Logo: to the web site of Uppsala University

uu.sePublications from Uppsala University
Change search
Refine search result
1234567 51 - 100 of 4207
CiteExportLink to result list
Permanent link
Cite
Citation style
  • apa
  • ieee
  • modern-language-association
  • vancouver
  • Other style
More styles
Language
  • de-DE
  • en-GB
  • en-US
  • fi-FI
  • nn-NO
  • nn-NB
  • sv-SE
  • Other locale
More languages
Output format
  • html
  • text
  • asciidoc
  • rtf
Rows per page
  • 5
  • 10
  • 20
  • 50
  • 100
  • 250
Sort
  • Standard (Relevance)
  • Author A-Ö
  • Author Ö-A
  • Title A-Ö
  • Title Ö-A
  • Publication type A-Ö
  • Publication type Ö-A
  • Issued (Oldest first)
  • Issued (Newest first)
  • Created (Oldest first)
  • Created (Newest first)
  • Last updated (Oldest first)
  • Last updated (Newest first)
  • Disputation date (earliest first)
  • Disputation date (latest first)
  • Standard (Relevance)
  • Author A-Ö
  • Author Ö-A
  • Title A-Ö
  • Title Ö-A
  • Publication type A-Ö
  • Publication type Ö-A
  • Issued (Oldest first)
  • Issued (Newest first)
  • Created (Oldest first)
  • Created (Newest first)
  • Last updated (Oldest first)
  • Last updated (Newest first)
  • Disputation date (earliest first)
  • Disputation date (latest first)
Select
The maximal number of hits you can export is 250. When you want to export more records please use the Create feeds function.
  • 51.
    Alatalo, Juha M.
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Little, Chelsea J.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Simulated global change: contrasting short and medium term growth and reproductive responses of a common alpine/Arctic cushion plant to experimental warming and nutrient enhancement2014In: SpringerPlus, E-ISSN 2193-1801, Vol. 3, article id 157Article in journal (Refereed)
    Abstract [en]

    Cushion plants are important components of alpine and Arctic plant communities around the world. They fulfill important roles as facilitators, nurse plants and foundation species across trophic levels for vascular plants, arthropods and soil microorganisms, the importance of these functions increasing with the relative severity of the environment. Here we report results from one of the few experimental studies simulating global change impacts on cushion plants; a factorial experiment with warming and nutrient enhancement that was applied to an alpine population of the common nurse plant, Silene acaulis, in sub-arctic Sweden. Experimental perturbations had significant short-term impacts on both stem elongation and leaf length. S. acaulis responded quickly by increasing stem elongation and (to a lesser extent) leaf length in the warming, nutrient, and the combined warming and nutrient enhancements. Cover and biomass also initially increased in response to the perturbations. However, after the initial positive short-term responses, S. acaulis cover declined in the manipulations, with the nutrient and combined warming and nutrient treatments having largest negative impact. No clear patterns were found for fruit production. Our results show that S. acaulis living in harsh environments has potential to react quickly when experiencing years with favorable conditions, and is more responsive to nutrient enhancement than to warming in terms of vegetative growth. While these conditions have an initial positive impact, populations experiencing longer-term increased nutrient levels will likely be negatively affected.

    Download full text (pdf)
    fulltext
  • 52.
    Alatalo, Juha M.
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Little, Chelsea J.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Jagerbrand, Annika K.
    Molau, Ulf
    Dominance hierarchies, diversity and species richness of vascular plants in an alpine meadow: contrasting short and medium term responses to simulated global change2014In: PeerJ, E-ISSN 2167-8359, Vol. 2, p. e406-Article in journal (Refereed)
    Abstract [en]

    We studied the impact of simulated global change on a high alpine meadow plant community. Specifically, we examined whether short-term (5 years) responses are good predictors for medium-term (7 years) changes in the system by applying a factorial warming and nutrient manipulation to 20 plots in Latnjajaure, subarctic Sweden. Seven years of experimental warming and nutrient enhancement caused dramatic shifts in dominance hierarchies in response to the nutrient and the combined warming and nutrient enhancement treatments. Dominance hierarchies in the meadow moved from a community being dominated by cushion plants, deciduous, and evergreen shrubs to a community being dominated by grasses, sedges, and forbs. Short-termresponses were shown to be inconsistent in their ability to predict medium-term responses for most functional groups, however, grasses showed a consistent and very substantial increase in response to nutrient addition over the seven years. The non-linear responses over time point out the importance of longer-term studies with repeated measurements to be able to better predict future changes. Forecasted changes to temperature and nutrient availability have implications for trophic interactions, and may ultimately influence the access to and palatability of the forage for grazers. Depending on what anthropogenic change will be most pronounced in the future (increase in nutrient deposits, warming, or a combination of them both), different shifts in community dominance hierarchies may occur. Generally, this study supports the productivity-diversity relationship found across arctic habitats, with community diversity peaking in mid-productivity systems and degrading as nutrient availability increases further. This is likely due the increasing competition in plant-plant interactions and the shifting dominance structure with grasses taking over the experimental plots, suggesting that global change could have high costs to biodiversity in the Arctic.

    Download full text (pdf)
    fulltext
  • 53.
    Alatalo, Juha M.
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Little, Chelsea J.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Jagerbrand, Annika K.
    Molau, Ulf
    Vascular plant abundance and diversity in an alpine heath under observed and simulated global change2015In: Scientific Reports, E-ISSN 2045-2322, Vol. 5, article id 10197Article in journal (Refereed)
    Abstract [en]

    Global change is predicted to cause shifts in species distributions and biodiversity in arctic tundra. We applied factorial warming and nutrient manipulation to a nutrient and species poor alpine/arctic heath community for seven years. Vascular plant abundance in control plots increased by 31%. There were also notable changes in cover in the nutrient and combined nutrient and warming treatments, with deciduous and evergreen shrubs declining, grasses overgrowing these plots. Sedge abundance initially increased significantly with nutrient amendment and then declined, going below initial values in the combined nutrient and warming treatment. Nutrient addition resulted in a change in dominance hierarchy from deciduous shrubs to grasses. We found significant declines in vascular plant diversity and evenness in the warming treatment and a decline in diversity in the combined warming and nutrient addition treatment, while nutrient addition caused a decline in species richness. The results give some experimental support that species poor plant communities with low diversity may be more vulnerable to loss of species diversity than communities with higher initial diversity. The projected increase in nutrient deposition and warming may therefore have negative impacts on ecosystem processes, functioning and services due to loss of species diversity in an already impoverished environment.

    Download full text (pdf)
    fulltext
  • 54.
    Alatalo, Juha M.
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Ostapenko, Oksana V.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    The Swedish system: The image cracking when taking a closer look2014In: Geoforum, ISSN 0016-7185, E-ISSN 1872-9398, Vol. 53, p. 82-83Article, review/survey (Refereed)
    Abstract [en]

    Sweden has a high international profile regarding social issues and projects an image as one of the best countries in the world in terms of social indicators. Here we argue for a revised view as the reality is that Swedish system is very segregated, particularly in terms of (1) relative lack of women in positions of high influence, (2) it is the worst country in the EU28 regarding long-term unemployment for people born outside the country, and (3) it has a education system that after a number of reforms is involved in a "race towards the bottom" to profit from students. At the same time Sweden undervalues foreign academic qualifications and getting work largely depends on "who you know", not "what you know".

  • 55. Alatalo, R. V.
    et al.
    Eriksson, D.
    Gustafsson, Lars
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology.
    Larsson, K.
    EXPLOITATION COMPETITION INFLUENCES THE USE OF FORAGING SITES BY TITS - EXPERIMENTAL-EVIDENCE1987In: Ecology, Vol. 68, no 2, p. 284-290Article in journal (Refereed)
  • 56. Alatalo, R. V.
    et al.
    Eriksson, D.
    Gustafsson, Lars
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology.
    Larsson, K.
    Exploitation competition influences the use of foraging sites by tits: experimental evidence.1987In: Ecology, Vol. 68, no 2, p. 284-290Article in journal (Refereed)
  • 57. Alatalo, R. V.
    et al.
    Eriksson, D.
    Gustafsson, Lars
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology.
    Lundberg, A.
    HYBRIDIZATION BETWEEN PIED AND COLLARED FLYCATCHERS - SEXUAL SELECTION AND SPECIATION THEORY1990In: Journal of Evolutionary Biology, Vol. 3, no 5-6, p. 375-389Article in journal (Refereed)
  • 58. Alatalo, R. V.
    et al.
    Gustafsson, Lars
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology.
    GENETIC COMPONENT OF MORPHOLOGICAL-DIFFERENTIATION IN COAL TITS UNDER COMPETITIVE RELEASE1988In: Evolution, Vol. 42, no 1, p. 200-203Article in journal (Refereed)
  • 59. Alatalo, R. V.
    et al.
    Gustafsson, Lars
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology.
    Linden, M.
    Lundberg, A.
    INTERSPECIFIC COMPETITION AND NICHE SHIFTS IN TITS AND THE GOLDCREST - AN EXPERIMENT1985In: Journal of Animal Ecology, Vol. 54, no 3, p. 977-984Article in journal (Refereed)
  • 60. Alatalo, R. V.
    et al.
    Gustafsson, Lars
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology.
    Linden, M.
    Lundberg, A.
    Interspecific competition and niche shifts in tits and the goldcrest: an experiment.1985In: Journal of Animal Ecology, Vol. 54, no 3, p. 977-984Article in journal (Refereed)
  • 61. Alatalo, R. V.
    et al.
    Gustafsson, Lars
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology.
    Lundberg, A.
    Breeding success and hybridization of collared flycatcher Ficedula albicollis, and pied flycatcher, Ficedula hypoleuca on Oland 19811982In: Calidris, Vol. 11, no 2, p. 103-108Article in journal (Refereed)
  • 62. Alatalo, R. V.
    et al.
    Gustafsson, Lars
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology.
    Lundberg, A.
    ( Breeding success and hybridization of collared flycatcher, Ficedula albicollis, and pied flycatcher, Ficedula hypoleuca, on Oland 1981). | Hackningsframgang och forekomst av halsbandsflugsnappare Ficedula albicollis, svartvit flugsnappare Ficedula hypoleuca samt blandpar pa Oland 1981.1982In: Calidris, Vol. 2, no 82, p. 103-108Article in journal (Refereed)
  • 63. Alatalo, R. V.
    et al.
    Gustafsson, Lars
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology.
    Lundberg, A.
    DO FEMALES PREFER OLDER MALES IN POLYGYNOUS BIRD SPECIES1986In: American Naturalist, Vol. 127, no 2, p. 241-245Article in journal (Refereed)
  • 64. Alatalo, R. V.
    et al.
    Gustafsson, Lars
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology.
    Lundberg, A.
    EXTRA-PAIR PATERNITY AND HERITABILITY ESTIMATES OF TARSUS LENGTH IN PIED AND COLLARED FLYCATCHERS1989In: Oikos, Vol. 56, no 1, p. 54-58Article in journal (Refereed)
  • 65. Alatalo, R. V.
    et al.
    Gustafsson, Lars
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology.
    Lundberg, A.
    Extra-pair paternity and heritability estimates of tarsus length in pied and collared flycatchers1989In: Oikos, Vol. 56, no 1, p. 54-58Article in journal (Refereed)
  • 66. Alatalo, R. V.
    et al.
    Gustafsson, Lars
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology.
    Lundberg, A.
    High frequency of cuckoldry in pied and collared flycatchers.1984In: Oikos, Vol. 42, no 1, p. 41-47Article in journal (Refereed)
  • 67. Alatalo, R. V.
    et al.
    Gustafsson, Lars
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology.
    Lundberg, A.
    Hybridization and breeding success of collared and pied flycatchers on the island of Gotland.1982In: Auk, Vol. 99, no 2, p. 285-291Article in journal (Refereed)
  • 68. Alatalo, R. V.
    et al.
    Gustafsson, Lars
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology.
    Lundberg, A.
    HYBRIDIZATION AND BREEDING SUCCESS OF COLLARED AND PIED FLYCATCHERS ON THE ISLAND OF GOTLAND1982In: Auk, Vol. 99, no 2, p. 285-291Article in journal (Refereed)
  • 69. Alatalo, R. V.
    et al.
    Gustafsson, Lars
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology.
    Lundberg, A.
    Interspecific competition and niche changes in tits ( Parus spp.): evaluation of nonexperimental data.1986In: American Naturalist, Vol. 127, no 6, p. 819-834Article in journal (Refereed)
  • 70. Alatalo, R. V.
    et al.
    Gustafsson, Lars
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology.
    Lundberg, A.
    INTERSPECIFIC COMPETITION AND NICHE CHANGES IN TITS (PARUS SPP) - EVALUATION OF NONEXPERIMENTAL DATA1986In: American Naturalist, Vol. 127, no 6, p. 819-834Article in journal (Refereed)
  • 71. Alatalo, R. V.
    et al.
    Gustafsson, Lars
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology.
    Lundberg, A.
    MALE COLORATION AND SPECIES RECOGNITION IN SYMPATRIC FLYCATCHERS1994In: Proceedings of the Royal Society B-Biological Sciences, Vol. 256, no 1346, p. 113-118Article in journal (Refereed)
  • 72. Alatalo, R. V.
    et al.
    Gustafsson, Lars
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology.
    Lundberg, A.
    PHENOTYPIC SELECTION ON HERITABLE SIZE TRAITS - ENVIRONMENTAL VARIANCE AND GENETIC RESPONSE1990In: American Naturalist, Vol. 135, no 3, p. 464-471Article in journal (Refereed)
  • 73. Alatalo, R. V.
    et al.
    Gustafsson, Lars
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology.
    Lundberg, A.
    WHY DO YOUNG PASSERINE BIRDS HAVE SHORTER WINGS THAN OLDER BIRDS1984In: Ibis, Vol. 126, no 3, p. 410-415Article in journal (Refereed)
  • 74. Alatalo, R. V.
    et al.
    Gustafsson, Lars
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology.
    Lundberg, A.
    Ulfstrand, S.
    HABITAT SHIFT OF THE WILLOW TIT PARUS MONTANUS IN THE ABSENCE OF THE MARSH TIT PARUS PALUSTRIS1985In: Ornis Scandinavica, Vol. 16, no 2, p. 121-128Article in journal (Refereed)
  • 75. Alatalo, R. V.
    et al.
    Gustafsson, Lars
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology.
    Lundberg, A.
    Ulfstrand, S.
    Habitat shift of the willow tit Parus montanus in the absence of the marsh tit Parus palustris.1985In: Ornis Scandinavica, Vol. 16, no 2, p. 121-128Article in journal (Refereed)
  • 76.
    Alavioon, Ghazal
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics.
    Haploid selection in animals: Exploring the fitness consequences and underlying mechanisms2018Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    A consequence of sexual reproduction in eukaryotes is the evolution of a biphasic life cycle with alternating diploid and haploid gametic phases. While our focus in evolutionary biology is on selection during the diploid phase, we know relatively little about selection occurring during the haploid gametic stage. This is particularly true in predominantly diploid animals, where gene expression and hence selection have long been thought to be absent in haploid cells like gametes and particularly sperm. During my PhD, I tested the idea of selection during the haploid gametic phase using zebrafish Danio rario as a study species. I combined a large-scale selection experiment over three generations with fitness assays and next-generation sequencing to assess the importance of haploid selection. We measured offspring fitness in all three generations.  In addition, we compared gene expression in brain and testes of F1 and F3 adult male from each treatment by RNA sequencing. We found that offspring sired by longer-lived sperm showed higher survival rate and higher early- and late-life reproductive fitness compared to offspring sired by shorter-lived sperm. We also found differentially expressed genes between the two treatments with functions in metabolic and developmental pathways. These findings suggest that the observed fitness differences to be caused by small expression changes in many basic genes. We also tested for a genetic underpinning of the selected sperm phenotypes and identified allelic differences across the entire genome. Finally, we investigated the additive genetic component and parental effect of different sperm phenotypes. We found generally low additive genetic variation and high parental effects on sperm performance traits. In conclusion, this thesis provides evidence that the phenotypic variation among intact fertile sperm within an ejaculate affects offspring fitness throughout life and provides a clear link between sperm phenotype and offspring fitness and between sperm phenotype and sperm genotype.

    List of papers
    1. Haploid selection within a single ejaculate increases offspring fitness
    Open this publication in new window or tab >>Haploid selection within a single ejaculate increases offspring fitness
    Show others...
    2017 (English)In: Proceedings of the National Academy of Sciences of the United States of America, ISSN 0027-8424, E-ISSN 1091-6490, no 30, p. 8053-8058Article in journal (Refereed) Published
    Abstract [en]

    An inescapable consequence of sex in eukaryotes is the evolution of a biphasic life cycle with alternating diploid and haploid phases. The occurrence of selection during the haploid phase can have far-reaching consequences for fundamental evolutionary processes including the rate of adaptation, the extent of inbreeding depression, and the load of deleterious mutations, as well as for applied research into fertilization technology. Although haploid selection is well established in plants, current dogma assumes that in animals, intact fertile sperm within a single ejaculate are equivalent at siring viable offspring. Using the zebrafish Danio rerio, we show that selection on phenotypic variation among intact fertile sperm within an ejaculate affects offspring fitness. Longer-lived sperm sired embryos with increased survival and a reduced number of apoptotic cells, and adult male offspring exhibited higher fitness. The effect on embryo viability was carried over into the second generation without further selection and was equally strong in both sexes. Sperm pools selected by motile phenotypes differed genetically at numerous sites throughout the genome. Our findings clearly link within-ejaculate variation in sperm phenotype to offspring fitness and sperm genotype in a vertebrate and have major implications for adaptive evolution.

    National Category
    Evolutionary Biology
    Identifiers
    urn:nbn:se:uu:diva-320335 (URN)10.1073/pnas.1705601114 (DOI)000406189900080 ()28698378 (PubMedID)
    Funder
    Swedish Research CouncilEU, European Research Council
    Available from: 2017-04-19 Created: 2017-04-19 Last updated: 2022-01-29Bibliographically approved
    2. Within-ejaculate selection for sperm longevity reduces male reproductive ageing
    Open this publication in new window or tab >>Within-ejaculate selection for sperm longevity reduces male reproductive ageing
    Show others...
    (English)Manuscript (preprint) (Other academic)
    Abstract [en]

    Males produce numerous sperm in the single ejaculate that greatly outnumber their potential egg targets. Recent studies found that phenotypic variation among sperm in the single ejaculate of a male reflects the phenotype and the genotype of the resulting offspring. Specifically, within-ejaculate sperm selection (WESS) for sperm longevity increased the performance of the resulting offspring in several key life-history traits in early-life. Because increased early-life reproductive performance often correlates with rapid ageing, it is possible that WESS increases early-life fitness at the cost of accelerated senescence. Alternatively, WESS can improve offspring quality throughout the life cycle, including reduced age-specific deterioration. We found that WESS for sperm longevity reduced age-specific deterioration of male fertility and embryo survival, while there is no effect on fertilization success. Remarkably, we found opposing effect of WESS on female fecundity, where selection for sperm longevity resulted in increased early-life performance followed by a slow decline, while unselected controls started low but increased their fecundity with age. Intriguingly, WESS also reduced the age-specific decline in fertilization success in females, suggesting that selection for sperm longevity improves at least some aspects of female reproductive ageing. These results demonstrate that within-ejaculate variation in sperm phenotype contributes to individual variation in animal life histories in the two sexes and have important implications for assisted fertilization programs in livestock and humans. 

    Keywords
    Ageing, Reproductive Success, Sperm Selection, Sperm Competition, Senescence
    National Category
    Evolutionary Biology
    Research subject
    Biology with specialization in Evolutionary Genetics
    Identifiers
    urn:nbn:se:uu:diva-350186 (URN)
    Available from: 2018-05-07 Created: 2018-05-07 Last updated: 2018-05-07
    3. The fitness consequences of selection among sperm within an ejaculate across generations
    Open this publication in new window or tab >>The fitness consequences of selection among sperm within an ejaculate across generations
    (English)Manuscript (preprint) (Other academic)
    Abstract [en]

    The evolution of a biphasic life cycle with alternating diploid and haploid phases is a necessary consequence of sexual reproduction in eukaryotes. Selection in each of the phases may have far reaching consequences for many evolutionary processes. While our focus in evolutionary biology lies mainly on selection during the diploid phase, we know relatively little about the role and consequences of selection occurring during the haploid gametic stage. This is particularly true in predominantly diploid animals where the haploid gametic phase is very short. To test the importance of haploid selection in animals, we performed a large-scale selection experiment with selection acting on haploid sperm. We selected on sperm longevity within an ejaculate and tested the effects of such selection over three generation. We performed fitness assays for every generation and found that offspring sired by longer-lived sperm generally exhibit higher fitness from early development into adulthood compared to offspring sired by their shorter-lived sibling sperm in all three generations. These fitness effects were carried over into the second generation without further selection in all three generations. Moreover, using RNA sequencing, we assessed differences in tissue specific gene expression between the offspring sired by the two sperm phenotypes in generation F1 and F3. The transcriptomes in both tissues differed significantly between the two treatments. Many very basic housekeeping genes involved in metabolism and development showed small differences in expression in both tissues. Our study provides solid evidence for the far-reaching consequences of selection on different sperm within a single ejaculate in three consecutive generations, and offers exciting new insights into the possible underlying mechanisms. Our results further highlight the importance of selection at the haploid gametic stages for fundamental evolutionary processes and assisted fertilization technologies.

    Keywords
    Haploid selection, sperm selection, offspring fitness, gene expression
    National Category
    Evolutionary Biology
    Research subject
    Biology with specialization in Evolutionary Genetics
    Identifiers
    urn:nbn:se:uu:diva-350190 (URN)
    Available from: 2018-05-07 Created: 2018-05-07 Last updated: 2018-05-07
    4. Sperm performance traits exhibit low additive genetic component and strong parental effects in external fertilizer
    Open this publication in new window or tab >>Sperm performance traits exhibit low additive genetic component and strong parental effects in external fertilizer
    (English)Manuscript (preprint) (Other academic)
    Abstract [en]

    Despite their key role in determining reproductive success and with that Darwinian fitness, the heritability and underlying additive genetic variance of reproductive traits is still not fully understood. While some traits show relatively high genetic variance, others show very low genetic variance, which is particularly true for complex non-morphological traits. In line with these general patterns, morphological sperm traits show surprisingly high heritability, whereas heritability reported for sperm quality and performance traits generally is lower. A possible explanation for this is the general notion that more fitness related traits show lower levels of additive genetic variance and heritability. We investigated the additive genetic variance and heritability of sperm swimming velocity, the percentage of motile sperm, sperm concentration in the ejaculate and sperm longevity in the externally fertilizing zebrafish Danio rerio. All sperm traits showed low but significant additive genetic variance and high parental components. While the additive genetic variance was significant it was lower than reported in many other studies. A possible explanation for this is that in externally fertilizing species, sperm traits are the prime determinant of fertilization success and high plasticity is crucial for swift adaptations to changes in the environmental conditions such as competition but also water temperature and currents. Given that this is the first study looking into the heritability of sperm traits in an external fertilizer it will be interesting to understand, whether this is true for other externally fertilizing species and taxa.

    Keywords
    additive genetic, parental effect, sperm traits, reproduction
    National Category
    Evolutionary Biology
    Research subject
    Biology with specialization in Evolutionary Genetics
    Identifiers
    urn:nbn:se:uu:diva-350191 (URN)
    Available from: 2018-05-07 Created: 2018-05-07 Last updated: 2018-06-01
    Download full text (pdf)
    fulltext
    Download (jpg)
    presentationsbild
  • 77.
    Alavioon, Ghazal
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics.
    Baños-Villalba, Adrian
    University Pablo de Olavide, Ctra.
    Schielzeth, Holger
    Friedrich Schiller University Jena.
    Immler, Simone
    University of East Anglia.
    Sperm performance traits exhibit low additive genetic component and strong parental effects in external fertilizerManuscript (preprint) (Other academic)
    Abstract [en]

    Despite their key role in determining reproductive success and with that Darwinian fitness, the heritability and underlying additive genetic variance of reproductive traits is still not fully understood. While some traits show relatively high genetic variance, others show very low genetic variance, which is particularly true for complex non-morphological traits. In line with these general patterns, morphological sperm traits show surprisingly high heritability, whereas heritability reported for sperm quality and performance traits generally is lower. A possible explanation for this is the general notion that more fitness related traits show lower levels of additive genetic variance and heritability. We investigated the additive genetic variance and heritability of sperm swimming velocity, the percentage of motile sperm, sperm concentration in the ejaculate and sperm longevity in the externally fertilizing zebrafish Danio rerio. All sperm traits showed low but significant additive genetic variance and high parental components. While the additive genetic variance was significant it was lower than reported in many other studies. A possible explanation for this is that in externally fertilizing species, sperm traits are the prime determinant of fertilization success and high plasticity is crucial for swift adaptations to changes in the environmental conditions such as competition but also water temperature and currents. Given that this is the first study looking into the heritability of sperm traits in an external fertilizer it will be interesting to understand, whether this is true for other externally fertilizing species and taxa.

  • 78.
    Alavioon, Ghazal
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics.
    Cabrera, Andrea
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics.
    LeChatelier, Magali
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics.
    Maklakov, Alexei A.
    University of East Anglia.
    Immler, Simone
    University of East Anglia.
    Within-ejaculate selection for sperm longevity reduces male reproductive ageingManuscript (preprint) (Other academic)
    Abstract [en]

    Males produce numerous sperm in the single ejaculate that greatly outnumber their potential egg targets. Recent studies found that phenotypic variation among sperm in the single ejaculate of a male reflects the phenotype and the genotype of the resulting offspring. Specifically, within-ejaculate sperm selection (WESS) for sperm longevity increased the performance of the resulting offspring in several key life-history traits in early-life. Because increased early-life reproductive performance often correlates with rapid ageing, it is possible that WESS increases early-life fitness at the cost of accelerated senescence. Alternatively, WESS can improve offspring quality throughout the life cycle, including reduced age-specific deterioration. We found that WESS for sperm longevity reduced age-specific deterioration of male fertility and embryo survival, while there is no effect on fertilization success. Remarkably, we found opposing effect of WESS on female fecundity, where selection for sperm longevity resulted in increased early-life performance followed by a slow decline, while unselected controls started low but increased their fecundity with age. Intriguingly, WESS also reduced the age-specific decline in fertilization success in females, suggesting that selection for sperm longevity improves at least some aspects of female reproductive ageing. These results demonstrate that within-ejaculate variation in sperm phenotype contributes to individual variation in animal life histories in the two sexes and have important implications for assisted fertilization programs in livestock and humans. 

  • 79.
    Alavioon, Ghazal
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Garcia, Andrea Cabrera
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    LeChatelier, Magali
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Maklakov, Alex A.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology. Univ East Anglia, Sch Biol Sci, Norwich Res Pk, Norwich, Norfolk, England.
    Immler, Simone
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology. Univ East Anglia, Sch Biol Sci, Norwich Res Pk, Norwich, Norfolk, England.
    Selection for longer lived sperm within ejaculate reduces reproductive ageing in offspring2019In: Evolution Letters, E-ISSN 2056-3744, Vol. 3, no 2, p. 198-206Article in journal (Refereed)
    Abstract [en]

    Males produce numerous sperm in a single ejaculate that greatly outnumber their potential egg targets. Recent studies found that phenotypic and genotypic variation among sperm in a single ejaculate of a male affects the fitness and performance of the resulting offspring. Specifically, within-ejaculate sperm selection for sperm longevity increased the performance of the resulting offspring in several key life-history traits in early life. Because increased early-life reproductive performance often correlates with rapid ageing, it is possible that within-ejaculate sperm selection increases early-life fitness at the cost of accelerated senescence. Alternatively, within-ejaculate sperm selection could improve offspring quality throughout the life cycle, including reduced age-specific deterioration. We tested the two alternative hypotheses in an experimental setup using zebrafish Danio rerio. We found that within-ejaculate sperm selection for sperm longevity reduced age-specific deterioration of fecundity and offspring survival but had no effect on fertilization success in males. Remarkably, we found an opposing effect of within-ejaculate sperm selection on female fecundity, where selection for sperm longevity resulted in increased early-life performance followed by a slow decline, while females sired by unselected sperm started low but increased their fecundity with age. Intriguingly, within-ejaculate sperm selection also reduced the age-specific decline in fertilization success in females, suggesting that selection for sperm longevity improves at least some aspects of female reproductive ageing. These results demonstrate that within-ejaculate variation in sperm phenotype contributes to individual variation in animal life histories in the two sexes and may have important implications for assisted fertilization programs in livestock and humans.

    Download full text (pdf)
    fulltext
  • 80.
    Alavioon, Ghazal
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Hotzy, Cosima
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Nakhro, Khriezhanuo
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Rudolf, Sandra
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Scofield, Douglas
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Zajitschek, Susanne
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology. Spanish Natl Res Council, Donana Biol Stn, Seville 41092, Spain.
    Maklakov, Alex A
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology. Univ East Anglia, Sch Biol Sci, Norwich NR4 7TJ, Norfolk, England.
    Immler, Simone
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology. Univ East Anglia, Sch Biol Sci, Norwich NR4 7TJ, Norfolk, England.
    Haploid selection within a single ejaculate increases offspring fitness2017In: Proceedings of the National Academy of Sciences of the United States of America, ISSN 0027-8424, E-ISSN 1091-6490, no 30, p. 8053-8058Article in journal (Refereed)
    Abstract [en]

    An inescapable consequence of sex in eukaryotes is the evolution of a biphasic life cycle with alternating diploid and haploid phases. The occurrence of selection during the haploid phase can have far-reaching consequences for fundamental evolutionary processes including the rate of adaptation, the extent of inbreeding depression, and the load of deleterious mutations, as well as for applied research into fertilization technology. Although haploid selection is well established in plants, current dogma assumes that in animals, intact fertile sperm within a single ejaculate are equivalent at siring viable offspring. Using the zebrafish Danio rerio, we show that selection on phenotypic variation among intact fertile sperm within an ejaculate affects offspring fitness. Longer-lived sperm sired embryos with increased survival and a reduced number of apoptotic cells, and adult male offspring exhibited higher fitness. The effect on embryo viability was carried over into the second generation without further selection and was equally strong in both sexes. Sperm pools selected by motile phenotypes differed genetically at numerous sites throughout the genome. Our findings clearly link within-ejaculate variation in sperm phenotype to offspring fitness and sperm genotype in a vertebrate and have major implications for adaptive evolution.

  • 81.
    Alavioon, Ghazal
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics.
    Roy M, Francis
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics.
    Wyszkowska, Julia
    Jagiellonian University.
    Immler, Simone
    University of East Anglia.
    The fitness consequences of selection among sperm within an ejaculate across generationsManuscript (preprint) (Other academic)
    Abstract [en]

    The evolution of a biphasic life cycle with alternating diploid and haploid phases is a necessary consequence of sexual reproduction in eukaryotes. Selection in each of the phases may have far reaching consequences for many evolutionary processes. While our focus in evolutionary biology lies mainly on selection during the diploid phase, we know relatively little about the role and consequences of selection occurring during the haploid gametic stage. This is particularly true in predominantly diploid animals where the haploid gametic phase is very short. To test the importance of haploid selection in animals, we performed a large-scale selection experiment with selection acting on haploid sperm. We selected on sperm longevity within an ejaculate and tested the effects of such selection over three generation. We performed fitness assays for every generation and found that offspring sired by longer-lived sperm generally exhibit higher fitness from early development into adulthood compared to offspring sired by their shorter-lived sibling sperm in all three generations. These fitness effects were carried over into the second generation without further selection in all three generations. Moreover, using RNA sequencing, we assessed differences in tissue specific gene expression between the offspring sired by the two sperm phenotypes in generation F1 and F3. The transcriptomes in both tissues differed significantly between the two treatments. Many very basic housekeeping genes involved in metabolism and development showed small differences in expression in both tissues. Our study provides solid evidence for the far-reaching consequences of selection on different sperm within a single ejaculate in three consecutive generations, and offers exciting new insights into the possible underlying mechanisms. Our results further highlight the importance of selection at the haploid gametic stages for fundamental evolutionary processes and assisted fertilization technologies.

  • 82. Alberts, Susan C.
    et al.
    Altmann, Jeanne
    Brockman, Diane K.
    Cords, Marina
    Fedigan, Linda M.
    Pusey, Anne
    Stoinski, Tara S.
    Strier, Karen B.
    Morris, William F.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Bronikowski, Anne M.
    Reproductive aging patterns in primates reveal that humans are distinct2013In: Proceedings of the National Academy of Sciences of the United States of America, ISSN 0027-8424, E-ISSN 1091-6490, Vol. 110, no 33, p. 13440-13445Article in journal (Refereed)
    Abstract [en]

    Women rarely give birth after similar to 45 y of age, and they experience the cessation of reproductive cycles, menopause, at similar to 50 y of age after a fertility decline lasting almost two decades. Such reproductive senescence in mid-lifespan is an evolutionary puzzle of enduring interest because it should be inherently disadvantageous. Furthermore, comparative data on reproductive senescence from other primates, or indeed other mammals, remains relatively rare. Here we carried out a unique detailed comparative study of reproductive senescence in seven species of nonhuman primates in natural populations, using long-term, individual-based data, and compared them to a population of humans experiencing natural fertility and mortality. In four of seven primate species we found that reproductive senescence occurred before death only in a small minority of individuals. In three primate species we found evidence of reproductive senescence that accelerated throughout adulthood; however, its initial rate was much lower than mortality, so that relatively few individuals experienced reproductive senescence before death. In contrast, the human population showed the predicted and well-known pattern in which reproductive senescence occurred before death for many women and its rate accelerated throughout adulthood. These results provide strong support for the hypothesis that reproductive senescence in midlife, although apparent in natural-fertility, natural-mortality populations of humans, is generally absent in other primates living in such populations.

  • 83.
    Aleix-Mata, Gael
    et al.
    Jaen Univ, Dept Expt Biol, E-23071 Jaen, Spain.;Jaen Univ, Dept Anim & Plant Biol & Ecol, E-23071 Jaen, Spain..
    Exposito, Miriam
    Jaen Univ, Dept Expt Biol, E-23071 Jaen, Spain..
    Ruiz-Ruano, Francisco J.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology. Granada Univ, Fac Sci, Dept Genet, E-18071 Granada, Spain..
    Maria Lopez-Beceiro, Ana
    Univ Santiago de Compostela, Dept Anat Anim Prod & Vet Clin Sci, E-27002 Lugo, Spain..
    Fidalgo, Luis E.
    Univ Santiago de Compostela, Dept Anat Anim Prod & Vet Clin Sci, E-27002 Lugo, Spain..
    Martinez-Carrasco, Carlos
    Murcia Univ, Dept Anim Hlth, E-30100 Murcia, Spain..
    Ruiz de Ybanez, Maria Rocio
    Murcia Univ, Dept Anim Hlth, E-30100 Murcia, Spain..
    Boos, Mathieu
    Naturaconst, Res Agcy Appl Ecol, F-67270 Wilshausen, France.;Federat Natl Chasseurs, Pole Sci, 13 Rue Gen Leclerc, F-92136 Issy Les Moulineaux, France..
    Perez, Jesus M.
    Jaen Univ, Dept Anim & Plant Biol & Ecol, E-23071 Jaen, Spain.;Wildlife Ecol & Hlth Grp WE&H, Barcelona, Spain..
    Sanchez, Antonio
    Jaen Univ, Dept Expt Biol, E-23071 Jaen, Spain..
    Development and characterization of 15 novel polymorphic microsatellite loci for two important bot flies (Diptera, Oestridae) by next-generation sequencing2020In: Parasitology Research, ISSN 0932-0113, E-ISSN 1432-1955, Vol. 119, no 9, p. 2829-2835Article in journal (Refereed)
    Abstract [en]

    Cephenemyia stimulatorandOestrus ovisare two important parasitic bot flies (Oestridae) species causing myiasis, with a potential negative impact on the welfare of the host. Using next-generation sequencing approach and bioinformatics tools, a large panel of possible microsatellites loci was obtained in both species. Primer pairs were designed for 15 selected microsatellite loci inC. stimulatorand other 15 loci inO. ovisfor PCR amplification. Loci amplification and analysis were performed in four populations of each species. The results demonstrated that all selected loci were polymorphic, with the number of alleles ranging from 2 to 6 per locus inC. stimulatorand 3 to 13 per locus inO. ovis. This is the first time to describe these microsatellite loci forC. stimulatorandO. ovis. These two sets of microsatellite markers could be further used for biogeographic and population genetics studies.

  • 84.
    Alessi, Nicola
    et al.
    Free Univ Bozen Bolzano, Fac Sci & Technol, Bozen Bolzano, Italy.
    Tesitel, Jakub
    Masaryk Univ, Dept Bot, Brno, Czech Republic.
    Zerbe, Stefan
    Free Univ Bozen Bolzano, Fac Sci & Technol, Bozen Bolzano, Italy.
    Spada, Francesco
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution. Sapienza Univ Roma, Dept Environm Biol, Rome, Italy.
    Agrillo, Emiliano
    Sapienza Univ Roma, Dept Environm Biol, Rome, Italy.
    Wellstein, Camilla
    Free Univ Bozen Bolzano, Fac Sci & Technol, Bozen Bolzano, Italy.
    Ancient refugia and present-day habitat suitability of native laurophylls in Italy2019In: Journal of Vegetation Science, ISSN 1100-9233, E-ISSN 1654-1103, Vol. 30, no 3, p. 564-574Article in journal (Refereed)
    Abstract [en]

    Questions European native laurophyllous species are interesting for their biogeography and evolutionary history, as well as for their responses to global changes. We identified Italian native laurophylls on the basis of morphology, biogeographical history and ecological niche to study whether these species are in equilibrium with the present-day climate. Furthermore, we localized Quaternary refugia and areas of potential spread of native laurophylls using distribution patterns of realized and potential aggregations of native laurophylls, respectively. Location Italy. Methods We extracted data for 17 087 forest plots from a phytosociological database. Detrended Correspondence Analysis of these plots with overlay of climatic and environmental variables was performed to identify native laurophylls, i.e., evergreen broad-leaved species of late Tertiary radiation, occupying a warm and humid niche. Potential ranges of laurophylls were calculated using Beals' index of sociological favourability. The realized/potential range-size ratio was calculated for each single laurophyll to understand whether it is in equilibrium with the present-day climate. Distribution patterns of realized and potential aggregations of laurophylls were mapped. Results Ordination analysis provided a selection of 11 species as Italian native laurophylls. Most of them occupied less than half of their estimated potential range. Realized aggregations richest in native laurophylls were localized in the central Apennines. However, the Italian forests showed high potential for native laurophylls with the richest potential aggregations in the whole Apennines and in the southern Alps. Conclusions Most of the Italian native laurophylls showed non-equilibrium with the current climate, suggesting that late-Quaternary events could better explain their present-day distribution than on-going climate change. Furthermore, their refugia in central Italy suggest the persistence in sites with temperate climate during Quaternary environmental changes. The high suitability of Italian forests for laurophylls, along with global changes, suggests possible future spreading of these species.

  • 85.
    Alessi, Nicola
    et al.
    Free Univ Bozen Bolzano, Fac Sci & Technol, Pzza Univ 5, I-39100 Bozen Bolzano, Italy.
    Wellstein, Camilla
    Free Univ Bozen Bolzano, Fac Sci & Technol, Pzza Univ 5, I-39100 Bozen Bolzano, Italy.
    Spada, Francesco
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution. Sapienza Univ Roma, Dept Environm Biol, Lgo Cristina di Svezia 24, I-00165 Rome.
    Zerbe, Stefan
    Free Univ Bozen Bolzano, Fac Sci & Technol, Pzza Univ 5, I-39100 Bozen Bolzano, Italy.
    Phytocoenological approach to the ecology of Laurus nobilis L. in Italy2018In: Rendiconti Lincei SCIENZE FISICHE E NATURALI, ISSN 2037-4631, E-ISSN 1720-0776, Vol. 29, no 2, p. 343-354Article in journal (Refereed)
    Abstract [en]

    Laurus nobilis L. (Laurel) is considered one of the most emblematic epigones of the late-Tertiary laurophyllous biome, persisting within the Mediterranean vegetation. Describing its present ecology and coenology is crucial to understand its biogeographical history as well as to develop consistent conservation and management practices in the context of the European Habitat Directive. We used recently available vegetation and environmental databases to investigate the coenological amplitude of Laurus in Italy, and to elucidate significant aspects of its persistence in the country. The coenological amplitude was assessed using the clustering method. Ordination techniques and regression trees were used to understand which environmental factors influence, respectively, the occurrence and the abundance of the species and, therefore, characterize its niche. Our results show a wide coenological amplitude of Laurus with respect to other laurophyllous species, growing within a wide range of forest communities. While the occurrence of the species is limited by winter temperature and favored by precipitation seasonality, changes in its abundance show a more refined pattern. In this latter case, two main groups of Laurus populations were differentiated based on water availability. The first group depends on abundant precipitations during the year while the second one buffers the summer aridity with soils rich in nutrients and moisture. Our findings provide crucial knowledge on Laurus habitats in Italy. However, discrepancies between our results and guidelines of the European Habitat Directive arose. The results presented here allow scientifically sound procedures for the regional conservation and management program.

  • 86.
    Alessi, Nicola
    et al.
    Free Univ Bozen Bolzano, Fac Sci & Technol, Bolzano, Italy.;Univ Bologna, Dept Biol Geol & Environm Sci, Geol & Environm Sci, Biodivers & Macroecol Grp,Alma Mater Studiorum, Via Irnerio 42, I-40126 Bologna, Italy..
    Wellstein, Camilla
    Free Univ Bozen Bolzano, Fac Sci & Technol, Bolzano, Italy..
    Spada, Francesco
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Zerbe, Stefan
    Free Univ Bozen Bolzano, Fac Sci & Technol, Bolzano, Italy..
    Population structure of Laurus nobilis L. in Central Italian forests: evidence for its ongoing expansion2021In: Rendiconti Lincei SCIENZE FISICHE E NATURALI, ISSN 2037-4631, E-ISSN 1720-0776, Vol. 32, p. 365-376Article in journal (Refereed)
    Abstract [en]

    During the last decades, an ongoing spread of broad-leaved evergreen laurophyllous species has been reported for forests of Southern Europe. Several factors were suggested as the main drivers of the phenomenon, namely global warming, land-use change, evolutionary history, and increase in atmospheric CO2. Among laurophylls, Laurus nobilis L. is considered one of the most prominent from the morphological, evolutionary, and ecological point of view. We studied the population structure of L. nobilis in Central Italy in its natural habitat to investigate its regeneration and potential expansion along with the influence biotic and abiotic factors. To define types of population structures, we collected proportions of six growth classes of L. nobilis in 16 sites. We obtained three types of population structure, i.e., (1) stable, (2) dynamic, and (3) regressive. The first two types are the most frequent, suggesting a potential increase of L. nobilis abundance within forests of Central Italy. The regressive population type occurs mainly in sites with heavy ungulate impact. High propagule pressure along with shaded and moist environmental conditions favor L. nobilis regeneration. Accordingly, we found evidence of a recent L. nobilis spread in Central Italian forests. We suggest the increase of forest cover and age, due to the abandonment of traditional rural practices, as key factors for the regeneration of this apparently late-successional laurophyll. In conclusion, the recent expansion of L. nobilis that we observed in the Italian forest stands can therefore be ascribed to a process of natural recover of a potential niche following land-use change.

    Download full text (pdf)
    FULLTEXT01
  • 87. Alho, J. S.
    et al.
    Herczeg, G.
    Laugen, A. T.
    Raesaenen, K.
    Laurila, Anssi
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Population and Conservation Biology.
    Merila, J.
    Allen's rule revisited: quantitative genetics of extremity length in the common frog along a latitudinal gradient2011In: Journal of Evolutionary Biology, ISSN 1010-061X, E-ISSN 1420-9101, Vol. 24, no 1, p. 59-70Article in journal (Refereed)
    Abstract [en]

    Ecogeographical rules linking climate to morphology have gained renewed interest because of climate change. Yet few studies have evaluated to what extent geographical trends ascribed to these rules have a genetic, rather than environmentally determined, basis. This applies especially to Allen's rule, which states that the relative extremity length decreases with increasing latitude. We studied leg length in the common frog (Rana temporaria) along a 1500 km latitudinal gradient utilizing wild and common garden data. In the wild, the body size-corrected femur and tibia lengths did not conform to Allen's rule but peaked at mid-latitudes. However, the ratio of femur to tibia length increased in the north, and the common garden data revealed a genetic cline consistent with Allen's rule in some trait and treatment combinations. While selection may have shortened the leg length in the north, the genetic trend seems to be partially masked by environmental effects.

  • 88. Ali El Hadi Mohamed, Rania
    et al.
    Abdelgadir, Deena M.
    Bashab, Hind M.
    Al-Shuraym, Laila A.
    Sfouq Aleanizy, Fadilah
    Alqahtani, Fulwah Y.
    Ahmed Al-Keridis, Lamya
    Mohamed, Nahla
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology. Princess Nourah Bint Abdurrahman University.
    First record of West Nile Virus detection inside wild mosquitoes in Khartoum capital of Sudan using PCR2020In: Saudi Journal of Biological Sciences, ISSN 1319-562X, Vol. 27, no 12, p. 3359-3364Article in journal (Refereed)
    Abstract [en]

    This study aimed to explore the presence of West Nile Virus (WNV) inside four species of mosquitoes: Culex univittatus (Theobald), Culex quinquefasciatus (Say) Aedes vittatus (Bigot) and Aedes vexans (Meigen). Adult wild mosquitoes were collected from different sites: Soba West, Hellat Kuku, Shambat, and Khartoum North Central Live Stock Market (KCLM). Surveys were carried out at Khartoum State during two phases: pre to the rainy season and post to the rainy season. Mosquito specimens were identified using classical keys then preserved at −80 °C freezer for two weeks till the virus examination using polymerase chain reaction (PCR) were carried out. WNV has been detected inside the three species of mosquitoes: A. vexans, C. univittatus, and C. quinquefasciatus. The species were collected from Hellat Kuku, (Shambat and Hellat Kuku), and (Shambat and KCLM) respectively. Two species of mosquitoes were positive for the virus: C. quinquefasciatus and C. univittatus. Positive results for the virus during the first phase of the study; males of C. quinquefasciatus and C. univittatus collected during the second phase of the study were also tested for the existence of the virus and they were positive. For our knowledge this study represents first record of WNV inside wild mosquitoes in Sudan. PCR technique provided reliable information because specific primer-probe sets were used for the detection of the virus. Extra studies are required to incriminate these species of mosquitoes as potential vectors of WNV.

    Download full text (pdf)
    fulltext
  • 89.
    Ali, Raja Hashim
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Bogusz, Marcin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Whelan, Simon
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    A graph-based approach for improving the homologyinference in multiple sequence alignmentsManuscript (preprint) (Other academic)
    Abstract [en]

    Multiple sequence alignment (MSA) is ubiquitous in evolutionary studies and other areas ofbioinformatics. In nearly all cases MSAs are taken to be a known and xed quantity on which toperform downstream analysis despite extensive evidence that MSA accuracy and uncertainty aectsresults. Mistakes in the MSA are known to cause a wide range of problems for downstream evolutionaryinference, ranging from false inference of positive selection to long branch attraction artifacts. The mostpopular approach to dealing with this problem is to remove (lter) specic columns in the MSA thatare thought to be prone to error, either through proximity to gaps or through some scoring function.Although popular, this approach has had mixed success and several studies have even suggested thatltering might be detrimental to phylogenetic studies. Here we present a dierent approach to dealingwith MSA accuracy and uncertainty through a graph-based approach implemented in the freely availablesoftware Divvier. The aim of Divvier is to identify clusters of characters that have strong statisticalevidence of shared homology, based on the output of a pair hidden Markov model. These clusters canthen be used to either lter characters out the MSA, through a process we call partial ltering, or torepresent each of the clusters in a new column, through a process we call divvying up. We validateour approach through its performance on real and simulated benchmarks, nding Divvier substantiallyoutperforms all other ltering software for treating MSAs by retaining more true positive homology callsand removing more false positive homology calls. We also nd that Divvier, in contrast to other lteringtools, can alleviate long branch attraction artifacts induced by MSA and reduces the variation in treeestimates caused by MSA uncertainty.

  • 90.
    Ali, Raja Hashim
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology. Ghulam Ishaq Khan Inst Engn Sci & Technol, Fac Comp Sci & Engn, Topi, Pakistan.
    Bogusz, Marcin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Whelan, Simon
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Identifying Clusters of High Confidence Homologies in Multiple Sequence Alignments2019In: Molecular biology and evolution, ISSN 0737-4038, E-ISSN 1537-1719, Vol. 36, no 10, p. 2340-2351Article in journal (Refereed)
    Abstract [en]

    Multiple sequence alignment (MSA) is ubiquitous in evolution and bioinformatics. MSAs are usually taken to be a known and fixed quantity on which to perform downstream analysis despite extensive evidence that MSA accuracy and uncertainty affect results. These errors are known to cause a wide range of problems for downstream evolutionary inference, ranging from false inference of positive selection to long branch attraction artifacts. The most popular approach to dealing with this problem is to remove (filter) specific columns in the MSA that are thought to be prone to error. Although popular, this approach has had mixed success and several studies have even suggested that filtering might be detrimental to phylogenetic studies. We present a graph-based clustering method to address MSA uncertainty and error in the software Divvier (available at https://github.com/simonwhelan/Divvier), which uses a probabilistic model to identify clusters of characters that have strong statistical evidence of shared homology. These clusters can then be used to either filter characters from the MSA (partial filtering) or represent each of the clusters in a new column (divvying). We validate Divvier through its performance on real and simulated benchmarks, finding Divvier substantially outperforms existing filtering software by retaining more true pairwise homologies calls and removing more false positive pairwise homologies. We also find that Divvier, in contrast to other filtering tools, can alleviate long branch attraction artifacts induced by MSA and reduces the variation in tree estimates caused by MSA uncertainty.

    Download full text (pdf)
    fulltext
  • 91. Allen, James E.
    et al.
    Whelan, Simon
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Assessing the State of Substitution Models Describing Noncoding RNA Evolution2014In: Genome Biology and Evolution, ISSN 1759-6653, E-ISSN 1759-6653, Vol. 6, no 1, p. 65-75Article in journal (Refereed)
    Abstract [en]

    Phylogenetic inference is widely used to investigate the relationships between homologous sequences. RNA molecules have played a key role in these studies because they are present throughout life and tend to evolve slowly. Phylogenetic inference has been shown to be dependent on the substitution model used. A wide range of models have been developed to describe RNA evolution, either with 16 states describing all possible canonical base pairs or with 7 states where the 10 mismatched nucleotides are reduced to a single state. Formal model selection has become a standard practice for choosing an inferential model and works well for comparing models of a specific type, such as comparisons within nucleotide models or within amino acid models. Model selection cannot function across different sized state spaces because the likelihoods are conditioned on different data. Here, we introduce statistical state-space projection methods that allow the direct comparison of likelihoods between nucleotide models and 7-state and 16-state RNA models. To demonstrate the general applicability of our new methods, we extract 287 RNA families from genomic alignments and perform model selection. We find that in 281/287 families, RNA models are selected in preference to nucleotide models, with simple 7-state RNA models selected for more conserved families with shorter stems and more complex 16-state RNA models selected for more divergent families with longer stems. Other factors, such as the function of the RNA molecule or the GC-content, have limited impact on model selection. Our models and model selection methods are freely available in the open-source software.

  • 92.
    Allesson, Lina
    et al.
    Univ Oslo, Dept Biosci, Oslo, Norway..
    Koehler, Birgit
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    Thrane, Jan-Erik
    Norwegian Inst Water Res, Oslo, Norway..
    Andersen, Tom
    Univ Oslo, Dept Biosci, Oslo, Norway..
    Hessen, Dag O.
    Univ Oslo, Dept Biosci, Oslo, Norway..
    The role of photomineralization for CO2 emissions in boreal lakes along a gradient of dissolved organic matter2021In: Limnology and Oceanography, ISSN 0024-3590, E-ISSN 1939-5590, Vol. 66, no 1, p. 158-170Article in journal (Refereed)
    Abstract [en]

    Many boreal lakes are experiencing an increase in concentrations of terrestrially derived dissolved organic matter (DOM)-a process commonly labeled "browning." Browning affects microbial and photochemical mineralization of DOM, and causes increased light attenuation and hence reduced photosynthesis. Consequently, browning regulates lake heterotrophy and net CO2-efflux to the atmosphere. Climate and environmental change makes ecological forecasting and global carbon cycle modeling increasingly important. A proper understanding of the magnitude and relative contribution from CO2-generating processes for lakes ranging in dissolve organic carbon (DOC) concentrations is therefore crucial for constraining models and forecasts. Here, we aim to study the relative contribution of photomineralization to total CO(2)production in 70 Scandinavian lakes along an ecosystem gradient of DOC concentration. We combined spectral data from the lakes with regression estimates between optical parameters and wavelength specific photochemical reactivity to estimate rates of photochemical DOC mineralization. Further, we estimated total in-lake CO2-production and efflux from lake chemical and physical data. Photochemical mineralization corresponded on average to 9% +/- 1% of the total CO2-evasion, with the highest contribution in clear lakes. The calculated relative contribution of photochemical mineralization to total in-lake CO2-production was about 3% +/- 0.2% in all lakes. Although lakes differed substantially in color, depth-integrated photomineralization estimates were similar in all lakes, regardless of DOC concentrations. DOC concentrations were positively related to CO2-efflux and total in-lake CO2-production but negatively related to primary production. We conclude that enhanced rates of photochemical mineralization will be a minor contributor to increased heterotrophy under increased browning.

    Download full text (pdf)
    fulltext
  • 93. Almeida, Erika
    et al.
    Nunes, Ana
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Population and Conservation Biology.
    Andrade, Pedro
    Alves, Susana
    Guerreiro, Catia
    Rebelo, Rui
    Antipredator responses of two anurans towards native and exotic predators2011In: Amphibia-Reptilia, ISSN 0173-5373, E-ISSN 1568-5381, Vol. 32, no 3, p. 341-350Article in journal (Refereed)
    Abstract [en]

    When faced with the risk of predation, tadpoles of many amphibian species are known to modify their phenotype. In this work we studied the effect of an exotic species, the red swamp crayfish (Procambarus clarkii), on the phenotype of two species of amphibians with different reproduction habitats: the Iberian painted frog, Discoglossus galganoi, that normally reproduces in temporary water bodies and the common toad, Bufo bufo, that reproduces in permanent water bodies. The responses were compared with the ones shown in the presence of a native predator, dragonfly (Aeshnidae) larvae. Behaviour, growth and morphology of tadpoles were monitored in a factorial experiment with five treatments. Our results showed that only the permanent habitat species altered its behaviour and life-history traits in the presence of P. clarkii; however, this was mediated by chemical cues from consumed conspecifics. Antipredator responses of B. bufo towards the exotic crayfish were similar to the ones towards the native predator, while D. galganoi responded to the dragonfly larvae but not to P. clarkii. This may be the result of infrequent colonization events of temporary habitats by the crayfish. Therefore, the consequences of the introduction of P. clarkii might be more serious for D. galganoi and other species living in temporary habitats. Species breeding in permanent habitats, more prone to having generalized antipredator responses, may be relatively protected against this exotic crayfish although the effectiveness of these responses still needs to be tested.

  • 94. Almeida, Rafael M.
    et al.
    Barros, Nathan
    Cole, Jonathan J.
    Tranvik, Lars
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    Roland, Fabio
    Correspondence: Emissions from Amazonian dams2013In: Nature Climate Change, ISSN 1758-678X, E-ISSN 1758-6798, Vol. 3, no 12, p. 1005-1005Article in journal (Other academic)
  • 95. Almeida, Rafael M.
    et al.
    Barros, Nathan
    Cole, Jonathan J.
    Tranvik, Lars
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    Roland, Fábio
    Emissions from Amazonian dams2013In: Nature Climate Change, ISSN 1758-678X, E-ISSN 1758-6798, Vol. 3, no 12, p. 1005-1005Article in journal (Refereed)
  • 96.
    Almeida, Rafael M.
    et al.
    Univ Fed Juiz de Fora, Inst Ciencias Biol, Dept Biol, Aquat Ecol Lab, Juiz De Fora, Brazil..
    Nobrega, Gabriel N.
    Univ Sao Paulo, Escola Super Agr Luiz de Queiroz, Dept Ciencia Solo, Piracicaba, Brazil..
    Junger, Pedro C.
    Univ Fed Rio de Janeiro, Lab Limnol, Rio De Janeiro, Brazil..
    Figueiredo, Aline V.
    Univ Fed Rio Grande do Norte, Lab Water Resources & Environm Sanitat, BR-59072970 Natal, RN, Brazil..
    Andrade, Anizio S.
    Univ Fed Rio Grande do Norte, Lab Limnol, BR-59072970 Natal, RN, Brazil..
    de Moura, Caroline G. B.
    Univ Fed Rio Grande do Norte, Lab Limnol, BR-59072970 Natal, RN, Brazil..
    Tonetta, Denise
    Univ Fed Santa Catarina, Lab Freshwater Ecol, Florianopolis, SC, Brazil..
    Oliveira, Ernandes S., Jr.
    Radboud Univ Nijmegen, Dept Aquat Ecol & Environm Biol, Inst Water & Wetland Res, NL-6525 ED Nijmegen, Netherlands..
    Araujo, Fabiana
    Univ Fed Rio Grande do Norte, Lab Water Resources & Environm Sanitat, BR-59072970 Natal, RN, Brazil..
    Rust, Felipe
    Univ Fed Juiz de Fora, Inst Ciencias Biol, Dept Biol, Aquat Ecol Lab, Juiz De Fora, Brazil..
    Pineiro-Guerra, Juan M.
    Univ Republica, Dept Ecol Teor & Aplicada, Ctr Univ Reg Este, Montevideo, Uruguay.;Univ Republica, Fac Ciencias, Montevideo, Uruguay..
    Mendonca, Jurandir R., Jr.
    Univ Fed Rio Grande do Norte, Lab Water Resources & Environm Sanitat, BR-59072970 Natal, RN, Brazil..
    Medeiros, Leonardo R.
    Univ Fed Rio Grande do Norte, Lab Limnol, BR-59072970 Natal, RN, Brazil..
    Pinheiro, Lorena
    Univ Fed Estado Rio de Janeiro, Dept Ciencias Nat, Rio De Janeiro, Brazil..
    Miranda, Marcela
    Univ Fed Juiz de Fora, Inst Ciencias Biol, Dept Biol, Aquat Ecol Lab, Juiz De Fora, Brazil..
    Costa, Mariana R. A.
    Univ Fed Rio Grande do Norte, Lab Water Resources & Environm Sanitat, BR-59072970 Natal, RN, Brazil..
    Melo, Michaela L.
    Univ Fed Sao Carlos, Lab Microbial Proc & Biodivers, BR-13560 Sao Carlos, SP, Brazil..
    Nobre, Regina L. G.
    Univ Fed Rio Grande do Norte, Lab Limnol, BR-59072970 Natal, RN, Brazil..
    Benevides, Thiago
    Univ Fed Rio de Janeiro, Lab Limnol, Rio De Janeiro, Brazil..
    Roland, Fabio
    Univ Fed Juiz de Fora, Inst Ciencias Biol, Dept Biol, Aquat Ecol Lab, Juiz De Fora, Brazil..
    de Klein, Jeroen
    Wageningen Univ, Aquat Ecol & Environm Sci, NL-6700 AP Wageningen, Netherlands..
    Barros, Nathan O.
    Univ Fed Juiz de Fora, Inst Ciencias Biol, Dept Biol, Aquat Ecol Lab, Juiz De Fora, Brazil..
    Mendonca, Raquel
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology. Univ Fed Juiz de Fora, Inst Ciencias Biol, Dept Biol, Aquat Ecol Lab, Juiz De Fora, Brazil.
    Becker, Vanessa
    Univ Fed Rio Grande do Norte, Lab Water Resources & Environm Sanitat, BR-59072970 Natal, RN, Brazil..
    Huszar, Veral. M.
    Univ Fed Rio de Janeiro, Museu Nacl, Lab Ficol, Rio De Janeiro, Brazil..
    Kosten, Sarian
    Radboud Univ Nijmegen, Dept Aquat Ecol & Environm Biol, Inst Water & Wetland Res, NL-6525 ED Nijmegen, Netherlands..
    High Primary Production Contrasts with Intense Carbon Emission in a Eutrophic Tropical Reservoir2016In: Frontiers in Microbiology, E-ISSN 1664-302X, Vol. 7, article id 717Article in journal (Refereed)
    Abstract [en]

    Recent studies from temperate lakes indicate that eutrophic systems tend to emit less carbon dioxide (Co-2) and bury more organic carbon (OC) than oligotrophic ones, rendering them CO2 sinks in some cases. However, the scarcity of data from tropical systems is critical for a complete understanding of the interplay between eutrophication and aquatic carbon (C) fluxes in warm waters. We test the hypothesis that a warm eutrophic system is a source of both CO2 and CH4 to the atmosphere, and that atmospheric emissions are larger than the burial of OC in sediments. This hypothesis was based on the following assumptions: (i) OC mineralization rates are high in warm water systems, so that water column CO2 production overrides the high C uptake by primary producers, and (ii) increasing trophic status creates favorable conditions for CH4 production. We measured water-air and sediment-water CO2 fluxes, CH4 diffusion, ebullition and oxidation, net ecosystem production (NEP) and sediment OC burial during the dry season in a eutrophic reservoir in the semiarid northeastern Brazil. The reservoir was stratified during daytime and mixed during nighttime. In spite of the high rates of primary production (4858 +/- 934 mg C m(-2) d(-1)), net heterotrophy was prevalent due to high ecosystem respiration (5209 +/- 992 mg C m(-2) d(-1)). Consequently, the reservoir was a source of atmospheric CO2 (518 +/- 182 mg C m(-2) d(-1)). In addition, the reservoir was a source of ebullitive (17 +/- 10 mg C m(-2) d(-1)) and diffusive CH4 (11 +/- 6 mg C m(-2) d(-1)). OC sedimentation was high (1162 mg C m(-2) d(-1)), but our results suggest that the majority of it is mineralized to CO2 (722 +/- 182 mg C m(-2) d(-1)) rather than buried as OC (440 mg C m(-2) d(-1)). Although temporally resolved data would render our findings more conclusive, our results suggest that despite being a primary production and OC burial hotspot, the tropical eutrophic system studied here was a stronger CO2 and CH4 source than a C sink, mainly because of high rates of OC mineralization in the water column and sediments.

    Download full text (pdf)
    fulltext
  • 97.
    Almeida, Rafael M.
    et al.
    Cornell University, USA.
    Paranaíba, José R.
    Federal University of Juiz de Fora, Brazil.
    Barbosa, Ícaro
    Federal University of Juiz de Fora, Brazil.
    Sobek, Sebastian
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    Kosten, Sarian
    University Nijmegen, The Netherlands.
    Linkhorst, Annika
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    Mendonça, Raquel
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology. Federal University of Juiz de Fora, Brazil.
    Quadra, Gabrielle
    Federal University of Juiz de Fora, Brazil.
    Roland, Fábio
    Federal University of Juiz de Fora, Brazil.
    Barros, Nathan
    Federal University of Juiz de Fora, Brazil.
    Carbon dioxide emission from drawdown areas of a Brazilian reservoir is linked to surrounding land cover2019In: Aquatic Sciences, ISSN 1015-1621, E-ISSN 1420-9055, Vol. 81, article id 68Article in journal (Refereed)
    Abstract [en]

    Reservoir sediments exposed to air due to water level fluctuations are strong sources of atmospheric carbon dioxide (CO2). The spatial variability of CO2 fluxes from these drawdown areas are still poorly understood. In a reservoir in southeastern Brazil, we investigated whether CO2 emissions from drawdown areas vary as a function of neighboring land cover types and assessed the magnitude of CO2 fluxes from drawdown areas in relation to nearby water surface. Exposed sediments near forestland (average = 2733 mg C m−2 day−1) emitted more CO2 than exposed sediments near grassland (average = 1261 mg C m−2 day−1), congruent with a difference in organic matter content between areas adjacent to forestland (average = 12.2%) and grassland (average = 10.9%). Moisture also had a significant effect on CO2 emission, with dry exposed sediments (average water content: 13.7%) emitting on average 2.5 times more CO2 than wet exposed sediments (average water content: 23.5%). We carried out a systematic comparison with data from the literature, which indicates that CO2 efflux from drawdown areas globally is about an order of magnitude higher than CO2 efflux from adjacent water surfaces, and within the range of CO2 efflux from terrestrial soils. Our findings suggest that emissions from exposed sediments may vary substantially in space, possibly related to organic matter supply from uphill vegetation, and that drawdown areas play a disproportionately important role in total reservoir CO2 emissions with respect to the area they cover.

    Download full text (pdf)
    fulltext
  • 98. Almeida, Rafael M.
    et al.
    Tranvik, Lars
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    Huszar, Vera L. M.
    Sobek, Sebastian
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    Mendonca, Raquel
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    Barros, Nathan
    Boemer, Gina
    Arantes, Joao Durval, Jr.
    Roland, Fabio
    Phosphorus transport by the largest Amazon tributary (Madeira River, Brazil) and its sensitivity to precipitation and damming2015In: Inland Waters, ISSN 2044-2041, E-ISSN 2044-205X, Vol. 5, no 3, p. 275-282Article in journal (Refereed)
    Abstract [en]

    Originating in the Bolivian and Peruvian Andes, the Madeira River is the largest tributary of the Amazon River in terms of discharge. Andean rivers transport large quantities of nutrient-rich suspended sediments and are the main source of phosphorus (P) to the Amazon basin. Here, we show the seasonal variability in concentrations and loads of different P forms (total, particulate, dissolved, and soluble reactive P) in the Madeira River through 8 field campaigns between 2009 and 2011. At our sampling reach in Porto Velho, Brazil, the Madeira River transports similar to 177-247 Gg yr(-1) of P, mostly linked to particles (similar to 85%). Concentrations and loads of all P forms have a maximum at rising waters and a minimum at low waters. Total P concentrations were substantially higher at a given discharge at rising water than at a similar discharge at falling water. The peak of P concentrations matched the peak of rainfall in the upper basin, suggesting an influence of precipitation-driven erosion. Projected precipitation increase in the eastern slopes of the Andes could enhance sediment yield and hence the P transport in the Madeira River. Because most of the P is particulate, however, we hypothesize that the planned proliferation of hydropower dams in the Madeira basin has the potential to reduce P loads substantially, possibly counteracting any precipitation-related increases. In the long term, this could be detrimental to highly productive downstream floodplain forests that are seasonally fertilized with P-rich deposits.

    Download full text (pdf)
    fulltext
  • 99.
    Alneberg, Johannes
    et al.
    KTH Royal Inst Technol, Sch Engn Sci Chem Biotechnol & Hlth, Dept Gene Technol, Sci Life Lab, Stockholm, Sweden.
    Karlsson, Christofer M. G.
    Linnaeus Univ, Ctr Ecol & Evolut Microbial Model Syst, EEMiS, Kalmar, Sweden.
    Divne, Anna-Maria
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular Evolution. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Bergin, Claudia
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular Evolution. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Homa, Felix
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular Evolution. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Lindh, Markus V.
    Linnaeus Univ, Ctr Ecol & Evolut Microbial Model Syst, EEMiS, Kalmar, Sweden;Lund Univ, Dept Biol, Lund, Sweden.
    Hugerth, Luisa W.
    KTH Royal Inst Technol, Sch Engn Sci Chem Biotechnol & Hlth, Dept Gene Technol, Sci Life Lab, Stockholm, Sweden;Karolinska Inst, Ctr Translat Microbiome Res, Dept Mol Tumour & Cell Biol, Sci Life Lab, Solna, Sweden.
    Ettema, Thijs J. G.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular Evolution. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Bertilsson, Stefan
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Andersson, Anders F.
    KTH Royal Inst Technol, Sch Engn Sci Chem Biotechnol & Hlth, Dept Gene Technol, Sci Life Lab, Stockholm, Sweden.
    Pinhassi, Jarone
    Linnaeus Univ, Ctr Ecol & Evolut Microbial Model Syst, EEMiS, Kalmar, Sweden.
    Genomes from uncultivated prokaryotes: a comparison of metagenome-assembled and single-amplified genomes2018In: Microbiome, E-ISSN 2049-2618, Vol. 6, article id 173Article in journal (Refereed)
    Abstract [en]

    Background: Prokaryotes dominate the biosphere and regulate biogeochemical processes essential to all life. Yet, our knowledge about their biology is for the most part limited to the minority that has been successfully cultured. Molecular techniques now allow for obtaining genome sequences of uncultivated prokaryotic taxa, facilitating in-depth analyses that may ultimately improve our understanding of these key organisms.

    Results: We compared results from two culture-independent strategies for recovering bacterial genomes: single-amplified genomes and metagenome-assembled genomes. Single-amplified genomes were obtained from samples collected at an offshore station in the Baltic Sea Proper and compared to previously obtained metagenome-assembled genomes from a time series at the same station. Among 16 single-amplified genomes analyzed, seven were found to match metagenome-assembled genomes, affiliated with a diverse set of taxa. Notably, genome pairs between the two approaches were nearly identical (average 99.51% sequence identity; range 98.77-99.84%) across overlapping regions (30-80% of each genome). Within matching pairs, the single-amplified genomes were consistently smaller and less complete, whereas the genetic functional profiles were maintained. For the metagenome-assembled genomes, only on average 3.6% of the bases were estimated to be missing from the genomes due to wrongly binned contigs.

    Conclusions: The strong agreement between the single-amplified and metagenome-assembled genomes emphasizes that both methods generate accurate genome information from uncultivated bacteria. Importantly, this implies that the research questions and the available resources are allowed to determine the selection of genomics approach for microbiome studies.

    Download full text (pdf)
    FULLTEXT01
  • 100.
    Alonso-Saez, Laura
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Evolution. Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    Unanue, Marian
    Latatu, Ainhoa
    Azua, Inigo
    Ayo, Begona
    Artolozaga, Itxaso
    Iriberri, Juan
    Changes in marine prokaryotic community induced by varying types of dissolved organic matter and subsequent grazing pressure2009In: Journal of Plankton Research, ISSN 0142-7873, E-ISSN 1464-3774, Vol. 31, no 11, p. 1373-1383Article in journal (Refereed)
    Abstract [en]

    We analysed changes in the abundance, biomass, activity and composition of coastal marine prokaryotic communities after the addition of organic substrates, such as glucose, leucine and yeast extract, and the effect of grazing pressure exerted by nanoflagellates. The addition of a carbon source (i.e. glucose) promoted the growth of Gammaproteobacteria, while a combined source of C and N (i.e. leucine) favoured the development of Alphaproteobacteria. The addition of yeast extract, a complex substrate rich in N and growth factors, promoted the proliferation of Alphaproteobacteria and Gammaproteobacteria. Grazing pressure exerted by nanoflagellates produced marked differences on the size structure of the prokaryotic biomass. A pronounced tendency to filamentation and aggregation was observed in the glucose treatment, while in the case of yeast extract, small and mainly freely dispersed prokaryotes were maintained throughout the incubations. Thus, the final community in the yeast extract treatment showed a high percentage of edible biomass, while an important fraction of potentially grazing-resistant prokaryotes (more than 50% of total prokaryotic biomass) was detected in the microcosms enriched with glucose. These results suggest a marked effect of DOM sources on the development of grazing-resistant prokaryotes.

1234567 51 - 100 of 4207
CiteExportLink to result list
Permanent link
Cite
Citation style
  • apa
  • ieee
  • modern-language-association
  • vancouver
  • Other style
More styles
Language
  • de-DE
  • en-GB
  • en-US
  • fi-FI
  • nn-NO
  • nn-NB
  • sv-SE
  • Other locale
More languages
Output format
  • html
  • text
  • asciidoc
  • rtf