
    Univ Andres Bello, Fac Ecol & Recursos Nat, Ctr Invest Sustentabilidad, Republ 440, Santiago, Chile.
    Spagnoletti, Matteo
    UCL, Genet Inst, London WC1E 6BT, England.
    Tessa, Giulia
    Nonprofit Assoc Zirichiltaggi Sardinia Wildlife C, Str Vicinale Filigheddu 62-C, I-07100 Sassari, Italy.
    Toledo, Luis Felipe
    Univ Estadual Campinas, Inst Biol, Dept Biol Anim, Lab Hist Nat Anfibios Brasileiros LaHNAB, Campinas, SP, Brazil.
    Valenzuela-Sanchez, Andres
    Univ Andres Bello, Fac Ecol & Recursos Nat, Ctr Invest Sustentabilidad, Republ 440, Santiago, Chile;ONG Ranita Darwin, Nataniel Cox 152, Santiago, Chile.
    Verster, Ruhan
    North West Univ, Unit Environm Sci & Management, Private Bag X6001, ZA-2520 Potchefstroom, South Africa.
    Voros, Judit
    Hungarian Nat Hist Museum, Dept Zool, Collect Amphibians & Reptiles, Baross U 13, H-1088 Budapest, Hungary.
    Webb, Rebecca J.
    James Cook Univ, Coll Publ Hlth Med & Vet Sci, Hlth Res Grp 1, Townsville, Qld 4811, Australia.
    Wierzbicki, Claudia
    Imperial Coll London, Sch Publ Hlth, Dept Infect Dis Epidemiol, London W2 1PG, England;Imperial Coll London, Sch Publ Hlth, MRC Ctr Global Infect Dis Anal, London W2 1PG, England.
    Wombwell, Emma
    Inst Zool, Regents Pk, London NW1 4RY, England.
    Zamudio, Kelly R.
    Cornell Univ, Dept Ecol & Evolutionary Biol, Ithaca, NY 14853 USA.
    Aanensen, David M.
    Imperial Coll London, Sch Publ Hlth, Dept Infect Dis Epidemiol, London W2 1PG, England;Imperial Coll London, Sch Publ Hlth, MRC Ctr Global Infect Dis Anal, London W2 1PG, England;Ctr Genom Pathogen Surveillance, Wellcome Genome Campus, Hinxton, Cambs, England.
    James, Timothy Y.
    Univ Michigan, Dept Ecol & Evolutionary Biol, Ann Arbor, MI 48109 USA.
    Gilbert, M. Thomas P.
    Norwegian Univ Sci & Technol NTNU, NTNU Univ Museum, Dept Nat Hist, Erling Skakkes Gate 49, NO-7012 Trondheim, Norway;Univ Copenhagen, Nat Hist Museum Denmark, Ctr GeoGenet, Oster Voldgade 5-7, DK-1350 Copenhagen, Denmark.
    Weldon, Che
    North West Univ, Unit Environm Sci & Management, Private Bag X6001, ZA-2520 Potchefstroom, South Africa.
    Bosch, Jaime
    CSIC, Museo Nacl Ciencias Nat, C Jose Gutierrez Abascal 2, E-28006 Madrid, Spain.
    Balloux, Francois
    Garner, Trenton W. J.
    Inst Zool, Regents Pk, London NW1 4RY, England;North West Univ, Unit Environm Sci & Management, Private Bag X6001, ZA-2520 Potchefstroom, South Africa;Nonprofit Assoc Zirichiltaggi Sardinia Wildlife C, Str Vicinale Filigheddu 62-C, I-07100 Sassari, Italy.
    Fisher, Matthew C.
    Imperial Coll London, Sch Publ Hlth, Dept Infect Dis Epidemiol, London W2 1PG, England;Imperial Coll London, Sch Publ Hlth, MRC Ctr Global Infect Dis Anal, London W2 1PG, England.
    Recent Asian origin of chytrid fungi causing global amphibian declines2018In: Science, ISSN 0036-8075, E-ISSN 1095-9203, Vol. 360, no 6389, p. 621-+Article in journal (Refereed)
    Abstract [en]

    Globalized infectious diseases are causing species declines worldwide, but their source often remains elusive. We used whole-genome sequencing to solve the spatiotemporal origins of themost devastating panzootic to date, caused by the fungus Batrachochytrium dendrobatidis, a proximate driver of global amphibian declines. We traced the source of B. dendrobatidis to the Korean peninsula, where one lineage, BdASIA-1, exhibits the genetic hallmarks of an ancestral population that seeded the panzootic. We date the emergence of this pathogen to the early 20th century, coinciding with the global expansion of commercial trade in amphibians, and we show that intercontinental transmission is ongoing. Our findings point to East Asia as a geographic hotspot for B. dendrobatidis biodiversity and the original source of these lineages that now parasitize amphibians worldwide.

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