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  • 1. Alneberg, Johannes
    et al.
    Bennke, Christin
    Beier, Sara
    Bunse, Carina
    Quince, Christopher
    Ininbergs, Karolina
    Riemann, Lasse
    Ekman, Martin
    Jürgens, Klaus
    Labrenz, Matthias
    Pinhassi, Jarone
    Andersson, Anders F.
    Ecosystem-wide metagenomic binning enables prediction of ecological niches from genomes2020In: Communications Biology, ISSN 2399-3642, Vol. 3, no 1, article id 119Article in journal (Refereed)
    Abstract [en]

    The genome encodes the metabolic and functional capabilities of an organism and should be a major determinant of its ecological niche. Yet, it is unknown if the niche can be predicted directly from the genome. Here, we conduct metagenomic binning on 123 water samples spanning major environmental gradients of the Baltic Sea. The resulting 1961 metagenome-assembled genomes represent 352 species-level clusters that correspond to 1/3 of the metagenome sequences of the prokaryotic size-fraction. By using machine-learning, the placement of a genome cluster along various niche gradients (salinity level, depth, size-fraction) could be predicted based solely on its functional genes. The same approach predicted the genomes’ placement in a virtual niche-space that captures the highest variation in distribution patterns. The predictions generally outperformed those inferred from phylogenetic information. Our study demonstrates a strong link between genome and ecological niche and provides a conceptual framework for predictive ecology based on genomic data.

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  • 2.
    Andersson, Bea Angelica
    Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences.
    Analysis of Selection and Genetic Drift in a Dioecious Plant: Spatial Genetic Structure and Selection in Phenotypic Traits in a Young Island Population of Silene dioica2014Independent thesis Basic level (degree of Bachelor), 10 credits / 15 HE creditsStudent thesis
    Abstract [en]

    Selection and genetic drift are often competing forces in shaping genetic structure in populations. Genetic drift will often effectively cancel out the effect of selection when population sizes are small, such as in colonizing island populations. On a small island in the Skeppsvik Archipelago in northern Sweden, a newly founded population of Silene dioica has been monitored since it first established around 1993. Though inhabiting an area of merely 173 m2, the population has been shown to exhibit a genetically differentiated patch structure where closely related individuals are tightly grouped, distanced from other family groups. In this study, the effect of selection was evaluated as compared to that of genetic drift. Variation in phenotypic traits in flowers, leaves and stalks were compared to that of neutral markers, in the form of PST and FST measures, to assess a measure of what proportion of differentiation among patches in phenotypic traits could not be attributed to genetic drift. Males and females were analysed separately to obtain measures of sex specific selection. Signs of divergent and stabilizing selection were found in several traits in both males and females despite the small spatial scale and short time since colonization. Further analysis is needed to assess explanations for trait divergence among patches and direction of selection.

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  • 3. Araki, N.H.T.
    et al.
    Khatab, I.A.
    Hemamali, K.K.G.U.
    Inomata,, N.
    Wang, Xiao-Ru
    Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences.
    Szmidt, A.E.
    Phylogeography of Larix sukaczewii Dyl. and Larix sibirica L. inferred from nucleotide variation of nuclear genes2008In: Tree Genetics & Genomes, ISSN 1614-2942, E-ISSN 1614-2950, Vol. 4, p. 611-623Article in journal (Refereed)
    Abstract [en]

    We investigated phylogeography of Larix sukaczewii and Larix sibirica using nucleotide variation at three following nuclear gene regions: 5.8 S rDNA including two internal transcribed spacers (ITS), cinnamyl alcohol dehydrogenase (CAD), and phytochrome-O (PHYO). We also included sequences of the 4-coumarate: coenzyme A ligase (4CL) gene region obtained in our recent study. CAD and PHYO showed very low nucleotide variation, but ITS and 4CL had levels of variation similar to those reported for other conifers. Pleistocene refugia have been hypothesized to exist in the Southern Urals and South Central Siberia, where four out of nine of the investigated populations occur. We found moderate to high levels of population differentiation (FST=0.115–0.531) in some pairwise comparisons suggesting limited gene flow and independent evolution of some refugial populations. In L. sukaczewii, low levels of differentiation were found among populations from areas glaciated during the Pleistocene, indicating their recent origin. Our results also suggest these populations were created by migrants from multiple, genetically distinct refugia. Furthermore, some haplotypes observed in populations from previously glaciated areas were not found in putative refugial populations, suggesting these populations might have contributed little to the extant populations created after the Last Glacial Maximum. Some authors regard L. sukaczewii and L. sibirica as a single species, while others consider them as separate species. The observed conspicuous differences in haplotype composition and distribution between L. sukaczewii and L. sibirica, together with high values of FST between populations of the two species, appear to support the latter classification.

  • 4. Backhouse, Amy
    et al.
    Sait, Steven M.
    Cameron, Tom C.
    Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences.
    Multiple mating in the traumatically inseminating Warehouse pirate bug, Xylocoris flavipes: effects on fecundity and longevity2012In: Biology Letters, ISSN 1744-9561, E-ISSN 1744-957X, Vol. 8, no 5, p. 706-709Article in journal (Refereed)
    Abstract [en]

    Optimal mating frequencies differ between sexes as a consequence of the sexual differentiation of reproductive costs per mating, where mating is normally more costly to females than males. In mating systems where sexual reproduction is costly to females, sexual conflict may cause both direct (i.e. by reducing female fecundity or causing mortality) and indirect (i.e. increased risk of mortality, reduced offspring viability) reductions in lifetime reproductive success of females, which have individual and population consequences. We investigated the direct and indirect costs of multiple mating in a traumatically inseminating (TI) predatory Warehouse pirate bug, Xylocoris flavipes (Reuter) (Hemiptera: Anthocoridae), where the male penetrates the female's abdomen during copulation. This study aimed to quantify the effects of TI on female fecundity, egg viability, the lifetime fecundity schedule, longevity and prey consumption in this cosmopolitan biocontrol agent. We found no difference in the total reproductive output between mating treatments in terms of total eggs laid or offspring viability, but there were significant differences found in daily fecundity schedules and adult longevity. In terms of lifetime reproduction, female Warehouse pirate bugs appear to be adapted to compensate for the costs of TI mating to their longevity.

  • 5. Balint, Miklos
    et al.
    Pfenninger, Markus
    Grossart, Hans-Peter
    Taberlet, Pierre
    Vellend, Mark
    Leibold, Mathew A.
    Englund, Göran
    Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences.
    Bowler, Diana
    Environmental DNA time series in ecology2018In: Trends in Ecology & Evolution, ISSN 0169-5347, E-ISSN 1872-8383, Vol. 33, no 12, p. 945-957Article, review/survey (Refereed)
    Abstract [en]

    Ecological communities change in time and space, but long-term dynamics at the century-to-millennia scale are poorly documented due to lack of relevant data sets. Nevertheless, understanding long-term dynamics is important for explaining present-day biodiversity patterns and placing conservation goals in a historical context. Here, we use recent examples and new perspectives to highlight how environmental DNA (eDNA) is starting to provide a powerful new source of temporal data for research questions that have so far been overlooked, by helping to resolve the ecological dynamics of populations, communities, and ecosystems over hundreds to thousands of years. We give examples of hypotheses that may be addressed by temporal eDNA biodiversity data, discuss possible research directions, and outline related challenges.

  • 6. Berdahl, Andrew
    et al.
    Brelsford, Christa
    De Bacco, Caterina
    Dumas, Marion
    Ferdinand, Vanessa
    Grochow, Joshua A.
    Hebert-Dufresne, Laurent
    Kallus, Yoav
    Kempes, Christopher P.
    Kolchinsky, Artemy
    Larremore, Daniel B.
    Libby, Eric
    Umeå University, Faculty of Science and Technology, Department of Mathematics and Mathematical Statistics.
    Power, Eleanor A.
    Stern, Caitlin A.
    Tracey, Brendan D.
    Dynamics of beneficial epidemics2019In: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 9, article id 15093Article in journal (Refereed)
    Abstract [en]

    Pathogens can spread epidemically through populations. Beneficial contagions, such as viruses that enhance host survival or technological innovations that improve quality of life, also have the potential to spread epidemically. How do the dynamics of beneficial biological and social epidemics differ from those of detrimental epidemics? We investigate this question using a breadth-first modeling approach involving three distinct theoretical models. First, in the context of population genetics, we show that a horizontally-transmissible element that increases fitness, such as viral DNA, spreads superexponentially through a population, more quickly than a beneficial mutation. Second, in the context of behavioral epidemiology, we show that infections that cause increased connectivity lead to superexponential fixation in the population. Third, in the context of dynamic social networks, we find that preferences for increased global infection accelerate spread and produce superexponential fixation, but preferences for local assortativity halt epidemics by disconnecting the infected from the susceptible. We conclude that the dynamics of beneficial biological and social epidemics are characterized by the rapid spread of beneficial elements, which is facilitated in biological systems by horizontal transmission and in social systems by active spreading behavior of infected individuals.

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  • 7.
    Berggren, Hanna
    et al.
    Linnéuniversitetet, Institutionen för biologi och miljö (BOM).
    Nordahl, Oscar
    Linnéuniversitetet, Institutionen för biologi och miljö (BOM).
    Tibblin, Petter
    Linnéuniversitetet, Institutionen för biologi och miljö (BOM).
    Larsson, Per
    Linnéuniversitetet, Institutionen för biologi och miljö (BOM).
    Forsman, Anders
    Linnéuniversitetet, Institutionen för biologi och miljö (BOM).
    Testing for local adaptation to spawning habitat in sympatric subpopulations of pike by reciprocal translocation of embryos2016In: PLoS ONE, ISSN 1932-6203, E-ISSN 1932-6203, Vol. 11, no 5, article id e0154488Article in journal (Refereed)
    Abstract [en]

    We tested for local adaption in early life-history traits by performing a reciprocal translocation experiment with approximately 2,500 embryos of pike (Esox lucius) divided in paired split-family batches. The experiment indicated local adaptation in one of the two subpopulations manifested as enhanced hatching success of eggs in the native habitat, both when compared to siblings transferred to a non-native habitat, and when compared to immigrant genotypes from the other subpopulation. Gene-by-environment effects on viability of eggs and larvae were evident in both subpopulations, showing that there existed genetic variation allowing for evolutionary responses to divergent selection, and indicating a capacity for plastic responses to environmental change. Next, we tested for differences in female life-history traits. Results uncovered that females from one population invested more resources into reproduction and also produced more (but smaller) eggs in relation to their body size compared to females from the other population. We suggest that these females have adjusted their reproductive strategies as a counter-adaptation because a high amount of sedimentation on the eggs in that subpopulations spawning habitat might benefit smaller eggs. Collectively, our findings point to adaptive divergence among sympatric subpopulations that are physically separated only for a short period during reproduction and early development-which is rare. These results illustrate how combinations of translocation experiments and field studies of life-history traits might infer about local adaptation and evolutionary divergence among populations. Local adaptations in subdivided populations are important to consider in management and conservation of biodiversity, because they may otherwise be negatively affected by harvesting, supplementation, and reintroduction efforts targeted at endangered populations.

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  • 8.
    Berner, Daniel
    et al.
    Basel, Switzerland.
    Thibert-Plante, Xavier
    Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences. Knoxville, TN, USA; Uppsala, Sweden.
    How mechanisms of habitat preference evolve and promote divergence with gene flow2015In: Journal of Evolutionary Biology, ISSN 1010-061X, E-ISSN 1420-9101, Vol. 28, no 9, p. 1641-1655Article in journal (Refereed)
    Abstract [en]

    Habitat preference may promote adaptive divergence and speciation, yet the conditions under which this is likely are insufficiently explored. We use individual-based simulations to study the evolution and consequence of habitat preference during divergence with gene flow, considering four different underlying genetically based behavioural mechanisms: natal habitat imprinting, phenotype-dependent, competition-dependent and direct genetic habitat preference. We find that the evolution of habitat preference generally requires initially high dispersal, is facilitated by asymmetry in population sizes between habitats, and is hindered by an increasing number of underlying genetic loci. Moreover, the probability of habitat preference to emerge and promote divergence differs greatly among the underlying mechanisms. Natal habitat imprinting evolves most easily and can allow full divergence in parameter ranges where no divergence is possible in the absence of habitat preference. The reason is that imprinting represents a one-allele mechanism of assortative mating linking dispersal behaviour very effectively to local selection. At the other extreme, direct genetic habitat preference, a two-allele mechanism, evolves under restricted conditions only, and even then facilitates divergence weakly. Overall, our results indicate that habitat preference can be a strong reproductive barrier promoting divergence with gene flow, but that this is highly contingent on the underlying preference mechanism.

  • 9.
    Bernhardsson, Carolina
    Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences.
    Molecular population genetics of inducible defense genes in Populus tremula2012Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    Plant-herbivore interactions are among the most common of ecological interactions. It is therefore not surprising that plants have evolved multiple mechanisms to defend themselves, using both constitutive chemical and physical barriers and by induced responses which are only expressed after herbivory has occurred. Herbivores, on the other hand, respond to these plant defenses by evolving counter-adaptations which makes defenses less effective or even useless. Adaptation can occur at different geographical scales, with varying coevolutionary interactions across a spatially heterogenous landscape. By looking at the underlying genes responsible for these defensive traits and herbivore related phenotypic traits, it is possible to investigate the coevolutionary history of these plant- herbivore interactions. Here I use molecular population genetic tools to investigate the evolutionary history of several inducible defense genes in European Aspen (Populus tremula) in Sweden. Two genes, belonging to the Polyphenol oxidase gene-family (PPO1 and PPO2), show skews in their site frequency spectrum together with patterns of diversity and divergence from an outgroup which correspond to signatures of adaptive evolution (Paper II). 71 single nucleotide polymorphisms (SNPs) from seven inducible defense genes (PPO1-PPO3, TI2-TI5) show elevated levels of population differentiation compared to control genes (genes not involved in plant defense), and 10 of these defense SNPs show strong signatures of natural selection (Paper III). These 71 defense SNPs also divides a sample of Swedish P. tremula trees into three distinct geographical groups, corresponding to a Southern, Central and Northern cluster, a patterns that is not present in control SNPs (Paper III). The same geographical pattern, with a distinct Northern cluster, is also observed in several phenotypic traits related to herbivory in our common garden in Sävar (Paper IV). These phenotypic traits show patterns of apparent local maladaptation of the herbivore community to the host population which could indicate the presence of “information coevolution” between plants and herbivores (Paper IV). 15 unique defense SNPs also show significant associations to eight phenotypic traits but the causal effects of these SNP associations may be confounded by the geographic structure found in both the underlying genes and in the phenotypic traits. The co-occurrence of population structure in both defense genes and herbivore community traits may be the result from historical events during the post-glacial recolonization of Sweden.

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    Molecular population genetics of inducible defense genes in Populus tremula
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    Spikblad C. Bernhardsson
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    Omslag C. Bernhardsson
  • 10.
    Bernhardsson, Carolina
    et al.
    Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Ingvarsson, Pär
    Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Geographic structure and adaptive population differentiation in herbivore defence genes in European aspen (Populus tremula L., Salicaceae)2012In: Molecular Ecology, ISSN 0962-1083, E-ISSN 1365-294X, Vol. 21, no 9, p. 2197-2207Article in journal (Refereed)
    Abstract [en]

    When a phenotypic trait is subjected to spatially variable selection and local adaptation, the underlying genes controlling the trait are also expected to show strong patterns of genetic differentiation since alternative alleles are favored in different geographical locations. Here we study 71 SNPs from seven genes associated with inducible defense responses in a sample of P. tremula collected from across Sweden. Four of these genes (PPO2, TI2, TI4 and TI5) show substantial population differentiation and a PCA conducted on the defense SNPs divides the Swedish population into three distinct clusters. Several defense SNPs show latitudinal clines, although these were not robust to multiple testing. However, five SNPs (located within TI4 and TI5) show strong longitudinal clines that remain significant after multiple test correction. Genetic geographical variation, supporting local adaptation, has earlier been confirmed in genes involved in the photoperiod pathway in P. tremula, but this is, to our knowledge, one of the first times that geographic variation has been found in genes involved in plant defense against antagonists.

  • 11.
    Bernhardsson, Carolina
    et al.
    Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences.
    Robinson, Kathryn M.
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology.
    Abreu, Ilka N.
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology.
    Jansson, Stefan
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology.
    Ingvarsson, Pär K.
    Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences.
    Albrectsen, Benedicte R.
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology.
    Population differentiation in arthropod community structure and phenotypic association with inducible defense genes in European Aspen (Populus tremula L., salicaceae)Manuscript (preprint) (Other academic)
    Abstract [en]

    Plant-herbivore interactions are known to vary across a landscape due to both variation in abiotic and biotic factors. Such spatial variation tends to promoting local adaption of plants to the prevailing herbivore regime. Here we use data from a common garden to look for patterns across populations in the abundance and diversity of herbivorous insects. We also screen for variation in the untargeted metabolome of the foliage of a subset of the same trees. We also search for phenotypic associations between genetic variation in a number of wound-induced genes and phenotypic variation in herbivore abundance, diversity and in metabolomes. We observe significant genetic variation in a number of herbivore-related traits but low correlations between traits. We do observe substantial genetic structure in both herbivore community structure and in metabolic profiles and this structure is aligned with genetic structure we have previously documented for a set of defense genes. We also identify a number of significant associations between SNPs from wound-induced defense genes and a number of the herbivore traits and metabolic profiles. However, these associations are likely not causal, but are rather caused by the underlying population structure we observe. These results highlight to the importance of historical processes and the need to better understand both the current-day geographic distribution of different herbivore species as well as the post-glacial colonization history of both plants and herbivores.

  • 12.
    Bokma, Folmer
    Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences.
    Evolution as a Largely Autonomous Process2015In: Macroevolution: Explanation, Interpretation and Evidence / [ed] Emanuele Serrelli och Nathalie Gontier, Cham: Springer, 2015, p. 87-112Chapter in book (Refereed)
    Abstract [en]

    Evolutionary theory has proven generally successful in predicting phenotypic changes over one or a few generations of natural or artificial selection, but fails to predict evolutionary dynamics over longer periods of time, which is a major shortcoming: At longer timescales, existing theory is largely concerned with a posteriori explanations and cannot even predict whether a population or species will adapt to environmental change, or go extinct. Based on a review of key literature from before Darwin to today, I argue that the reason for this shortcoming is that in the Modern Synthesis fitness is regarded as determined exclusively by how well traits are suited to the biotic and abiotic environment. I argue that much can be gained by explicitly considering that fitness has a significant intrinsic component, determined by how well different traits are adapted to each other. Due to adaptation of traits to each other, those traits that are important for the functioning of many other traits can vary only within narrow tolerance limits. Short-term selection experiments and year-to-year fluctuations in natural populations taking place within these tolerance limits give the appearance of rapid evolution. Yet the tolerance limits will prevent changes to accumulate over time, and hence, these traits evolve in a million years no more than they do in a decade. Only traits like coloration that have little influence on other traits can evolve freely, but that will rarely be sufficient to prevent extinction. Significant evolutionary departures require a reshuffling of the interactions between traits and will often coincide with speciation. Emerging from a complex system of interacting traits, the magnitude and direction of these changes will be largely independent of the factors that triggered them, rendering macroevolution a largely autonomous process.

  • 13.
    Bokma, Folmer
    et al.
    Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences.
    Baek, Seung Ki
    Umeå University, Faculty of Science and Technology, Department of Physics.
    Minnhagen, Petter
    Umeå University, Faculty of Science and Technology, Department of Physics.
    50 years of inordinate fondness2014In: Systematic Biology, ISSN 1063-5157, E-ISSN 1076-836X, Vol. 63, no 2, p. 251-256Article in journal (Refereed)
  • 14.
    Bokma, Folmer
    et al.
    Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences.
    Godinot, Marc
    Maridet, Olivier
    Ladeveze, Sandrine
    Costeur, Loic
    Sole, Floreal
    Gheerbrant, Emmanuel
    Peigne, Stephane
    Jacques, Florian
    Laurin, Michel
    Testing for Deperet's Rule (Body Size Increase) in Mammals using Combined Extinct and Extant Data2016In: Systematic Biology, ISSN 1063-5157, E-ISSN 1076-836X, Vol. 65, no 1, p. 98-108Article in journal (Refereed)
    Abstract [en]

    Whether or not evolutionary lineages in general show a tendency to increase in body size has often been discussed. This tendency has been dubbed "Cope's rule" but because Cope never hypothesized it, we suggest renaming it after Deperet, who formulated it clearly in 1907. Deperet's rule has traditionally been studied using fossil data, but more recently a number of studies have used present-day species. While several paleontological studies of Cenozoic placental mammals have found support for increasing body size, most studies of extant placentals have failed to detect such a trend. Here, we present a method to combine information from present-day species with fossil data in a Bayesian phylogenetic framework. We apply the method to body mass estimates of a large number of extant and extinct mammal species, and find strong support for Deperet's rule. The tendency for size increase appears to be driven not by evolution toward larger size in established species, but by processes related to the emergence of new species. Our analysis shows that complementary data from extant and extinct species can greatly improve inference of macroevolutionary processes.

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  • 15.
    Bokma, Folmer
    et al.
    Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences.
    van den Brink, Valentijn
    Stadler, Tanja
    Unexpectedly many extinct hominins2012In: Evolution, ISSN 0014-3820, E-ISSN 1558-5646, Vol. 66, no 9, p. 2969-2974Article in journal (Refereed)
    Abstract [en]

    Recent studies indicate that Neanderthal and Denisova hominins may have been separate species, while debate continues on the status of Homo floresiensis. The decade-long debate between splitters, who recognize over 20 hominin species, and lumpers, who maintain that all these fossils belong to just a few lineages, illustrates that we do not know how many extinct hominin species to expect. Here, we present probability distributions for the number of speciation events and the number of contemporary species along a branch of a phylogeny. With estimates of hominin speciation and extincton rates, we then show that the expected total number of extinct hominin species is 8, but may be as high as 27. We also show that it is highly unlikely that three very recent species disappeared due to natural, background extinction. This may indicate that human-like remains are too easily considered distinct species. Otherwise, the evidence suggesting that Neanderthal and the Denisova hominin represent distinct species implies a recent wave of extinctions, ostensibly driven by the only survivor, H. sapiens.

  • 16. Bourque, S.
    et al.
    Jeandroz, S.
    Grandperret, V.
    Lehotai, Nora
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC). Agroécologie, AgroSup Dijon, Centre National de la Recherche Scientifique (CNRS), Institut National de la Recherche Agronomique (INRA), Université Bourgogne Franche-Comté, Dijon, France.
    Aime, S.
    Soltis, D. E.
    Miles, N. W.
    Melkonian, M.
    Deyholos, M. K.
    Leebens-Mack, J. H.
    Chase, M. W.
    Rothfels, C. J.
    Stevenson, D. W.
    Graham, S. W.
    Wang, X.
    Wu, S.
    Pires, J. C.
    Edger, P. P.
    Yan, Z.
    Xie, Y.
    Carpenter, E. J.
    Wong, G. K. S.
    Wendehenne, D.
    Nicolas-Frances, V.
    The Evolution of HD2 Proteins in Green Plants2016In: Trends in Plant Science, ISSN 1360-1385, E-ISSN 1878-4372, Vol. 21, no 12, p. 1008-1016Article, review/survey (Refereed)
    Abstract [en]

    In eukaryotes, protein deacetylation is carried out by two well-conserved his tone deacetylase (HDAC) families: RPD3/HDA1 and SIR2. Intriguingly, model plants such as Arabidopsis express an additional plant-specific HDAC family, termed type-2 HDACs (HD2s). Transcriptomic analyses from more than 1300 green plants generated by the 1000 plants (1KP) consortium showed that HD2s appeared early in green plant evolution, the first members being detected in several streptophyte green alga. The HD2 family has expanded via several rounds of successive duplication; members are expressed in all major green plant clades. Interestingly, angiosperm species express new HD2 genes devoid of a zinc-finger domain, one of the main structural features of HD2s. These variants may have been associated with the origin and/or the biology of the ovule/seed.

  • 17.
    Brännström, Åke
    et al.
    Umeå University, Faculty of Science and Technology, Department of Mathematics and Mathematical Statistics.
    Johansson, Jacob
    Loeuille, Nicolas
    Kristensen, Nadiah
    Troost, Tineke
    Hille Ris Lambers, Reinier
    Dieckmann, Ulf
    Modelling the ecology and evolution of communities: a review of past achievements, current efforts, and future promises2012In: Evolutionary Ecology Research, ISSN 1522-0613, E-ISSN 1937-3791, Vol. 14, no 5, p. 601-625Article in journal (Refereed)
    Abstract [en]

    Background: The complexity and dynamical nature of community interactions makemodelling a useful tool for understanding how communities develop over time and howthey respond to external perturbations. Large community-evolution models (LCEMs) areparticularly promising, since they can address both ecological and evolutionary questions, andcan give rise to richly structured and diverse model communities.Questions: Which types of models have been used to study community structure and what aretheir key features and limitations? How do adaptations and/or invasions affect communityformation? Which mechanisms promote diverse and stable communities? What are theimplications of LCEMs for management and conservation? What are the key challenges forfuture research?Models considered: Static models of community structure, demographic community models,and small and large community-evolution models.Conclusions: Large community-evolution models encompass a variety of modelled traits andinteractions, demographic dynamics, and evolutionary dynamics. They are able to reproduceempirical community structures. They have already generated new insights, such as the dual roleof competition, which limits diversity through competitive exclusion yet facilitates diversitythrough speciation. Other critical factors determining eventual community structure arethe shape of trade-off functions, inclusion of adaptive foraging, and energy availability. A particularly interesting feature of LCEMs is that these models not only help to contrast

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  • 18.
    Brännström, Åke
    et al.
    Umeå University, Faculty of Science and Technology, Department of Mathematics and Mathematical Statistics.
    Johansson, Jacob
    Lund University.
    von Festenberg, Niels
    The Hitchhiker’s Guide to Adaptive Dynamics2013In: Games, ISSN 2073-4336, E-ISSN 2073-4336, no 4, p. 304-328Article in journal (Refereed)
    Abstract [en]

    Adaptive dynamics is a mathematical framework for studying evolution. It extends evolutionary game theory to account for more realistic ecological dynamics and it can incorporate both frequency- and density-dependent selection. This is a practical guide to adaptive dynamics that aims to illustrate how the methodology can be applied to the study of specific systems. The theory is presented in detail for a single, monomorphic, asexually reproducing population. We explain the necessary terminology to understand the basic arguments in models based on adaptive dynamics, including invasion fitness, the selection gradient, pairwise invasibility plots (PIP), evolutionarily singular strategies, and the canonical equation. The presentation is supported with a worked-out example of evolution of arrival times in migratory birds. We show how the adaptive dynamics methodology can be extended to study evolution in polymorphic populations using trait evolution plots (TEPs). We give an overview of literature that generalises adaptive dynamics techniques to other scenarios, such as sexual, diploid populations, and spatially-structured populations. We conclude by discussing how adaptive dynamics relates to evolutionary game theory and how adaptive-dynamics techniques can be used in speciation research.

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  • 19.
    Burdon, Jeremy J.
    et al.
    CSIRO-Plant Industry, Canberra, Australia.
    Thrall, Peter H.
    CSIRO-Plant Industry, Canberra, Australia.
    Ericson, Lars
    Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences.
    The current and future dynamics of disease in plant communities2006In: Annual Review of Phytopathology, ISSN 0066-4286, E-ISSN 1545-2107, Vol. 44, p. 19-39Article in journal (Refereed)
    Abstract [en]

    Pathogens are powerful evolutionary forces shaping the structure and dynamics of both individual species and of the communities of which they are part, at a broad range of genetic, ecological, spatial, and temporal scales. At all these levels their impact varies from the subtle and little recognized through to the most obvious destruction. Today the direct role of pathogens in natural plant communities is better recognized than at previous times, although the nuances of their interactions and the cascade of ramifications that can flow through changing biotic and abiotic effects are only now gaining recognition. However, as human influence on pathogens increases either directly through enhanced if accidental dispersal, or through anthropogenic impacts on climate-we may expect to see increasing evidence of pathogens affecting plant species, community structure, and ecosystem function.

  • 20.
    Calatayud, Joaquín
    et al.
    Umeå University, Faculty of Science and Technology, Department of Physics. Departamento de Biogeografía y Cambio Global, Museo Nacional de Ciencias Naturales, Madrid, Spain.
    Andivia, Enrique
    Escudero, Adrian
    Melian, Carlos J.
    Bernardo-Madrid, Ruben
    Stoffel, Markus
    Aponte, Cristina
    Medina, Nagore G.
    Molina-Venegas, Rafael
    Arnan, Xavier
    Rosvall, Martin
    Umeå University, Faculty of Science and Technology, Department of Physics.
    Neuman, Magnus
    Umeå University, Faculty of Science and Technology, Department of Physics.
    Ari Noriega, Jorge
    Alves-Martins, Fernanda
    Draper, Isabel
    Luzuriaga, Arantzazu
    Ballesteros-Canovas, Juan Antonio
    Morales-Molino, Cesar
    Ferrandis, Pablo
    Herrero, Asier
    Pataro, Luciano
    Juen, Leandro
    Cea, Alex
    Madrigal-Gonzalez, Jaime
    Positive associations among rare species and their persistence in ecological assemblages2020In: Nature Ecology & Evolution, E-ISSN 2397-334X, Vol. 4, no 1, p. 40-45Article in journal (Refereed)
    Abstract [en]

    According to the competitive exclusion principle, species with low competitive abilities should be excluded by more efficient competitors; yet, they generally remain as rare species. Here, we describe the positive and negative spatial association networks of 326 disparate assemblages, showing a general organization pattern that simultaneously supports the primacy of competition and the persistence of rare species. Abundant species monopolize negative associations in about 90% of the assemblages. On the other hand, rare species are mostly involved in positive associations, forming small network modules. Simulations suggest that positive interactions among rare species and microhabitat preferences are the most probable mechanisms underpinning this pattern and rare species persistence. The consistent results across taxa and geography suggest a general explanation for the maintenance of biodiversity in competitive environments. Analysing spatial association networks among >300 terrestrial and aquatic assemblages, the authors find that the majority of negative associations involve abundant species. In contrast, rare species form mostly positive associations, potentially explaining their persistence in natural communities.

  • 21.
    Calatayud, Joaquín
    et al.
    Umeå University, Faculty of Science and Technology, Department of Physics. Departamento de Ciencias de la Vida, Universidad de Alcala´, Edificio de Ciencias, Ctra. Madrid-Barcelona km. 33,6, Alcala´ de Henares, 28871 Madrid, Spain; Department of Biogeography and Global Change, Museo Nacional de Ciencias Naturales (MNCN-CSIC), C/Jose´ Gutie´rrez Abascal 2, 28006 Madrid, Spain.
    Angel Rodriguez, Miguel
    Molina-Venegas, Rafael
    Leo, Maria
    Luis Horreo, Jose
    Hortal, Joaquin
    Pleistocene climate change and the formation of regional species pools2019In: Proceedings of the Royal Society of London. Biological Sciences, ISSN 0962-8452, E-ISSN 1471-2954, Vol. 286, no 1905, article id 20190291Article in journal (Refereed)
    Abstract [en]

    Although the description of bioregions dates back to the origin of biogeography, the processes originating their associated species pools hive been seldom studied. Ancient historical events are thought to play a fundamental role in configuring bioregions, but the effects of more recent events on these regional biotas are largely unknown. We used a network approach to identify regional and sub-regional faunas of European Carabus beetles and developed a method to explore the relative contribution of dispersal barriers, niche similarities and phylogenetic history on their configuration. We identify a transition zone matching the limit of the ice sheets at the Last Glacial Maximum. While southern species pools are mostly separated by dispersal barriers, in the north species are mainly sorted by their environmental niches. Strikingly, most phylogenetic structuration of Carabus faunas occurred during the Pleistocene. Our results show how extreme recent historical events - such as Pleistocene climate cooling, rather than just deep-time evolutionary processes-can profoundly modify the composition and structure of geographical species pools.

  • 22.
    Carlsson-Graner, Ulla
    et al.
    Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences.
    Thrall, Peter H.
    Host resistance and pathogen infectivity in host populations with varying connectivity2015In: Evolution, ISSN 0014-3820, E-ISSN 1558-5646, Vol. 69, no 4, p. 926-938Article in journal (Refereed)
    Abstract [en]

    Theory predicts that hosts and pathogens will evolve higher resistance and aggressiveness in systems where populations are spatially connected than in situations in which populations are isolated and dispersal is more local. In a large cross-inoculation experiment we surveyed patterns of host resistance and pathogen infectivity in anther-smut diseased Viscaria alpina populations from three contrasting areas where populations range from continuous, through patchy but spatially connected to highly isolated demes. In agreement with theory, isolated populations of V. alpina were more susceptible on average than either patchily distributed or continuous populations. While increased dispersal in connected systems increases disease spread, it may also increase host gene flow and the potential for greater host resistance to evolve. In the Viscaria-Microbotryum system, pathogen infectivity mirrored patterns of host resistance with strains from the isolated populations being the least infective and strains from the more resistant continuous populations being the most infective on average, suggesting that high resistance selects for high infectivity. To our knowledge this study is the first to characterize the impacts of varying spatial connectivity on patterns of host resistance and pathogen infectivity in a natural system.

  • 23. Chen, Xiaojie
    et al.
    Brännström, Åke
    Umeå University, Faculty of Science and Technology, Department of Mathematics and Mathematical Statistics. Evolution and Ecology Program, International Institute for Applied Systems Analysis (IIASA), Laxenburg, Austria.
    Dieckmann, Ulf
    Parent-preferred dispersal promotes cooperation in structured populations2019In: Proceedings of the Royal Society of London. Biological Sciences, ISSN 0962-8452, E-ISSN 1471-2954, Vol. 286, no 1895, article id 20181949Article in journal (Refereed)
    Abstract [en]

    Dispersal is a key process for the emergence of social and biological behaviours. Yet, little attention has been paid to dispersal's effects on the evolution of cooperative behaviour in structured populations. To address this issue, we propose two new dispersal modes, parent-preferred and offspring-preferred dispersal, incorporate them into the birth-death update rule, and consider the resultant strategy evolution in the prisoner's dilemma on random-regular, small-world, and scale-free networks, respectively. We find that parent-preferred dispersal favours the evolution of cooperation in these different types of population structures, while offspring-preferred dispersal inhibits the evolution of cooperation in homogeneous populations. On scale-free networks when the strength of parent-preferred dispersal is weak, cooperation can be enhanced at intermediate strengths of offspring-preferred dispersal, and cooperators can coexist with defectors at high strengths of offspring-preferred dispersal. Moreover, our theoretical analysis based on the pair-approximation method corroborates the evolutionary outcomes on random-regular networks. We also incorporate the two new dispersal modes into three other update rules (death-birth, imitation, and pairwise comparison updating), and find that similar results about the effects of parent-preferred and offspring-preferred dispersal can again be observed in the aforementioned different types of population structures. Our work, thus, unveils robust effects of preferential dispersal modes on the evolution of cooperation in different interactive environments.

  • 24.
    Cherif, Mehdi
    Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences.
    Stoichiometry and Population Growth in Osmotrophs and Non‐Osmotrophs2016In: eLS, John Wiley & Sons, 2016, p. 1-6Chapter in book (Refereed)
    Abstract [en]

    Growth is a process fundamental to life. It implies an increase in not only energy and information but also matter content. Recent advances in ecology have demonstrated that the elemental composition of organisms – their stoichiometry – is inextricably linked to their growth rate. Unbalances between the demands of elements for growth and their relative availabilities often result in elemental limitation. Also, different cellular components have different elemental compositions, and thus changes in allocation between uptake and assembly machineries affect both growth rate and elemental composition at the organismal level. Osmotrophs (including autotrophs) acquire essential elements through a vast set of separate molecules, resulting in more flexible stoichiometries compared to non-osmotrophs that ingest their preys in one package. Relationships between elemental composition and growth rate should be considered differently for individuals and for populations, as processes and mechanisms differ between the two scales, and more generally among the various biological scales.

  • 25. Cornforth, Daniel M
    et al.
    Sumpter, David J T
    Brown, Sam P
    Brännström, Åke
    Umeå University, Faculty of Science and Technology, Department of Mathematics and Mathematical Statistics.
    Synergy and group size in microbial cooperation2012In: American Naturalist, ISSN 0003-0147, E-ISSN 1537-5323, Vol. 180, no 3, p. 296-305Article in journal (Refereed)
    Abstract [en]

    Abstract Microbes produce many molecules that are important for their growth and development, and the exploitation of these secretions by nonproducers has recently become an important paradigm in microbial social evolution. Although the production of these public-goods molecules has been studied intensely, little is known of how the benefits accrued and the costs incurred depend on the quantity of public-goods molecules produced. We focus here on the relationship between the shape of the benefit curve and cellular density, using a model assuming three types of benefit functions: diminishing, accelerating, and sigmoidal (accelerating and then diminishing). We classify the latter two as being synergistic and argue that sigmoidal curves are common in microbial systems. Synergistic benefit curves interact with group sizes to give very different expected evolutionary dynamics. In particular, we show that whether and to what extent microbes evolve to produce public goods depends strongly on group size. We show that synergy can create an "evolutionary trap" that can stymie the establishment and maintenance of cooperation. By allowing density-dependent regulation of production (quorum sensing), we show how this trap may be avoided. We discuss the implications of our results on experimental design.

  • 26. Crispo, Erika
    et al.
    DiBattista, Joseph D.
    Correa, Cristian
    Thibert-Plante, Xavier
    Department of Biology and Redpath Museum, McGill University, Montreal, Quebec, Canada.
    McKellar, Ann E.
    Schwartz, Amy K.
    Berner, Daniel
    De Leon, Luis F.
    Hendry, Andrew P.
    The evolution of phenotypic plasticity in response to anthropogenic disturbance2010In: Evolutionary Ecology Research, ISSN 1522-0613, E-ISSN 1937-3791, Vol. 12, no 1, p. 47-66Article in journal (Refereed)
    Abstract [en]

    Questions: Do evolutionary changes in phenotypic plasticity occur after anthropogenic disturbance? Do these changes tend to be increases or decreases in plasticity? How do these evolutionary patterns differ among taxa and trait types? Does evolution of plasticity change with time since the disturbance?

    Data incorporated: Evolutionary rates for plasticity estimated from 20 studies that have compared a plastic response in two or more populations, at least one of which had experienced an anthropogenic disturbance in nature and at least one of which had not.

    Method of analysis: We estimate evolutionary rates (darwins and haldanes) for plasticity for each study, which represent the amount of evolutionary change in plasticity. We then perform analyses of covariance, with the evolutionary rate numerator (amount of evolutionary change) as a response variable, taxa and trait type as predictor variables, and the amount of evolutionary time as a covariate.

    Conclusions:We find that plasticity has evolved in several cases, including both increases and decreases in the levels of plasticity following anthropogenic disturbances. The typical direction of this evolutionary response depends on an interaction between taxon and trait type. For instance, invertebrates sometimes show the evolution of increased  plasticity for life-history traits, but the evolution of decreased plasticity for morphological traits. Plants, on the other hand, show no trends in the direction of plasticity evolution.

  • 27. De Block, Marjan
    et al.
    Slos, Stefanie
    Johansson, Frank
    Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences.
    Stoks, Robby
    Integrating life history and physiology to understand latitudinal size variation in a damselfly2008In: Ecography, ISSN 0906-7590, E-ISSN 1600-0587, Vol. 31, p. 115-123Article in journal (Refereed)
    Abstract [en]

    Our understanding of latitudinal life history patterns may benefit by jointly considering age and mass at maturity and growth rate. Additional insight may be gained by exploring potential constraints through pushing growth rates to their maximum and scoring physiological cost-related variables. Therefore, we reared animals of a univoltine Spanish and Belgian population and of a semivoltine Swedish population of the damselfly Enallagma cyathigerum (spanning a latitude gradient of ca 2350 km) in a common environment from the eggs until adult emergence and exposed them to a transient starvation period to induce compensatory growth. Besides age and mass at maturity and growth rate we also scored investment in energy storage (i.e. triglycerides) and immune function (i.e. total activity of phenoloxidase). At emergence, body mass was greater in Spain and Sweden and lower in Belgium, suggesting a genetic component for the U-shaped latitudinal pattern that was found also in a previous study based on field-collected adults. The mass difference between univoltine populations can be explained by the shorter development time in the Belgian population, and this despite a higher growth rate, a pattern consistent with undercompensating countergradient variation. In line with the assumed shorter growth seasons, Belgian and Swedish animals showed higher routine growth rates and compensatory growth after transient starvation. Despite a strong link with metabolic rates (as measured by oxygen consumption) populations with higher routine growth rates had no lower fat content and had higher immune function (i.e. immune function decreased from Sweden to Spain), which was unexpected. Rapid compensatory growth did, however, result in a lowered immune function. This may contribute to the absence of perfect compensating countergradient variation in the Belgian population and the lowest routine growth rates in the Spanish population. Our results underscore the importance of integrating key life historical with physiological traits for understanding latitudinal population differentiation.

  • 28.
    de La Torre, Amanda R.
    et al.
    Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences. Department of Plant Sciences, University of California–Davis, Davis, CA.
    Li, Zhen
    Van de Peer, Yves
    Ingvarsson, Pär K.
    Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences. Department of Plant Biology, Uppsala Biocenter, Swedish University of Agr icultural Sciences, Uppsala, Sweden.
    Contrasting Rates of Molecular Evolution and Patterns of Selection among Gymnosperms and Flowering Plants2017In: Molecular biology and evolution, ISSN 0737-4038, E-ISSN 1537-1719, Vol. 34, no 6, p. 1363-1377Article in journal (Refereed)
    Abstract [en]

    The majority of variation in rates of molecular evolution among seed plants remains both unexplored and unexplained. Although some attention has been given to flowering plants, reports of molecular evolutionary rates for their sister plant clade (gymnosperms) are scarce, and to our knowledge differences in molecular evolution among seed plant clades have never been tested in a phylogenetic framework. Angiosperms and gymnosperms differ in a number of features, of which contrasting reproductive biology, life spans, and population sizes are the most prominent. The highly conserved morphology of gymnosperms evidenced by similarity of extant species to fossil records and the high levels of macrosynteny at the genomic level have led scientists to believe that gymnosperms are slow-evolving plants, although some studies have offered contradictory results. Here, we used 31,968 nucleotide sites obtained from orthologous genes across a wide taxonomic sampling that includes representatives of most conifers, cycads, ginkgo, and many angiosperms with a sequenced genome. Our results suggest that angiosperms and gymnosperms differ considerably in their rates of molecular evolution per unit time, with gymnosperm rates being, on average, seven times lower than angiosperm species. Longer generation times and larger genome sizes are some of the factors explaining the slow rates of molecular evolution found in gymnosperms. In contrast to their slow rates of molecular evolution, gymnosperms possess higher substitution rate ratios than angiosperm taxa. Finally, our study suggests stronger and more efficient purifying and diversifying selection in gymnosperm than in angiosperm species, probably in relation to larger effective population sizes.

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  • 29.
    De La Torre, Amanda R
    et al.
    Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences.
    Lin, Yao-Cheng
    Van de Peer, Yves
    Ingvarsson, Pär K
    Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Genome-wide analysis reveals diverged patterns of codon bias, gene expression, and rates of sequence evolution in Picea gene families2015In: Genome Biology and Evolution, ISSN 1759-6653, E-ISSN 1759-6653, Vol. 7, no 4, p. 1002-1015Article in journal (Refereed)
    Abstract [en]

    The recent sequencing of several gymnosperm genomes has greatly facilitated studying the evolution of their genes and gene families. In this study, we examine the evidence for expression-mediated selection in the first two fully sequenced representatives of the gymnosperm plant clade (Picea abies and Picea glauca). We use genome-wide estimates of gene expression (> 50,000 expressed genes) to study the relationship between gene expression, codon bias, rates of sequence divergence, protein length, and gene duplication. We found that gene expression is correlated with rates of sequence divergence and codon bias, suggesting that natural selection is acting on Picea protein-coding genes for translational efficiency. Gene expression, rates of sequence divergence, and codon bias are correlated with the size of gene families, with large multicopy gene families having, on average, a lower expression level and breadth, lower codon bias, and higher rates of sequence divergence than single-copy gene families. Tissue-specific patterns of gene expression were more common in large gene families with large gene expression divergence than in single-copy families. Recent family expansions combined with large gene expression variation in paralogs and increased rates of sequence evolution suggest that some Picea gene families are rapidly evolving to cope with biotic and abiotic stress. Our study highlights the importance of gene expression and natural selection in shaping the evolution of protein-coding genes in Picea species, and sets the ground for further studies investigating the evolution of individual gene families in gymnosperms.

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  • 30.
    Dibattista, Joseph D.
    et al.
    Redpath Museum and Department of Biology, McGill University, Montréal, Québec, Canada .
    Feldheim, Kevin A.
    Field Museum, Pritzker Laboratory for Molecular Systematics and Evolution, Chicago, IL, USA.
    Thibert-Plante, Xavier
    Redpath Museum and Department of Biology, McGill University, Montréal, Québec, Canada.
    Gruber, Samuel H.
    Division of Marine Biology and Fisheries, Rosenstiel School of Marine and Atmospheric Science, Miami, FL, USA.
    Hendry, Andrew P.
    Redpath Museum and Department of Biology, McGill University, Montréal, Québec, Canada.
    A genetic assessment of polyandry and breeding-site fidelity in lemon sharks2008In: Molecular Ecology, ISSN 0962-1083, E-ISSN 1365-294X, Vol. 17, no 14, p. 3337-3351Article in journal (Refereed)
    Abstract [en]

    We here employ 11 microsatellite markers and recently developed litter reconstruction methods to infer mating system parameters (i.e. polyandry and breeding-site fidelity) at a lemon shark nursery site in Marquesas Key, Florida. Four hundred and eight juvenile or subadult sharks were genotyped over eight complete breeding seasons. Using this information, we were able to infer family structure, as well as fully or partially reconstruct genotypes of 46 mothers and 163 fathers. Multiple litter reconstruction methods were used, and novel simulations helped define apparent bias and precision of at least some mating system parameters. For Marquesas Key, we find that adult female lemon sharks display high levels of polyandry (81% of all litters sampled) and stronger fidelity to the nursery site than do males. Indeed, few male sharks sired offspring from more than one litter during the course of the study. These findings were quite similar to previous results from another lemon shark nursery site (Bimini, Bahamas), suggesting conserved mating system parameters despite significant variation in early life-history traits (i.e. body size and growth) among sites. The finding of at least some site fidelity in females also supports the need for careful conservation of each nursery.

  • 31. Dixon, Christopher J
    et al.
    Schoenswetter, Peter
    Suda, Jan
    Wiedermann, Magdalena M
    Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences.
    Schneeweiss, Gerald M
    Reciprocal Pleistocene origin and postglacial range formation of an allopolyploid and its sympatric ancestors (Androsace adfinis group, Primulaceae)2009In: Molecular Phylogenetics and Evolution, ISSN 1055-7903, E-ISSN 1095-9513, Vol. 50, no 1, p. 74-83Article in journal (Refereed)
    Abstract [en]

    The biogeographic history of polyploids and their lower-ploid ancestors is an important feature to achieve a better understanding of polyploid evolution. This is exemplified here using the ecologically congruent members of the Androsace adfinis group (Primulaceae) endemic to the southwestern European Alps. Employing relative genome size, AFLP fingerprint and chloroplast sequence haplotype data, we show that Androsace brigantiaca is a recent (probably no more than 0.2 million years) allopolyploid derivative of the geographically close A adfinis and A puberula, which formed reciprocally in a comparatively restricted area in the southern Southwestern Alps. Bayesian admixture analysis-also of artificial additive AFLP profiles-shows that the nuclear genome of A. brigantiaca is significantly biased towards the puberula-genome irrespective of maternal parentage. Nevertheless, there is no evidence for genetic interaction (hybridization, introgression) of A brigantiaca with either of its ancestors, including the widely sympatric A. puberula. Sympatry might be facilitated by ecological displacement on a local scale or might be a transitory phase on the way to competitive replacement via, for instance, polyploid superiority.

  • 32. Drotz, Marcus K
    et al.
    Brodin, Tomas
    Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences.
    Nilsson, Anders N
    Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences.
    Changing Names with Changed Address: Integrated Taxonomy and Species Delimitation in the Holarctic Colymbetes paykulli Group (Coleoptera: Dytiscidae)2015In: PLoS ONE, ISSN 1932-6203, E-ISSN 1932-6203, Vol. 10, no 11, article id e0143577Article in journal (Refereed)
    Abstract [en]

    Species delimitation of geographically isolated forms is a long-standing problem in less studied insect groups. Often taxonomic decisions are based directly on morphologic variation, and lack a discussion regarding sample size and the efficiency of migration barriers or dispersal/migration capacity of the studied species. These problems are here exemplified in a water beetle complex from the Bering Sea region that separates North America from Eurasia. Only a few sampled specimens occur from this particular area and they are mostly found in museum and private collections. Here we utilize the theory of integrated taxonomy to discuss the speciation of the Holarctic Colymbetes paykulli water beetle complex, which historically has included up to five species of which today only two are recognized. Three delimitation methods are used; landmark based morphometry of body shape, variation in reticulation patterns of the pronotum exo-skeleton and sequence variation of the partial mitochondrial gene Cyt b. Our conclusion is that the Palearctic and Nearctic populations of C. paykulli are given the status of separate species, based on the fact that all methods showed significant separation between populations. As a consequence the name of the Palearctic species is C. paykulli Erichson and the Nearctic species should be known as C. longulus LeConte. There is no clear support for delineation between Palearctic and Nearctic populations of C. dahuricus based on mtDNA. However, significant difference in size and reticulation patterns from the two regions is shown. The combined conclusion is that the C. dahuricus complex needs a more thorough investigation to fully disentangle its taxonomic status. Therefore it is here still regarded as a Holarctic species. This study highlights the importance to study several diagnosable characters that has the potential to discriminate evolutionary lineage during speciation.

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  • 33. Du, Shuhui
    et al.
    Wang, Zhaoshan
    Ingvarsson, Pär K
    Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Wang, Dongsheng
    Wang, Junhui
    Wu, Zhiqiang
    Tembrock, Luke R.
    Zhang, Jianguo
    Multilocus analysis of nucleotide variation and speciation in three closely related Populus (Salicaceae) species2015In: Molecular Ecology, ISSN 0962-1083, E-ISSN 1365-294X, Vol. 24, no 19, p. 4994-5005Article in journal (Refereed)
    Abstract [en]

    Historical tectonism and climate oscillations can isolate and contract the geographical distributions of many plant species, and they are even known to trigger species divergence and ultimately speciation. Here, we estimated the nucleotide variation and speciation in three closely related Populus species, Populus tremuloides, P.tremula and P.davidiana, distributed in North America and Eurasia. We analysed the sequence variation in six single-copy nuclear loci and three chloroplast (cpDNA) fragments in 497 individuals sampled from 33 populations of these three species across their geographic distributions. These three Populus species harboured relatively high levels of nucleotide diversity and showed high levels of nucleotide differentiation. Phylogenetic analysis revealed that P.tremuloides diverged earlier than the other two species. The cpDNA haplotype network result clearly illustrated the dispersal route from North America to eastern Asia and then into Europe. Molecular dating results confirmed that the divergence of these three species coincided with the sundering of the Bering land bridge in the late Miocene and a rapid uplift of the Qinghai-Tibetan Plateau around the Miocene/Pliocene boundary. Vicariance-driven successful allopatric speciation resulting from historical tectonism and climate oscillations most likely played roles inthe formation of the disjunct distributions and divergence of these three Populus species.

  • 34. Dunny, Gary
    et al.
    Berntsson, Ronnie Per-Arne
    Umeå University, Faculty of Medicine, Department of Medical Biochemistry and Biophysics.
    Enterococcal sex pheromones: evolutionary pathways to complex, two-signal systems2016In: Journal of Bacteriology, ISSN 0021-9193, E-ISSN 1098-5530, Vol. 198, no 11, p. 1556-1562Article, review/survey (Refereed)
    Abstract [en]

    Gram-positive bacteria carry out intercellular communication using secreted peptides. Important examples of this type of communication are the enterococcal sex pheromone systems, in which the transfer of conjugative plasmids is controlled by intercellular signaling among populations of donors and recipients. This review focuses on the pheromone response system of the conjugative plasmid pCF10. The peptide pheromones regulating pCF10 transfer act by modulating the ability of the PrgX transcription factor to repress the transcription of an operon encoding conjugation functions. Many Gram-positive bacteria regulate important processes, including the production of virulence factors, biofilm formation, sporulation, and genetic exchange using peptide-mediated signaling systems. The key master regulators of these systems comprise the RRNPP (RggRap/NprR/PlcR/PrgX) family of intracellular peptide receptors; these regulators show conserved structures. While many RRNPP systems include a core module of two linked genes encoding the regulatory protein and its cognate signaling peptide, the enterococcal sex pheromone plasmids have evolved to a complex system that also recognizes a second host-encoded signaling peptide. Additional regulatory genes not found in most RRNPP systems also modulate signal production and signal import in the enterococcal pheromone plasmids. This review summarizes several structural studies that cumulatively demonstrate that the ability of three pCF10 regulatory proteins to recognize the same 7-amino-acid pheromone peptide arose by convergent evolution of unrelated proteins from different families. We also focus on the selective pressures and structure/function constraints that have driven the evolution of pCF10 from a simple, single-peptide system resembling current RRNPPs in other bacteria to the current complex inducible plasmid transfer system.

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  • 35. Dutton, Edward
    et al.
    Madison, Guy
    Umeå University, Faculty of Social Sciences, Department of Psychology.
    Why do middle-class couples of European descent adopt children from Africa and Asia? Some Support for the Differential K Model2018In: Personality and Individual Differences, ISSN 0191-8869, E-ISSN 1873-3549, Vol. 130, p. 156-160Article in journal (Refereed)
    Abstract [en]

    Patterns of adoption behaviour are starkly asymmetric across populations. To better understand this phenomenon we conducted a systematic review of transracial adoption and adoption in general. We found six quantitative studies from the USA (with representative samples comprising a total of 117,000 participants) which had examined sex, race, and SES in relation to differences in behaviours and attitudes regarding both transracial adoption and adoption in general. A secondary analysis of these data found that transracial adopting is predicted by being female, white (as opposed to black), and of higher SES. These data are consistent with group differences in Life History Strategy – the Differential K model – regarding males and females, SES differences, and white and black people, but not with the fact that both transracial adoption and adoption rates in general seem to be lower in Northeast Asian countries. The influence of cultural factors upon these patterns may be addressed by future studies.

  • 36.
    Dwibedi, Chinmay Kumar
    et al.
    Umeå University, Faculty of Medicine, Department of Clinical Microbiology. Umeå University, Faculty of Medicine, Molecular Infection Medicine Sweden (MIMS). Division of CBRN Security and Defence, Swedish Defense Research Agency, Umeå, Sweden.
    Birdsell, Dawn
    Larkeryd, Adrian
    Myrtennas, Kerstin
    Ohrman, Caroline
    Nilsson, Elin
    Karlsson, Edvin
    Hochhalter, Christian
    Rivera, Andrew
    Maltinsky, Sara
    Bayer, Brittany
    Keim, Paul
    Scholz, Holger C.
    Tomaso, Herbert
    Wittwer, Matthias
    Beuret, Christian
    Schuerch, Nadia
    Pilo, Paola
    Hernandez Perez, Marta
    Rodriguez-Lazaro, David
    Escudero, Raquel
    Anda, Pedro
    Forsman, Mats
    Wagner, David M.
    Larsson, Par
    Johansson, Anders
    Umeå University, Faculty of Medicine, Department of Clinical Microbiology. Umeå University, Faculty of Medicine, Molecular Infection Medicine Sweden (MIMS).
    Long-range dispersal moved Francisella tularensis into Western Europe from the East2016In: Microbial Genomics, ISSN 2057-5858, Vol. 2, no 12Article in journal (Refereed)
    Abstract [en]

    For many infections transmitting to humans from reservoirs in nature, disease dispersal patterns over space and time are largely unknown. Here, a reversed genomics approach helped us understand disease dispersal and yielded insight into evolution and biological properties of Francisella tularensis, the bacterium causing tularemia. We whole-genome sequenced 67 strains and characterized by single-nucleotide polymorphism assays 138 strains, collected from individuals infected 1947-2012 across Western Europe. We used the data for phylogenetic, population genetic and geographical network analyses. All strains (n= 205) belonged to a monophyletic population of recent ancestry not found outside Western Europe. Most strains (n= 195) throughout the study area were assigned to a star-like phylogenetic pattern indicating that colonization of Western Europe occurred via clonal expansion. In the East of the study area, strains were more diverse, consistent with a founder population spreading from east to west. The relationship of genetic and geographic distance within the F. tularensis population was complex and indicated multiple long-distance dispersal events. Mutation rate estimates based on year of isolation indicated null rates; in outbreak hotspots only, there was a rate of 0.4 mutations/genome/year. Patterns of nucleotide substitution showed marked AT mutational bias suggestive of genetic drift. These results demonstrate that tularemia has moved from east to west in Europe and that F. tularensis has a biology characterized by long-range geographical dispersal events and mostly slow, but variable, replication rates. The results indicate that mutation-driven evolution, a resting survival phase, genetic drift and long-distance geographical dispersal events have interacted to generate genetic diversity within this species.

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  • 37.
    Dynesius, Mats
    et al.
    Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences.
    Jansson, Roland
    Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences.
    Persistence of within-species lineages: a neglected control of speciation rates2014In: Evolution, ISSN 0014-3820, E-ISSN 1558-5646, Vol. 68, no 4, p. 923-934Article in journal (Refereed)
    Abstract [en]

    We present a framework distinguishing three principal controls of speciation rate: rate of splitting, level of persistence, and length of speciation duration. We contend that discussions on diversification become clearer in the light of this framework, because speciation rate variation could be attributed to any of these controls. In particular, we claim that the role of persistence of within-species lineages in controlling speciation rates has been greatly underappreciated. More emphasis on the persistence control would change expectations of the role of several biological traits and environmental factors, because they may drive speciationrate in one direction through the persistence control and in the opposite direction through the other two controls. Traits and environments have been little studied regarding their influence on speciation rate through the persistence control, with climatic fluctuations being a relatively well-studied exception. Considering the recent advances in genomic and phylogenetic analysis, we think that the time is ripe for applying the framework in empirical research. Variation among clades and areas (and thus among traits and environments) in the importance of the three rate controls could be addressed for example by dating splitting events, detecting within-species lineages, and scanning genomes for evidence of divergent selection.

  • 38. Estrela, Sylvie
    et al.
    Libby, Eric
    Umeå University, Faculty of Science and Technology, Department of Mathematics and Mathematical Statistics. Santa Fe Institute, Santa Fe, NM, USA.
    Van Cleve, Jeremy
    Debarre, Florence
    Deforet, Maxime
    Harcombe, William R.
    Pena, Jorge
    Brown, Sam P.
    Hochberg, Michael E.
    Environmentally Mediated Social Dilemmas2019In: Trends in Ecology & Evolution, ISSN 0169-5347, E-ISSN 1872-8383, Vol. 34, no 1, p. 6-18Article, review/survey (Refereed)
    Abstract [en]

    By consuming and producing environmental resources, organisms inevitably change their habitats. The consequences of such environmental modifications can be detrimental or beneficial not only to the focal organism but also to other organisms sharing the same environment. Social evolution theory has been very influential in studying how social interactions mediated by public 'goods' or 'bads' evolve by emphasizing the role of spatial structure. The environmental dimensions driving these interactions, however, are typically abstracted away. We propose here a new, environment-mediated taxonomy of social behaviors where organisms are categorized by their production or consumption of environmental factors that can help or harm others in the environment. We discuss microbial examples of our classification and highlight the importance of environmental intermediates more generally.

  • 39. Evans, Alistair R.
    et al.
    Jones, David
    Boyer, Alison G.
    Brown, James H.
    Costa, Daniel P.
    Ernest, S. K. Morgan
    Fitzgerald, Erich M. G.
    Fortelius, Mikael
    Gittleman, John L.
    Hamilton, Marcus J.
    Harding, Larisa E
    Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences.
    Lintulaakso, Kari
    Lyons, S. Kathleen
    Okie, Jordan G.
    Saarinen, Juha J.
    Sibly, Richard M.
    Smith, Felisa A.
    Stephens, Patrick R.
    Theodor, Jessica M.
    Uhen, Mark D.
    The maximum rate of mammal evolution2012In: Proceedings of the National Academy of Sciences of the United States of America, ISSN 0027-8424, E-ISSN 1091-6490, Vol. 109, no 11, p. 4187-4190Article in journal (Refereed)
    Abstract [en]

    How fast can a mammal evolve from the size of a mouse to the size of an elephant? Achieving such a large transformation calls for major biological reorganization. Thus, the speed at which this occurs has important implications for extensive faunal changes, including adaptive radiations and recovery from mass extinctions. To quantify the pace of large-scale evolution we developed a metric, clade maximum rate, which represents the maximum evolutionary rate of a trait within a clade. We applied this metric to body mass evolution in mammals over the last 70 million years, during which multiple large evolutionary transitions occurred in oceans and on continents and islands. Our computations suggest that it took a minimum of 1.6, 5.1, and 10 million generations for terrestrial mammal mass to increase 100-, and 1,000-, and 5,000-fold, respectively. Values for whales were down to half the length (i.e., 1.1, 3, and 5 million generations), perhaps due to the reduced mechanical constraints of living in an aquatic environment. When differences in generation time are considered, we find an exponential increase in maximum mammal body mass during the 35 million years following the Cretaceous-Paleogene (K-Pg) extinction event. Our results also indicate a basic asymmetry in macroevolution: very large decreases (such as extreme insular dwarfism) can happen at more than 10 times the rate of increases. Our findings allow more rigorous comparisons of microevolutionary and macroevolutionary patterns and processes.

  • 40.
    Fagernäs, Zandra
    Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences.
    Biogeography of Norway spruce (Picea abies (L.) Karst.): Insights from a genome-wide study2017Independent thesis Advanced level (degree of Master (Two Years)), 40 credits / 60 HE creditsStudent thesis
    Abstract [en]

    Norway spruce (Picea abies (L.) Karst.) together with the sister species Siberian spruce (P. obovata Ledeb.) form a vast continuous distribution over Eurasia. The present distribution of P. abies in Europe was formed recently, after the last glacial maximum. Theories about the colonization routes and history of this species differ depending on the datasets examined to date. This thesis aims to investigate the genetic structure and diversity of P. abies and establish its glacial refugia and postglacial migration. A range-wide sampling was performed of both P. abies and P. obovata, and a genotyping-by-sequencing approach was used to obtain whole-genome single nucleotide polymorphism (SNP) data. Two major genetic lineages of P. abies were found; northern and central Europe. The northern lineage was further divided into a Scandinavian and a north-east European cluster; the Scandinavian cluster being more closely related to P. obovata and the north-east European cluster to the central European lineage. Introgression from P. obovata was detected far into northern Fennoscandia. The central European lineage was divided into an Alpine and a Carpathian cluster, originating from different glacial refugia. Genetic diversity was higher in the northern part of the range, which can be attributed to the relatively large refugium that recolonized this area, as well as introgression from P. obovata. Genetic diversity was also somewhat elevated where the two central European clusters meet, as is expected in areas where two previously isolated lineages admix. This study is the first range-wide investigation of P. abies using whole-genome SNP information, and shows how the genetic structure of the species has been shaped by the last glacial maximum and postglacial recolonization.

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  • 41.
    Faucillion, Marie-Line
    et al.
    Umeå University, Faculty of Science and Technology, Department of Molecular Biology (Faculty of Science and Technology).
    Larsson, Jan
    Umeå University, Faculty of Science and Technology, Department of Molecular Biology (Faculty of Science and Technology).
    Increased expression of X-linked genes in mammals is associated with a higher stability of transcripts and an increased ribosome density2015In: Genome Biology and Evolution, ISSN 1759-6653, E-ISSN 1759-6653, Vol. 7, no 4, p. 1039-1052Article in journal (Refereed)
    Abstract [en]

    Mammalian sex chromosomes evolved from the degeneration of one homolog of a pair of ancestral autosomes, the proto-Y. This resulted in a gene dose imbalance that is believed to be restored (partially or fully) through up-regulation of gene expression from the single active X-chromosome in both sexes by a dosage compensatory mechanism. We analyzed multiple genome-wide RNA stability datasets and found significantly longer average half-lives for X-chromosome transcripts than for autosomal transcripts in various human cell lines, both male and female, and in mice. Analysis of ribosome profiling data shows that ribosome density is higher on X-chromosome transcripts than on autosomal transcripts in both humans and mice, suggesting that the higher stability is causally linked to a higher translation rate. Our results and observations are in accordance with a dosage compensatory upregulation of expressed X-linked genes. We therefore propose that differential mRNA stability and translation rates of the autosomes and sex chromosomes contribute to an evolutionarily conserved dosage compensation mechanism in mammals.

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  • 42. Fritsch, Peter W.
    et al.
    Schiller, Anja M.
    Larson, Keith W.
    Department of Animal Ecology, Lund University, Sölvegatan 37, Lund 22362, Sweden .
    Taxonomic Implications of Morphological Variation in Cercis canadensis (Fabaceae) from Mexico and Adjacent Parts of Texas2009In: Systematic Botany, ISSN 0363-6445, E-ISSN 1548-2324, Vol. 34, no 3, p. 510-520Article in journal (Refereed)
    Abstract [en]

    Taxonomic treatments recognize three varieties of Cercis canadensis: with variety canadensis, widespread throughout the eastern United States, and varieties texensis and mexicana, found east and west of the Pecos River in Texas, respectively. The distribution of Cercis continues southward into northeastern Mexico, but complex variation in leaf shape has confounded straightforward application of varietal names to the Mexican plants. To clarify the taxonomy of Cercis in Mexico, we conducted a morphometric analysis with 281 herbarium specimens, including a representative set of samples from Texas. Correlation and principal component analysis of 12 characters recovered two groups that correspond to the presence versus absence of branchlet pubescence. These groups are geographically distinct at the northern and southern extremes of the focus area but exhibit a large central region of overlap. No other discontinuities in character states were discovered to corroborate this division. Leaf shape varies continuously from ovate-acuminate at the northern and southern extremes to subreniform in the central region, suggesting clinal adaptation to the mesic versus xeric environments in which the plants occur. Based on our data, we apply the varietal epithets mexicana and, provisionally, texensis to Mexican C. canadensis with pubescent and glabrous branchlets, respectively, the latter based on geographic proximity to plants in Texas in the absence of definitive evidence on the phenotypic distinction between varieties canadensis and texensis.

  • 43. Garcia-Cisneros, A.
    et al.
    Perez-Portela, R.
    Almroth, B. C.
    Degerman, Sofie
    Umeå University, Faculty of Medicine, Department of Medical Biosciences.
    Palacin, C.
    Skold, H. Nilsson
    Long telomeres are associated with clonality in wild populations of the fissiparous starfish Coscinasterias tenuispina2015In: Heredity, ISSN 0018-067X, E-ISSN 1365-2540, Vol. 115, no 5, p. 437-443Article in journal (Refereed)
    Abstract [en]

    Telomeres usually shorten during an organism's lifespan and have thus been used as an aging and health marker. When telomeres become sufficiently short, senescence is induced. The most common method of restoring telomere length is via telomerase reverse transcriptase activity, highly expressed during embryogenesis. However, although asexual reproduction from adult tissues has an important role in the life cycles of certain species, its effect on the aging and fitness of wild populations, as well as its implications for the long-term survival of populations with limited genetic variation, is largely unknown. Here we compare relative telomere length of 58 individuals from four populations of the asexually reproducing starfish Coscinasterias tenuispina. Additionally, 12 individuals were used to compare telomere lengths in regenerating and non-regenerating arms, in two different tissues (tube feet and pyloric cecum). The level of clonality was assessed by genotyping the populations based on 12 specific microsatellite loci and relative telomere length was measured via quantitative PCR. The results revealed significantly longer telomeres in Mediterranean populations than Atlantic ones as demonstrated by the Kruskal-Wallis test (K=24.17, significant value: P-value <0.001), with the former also characterized by higher levels of clonality derived from asexual reproduction. Telomeres were furthermore significantly longer in regenerating arms than in non-regenerating arms within individuals (pyloric cecum tissue: Mann-Whitney test, V=299, P-value <10(-6); and tube feet tissue Student's t=2.28, P-value = 0.029). Our study suggests that one of the mechanisms responsible for the long-term somatic maintenance and persistence of clonal populations is telomere elongation.

  • 44. Hart, Nathan S.
    et al.
    Lamb, Trevor D.
    Patel, Hardip R.
    Chuah, Aaron
    Natoli, Riccardo C.
    Hudson, Nicholas J.
    Cutmore, Scott C.
    Davies, Wayne I. L.
    Umeå University, Faculty of Medicine, Umeå Centre for Molecular Medicine (UCMM).
    Collin, Shaun P.
    Hunt, David M.
    Visual Opsin Diversity in Sharks and Rays2020In: Molecular biology and evolution, ISSN 0737-4038, E-ISSN 1537-1719, Vol. 37, no 3, p. 811-827Article in journal (Refereed)
    Abstract [en]

    The diversity of color vision systems found in extant vertebrates suggests that different evolutionary selection pressures have driven specializations in photoreceptor complement and visual pigment spectral tuning appropriate for an animal's behavior, habitat, and life history. Aquatic vertebrates in particular show high variability in chromatic vision and have become important models for understanding the role of color vision in prey detection, predator avoidance, and social interactions. In this study, we examined the capacity for chromatic vision in elasmobranch fishes, a group that have received relatively little attention to date. We used microspectrophotometry to measure the spectral absorbance of the visual pigments in the outer segments of individual photoreceptors from several ray and shark species, and we sequenced the opsin mRNAs obtained from the retinas of the same species, as well as from additional elasmobranch species. We reveal the phylogenetically widespread occurrence of dichromatic color vision in rays based on two cone opsins, RH2 and LWS. We also confirm that all shark species studied to date appear to be cone monochromats but report that in different species the single cone opsin may be of either the LWS or the RH2 class. From this, we infer that cone monochromacy in sharks has evolved independently on multiple occasions. Together with earlier discoveries in secondarily aquatic marine mammals, this suggests that cone-based color vision may be of little use for large marine predators, such as sharks, pinnipeds, and cetaceans.

  • 45.
    Hatchett, William
    Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences.
    The road toward sympatric speciation in whitefish.: The effects of divergent selection on European whitefish (Coregonus lavaretus) size and behavior, and effects on zooplankton communities.2015Independent thesis Advanced level (degree of Master (Two Years)), 40 credits / 60 HE creditsStudent thesis
    Abstract [en]

    For almost every organism there are large gaps in our knowledge about the processes that leads to speciation. The changes an organism undergoes before divergence has occurred have remained a mystery, as it is difficult to say whether or not a species is going to diverge and when. To investigate this unknown the European whitefish (Coregonus lavaretus) and the northern pike (Esox lucius) were studied, as they produce a repeatable and predictable pattern of speciation in sympatry. To investigate the changes in phenotypes and behaviour in whitefish that precedes divergence, two lake populations were examined, Gräsvattnet and Ringsjön. Gräsvattnet was used as a control, with a population of whitefish but an absence of pike, whereas Ringsjön has a population of whitefish that invaded from Gräsvattnet and a pike population. The presence of pike presumably exerts divergent selection on the whitefish population. Fish and zooplankton were surveyed in both lakes from 1970 to the present day, which allows us to compare how whitefish populations and their resources change in the presence and absence of pike. The results found in Ringsjön show; (1) a change in habitat use, (2) a change in diet from pelagic to benthic, (3) an increase in the relationship between individual body size and diet and (4) a decrease in average size over the course of the study. (1)The presence of pike is believed to have forced the whitefish into the pelagic which could be seen in the result, with an increase in individuals caught in the pelagic. (2) The change in diet is thought to be caused by a resource competition created by individuals being forced to use the pelagic. Although insignificant this led to an overall reduction in zooplankton abundance by almost 40% which could have intensified competition. The resource competition could then have been intensified further by the change in composition of zooplankton relative abundance. (3) The increase in relationship between individual body size and diet is thought to increase due to the resource competition between smaller and larger individuals in the pelagic. Smaller individuals are better competitors than larger individuals for pelagic resource which could have led to the larger individuals switching to a more benthic diet. (4) The decrease in average size is thought to be caused by negative selection for larger individuals. Larger individuals have switched to a more benthic diet, and although the individuals are larger they still face the risk of predation in the littoral zone as they have not outgrown the gape size of the pike. This could have led to the average size reduction that may be the first steps in speciation, and ultimately leading to the divergence of two morphs by sympatric speciation in Ringsjön. In Gräsvattnet over the course of the study there were few and small changes in whitefish size, zooplankton relative abundance in the diet and in the environment. The results in Gräsvattnet could however suggest resource competition for benthic resources. Although resource competition is thought to be an important factor in the speciation of whitefish, without predation pressure no speciation occurs. This result could suggest the importance of predation pressure in the speciation of whitefish. 

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  • 46.
    Hein, Catherine L.
    et al.
    Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences. Climate Impacts Research Centre, Abisko Scientific Research Station, Abisko, Sweden .
    Öhlund, Gunnar
    Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences.
    Englund, Göran
    Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences.
    Fish introductions reveal the temperature dependence of species interactions2014In: Proceedings of the Royal Society of London. Biological Sciences, ISSN 0962-8452, E-ISSN 1471-2954, Vol. 281, no 1775, p. 20132641-Article in journal (Refereed)
    Abstract [en]

    A major area of current research is to understand how climate change will impact species interactions and ultimately biodiversity. A variety of environmental conditions are rapidly changing owing to climate warming, and these conditions often affect both the strength and outcome of species interactions. We used fish distributions and replicated fish introductions to investigate environmental conditions influencing the coexistence of two fishes in Swedish lakes: brown trout (Salmo trutta) and pike (Esox lucius). A logistic regression model of brown trout and pike coexistence showed that these species coexist in large lakes (more than 4.5 km(2)), but not in small, warm lakes (annual air temperature more than 0.9-1.5 degrees C). We then explored how climate change will alter coexistence by substituting climate scenarios for 2091-2100 into our model. The model predicts that brown trout will be extirpated from approximately half of the lakes where they presently coexist with pike and from nearly all 9100 lakes where pike are predicted to invade. Context dependency was critical for understanding pike-brown trout interactions, and, given the widespread occurrence of context-dependent species interactions, this aspect will probably be critical for accurately predicting climate impacts on biodiversity.

  • 47.
    Hellekant, Nils
    Umeå University, Faculty of Science and Technology, Department of Physics.
    Adaptive Evolution of Resource Use, Phenotypic Diversity, and Productivity of Phytoplankton Communities2019Independent thesis Advanced level (professional degree), 20 credits / 30 HE creditsStudent thesis
    Abstract [en]

    There is growing concern that the worldwide loss in biodiversity will harm the stability of the ecosystems, and thereby, the carrying capacity and critical ecosystem services the biosphere provides. Phytoplankton (microalgae) in lakes and oceans are arguably the most important primary producers. They are responsible for approximately half of the earth's primary production. However, there is little research into what influences the biodiversity of phytoplankton communities and of those studies the mechanisms for coexistence of phytoplankton have so far almost exclusively been studied on ecological time scales. We, therefore, explored how biodiversity and biomass (a proxy to primary production) of phytoplankton communities respond to co-varied environmental drivers over evolutionary time scales. We model adaptive evolution of phytoplankton' resource use, with a non-dimensionalized model of negatively buoyant phytoplankton inhabiting a partially mixed one-dimensional water column using reaction-advection-diffusion equations.

    We show that a number of environmental drivers have novel effects on biodiversity and biomass on evolutionary timescales. In contrast with previous non-evolutionary work, we found that decreasing light attenuation or increasing resource use efficiency can result in decreased biomass of plankton communities and nutrient-poor environments. One novel driver of species diversity was the combination of low rates of diffusion with relatively intermediate rates of sinking promote species diversity. Furthermore, we show that the phytoplankton turnover rate affects environmental heterogeneity and is, therefore, a contributing driver to species diversity.The evolution of half saturation constants can produce a variety of biodiversity-ecosystem function patterns as two positive, one unimodal, and one negative association were found when comparing biodiversity-ecosystem function.

    Collectively, our analyses suggest that environmental drivers can have substantially different effects over evolutionary timescales than those effects ecological modeling has previously shown.

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  • 48.
    Hudson, Alan G.
    et al.
    Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences. Division of Aquatic Ecology & Macroevolution, Institute of Ecology & Evolution, University of Bern, Bern, Switzerland and Department of Fish Ecology & Evolution, EAWAG Centre of Ecology, Evolution and Biogeochemistry, Kastanienbaum, Switzerland.
    Vonlanthen, Pascal
    Division of Aquatic Ecology & Macroevolution, Institute of Ecology & Evolution, University of Bern, Bern, Switzerland and Department of Fish Ecology & Evolution, EAWAG Centre of Ecology, Evolution and Biogeochemistry, Kastanienbaum, Switzerland.
    Bezault, Etienne
    Department of Biology, Reed College, Portland, USA, Division of Aquatic Ecology & Macroevolution, Institute of Ecology & Evolution, University of Bern, Bern, Switzerland and Department of Fish Ecology & Evolution, EAWAG Centre of Ecology, Evolution and Biogeochemistry, Kastanienbaum, Switzerland.
    Seehausen, Ole
    Division of Aquatic Ecology & Macroevolution, Institute of Ecology & Evolution, University of Bern, Bern, Switzerland and Department of Fish Ecology & Evolution, EAWAG Centre of Ecology, Evolution and Biogeochemistry, Kastanienbaum, Switzerland.
    Genomic signatures of relaxed disruptive selection associated with speciation reversal in whitefish2013In: BMC Evolutionary Biology, ISSN 1471-2148, E-ISSN 1471-2148, Vol. 13, p. 108-Article in journal (Refereed)
    Abstract [en]

    Background: Speciation reversal: the erosion of species differentiation via an increase in introgressive hybridization due to the weakening of previously divergent selection regimes, is thought to be an important, yet poorly understood, driver of biodiversity loss. Our study system, the Alpine whitefish (Coregonus spp.) species complex is a classic example of a recent postglacial adaptive radiation: forming an array of endemic lake flocks, with the independent origination of similar ecotypes among flocks. However, many of the lakes of the Alpine radiation have been seriously impacted by anthropogenic nutrient enrichment, resulting in a collapse in neutral genetic and phenotypic differentiation within the most polluted lakes. Here we investigate the effects of eutrophication on the selective forces that have shaped this radiation, using population genomics. We studied eight sympatric species assemblages belonging to five independent parallel adaptive radiations, and one species pair in secondary contact. We used AFLP markers, and applied F-ST outlier (BAYESCAN, DFDIST) and logistic regression analyses (MATSAM), to identify candidate regions for disruptive selection in the genome and their associations with adaptive traits within each lake flock. The number of outlier and adaptive trait associated loci identified per lake were then regressed against two variables (historical phosphorus concentration and contemporary oxygen concentration) representing the strength of eutrophication. Results: Whilst we identify disruptive selection candidate regions in all lake flocks, we find similar trends, across analysis methods, towards fewer disruptive selection candidate regions and fewer adaptive trait/candidate loci associations in the more polluted lakes. Conclusions: Weakened disruptive selection and a concomitant breakdown in reproductive isolating mechanisms in more polluted lakes has lead to increased gene flow between coexisting Alpine whitefish species. We hypothesize that the resulting higher rates of interspecific recombination reduce either the number or extent of genomic islands of divergence surrounding loci evolving under disruptive natural selection. This produces the negative trend seen in the number of selection candidate loci recovered during genome scans of whitefish species flocks, with increasing levels of anthropogenic eutrophication: as the likelihood decreases that AFLP restriction sites will fall within regions of heightened genomic divergence and therefore be classified as F-ST outlier loci. This study explores for the first time the potential effects of human-mediated relaxation of disruptive selection on heterogeneous genomic divergence between coexisting species.

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  • 49. Ingvarsson, Par K.
    et al.
    Bernhardsson, Carolina
    Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences. Department of Plant Biology, Linnean Centre for Plant Biology, Swedish University of Agricultural Sciences, Uppsala, Sweden.
    Genome-wide signatures of environmental adaptation in European aspen (Populus tremula) under current and future climate conditions2020In: Evolutionary Applications, ISSN 1752-4571, E-ISSN 1752-4571, Vol. 13, no 1, p. 132-142Article in journal (Refereed)
    Abstract [en]

    Future climate change has been predicted to disrupt local adaptation in many perennial plants, such as forest trees, but the magnitude and location of these effects are thus far poorly understood. Here, we assess local adaptation to current climate in European aspen (Populus tremula) by using environmental association analyses to identify genetic variants associated with two representative climate variables describing current day variation in temperature and precipitation. We also analysed patterns of genetic differentiation between southern and northern populations and observe that regions of high genetic differentiation are enriched for SNPs that are significantly associated with climate. Using variants associated with climate, we examined patterns of isolation by distance and environment and used spatial modelling to predict the geographic distribution of genomic variation in response to two scenarios of future climate change. We show that climate conditions at a northern reference site will correspond to climate conditions experienced by current day populations located 4-8 latitude degrees further south. By assessing the relationship between phenotypic traits and vegetative fitness, we also demonstrate that southern populations harbour genetic variation that likely would be adaptive further north under both climate change scenarios. Current day populations at the lagging edge of the distribution in Sweden can therefore serve as sources for introducing adaptive alleles onto northern populations, but the likelihood of this largely depends on naturally occurring levels of gene flow.

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  • 50.
    Ingvarsson, Pär
    Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences.
    Molecular evolution of synonymous codon usage in Populus2008In: BMC Evolutionary Biology, ISSN 1471-2148, E-ISSN 1471-2148, Vol. 8, p. 307-Article in journal (Refereed)
    Abstract [en]

    Background Evolution of synonymous codon usage is thought to be determined by a balance between mutation, genetic drift andnatural selection on translational efficiency. However, natural selection on codon usage is considered to be a weak evolutionary force and selection on codon usage is expected to be strongest in species with large effective population sizes. Results I examined the evolution of synonymous codons using EST data from five species of Populus. Data on relative synonymous codon usage in genes with high and low gene expression were used to identify 25 codons from 18 different amino acids that were deemed to be preferred codons across all five species.All five species show significant correlations between codon bias and gene expression, independent of base composition, thus indicating that translational selection has shaped synonymous codon usage. Using a set of 158 orthologous genes I detected an excess of unpreferred to preferred (U->P) mutations in two lineages, P. tremula and P. deltoides. Maximum likelihood estimates of the strength of selection acting on synonymous codons was also significantly greater than zero in P. tremula, with the ML estimate of 4N[es]=0.720. Conclusions The data is consistent with weak selection on preferred codons in all five species. There is also evidence suggesting that selection on synonymous codons has increased in P. tremula. Although the reasons for the increase in selection on codon usage in the P. tremula lineage are not clear, one possible explanation is an increase in the effective population size in P. tremula.

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