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  • 1.
    Andreasen, Katarina
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för evolution, genomik och systematik, Systematisk botanik. Systematisk botanik.
    Implications of molecular systematic analyses on the conservation of rare and threatened taxa: contrasting examples from Malvaceae2005Inngår i: Conservation Genetics, ISSN 1566-0621, E-ISSN 1572-9737, Vol. 6, nr 3, s. 399-412Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Systematic research provides essential evidence for setting conservation priorities for rare and endangered taxa. Phylogenetic analyses can identify cryptic, genetically distinct lineages as well as actively interbreeding, and hence, non-distinctive lineages earlier perceived as separate taxa. A major aim of this study was to identify genetically distinct, rare lineages within two Malvaceae sister-genera, Sidalcea and Eremalche. The focus was two taxon-pairs each consisting of one rare and one more common taxon. The results demonstrate that even within two closely related genera, with a large number of rare taxa, molecular phylogenetic analyses can reveal contrasting degrees of evolutionary divergence and thus contrasting conservation implications for threatened taxa. Contrary to expectations, the substitution rate in the nuclear ribosomal transcribed spacers for annualEremalche did not correspond to the faster evolutionary rate of annuals – compared to perennials – detected earlier within Sidalcea. Branch lengths in the (annual) Eremalche clade were shorter than those of annual members of Sidalcea. The phylogenetic analyses showed that the rare and endangered S. keckii and E. kernensis each are most closely related to a common species that has been regarded as insufficiently distinct to warrant separate taxonomic status. An additional aim of the study was to test the utility of the Phylogenetic Diversity (PD) measure to formalize the procedure of prioritizing conservation efforts. The measure demonstrated S. keckii (but not E. kernensis) to be genetically distinct from its closest relative and a good candidate for conservation. The PD measure was earlier used for assessing conservation priorities for areas, but proved useful to more objectively suggest conservation priorities among threatened taxa. Because this measure is calculated directly from the data, it retains more character information and gives a better representation of genetic diversity than other measures relying on tree topologies.

  • 2.
    Arrendal, Johanna
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och evolution, Zooekologi.
    Vilà, Carles
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för evolution, genomik och systematik, Evolutionsbiologi.
    Björklund, Mats
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och evolution, Zooekologi.
    Reliability of noninvasive genetic census of otters compared to field censuses2007Inngår i: Conservation Genetics, ISSN 1566-0621, E-ISSN 1572-9737, Vol. 8, nr 5, s. 1097-1107Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Conservation and management actions are often highly dependent on accurate estimations of population sizes. However, these estimates are difficult to obtain for elusive and rare species. We compared two census methods for Eurasian otter: snow tracking and noninvasive genetic census based on the genotyping of faecal samples. With the noninvasive genetic census we detected the presence of almost twice as many otters as with snow tracking (23 and 10–15, respectively), and mark-recapture estimates based on the genetic census indicated that the real number of otters could be even higher. Our results indicate that snow tracking tends to underestimate the number of individuals and also that it is more susceptible to subjective assessment. We compared the strengths and weaknesses of the two methods.

  • 3.
    Björnerfeldt, Susanne
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för evolution, genomik och systematik, Evolutionsbiologi.
    Vilà, Carles
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för evolution, genomik och systematik, Evolutionsbiologi.
    Evaluation of methods for single hair DNA amplification2007Inngår i: Conservation Genetics, ISSN 1566-0621, E-ISSN 1572-9737, Vol. 8, nr 4, s. 977-981Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Because of the low amount of DNA in single hairs, it may be difficult to obtain reliable genotypes for forensic and conservation genetics studies. We therefore compared different methods for reliably genotyping single hair samples. Our results indicate that preliminary whole genome amplification can increase the likelihood of successfully genotyping a single hair compared to other commonly used protocols. The difference between the methods is small for single locus comparisons, but it becomes more important in multi-locus comparisons. The economic and time costs of the whole genome amplification may prevent its large-scale use in non-invasive monitoring programs. Nevertheless, it may be a very useful approach for the analysis of especially valuable samples.

  • 4.
    Bodare, Sofia
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Växtekologi och evolution.
    Ravikanth, Gudasalamani
    Ashoka Trust Res Ecol & Environm, Bangalore 560064, Karnataka, India.;Univ Agr Sci, Sch Ecol & Conservat, Bangalore 560065, Karnataka, India..
    Ismail, Sascha A.
    Swiss Fed Inst Technol, Dept Environm Syst Sci, Ecosyst Management, Univ Str 16, CH-8092 Zurich, Switzerland..
    Patel, Mohana Kumara
    Univ Agr Sci, Sch Ecol & Conservat, Bangalore 560065, Karnataka, India..
    Spanu, Ilaria
    CNR, Inst Biosci & Bioresources, Via Madonna del Piano 10, I-50019 Florence, Italy..
    Vasudeva, Ramesh
    Univ Agr Sci, Dept Forest Biol, Coll Forestry, Sirsi 581401, Karnataka, India..
    Shaanker, Ramanan Uma
    Ashoka Trust Res Ecol & Environm, Bangalore 560064, Karnataka, India.;Univ Agr Sci, Sch Ecol & Conservat, Bangalore 560065, Karnataka, India.;Univ Agr Sci, Dept Crop Physiol, Bangalore 560065, Karnataka, India..
    Vendramin, Giovanni Giuseppe
    CNR, Inst Biosci & Bioresources, Via Madonna del Piano 10, I-50019 Florence, Italy..
    Lascoux, Martin
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Växtekologi och evolution.
    Tsuda, Yoshiaki
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Växtekologi och evolution. Univ Tsukuba, Sugadaira Montane Res Ctr, 1278-294 Sugadairakogen, Ueda, Nagano 3862204, Japan..
    Fine- and local- scale genetic structure of Dysoxylum malabaricum, a late-successional canopy tree species in disturbed forest patches in the Western Ghats, India2017Inngår i: Conservation Genetics, ISSN 1566-0621, E-ISSN 1572-9737, Vol. 18, nr 1, s. 1-15Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Dysoxylum malabaricum (white cedar) is an economically important tree species, endemic to the Western Ghats, India, which is the world's most densely populated biodiversity hotspot. In this study, we used variation at ten nuclear simple sequence repeat loci to investigate genetic diversity and fine scale spatial genetic structure (FSGS) in seedlings and adults of D. malabaricum from four forest patches in the northern part of the Western Ghats. When genetic variation was compared between seedlings and adults across locations, significant differences were detected in allelic richness, observed heterozygosity, fixation index (F (IS)), and relatedness (P < 0.05). Reduced genetic diversity and increased relatedness at the seedling stage might be due to fragmentation and disturbance. There was no FSGS at the adult stage and FSGS was limited to shorter distance classes at the seedling stage. However, there was clear spatial genetic structure at the landscape level (< 50 km), regardless of age class, due to limited gene flow between forest patches. A comparison of the distributions of size classes in the four locations with published data from a more southern area, showed that large trees (diameter at breast height, DBH, > 130 cm) are present in the southern sacred forests but not in the northern forest reserves. This pattern is likely due to stronger harvesting pressure in the north compared to the south, because in the north there are no cultural taboos regulating the extraction of natural resources. The implications for forest conservation in this biodiversity hotspot are discussed.

  • 5.
    Breed, Martin F.
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Växtekologi och evolution.
    Stead, Michael G.
    Australian Centre for Evolutionary Biology and Biodiversity (ACEBB) and School of Earth and Environmental Sciences, University of Adelaide.
    Ottewell, Kym M.
    Australian Centre for Evolutionary Biology and Biodiversity (ACEBB) and School of Earth and Environmental Sciences, University of Adelaide.
    Gardner, Michael G.
    Australian Centre for Evolutionary Biology and Biodiversity (ACEBB) and School of Earth and Environmental Sciences, University of Adelaide.
    Lowe, Andrew J.
    Australian Centre for Evolutionary Biology and Biodiversity (ACEBB) and School of Earth and Environmental Sciences, University of Adelaide.
    Which provenance and where?: Seed sourcing strategies for revegetation in a changing environment2013Inngår i: Conservation Genetics, ISSN 1566-0621, E-ISSN 1572-9737, Vol. 14, nr 1, s. 1-10Artikkel, forskningsoversikt (Fagfellevurdert)
    Abstract [en]

    Revegetation is one practical application of science that should ideally aim to combine ecology with evolution to maximise biodiversity and ecosystem outcomes. The strict use of locally sourced seed in revegetation programs is widespread and is based on the expectation that populations are locally adapted. This practice does not fully integrate two global drivers of ecosystem change and biodiversity loss: habitat fragmentation and climate change. Here, we suggest amendments to existing strategies combined with a review of alternative seed-sourcing strategies that propose to mitigate against these drivers. We present a provenancing selection guide based on confidence surrounding climate change distribution modelling and data on population genetic and/or environmental differences between populations. Revegetation practices will benefit from greater integration of current scientific developments and establishment of more long-term experiments is key to improving the long-term success. The rapid growth in carbon and biodiversity markets creates a favourable economic climate to achieve these outcomes.

  • 6.
    Demandt, Marnie H.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Zooekologi.
    Temporal changes in genetic diversity of isolated populations of perch and roach2010Inngår i: Conservation Genetics, ISSN 1566-0621, E-ISSN 1572-9737, Vol. 11, nr 1, s. 249-255Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Genetic drift, together with natural selection and gene flow, affects genetic variation and is the major source of changes in allele frequencies in small and isolated populations. Temporal shifts in allele frequencies at five polymorphic loci were used to estimate the amount of genetic drift in an isolated population of perch (Perca fluviatilis L.) and roach (Rutilus rutilus L.). Here, I used the populations from the Biotest basin at Forsmark, Sweden, to investigate genetic diversity between 1977 and 2000, during which time the population can be considered to be totally isolated from other populations. Microsatellite data reveal stable levels of gene diversity over time for both species. Estimates of genetic differentiation (F-ST) showed a significant divergence between 1977 and 2000 for both perch and roach. A positive correlation between genetic distance and time was found (Mantel test, perch: r = 0.724, P = 0.0112; roach: r = 0.59, P = 0.036). Estimates of effective population size (N-e) differed with a factor six between two different estimators (NeEstimator and TempoFS) applying the temporal method. Ratios of Ne/N ranged between 10(-2) and 10(-3), values normally found in marine species. Despite low Ne the populations have not lost their evolutionary potential due to drift. But two decades of isolation have lead to isolation by time for populations of perch and roach, respectively.

  • 7.
    Graham, Stuart
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Zooekologi. Department of Ecology, Evolution and Marine Biology, University of California, Santa Barbara, CA 93106, USA..
    Kozma, Radoslav
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Zooekologi.
    Höglund, Jacob
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Zooekologi.
    The utility of effective population size in population management 1:estimating contemporary effective size2016Inngår i: Conservation Genetics, ISSN 1566-0621, E-ISSN 1572-9737Artikkel i tidsskrift (Fagfellevurdert)
    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.

  • 8.
    Guschanski, Katerina
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Zooekologi.
    Olivieri, G.
    Funk, S. M.
    Radespiel, U.
    MtDNA reveals strong genetic differentiation among geographically isolated populations of the golden brown mouse lemur, Microcebus ravelobensis2007Inngår i: Conservation Genetics, ISSN 1566-0621, E-ISSN 1572-9737, Vol. 8, nr 4, s. 809-821Artikkel i tidsskrift (Fagfellevurdert)
  • 9.
    Hedmark, Eva
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för evolution, genomik och systematik. Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Evolutionsbiologi.
    Ellegren, Hans
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för evolution, genomik och systematik. Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Evolutionsbiologi.
    DNA-based monitoring of two newly founded Scandinavian wolverine populations2007Inngår i: Conservation Genetics, ISSN 1566-0621, E-ISSN 1572-9737, Vol. 8, nr 4, s. 843-852Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    The wolverine is an endangered carnivore that in northwestern Europe is restricted to the mountain range along the border between Sweden and Norway. The Scandinavian wolverine population experienced a severe decline in numbers due to human persecution during the 20th century, although with legislative protection the population has recently implied that the population slowly has started to recover (current population size estimate of 800 individuals). In the mid 1990s, wolverines appeared in two new and isolated areas east of the mountain range, in the forest landscape close to the Gulf of Bothnia. Using non-invasive, DNA-based monitoring, we show here that these new subpopulations were likely founded by as few as 2 and 2-4 individuals, respectively, and that little, if any, genetic contact with the main population since colonisation has been established. A high degree of genetic similarity among individuals in the two areas indicates inbreeding. We estimate the minimum number of wolverines known to be alive in these areas during the period of 2001-2005 to 5 and 17, respectively, with one subpopulation showing decreasing (currently 2) numbers and the other increasing (10). For the somewhat larger population, we infer a tentative pedigree from relatedness values and parentage tests, which indicates the occurrence of brother-sister matings. This study illustrates the usefulness of non-invasive monitoring in the management of endangered carnivore populations.

  • 10.
    Hefti-Gautschi, Barbara
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för evolutionsbiologi.
    Pfunder, Monika
    Jenni, Lukas
    Keller, Verena
    Ellegren, Hans
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för evolutionsbiologi.
    Identification of conservation units in the European Mergus merganser based on nuclear and mitochondrial DNA markers2009Inngår i: Conservation Genetics, ISSN 1566-0621, E-ISSN 1572-9737, Vol. 10, nr 1, s. 87-99Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    The conservation status of small breeding areas of the Goosander (Mergus merganser merganser) in Central Europe is unclear. Geographic isolation of these areas suggests restricted gene flow to and from large North-European populations. On the other hand, migrating Goosanders from northern Europe join the Central European breeding population for wintering. To evaluate the conservation status of the small breeding areas we assessed the genetic structure of M. merganser populations in Europe by examining two nuclear marker systems (microsatellites and Single Nucleotide Polymorphisms, SNP) and mitochondrial (mtDNA) control region sequence variation for Goosanders in 11 sampling areas representing three of five distinct breeding areas and two subspecies (M. m. merganser and M. m. americanus). Overall population differentiation estimates including both subspecies were high, both based on mtDNA (Phi(ST) = 0.899; P < 0.0001) and nuclear markers (theta(ST) = 0.219; 95% CI 0.088-0.398, SNP and microsatellites combined). Within Europe, mtDNA revealed a strong overall (Phi(ST) = 0.426; P < 0.0001) and significant pairwise population differentiation between almost all comparisons. In contrast, both nuclear marker systems combined revealed only a small overall genetic differentiation (theta(ST) = 0.022; 95% CI 0.003-0.041). The strong genetic differentiation based on female-inherited mtDNA but not on biparentally inherited nuclear markers can be explained by sex-biased dispersal and strong female philopatry. Therefore, small breeding areas in Europe are endangered despite large male-mediated gene-flow, because when these populations decline, only males-but due to strong philopatry not females-can be efficiently supplemented by migration from the large North European populations. We therefore propose to manage the small breeding areas independently and to strengthen conservation efforts for this species in Central Europe.

  • 11.
    Höglund, Jacob
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och evolution, Populationsbiologi.
    Larsson, Jobs Karl
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och evolution, Populationsbiologi.
    Jansman, Hugh A.H.
    Segelbacher, Gernot
    Genetic variability in European black grouse (Tetrao tetrix)2007Inngår i: Conservation Genetics, ISSN 1566-0621, E-ISSN 1572-9737, Vol. 8, nr 1, s. 239-243Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    We studied microsatellite genetic variation in 14 different geographic populations of black grouse (Tetrao tetrix) across the European range. Populations were grouped in three different fragmentation categories: isolated, contiguous and continuous, respectively. Genetic diversity, measured as observed heterozygosity (H O), expected heterozygosity (H E) and allelic richness, were lower in isolated populations as compared to the other two categories that did not differ amongst one another. These results imply that lowered genetic variability in black grouse populations is negatively affected by population isolation. Our results suggest that the connectivity of small and isolated populations in Western Europe should be improved or else these face an increased risk of extinction due to genetic and demographic stochasticity.

  • 12.
    Höglund, Jacob
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Zooekologi.
    Wengström, Åsa
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Zooekologi.
    Rogell, Björn
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Zooekologi.
    Meyer-Lucht, Yvonne
    Low MHC variation in isolated island populations of the Natterjack toad (Bufo calamita)2015Inngår i: Conservation Genetics, ISSN 1566-0621, E-ISSN 1572-9737, Vol. 16, nr 4, s. 1007-1010Artikkel i tidsskrift (Fagfellevurdert)
    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.

  • 13.
    Kireta, Dona
    et al.
    Univ Adelaide, Sch Biol Sci, North Terrace, Adelaide, SA 5005, Australia;Univ Adelaide, Environm Inst, North Terrace, Adelaide, SA 5005, Australia.
    Christmas, Matthew
    Uppsala universitet, Medicinska och farmaceutiska vetenskapsområdet, Medicinska fakulteten, Institutionen för medicinsk biokemi och mikrobiologi.
    Lowe, Andrew J.
    Univ Adelaide, Sch Biol Sci, North Terrace, Adelaide, SA 5005, Australia;Univ Adelaide, Environm Inst, North Terrace, Adelaide, SA 5005, Australia.
    Breed, Martin F.
    Univ Adelaide, Sch Biol Sci, North Terrace, Adelaide, SA 5005, Australia;Univ Adelaide, Environm Inst, North Terrace, Adelaide, SA 5005, Australia.
    Disentangling the evolutionary history of three related shrub species using genome-wide molecular markers2019Inngår i: Conservation Genetics, ISSN 1566-0621, E-ISSN 1572-9737, Vol. 20, nr 5, s. 1101-1112Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Understanding population genetic structure provides insight into historic population connectivity, and is largely driven by migration, population size, and species life history. During the last glacial maximum, sea levels around the biogeographically interesting, but poorly studied, South Australian coastal plains and geosyncline were thought to be sufficiently low that three prominent peninsulas (Fleurieu, Yorke, Eyre) and a large offshore island (Kangaroo Island) formed a continuous landmass. However, the degree to which population genetic structure in this region has been shaped by biogeography remains largely untested. Here, we use genome-wide SNP data from three Goodenia shrub species with contrasting growth forms to assess how historical and contemporary processes have shaped population genetic structure. These species occur commonly throughout South Australia and are used extensively in revegetation. The two woody species (Goodenia varia, G. ovata) displayed low genetic differentiation across the southern parts of the peninsulas and island, reflecting historical landscape connectivity. The third more-herbaceous species (G. amplexans) displayed higher genetic structure across the land features, reflecting contemporary disconnectivity. Kangaroo Island and the southern Flinders Ranges had relatively high genetic diversity, providing further evidence that they were important putative Pleistocene refugia. We demonstrate that historic changes in landscape and possible migration to and from refugia, have shaped the population genetic structure in these closely related shrubs, which may have been influenced by contemporary factors and small population sizes. We highlight the importance of using multi-species designs when studying historical population connectivity in understudied regions of the world.

  • 14. Knopp, T.
    et al.
    Cano, José M.
    Crochet, Pierre-André
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och evolution, Zooekologi.
    Merilä, J.
    Contrasting levels of variation in neutral and quantitative genetic loci on island populations of moor frogs (Rana arvalis)2007Inngår i: Conservation Genetics, ISSN 1566-0621, E-ISSN 1572-9737, Vol. 8, nr 1, s. 45-56Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Reduced levels of genetic variability and a prominent differentiation in both neutral marker genes and phenotypic traits are typical for many island populations as compared to their mainland conspecifics. However, whether genetic diversity in neutral marker genes reflects genetic variability in quantitative traits, and thus, their evolutionary potential, remains typically unclear. Moreover, the phenotypic differentiation on islands could be attributable to phenotypic plasticity, selection or drift; something which seldom has been tested. Using eight polymorphic microsatellite loci and quantitative genetic breeding experiments we conducted a detailed comparison on genetic variability and differentiation between Nordic islands (viz. Gotland, Öland and Læsø) and neighbouring mainland populations of moor frogs (Rana arvalis). As expected, the neutral variation was generally lower in island than in mainland populations. But as opposed to this, higher levels of additive genetic variation (V A) in body size and tibia length were found on the island of Gotland as compared to the mainland population. When comparing the differentiation seen in neutral marker genes (F ST) with the differentiation in genes coding quantitative traits (Q ST) two different evolutionary scenarios were found: while selection might explain a smaller size of moor frogs on Gotland, the differentiation seen in tibia length could be explained by genetic drift. These results highlight the limited utility of microsatellite loci alone in inferring the causes behind an observed phenotypic differentiation, or in predicting the amount of genetic variation in ecologically important quantitative traits.

  • 15.
    Kozma, Radoslav
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Zooekologi.
    Graham, Stuart
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Zooekologi. Department of Ecology, Evolution and Marine Biology, University of California, Santa Barbara, CA 93106, USA.
    Höglund, Jacob
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Zooekologi.
    The utility of effective population size in population management 2:estimating demographic history2016Inngår i: Conservation Genetics, ISSN 1566-0621, E-ISSN 1572-9737Artikkel i tidsskrift (Fagfellevurdert)
    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.

  • 16.
    Larsson, Kjell
    et al.
    Högskolan på Gotland, Avdelningen för Biologi.
    Ottvall, Richard
    Högskolan på Gotland, Avdelningen för Biologi.
    Höglund, Jacob
    Bensch, Staffan
    Population differentiation in the redshank (Tringa totanus) as revealed by mitochondrial DNA and amplified fragment length polymorphism markers2005Inngår i: Conservation Genetics, ISSN 1566-0621, E-ISSN 1572-9737, Vol. 6, nr 3, s. 321-331Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    The redshank (Tringa totanus) is declining throughout Europe and to implement efficient conservation measures, it is important to obtain information about the population genetic structure. The aim of the present study was two-fold. First, we analysed the genetic variation within and between populations in the Baltic region in southern Scandinavia. Evidence of genetic structure would suggest that different populations might require separate management strategies. Second, in an attempt to study large-scale genetic structure we compared the Baltic populations with redshanks from northern Scandinavia and Iceland. This analysis could reveal insights into phylogeography and long-term population history. DNA samples were collected from six breeding sites in Scandinavia presumed to include two subspecies (totanus and britannica) and a further sample from Iceland (subspecies robusta). Two methods were used to study the population genetic structure. Domain II and III of the mitochondrial control region was analysed by DNA sequencing and nuclear DNA was analysed by screening amplified fragment length polymorphism (AFLP) markers. Mitochondrial DNA showed no variation between individuals in domain II. When analysing an 481 bp fragment of domain III seven haplotypes were found among birds. On the basis of mtDNA sequences, redshanks showed some evidence of a recent expansion from a bottlenecked refugial population. Bayesian analyses of AFLP data revealed a significant genetic differentiation between suggested subspecies but not between populations within the Baltic region. Our results indicate that populations of redshanks in Europe constitute at least three separate management units corresponding to the recognised subspecies.

  • 17.
    Lopes, Fernando
    et al.
    Univ Vale Rio dos Sinos UNISINOS, BR-93022000 Sao Leopoldo, RS, Brazil.;Pontificia Univ Catolica Rio Grande sul PUCRS, BR-90619900 Porto Alegre, RS, Brazil..
    Hoffman, Joseph Ivan
    Univ Bielefeld, D-33501 Bielefeld, Germany..
    Valiati, Victor Hugo
    Univ Vale Rio dos Sinos UNISINOS, BR-93022000 Sao Leopoldo, RS, Brazil..
    Bonatto, Sandro L.
    Pontificia Univ Catolica Rio Grande sul PUCRS, BR-90619900 Porto Alegre, RS, Brazil..
    Wolf, Jochen B. W.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Evolutionsbiologi.
    Trillmich, Fritz
    Univ Bielefeld, D-33501 Bielefeld, Germany..
    Oliveira, Larissa R.
    Univ Vale Rio dos Sinos UNISINOS, BR-93022000 Sao Leopoldo, RS, Brazil.;Grp Estudos Mamiferos Aquaticos Rio Grande Sul GE, BR-95625000 Imbe, RS, Brazil..
    Fine-scale matrilineal population structure in the Galapagos fur seal and its implications for conservation management2015Inngår i: Conservation Genetics, ISSN 1566-0621, E-ISSN 1572-9737, Vol. 16, nr 5, s. 1099-1113Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Females of many pinniped species generally exhibit strong fine-scale philopatry, but it is unclear over what spatial scale this behavior may translate into genetic population structure. We conducted a population genetic survey in the Galapagos fur seal, Arctocephalus galapagoensis, an endangered pinniped endemic to a small geographic range in the northwest of the Galapagos archipelago. To assess patterns of genetic diversity levels and population differentiation, we analyzed part of the mitochondrial control region (mtDNA) and 18 microsatellites DNA markers. We detected similar levels of genetic diversity to many other pinniped species (h = 0.86, pi = 0.012, A = 7.44) despite severe anthropogenic exploitation in the nineteenth century and recurrent population crashes due to recent climatic perturbations associated with El Nio Southern Oscillation events. We further found remarkably strong fine-scale matrilineal population structure, with 33.9 % of the mtDNA variation being partitioned among colonies separated by as little as 70 km swimming distance. In contrast, population structure inferred from nuclear markers was weak. Our findings provide further evidence that natal philopatry can translate into fine-scale genetic population structure in highly mobile species. We discuss the relevance of our results for the fine-scale conservation management of this species with a very restricted geographic range.

  • 18. McMahon, Barry J.
    et al.
    Johansson, Magnus P.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Populationsbiologi och naturvårdsbiologi.
    Piertney, Stuart B.
    Buckley, Kieran
    Höglund, Jacob
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Populationsbiologi och naturvårdsbiologi.
    Genetic variation among endangered Irish red grouse (Lagopus lagopus hibernicus) populations: implications for conservation and management2012Inngår i: Conservation Genetics, ISSN 1566-0621, E-ISSN 1572-9737, Vol. 13, nr 3, s. 639-647Artikkel i tidsskrift (Fagfellevurdert)
    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.

  • 19. Merilä, Juha
    et al.
    Söderman, Fredrik
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och evolution, Populationsbiologi.
    O'Hara, Robert
    Räsänen, Katja
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och evolution, Populationsbiologi.
    Laurila, Anssi
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och evolution, Populationsbiologi.
    Local adaptation and genetics of acid-stress tolerance in the moor frog, Rana arvalis2004Inngår i: Conservation Genetics, ISSN 1566-0621, E-ISSN 1572-9737, Vol. 5, nr 4, s. 513-527Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    As potential to adapt to environmental stress can be essential for population persistence, knowledge on the genetic architecture of local adaptation is important for conservation genetics. We investigated the relative importance of additive genetic, dominance and maternal effects contributions to acid stress tolerance in two moor frog (Rana arvalis) populations originating from low and neutral pH habitats. Experiments with crosses obtained from artificial matings revealed that embryos from the acid origin population were more tolerant to low pH than embryos from the neutral origin population in embryonic survival rates, but not in terms of developmental stability, developmental and growth rates. Strong maternal effect and small additive genetic contributions to variation were detected in all traits in both populations. In general, dominance contributions to variance in different traits were of similar magnitude to the additive genetic effects, but dominance effects outweighed the additive genetic and maternal effects contributions to early growth in both populations. Furthermore, the expression of additive genetic variance was independent of pH treatment, suggesting little additive genetic variation in acid stress tolerance. The results suggest that although local genetic adaptation to acid stress has taken place, the current variation in acid stress tolerance in acidified populations may owe largely to non-genetic effects. However, low but significant heritabilities ( h(2) approximate to 0.07 - 0.22) in all traits - including viability itself - under a wide range of pH conditions suggests that environmental stress created by low pH is unlikely to lower moor frog populations' ability to respond to selection in the traits studied. Nevertheless, acid conditions could lower populations' ability to respond to selection in the long run through reduction in effective population size.

  • 20.
    Meyer-Lucht, Yvonne
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Zooekologi.
    Mulder, Kevin P.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Zooekologi. Univ Porto, CIBIO InBIO, Ctr Invest Biodiversidade & Recursos Genet, Campus Agr Vairao, Vairao, Portugal..
    James, Marianne C.
    Univ Aberdeen, Inst Biol & Environm Sci, Aberdeen, Scotland.;Food Stand Agcy Scotland, Aberdeen, Scotland..
    McMahon, Barry J.
    Univ Coll Dublin, UCD Sch Agr & Food Sci, Dublin 4, Ireland..
    Buckley, Kieran
    Natl Pk & Wildlife Serv, Dept Arts Heritage & Gaeltacht, 4 Claremont Rd, Dublin 4, Ireland..
    Piertney, Stuart B.
    Univ Aberdeen, Inst Biol & Environm Sci, Aberdeen, Scotland..
    Höglund, Jacob
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Zooekologi.
    Adaptive and neutral genetic differentiation among Scottish and endangered Irish red grouse (Lagopus lagopus scotica)2016Inngår i: Conservation Genetics, ISSN 1566-0621, E-ISSN 1572-9737, Vol. 17, nr 3, s. 615-630Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Studying patterns of intra-specific genetic variation among populations allows for a better understanding of population structure and local adaptation. However, those patterns may differ according to the genetic markers applied, as neutral genetic markers reflect demographic processes and random genetic drift, whereas adaptive markers also carry the footprint of selection. In combination, neutral and adaptive genetic markers permit to assess the relative roles of drift and selection in shaping population structure. Among the best understood adaptive genetic loci are the genes of the major histocompatibility complex (MHC). We here study variation and differentiation at neutral SNP markers and MHC class II genes in red grouse (Lagopus lagopus scotica) from Ireland and Scotland. Irish red grouse populations are fragmented and drastically declining, but red grouse are abundant in Scotland. We find evidence for positive selection acting on the MHC genes and variation in MHC gene copy numbers among Irish individuals. Furthermore, there was significant population differentiation among red grouse from Ireland and Scotland at the neutral SNP markers (F-ST = 0.084) and the MHC-BLB genes (F-ST: BLB1 = 0.116, BLB2 = 0.090, BLB3 = 0.104). Differentiation at the MHC-BLB1 was significantly higher than at the neutral SNP markers, suggesting that selection plays an important role in shaping MHC variation, in addition to genetic drift. We speculate that the observed differentiation pattern might be due to local adaptation to different parasite regimes. These findings have strong conservation implications and we advise against the introduction of Scottish red grouse to supplement Irish populations.

  • 21.
    Meyer-Lucht, Yvonne
    et al.
    Leibniz-Institute for Zoo- and Wildlife Research.
    Otten, Celine
    Leibniz-Institute for Zoo- and Wildlife Research.
    Puettker, Thomas
    Leibniz-Institute for Zoo- and Wildlife Research.
    Pardini, Renata
    Universidade de Sao Paulo.
    Paul Metzger, Jean
    Universidade de Sao Paulo.
    Sommer, Simone
    Leibniz-Institute for Zoo- and Wildlife Research.
    Variety matters: adaptive genetic diversity and parasite load in two mouse opossums from the Brazilian Atlantic forest2010Inngår i: Conservation Genetics, ISSN 1566-0621, E-ISSN 1572-9737, Vol. 11, nr 5, s. 2001-2013Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    The adaptive potential of a species to a changing environment and in disease defence is primarily based on genetic variation. Immune genes, such as genes of the major histocompatibility complex (MHC), may thereby be of particular importance. In marsupials, however, there is very little knowledge about natural levels and functional importance of MHC polymorphism, despite their key role in the mammalian evolution. In a previous study, we discovered remarkable differences in the MHC class II diversity between two species of mouse opossums (Gracilinanus microtarsus, Marmosops incanus) from the Brazilian Atlantic forest, which is one of the most endangered hotspots for biodiversity conservation. Since the main forces in generating MHC diversity are assumed to be pathogens, we investigated in this study gastrointestinal parasite burden and functional associations between the individual MHC constitution and parasite load. We tested two contrasting scenarios, which might explain differences in MHC diversity between species. We predicted that a species with low MHC diversity would either be under relaxed selection pressure by low parasite diversity ('Evolutionary equilibrium' scenario), or there was a recent loss in MHC diversity leading to a lack of resistance alleles and increased parasite burden ('Unbalanced situation' scenario). In both species it became apparent that the MHC class II is functionally important in defence against gastrointestinal helminths, which was shown here for the first time in marsupials. On the population level, parasite diversity did not markedly differ between the two host species. However, we did observe considerable differences in the individual parasite load (parasite prevalence and infection intensity): while M. incanus revealed low MHC DAB diversity and high parasite load, G. microtarsus showed a tenfold higher population wide MHC DAB diversity and lower parasite burden. These results support the second scenario of an unbalanced situation.

  • 22.
    Morandin, C.
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik.
    Loveridge, A. J.
    Segelbacher, G.
    Elliot, N.
    Madzikanda, H.
    Macdonald, D. W.
    Höglund, Jacob
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Zooekologi.
    Gene flow and immigration: genetic diversity and population structure of lions (Panthera leo) in Hwange National Park, Zimbabwe2014Inngår i: Conservation Genetics, ISSN 1566-0621, E-ISSN 1572-9737, Vol. 15, nr 3, s. 697-706Artikkel i tidsskrift (Fagfellevurdert)
    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.

  • 23. Mucci, Nadia
    et al.
    Arrendal, Johanna
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Zooekologi.
    Ansorge, Hermann
    Bailey, Michael
    Bodner, Michaela
    Delibes, Miguel
    Ferrando, Ainhoa
    Fournier, Pascal
    Fournier, Christine
    Godoy, Jose A.
    Hajkova, Petra
    Hauer, Silke
    Heggberget, Thrine Moen
    Heidecke, Dietrich
    Kirjavainen, Harri
    Krueger, Hans-Heinrich
    Kvaloy, Kirsti
    Lafontaine, Lionel
    Lanszki, Jozsef
    Lemarchand, Charles
    Liukko, Ulla-Maija
    Loeschcke, Volker
    Ludwig, Gilbert
    Madsen, Aksel Bo
    Mercier, Laurent
    Ozolins, Janis
    Paunovic, Momir
    Pertoldi, Cino
    Piriz, Ana
    Prigioni, Claudio
    Santos-Reis, Margarida
    Luis, Teresa Sales
    Stjernberg, Torsten
    Schmid, Hans
    Suchentrunk, Franz
    Teubner, Jens
    Tornberg, Risto
    Zinke, Olaf
    Randi, Ettore
    Genetic diversity and landscape genetic structure of otter (Lutra lutra) populations in Europe2010Inngår i: Conservation Genetics, ISSN 1566-0621, E-ISSN 1572-9737, Vol. 11, nr 2, s. 583-599Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Eurasian otter populations strongly declined and partially disappeared due to global and local causes (habitat destruction, water pollution, human persecution) in parts of their continental range. Conservation strategies, based on reintroduction projects or restoration of dispersal corridors, should rely on sound knowledge of the historical or recent consequences of population genetic structuring. Here we present the results of a survey performed on 616 samples, collected from 19 European countries, genotyped at the mtDNA control-region and 11 autosomal microsatellites. The mtDNA variability was low (nucleotide diversity = 0.0014; average number of pairwise differences = 2.25), suggesting that extant otter mtDNA lineages originated recently. A star-shaped mtDNA network did not allow outlining any phylogeographic inference. Microsatellites were only moderately variable (H (o) = 0.50; H (e) = 0.58, on average across populations), the average allele number was low (observed A (o) = 4.9, range 2.5-6.8; effective A (e) = 2.8; range 1.6-3.7), suggesting small historical effective population size. Extant otters likely originated from the expansion of a single refugial population. Bayesian clustering and landscape genetic analyses however indicate that local populations are genetically differentiated, perhaps as consequence of post-glacial demographic fluctuations and recent isolation. These results delineate a framework that should be used for implementing conservation programs in Europe, particularly if they are based on the reintroduction of wild or captive-reproduced otters.

  • 24.
    Muñoz-Fuentes, Violeta
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Evolutionsbiologi.
    Darimont, Chris T.
    University of California.
    Paquet, Paul C.
    University of Calgary.
    Leonard, Jennifer A.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Evolutionsbiologi.
    The genetic legacy of extirpation and re-colonization in Vancouver Island wolves2010Inngår i: Conservation Genetics, ISSN 1566-0621, E-ISSN 1572-9737, Vol. 11, nr 2, s. 547-556Artikkel i tidsskrift (Fagfellevurdert)
  • 25.
    Nota, Kevin
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Växtekologi och evolution. Univ Cent Lancashire, Sch Forens & Appl Sci, Preston PR1 2HE, Lancs, England.
    Downing, Stephen
    Northern England Raptor Forum, Hebden Bridge, England.
    Iyengar, Arati
    Univ Cent Lancashire, Sch Forens & Appl Sci, Preston PR1 2HE, Lancs, England;SUNY Albany, Dept Biol Sci, 1400 Washington Ave, Albany, NY 12222 USA.
    Metabarcoding-based dietary analysis of hen harrier (Circus cyaneus) in Great Britain using buccal swabs from chicks2019Inngår i: Conservation Genetics, ISSN 1566-0621, E-ISSN 1572-9737, Vol. 20, nr 6, s. 1389-1404Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    The hen harrier is a heavily persecuted bird of prey in Great Britain since its diet includes Red grouse, a game bird shot in driven and walked-up grouse shooting. Unlike walked-up shooting where shooters walk up moors and flush grouse with dogs, in driven grouse shooting the grouse are driven by beaters towards static shooters. Driven grouse moors (DGMs) are increasingly being managed to sustain high densities of Red grouse intensifying a long-standing conservation conflict between conservationists and grouse moor keepers. A metabarcoding approach was used with degenerate universal cytochrome oxidase I and cytochrome b primers along with hen harrier blocking primers. A novel sampling method was used to detect prey in buccal swab samples from chicks from broods across Great Britain from both managed and unmanaged moorland habitats. This resulted in detection of 62 species of prey across 51 broods with Meadow pipit, Red grouse, Wren, Skylark, and voles being most frequently detected. Frequency of occurrence data and species accumulation curves reveal high incidence of Red grouse and low prey species richness in the diet of hen harriers in DGMs but low incidence of Red grouse and high prey species richness in walked-up and unmanaged moors. Waders were only detected within walked-up and unmanaged moors and not within DGMs where they have been reported to occur at high densities. Regional species detected included endemic species such as the Orkney vole seen only in Orkney. This study represents the first metabarcoding-based dietary analysis in a raptor using buccal swabs.

  • 26.
    Quintela, Maria
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och evolution, Populationsbiologi och naturvårdsbiologi.
    Thulin, Carl-Gustaf
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och evolution, Populationsbiologi och naturvårdsbiologi.
    Höglund, Jacob
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och evolution, Populationsbiologi och naturvårdsbiologi.
    Detecting hybridization between willow grouse (Lagopus lagopus) and rock ptarmigan (L. muta) in Central Sweden through Bayesian admixture analyses and mtDNA screening2010Inngår i: Conservation Genetics, ISSN 1566-0621, E-ISSN 1572-9737, Vol. 11, nr 2, s. 557-569Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Willow grouse (L. lagopus) and rock ptarmigan (L. muta) are sibling species with similar phenotypic and life histories that coexist sympatrically in wide areas of their distribution range. These grouse are amongst the most popular game birds in Scandinavia but contrary to other quarry species, no restocking with captive-bred animals has ever been performed. The discovery of two individuals with intermediate plumage features evoked the question of possible hybridization events between both species, an idea that did not seem too unlikely on the basis of habitat overlap. Thus, to assess whether any genetic exchange is occurring, we used different Bayesian-based admixture analyses of multilocus genotypes determined at twelve microsatellite loci. We also obtained mitochondrial COI-sequences from a selected number of individuals to infer the maternal geneflow and potential introgression. The capacity of our panel of microsatellite markers to detect hybridization was verified using assignments of simulated genotypes. We then evaluated the extent of hybridization in an actual sample of 111 individuals collected in a 100-km(2) area in the Scandinavian mountain range. An admixed condition was verified in one of the suspected hybrids, that seemed to carry a L. muta genotype with partial L. lagopus introgression. In addition, more than 4% of L. lagopus showed signs of hybridization under the most conservative scenario with respect to discrepancies between population assignment methods. This was unexpected, given that no L. lagopus displayed any apparent intermediate plumage features. Furthermore, interspecific geneflow of mtDNA haplotypes was lower than expected; which suggests that Haldane's rule might apply for these two grouse species. Hence, plumage identification of hybrid ancestry is not always reliable and might lead to biases in the estimation of hybridization rates. Hybridisation may be expected to increase if the climate gets warmer as the habitat overlap between the species will become more extensive. We discuss whether hybridisation is a threat to the long-term survival of any of the two species.

  • 27. Ramirez, O.
    et al.
    Altet, L.
    Enseñat, C.
    Vilà, Carles
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för evolution, genomik och systematik, Evolutionsbiologi.
    Sanchez, A.
    Ruiz, A.
    Genetic assessment of the Iberian wolf Canis lupus signatus captive breeding program2006Inngår i: Conservation Genetics, ISSN 1566-0621, E-ISSN 1572-9737, Vol. 7, nr 6, s. 861-878Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    The main goal of ex situ conservation programs is to improve the chances of long term survival of natural populations by founding and managing captive colonies that can serve as a source of individuals for future reintroductions or to reinforce existing populations. The degree in which a captive breeding program has captured the genetic diversity existing in the source wild population has seldom been evaluated. In this study we evaluate the genetic diversity in wild and captive populations of the Iberian wolf, Canis lupus signatus, in order to assess how much genetic diversity is being preserved in the ongoing ex situ conservation program for this subspecies. A sample of domestic dogs was also included in the analysis for comparison. Seventy-four wolves and 135 dogs were genotyped at 13 unlinked microsatellite loci. The results show that genetic diversity in Iberian wolves is comparable in magnitude to that of other wild populations of gray wolf. Both the wild and the captive Iberian wolf populations have a similarly high genetic diversity indicating that no substantial loss of diversity has occurred in the captive-breeding program. The effective number of founders of the program was estimated as similar to 16, suggesting that all founders in the studbook pedigree were genetically independent. Our results emphasize also the genetic divergence between wolves and domestic dogs and indicate that our set of 13 microsatellite loci provide a powerful diagnostic test to distinguish wolves, dogs and their hybrids.

  • 28.
    Rogell, Björn
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och evolution, Populationsbiologi och naturvårdsbiologi.
    Thörngren, Hanna
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och evolution, Zooekologi.
    Laurila, Anssi
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och evolution, Populationsbiologi och naturvårdsbiologi.
    Höglund, Jacob
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och evolution, Populationsbiologi och naturvårdsbiologi.
    Fitness costs associated with low genetic variation are reduced in a harsher environment in amphibian island populations2010Inngår i: Conservation Genetics, ISSN 1566-0621, E-ISSN 1572-9737, Vol. 11, nr 2, s. 489-496Artikkel i tidsskrift (Annet (populærvitenskap, debatt, mm))
    Abstract [en]

    A basic premise of conservation geneticists is that low levels of genetic variation are associated with fitness costs in terms of reduced survival and fecundity. These fitness costs may frequently vary with environmental factors and should increase under more stressful conditions. However, there is no consensus on how fitness costs associated with low genetic variation change under natural conditions in relation to the stressfulness of the environment. On the Swedish west coast, natterjack toad Bufo calamita populations show a strong population genetic structure and large variation in the amount of within-population genetic variation. We experimentally examined the survival of natterjack larvae from six populations with different genetic variation in three thermal environments corresponding to (a) the mean temperature of natural ponds (stable, laboratory), (b) a high temperature environment occurring in desiccating ponds (stable, laboratory) and (c) an outdoor treatment mimicking the natural, variable thermal conditions (fluctuating, semi-natural). We found that larvae in the outdoor treatment had poorer survival than larvae in the stable environments suggesting that the outdoor treatment was more stressful. Overall, populations with higher genetic variation had higher larval survival. However, a significant interaction between treatments and genetic variation indicated that fitness costs associated with low genetic variation were less severe in the outdoor treatment. Thus, we found no support for the hypothesis that fitness costs associated with low genetic variation increase under more stressful conditions. Our results suggest that natural thermal stress may mask fitness losses associated with low genetic variation in these populations.

  • 29.
    Rogell, Björn
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och evolution, Populationsbiologi och naturvårdsbiologi.
    Thörngren, Hanna
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och evolution, Populationsbiologi och naturvårdsbiologi. Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och evolution, Zooekologi.
    Palm, Stefan
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och evolution, Populationsbiologi och naturvårdsbiologi.
    Laurila, Anssi
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och evolution, Populationsbiologi och naturvårdsbiologi.
    Höglund, Jacob
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och evolution, Populationsbiologi och naturvårdsbiologi.
    Genetic structure in peripheral populations of the natterjack toad, Bufo calamita, as revealed by AFLP2010Inngår i: Conservation Genetics, ISSN 1566-0621, E-ISSN 1572-9737, Vol. 11, nr 1, s. 173-181Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Decreased fitness due to loss of genetic variation is a well recognised issue in conservation biology. Along the Swedish west coast, the endangered natterjack toad (Bufo calamita) occurs on, for the species, highly unusual habitat of rocky islands. Although the toads inhabit a restricted geographical area (maximum distance between the populations is 71 km), the fragmented nature of the landscape makes the genetic properties of the populations of conservation interest. However, lack of genetic variation found using conventional methods (microsatellites) has impeded genetic studies within these peripheral populations so far. In this study we assess population structure and genetic variation among seven of these fringe populations using 105 polymorphic Amplified Fragment Length Polymorphism (AFLP) loci. We found a well-defined population structure without evidence for isolation by distance, implying restricted gene flow between populations. Additionally, the populations differed in their amount of genetic variation, emphasizing the need to monitor genetically impoverished populations for possible declines mediated by inbreeding depression and reduced adaptive potential. Conservation implications for these unique populations are discussed in the light of our results.

  • 30. Ruokonen, Minna
    et al.
    Andersson, Anna-Carin
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för evolution, genomik och systematik, Evolutionär funktionsgenomik.
    Tegelström, Håkan
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och evolution, Populationsbiologi och naturvårdsbiologi.
    Using historical captive stocks in conservation. The case of the lesser white-fronted goose2007Inngår i: Conservation Genetics, ISSN 1566-0621, E-ISSN 1572-9737, Vol. 8, nr 1, s. 197-207Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Many captive stocks of economically or otherwise valuable species were established before the decline of the wild population. These stocks are potentially valuable sources of genetic variability, but their taxonomic identity and actual value is often uncertain. We studied the genetics of captive stocks of the threatened lesser white-fronted goose Anser erythropus maintained in Sweden and elsewhere in Europe. Analyses of mtDNA and nuclear microsatellite markers revealed that 36% of the individuals had a hybrid ancestry. Because the parental species are closely related it is unlikely that our analyses detected all hybrid individuals in the material. Because no ancestral polymorphism or introgression was observed in samples of wild populations, it is likely that the observed hybridisation has occurred in captivity. As a consequence of founder effect, drift and hybridisation, captive stocks were genetically differentiated from the wild populations of the lesser white-fronted goose. The high level of genetic diversity in the captive stocks is explained at least partially by hybridisation. The present captive stocks of the lesser white-fronted goose are considered unsuitable for further reintroduction, or supplementation: hybridisation has involved three species, the number of hybrids is high, and all the investigated captive stocks are similarly affected. The results highlight the potential shortcomings of using captive-bred individuals in supplementation and reintroduction projects, when the captive stocks have not been pedigreed and bred according to conservation principles.

  • 31.
    Rózsa, Jani
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Evolutionsbiologi.
    Strand, Tanja
    Uppsala universitet, Medicinska och farmaceutiska vetenskapsområdet, Medicinska fakulteten, Institutionen för medicinsk biokemi och mikrobiologi. Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik.
    Montadert, Marc
    Univ Franche Comte, UC INRA, MRT, Lab Ecol & Ecophysiol,EA 3184, Pl Leclercq, F-25300 Besancon, France.
    Kozma, Radoslav
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Zooekologi.
    Höglund, Jacob
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Zooekologi.
    Effects of a range expansion on adaptive and neutral genetic diversity in dispersal limited Hazel grouse (Bonasa bonasia) in the French Alps2016Inngår i: Conservation Genetics, ISSN 1566-0621, E-ISSN 1572-9737, Vol. 17, nr 2, s. 401-412Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Biogeographic range expansions, when related to dispersal limitation, may have counter intuitive effects on genetic diversity. At range margins the relative roles of demographic changes, connectivity and genetic diversity need to be integrated for a successful assessment of population viability. Historically the Hazel grouse (Bonasa bonasia) in France was found in the north of the French Alps and also in a disjunct population in the nearby Jura Mountains. The species has recently undergone a range expansion in a north to south axis in the Alps. Local population size estimates and migration patterns during expansion have previously been studied. In this study, we performed genotyping at neutral (microsatellite) and adaptive (MHC) genetic markers in Hazel grouse. We compared diversity and differentiation (FST and DEST) at three sampling localities along the expansion axis in the French Alps and Jura, as well as at two sampling localities in Sweden, where the population has had a long-term continuous and stable distribution. Strong serial founder effects were found between the French localities, resulting in stronger isolation further south, with a relatively high neutral differentiation (pair-wise FST = 0.117). However, the loss of adaptive diversity MHC was slight. No adaptive differentiation (MHC DEST = −0.015) was observed, thus, the French localities can be considered uniform units with regard to MHC diversity, a criterion to treat populations in these localities as a management unit.

  • 32.
    Segelbacher, Gernot
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Zooekologi.
    Strand, Tanja M.
    Uppsala universitet, Medicinska och farmaceutiska vetenskapsområdet, Medicinska fakulteten, Institutionen för medicinsk biokemi och mikrobiologi. Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Zooekologi.
    Quintela, Maria
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Zooekologi.
    Axelsson, Tomas
    Uppsala universitet, Medicinska och farmaceutiska vetenskapsområdet, Medicinska fakulteten, Institutionen för medicinska vetenskaper, Molekylär medicin.
    Jansman, Hugh A.H.
    Koelewijn, Hans-Peter
    Höglund, Jacob
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Zooekologi.
    Analyses of historical and current populations of black grouse in Central Europe reveal strong effects of genetic drift and loss of genetic diversity2014Inngår i: Conservation Genetics, ISSN 1566-0621, E-ISSN 1572-9737, Vol. 15, nr 5, s. 1183-1195Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Black grouse (Tetrao tetrix) in Central Europe have undergone a severe contraction of their range in recent decades with only a few small isolated remaining populations. Here we compare genetic diversity of two contemporary isolated populations (Sallandse Heuvelrug, Netherlands and Lüneburger Heide, Germany) with historical samples from the same region collected within the last one hundred years. We use markers with both putatively neutral and functional variation to test whether the present small and highly fragmented populations hold lower genetic diversity compared to the former larger population. For this we applied three different types of genetic markers: nine microsatellites and 21 single nucleotide polymorphisms (SNPs), both sets which have been found to be neutral, and two functional major histocompatibility complex (MHC) genes for which there is evidence they are under selection. The contemporary small isolated populations displayed lower neutral genetic diversity compared to the corresponding historical samples. Furthermore, samples from Denmark showed that this now extinct population displayed lower genetic variation in the period immediately prior to the local extinction. Population structure was more pronounced among contemporary populations compared to historical populations for microsatellites and SNPs. This effect was not as distinct for MHC which is consistent with the possibility that MHC has been subjected to balancing selection in the past, a process which maintains genetic variation and may minimize population structure for such markers. Genetic differentiation among the present populations highlights the strong effects of population decline on the genetic structure of natural populations, which can be ultimately attributed to habitat loss following anthropogenic land use changes.

  • 33.
    Semerikov, Vladimir L.
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för evolution, genomik och systematik, Evolutionär funktionsgenomik.
    Vendramin, Giovanni G.
    Sebastiani, Federico
    Lascoux, Martin
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för evolution, genomik och systematik, Evolutionär funktionsgenomik.
    RAPD-derived, PCR-based mitochondrial markers for Larix species and their usefulness in phylogeny2006Inngår i: Conservation Genetics, ISSN 1566-0621, E-ISSN 1572-9737, Vol. 7, nr 4, s. 621-625Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Random amplified polymorphic DNA (RAPDs) from plants contains numerous fragments of mitochondrial origin. In the present study, the association between RAPD bands and previously recognized mitochondrial polymorphism in a Larix population was used to identify fragments of mitochondrial origin and to develop PCR-based mitochondrial DNA markers useful to study phylogeny in larches, Larix sp. (Pinaceae).

  • 34.
    Sletvold, Nina
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Växtekologi och evolution.
    Grindeland, John Magne
    Zu, Pengjuan
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Växtekologi och evolution.
    Ågren, Jon
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Växtekologi och evolution.
    Strong inbreeding depression and local outbreeding depression in the rewarding orchid Gymnadenia conopsea2012Inngår i: Conservation Genetics, ISSN 1566-0621, E-ISSN 1572-9737, Vol. 13, nr 5, s. 1305-1315Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Conservation of species threatened by habitat fragmentation is a major global challenge, and determining the genetic and demographic processes associated with isolation and reductions in population size will be critical for an increasing number of species. We conducted controlled crosses and field germination experiments to quantify the effects of inbreeding and outbreeding in the declining orchid Gymnadenia conopsea in two Norwegian populations that differ in size. We further compared our results with published estimates of inbreeding depression in orchids. There was severe inbreeding depression for seed production (delta = 0.41-0.67) and germination (delta = 0.46-0.66) in both populations, with stronger inbreeding depression in the large population. Compared to outcrossing, selfing reduced female fitness (number of seeds per fruit x proportion of seeds germinating) by 76 and 54 % in the large and small population, respectively. The magnitude of inbreeding depression for seed production was higher than the average reported for orchids, while for germination it was similar to earlier estimates. The large population also experienced considerable outbreeding depression for seed production (delta = 0.23-0.27), germination (delta = 0.33) and female fitness (delta = 0.47) following crosses with a population 1.6 km away. The strong inbreeding depression indicates that both populations harbour a substantial genetic load, and suggests that fragmentation may reinforce population decline in G. conopsea via increased inbreeding. Moreover, the local outbreeding depression indicates substantial genetic differentiation at a moderate spatial scale. This has important implications for the use of crosses between populations or plant translocations as conservation approaches.

  • 35.
    Sundqvist, Anna-Karin
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för evolution, genomik och systematik, Evolutionsbiologi.
    Ellegren, Hans
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för evolution, genomik och systematik, Evolutionsbiologi.
    Vilà, Carles
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för evolution, genomik och systematik, Evolutionsbiologi.
    Wolf or dog? Genetic identification of predator from saliva collected around bite wounds on prey2008Inngår i: Conservation Genetics, ISSN 1566-0621, E-ISSN 1572-9737, Vol. 9, nr 5, s. 1275-1279Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Wolf predation on livestock is a management problem in many areas and is often used to justify control measures against the wolves. However, wolves coexist with dogs across their range, and dogs could be responsible for attacks blamed on wolves. In this study we evaluate the possibility of obtaining sufficient DNA for species identification of the predator from saliva remaining close to bite wounds following a canid attack. Predator DNA of reasonably high quality was successfully extracted from bite wounds on two sheep that had been attacked on a farm and were genotyped using six informative microsatellite markers. A single consensus genotype could be constructed from the bite wounds of both sheep which we compared to genotypes obtained from Scandinavian wolves and dogs. The results clearly showed that the saliva sampled originated from a single dog. This report thus demonstrates the feasibility of predator species identification from bite wounds and also illustrates that it can not be taken for granted that wolves are responsible for canid livestock kills.

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