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  • 51.
    Hou, Chen
    Stockholm University, Faculty of Science, Department of Ecology, Environment and Plant Sciences.
    Proteomics and phylogenetics of the Gnetales2014Licentiate thesis, comprehensive summary (Other academic)
    Abstract [en]

    A central point of Darwin’s theory of evolution is that accumulation of many small changes during the evolutionary process can result in significant change over time. In light of his theory, plant scientists seek for and compare different plant traits among species e.g., from morphology, DNA or proteins in order to discover the underlying evolutionary patterns and processes. The Gnetales, an intriguing family that comprises Ephedra, Gnetum and Welwitschia, have puzzled scientists for over a century. Their features are evolutionarily difficult to understand in comparison with other seed plants and this has hampered analyses of evolution and phylogeny regardless of whether morphological or molecular data has been utilized. In this thesis, I first attempt (Paper I) to seek for a new evolutionary indicator; a protein profile from pollination drops of Ephedra is compiled, and the results are compared with those from conifers and other seed plants. The aim of this proteomic study was also to investigate whether proteomic profiles vary among Ephedra species and are affected by different selection factors, e.g., pollination mode, ovule protection etc. The results indicate, however, that proteins are present only in very small amounts in pollination drops of Ephedra, and mainly as waste products from degrading cells. This is surprising since proteins are considered important for defense of the naked ovules of gymnosperms, e.g., against pathogens. Pollination drops of Ephedra have a very high sugar concentration and it is possible that carbohydrates are responsible for ovule defense in Ephedra. The second chapter of my thesis (Paper II) is devoted to Gnetum; a phylogenetic study based on genetic markers derived from both nuclear ribosomal regions and chloroplast regions is conducted. Previous studies have been hampered by difficulties with outgroup comparison and homology assessments of informative gene regions. A few attempts have been made to estimate the deepest splits in the genus, all with a limited ingroup sampling. We address the phylogeny of Gnetum and make a first assessment of the monophyly of species, using a denser sampling of taxa and a combination of faster and more slowly evolving molecular markers. The results are discussed in comparison with previous classification and morphology, and will provide a basis for further studies of taxonomy, ecology, and biogeography in Gnetum

  • 52.
    Hughes, P. William
    Carleton University, Canada.
    Are Species Special?: The Ethics of Species An Introduction by Ronald L. Sandler Cambridge University Press, Cambridge, 20122013In: Science, ISSN 0036-8075, E-ISSN 1095-9203, Vol. 339, no 6123, p. 1035-1035Article, book review (Other academic)
  • 53.
    Hughes, P. William
    Max Planck Institute for Plant Breeding Research, Germany; University of Cologne, Germany.
    How universal is the evolution of senescence?2017In: Evolution, ISSN 0014-3820, E-ISSN 1558-5646, Vol. 71, no 7, p. 1919-1921Article in journal (Refereed)
  • 54.
    Hughes, P. William
    Max Planck Institute for Plant Breeding Research, Germany; University of Cologne, Germany.
    Minimal-Risk Seed Heteromorphism: Proportions of Seed Morphs for Optimal Risk-Averse Heteromorphic Strategies2018In: Frontiers in Plant Science, ISSN 1664-462X, E-ISSN 1664-462X, Vol. 9, article id 1412Article in journal (Refereed)
    Abstract [en]

    Seed heteromorphism is the reproductive strategy characterized by the simultaneous production of multiple seed types. While comparing heteromorphic to monomorphic strategies is mathematically simple, there is no explicit test for assessing which ratio of seed morphs minimizes fitness variance, and hence offers a basis for comparing different heteromorphic strategies. Such a test may be particularly valuable when more than two distinct morphs are present, since many strategies may have equivalent geometric fitnesses. As noted by Gillespie (1974), in these cases avoiding rare but evolutionarily important instances of severe reductions in fitness involves the minimization of variation in fitness—i.e., risk. Here I compute the optimal proportions of two or more seed morphs for heteromorphic strategies that either: (1) minimize total fitness variance; or (2) maximize the fitness-risk ratio—i.e., the “extra” fitness accrued per unit of “extra” fitness variance. This work thereby provides a testable null hypothesis to estimate the optimal frequencies of seed morphs when multiple heteromorphic strategies have evolved in environments with severe fitness risks. Moreover, it also permits the calculation of expected seed morph frequencies when more than two seed morphs are produced.

  • 55.
    Hughes, Patrick William
    Max Planck Institute for Plant Breeding Research, Germany.
    Between semelparity and iteroparity: Empirical evidence for a continuum of modes of parity2017In: Ecology and Evolution, ISSN 2045-7758, E-ISSN 2045-7758, Vol. 7, no 20, p. 8232-8261Article in journal (Refereed)
    Abstract [en]

    The number of times an organism reproduces (i.e., its mode of parity) is a fundamental life‐history character, and evolutionary and ecological models that compare the relative fitnesses of different modes of parity are common in life‐history theory and theoretical biology. Despite the success of mathematical models designed to compare intrinsic rates of increase (i.e., density‐independent growth rates) between annual‐semelparous and perennial‐iteroparous reproductive schedules, there is widespread evidence that variation in reproductive allocation among semelparous and iteroparous organisms alike is continuous. This study reviews the ecological and molecular evidence for the continuity and plasticity of modes of parity—that is, the idea that annual‐semelparous and perennial‐iteroparous life histories are better understood as endpoints along a continuum of possible strategies. I conclude that parity should be understood as a continuum of different modes of parity, which differ by the degree to which they disperse or concentrate reproductive effort in time. I further argue that there are three main implications of this conclusion: (1) that seasonality should not be conflated with parity; (2) that mathematical models purporting to explain the general evolution of semelparous life histories from iteroparous ones (or vice versa) should not assume that organisms can only display either an annual‐semelparous life history or a perennial‐iteroparous one; and (3) that evolutionary ecologists should base explanations of how different life‐history strategies evolve on the physiological or molecular basis of traits underlying different modes of parity.

  • 56.
    Hylander, Kristoffer
    et al.
    Stockholm University, Faculty of Science, Department of Ecology, Environment and Plant Sciences.
    Ehrlen, Johan
    Stockholm University, Faculty of Science, Department of Ecology, Environment and Plant Sciences.
    The mechanisms causing extinction debts2013In: Trends in Ecology & Evolution, ISSN 0169-5347, E-ISSN 1872-8383, Vol. 28, no 6, p. 341-346Article in journal (Refereed)
    Abstract [en]

    Extinction debts can result from many types of habitat changes involving mechanisms other than metapopulation processes. This is a fact that most recent literature on extinction debts pays little attention to. We argue that extinction debts can arise because (i) individuals survive in resistant life-cycle stages long after habitat quality change, (ii) stochastic extinctions of populations that have become small are not immediate, and (iii) metapopulations survive long after that connectivity has decreased if colonization-extinction dynamics is slow. A failure to distinguish between these different mechanisms and to simultaneously consider both the size of the extinction debt and the relaxation time hampers our understanding of how extinction debts arise and our ability to prevent ultimate extinctions.

  • 57.
    Höhna, Sebastian
    Stockholm University, Faculty of Science, Department of Mathematics.
    Bayesian Phylogenetic Inference2011Licentiate thesis, comprehensive summary (Other academic)
    Abstract [en]

    In this thesis we consider two very different topics in Bayesian phylogenetic inference. The first paper, "Inferring speciation and extinction rates under different sampling schemes" by Sebastian Höhna, Tanja Stadler, Fredrik Ronquist and Tom Britton, focuses on estimating the rates of speciation and extinction of species when only a subsample of the present day species is available. The second paper "Burnin Estimation and Convergence Assessment" by Sebastian Höhna and Kristoffer Sahlin focuses on how to analyze the output of Markov chain Monte Carlo (MCMC) runs with respect to convergence to the stationary distribution and approximation of the posterior probability distribution.

    The birth-death process is used to describe the evolution of species diversity. Previous work enabled the estimation of speciation and extinction rates under the assumption of a constant rate birth-death process and complete sampling of all extant species. We extend the complete sampled birth-death process to incomplete sampling with three different types of sampling schemes: random sampling, diversified sampling and clustered sampling. On a set of empirical phylogenies with known sampling fraction we observe that taking the sampling fraction into account gives better fitting models, either by random sampling or diversified sampling.

    The current trend in Bayesian phylogenetic inference is to extend the available models by using more complex models and/or hierarchical models. This renders Bayesian inference by means of the MCMC algorithm very intricate. Performance of single or multiple MCMC runs need to be assessed. We investigate which methods are used in Bayesian phylogenetics to assess the performance of MCMC runs, which methods are available from other research areas and compile a strategy on how to assess convergence and how to estimate the burnin automatically in a statistically sound framework.

  • 58.
    Höhna, Sebastian
    Stockholm University, Faculty of Science, Department of Mathematics.
    Bayesian Phylogenetic Inference: Estimating Diversification Rates from Reconstructed Phylogenies2013Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    Phylogenetics is the study of the evolutionary relationship between species. Inference of phylogeny relies heavily on statistical models that have been extended and refined tremendously over the past years into very complex hierarchical models. Paper I introduces probabilistic graphical models to statistical phylogenetics and elaborates on the potential advantages a unified graphical model representation could have for the community, e.g., by facilitating communication and improving reproducibility of statistical analyses of phylogeny and evolution.

    Once the phylogeny is reconstructed it is possible to infer the rates of diversification (speciation and extinction). In this thesis I extend the birth-death process model, so that it can be applied to incompletely sampled phylogenies, that is, phylogenies of only a subsample of the presently living species from one group. Previous work only considered the case when every species had the same probability to be included and here I examine two alternative sampling schemes: diversified taxon sampling and cluster sampling. Paper II introduces these sampling schemes under a constant rate birth-death process and gives the probability density for reconstructed phylogenies. These models are extended in Paper IV to time-dependent diversification rates, again, under different sampling schemes and applied to empirical phylogenies. Paper III focuses on fast and unbiased simulations of reconstructed phylogenies. The efficiency is achieved by deriving the analytical distribution and density function of the speciation times in the reconstructed phylogeny.

  • 59.
    Höhna, Sebastian
    Stockholm University, Faculty of Science, Department of Mathematics.
    Likelihood Inference of Non-Constant Diversification Rates with Incomplete Taxon Sampling2014In: PLoS ONE, ISSN 1932-6203, E-ISSN 1932-6203, Vol. 9, no 1, article id e84184Article in journal (Refereed)
    Abstract [en]

    Large-scale phylogenies provide a valuable source to study background diversification rates and investigate if the rates have changed over time. Unfortunately most large-scale, dated phylogenies are sparsely sampled (fewer than 5% of the described species) and taxon sampling is not uniform. Instead, taxa are frequently sampled to obtain at least one representative per subgroup (e. g. family) and thus to maximize diversity (diversified sampling). So far, such complications have been ignored, potentially biasing the conclusions that have been reached. In this study I derive the likelihood of a birth-death process with non-constant (time-dependent) diversification rates and diversified taxon sampling. Using simulations I test if the true parameters and the sampling method can be recovered when the trees are small or medium sized (fewer than 200 taxa). The results show that the diversification rates can be inferred and the estimates are unbiased for large trees but are biased for small trees (fewer than 50 taxa). Furthermore, model selection by means of Akaike's Information Criterion favors the true model if the true rates differ sufficiently from alternative models (e. g. the birth-death model is recovered if the extinction rate is large and compared to a pure-birth model). Finally, I applied six different diversification rate models - ranging from a constant-rate pure birth process to a decreasing speciation rate birth-death process but excluding any rate shift models - on three large-scale empirical phylogenies (ants, mammals and snakes with respectively 149, 164 and 41 sampled species). All three phylogenies were constructed by diversified taxon sampling, as stated by the authors. However only the snake phylogeny supported diversified taxon sampling. Moreover, a parametric bootstrap test revealed that none of the tested models provided a good fit to the observed data. The model assumptions, such as homogeneous rates across species or no rate shifts, appear to be violated.

  • 60.
    Höhna, Sebastian
    et al.
    Stockholm University, Faculty of Science, Department of Mathematics.
    Heath, Tracy A.
    University of California, Berkeley.
    Boussau, Bastien
    University of California, Berkeley .
    Landis, Michael J.
    University of California, Berkeley .
    Ronquist, Fredrik
    Swedish Museum of Natural History.
    Huelsenbeck, John P.
    University of California, Berkeley .
    Probabilistic Graphical Model Representation in PhylogeneticsManuscript (preprint) (Other academic)
    Abstract [en]

    Recent years have seen a rapid expansion of the model space explored in statistical phylogenetics, emphasizing the need for new approaches to model representation and software development. Clear communication and representation of the chosen model is crucial for: (1) reproducibility of an analysis, (2) model development and (3) software design. Moreover, a unified, clear and understandable framework formodel representation lowers the barrier for beginning scientists and non-specialists to grasp the model including the assumptions and parameter/variable dependencies.

    Graphical models is such a unifying framework that has gained in popularity in the statistical literature in recent years. The core idea isto break complex models into conditionally independent distributions and the strength lies in, amongst others: comprehensibility, flexibility, adaptability and computational algorithms. Graphical models can be used to teach statistical models, to facilitate communication among phylogeneticists and in the development of generic software for simulation and statistical inference.

    Here, we provide an introduction to graphical models for phylogeneticists and extend the standard graphical model representation to the realm of phylogenetics. We introduce a new graphical model component, tree plates, to capture the changing structure of the subgraph corresponding to a phylogenetic tree. We describe a range of phylogenetic models using the graphical model framework and built these into separate, interchangeable modules. Phylogenetic model graphs can be readily used in simulation, maximum likelihood inference, and Bayesian inference using either Metropolis-Hastings or Gibbs sampling of the posterior distribution.

  • 61.
    Höhna, Sebastian
    et al.
    Stockholm University, Faculty of Science, Department of Mathematics.
    Stadler, Tanja
    Ronquist, Fredrik
    Britton, Tom
    Stockholm University, Faculty of Science, Department of Mathematics.
    Inferring Speciation and Extinction Rates under Different Sampling Schemes2011In: Molecular biology and evolution, ISSN 0737-4038, E-ISSN 1537-1719, Vol. 28, no 9, p. 2577-2589Article in journal (Refereed)
    Abstract [en]

    The birth-death process is widely used in phylogenetics to model speciation and extinction. Recent studies have shown that the inferred rates are sensitive to assumptions about the sampling probability of lineages. Here, we examine the effect of the method used to sample lineages. Whereas previous studies have assumed random sampling (RS), we consider two extreme cases of biased sampling: diversified sampling (DS), where tips are selected to maximize diversity and cluster sampling (CS), where sample diversity is minimized. DS appears to be standard practice, for example, in analyses of higher taxa, whereas CS may occur under special circumstances, for example, in studies of geographically defined floras or faunas. Using both simulations and analyses of empirical data, we show that inferred rates may be heavily biased if the sampling strategy is not modeled correctly. In particular, when a diversified sample is treated as if it were a random or complete sample, the extinction rate is severely underestimated, often close to 0. Such dramatic errors may lead to serious consequences, for example, if estimated rates are used in assessing the vulnerability of threatened species to extinction. Using Bayesian model testing across 18 empirical data sets, we show that DS is commonly a better fit to the data than complete, random, or cluster sampling (CS). Inappropriate modeling of the sampling method may at least partly explain anomalous results that have previously been attributed to variation over time in birth and death rates.

  • 62. Ickert-Bond, Stefanie M.
    et al.
    Rydin, Catarina
    University of Munich, Germany.
    Renner, Susanne S.
    A fossil-calibrated relaxed clock for Ephedra indicates an Oligocene age for the divergence of Asian and New World clades and Miocene dispersal into South America2009In: Journal of Systematics and Evolution, ISSN 1674-4918, E-ISSN 1759-6831, Vol. 47, no 5, p. 444-456Article in journal (Refereed)
    Abstract [en]

    Ephedra comprises approximately 50 species, which are roughly equally distributed between the Old and New World deserts, but not in the intervening regions (amphitropical range). Great heterogeneity in the substitution rates of Gnetales (EphedraGnetum, and Welwitschia) has made it difficult to infer the ages of the major divergence events in Ephedra, such as the timing of the Beringian disjunction in the genus and the entry into South America. Here, we use data from as many Gnetales species and genes as available from GenBank and from a recent study to investigate the timing of the major divergence events. Because of the tradeoff between the amount of missing data and taxon/gene sampling, we reduced the initial matrix of 265 accessions and 12 loci to 95 accessions and 10 loci, and further to 42 species (and 7736 aligned nucleotides) to achieve stationary distributions in the Bayesian molecular clock runs. Results from a relaxed clock with an uncorrelated rates model and fossil‐based calibration reveal that New World species are monophyletic and diverged from their mostly Asian sister clade some 30 mya, fitting with many other Beringian disjunctions. The split between the single North American and the single South American clade occurred approximately 25 mya, well before the closure of the Panamanian Isthmus. Overall, the biogeographic history of Ephedra appears dominated by long‐distance dispersal, but finer‐scale studies are needed to test this hypothesis.

  • 63. Irestedt, Martin
    et al.
    Fabre, Pierre-Henri
    Batalha-Filho, Henrique
    Jønsson, Knud A.
    Roselaar, Cees S
    Sangster, George
    Stockholm University, Faculty of Science, Department of Zoology, Systematic Zoology.
    Ericson, Per GP
    Stockholm University, Faculty of Science, Department of Zoology. Swedish Museum of Natural History.
    The spatio-temporal colonization and diversification across the Indo-Pacific by a ‘great speciator’ (Aves, Erythropitta erythrogaster)2013In: Proceedings of the Royal Society of London. Biological Sciences, ISSN 0962-8452, E-ISSN 1471-2954, Vol. 280, no 1759, p. 20130309-Article in journal (Refereed)
    Abstract [en]

    The Indo-Pacific region has arguably been the most important area for the formulation of theories about biogeography and speciation, but modern studies of the tempo, mode and magnitude of diversification across this region are scarce. We study the biogeographical history and characterize levels of diversification in the wide-ranging passerine bird Erythropitta erythrogaster using molecular, phylogeographic and population genetics methods, as well as morphometric and plumage analyses. Our results suggest that E. erythrogaster colonized the Indo-Pacific during the Pleistocene in an eastward direction following a stepping stone pathway, and that sea level fluctuations during the Pleistocene only locally may have promoted gene flow. A molecular species delimitation test suggests that several allopatric island populations of E. erythrogaster may be regarded as species. Most of these putative new species are further characterized by diagnostic differences in plumage. Our study reconfirms the E. erythrogaster complex as a ‘great speciator’: it represents a complex of up to 17 allopatrically distributed, reciprocally monophyletic and/or morphologically diagnosable species that originated during the Pleistocene. Our results support the view that observed latitudinal gradients of genetic divergence among avian sister-species may have been affected by incomplete knowledge of taxonomic limits in tropical bird species.

  • 64.
    Janz, Niklas
    Stockholm University, Faculty of Science, Department of Zoology.
    Ehrlich and Raven Revisited: Mechanisms Underlying Codiversification of Plants and Enemies2011In: Annual Review of Ecology, Evolution and Systematics, ISSN 1543-592X, E-ISSN 1545-2069, Vol. 42, p. 71-89Article, review/survey (Refereed)
    Abstract [en]

    After almost 50 years of scrutiny, the ideas that Ehrlich and Raven presented in their classical paper on the coevolution between butterflies and plants are still very much alive. Much of this interest has involved the potential for codiversification, both in how the interaction itself diversifies and how the interaction affects modes and rates of speciation. Despite high levels of conservatism and specialization, diversification of the interaction appears to be mainly a consequence of host shifts, but this somewhat paradoxical conclusion can be understood by an appreciation of the ecological as well as genetic mechanisms behind host shifts. There are several ways that the interaction can influence speciation, with or without host-plant-based di-vergent selection on reproductive barriers. One current debate is over the relative importance of radiations following shifts to new adaptive zones and elevated rates of speciation in groups with plastic and diverse host use.

  • 65.
    Janz, Niklas
    et al.
    Stockholm University, Faculty of Science, Department of Zoology.
    Braga, Mariana P
    Stockholm University, Faculty of Science, Department of Zoology.
    Wahlberg, Niklas
    Nylin, Sören
    Stockholm University, Faculty of Science, Department of Zoology.
    On oscillations and flutterings - A reply to Hamm and Fordyce2016In: Evolution, ISSN 0014-3820, E-ISSN 1558-5646, Vol. 70, no 5, p. 1150-1155Article in journal (Refereed)
    Abstract [en]

    The diversification of plant-feeding insects is seen as a spectacular example of evolutionary radiation. Hence, developing hypotheses to explain this diversification, and methods to test them, is an important undertaking. Some years ago, we presented the oscillation hypothesis as a general process that could drive diversification of this and similar interactions, through repeated expansions and contractions of host ranges. Hamm and Fordyce recently presented a study with the outspoken intention of testing this hypothesis where they concluded that the oscillation hypothesis was not supported. We point out several problems with their study, owing both to a misrepresentation of our hypothesis and to the methods. We provide a clarifying description of the oscillation hypothesis, and detail some predictions that follow from it. A reanalysis of the data demonstrated a troubling sensitivity of the "SSE" class of models to small changes in model specification, and we caution against using them for tests of trait-based diversification. Future tests of the hypothesis also need to better acknowledge the processes behind the host range oscillations. We suspect that doing so will resolve some of the apparent conflicts between our hypothesis and the view presented by Hamm and Fordyce.

  • 66.
    Jörgensen, Annelie
    Stockholm University, Faculty of Science, Department of Ecology, Environment and Plant Sciences.
    Reproduktiv morfologi hos Gnetum cuspidatum-gruppen och dess implikationer för evolution av pollinationsbiologi inom Gnetales2014Independent thesis Basic level (degree of Bachelor), 10 credits / 15 HE creditsStudent thesis
  • 67. Jønsson, Knud Andreas
    et al.
    Delhey, Kaspar
    Sangster, George
    Swedish Museum of Natural History, Sweden.
    Ericson, Per G. P.
    Irestedt, Martin
    The evolution of mimicry of friarbirds by orioles (Aves: Passeriformes) in Australo-Pacific archipelagos2016In: Proceedings of the Royal Society of London. Biological Sciences, ISSN 0962-8452, E-ISSN 1471-2954, Vol. 283, no 1833, article id 20160409Article in journal (Refereed)
    Abstract [en]

    Observations by Alfred Wallace and Jared Diamond of plumage similarities between co-occurring orioles (Oriolus) and friarbirds (Philemon) in the Malay archipelago led them to conclude that the former represent visual mimics of the latter. Here, we use molecular phylogenies and plumage reflectance measurements to test several key predictions of the mimicry hypothesis. We show that friarbirds originated before brown orioles, that the two groups did not co-speciate, although there is one plausible instance of co-speciation among species on the neighbouring Moluccan islands of Buru and Seram. Furthermore, we show that greater size disparity between model and mimic and a longer history of co-occurrence have resulted in a stronger plumage similarity (mimicry). This suggests that resemblance between orioles and friarbirds represents mimicry and that colonization of islands by brown orioles has been facilitated by their ability to mimic the aggressive friarbirds.

  • 68.
    Karlsson, Konrad
    Stockholm University, Faculty of Science, Department of Ecology, Environment and Plant Sciences.
    Local adaptation in life history traits and population size estimation of aquatic organisms2019Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    Human society is dependent on healthy aquatic ecosystems for our basic needs and well-being. Therefore, knowledge about how organisms respond and interact with their environments is pivotal. The Baltic Sea is highly affected by human activity and future populations living in its catchment area will have to respond to multiple set of changing abiotic and biotic predictors.

    The first two papers of this thesis focus on local adaptation, adaptive capacity, and the response to changing temperature, salinity, and food conditions of different Eurytemora affinis populations, a ubiquitous zooplankton species in the Baltic Sea. Development time of zooplankton is an important trait and relates to how fast a population can increase in number. Common garden experiments showed that E. affinis populations from warmer southern areas had shorter development time from nauplii to adult at high temperature compared to populations from colder areas, which indicates an adaptation to temperature. The adaptation was explained by a correlation in development time between higher temperatures, 17 and 22.5 °C, while development between a colder temperature, 12 °C, and the two higher temperatures was uncorrelated. This implies that adaption to short development time at high temperature is unlikely for populations originating from cold temperatures. Hence, global warming will be disadvantageous for northern, compared to southern populations. However, development time is heritable and may change under selection, and may improve the competitive advantage of northern populations. The population with the shortest development time had comparably lower survival at high temperature and low food quality. This represents a cost of fast development, and emphasizes the importance of including multiple stressors when investigating potential effects of climate change.

    E. affinis inhabits a broad range of habitats from an epi-benthic life in freshwater lakes and river mouths, to pelagic life in estuaries. Paper III aims to link the morphology of different populations to habitat and resource utilization. Results showed that the individuals of a pelagic population were smaller in size and more slender, compared to a littoral population of larger and more fecund individuals. In experimentally constructed benthic and pelagic algae communities, the littoral population produced less offspring than the pelagic population when filamentous benthic diatoms were included. This suggests that filaments disturb their feeding and that littoral populations of E. affinis stay epi-benthic. As pelagic fish typically select larger prey, living close to the bottom probably allows the littoral population to grow larger than the pelagic. These results link morphology to habitat specialization, and show contrasting ecological effects of two E. affinis populations.

    Paper IV focuses on the recreational angler’s potential role as a citizen scientist. The pike Esox lucius has a stabilizing role in ecosystems as a top consumer and is highly valued by recreational anglers in European lakes and estuaries. Results showed that recreational angling could be used to estimate population size and connectivity of E. lucius in spatial capture-recapture models. The only prerequisite is that anglers practice catch and release, retain spatial data, and take photos of their caught fish. These results show that data from recreational angling can be of potential use for fisheries managers and researchers.

  • 69.
    Karlsson, Konrad
    et al.
    Stockholm University, Faculty of Science, Department of Ecology, Environment and Plant Sciences.
    Winder, Monika
    Stockholm University, Faculty of Science, Department of Ecology, Environment and Plant Sciences.
    Ecosystem Effects of Morphological and Life History Traits in Two Divergent Zooplankton Populations2018In: Frontiers in Marine Science, E-ISSN 2296-7745, Vol. 5, article id 408Article in journal (Refereed)
    Abstract [en]

    Little is known about the ecosystem effects of locally adapted populations. The filter feeding copepod Eurytemora affinis is an abundant and important zooplankton in coastal waters that consist of a cryptic species complex with locally adapted populations. We used a mesocosm setup to investigate population and ecosystem interactions of two populations from the Baltic Sea with different morphology and life history traits. One population is laterally wider, larger-sized, more fecund, and have higher growth rate than the other. The experimental ecosystems varied in algae community (pelagic algae, and pelagic algae + benthic diatoms) with two resource supply scenarios. Results showed that the large-sized population is a more effective grazer. In low resource supply the small-sized population starved, whereas the large-sized population was unaffected, resulting in a larger population increase of both nauplii and copepodites than for the small-sized population. Addition of benthic diatoms to the pelagic algae community had much more negative effects on the reproduction of the large-sized population. This suggests that the large-sized population feeds near benthic to a greater extent than the small-sized population, and that filamentous benthic diatoms interfere with the grazing process. Despite the negative effects of benthic diatoms, the large-sized population could maintain similar or higher reproduction than the small-sized population. In addition, the high grazing efficiency of the large-sized population resulted in a different community composition of algae. Specifically, flagellated species and small sized benthic diatoms were more grazed upon by the large-sized population. Our results show that morphologically divergent, yet phylogenetically closely related zooplankton populations can have different ecosystem functions, and in turn have different population increase in response to resource supply and algae community.

  • 70.
    Karlsson, Konrad
    et al.
    Stockholm University, Faculty of Science, Department of Ecology, Environment and Plant Sciences.
    Winder, Monika
    Stockholm University, Faculty of Science, Department of Ecology, Environment and Plant Sciences.
    Local adaptation and phenotypic plasticity in populations of the Baltic Sea copepod Eurytemora affinisManuscript (preprint) (Other academic)
  • 71.
    Keehnen, Naomi
    et al.
    Stockholm University, Faculty of Science, Department of Zoology, Population Genetics.
    Fors, Lisa
    Stockholm University, Faculty of Science, Department of Zoology, Population Genetics.
    Integrating immune cell expression with signatures of selection suggests novel targets in melanin trafficking for geographic differences in melanin-related immune performanceManuscript (preprint) (Other academic)
  • 72.
    Keehnen, Naomi
    et al.
    Stockholm University, Faculty of Science, Department of Zoology, Population Genetics.
    Fors, Lisa
    Stockholm University, Faculty of Science, Department of Zoology, Population Genetics.
    Järver, Peter
    Stockholm University, Faculty of Science, Department of Molecular Biosciences, The Wenner-Gren Institute.
    Spetz, Anna-Lena
    Stockholm University, Faculty of Science, Department of Molecular Biosciences, The Wenner-Gren Institute.
    Nylin, Sören
    Stockholm University, Faculty of Science, Department of Zoology, Animal Ecology.
    Theopold, Ulrich
    Stockholm University, Faculty of Science, Department of Molecular Biosciences, The Wenner-Gren Institute.
    Wheat, Christopher
    Stockholm University, Faculty of Science, Department of Zoology, Population Genetics.
    Geographic variation in hemocyte diversity and phagocytic propensity shows a diffuse genomic signature in the green veined white butterflyManuscript (preprint) (Other academic)
    Abstract [en]

    Insects rely on their innate immune system to successfully mediate complex interactions with their internal microbiota, as well as the microbes present in the environment. Given the variation in microbes across habitats, the challenges to respond to them is likely to result in local adaptation in the immune system. Here we focus upon phagocytosis, a mechanism by which pathogens and foreign particles are engulfed in order to be contained, killed and processed for antigen presentation. We investigated the phenotypic and genetic variation related to phagocytosis, in two allopatric populations of the butterfly Pieris napi. We found that the populations differ in their hemocyte composition, and overall phagocytic capability, driven by the increased phagocytic propensity of each cell type. However, no evidence for divergence in phagocytosis-related genes was observed, though an enrichment of genes involved in glutamine metabolism was found, which have recently been linked to immune cell differentiation in mammals.

  • 73.
    Keehnen, Naomi L. P.
    et al.
    Stockholm University, Faculty of Science, Department of Zoology, Population Genetics.
    Kučerova, Lucie
    Stockholm University, Faculty of Science, Department of Molecular Biosciences, The Wenner-Gren Institute. Biology Centre CAS, Czech Republic.
    Nylin, Sören
    Stockholm University, Faculty of Science, Department of Zoology, Animal Ecology.
    Theopold, Ulrich
    Stockholm University, Faculty of Science, Department of Molecular Biosciences, The Wenner-Gren Institute.
    Wheat, Christopher W.
    Stockholm University, Faculty of Science, Department of Zoology, Population Genetics.
    The consequences of surviving infection across the metamorphic boundary: tradeoff insights from RNAseq and life history measuresManuscript (preprint) (Other academic)
    Abstract [en]

    The broad diversity of insect life has been shaped, in part, by pathogen pressure, yet the influence of injury and infection during critical periods of development is understudied. During development, insects undergo metamorphosis, wherein the organism experiences a dramatic shift in their overall morphology, and physiology. In temperate zones, metamorphosis is often directly followed by a developmental arrest called diapause, for which the insect needs to acquire enough energy reserves before the onset of winter. We investigated the long-term effects of injury and infection using two bacteria in the butterfly Pieris napi, revealing that the negative consequences of bacterial infection carry across the metamorphic boundary. Initial direct effects of infection were weight loss and slower development, as well as an increased mortality at higher infection levels. The detrimental effects were stronger in the gram-positive Micrococcus luteus compared to gram-negative Escherichia coli. Transcriptome-wide differences between the two bacteria were already observed in the gene expression profile of the first 24 hours after infection. Larvae infected with M. luteus showed a strong suppression of all non-immunity related processes, with several types of immune responses being activated. The impact of these transcriptomic changes, a tradeoff between homeostasis and immune response, were visible in the life history data, wherein individuals infected with M. luteus had the highest mortality rate, along with the lowest pupal weight, developmental rate and adult weight of all the treatments. Overall, we find that the cost of infection and wounding in the final larval instar carries over the metamorphic boundary, and is expected to negatively affect their lifetime fitness.

  • 74.
    Keehnen, Naomi L. P.
    et al.
    Stockholm University, Faculty of Science, Department of Zoology.
    Rolff, Jens
    Theopold, Ulrich
    Stockholm University, Faculty of Science, Department of Molecular Biosciences, The Wenner-Gren Institute.
    Wheat, Christopher W.
    Stockholm University, Faculty of Science, Department of Zoology.
    Insect Antimicrobial Defences: A Brief History, Recent Findings, Biases, and a Way Forward in Evolutionary Studies2017In: Advances in Insect Physiology, ISSN 0065-2806, E-ISSN 2213-6800, Vol. 52, p. 1-33Article in journal (Refereed)
    Abstract [en]

    We propose that an evolutionary and phenotype-driven approach, harnessing current technological developments, has much to offer for our understanding of insect immunity. After briefly reviewing the history of the discovery of canonical immune system, the current understanding of its components is reviewed and then we argue that the current paradigm of research may be biassed due to (a) its limited taxonomic perspective, (b) the evolutionary time scale being studied, and (c) a focus primarily if not exclusively, upon the canonical, humoural gene set. For the rest of the review, we then discuss the importance of a phenotype down approach as an understudied perspective, exemplified by the need for understanding the basis of cellular responses and wounding as a source of selection on immunity in the wild. We propose that research on those topics almost certainly will provide new insights into the evolution of the insect immune system.

  • 75.
    Keehnen, Naomi L.P.
    Stockholm University, Faculty of Science, Department of Zoology.
    Immunity & the butterfly: A functional genomic study of natural variation in immunity2019Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    Butterflies are ubiquitous and abundant, occurring in a wide variety of environments that contain diverse microbial communities with varied pathogenic pressures. These pathogens and parasites present a constant threat to organisms, and have led to the evolution of complex and intricate immune responses. Despite strong selection against immunological threats, organisms display great variation in their immune capabilities, both on the genetic and physiological level. Investigating this variation remains challenging, since differences in immune responses might arise from changes in the amount, size or performance of cells or organs. Disentangling these relative contributions is important, as the targets of selection are expected to differ, ranging from immune genes directly related to the phenotype to genes indirectly involved via cell proliferation. This thesis focuses on characterizing the immune system of the butterfly Pieris napi and investigating its remarkable variation across populations by using both phenotypic and genotypic measurements. By integrating RNA-seq with life history measurements, I found that the cost of infection and wounding in the final larval stage carries over the metamorphic boundary in P. napi (Paper II). Using population comparisons, I identified both the action and potential targets of natural selection in wild populations within their respective immune responses (Paper I, III & IV). The immune genes in P. napi show increased genetic variation compared to the rest of the genome, and microevolutionary selection dynamics act on these genes between and among populations (Paper I). I measured the cellular immune responses related to phagocytosis and melanization in common garden reared larvae originating from two allopatric populations (Spain, Sweden) (Paper III & IV). The two populations were found to differ in their blood cell composition, and overall phagocytic capability, driven by the increased phagocytic propensity of each cell type (Paper III). However, genome wide analysis of divergence between these populations found no excess genetic differentiation in genes annotated to phagocytic capacity, suggesting that our observed population differences might arise from genes affecting the activation or transdifferentiation of cells, which currently lack functional annotation. Interestingly, genes involved in glutamine metabolism, which have been linked to immune cell differentiation in mammals, did show divergence between the populations. In addition, the populations also differed in prophenoloxidase activity, a common method for quantifying immune related melanization in insects, along with the abundance of the cell-type (oenocytoids) related to this important immune function (Paper IV). Integrative analysis using both transcriptomic and genomic data revealed that the genes involved in this phenotype showed no significant differentiation between the populations. However, a gene involved with proper trafficking of melanogenic enzymes in vertebrates was found to be highly expressed and highly diverged between the two populations, providing an interesting candidate for future studies. This thesis demonstrates the advantages of integrating several genomic tools with lab experiments to quantify natural variation in the immune system of butterflies.

     

  • 76.
    Kivela, Sami M.
    et al.
    Stockholm University, Faculty of Science, Department of Zoology. University of Oulu.
    Valimaki, Panu
    Gotthard, Karl
    Stockholm University, Faculty of Science, Department of Zoology.
    SEASONALITY MAINTAINS ALTERNATIVE LIFE-HISTORY PHENOTYPES2013In: Evolution, ISSN 0014-3820, E-ISSN 1558-5646, Vol. 67, no 11, p. 3145-3160Article in journal (Refereed)
    Abstract [en]

    Many organisms express discrete alternative phenotypes (polyphenisms) in relation to predictable environmental variation. However, the evolution of alternative life-history phenotypes remains poorly understood. Here, we analyze the evolution of alternative life histories in seasonal environments by using temperate insects as a model system. Temperate insects express alternative developmental pathways of diapause and direct development, the induction of a certain pathway affecting fitness through its life-history correlates. We develop a methodologically novel and holistic simulation model and optimize development time, growth rate, body size, reproductive effort, and adult life span simultaneously in both developmental pathways. The model predicts that direct development should be associated with shorter development time (duration of growth) and adult life span, higher growth rate and reproductive effort, smaller body size as well as lower fecundity compared to the diapause pathway, because the two generations divide the available time unequally. These predictions are consistent with many empirical data. Our analysis shows that seasonality alone can explain the evolution of alternative life histories.

  • 77.
    Kodandaramaiah, Ullasa
    et al.
    Stockholm University, Faculty of Science, Department of Zoology.
    Weingartner, Elisabet
    Stockholm University, Faculty of Science, Department of Zoology.
    Janz, Niklas
    Stockholm University, Faculty of Science, Department of Zoology.
    Dalén, L.
    Nylin, Sören
    Stockholm University, Faculty of Science, Department of Zoology.
    Population structure in relation to host-plant ecology and Wolbachia infestation in the comma butterfly2011In: Journal of Evolutionary Biology, ISSN 1010-061X, E-ISSN 1420-9101, Vol. 24, no 10, p. 2173-2185Article in journal (Refereed)
    Abstract [en]

    Experimental work on Polygonia c-album, a temperate polyphagous butterfly species, has shown that Swedish, Belgian, Norwegian and Estonian females are generalists with respect to host-plant preference, whereas females from UK and Spain are specialized on Urticaceae. Female preference is known to have a strong genetic component. We test whether the specialist and generalist populations form respective genetic clusters using data from mitochondrial sequences and 10 microsatellite loci. Results do not support this hypothesis, suggesting that the specialist and generalist traits have evolved more than once independently. Mitochondrial DNA variation suggests a rapid expansion scenario, with a single widespread haplotype occurring in high frequency, whereas microsatellite data indicate strong differentiation of the Moroccan population. Based on a comparison of polymorphism in the mitochondrial data and sequences from a nuclear gene, we show that the diversity in the former is significantly less than that expected under neutral evolution. Furthermore, we found that almost all butterfly samples were infected with a single strain of Wolbachia, a maternally inherited bacterium. We reason that indirect selection on the mitochondrial genome mediated by a recent sweep of Wolbachia infection has depleted variability in the mitochondrial sequences. We also surmise that P. c-album could have expanded out of a single glacial refugium and colonized Morocco recently.

  • 78.
    Kodandaramaiah, Ullasa
    et al.
    Stockholm University, Faculty of Science, Department of Zoology.
    Weingartner, Elisabet
    Stockholm University, Faculty of Science, Department of Botany.
    Janz, Niklas
    Stockholm University, Faculty of Science, Department of Zoology.
    Leski, Michael
    Slove, Jessica
    Stockholm University, Faculty of Science, Department of Zoology.
    Warren, Andrew
    Nylin, Sören
    Stockholm University, Faculty of Science, Department of Zoology.
    Investigating concordance among genetic data, subspecies circumscriptions and hostplant use in the nymphalid butterfly polygonia faunus2012In: PLoS ONE, ISSN 1932-6203, E-ISSN 1932-6203, Vol. 7, no 7, p. e41058-Article in journal (Refereed)
    Abstract [en]

    Subspecies are commonly used taxonomic units to formally describe intraspecific geographic variation in morphological traits. However, the concept of subspecies is not clearly defined, and there is little agreement about what they represent in terms of evolutionary units, and whether they can be used as reliably useful units in conservation, evolutionary theory and taxonomy. We here investigate whether the morphologically well-characterized subspecies in the North American butterfly Polygonia faunus are supported by genetic data from mitochondrial sequences and eight microsatellite loci. We also investigate the phylogeographic structure of P. faunus and test whether similarities in host-plant use among populations are related to genetic similarity. Neither the nuclear nor the mitochondrial data corroborated subspecies groupings. We found three well defined genetic clusters corresponding to California, Arizona and (New Mexico+Colorado). There was little structuring among the remaining populations, probably due to gene flow across populations. We found no support for the hypothesis that similarities in host use are related to genetic proximity. The results indicate that the species underwent a recent rapid expansion, probably from two glacial refugia in western North America. The mitochondrial haplotype network indicates at least two independent expansion phases into eastern North America. Our results clearly demonstrate that subspecies in P. faunus do not conform to the structuring of genetic variation. More studies on insects and other invertebrates are needed to better understand the scope of this phenomenon. The results of this study will be crucial in designing further experiments to understand the evolution of hostplant utilization in this species.

  • 79. Koren, Lee
    et al.
    Matas, Devorah
    Pečnerová, Patrícia
    Stockholm University, Faculty of Science, Department of Zoology. Swedish Museum of Natural History, Sweden.
    Dalén, Love
    Stockholm University, Faculty of Science, Department of Zoology. Swedish Museum of Natural History, Sweden.
    Tikhonov, Alexei
    Gilbert, M. Thomas P.
    Geffen, Eli
    Testosterone in ancient hair from an extinct speciesManuscript (preprint) (Other academic)
  • 80.
    Kotrschal, Alexander
    et al.
    Stockholm University, Faculty of Science, Department of Zoology, Ethology. University of Veterinary Medicine, Austria.
    Buechel, Séverine D.
    Stockholm University, Faculty of Science, Department of Zoology, Ethology. University of Veterinary Medicine, Austria.
    Zala, Sarah M.
    Corral Lopez, Alberto
    Stockholm University, Faculty of Science, Department of Zoology, Ethology.
    Penn, Dustin J.
    Kolm, Niclas
    Stockholm University, Faculty of Science, Department of Zoology, Ethology.
    Brain size affects female but not male survival under predation threat2015In: Ecology Letters, ISSN 1461-023X, E-ISSN 1461-0248, Vol. 18, no 7, p. 646-652Article in journal (Refereed)
    Abstract [en]

    There is remarkable diversity in brain size among vertebrates, but surprisingly little is known about how ecological species interactions impact the evolution of brain size. Using guppies, artificially selected for large and small brains, we determined how brain size affects survival under predation threat in a naturalistic environment. We cohoused mixed groups of small- and large-brained individuals in six semi-natural streams with their natural predator, the pike cichlid, and monitored survival in weekly censuses over 5 months. We found that large-brained females had 13.5% higher survival compared to small-brained females, whereas the brain size had no discernible effect on male survival. We suggest that large-brained females have a cognitive advantage that allows them to better evade predation, whereas large-brained males are more colourful, which may counteract any potential benefits of brain size. Our study provides the first experimental evidence that trophic interactions can affect the evolution of brain size.

  • 81.
    Krüger, Åsa
    et al.
    Stockholm University, Faculty of Science, Department of Botany. Stockholm University, Faculty of Science, The Bergius Botanical Garden Museum.
    Razafimandimbison, Sylvain G.
    Stockholm University, Faculty of Science, The Bergius Botanical Garden Museum.
    Bremer, Birgitta
    Stockholm University, Faculty of Science, The Bergius Botanical Garden Museum.
    Molecular phylogeny of the tribe Danaideae (Rubiaceae: Rubioideae): Another example of out-of-Madagascar dispersal2012In: Taxon, ISSN 0040-0262, E-ISSN 1996-8175, Vol. 61, no 3, p. 629-636Article in journal (Refereed)
    Abstract [en]

    Extensive efforts have been made to resolve the phylogeny of the large coffee family (Rubiaceae) based on molecular data. As a result, several small tribes have been described, but the phylogenies and generic delimitations for many of these groups remain unclear. This study focuses on the small tribe Danaideae that belongs to subfamily Rubioideae and whose generic limits have not previously been addressed with molecular data. It is the sole rubiaceous tribe distributed almost entirely in the Western Indian Ocean region, with the exception of the East African Danais xanthorrhoea. The tribe consists of three genera: Danais, Payera (including the monotypic genus Coursiana), and Schismatoclada. We present the first molecular phylogenetic study of Danaideae including representatives from all three genera and using Bayesian and maximum parsimony methods and sequence data from nuclear DNA (nrITS) and chloroplast DNA (petD, psbA-trnH, rpl32-trnL(UAG), rps16). Our main objectives were to rigorously test the monophyly of Danaideae as currently circumscribed and assess phylogenetic relationships within the tribe. The findings of this study shed light on the colonization history of the tribe. Our analyses reaffirm the monophyly of Danaideae and Danais but reveal the paraphyly of Payera and Schismatoclada. The close relationship between the three Danaideae genera and Coursiana is supported. However, we found very little support for the inclusion of the latter genus in Payera as proposed earlier. The tribe is resolved in two morphologically distinct major lineages, the highly supported Damns clade with lianescent habit (= Danais sensu Buchner & Puff) and the Payera-Schismatoclada clade with arborescent habit. The Malagasy and Mauritian specimens of Danais fragrans are not closely related, and we restrict D. fragrans to the Mauritian taxa and resurrect Danais lyallii Baker to accommodate the Malagasy D. fragrans. According to our analysis. Madagascar is the origin of all species of Danaideae occurring in the Comoro archipelago, East Africa, and Mauritius. The Mauritian and East African Danais each is the result of a single colonization event, while there were at least two independent colonization events to the Comoros.

  • 82.
    Larsson, Josefine
    et al.
    Södertörns högskola.
    Lind, Emma
    Stockholm University, Faculty of Science, Department of Zoology. Södertörns högskola.
    Hallgren, Stefan
    Södertörns högskola.
    From AFLP to sequence specific markers: Identifying genomic regions under selection in the three-spined stickleback caused by pulp mill effluentsManuscript (preprint) (Other academic)
    Abstract [en]

    The processes underlying divergent selection and genetic adaptation have been on the evolutionary biologists agenda for a long time. In this study we used the three-spined stickleback (Gasterosteus aculeatus) study system, a perfect system to study the evolution of similar traits in different lineages exposed to similar environmental conditions. Lind and Grahn (2011) have found directional selection caused by pulp mill effluent on populations of three-spined stickleback along the Swedish coast. In their study, they identified 21 AFLP- outlier loci indicated to be under selection. Here we converted some of these anonymous AFLP loci into sequenced markers and aligned them to the stickleback genome. Four out of five loci, aligned within or close to coding regions, on chromosome I, chromosome VIII, chromosome XIX and chromosome XX. One of the locus, located on chromosome VIII, have been identified to be under selection for fresh water adaption in other studies, including Baltic Sea stickleback populations (Mäkinen et al. 2008a,b). We believe that this is feasibly method that can be used as a starting point for identification of genes and genomic regions possible involved in adaptation, both for model and non-model organisms. 

  • 83.
    Lehmann, Philipp
    et al.
    Stockholm University, Faculty of Science, Department of Zoology.
    Van der Bijl, Wouter
    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.
    Gotthard, Karl
    Stockholm University, Faculty of Science, Department of Zoology.
    Timing of diapause termination in relation to variation in winter climate2017In: Physiological entomology (Print), ISSN 0307-6962, E-ISSN 1365-3032, Vol. 42, no 3, p. 232-238Article in journal (Refereed)
    Abstract [en]

    In temperate insects, winters are typically endured by entering diapause, which comprises a deep resting stage. Correct timing of diapause termination is vital for synchronization of emergence with conspecifics and for mobilizing resources when conditions for growth and reproduction become favourable. Although critical to survival, the intrinsic and extrinsic drivers of diapause termination timing are poorly understood. In the present study, we investigate diapause development under a range of durations (10-24weeks) spent at different temperatures (-2 to 10 degrees C) in the pupal diapausing butterfly Pieris napi Linnaeus (Lepidoptera: Pieridae). We determine: (i) the maximum cold temperature for diapause development; (ii) if pupae in diapause count cold days or cold sums; and (iii) whether diapause termination is distinct or gradual. The results indicate large and idiosyncratic effects of high and low nonlethal temperatures on diapause development in P. napi. Although all temperatures tested lead to diapause termination, a thermal optimum between 2 and 4 degrees C is observed. Lower temperatures lead to decreased eclosion propensity, whereas higher temperatures slow down development and increase emergence desynchronization. These data suggest that, rather than a simple cold-summing process with a distinct diapause termination point, there are trade-offs between time and temperature at the low and high end of the thermal range, resulting in a nonlinear thermal landscape showing a ridge of increasing eclosion propensity at moderate temperatures. The present study suggests that the effects of temperature on diapause development should be included in projections on post-winter phenology models of insects, including pest species.

  • 84.
    Leimar, Olof
    et al.
    Stockholm University, Faculty of Science, Department of Zoology.
    Hartfelder, Klaus
    Laubichler, Manfred D.
    Page, Robert E., Jr.
    Development and evolution of caste dimorphism in honeybees: a modeling approach2012In: Ecology and Evolution, ISSN 2045-7758, Vol. 2, no 12, p. 3098-3109Article in journal (Refereed)
    Abstract [en]

    The difference in phenotypes of queens and workers is a hallmark of the highly eusocial insects. The caste dimorphism is often described as a switch-controlled polyphenism, in which environmental conditions decide an individual's caste. Using theoretical modeling and empirical data from honeybees, we show that there is no discrete larval developmental switch. Instead, a combination of larval developmental plasticity and nurse worker feeding behavior make up a colony-level social and physiological system that regulates development and produces the caste dimorphism. Discrete queen and worker phenotypes are the result of discrete feeding regimes imposed by nurses, whereas a range of experimental feeding regimes produces a continuous range of phenotypes. Worker ovariole numbers are reduced through feeding-regime-mediated reduction in juvenile hormone titers, involving reduced sugar in the larval food. Based on the mechanisms identified in our analysis, we propose a scenario of the evolutionary history of honeybee development and feeding regimes.

  • 85.
    Leimar, Olof
    et al.
    Stockholm University, Faculty of Science, Department of Zoology, Ethology.
    Norberg, Ulf
    Stockholm University, Faculty of Science, Department of Zoology, Animal Ecology.
    Metapopulation extinction and genetic variation in dispersal-related traits1997In: Oikos, ISSN 0030-1299, E-ISSN 1600-0706, Vol. 80, p. 448-458Article in journal (Refereed)
  • 86.
    Leimar, Olof
    et al.
    Stockholm University, Faculty of Science, Department of Zoology.
    Tullberg, Birgitta S.
    Stockholm University, Faculty of Science, Department of Zoology.
    Mallet, James
    Mimicry, saltational evolution, and the crossing of fitness valleys2012In: The adaptive landscape in evolutionary biology / [ed] Erik I. Svensson, Ryan Calsbeek, New York: Oxford University Press, 2012, p. 259-270Chapter in book (Refereed)
  • 87.
    Liao, Te-Yu
    et al.
    Stockholm University, Faculty of Science, Department of Zoology.
    Kullander, Sven O.
    Fang, Fang
    Phylogenetic position of rasborin cyprinids and monophyly of major lineages among the Danioninae, based on morphological characters (Cypriniformes: Cyprinidae)2011In: Journal of Zoological Systematics and Evolutionary Research, ISSN 0947-5745, E-ISSN 1439-0469, Vol. 49, no 3, p. 224-232Article in journal (Refereed)
    Abstract [en]

    The cyprinid subfamily Danioninae is one of the most important fish groups due to its inclusion of the model fish, Danio rerio. Molecular investigations have shown that species traditionally placed in the Danioninae are non-monophyletic, divided into two groups corresponding to the Danioninae and Opsariichthyinae. The Danioninae are further divided into three lineages, i.e. chedrins, danionins and rasborins. However, morphological characters determining the foregoing groups are unknown. To investigate the interrelationships among major lineages within the Danioninae, a phylogenetic analysis based on 43 morphological characters from 34 taxa was conducted. Parsimony analysis recovers the Danioninae and Opsariichthyinae to be distinguished by the Y-shaped ligament, absent in the Danioninae while present in the Opsariichthyinae. The Danioninae are divided into two tribes, Danionini and Rasborini. The Rasborini, including Boraras, Brevibora, Horadandia, Kottelatia, Rasbora, Rasboroides, Rasbosoma, Trigonopoma and Trigonostigma, are diagnosed by presence of dark supra-anal pigment and subpeduncular streak as well as presence of the rasborin process on epibranchial 4. The Danionini are composed of two subtribes, Danionina and Chedrina, the Danionina including Chela, Danio, Devario, Microdevario and Microrasbora, and the Chedrina comprising Chelaethiops, Esomus, Luciosoma, Megarasbora, Mesobola, Nematabramis, Opsarius, Raiamas and Salmophasia. The Danionina are diagnosed by the unossified interhyal and presence of the danionin foramen in the horizontal limb of the cleithrum while the Chedrina are characterized by the postcleithrum absent or greatly reduced and approximately normal to abdominal ribs when present.

  • 88.
    Lind, Emma
    Stockholm University, Faculty of Science, Department of Zoology.
    Genetic response to pollution in sticklebacks; natural selection in the wild2013Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    The last century, humans have been altering almost all natural environments at an accelerating rate, including the Baltic Sea that has highly eutrophicated areas and many coastal industries such as Pulp-mills. For animals living in a habitat that changes there are basically two alternatives, either to cope with the change or become locally extinct. This thesis aims to investigate if recent anthropogenic disturbance in the Baltic Sea can affect natural populations on a genetic level through natural selection.

    First, we found a fine-scale genetic structure in three-spine sticklebacks (Gasterosteus aculeatus) populations along the Swedish coast (paper I), indicating limited gene-flow between populations in geographic proximity. Different genetic markers, specifically Amplified Fragment Lenght Polymorpism (AFLP, and microsatellites,  gave different results, highlighting the heterogeneous character of genomes which demonstrates that it is important to choose a genetic marker that is relevant for the question at hand. With a population genomic approach, and a multilocus genetic marker (AFLP), we detected convergent evolution in genotype composition in stickleback populations living in environments affected by pulp-mill effluent (paper II) and in highly eutrophicated environments (paper III), compared to adjacent reference populations. We found loci, in both studies (paper II, III), that were different from a neutral distribution and thus probably under divergent selection for the habitat differences investigated. The selective effect from pulp-mill effluents were more pronounced, but the two different habitats had mutual characters (AFLP loci). In paper IV, we converted five anonymous AFLP loci to sequenced markers and aligned them to the stickleback genome. Four out of five loci aligned within, or close to, coding regions on chromosome I, chromosome VIII, chromosome XIX and chromosome XX. One of the loci, located on chromosome VIII and identified as under divergent selection in both paper II and III, has been identified in other studies as to be under selection for fresh water adaptation, including Baltic Sea stickleback populations.

    In conclusion, anthropogenic alterations of natural environments can have evolutionary consequences, probably adaptive, for the animals living there and the evolutionary response exhibited by natural populations can be very fast.

  • 89.
    Lind, Emma E.
    et al.
    Södertörns högskola.
    Grahn, Mats
    Södertörns högskola.
    Directional genetic selection by pulp mill effluent on multiple populations of three-spined stickleback (Gasterosteus aculeatus)2011In: Ecotoxicology, ISSN 0963-9292, E-ISSN 1573-3017, Vol. 20, no 3, p. 503-512Article in journal (Refereed)
    Abstract [en]

    Contamination can cause a rapid environmental change which may require populations to respond with evolutionary changes. To evaluate the effects of pulp mill effluents on population genetics, we sampled three-spined sticklebacks (Gasterosteus aculeatus) near four pulp mills and four adjacent reference sites and analyzed Amplified Fragment Length Polymorphism (AFLP) to compare genetic variability. A fine scale genetic structure was detected and samples from polluted sites separated from reference sites in multidimensional scaling plots (P < 0.005, 1000 permutations) and locus-by-locus Analysis of Molecular Variance (AMOVA) further confirmed that habitats are significantly separated (F-ST = 0.021, P < 0.01, 1023 permutations). The amount of genetic variation between populations did not differ between habitats, and populations from both habitats had similar levels of heterozygosity (polluted sites Nei's Hs = 0.11, reference sites Nei's Hs = 0.11). Still, pairwise F-ST: s between three, out of four, pairs of polluted-reference sites were significant. A F-ST-outlier analysis showed that 21 (8.4%) loci were statistically different from a neutral distribution at the P < 0.05 level and therefore indicated to be under divergent selection. When removing 13 F-ST-outlier loci, significant at the P < 0.01 level, differentiation between habitats disappeared in a multidimensional scaling plot. In conclusion, pulp mill effluence has acted as a selective agent on natural populations of G. aculeatus, causing a convergence in genotype composition change at multiple sites in an open environment.

  • 90.
    Lind, Emma
    et al.
    Stockholm University, Faculty of Science, Department of Zoology. Södertörns högskola.
    Larsson, Josefine
    Södertörns högskola.
    Tuomainen, Ulla
    University of Helsinki.
    Borg, Malin
    Södertörns högskola.
    Candolin, Ulrika
    University of Helsinki.
    Grahn, ts
    Södertörns högskola.
    Genetic response to eutrophication in three-spined sticklebacks (Gasterosteus aculeatus): A study of multiple Baltic Sea populationsManuscript (preprint) (Other academic)
    Abstract [en]

    Anthropogenic activities are causing change in natural habitats at an accelerating rate and affecting populations by altered selection pressures. One example is human-induced eutrophication in the Baltic Sea, were behaviour alterations are well documented in three-spined sticklebacks (Gasterosteus aculeatus). Here we have used 204 variable Amplified Fragment Length Polymorphism (AFLP) markers to investigate genetic differences between a set of ten hierarchal sampled populations of sticklebacks, five populations inhabiting eutrophicated habitats and five from control populations, in total 292 individuals. We found significant genetic variation that could be attributed to habitat (4.3% AMOVA). A combination of FST outlier analysis and classification analysis revealed seven AFLP-loci likely to be affected by divergent selection by eutrophication. Four of these seven loci have earlier been identified as under selection in stickleback populations living in pulp-mill effluents suggesting some similar selective factors between eutrophication and pulp-mill effluent effected habitats. 

  • 91.
    Lind, Johan
    Stockholm University, Faculty of Humanities, Department of Archaeology and Classical Studies, Centre for the Study of Cultural Evolution.
    Näbbars ursprung2017In: Vår fågelvärld med Fågelvännen, ISSN 2002-2743, no 4, p. 20-24Article in journal (Other (popular science, discussion, etc.))
  • 92.
    Lindenfors, Patrik
    Stockholm University, Faculty of Science, Department of Zoology, Animal Ecology. Stockholm University, Faculty of Humanities, Centre for Cultural Evolution.
    Claphaminstitutets lögner om evolutionsteorin2010In: NewsmillArticle in journal (Other (popular science, discussion, etc.))
  • 93.
    Lindenfors, Patrik
    Stockholm University, Faculty of Science, Department of Zoology, Animal Ecology. Stockholm University, Faculty of Humanities, Centre for the Study of Cultural Evolution.
    Det ligger i människans natur att ha kultur2010In: Tvärsnitt, no 2Article in journal (Other academic)
  • 94.
    Lindenfors, Patrik
    Stockholm University, Faculty of Science, Department of Zoology, Animal Ecology. Stockholm University, Faculty of Humanities, Department of Archaeology and Classical Studies, Centre for the Study of Cultural Evolution.
    For Whose Benefit? The Biological and Cultural Evolution of Human Cooperation2017Book (Refereed)
    Abstract [en]

    This book takes the reader on a journey, navigating the enigmatic aspects of cooperation; a journey that starts inside the body and continues via our thoughts to the human super-organism.

    Cooperation is one of life’s fundamental principles. We are all made of parts – genes, cells, organs, neurons, but also of ideas, or ‘memes’. Our societies too are made of parts – us humans. Is all this cooperation fundamentally the same process?

    From the smallest component parts of our bodies and minds to our complicated societies, everywhere cooperation is the organizing principle. Often this cooperation has emerged because the constituting parts have benefited from the interactions, but not seldom the cooperating units appear to lose on the interaction. How then to explain cooperation? How can we understand our intricate societies where we regularly provide small and large favors for people we are unrelated to, know, or even never expect to meet again? Where does the idea come from that it is right to risk one’s life for country, religion or freedom? The answers seem to reside in the two processes that have shaped humanity: biological and cultural evolution.

  • 95.
    Lindenfors, Patrik
    Stockholm University, Faculty of Science, Department of Zoology, Animal Ecology. Stockholm University, Faculty of Humanities, Centre for the Study of Cultural Evolution.
    Memetik, teori om hur mem uppstår, sprids och är utsatta för urval2017In: Nationalencyklopedin: 2016, Malmö: NE Nationalencyklopedin , 2017Chapter in book (Other academic)
  • 96.
    Lindenfors, Patrik
    Stockholm University, Faculty of Science, Department of Zoology, Animal Ecology. Stockholm University, Faculty of Humanities, Centre for Cultural Evolution.
    Om konsten att vara tacksam2015In: Uppdrag mission, ISSN 2001-0087, Vol. 169, no 1Article in journal (Other (popular science, discussion, etc.))
  • 97.
    Lindenfors, Patrik
    Stockholm University, Faculty of Science, Department of Zoology, Animal Ecology. Stockholm University, Faculty of Humanities, Department of Archaeology and Classical Studies, Centre for Cultural Evolution. Institute for Future Studies, Sweden.
    Primate Social Evolution2018In: The International Encyclopedia of Anthropology, John Wiley & Sons, 2018Chapter in book (Refereed)
    Abstract [en]

    Primates display a remarkable diversity of types of social organization—a diversity that, according to the socioecological model of social evolution, is ultimately determined by ecological factors limiting female fitness and the number of matings limiting male fitness. The foremost ecological determinants of female sociality are the degree to which food resources are defendable, either alone or in a group, and the level of protection from predators gained from being part of a group. Further factors that have been proposed are the presence of infanticide, coalitions, and dominance hierarchies; general population density and habitat saturation; whether competition is mainly intra‐ or intergroup; and which sex disperses. Male sociality is instead mainly determined by the spatiotemporal spacing of mating opportunities with females. Some researchers have also proposed that cognitive abilities impose a limit on group size, since primate sociality demands competent navigation of social networks.

  • 98.
    Lindenfors, Patrik
    Stockholm University, Faculty of Science, Department of Zoology, Animal Ecology. Stockholm University, Faculty of Humanities, Centre for the Study of Cultural Evolution.
    Religion har evolverat för att passa våra psyken2013Other (Other (popular science, discussion, etc.))
  • 99.
    Lindenfors, Patrik
    Stockholm University, Faculty of Science, Department of Zoology, Animal Ecology. Stockholm University, Faculty of Humanities, Centre for the Study of Cultural Evolution.
    Samarbete: människans väg till framgång - om de många nivåer av samarbete som bygger upp oss och våra samhällen2011Book (Other academic)
  • 100.
    Lindenfors, Patrik
    Stockholm University, Faculty of Science, Department of Zoology, Animal Ecology. Stockholm University, Faculty of Humanities, Centre for the Study of Cultural Evolution.
    Varifrån kommer känslor och värderingar?2013In: Sans, ISSN 2000-9690, Vol. 1Article in journal (Other (popular science, discussion, etc.))
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