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1.
  • Abalaka, Jacinta, et al. (author)
  • Genetic diversity and population structure of the range restricted rock firefinch Lagonosticta sanguinodorsalis
  • 2015
  • In: Conservation Genetics. - : Springer Science and Business Media LLC. - 1566-0621 .- 1572-9737. ; 16:2, s. 411-418
  • Journal article (peer-reviewed)abstract
    • Understanding the degree of genetic population differentiation is important in conservation genetics for inferring gene flow between populations and for identifying small and isolated threatened populations. We evaluated the genetic variation within and between three populations of the rock firefinch (Lagonosticta sanguinodorsalis), a range restricted firefinch endemic to Nigeria and Cameroon. The populations were closely located (c. 100 km apart) within the species' core distribution in Central Nigeria. We found that the populations had similar levels of gene diversities (H (E) ) and low but significant inbreeding coefficients (F (IS) ). Despite the short distance between populations there was a weak but significant population structure, which indicates that the populations are somewhat isolated and affected by drift within the species' core distribution in Nigeria. The knowledge of the genetic status of the rock firefinch will serve as a foundation to future studies to help understand population demography and for managing and maintaining viable populations.
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2.
  • Andersson, Anastasia, et al. (author)
  • Complex genetic diversity patterns of cryptic, sympatric brown trout (Salmo trutta) populations in tiny mountain lakes
  • 2017
  • In: Conservation Genetics. - : Springer Science and Business Media LLC. - 1566-0621 .- 1572-9737. ; 18:5, s. 1213-1227
  • Journal article (peer-reviewed)abstract
    • Intraspecific genetic variation can have similar effects as species diversity on ecosystem function; understanding such variation is important, particularly for ecological key species. The brown trout plays central roles in many northern freshwater ecosystems, and several cases of sympatric brown trout populations have been detected in freshwater lakes based on apparent morphological differences. In some rare cases, sympatric, genetically distinct populations lacking visible phenotypic differences have been detected based on genetic data alone. Detecting such cryptic sympatric populations without prior grouping of individuals based on phenotypic characteristics is more difficult statistically, though. The aim of the present study is to delineate the spatial connectivity of two cryptic, sympatric genetic clusters of brown trout discovered in two interconnected, tiny subarctic Swedish lakes. The structures were detected using allozyme markers, and have been monitored over time. Here, we confirm their existence for almost three decades and report that these cryptic, sympatric populations exhibit very different connectivity patterns to brown trout of nearby lakes. One of the clusters is relatively isolated while the other one shows high genetic similarity to downstream populations. There are indications of different spawning sites as reflected in genetic structuring among parr from different creeks. We used > 3000 SNPs on a subsample and find that the SNPs largely confirm the allozyme pattern but give considerably lower F (ST) values, and potentially indicate further structuring within populations. This type of complex genetic substructuring over microgeographical scales might be more common than anticipated and needs to be considered in conservation management.
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3.
  • Andreasen, Katarina (author)
  • Implications of molecular systematic analyses on the conservation of rare and threatened taxa : contrasting examples from Malvaceae
  • 2005
  • In: Conservation Genetics. - : Springer Science and Business Media LLC. - 1566-0621 .- 1572-9737. ; 6:3, s. 399-412
  • Journal article (peer-reviewed)abstract
    • 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.
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5.
  • Arrendal, Johanna, et al. (author)
  • Reliability of noninvasive genetic census of otters compared to field censuses
  • 2007
  • In: Conservation Genetics. - : Springer Science and Business Media LLC. - 1566-0621 .- 1572-9737. ; 8:5, s. 1097-1107
  • Journal article (peer-reviewed)abstract
    • 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.
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7.
  • Bererhi, Badreddine, et al. (author)
  • Inconsistent inbreeding effects during lizard ontogeny
  • 2019
  • In: Conservation Genetics. - : Springer Science and Business Media LLC. - 1566-0621 .- 1572-9737. ; 20:4, s. 865-874
  • Journal article (peer-reviewed)abstract
    • Reported effects of inbreeding vary among taxa and may depend on a number of factors, including what trait is measured, temporal variability, parental effects, or life history stage. To understand the effects of inbreeding during early life history stages, we estimated the effects of individual-level heterozygosity on hatching success and first year survival in a Swedish population of sand lizards (Lacerta agilis) over a period of almost a decade, using over 4000 eggs, 400 clutches, and over 3000 juveniles. Heterozygosity had a positive effect on hatching success, in standardized laboratory conditions, but no effect on first year survival. Also, both of these measures of viability varied across the years of the study, demonstrating the importance of temporal heterogeneity in pre and post-hatching conditions. Finally, we identified both paternal and maternal identity effects on hatching success. Thus, we show that selection on heterozygosity was not consistent across developmental life stages, emphasizing the need of considering a number of ontogenic stages, as well as potential parental and environmental effects, when studying the effects of heterozygosity on viability in natural populations.
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8.
  • Besnier, Francois, et al. (author)
  • Applying QTL analysis to conservation genetics
  • 2010
  • In: Conservation Genetics. - : Springer Science and Business Media LLC. - 1566-0621 .- 1572-9737. ; 11, s. 399-408
  • Journal article (peer-reviewed)abstract
    • Both analytical and molecular tools currently exist that can be used to prolifically apply quantitative trait loci (QTL) analysis to the study of natural populations. In this communication, we review and exemplify the use of QTL mapping tools and genetic modeling for conservation geneticists. We simulate populations inspired by relevant cases that can be encountered in the field and analyze them using the recently developed flexible intercross analysis (FIA) method. We then reanalyze these results with the also recently developed natural and orthogonal interactions (NOIA) model of genetic effects. Next, we further exemplify the potential of genetic modeling for the interpretation of the output of QTL analyses by reviewing studies on hybrids between wild individuals and their domesticated relatives. Based on the results here presented we emphasize several points that are pertinent in conservation genetics including (i) the advantages of FIA as a powerful tool to be applied to line crosses in which the parental lines are not inbred, (ii) the importance of obtaining estimates of genetic effects that are adequate to address the research issue under consideration, (iii) the versatility of genetic modeling, particularly NOIA, to dissect complex genetic architectures and (iv) the possibility of using currently available methods to address non-equilibrium multiallelic systems.
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9.
  • Björnerfeldt, Susanne, et al. (author)
  • Evaluation of methods for single hair DNA amplification
  • 2007
  • In: Conservation Genetics. - : Springer Science and Business Media LLC. - 1566-0621 .- 1572-9737. ; 8:4, s. 977-981
  • Journal article (peer-reviewed)abstract
    • 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.
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10.
  • Bodare, Sofia, et al. (author)
  • Fine- and local- scale genetic structure of Dysoxylum malabaricum, a late-successional canopy tree species in disturbed forest patches in the Western Ghats, India
  • 2017
  • In: Conservation Genetics. - : SPRINGER. - 1566-0621 .- 1572-9737. ; 18:1, s. 1-15
  • Journal article (peer-reviewed)abstract
    • 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.
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11.
  • Breed, Martin F., 1981-, et al. (author)
  • Which provenance and where? : Seed sourcing strategies for revegetation in a changing environment
  • 2013
  • In: Conservation Genetics. - : Springer Science and Business Media LLC. - 1566-0621 .- 1572-9737. ; 14:1, s. 1-10
  • Research review (peer-reviewed)abstract
    • 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.
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12.
  • Dalen, L, et al. (author)
  • Identifying species from pieces of faeces
  • 2004
  • In: Conservation Genetics. - DORDRECHT : KLUWER ACADEMIC PUBL. - 1566-0621 .- 1572-9737. ; 5:1, s. 109-111
  • Journal article (peer-reviewed)
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13.
  • Demandt, Marnie H. (author)
  • Temporal changes in genetic diversity of isolated populations of perch and roach
  • 2010
  • In: Conservation Genetics. - : Springer Science and Business Media LLC. - 1566-0621 .- 1572-9737. ; 11:1, s. 249-255
  • Journal article (peer-reviewed)abstract
    • 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.
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14.
  • Gardeström, J., et al. (author)
  • Characterization of six microsatellite loci in the Baltic blue mussel Mytilus trossulus and cross-species amplification in North Sea Mytilus edulis
  • 2008
  • In: Conservation Genetics. - : Springer Science and Business Media LLC. - 1566-0621 .- 1572-9737. ; 9:4, s. 1003-1005
  • Journal article (peer-reviewed)abstract
    • The blue mussel Mytilus trossulus occurs in the Pacific and in the North Atlantic. We developed and characterized six microsatellite loci for Baltic M. trossulus. Seventeen microsatellite loci were screened, of which six were polymorphic. The number of alleles among 50 individuals ranged from 3 to 13 and the observed and expected heterozygosity were 0.09-0.46 and 0.34-0.86, respectively. The loci were also tested for cross amplification in M. edulis, in which four of the six microsatellite loci were successfully amplified.
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15.
  • Graves, JA, et al. (author)
  • Microsatellite and mtDNA analysis of the population structure of grey seals (Halichoerus grypus) from three breeding areas in the Baltic Sea
  • 2009
  • In: Conservation Genetics. - : Springer Science and Business Media LLC. - 1566-0621 .- 1572-9737. ; 10, s. 59-68
  • Journal article (peer-reviewed)abstract
    • The growing number of grey seals in the Baltic Sea has led to a dramatic increase in interactions between seals and fisheries. The conflict has become such a problem that hunting was introduced in Finland in 1998 and the Swedish Environment Protection Agency recommended a cull of grey seals starting in 2001. Culling has been implemented despite the lack of data on population structure. Low levels of migration between regions would mean that intensive culling in specific geographic areas would have disproportionate effects on local population structure and genetic diversity. We used eight microsatellite loci and a 489 bp section of the mtDNA control region to examine the genetic variability and differentiation between three breeding sites in the Baltic Sea and two in the UK. We found high levels of genetic variability in all sampled Baltic groups for both the microsatellites and the control region. There were highly significant differences in microsatellite allele frequencies between all three Baltic breeding sites and between the Baltic sites and the UK sites. However, there were no significant differences in mtDNA control region haplotypes between the Baltic sites. This genetic substructure of the Baltic grey seal populations should be taken into consideration when managing the seal population to prevent the hunting regime from having an adverse effect on genetic diversity by setting hunting quotas separately for the different subpopulations.
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17.
  • Hansson, Bengt, et al. (author)
  • Heterozygosity-fitness correlations within inbreeding classes : Local or genome-wide effects?
  • 2008
  • In: Conservation Genetics. - : Springer Science and Business Media LLC. - 1566-0621 .- 1572-9737. ; 9:1, s. 73-83
  • Journal article (peer-reviewed)abstract
    • Marker-based studies of inbreeding may lead to an enhanced understanding of inbreeding depression in natural populations, which is a major concern in conservation genetics. Correlations between marker heterozygosity and variation in fitness-associated traits-'heterozygosity-fitness correlations' (HFCs)-are of particular importance and have been widely applied in natural populations. In partially inbred populations, HFCs can be driven by selection against inbred individuals and thus reflect inbreeding depression. However, other explanations for HFCs also exist, such as functional effects of the markers per se or that the markers reveal selection on linked fitness genes due to extended linkage disequilibrium (LD) in the population. Accordingly, HFCs do not only arise in partially inbred populations, they may also occur within inbreeding classes such as families, i.e. in situations when there is no variation in the inbreeding coefficient. In this study we focus on the importance of LD for within-family HFCs, thereby aiming at enhancing our general understanding of HFCs. For non-coding markers, within-family HFCs have been proposed to be caused in two ways: either by 'local effects' at linked fitness genes in LD with the markers, or by 'general effects' due to a correlation between proportion of heterozygous markers (H M ) and heterozygosity at genome-wide distributed fitness genes (H GW ). To evaluate these contrasting hypotheses for within-family HFCs, we analysed simulated data sets of sexually reproducing populations with varying levels of LD. The results confirmed that segregation induces variation in both H M and H GW at a fixed level of inbreeding, as expected, the variation in H M declined with increasing number of markers, whereas the variation in H GW declined with decreasing LD. However, less intuitively, there was no positive correlation between the variation in H M and H GW within inbreeding classes when the local component of H GW was accounted for (i.e. when the part of the chromosome in LD with the markers was excluded). This strongly suggests that within-family HFCs are not caused by general effects. Instead, our results support the idea that HFCs at a known level of inbreeding can be driven by local effects in populations with high to moderate LD. Note however that we define the local component of H GW as the part of the chromosomes in LD with the markers. This implies that when LD is high, the local component will consist of a substantial part of the genome and thus provides a rather 'genome-wide' view. We caution against routinely interpreting positive HFCs as evidence of inbreeding depression and non-significant HFCs as lack thereof, especially when few markers are used. © 2007 Springer Science+Business Media, Inc.
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18.
  • Hedmark, Eva, et al. (author)
  • DNA-based monitoring of two newly founded Scandinavian wolverine populations
  • 2007
  • In: Conservation Genetics. - : Springer Science and Business Media LLC. - 1566-0621 .- 1572-9737. ; 8:4, s. 843-852
  • Journal article (peer-reviewed)abstract
    • 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.
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19.
  • Hefti-Gautschi, Barbara, et al. (author)
  • Identification of conservation units in the European Mergus merganser based on nuclear and mitochondrial DNA markers
  • 2009
  • In: Conservation Genetics. - : Springer Science and Business Media LLC. - 1566-0621 .- 1572-9737. ; 10:1, s. 87-99
  • Journal article (peer-reviewed)abstract
    • 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.
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20.
  • Hoban, Sean, et al. (author)
  • Genetic diversity goals and targets have improved, but remain insufficient for clear implementation of the post-2020 global biodiversity framework
  • 2023
  • In: Conservation Genetics. - : Springer Science and Business Media LLC. - 1566-0621 .- 1572-9737. ; 24:2, s. 181-191
  • Journal article (peer-reviewed)abstract
    • Genetic diversity among and within populations of all species is necessary for people and nature to survive and thrive in a changing world. Over the past three years, commitments for conserving genetic diversity have become more ambitious and specific under the Convention on Biological Diversity’s (CBD) draft post-2020 global biodiversity framework (GBF). This Perspective article comments on how goals and targets of the GBF have evolved, the improvements that are still needed, lessons learned from this process, and connections between goals and targets and the actions and reporting that will be needed to maintain, protect, manage and monitor genetic diversity. It is possible and necessary that the GBF strives to maintain genetic diversity within and among populations of all species, to restore genetic connectivity, and to develop national genetic conservation strategies, and to report on these using proposed, feasible indicators.
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21.
  • Hudson, Alan G., et al. (author)
  • Population structure, inbreeding and local adaptation within an endangered riverine specialist : the nase (Chondrostoma nasus)
  • 2014
  • In: Conservation Genetics. - : Springer Science+Business Media B.V.. - 1566-0621 .- 1572-9737. ; 15:4, s. 933-951
  • Journal article (peer-reviewed)abstract
    • Chondrostoma nasus is a cyprinid fish with highly specialized, ecologically and geographically distinct, ontogenetic trophic niches. Nase population numbers across their Swiss range have shown massive declines and many localized extinctions. In this study, we integrate genetic data (AFLP, microsatellite, mtDNA sequence) with phenotypic and demographic analyses to survey patterns of neutral and adaptive genetic diversity in all extant (and one extinct) Swiss nase populations, with the aim to delineate intraspecific conservation units (CUs) and to inform future population management strategies. We discovered two major genetically and geographically distinct population groupings. The first population grouping comprises nase inhabiting rivers flowing into Lake Constance; the second comprises nase populations from Rhine drainages below Lake Constance. Within these clusters there is generally limited genetic differentiation among populations. Genomic outlier scans based on 256 to 377 polymorphic AFLP loci revealed little evidence of local adaptation both within and among population clusters, with the exception of one candidate locus identified in scans involving the low genetic diversity Schanzengraben population. However, significant phenotypic differentiation in body shape between certain populations suggests a need for more intensive future studies of local adaptation. Our data strongly suggests that the two major population groups should be treated as distinct CUs, with any supplemental stocking and reintroductions sourced only from within the range of the CU concerned.
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22.
  • Höglund, Jacob, et al. (author)
  • Genetic variability in European black grouse (Tetrao tetrix)
  • 2007
  • In: Conservation Genetics. - : Springer Science and Business Media LLC. - 1566-0621 .- 1572-9737. ; 8:1, s. 239-243
  • Journal article (peer-reviewed)abstract
    • 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.
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23.
  • Höglund, Jacob, et al. (author)
  • Low MHC variation in isolated island populations of the Natterjack toad (Bufo calamita)
  • 2015
  • In: Conservation Genetics. - : Springer Science and Business Media LLC. - 1566-0621 .- 1572-9737. ; 16:4, s. 1007-1010
  • Journal article (peer-reviewed)abstract
    • 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.
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24.
  • Höglund, Jacob, et al. (author)
  • Low neutral and immunogenetic diversity in northern fringe populations of the green toad Bufotes viridis : implications for conservation
  • 2022
  • In: Conservation Genetics. - : Springer Nature. - 1566-0621 .- 1572-9737. ; 23, s. 139-149
  • Journal article (peer-reviewed)abstract
    • Genetic variation is often lower at high latitudes, which may compromise the adaptability and hence survival of organisms. Here we show that genetic variability is negatively correlated with northern latitude in European green toads (Bufotes viridis). The result holds true for both putatively neutral microsatellite variation and supposedly adaptive MHC Class IIB variation. In particular, our findings have bearing on the conservation status of this species in Sweden, on the northern limit of its distribution where local populations are small and fragmented. These genetically impoverished populations are closely related to other populations found around the Baltic Sea basin. The low neutral and adaptive variation in these fringe populations compared to population at central ranges confirms a pattern shared across all other amphibians so far studied. In Sweden, the situation of green toads is of concern as the remaining populations may not have the evolutionary potential to cope with present and future environmental challenges.
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25.
  • Jansson, Mija, et al. (author)
  • Genetic contribution from a zoo population can increase genetic variation in the highly inbred wild Swedish wolf population
  • 2015
  • In: Conservation Genetics. - : Springer Science and Business Media LLC. - 1566-0621 .- 1572-9737. ; 16:6, s. 1501-1505
  • Journal article (peer-reviewed)abstract
    • The Swedish wolf population (Canis lupus) descends from five individuals and is isolated and highly inbred with an average inbreeding coefficient of 0.27. In addition, inbreeding depression has led to reduced litter size and a high frequency of spinal disorders. To achieve the management goal of reducing the mean level of inbreeding, introductions into the wild population from a zoo conservation breeding program have been proposed by authorities. We used pedigree data of the wild and zoo populations to evaluate the extent to which the captive population can contribute genetic variation to the wild one. We measure genetic variation as founder alleles and founder genome equivalents. The two populations have three founders in common, but in spite of this common ancestry, our results show a potential to almost double genetic variation from 11.2 to 21.1 founder alleles. Similarly, the number of founder genome equivalents in the wild population can increase from the present 1.8 to 3.2, but this requires that almost 50 % of the wild gene pool consists of genes from the zoo population. Average kinship in the joint zoo and wild population is 0.15, which is above the management target of 0.1. Genetic contribution from the zoo has the potential to improve, but not solve, the genetically precarious situation of the wild population.
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26.
  • Kireta, Dona, et al. (author)
  • Disentangling the evolutionary history of three related shrub species using genome-wide molecular markers
  • 2019
  • In: Conservation Genetics. - : Springer Science and Business Media LLC. - 1566-0621 .- 1572-9737. ; 20:5, s. 1101-1112
  • Journal article (peer-reviewed)abstract
    • 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.
  •  
27.
  • Knopp, T., et al. (author)
  • Contrasting levels of variation in neutral and quantitative genetic loci on island populations of moor frogs (Rana arvalis)
  • 2007
  • In: Conservation Genetics. - : Springer Science and Business Media LLC. - 1566-0621 .- 1572-9737. ; 8:1, s. 45-56
  • Journal article (peer-reviewed)abstract
    • 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.
  •  
28.
  • Kurland, Sara, 1989-, et al. (author)
  • Effects of subpopulation extinction on effective size (Ne) of metapopulations
  • 2023
  • In: Conservation Genetics. - : Springer Science and Business Media LLC. - 1566-0621 .- 1572-9737. ; 24:4, s. 417-433
  • Journal article (peer-reviewed)abstract
    • Population extinction is ubiquitous in all taxa. Such extirpations can reduce intraspecific diversity, but the extent to which genetic diversity of surviving populations are affected remains largely unclear. A key concept in this context is the effective population size (Ne), which quantifies the rate at which genetic diversity within populations is lost. Ne was developed for single, isolated populations while many natural populations are instead connected to other populations via gene flow. Recent analytical approaches and software permit modelling of Ne of interconnected populations (metapopulations). Here, we apply such tools to investigate how extinction of subpopulations affects Ne of the metapopulation (NeMeta) and of separate surviving subpopulations (NeRx) under different rates and patterns of genetic exchange between subpopulations. We assess extinction effects before and at migration-drift equilibrium. We find that the effect of extinction on NeMeta increases with reduced connectivity, suggesting that stepping stone models of migration are more impacted than island-migration models when the same number of subpopulations are lost. Furthermore, in stepping stone models, after extinction and before a new equilibrium has been reached, NeRx can vary drastically among surviving subpopulations and depends on their initial spatial position relative to extinct ones. Our results demonstrate that extinctions can have far more complex effects on the retention of intraspecific diversity than typically recognized. Metapopulation dynamics need heightened consideration in sustainable management and conservation, e.g., in monitoring genetic diversity, and are relevant to a wide range of species in the ongoing extinction crisis. 
  •  
29.
  • Laikre, Linda, 1960- (author)
  • Genetic diversity is overlooked in international conservation policy implementation.
  • 2010
  • In: Conservation Genetics. - : Springer Science and Business Media LLC. - 1566-0621 .- 1572-9737. ; 11, s. 349-354
  • Journal article (peer-reviewed)abstract
    • The importance of genetic variation for maintaining biological diversity and evolutionary processes has been recognized by researchers for decades. This realization has prompted agreements by world leaders toconserve genetic diversity, and this is an explicit goal of the Convention on Biological Diversity (CBD). Nevertheless, very limited action has been taken to protect genetic diversity on a global scale. International conservation efforts to halt biodiversity loss focus on habitats and species,whereas little or no attention is paid to gene level variation. By this year, 2010, world leaders have agreed that a significant reduction of the rate of biodiversity loss should have been achieved. However, gene level diversity is still not monitored, indicators that can help identify threats to genetic variation are missing, and there is no strategy for how genetic aspects can be included in biodiversity targets beyond 2010. Important findings and conclusions from decades of conservation genetic research are not translated into concrete conservation action in the arena of international policy development. There is an urgent need for conservation geneticists worldwide to become involved in policy and practical conservation work beyond the universities and research institutions.
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30.
  • Larsson, Kjell, 1958-, et al. (author)
  • Population differentiation in the redshank (Tringa totanus) as revealed by mitochondrial DNA and amplified fragment length polymorphism markers
  • 2005
  • In: Conservation Genetics. - : Springer Science and Business Media LLC. - 1566-0621 .- 1572-9737. ; 6:3, s. 321-331
  • Journal article (peer-reviewed)abstract
    • 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.
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31.
  • Larsson, Lena C., et al. (author)
  • Statistical power for detecting genetic divergence–organelle versus nuclear markers
  • 2009
  • In: Conservation Genetics. - : Springer Science and Business Media LLC. - 1566-0621 .- 1572-9737. ; 10:5, s. 1255-1264
  • Journal article (peer-reviewed)abstract
    • Statistical power is critical in conservation for detecting genetic differences in space or time from allele frequency data. Organelle and nuclear genetic markers have fundamentally different transmission dynamics; the potential effect of these differences on power to detect divergence have been speculated on but not investigated. We examine, analytically and with computer simulations, the relative performance of organelle and nuclear markers under basic, ideal situations. We conclude that claims of a generally higher resolving power of either marker type are not correct. The ratio R = FST,organelle/FST,nuclear varies between 1 and 4 during differentiation and this greatly affects the power relationship. When nuclear FST is associated with organelle differentiation four times higher, the power of the organelle marker is similar to two nuclear loci with the same allele frequency distribution. With large sample sizes (n C 50) and several populations or many alleles per locus (C5), the power difference may typically be disregarded when nuclear FST[0.05. To correctly interpret observed patterns of genetic differentiation in practical situations, the expected FSTs and the statistical properties (i.e., power analysis) of the genetic markers used should be evaluated, taking the observed allele frequency distributions into consideration.
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32.
  • Lopes, Fernando, et al. (author)
  • Fine-scale matrilineal population structure in the Galapagos fur seal and its implications for conservation management
  • 2015
  • In: Conservation Genetics. - : Springer Science and Business Media LLC. - 1566-0621 .- 1572-9737. ; 16:5, s. 1099-1113
  • Journal article (peer-reviewed)abstract
    • 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.
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33.
  • Luikart, Gordon, et al. (author)
  • Estimation of census and effective population sizes : the increasing usefulness of DNA-based approaches
  • 2010
  • In: Conservation Genetics. - : Springer Science and Business Media LLC. - 1566-0621 .- 1572-9737. ; 11, s. 355-373
  • Journal article (peer-reviewed)abstract
    • Population census size (N C) and effective population sizes (N e) are two crucial parameters that influence population viability, wildlife management decisions, and conservation planning. Genetic estimators of both N C and N e are increasingly widely used because molecular markers are increasingly available, statistical methods are improving rapidly, and genetic estimators complement or improve upon traditional demographic estimators. We review the kinds and applications of estimators of both N C and N e, and the often undervalued and misunderstood ratio of effective-to-census size (N e /N C). We focus on recently improved and well evaluated methods that are most likely to facilitate conservation. Finally, we outline areas of future research to improve N e and N C estimation in wild populations
  •  
34.
  • McMahon, Barry J., et al. (author)
  • Genetic variation among endangered Irish red grouse (Lagopus lagopus hibernicus) populations : implications for conservation and management
  • 2012
  • In: Conservation Genetics. - : Springer Science and Business Media LLC. - 1566-0621 .- 1572-9737. ; 13:3, s. 639-647
  • Journal article (peer-reviewed)abstract
    • 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.
  •  
35.
  • Merilä, Juha, et al. (author)
  • Local adaptation and genetics of acid-stress tolerance in the moor frog, Rana arvalis
  • 2004
  • In: Conservation Genetics. - 1566-0621 .- 1572-9737. ; 5:4, s. 513-527
  • Journal article (peer-reviewed)abstract
    • 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.
  •  
36.
  • Meyer-Lucht, Yvonne, et al. (author)
  • Adaptive and neutral genetic differentiation among Scottish and endangered Irish red grouse (Lagopus lagopus scotica)
  • 2016
  • In: Conservation Genetics. - : Springer Science and Business Media LLC. - 1566-0621 .- 1572-9737. ; 17:3, s. 615-630
  • Journal article (peer-reviewed)abstract
    • 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.
  •  
37.
  • Meyer-Lucht, Yvonne, et al. (author)
  • Variety matters : adaptive genetic diversity and parasite load in two mouse opossums from the Brazilian Atlantic forest
  • 2010
  • In: Conservation Genetics. - : Springer Science and Business Media LLC. - 1566-0621 .- 1572-9737. ; 11:5, s. 2001-2013
  • Journal article (peer-reviewed)abstract
    • 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.
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38.
  • Morandin, C., et al. (author)
  • Gene flow and immigration : genetic diversity and population structure of lions (Panthera leo) in Hwange National Park, Zimbabwe
  • 2014
  • In: Conservation Genetics. - : Springer Science and Business Media LLC. - 1566-0621 .- 1572-9737. ; 15:3, s. 697-706
  • Journal article (peer-reviewed)abstract
    • 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.
  •  
39.
  • Moussy, Caroline, et al. (author)
  • The genetic structure of the European breeding populations of a declining farmland bird, the ortolan bunting (Emberiza hortulana), reveals conservation priorities
  • 2018
  • In: Conservation Genetics. - : Springer. - 1566-0621 .- 1572-9737. ; 19:4, s. 909-922
  • Journal article (peer-reviewed)abstract
    • Anthropogenic activities, such as agricultural intensification, caused large declines in biodiversity, including farmland birds. In addition to demographic consequences, anthropogenic activities can result in loss of genetic diversity, reduction of gene flow and altered genetic structure. We investigated the distribution of the genetic variation of a declining farmland and long-distance migratory bird, the ortolan bunting Emberiza hortulana, across its European breeding range to assess the impact of human-driven population declines on genetic diversity and structure in order to advise conservation priorities. The large population declines observed have not resulted in dramatic loss of genetic diversity, which is moderate to high and constant across all sampled breeding sites. Extensive gene flow occurs across the breeding range, even across a migratory divide, which contributes little to genetic structuring. However, gene flow is asymmetric, with the large eastern populations acting as source populations for the smaller western ones. Furthermore, breeding populations that underwent the largest declines, in Fennoscandia and Baltic countries, appear to be recently isolated, with no gene exchange occurring with the eastern or the western populations. These are signs for concern as declines in the eastern populations could affect the strength of gene flow and in turn affect the western populations. The genetic, and demographic, isolation of the northern populations make them particularly sensitive to loss of genetic diversity and to extinction as no immigration is occurring to counter-act the drastic declines. In such a situation, conservation efforts are needed across the whole breeding range: in particular, protecting the eastern populations due to their key role in maintaining gene flow across the range, and focussing on the northern populations due to their recent isolation and endangered status.
  •  
40.
  • Mucci, Nadia, et al. (author)
  • Genetic diversity and landscape genetic structure of otter (Lutra lutra) populations in Europe
  • 2010
  • In: Conservation Genetics. - : Springer Science and Business Media LLC. - 1566-0621 .- 1572-9737. ; 11:2, s. 583-599
  • Journal article (peer-reviewed)abstract
    • 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.
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41.
  •  
42.
  •  
43.
  • Norén, Karin, et al. (author)
  • Red foxes colonizing the tundra : genetic analysis as a tool for population management
  • 2017
  • In: Conservation Genetics. - : Springer Science and Business Media LLC. - 1566-0621 .- 1572-9737. ; 18:2, s. 359-370
  • Journal article (peer-reviewed)abstract
    • Climate change accelerates biodiversity alterations in northern ecosystems. A prevalent example is that tundra regions are invaded by boreal species. This impacts negatively on native species through competition, predation and transmission of zoonoses. Scandinavian red foxes (Vulpes vulpes) have emerged into the tundra and have altered the structure and function of the tundra community. For instance, they threaten persistence of the endangered Swedish Arctic fox (Vulpes lagopus). County board administrations implement control of the tundra red foxes, but little is known about the underlying expansion dynamics. A broad-scale study revealed high connectivity where northern areas were supplemented with red foxes from surrounding population. However, red fox expansion is most prevalent in tundra regions and the fine-scaled expansion dynamics in these areas have not yet been disseminated. With the aim of identifying the invasive pathways of tundra red foxes, we present microsatellite data for 205 Swedish red foxes and mitochondrial sequence variation in 102 foxes sampled across the historical boreo-nemoral distribution and recently colonized tundra regions. Genetic structuring was low with high levels of ongoing, asymmetric dispersal from surrounding boreal zones into tundra habitats causing high genetic admixture. In both tundra and boreo-nemoral regions, inter-individual relatedness decreased with increasing geographic distance and data suggests male-biased dispersal patterns. Overall, fine-scaled expansion patterns were affected by multiple factors and we discuss its implications for future red fox management.
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44.
  • Norman, Anita, et al. (author)
  • Moving far, staying close: red fox dispersal patterns revealed by SNP genotyping
  • 2021
  • In: Conservation Genetics. - : Springer Science and Business Media LLC. - 1566-0621 .- 1572-9737. ; 22, s. 249-257
  • Journal article (peer-reviewed)abstract
    • The genetic structure of a population can provide important insights into animal movements at varying geographical scales. Individual and social behaviors, such as philopatry and dispersal, affect patterns of relatedness, age and sex structure, shaping the local genetic structure of populations. However, these fine scale patterns may not be detected within broader population genetic structure. Using SNP genotyping for pairwise relatedness estimates, we investigated the spatial and genetic structuring of 141 red foxes within south-central Sweden at two scales. First, we looked at broad scale population structuring among red foxes at the regional level. We then estimated pairwise relatedness values to evaluate the spatial and genetic structure of male, female and mixed sex pairs for patterns of philopatry and dispersal at a more localized scale. We found limited genetic differentiation at the regional scale. However, local investigations revealed patterns of female philopatry and male biased dispersal. There were significant differences in pairwise geographic distances between highly related same sex pairs with the average distance between related males, 37.8 km, being six times farther than that of related females, averaging 6.3 km. In summary, the low levels of genetic differentiation found in this study illustrates the mobility and dispersal ability of red foxes across scales. However, relatedness plays a strong role in the spatial organization of red foxes locally, ultimately contributing to male biased dispersal patterns.
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45.
  • Nota, Kevin, et al. (author)
  • Metabarcoding-based dietary analysis of hen harrier (Circus cyaneus) in Great Britain using buccal swabs from chicks
  • 2019
  • In: Conservation Genetics. - : Springer. - 1566-0621 .- 1572-9737. ; 20:6, s. 1389-1404
  • Journal article (peer-reviewed)abstract
    • 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.
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46.
  • Palm, Stefan, et al. (author)
  • A large wild salmon stock shows genetic and life history differentiation within, but not between, rivers
  • 2021
  • In: Conservation Genetics. - : Springer Science and Business Media LLC. - 1566-0621 .- 1572-9737. ; 22
  • Journal article (peer-reviewed)abstract
    • Anadromous salmonid fishes frequently exhibit strong geographic population structuring. However, population genetic differentiation of Atlantic salmon (Salmo salar) at fine geographic scales differs across equivalent spatial extents in different regions. So far, fine-scale genetic differentiation has not been assessed in rivers of the Baltic Sea, a region that contains an evolutionarily distinct Atlantic salmon lineage. Thus, Baltic salmon are currently managed on the river level, without focus on potential genetic structure and diversity within rivers. Here, we used microsatellites to characterize the genetic structure of wild juvenile salmon sampled throughout the interconnected, northern Baltic Tornio and Kalix Rivers. We found genetic differentiation within the two rivers, but not between them: salmon in the upper reaches differed from individuals in the lower reaches, regardless of river system. Further, examining smolts migrating from the river to the sea and adults returning from the sea to spawn, we found an association between the genetic structure and seasonal migration timing. Out-migrating smolts genetically assigned to upper river reaches were older and tended to reach the sea later in the season than smolts from the lower reaches. In contrast, mature adults originating from the upper reaches returned to the river early in the season. Our observation of genetic population structuring between downstream and upstream reaches of the large Tornio and Kalix rivers, and its association with migration timing, implies that careful temporal management of the northern Baltic fisheries would help to preserve the diversity and sustainability of the wild salmon stocks of these rivers.
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47.
  • Palm, Stefan, et al. (author)
  • Microsatellite markers reveal clear geographic structuring among threatened noble crayfish (Astacus astacus) populations in Northern and Central Europe
  • 2013
  • In: Conservation Genetics. - : Springer Science and Business Media LLC. - 1566-0621 .- 1572-9737. ; 14, s. 809-821
  • Journal article (peer-reviewed)abstract
    • Noble crayfish (Astacus astacus L.), the most highly valued freshwater crayfish in Europe, is threatened due to a long-term population decline caused mainly by the spread of crayfish plague. Reintroduction of the noble crayfish into restored waters is a common practice but the geographic and genetic origin of stocking material has rarely been considered, partially because previous genetic studies have been hampered by lack of nuclear gene markers with known inheritance. This study represents the first large scale population genetic survey of the noble crayfish (633 adults from 18 locations) based on 10 newly developed microsatellite markers. We focused primarily on the Baltic Sea area (Estonia, Finland and Sweden) where the largest proportion of the remaining populations exists. To allow comparisons, samples from the Black Sea catchment (the Danube drainage) were also included. Two highly differentiated population groups were identified corresponding to the Baltic Sea and the Black Sea catchments, respectively. The Baltic Sea catchment populations had significantly lower genetic variation and private allele numbers than the Black Sea catchment populations. Within the Baltic Sea area, a clear genetic structure was revealed with population samples corresponding well to their geographic origin, suggesting little impact of long-distance translocations. The clear genetic structure strongly suggests that the choice of stocking material for re-introductions and supplemental releases needs to be based on empirical genetic knowledge.
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48.
  • Palme, Anna, et al. (author)
  • Monitoring reveals two genetically distinct brown trout populations remaining in stable sympatry over 20 years in tiny mountain lakes
  • 2013
  • In: Conservation Genetics. - : Springer Science and Business Media LLC. - 1566-0621 .- 1572-9737. ; 14:4, s. 795-808
  • Journal article (peer-reviewed)abstract
    • Detecting population subdivision when apparent barriers to gene flow are lacking is important in evolutionary and conservation biology. Recent research indicates that intraspecific population complexity can be crucial for maintaining a species' evolutionary potential, productivity, and ecological role. We monitored the genetic relationships at 14 allozyme loci among similar to 4,000 brown trout (Salmo trutta) collected during 19 years from two small interconnected mountain lakes (0.10 and 0.17 km(2), respectively) in central Sweden. There were no allele frequency differences between the lakes. However, heterozygote deficiencies within lakes became obvious after a few years of monitoring. Detailed analyses were then carried out without a priori grouping of samples, revealing unexpected differentiation patterns: (i) the same two genetically distinct (F (ST) a parts per thousand yen 0.10) populations occur sympatrically at about equal frequencies within both lakes, (ii) the genetic subdivision is not coupled with apparent phenotypical dichotomies, (iii) this cryptic structure remains stable over the two decades monitored, and (iv) the point estimates of effective population size are c. 120 and 190, respectively, indicating that genetic drift is important in this system. A subsample of 382 fish was also analyzed for seven microsatellites. The genetic pattern does not follow that of the allozymes, and in this subsample the presence of multiple populations would have gone undetected if only scoring microsatellites. Sympatric populations may be more common than anticipated, but difficult to detect when individuals cannot be grouped appropriately, or when markers or sample sizes are insufficient to provide adequate statistical power with approaches not requiring prior grouping.
  •  
49.
  • Ponnikas, Suvi, et al. (author)
  • Genetic structure of an endangered raptor at individual and population levels
  • 2013
  • In: Conservation Genetics. - : Springer Science and Business Media LLC. - 1566-0621 .- 1572-9737. ; 14:6, s. 1135-1147
  • Journal article (peer-reviewed)abstract
    • The Finnish population of White-tailed Eagle (Haliaeetus albicilla) has gone through two major demographic bottlenecks during the last two centuries. Strong conservation measures have allowed the population to recover, but despite the rapid population growth during recent years the species is still classified as endangered. We studied the genetic population structure at both individual and population levels in an attempt to recognize the processes shaping it. We used 9 microsatellite loci and 473 base pair fragment of the mitochondrial DNA control region on samples collected between the years 2003 and 2007 (N = 489). We found a clear isolation by distance pattern at fine scale (i.e. individual level) which is most likely a result of species' philopatric behaviour. Although we did not find signs of the recent bottlenecks, we did find evidence of an ancient bottleneck that has occurred most likely over 21,000 years ago, long before the genetic divergence of the two present Finnish subpopulations (one along the Baltic Sea coast line and another in Lapland and easternmost Finland). We conclude that the present population structure is mainly a consequence of the species philopatric behaviour over a long time period instead of recent population bottlenecks. Based on our results, the Finnish population seems to have ongoing immigration from neighbouring populations. Hence, even though the population has recovered mainly through local growth, our results suggest that gene flow from genetically differentiated populations have had an impact as well.
  •  
50.
  • Quintela, Maria, et al. (author)
  • Detecting hybridization between willow grouse (Lagopus lagopus) and rock ptarmigan (L. muta) in Central Sweden through Bayesian admixture analyses and mtDNA screening
  • 2010
  • In: Conservation Genetics. - : Springer Science and Business Media LLC. - 1566-0621 .- 1572-9737. ; 11:2, s. 557-569
  • Journal article (peer-reviewed)abstract
    • 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.
  •  
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