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  • 1. Allendorf, Fred W.
    et al.
    Berry, Oliver
    Ryman, Nils
    Stockholm University, Faculty of Science, Department of Zoology.
    So long to genetic diversity, and thanks for all the fish2014In: Molecular Ecology, ISSN 0962-1083, E-ISSN 1365-294X, Vol. 23, no 1, p. 23-25Article in journal (Refereed)
    Abstract [en]

    The world faces a global fishing crisis. Wild marine fisheries comprise nearly 15% of all animal protein in the human diet, but, according to the U.N. Food and Agriculture Organization, nearly 60% of all commercially important marine fish stocks are overexploited, recovering, or depleted (FAO 2012; Fig. 1). Some authors have suggested that the large population sizes of harvested marine fish make even collapsed populations resistant to the loss of genetic variation by genetic drift (e. g. Beverton 1990). In contrast, others have argued that the loss of alleles because of overfishing may actually be more dramatic in large populations than in small ones (Ryman et al. 1995). In this issue, Pinsky & Palumbi (2014) report that overfished populations have approximately 2% lower heterozygosity and 12% lower allelic richness than populations that are not overfished. They also performed simulations which suggest that their estimates likely underestimate the actual loss of rare alleles by a factor of three or four. This important paper shows that the harvesting of marine fish can have genetic effects that threaten the long-term sustainability of this valuable resource.

  • 2.
    Broman, Elias
    et al.
    Stockholm University, Faculty of Science, Department of Ecology, Environment and Plant Sciences. Stockholm University, Faculty of Science, Stockholm University Baltic Sea Centre.
    Raymond, Caroline
    Stockholm University, Faculty of Science, Department of Ecology, Environment and Plant Sciences.
    Sommer, Christian
    Gunnarsson, Jonas S.
    Stockholm University, Faculty of Science, Department of Ecology, Environment and Plant Sciences.
    Creer, Simon
    Nascimento, Francisco J. A.
    Stockholm University, Faculty of Science, Department of Ecology, Environment and Plant Sciences. Stockholm University, Faculty of Science, Stockholm University Baltic Sea Centre.
    Salinity drives meiofaunal community structure dynamics across the Baltic ecosystem2019In: Molecular Ecology, ISSN 0962-1083, E-ISSN 1365-294X, Vol. 28, no 16, p. 3813-3829Article in journal (Refereed)
    Abstract [en]

    Coastal benthic biodiversity is under increased pressure from climate change, eutrophication, hypoxia, and changes in salinity due to increase in river runoff. The Baltic Sea is a large brackish system characterized by steep environmental gradients that experiences all of the mentioned stressors. As such it provides an ideal model system for studying the impact of on‐going and future climate change on biodiversity and function of benthic ecosystems. Meiofauna (animals < 1 mm) are abundant in sediment and are still largely unexplored even though they are known to regulate organic matter degradation and nutrient cycling. In this study, benthic meiofaunal community structure was analysed along a salinity gradient in the Baltic Sea proper using high‐throughput sequencing. Our results demonstrate that areas with higher salinity have a higher biodiversity, and salinity is probably the main driver influencing meiofauna diversity and community composition. Furthermore, in the more diverse and saline environments a larger amount of nematode genera classified as predators prevailed, and meiofauna‐macrofauna associations were more prominent. These findings show that in the Baltic Sea, a decrease in salinity resulting from accelerated climate change will probably lead to decreased benthic biodiversity, and cause profound changes in benthic communities, with potential consequences for ecosystem stability, functions and services.

  • 3.
    Buechel, Séverine D.
    et al.
    University of Lausanne, Switzerland; Institute of Integrative Biology (IBZ), Switzerland.
    Wurm, Yanick
    Keller, Laurent
    Social chromosome variants differentially affect queen determination and the survival of workers in the fire ant Solenopsis invicta2014In: Molecular Ecology, ISSN 0962-1083, E-ISSN 1365-294X, Vol. 23, no 20, p. 5117-5127Article in journal (Refereed)
    Abstract [en]

    Intraspecific variation in social organization is common, yet the underlying causes are rarely known. An exception is the fire ant Solenopsis invicta in which the existence of two distinct forms of social colony organization is under the control of the two variants of a pair of social chromosomes, SB and Sb. Colonies containing exclusively SB/SB workers accept only one single queen and she must be SB/SB. By contrast, when colonies contain more than 10% of SB/Sb workers, they accept several queens but only SB/Sb queens. The variants of the social chromosome are associated with several additional important phenotypic differences, including the size, fecundity and dispersal strategies of queens, aggressiveness of workers, and sperm count in males. However, little is known about whether social chromosome variants affect fitness in other life stages. Here, we perform experiments to determine whether differential selection occurs during development and in adult workers. We find evidence that the Sb variant of the social chromosome increases the likelihood of female brood to develop into queens and that adult SB/Sb workers, the workers that cull SB/SB queens, are overrepresented in comparison to SB/SB workers. This demonstrates that supergenes such as the social chromosome can have complex effects on phenotypes at various stages of development.

  • 4.
    Celorio-Mancera, Maria de la Paz
    et al.
    Stockholm University, Faculty of Science, Department of Zoology, Animal Ecology.
    Wheat, Christopher W.
    Stockholm University, Faculty of Science, Department of Zoology, Population Genetics.
    Vogel, Heiko
    Söderlind, Lina
    Stockholm University, Faculty of Science, Department of Zoology, Animal Ecology.
    Janz, Niklas
    Stockholm University, Faculty of Science, Department of Zoology, Animal Ecology.
    Nylin, Sören
    Stockholm University, Faculty of Science, Department of Zoology, Animal Ecology.
    Mechanisms of macroevolution: polyphagous plasticity in butterfly larvae revealed by RNA-Seq2013In: Molecular Ecology, ISSN 0962-1083, E-ISSN 1365-294X, Vol. 22, no 19, p. 4884-4895Article in journal (Refereed)
    Abstract [en]

    Transcriptome studies of insect herbivory are still rare, yet studies in model systems have uncovered patterns of transcript regulation that appear to provide insights into how insect herbivores attain polyphagy, such as a general increase in expression breadth and regulation of ribosomal, digestion- and detoxification-related genes. We investigated the potential generality of these emerging patterns, in the Swedish comma, Polygonia c-album, which is a polyphagous, widely-distributed butterfly. Urtica dioica and Ribes uva-crispa are hosts of P. c-album, but Ribes represents a recent evolutionary shift onto a very divergent host. Utilizing the assembled transcriptome for read mapping, we assessed gene expression finding that caterpillar life-history (i.e. 2nd vs. 4th-instar regulation) had a limited influence on gene expression plasticity. In contrast, differential expression in response to host-plant identified genes encoding serine-type endopeptidases, membrane-associated proteins and transporters. Differential regulation of genes involved in nucleic acid binding was also observed suggesting that polyphagy involves large scale transcriptional changes. Additionally, transcripts coding for structural constituents of the cuticle were differentially expressed in caterpillars in response to their diet indicating that the insect cuticle may be a target for plant defence. Our results state that emerging patterns of transcript regulation from model species appear relevant in species when placed in an evolutionary context.

  • 5.
    Dalén, Love
    et al.
    Stockholm University, Faculty of Science, Department of Zoology.
    Kvaloy, K.
    Linnell, J. D. C.
    Elmhagen, Bodil
    Stockholm University, Faculty of Science, Department of Zoology.
    Strand, O.
    Tannerfeldt, M.
    Henttonen, H.
    Fuglei, E.
    Landa, A.
    Angerbjörn, Anders
    Stockholm University, Faculty of Science, Department of Zoology.
    Population structure in a critically endangered arctic fox population: does genetics matter?2006In: Molecular Ecology, ISSN 0962-1083, E-ISSN 1365-294X, Vol. 15, no 10, p. 2809-2819Article in journal (Refereed)
    Abstract [en]

    The arctic fox (Alopex lagopus) in Scandinavia is classified as critically endangered after having gone through a severe decline in population size in the beginning of the 20th century, from which it has failed to recover despite more than 65 years of protection. Arctic foxes have a high dispersal rate and often disperse over long distances, suggesting that there was probably little population differentiation within Scandinavia prior to the bottleneck. It is, however, possible that the recent decline in population size has led to a decrease in dispersal and an increase in population fragmentation. To examine this, we used 10 microsatellite loci to analyse genetic variation in 150 arctic foxes from Scandinavia and Russia. The results showed that the arctic fox in Scandinavia presently is subdivided into four populations, and that the Kola Peninsula and northwest Russia together form a large fifth population. Current dispersal between the populations seemed to be very low, but genetic variation within them was relatively high. This and the relative F-ST values among the populations are consistent with a model of recent fragmentation within Scandinavia. Since the amount of genetic variation is high within the populations, but the populations are small and isolated, demographic stochasticity seems to pose a higher threat to the populations' persistence than inbreeding depression and low genetic variation.

  • 6. Desamore, Aurelie
    et al.
    Patino, Jairo
    Mardulyn, Patrick
    Mcdaniel, Stuart F.
    Zanatta, Florian
    Laenen, Benjamin
    Stockholm University, Faculty of Science, Department of Ecology, Environment and Plant Sciences. Stockholm University, Science for Life Laboratory (SciLifeLab). University of Liège, Belgium.
    Vanderpoorten, Alain
    High migration rates shape the postglacial history of amphi-Atlantic bryophytes2016In: Molecular Ecology, ISSN 0962-1083, E-ISSN 1365-294X, Vol. 25, no 21, p. 5568-5584Article in journal (Refereed)
    Abstract [en]

    Paleontological evidence and current patterns of angiosperm species richness suggest that European biota experienced more severe bottlenecks than North American ones during the last glacial maximum. How well this pattern fits other plant species is less clear. Bryophytes offer a unique opportunity to contrast the impact of the last glacial maximum in North America and Europe because about 60% of the European bryoflora is shared with North America. Here, we use population genetic analyses based on approximate Bayesian computation on eight amphi-Atlantic species to test the hypothesis that North American populations were less impacted by the last glacial maximum, exhibiting higher levels of genetic diversity than European ones and ultimately serving as a refugium for the postglacial recolonization of Europe. In contrast with this hypothesis, the best-fit demographic model involved similar patterns of population size contractions, comparable levels of genetic diversity and balanced migration rates between European and North American populations. Our results thus suggest that bryophytes have experienced comparable demographic glacial histories on both sides of the Atlantic. Although a weak, but significant genetic structure was systematically recovered between European and North American populations, evidence for migration from and towards both continents suggests that amphi-Atlantic bryophyte population may function as a metapopulation network. Reconstructing the biogeographic history of either North American or European bryophyte populations therefore requires a large, trans-Atlantic geographic framework.

  • 7. Désamoré, Aurélie
    et al.
    Laenen, Benjamin
    Stockholm University, Faculty of Science, Department of Ecology, Environment and Plant Sciences.
    Miller, Kelly B.
    Bergsten, Johannes
    Early burst in body size evolution is uncoupled from species diversification in diving beetles (Dytiscidae)2018In: Molecular Ecology, ISSN 0962-1083, E-ISSN 1365-294X, Vol. 27, no 4, p. 979-993Article in journal (Refereed)
    Abstract [en]

    Changes in morphology are often thought to be linked to changes in species diversification, which is expected to leave a signal of early burst (EB) in phenotypic traits. However, such signal is rarely recovered in empirical phylogenies, even for groups with well-known adaptive radiation. Using a comprehensive phylogenetic approach in Dytiscidae, which harbours similar to 4,300 species with as much as 50-fold variation in body size among them, we ask whether pattern of species diversification correlates with morphological evolution. Additionally, we test whether the large variation in body size is linked to habitat preference and whether the latter influences species turnover. We found, in sharp contrast to most animal groups, that Dytiscidae body size evolution follows an early-burst model with subsequent high phylogenetic conservatism. However, we found no evidence for associated shifts in species diversification, which point to an uncoupled evolution of morphology and species diversification. We recovered the ancestral habitat of Dytiscidae as lentic (standing water), with many transitions to lotic habitat (running water) that are concomitant to a decrease in body size. Finally, we found no evidence for difference in net diversification rates between habitats nor difference in turnover in lentic and lotic species. This result, together with recent findings in dragonflies, contrasts with some theoretical expectations of the habitat stability hypothesis. Thus, a thorough reassessment of the impact of dispersal, gene flow and range size on the speciation process is needed to fully encompass the evolutionary consequences of the lentic-lotic divide for freshwater fauna.

  • 8. Geffen, E.
    et al.
    Kam, Michael
    Hefner, R.
    Hersteinsson, P.
    Angerbjörn, Anders
    Stockholm University, Faculty of Science, Department of Zoology.
    Dalén, Love
    Naturhistoriska riksmuseet, Molekylärsystematik.
    Fuglei, E.
    Norén, Karin
    Stockholm University, Faculty of Science, Department of Zoology.
    Adams, J. R.
    Vucetich, J.
    Meier, T. J.
    Mech, L. D.
    von Holdt, B. M.
    Stahler, D. R.
    Wayne, R. K.
    Kin encounter rate and inbreeding avoidance in canids2011In: Molecular Ecology, ISSN 0962-1083, E-ISSN 1365-294X, Vol. 20, no 24, p. 5348-5358Article in journal (Refereed)
    Abstract [en]

    Mating with close kin can lead to inbreeding depression through the expression of recessive deleterious alleles and loss of heterozygosity. Mate selection may be affected by kin encounter rate, and inbreeding avoidance may not be uniform but associated with age and social system. Specifically, selection for kin recognition and inbreeding avoidance may be more developed in species that live in family groups or breed cooperatively. To test this hypothesis, we compared kin encounter rate and the proportion of related breeding pairs in noninbred and highly inbred canid populations. The chance of randomly encountering a full sib ranged between 1–8% and 20–22% in noninbred and inbred canid populations, respectively. We show that regardless of encounter rate, outside natal groups mates were selected independent of relatedness. Within natal groups, there was a significant avoidance of mating with a relative. Lack of discrimination against mating with close relatives outside packs suggests that the rate of inbreeding in canids is related to the proximity of close relatives, which could explain the high degree of inbreeding depression observed in some populations. The idea that kin encounter rate and social organization can explain the lack of inbreeding avoidance in some species is intriguing and may have implications for the management of populations at risk

  • 9. Hoffman, Eric A.
    et al.
    Kolm, Niclas
    Uppsala universitet, Zooekologi.
    Berglund, Anders
    Uppsala universitet, Zooekologi.
    Arquello, J. Roman
    Jones, A dam G.
    Genetic structure in the coral-reef-associated Banggai cardinalfish, Pterapogon kauderni2005In: Molecular Ecology, ISSN 0962-1083, E-ISSN 1365-294X, Vol. 14, no 5, p. 1367-1375Article in journal (Refereed)
    Abstract [en]

    In this study, we used 11 polymorphic microsatellite loci to show that oceanic distances as small as 2–5 km are sufficient to produce high levels of population genetic structure (multilocus FST as high as 0.22) in the Banggai cardinalfish(Pterapogon kauderni), a heavily exploited reef fish lacking a pelagic larval dispersal phase. Global FST among all populations, separated by a maximum distance of 203 km, was 0.18 (RST = 0.35). Moreover, two lines of evidence suggest that estimates of FST may actually underestimate the true level of genetic structure. First, within-locus FST values were consistently close to the theoretical maximum set by the average within-population heterozygosity. Second, the allele size permutation test showed that RST values were significantly larger than FST values, indicating that populations have been isolated long enough for mutation to have played a role in generating allelic variation among populations. The high level of microspatial structure observed in this marine fish indicates that life history traits such as lack of pelagic larval phase and a good homing ability do indeed play a role in shaping population genetic structure in the marine realm.

  • 10.
    Hughes, Patrick William
    et al.
    Max Planck Institute for Plant Breeding Research, Germany; University of Cologne, Germany.
    Soppe, Wim J. J.
    Albani, Maria C.
    Seed traits are pleiotropically regulated by the flowering time gene PERPETUAL FLOWERING 1 (PEP1) in the perennial Arabis alpina2019In: Molecular Ecology, ISSN 0962-1083, E-ISSN 1365-294X, Vol. 28, no 5, p. 1183-1201Article in journal (Refereed)
    Abstract [en]

    The life cycles of plants are characterized by two major life history transitions—germination and the initiation of flowering—the timing of which are important determinants of fitness. Unlike annuals, which make the transition from the vegetative to reproductive phase only once, perennials iterate reproduction in successive years. The floral repressor PERPETUAL FLOWERING 1 (PEP1), an ortholog of FLOWERING LOCUS C, in the alpine perennial Arabis alpina ensures the continuation of vegetative growth after flowering and thereby restricts the duration of the flowering episode. We performed greenhouse and garden experiments to compare flowering phenology, fecundity and seed traits between A. alpina accessions that have a functional PEP1 allele and flower seasonally and pep1 mutants and accessions that carry lesions in PEP1 and flower perpetually. In the garden, perpetual genotypes flower asynchronously and show higher winter mortality than seasonal ones. PEP1 also pleiotropically regulates seed dormancy and longevity in a way that is functionally divergent from FLC. Seeds from perpetual genotypes have shallow dormancy and reduced longevity regardless of whether they after‐ripened in plants grown in the greenhouse or in the experimental garden. These results suggest that perpetual genotypes have higher mortality during winter but compensate by showing higher seedling establishment. Differences in seed traits between seasonal and perpetual genotypes are also coupled with differences in hormone sensitivity and expression of genes involved in hormonal pathways. Our study highlights the existence of pleiotropic regulation of seed traits by hub developmental regulators such as PEP1, suggesting that seed and flowering traits in perennial plants might be optimized in a coordinated fashion.

  • 11.
    Johansson, Veronika A.
    et al.
    Stockholm University, Faculty of Science, Department of Ecology, Environment and Plant Sciences.
    Bahram, M.
    Tedersoo, L.
    Koljalg, U.
    Eriksson, Ove
    Stockholm University, Faculty of Science, Department of Ecology, Environment and Plant Sciences.
    Specificity of fungal associations of Pyroleae and Monotropa hypopitys during germination and seedling development2017In: Molecular Ecology, ISSN 0962-1083, E-ISSN 1365-294X, Vol. 26, no 9, p. 2591-2604Article in journal (Refereed)
    Abstract [en]

    Mycoheterotrophic plants obtain organic carbon from associated mycorrhizal fungi, fully or partially. Angiosperms with this form of nutrition possess exceptionally small 'dust seeds' which after germination develop 'seedlings' that remain subterranean for several years, fully dependent on fungi for supply of carbon. Mycoheterotrophs which as adults have photosynthesis thus develop from full to partial mycoheterotrophy, or autotrophy, during ontogeny. Mycoheterotrophic plants may represent a gradient of variation in a parasitism-mutualism continuum, both among and within species. Previous studies on plant-fungal associations in mycoheterotrophs have focused on either germination or the adult life stages of the plant. Much less is known about the fungal associations during development of the subterranean seedlings. We investigated germination and seedling development and the diversity of fungi associated with germinating seeds and subterranean seedlings (juveniles) in five Monotropoideae (Ericaceae) species, the full mycoheterotroph Monotropa hypopitys and the putatively partial mycoheterotrophs Pyrola chlorantha, P. rotundifolia, Moneses uniflora and Chimaphila umbellata. Seedlings retrieved from seed sowing experiments in the field were used to examine diversity of fungal associates, using pyrosequencing analysis of ITS2 region for fungal identification. The investigated species varied with regard to germination, seedling development and diversity of associated fungi during juvenile ontogeny. Results suggest that fungal host specificity increases during juvenile ontogeny, most pronounced in the fully mycoheterotrophic species, but a narrowing of fungal associates was found also in two partially mycoheterotrophic species. We suggest that variation in specificity of associated fungi during seedling ontogeny in mycoheterotrophs represents ongoing evolution along a parasitism-mutualism continuum.

  • 12. Jorde, Per Erik
    et al.
    Andersson, Anastasia
    Stockholm University, Faculty of Science, Department of Zoology.
    Ryman, Nils
    Stockholm University, Faculty of Science, Department of Zoology.
    Laikre, Linda
    Stockholm University, Faculty of Science, Department of Zoology.
    Are we underestimating the occurrence of sympatric populations?2018In: Molecular Ecology, ISSN 0962-1083, E-ISSN 1365-294X, Vol. 27, no 20, p. 4011-4025Article in journal (Refereed)
    Abstract [en]

    Sympatric populations are conspecific populations that coexist spatially. They are of interest in evolutionary biology by representing the potential first steps of sympatric speciation and are important to identify and monitor in conservation management. Reviewing the literature pertaining to sympatric populations, we find that most cases of sympatry appear coupled to phenotypic divergence, implying ease of detection. In comparison, phenotypically cryptic, sympatric populations seem rarely documented. We explore the statistical power for detecting population mixtures from genetic marker data, using commonly applied tests for heterozygote deficiency (i.e., Wahlund effect) and the structure software, through computer simulations. We find that both tests are efficient at detecting population mixture only when genetic differentiation is high, sample size and number of genetic markers are reasonable and the sympatric populations happen to occur in similar proportions in the sample. We present an approximate expression based on these experimental factors for the lower limit of F-ST, beyond which power for structure collapses and only the heterozygote-deficiency tests retain some, although low, power. The findings suggest that cases of cryptic sympatry may have passed unnoticed in population genetic screenings using number of loci typical of the pre-genomics era. Hence, cryptic sympatric populations may be more common than hitherto thought, and we urge more attention being diverted to their detection and characterization.

  • 13.
    Keehnen, Naomi L. P.
    et al.
    Stockholm University, Faculty of Science, Department of Zoology.
    Hill, Jason
    Stockholm University, Faculty of Science, Department of Zoology.
    Nylin, Sören
    Stockholm University, Faculty of Science, Department of Zoology.
    Wheat, Christopher W.
    Stockholm University, Faculty of Science, Department of Zoology.
    Microevolutionary selection dynamics acting on immune genes of the green-veined white butterfly, Pieris napi2018In: Molecular Ecology, ISSN 0962-1083, E-ISSN 1365-294X, Vol. 27, no 13, p. 2807-2822Article in journal (Refereed)
    Abstract [en]

    Insects rely on their innate immune system to successfully mediate complex interactions with their microbiota, as well as the microbes present in the environment. Previous work has shown that components of the canonical immune gene repertoire evolve rapidly and have evolutionary characteristics originating from interactions with fast-evolving microorganisms. Although these interactions are likely to vary among populations, there is a poor understanding of the microevolutionary dynamics of immune genes, especially in non-Dipteran insects. Here, we use the full set of canonical insect immune genes to investigate microevolutionary dynamics acting on these genes between and among populations by comparing three allopatric populations of the green-veined white butterfly, Pieris napi (Linne; Lepidoptera, Pieridae). Immune genes showed increased genetic diversity compared to genes from the rest of the genome and various functional categories exhibited different types of signatures of selection, at different evolutionary scales, presenting a complex pattern of selection dynamics. Signatures of balancing selection were identified in 10 genes, and 17 genes appear to be under positive selection. Genes involved with the cellular arm of the immune response as well as the Toll pathway appear to be enriched among our outlier loci, regardless of functional category. This suggests that the targets of selection might focus upon an entire pathway, rather than functional subsets across pathways. Our microevolutionary results are similar to previously observed macroevolutionary patterns from diverse taxa, suggesting that either the immune system is robust to dramatic differences in life history and microbial communities, or that diverse microbes exert similar selection pressures.

  • 14.
    Lagerholm, Vendela K.
    et al.
    Stockholm University, Faculty of Science, Department of Zoology. Swedish Museum of Natural History, Sweden.
    Sandoval-Castellanos, Edson
    Stockholm University, Faculty of Science, Department of Zoology. Swedish Museum of Natural History, Sweden.
    Ehrich, Dorothee
    Abramson, Natalia I.
    Nadachowski, Adam
    Kalthoff, Daniela C.
    Germonpre, Mietje
    Angerbjörn, Anders
    Stockholm University, Faculty of Science, Department of Zoology.
    Stewart, John R.
    Dalén, Love
    On the origin of the Norwegian lemming2014In: Molecular Ecology, ISSN 0962-1083, E-ISSN 1365-294X, Vol. 23, no 8, p. 2060-2071Article in journal (Refereed)
    Abstract [en]

    The Pleistocene glacial cycles resulted in significant changes in species distributions, and it has been discussed whether this caused increased rates of population divergence and speciation. One species that is likely to have evolved during the Pleistocene is the Norwegian lemming (Lemmus lemmus). However, the origin of this species, both in terms of when and from what ancestral taxon it evolved, has been difficult to ascertain. Here, we use ancient DNA recovered from lemming remains from a series of Late Pleistocene and Holocene sites to explore the species' evolutionary history. The results revealed considerable genetic differentiation between glacial and contemporary samples. Moreover, the analyses provided strong support for a divergence time prior to the Last Glacial Maximum (LGM), therefore likely ruling out a postglacial colonization of Scandinavia. Consequently, it appears that the Norwegian lemming evolved from a small population that survived the LGM in an ice-free Scandinavian refugium.

  • 15.
    Laikre, Linda
    et al.
    Stockholm University, Faculty of Science, Department of Zoology, Population Genetics.
    Miller, Loren M.
    University of Minnesota.
    Palmé, Anna
    Stockholm University, Faculty of Science, Department of Zoology, Population Genetics.
    Palm, Stefan
    Stockholm University, Faculty of Science, Department of Zoology, Population Genetics.
    Kapuscinski, Anne R.
    University of Minnesota.
    Thoresson, Gunnar
    National Board of Fisheries.
    Ryman, Nils
    Stockholm University, Faculty of Science, Department of Zoology, Population Genetics.
    Spatial genetic structure of northern pike (Esox lucius) in the Baltic Sea2005In: Molecular Ecology, ISSN 0962-1083, E-ISSN 1365-294X, Vol. 14, no 7, p. 1955-1964Article in journal (Refereed)
    Abstract [en]

    The genetic relationships among 337 northern pike (Esox lucius) collected from the coastal zone of the central Baltic region and the Finnish islands of Åland were analysed using five microsatellite loci. Spatial structure was delineated using both traditional F-statistics and individually based approaches including spatial autocorrelation analysis. Our results indicate that the observed genotypic distribution is incompatible with that of a single, panmictic population. Isolation by distance appears important for shaping the genetic structure of pike in this region resulting in a largely continuous genetic change over the study area. Spatial autocorrelation analysis (Moran’s I) of individual pairwise genotypic data show significant positive genetic correlation among pike collected within geographical distances of less than c. 100–150 km (genetic patch size). We suggest that the genetic patch size may be used as a preliminary basis for identifying management units for pike in the Baltic Sea.

  • 16. Leal, Luis
    et al.
    Talla, Venkat
    Källman, Thomas
    Friberg, Magne
    Wiklund, Christer
    Stockholm University, Faculty of Science, Department of Zoology.
    Dincă, Vlad
    Vila, Roger
    Backström, Niclas
    Gene expression profiling across ontogenetic stages in the wood white (Leptidea sinapis) reveals pathways linked to butterfly diapause regulation2018In: Molecular Ecology, ISSN 0962-1083, E-ISSN 1365-294X, Vol. 27, no 4, p. 935-948Article in journal (Refereed)
    Abstract [en]

    In temperate latitudes, many insects enter diapause (dormancy) during the cold season, a period during which developmental processes come to a standstill. The wood white (Leptidea sinapis) is a butterfly species distributed across western Eurasia that shows photoperiod-induced diapause with variation in critical day-length across populations at different latitudes. We assembled transcriptomes and estimated gene expression levels at different developmental stages in experimentally induced directly developing and diapausing cohorts of a single Swedish population of L. sinapis to investigate the regulatory mechanisms underpinning diapause initiation. Different day lengths resulted in expression changes of developmental genes and affected the rate of accumulation of signal molecules, suggesting that diapause induction might be controlled by increased activity of monoamine neurotransmitters in larvae reared under short-day light conditions. Expression differences between light treatment groups of two monoamine regulator genes (DDC and ST) were observed already in instar III larvae. Once developmental pathways were irreversibly set at instar V, a handful of genes related to dopamine production were differentially expressed leading to a significant decrease in expression of global metabolic genes and increase in expression of genes related to fatty acid synthesis and sequestration. This is in line with a time-dependent (hour-glass) model of diapause regulation where a gradual shift in the concentration of monoamine neurotransmitters and their metabolites during development of larvae under short-day conditions leads to increased storage of fat, decreased energy expenditures, and ultimately developmental stasis at the pupal stage.

  • 17. Lira, Jaime
    et al.
    Linderholm, Anna
    Stockholm University, Faculty of Humanities, Department of Archaeology and Classical Studies, Archaeological Research Laboratory.
    Olaria, C
    Brändström Durling, Michael
    Gilbert, Tom
    Ellegren, Hans
    Willerslev, Eske
    Lidén, Kerstin
    Stockholm University, Faculty of Humanities, Department of Archaeology and Classical Studies, Archaeological Research Laboratory. Stockholm University, Faculty of Humanities, Centre for the Study of Cultural Evolution.
    Arsuaga, JL
    Götherström, Anders
    Ancient DNA reveals traces of Iberian Neolithic and Bronze age lineages in modern Iberian horses2010In: Molecular Ecology, ISSN 0962-1083, E-ISSN 1365-294X, Vol. 19, no 1, p. 64-78Article in journal (Refereed)
    Abstract [en]

    Multiple geographical regions have been proposed for the domestication of Equus caballus. It has been suggested, based on zooarchaeological and genetic analyses that wild horses from the Iberian Peninsula were involved in the process, and the overrepresentation of mitochondrial D1 cluster in modern Iberian horses supports this suggestion. To test this hypothesis, we analysed mitochondrial DNA from 22 ancient Iberian horse remains belonging to the Neolithic, the Bronze Age and the Middle Ages, against previously published sequences. Only the medieval Iberian sequence appeared in the D1 group. Neolithic and Bronze Age sequences grouped in other clusters, one of which (Lusitano group C) is exclusively represented by modern horses of Iberian origin. Moreover, Bronze Age Iberian sequences displayed the lowest nucleotide diversity values when compared with modern horses, ancient wild horses and other ancient domesticates using nonparametric bootstrapping analyses. We conclude that the excessive clustering of Bronze Age horses in the Lusitano group C, the observed nucleotide diversity and the local continuity from wild Neolithic Iberian to modern Iberian horses, could be explained by the use of local wild mares during an early Iberian domestication or restocking event, whereas the D1 group probably was introduced into Iberia in later historical times.

  • 18. Mendez, Martin
    et al.
    Jefferson, Thomas A.
    Kolokotronis, Sergios-Orestis
    Kruetzen, Michael
    Parra, Guido J.
    Collins, Tim
    Minton, Giana
    Baldwin, Robert
    Berggren, Per
    Särnblad, Anna
    Stockholm University, Faculty of Science, Department of Zoology.
    Amir, Omar A.
    Peddemors, Vic M.
    Karczmarski, Leszek
    Guissamulo, Almeida
    Smith, Brian
    Sutaria, Dipani
    Amato, George
    Rosenbaum, Howard C.
    Integrating multiple lines of evidence to better understand the evolutionary divergence of humpback dolphins along their entire distribution range: a new dolphin species in Australian waters?2013In: Molecular Ecology, ISSN 0962-1083, E-ISSN 1365-294X, Vol. 22, no 23, p. 5936-5948Article in journal (Refereed)
    Abstract [en]

    The conservation of humpback dolphins, distributed in coastal waters of the Indo-West Pacific and eastern Atlantic Oceans, has been hindered by a lack of understanding about the number of species in the genus (Sousa) and their population structure. To address this issue, we present a combined analysis of genetic and morphologic data collected from beach-cast, remote-biopsied and museum specimens from throughout the known Sousa range. We extracted genetic sequence data from 235 samples from extant populations and explored the mitochondrial control region and four nuclear introns through phylogenetic, population-level and population aggregation frameworks. In addition, 180 cranial specimens from the same geographical regions allowed comparisons of 24 morphological characters through multivariate analyses. The genetic and morphological data showed significant and concordant patterns of geographical segregation, which are typical for the kind of demographic isolation displayed by species units, across the Sousa genus distribution range. Based on our combined genetic and morphological analyses, there is convincing evidence for at least four species within the genus (S.teuszii in the Atlantic off West Africa, S.plumbea in the central and western Indian Ocean, S.chinensis in the eastern Indian and West Pacific Oceans, and a new as-yet-unnamed species off northern Australia).

  • 19.
    Neethiraj, Ramprasad
    et al.
    Stockholm University, Faculty of Science, Department of Zoology. Pennsylvania State University, USA.
    Hornett, Emily A.
    Hill, Jason A.
    Stockholm University, Faculty of Science, Department of Zoology.
    Wheat, Christopher W.
    Stockholm University, Faculty of Science, Department of Zoology.
    Investigating the genomic basis of discrete phenotypes using a Pool-Seq-only approach: New insights into the genetics underlying colour variation in diverse taxa2017In: Molecular Ecology, ISSN 0962-1083, E-ISSN 1365-294X, Vol. 26, no 19, p. 4990-5002Article in journal (Refereed)
    Abstract [en]

    While large-scale genomic approaches are increasingly revealing the genetic basis of polymorphic phenotypes such as colour morphs, such approaches are almost exclusively conducted in species with high-quality genomes and annotations. Here, we use Pool-Seq data for both genome assembly and SNP frequency estimation, followed by scanning for F-ST outliers to identify divergent genomic regions. Using paired-end, short-read sequencing data from two groups of individuals expressing divergent phenotypes, we generate a de novo rough-draft genome, identify SNPs and calculate genomewide F-ST differences between phenotypic groups. As genomes generated by Pool-Seq data are highly fragmented, we also present an approach for super-scaffolding contigs using existing protein-coding data sets. Using this approach, we reanalysed genomic data from two recent studies of birds and butterflies investigating colour pattern variation and replicated their core findings, demonstrating the accuracy and power of a Pool-Seq-only approach. Additionally, we discovered new regions of high divergence and new annotations that together suggest novel parallels between birds and butterflies in the origins of their colour pattern variation.

  • 20.
    Norén, Karin
    et al.
    Stockholm University, Faculty of Science, Department of Zoology.
    Godoy, Erika
    Stockholm University, Faculty of Science, Department of Zoology.
    Dalén, Love
    Stockholm University, Faculty of Science, Department of Zoology. Swedish Museum of Natural History, Sweden.
    Meijer, Tomas
    Stockholm University, Faculty of Science, Department of Zoology. National Veterinary Institute, Sweden.
    Angerbjörn, Anders
    Stockholm University, Faculty of Science, Department of Zoology.
    Inbreeding depression in a critically endangered carnivore2016In: Molecular Ecology, ISSN 0962-1083, E-ISSN 1365-294X, Vol. 25, no 14, p. 3309-3318Article in journal (Refereed)
    Abstract [en]

    Harmful effects arising from matings between relatives (inbreeding) is a long-standing observation that is well founded in theory. Empirical evidence for inbreeding depression in natural populations is however rare because of the challenges of assembling pedigrees supplemented with fitness traits. We examined the occurrence of inbreeding and subsequent inbreeding depression using a unique data set containing a genetically verified pedigree with individual fitness traits for a critically endangered arctic fox (Vulpes lagopus) population. The study covered nine years and was comprised of 33 litters with a total of 205 individuals. We recorded that the present population was founded by only five individuals. Over the study period, the population exhibited a tenfold increase in average inbreeding coefficient with a final level corresponding to half-sib matings. Inbreeding mainly occurred between cousins, but we also observed two cases of full-sib matings. The pedigree data demonstrated clear evidence of inbreeding depression on traditional fitness traits where inbred individuals displayed reduced survival and reproduction. Fitness traits were however differently affected by the fluctuating resource abundande. Inbred individuals born at low-quality years displayed reduced first-year survival, while inbred individuals born at high-quality years were less likely to reproduce. The documentation of inbreeding depression in fundamental fitness traits suggests that inbreeding depression can limit population recovery. Introducing new genetic material to promote a genetic rescue effect may thus be necessary for population long-term persistence.

  • 21.
    Nyström, Veronica
    et al.
    Stockholm University, Faculty of Science, Department of Zoology.
    Humphrey, Joanne
    Skoglund, Pontus
    McKeown, Niall J.
    Vartanyan, Sergey
    Shaw, Paul W.
    Lidén, Kerstin
    Stockholm University, Faculty of Humanities, Department of Archaeology and Classical Studies, Archaeological Research Laboratory.
    Jakobsson, Mattias
    Barnes, Ian
    Angerbjörn, Anders
    Stockholm University, Faculty of Science, Department of Zoology.
    Lister, Adrian
    Dalen, Love
    Microsatellite genotyping reveals end-Pleistocene decline in mammoth autosomal genetic variation2012In: Molecular Ecology, ISSN 0962-1083, E-ISSN 1365-294X, Vol. 21, no 14, p. 3391-3402Article in journal (Refereed)
    Abstract [en]

    The last glaciation was a dynamic period with strong impact on the demography of many species and populations. In recent years, mitochondrial DNA sequences retrieved from radiocarbon-dated remains have provided novel insights into the history of Late Pleistocene populations. However, genotyping of loci from the nuclear genome may provide enhanced resolution of population-level changes. Here, we use four autosomal microsatellite DNA markers to investigate the demographic history of woolly mammoths (Mammuthus primigenius) in north-eastern Siberia from before 60 000 years ago up until the species final disappearance c. 4000 years ago. We identified two genetic groups, implying a marked temporal genetic differentiation between samples with radiocarbon ages older than 12 thousand radiocarbon years before present (ka) and those younger than 9 ka. Simulation-based analysis indicates that this dramatic change in genetic composition, which included a decrease in individual heterozygosity of approximately 30%, was due to a multifold reduction in effective population size. A corresponding reduction in genetic variation was also detected in the mitochondrial DNA, where about 65% of the diversity was lost. We observed no further loss in genetic variation during the Holocene, which suggests a rapid final extinction event.

  • 22. Palsboll, Per J.
    et al.
    Peery, M. Zachariah
    Olsen, Morten T.
    Stockholm University, Faculty of Science, Department of Genetics, Microbiology and Toxicology.
    Beissinger, Steven R.
    Berube, Martine
    Inferring recent historic abundance from current genetic diversity2013In: Molecular Ecology, ISSN 0962-1083, E-ISSN 1365-294X, Vol. 22, no 1, p. 22-40Article, review/survey (Refereed)
    Abstract [en]

    Recent historic abundance is an elusive parameter of great importance for conserving endangered species and understanding the pre-anthropogenic state of the biosphere. The number of studies that have used population genetic theory to estimate recent historic abundance from contemporary levels of genetic diversity has grown rapidly over the last two decades. Such assessments often yield unexpectedly large estimates of historic abundance. We review the underlying theory and common practices of estimating recent historic abundance from contemporary genetic diversity, and critically evaluate the potential issues at various estimation steps. A general issue of mismatched spatio-temporal scales between the estimation itself and the objective of the estimation emerged from our assessment; genetic diversitybased estimates of recent historic abundance represent long-term averages, whereas the objective typically is an estimate of recent abundance for a specific population. Currently, the most promising approach to estimate the difference between recent historic and contemporary abundance requires that genetic data be collected from samples of similar spatial and temporal duration. Novel genome-enabled inference methods may be able to utilize additional information of dense genome-wide distributions of markers, such as of identity-by-descent tracts, to infer recent historic abundance from contemporary samples only.

  • 23. Pastene, Luis A.
    et al.
    Goto, Mutsuo
    Kanda, Naohisa
    Zerbini, Alexandre N.
    Kerem, Dan
    Watanabe, Kazuo
    Bessho, Yoshitaka
    Hasegawa, Masami
    Nielsen, Rasmus
    Larsen, Finn
    Palsböll, Per J.
    Stockholm University, Faculty of Science, Department of Genetics, Microbiology and Toxicology.
    Radiation and speciation of pelagic organisms during periods of global warming: the case of the common minke whale, Balaenoptera acutorostrata2007In: Molecular Ecology, ISSN 0962-1083, E-ISSN 1365-294X, Vol. 16, no 7, p. 1481-1495Article in journal (Refereed)
    Abstract [en]

    How do populations of highly mobile species inhabiting open environments become reproductively isolated and evolve into new species? We test the hypothesis that elevated ocean-surface temperatures can facilitate allopatry among pelagic populations and thus promote speciation. Oceanographic modelling has shown that increasing surface temperatures cause localization and reduction of upwelling, leading to fragmentation of feeding areas critical to pelagic species. We test our hypothesis by genetic analyses of populations of two closely related baleen whales, the Antarctic minke whale (Balaenoptera bonaerensis) and common minke whale (Balaenoptera acutorostrata) whose current distributions and migration patterns extent are largely determined by areas of consistent upwelling with high primary production. Phylogeographic and population genetic analyses of mitochondrial DNA control-region nucleotide sequences collected from 467 whales sampled in four different ocean basins were employed to infer the evolutionary relationship among populations of B. acutorostrata by rooting an intraspecific phylogeny with a population of B. bonaerensis. Our findings suggest that the two species diverged in the Southern Hemisphere less than 5 million years ago (Ma). This estimate places the speciation event during a period of extended global warming in the Pliocene. We propose that elevated ocean temperatures in the period facilitated allopatric speciation by disrupting the continuous belt of upwelling maintained by the Antarctic Circumpolar Current. Our analyses revealed that the current populations of B. acutorostrata likely diverged after the Pliocene some 1.5 Ma when global temperatures had decreased and presumably coinciding with the re-establishment of the polar-equatorial temperature gradient that ultimately drives upwelling. In most population samples, we detected genetic signatures of exponential population expansions, consistent with the notion of increasing carrying capacity after the Pliocene. Our hypothesis that prolonged periods of global warming facilitate speciation in pelagic marine species that depend on upwelling should be tested by comparative analyses in other pelagic species.

  • 24.
    Pruisscher, Peter
    et al.
    Stockholm University, Faculty of Science, Department of Zoology.
    Nylin, Sören
    Stockholm University, Faculty of Science, Department of Zoology.
    Gotthard, Karl
    Stockholm University, Faculty of Science, Department of Zoology.
    Wheat, Christopher W.
    Stockholm University, Faculty of Science, Department of Zoology.
    Genetic variation underlying local adaptation of diapause induction along a cline in a butterfly2018In: Molecular Ecology, ISSN 0962-1083, E-ISSN 1365-294X, Vol. 27, no 18, p. 3613-3626Article in journal (Refereed)
    Abstract [en]

    Diapause is a life history strategy allowing individuals to arrest development until favourable conditions return, and it is commonly induced by shortened day length that is latitude specific for local populations. Although understanding the evolutionary dynamics of a threshold trait like diapause induction provides insights into the adaptive process and adaptive potential of populations, the genetic mechanism of variation in photoperiodic induction of diapause is not well understood. Here, we investigate genetic variation underlying latitudinal variation in diapause induction and the selection dynamics acting upon it. Using a genomewide scan for divergent regions between two populations of the butterfly Pararge aegeria that differ strongly in their induction thresholds, we identified and investigated the patterns of variation in those regions. We then tested the association of these regions with diapause induction using between-population crosses, finding significant SNP associations in four genes present in two chromosomal regions, one with the gene period, and the other with the genes kinesin, carnitine O-acetyltransferase and timeless. Patterns of allele frequencies in these two regions in population samples along a latitudinal cline suggest strong selection against heterozygotes at two genes within these loci (period, timeless). Evidence for additional loci modifying the diapause decision was found in patterns of allelic change in relation to induction thresholds over the cline, as well as in backcross analyses. Taken together, population-specific adaptations of diapause induction appear to be due to a combination of alleles of larger and smaller effect size, consistent with an exponential distribution of effect sizes involved in local adaption.

  • 25.
    Ryman, Nils
    et al.
    Stockholm University, Faculty of Science, Department of Zoology.
    Laikre, Linda
    Stockholm University, Faculty of Science, Department of Zoology.
    Hössjer, Ola
    Stockholm University, Faculty of Science, Department of Mathematics.
    Do estimates of contemporary effective population size tell us what we want to know?2019In: Molecular Ecology, ISSN 0962-1083, E-ISSN 1365-294X, Vol. 28, no 8, p. 1904-1918Article in journal (Refereed)
    Abstract [en]

    Estimation of effective population size (N-e) from genetic marker data is a major focus for biodiversity conservation because it is essential to know at what rates inbreeding is increasing and additive genetic variation is lost. But are these the rates assessed when applying commonly used N-e estimation techniques? Here we use recently developed analytical tools and demonstrate that in the case of substructured populations the answer is no. This is because the following: Genetic change can be quantified in several ways reflecting different types of N-e such as inbreeding (N-eI), variance (N-eV), additive genetic variance (N-eAV), linkage disequilibrium equilibrium (N-eLD), eigenvalue (N-eE) and coalescence (N-eCo) effective size. They are all the same for an isolated population of constant size, but the realized values of these effective sizes can differ dramatically in populations under migration. Commonly applied N-e-estimators target N-eV or N(eLD )of individual subpopulations. While such estimates are safe proxies for the rates of inbreeding and loss of additive genetic variation under isolation, we show that they are poor indicators of these rates in populations affected by migration. In fact, both the local and global inbreeding (N-eI) and additive genetic variance (N-eAV) effective sizes are consistently underestimated in a subdivided population. This is serious because these are the effective sizes that are relevant to the widely accepted 50/500 rule for short and long term genetic conservation. The bias can be infinitely large and is due to inappropriate parameters being estimated when applying theory for isolated populations to subdivided ones.

  • 26.
    Ryman, Nils
    et al.
    Stockholm University, Faculty of Science, Department of Zoology, Population Genetics.
    Leimar, Olof
    Stockholm University, Faculty of Science, Department of Zoology, Ethology.
    GST is still a useful measure of genetic differentation - a comment on Jost's D2009In: Molecular Ecology, ISSN 0962-1083, E-ISSN 1365-294X, Vol. 18, p. 2084-2087Article in journal (Refereed)
  • 27. Talla, Venkat
    et al.
    Johansson, Anna
    Dincă, Vlad
    Vila, Roger
    Friberg, Magne
    Wiklund, Christer
    Stockholm University, Faculty of Science, Department of Zoology.
    Backström, Niclas
    Lack of gene flow: Narrow and dispersed differentiation islands in a triplet of Leptidea butterfly species2019In: Molecular Ecology, ISSN 0962-1083, E-ISSN 1365-294X, Vol. 28, no 16, p. 3756-3770Article in journal (Refereed)
    Abstract [en]

    Genome scans in recently separated species can inform on molecular mechanisms and evolutionary processes driving divergence. Large-scale polymorphism data from multiple species pairs are also key to investigate the repeatability of divergence-whether radiations tend to show parallel responses to similar selection pressures and/or underlying molecular forces. Here, we used whole-genome resequencing data from six wood white (Leptidea sp.) butterfly populations, representing three closely related species with karyomorph variation, to infer the species' demographic history and characterize patterns of genomic diversity and differentiation. The analyses supported previously established species relationships, and there was no evidence for postdivergence gene flow. We identified significant intraspecific genetic structure, in particular between karyomorph extremes in the wood white (L. sinapis)-a species with a remarkable chromosome number cline across the distribution range. The genomic landscapes of differentiation were erratic, and outlier regions were narrow and dispersed. Highly differentiated (F-ST) regions generally had low genetic diversity (theta(pi)), but increased absolute divergence (D-XY) and excess of rare frequency variants (low Tajima's D). A minority of differentiation peaks were shared across species and population comparisons. However, highly differentiated regions contained genes with overrepresented functions related to metabolism, response to stimulus and cellular processes, indicating recurrent directional selection on a specific set of traits in all comparisons. In contrast to the majority of genome scans in recently diverged lineages, our data suggest that divergence landscapes in Leptidea have been shaped by directional selection and genetic drift rather than stable recombination landscapes and/or introgression.

  • 28. Tedersoo, Leho
    et al.
    Bahram, Mohammad
    Jairus, Teele
    Bechem, Eneke
    Chinoya, Stephen
    Mpumba, Rebecca
    Leal, Miguel
    Randrianjohany, Emile
    Razafimandimbison, Sylvain
    Stockholm University, Faculty of Science, Department of Botany.
    Sadam, Ave
    Naadel, Triin
    Koljalg, Urmas
    Spatial structure and the effects of host and soil environments on communities of ectomycorrhizal fungi in wooded savannas and rain forests of Continental Africa and Madagascar2011In: Molecular Ecology, ISSN 0962-1083, E-ISSN 1365-294X, Vol. 20, no 14, p. 3071-3080Article in journal (Refereed)
    Abstract [en]

    Mycorrhizal fungi play a key role in mineral nutrition of terrestrial plants, but the factors affecting natural distribution, diversity and community composition of particularly tropical fungi remain poorly understood. This study addresses shifts in community structure and species frequency of ectomycorrhizal (EcM) fungi in relation to host taxa, soil depth and spatial structure in four contrasting African ecosystems. We used the rDNA and plastid trnL intron sequence analysis for identification of fungi and host plants, respectively. By partitioning out spatial autocorrelation in plant and fungal distribution, we suggest that African EcM fungal communities are little structured by soil horizon and host at the plant species and family levels. These findings contrast with patterns of vegetation in these forests and EcM fungal communities in other tropical and temperate ecosystems. The low level of host preference indirectly supports an earlier hypothesis that pioneer Phyllanthaceae may facilitate the establishment of late successional Fabaceae and potentially other EcM host trees by providing compatible fungal inoculum in deforested and naturally disturbed ecosystems of tropical Africa.

  • 29. Tuda, Midori
    et al.
    Liljestrand Rönn, Johanna
    Uppsala universitet.
    Buranapanichpan, S.
    Wasano, N.
    Arnqvist, Göran
    Evolutionary diversification of the bean beetle genus Callosobruchus (Coleoptera: Bruchidae): Traits associated with stored-product pest status2006In: Molecular Ecology, ISSN 0962-1083, E-ISSN 1365-294X, Vol. 15, no 12, p. 3541-3551Article in journal (Refereed)
    Abstract [en]

    Despite the fact that many plant-feeding insects are pests, little effort has been paid to elucidating key evolutionary trait transitions that allow taxa to acquire or lose pest status. A large proportion of species in the genus Callosobruchus are economically important pests of stored, dry post-harvest beans of the tribe Phaseoleae. However, the evolution of this feeding habit is poorly understood. Here, we present a reconstruction of the phylogeny of the Asian and African Callosobruchus based on three mitochondrial genes, and assess which traits have been associated with the evolutionary origin or loss of ability to reproduce on dry beans. Our phylogenetic analysis showed that species group into the chinensis and the maculatus clades, which are also supported by genital morphology, and an additional paraphyletic group. Ancestral ability to use dry beans has been lost in the chinensis clade but acquired again in C. chinensis. Dry-bean use and host-plant use were both phylogenetically constrained and transitions in the two were significantly correlated. Host shifts from the subtribe Phaseolinae to Cajaninae were more common than the reverse and were more likely in species using young beans. Ability to use dry beans was more likely gained when using Phaseolinae hosts and promoted habitat shifts from tropical to temperate regions. Adaptation to arid climate was associated with ability to reproduce on dry beans and on Phaseolinae. Thus, our analysis suggests that physiological adaptations to arid season and to Phaseolinae hosts both render beetles predisposed to become pests of cultivated beans.

  • 30.
    Verschut, Vasiliki
    et al.
    Stockholm University, Faculty of Science, Department of Ecology, Environment and Plant Sciences.
    Strandmark, Alma
    Stockholm University, Faculty of Science, Department of Ecology, Environment and Plant Sciences.
    Esparza-Salas, Rodrigo
    Hambäck, Peter A.
    Stockholm University, Faculty of Science, Department of Ecology, Environment and Plant Sciences.
    Seasonally varying marine influences on the coastal ecosystem detected through molecular gut analysis2019In: Molecular Ecology, ISSN 0962-1083, E-ISSN 1365-294X, Vol. 28, no 2, p. 307-317Article in journal (Refereed)
    Abstract [en]

    Terrestrial predators on marine shores benefit from the inflow of organisms and matter from the marine ecosystem, often causing very high predator densities and indirectly affecting the abundance of other prey species on shores. This indirect effect may be particularly strong if predators shift diets between seasons. We therefore quantified the seasonal variation in diet of two wolf spider species that dominate the shoreline predator community, using molecular gut content analyses with general primers to detect the full prey range. Across the season, spider diets changed, with predominantly terrestrial prey from May until July and predominantly marine prey (mainly chironomids) from August until October. This pattern coincided with a change in the spider age and size structure, and prey abundance data and resource selection analyses suggest that the higher consumption of chironomids during autumn is due to an ontogenetic diet shift rather than to variation in prey abundance. The analyses suggested that small dipterans with a weak flight capacity, such as Chironomidae, Sphaeroceridae, Scatopsidae and Ephydridae, were overrepresented in the gut of small juvenile spiders during autumn, whereas larger, more robust prey, such as Lepidoptera, Anthomyidae and Dolichopodidae, were overrepresented in the diet of adult spiders during spring. The effect of the inflow may be that the survival and growth of juvenile spiders is higher in areas with high chironomid abundances, leading to higher densities of adult spiders and higher predation rates on the terrestrial prey next spring.

  • 31.
    Xenikoudakis, Georgios
    et al.
    Stockholm University, Faculty of Science, Department of Zoology. Swedish Museum of National History, Sweden.
    Ersmark, Erik
    Stockholm University, Faculty of Science, Department of Zoology. Swedish Museum of National History, Sweden.
    Tison, J. -L.
    Waits, L.
    Kindberg, J.
    Swenson, J. E.
    Dalén, Love
    Swedish Museum of National History, Sweden.
    Consequences of a demographic bottleneck on geneticstructure and variation in the Scandinavian brown bear2015In: Molecular Ecology, ISSN 0962-1083, E-ISSN 1365-294X, Vol. 24, no 13, p. 3441-3454Article in journal (Refereed)
    Abstract [en]

    The Scandinavian brown bear went through a major decline in population size approximately 100years ago, due to intense hunting. After being protected, the population subsequently recovered and today numbers in the thousands. The genetic diversity in the contemporary population has been investigated in considerable detail, and it has been shown that the population consists of several subpopulations that display relatively high levels of genetic variation. However, previous studies have been unable to resolve the degree to which the demographic bottleneck impacted the contemporary genetic structure and diversity. In this study, we used mitochondrial and microsatellite DNA markers from pre- and postbottleneck Scandinavian brown bear samples to investigate the effect of the bottleneck. Simulation and multivariate analysis suggested the same genetic structure for the historical and modern samples, which are clustered into three subpopulations in southern, central and northern Scandinavia. However, the southern subpopulation appears to have gone through a marked change in allele frequencies. When comparing the mitochondrial DNA diversity in the whole population, we found a major decline in haplotype numbers across the bottleneck. However, the loss of autosomal genetic diversity was less pronounced, although a significant decline in allelic richness was observed in the southern subpopulation. Approximate Bayesian computations provided clear support for a decline in effective population size during the bottleneck, in both the southern and northern subpopulations. These results have implications for the future management of the Scandinavian brown bear because they indicate a recent loss in genetic diversity and also that the current genetic structure may have been caused by historical ecological processes rather than recent anthropogenic persecution.

1 - 31 of 31
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