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  • 1301. Shoda-Kagaya, E.
    et al.
    Saito, S.
    Okada, M.
    Nozaki, A.
    Nunokawa, K.
    Tsuda, Yoshiaki
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Evolutionär funktionsgenomik.
    Genetic structure of the oak wilt vector beetle Platypus quercivorus: inferences toward the process of damaged area expansion2010Inngår i: BMC Ecology, ISSN 1472-6785, E-ISSN 1472-6785, Vol. 10, nr 21Artikkel i tidsskrift (Fagfellevurdert)
  • 1302.
    Sigurdardóttir, Sunniva Samson
    Linnéuniversitetet, Fakulteten för Hälso- och livsvetenskap (FHL), Institutionen för biologi och miljö (BOM).
    Hit and Miss: The Complexity of Admixture2014Independent thesis Basic level (degree of Bachelor), 10 poäng / 15 hpOppgave
    Abstract [en]

    With massive population declines all over the world, conservationists are faced with a serious threat of extinctions with a need to explore possibilities of translocations and interbreeding programs. While admixture, mixing of separate gene pools, can have beneficial effects, scientists have become aware of the risk of outbreeding depression. The aim of the present study was to investigate the symmetry in outcome in interbreeding population pairs and examine if there are any general patterns. A systematic review was conducted on 28 experimental studies about interbreeding and admixture in plants and animals with comparisons between purebred groups and hybrid groups. Three main types of traits were investigated, chosen to represent quantity, quality and body size of offspring. Overall, symmetrical outcomes were most frequent (62.8 ± 2.6 %), most commonly with a neutral outcome (i.e. none of the populations significantly affected by admixture) in both populations (40.6  ± 3.9 % of all outcome possibilities), which even might be an underestimate because of potential publication bias. Positive and negative outcomes were similar in frequency (11.5 and 11.2 %, respectively, in symmetrical outcomes; 18.1 and 14.4 % in asymmetrical outcomes). The results indicate that consequences of admixture differed between experiments conducted in the laboratory versus semi-natural or natural conditions, between plants and animals, and between the three types of traits. The effects of admixture depended on whether the response was measured in first, second, third generation hybrids, or backcrosses. However, there was no difference in outcome between first and second generation hybrids, which is not in agreement with theory where a more frequent and/or severe negative outcome is expected in later generations. The cause of positive or negative admixture could not be identified, although the heterogenous outcome might indicate that interactions in population pairs are unique. Accordingly, no translocation should be carried out into endangered populations before cautious investigation of possible admixture outcomes. Future research should aim to disentangle the cause and effect of admixture and, preferably, use genetic divergence as an explanatory variable.

  • 1303.
    Siljestam, Mattias
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Zooekologi.
    Östman, Örjan
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Zooekologi.
    The combined effects of temporal autocorrelation and the costs of plasticity on the evolution of plasticity2017Inngår i: Journal of Evolutionary Biology, ISSN 1010-061X, E-ISSN 1420-9101, Vol. 30, nr 7, s. 1361-1371Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Adaptive phenotypic plasticity is an important source of intraspecific variation, and for many plastic traits, the costs or factors limiting plasticity seem cryptic. However, there are several different factors that may constrain the evolution of plasticity, but few models have considered costs and limiting factors simultaneously. Here we use a simulation model to investigate how the optimal level of plasticity in a population depends on a fixed maintenance fitness cost for plasticity or an incremental fitness cost for producing a plastic response in combination with environmental unpredictability (environmental fluctuation speed) limiting plasticity. Our model identifies two mechanisms that act, almost separately, to constrain the evolution of plasticity: (i) the fitness cost of plasticity scaled by the nonplastic environmental tolerance, and (ii) the environmental fluctuation speed scaled by the rate of phenotypic change. That is, the evolution of plasticity is constrained by the high cost of plasticity in combination with high tolerance for environmental variation, or fast environmental changes in combination with slow plastic response. Qualitatively similar results are found when maintenance and incremental fitness costs of plasticity are incorporated, although a larger degree of plasticity is selected for with an incremental cost. Our model highlights that it is important to consider direct fitness costs and phenotypic limitations in relation to nonplastic environmental tolerance and environmental fluctuations, respectively, to understand what constrains the evolution of phenotypic plasticity.

  • 1304.
    Sjödin, Henrik
    et al.
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för ekologi, miljö och geovetenskap. Evolution and Ecology Program, International Institute for Applied Systems Analysis, 2361 Laxenburg, Austria.
    Brännström, Åke
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för matematik och matematisk statistik. Evolution and Ecology Program, International Institute for Applied Systems Analysis, 2361 Laxenburg, Austria.
    Dieckmann, Ulf
    Evolution and Ecology Program, International Institute for Applied Systems Analysis, 2361 Laxenburg, Austria.
    Mazzucco, Rupert
    Evolution and Ecology Program, International Institute for Applied Systems Analysis, 2361 Laxenburg, Austria.
    Contingent dispersal and the formation of cooperative groupsManuskript (preprint) (Annet vitenskapelig)
  • 1305.
    Sjödin, Per
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Evolutionsbiologi.
    Skoglund, Pontus
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Evolutionsbiologi.
    Jakobsson, Mattias
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Evolutionsbiologi. Uppsala universitet, Science for Life Laboratory, SciLifeLab.
    Assessing the Maximum Contribution from Ancient Populations2014Inngår i: Molecular biology and evolution, ISSN 0737-4038, E-ISSN 1537-1719, Vol. 31, nr 5, s. 1248-1260Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Ancestral relationships between populations separated by time represent an often neglected dimension in population genetics, a field which historically has focused on analysis of spatially distributed samples from the same point in time. Models are usually straightforward when two time-separated populations are assumed to be completely isolated from all other populations. However, this is usually an unrealistically stringent assumption when there is gene flow with other populations. Here, we investigate continuity in the presence of gene flow from unknown populations. This setup allows a more nuanced treatment of questions regarding population continuity in terms of "level of contribution" from a particular ancient population to a more recent population. We propose a statistical framework which makes use of a biallelic marker sampled at two different points in time to assess population contribution, and present two different interpretations of the concept. We apply the approach to published data from a prehistoric human population in Scandinavia (Malmstrom H, Gilbert MTP, Thomas MG, Brandstrom M, StorAyen J, Molnar P, Andersen PK, Bendixen C, Holmlund G, Gotherstrom A, et al. 2009. Ancient DNA reveals lack of continuity between Neolithic hunter-gatherers and contemporary Scandinavians. Curr Biol. 19:1758-1762) and Pleistocene woolly mammoth (Barnes I, Shapiro B, Lister A, Kuznetsova T, Sher A, Guthrie D, Thomas MG. 2007. Genetic structure and extinction of the woolly mammoth, Mammuthus primigenius. Curr Biol. 17:1072-1075; Debruyne R, Chu G, King CE, Bos K, Kuch M, Schwarz C, Szpak P, Grocke DR, Matheus P, Zazula G, et al. 2008. Out of America: ancient DNA evidence for a new world origin of late quaternary woolly mammoths. Curr Biol. 18:1320-1326).

  • 1306.
    Sjöstrand, Agnès E.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Evolutionsbiologi.
    Origins and Adaptation in Humans: A Case Study of Taste and Lifestyle2015Doktoravhandling, med artikler (Annet vitenskapelig)
    Abstract [en]

    In this thesis, I use population genetics and statistical approaches to investigate early human demography, infer local adaptation in diverse sets of populations, and study the genetic basis for taste perception.

    In the first paper, I examine the genomic evidence for a severe bottleneck, which has been suggested based on paleontological and climate studies to coincide with the emergence of anatomically modern humans. Using a Bayesian approach, I evaluate the genetic evidence of a bottleneck between 190,000 and 130,000 years ago and find that the data is in favor of a model without bottleneck at this time point.

    I further develop a method to detect local adaptation based on frequencies of private haplotypes. I first show, using simulated data, that this method can detect local adaption. Applied to large-scale human genotype data, this method detects known signals of positive selection in human data such as the positive selection around the lactase gene in Europeans and East Africans. Also, this method permits to improve knowledge on potential adaptation events in humans as it finds several regions potentially selected that were not previously described. I further investigate patterns of adaptation in whole genome data based on a diverse set of African populations. The results from the regions potentially selected show that diet and pathogens are the common driving forces of adaptation in all studied populations.

    There is evidence that taste perception have evolved in concert with diet, environment, and the organismal needs in humans. For this reason, I study taste perception in populations differing on lifestyle (hunter-gatherers, farmers and nomad herders). I present taste perception phenotypes for all tastes (sweet, bitter, sour, salty and umami) and relate them to high density genotype data. I show that taste and taste-involved genes have evolved with lifestyle. By performing an association study, I also show that variation in taste perception involves more genes than only the taste receptors genes.

    In this thesis, by analyzing human genetic data with a population genetics approaches, I covered several topics of human ancient demography and adaptation and show the utility of using large-scale genetic data to better understand human history.

  • 1307. Sjöstrand, Joel
    et al.
    Tofigh, Ali
    Daubin, Vincent
    Arvestad, Lars
    KTH, Skolan för datavetenskap och kommunikation (CSC), Beräkningsbiologi, CB. KTH, Centra, Science for Life Laboratory, SciLifeLab.
    Sennblad, Bengt
    Lagergren, Jens
    KTH, Skolan för datavetenskap och kommunikation (CSC), Beräkningsbiologi, CB. KTH, Centra, Science for Life Laboratory, SciLifeLab.
    A Bayesian Method for Analyzing Lateral Gene Transfer2014Inngår i: Systematic Biology, ISSN 1063-5157, E-ISSN 1076-836X, Vol. 63, nr 3, s. 409-420Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Lateral gene transfer (LGT)uwhich transfers DNA between two non-vertically related individuals belonging to the same or different speciesuis recognized as a major force in prokaryotic evolution, and evidence of its impact on eukaryotic evolution is ever increasing. LGT has attracted much public attention for its potential to transfer pathogenic elements and antibiotic resistance in bacteria, and to transfer pesticide resistance from genetically modified crops to other plants. In a wider perspective, there is a growing body of studies highlighting the role of LGT in enabling organisms to occupy new niches or adapt to environmental changes. The challenge LGT poses to the standard tree-based conception of evolution is also being debated. Studies of LGT have, however, been severely limited by a lack of computational tools. The best currently available LGT algorithms are parsimony-based phylogenetic methods, which require a pre-computed gene tree and cannot choose between sometimes wildly differing most parsimonious solutions. Moreover, in many studies, simple heuristics are applied that can only handle putative orthologs and completely disregard gene duplications (GDs). Consequently, proposed LGT among specific gene families, and the rate of LGT in general, remain debated. We present a Bayesian Markov-chain Monte Carlo-based method that integrates GD, gene loss, LGT, and sequence evolution, and apply the method in a genome-wide analysis of two groups of bacteria: Mollicutes and Cyanobacteria. Our analyses show that although the LGT rate between distant species is high, the net combined rate of duplication and close-species LGT is on average higher. We also show that the common practice of disregarding reconcilability in gene tree inference overestimates the number of LGT and duplication events. [Bayesian; gene duplication; gene loss; horizontal gene transfer; lateral gene transfer; MCMC; phylogenetics.].

  • 1308.
    Skar, Helena
    et al.
    Linköpings universitet, Institutionen för teknik och naturvetenskap, Medie- och Informationsteknik. Linköpings universitet, Tekniska fakulteten.
    Tibell, Lena A E
    Linköpings universitet, Institutionen för teknik och naturvetenskap, Medie- och Informationsteknik. Linköpings universitet, Tekniska fakulteten. Linköpings universitet.
    The potential of the evolutionary tree as mediational means in museum exhibitions containing key evolutionary concepts2015Inngår i: Non-formal Learning Environments, 2015Konferansepaper (Fagfellevurdert)
    Abstract [en]

    Diagrams have been used to visualize evolutionary relationships for more than 150 years, and are today readily found in many areas such as textbooks, media, museums and the scientific literature. The tree of life metaphor, where the diagram takes the form of an organic vertical tree has been used almost as long and is still used to a high degree in textbooks and at museums. Despite this high prevalence the instructional needed to develop tree-thinking abilities are often lacking, potentially leading to interpretational misconceptions of the evolutionary concepts presented.

    In this study 5 exhibitions with evolutionary content in natural science museums in the Nordic countries have been analysed in order to understand how evolutionary tree diagrams are incorporated in these exhibitions, what design is used and what instructional support is available to the visitor. A multi-modal social semiotic approach was used, where 3 functional levels were analysed together in order to assess the meaning making potential of the evolutionary trees in these exhibitions; i) content, representational process and design. ii) instruction and interactivity. iii) spatial and organizational composition. The analyses show a wide range of communication strategies; reaching from the evolutionary tree diagrams having a pivotal role in the exhibition narrative to being placed purely in the margin with no explicit connection to the overall evolutionary content. The instructional support is in many cases lacking but is sometimes incorporated in the presentational text of specific parts of the evolutionary tree, and the design ranges from tree of life type iconic visualisations to highly abstract renderings. Overall the evolutionary tree as a visual tool to communicate important evolutionary concepts seems to be used to a high degree but important aspects in order to better afford scientific correct interpretations of the trees are sometimes lacking.

  • 1309. Skarpe, C.
    et al.
    Bergström, R.
    Makhabu, S.
    Rooke, T.
    Hytteborn, Håkan
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Växtekologi och evolution.
    Danell, K.
    Plant-Herbivore Interactions2014Inngår i: Elephants and Savanna Woodland Ecosystems: A Study from Chobe National Park, Botswana / [ed] C. Skarpe, J. T. du Toit and S. R. Moe, Wiley-Blackwell, 2014, s. 189-206Kapittel i bok, del av antologi (Fagfellevurdert)
    Abstract [en]

    To a casual observer, the importance of large herbivores for ecosystem structure and dynamics can seem more obvious in African savannas than in many other ecosystems because of their high abundance, diversity and species richness of ungulates. African savannas have also had a long uninterrupted history of mammalian herbivory, leading to the evolution of plant traits adapted to herbivory and to reciprocal traits in herbivores. In nutrient-poor savannas such as those on Kalahari sand in the Chobe National Park, Botswana, elephants, Loxodonta africana, are a main agent creating spatial and temporal variation in the vegetation and ecosystems. Within this framework, elephants and smaller herbivores interact with individual plants and plant populations, exploiting and modifying heterogeneity at many scales. Intermittent grazing in systems of migratory or highly mobile herbivores provides food plants with a recovery period, and could be one reason for the 'success' and abundance of many migratory herbivore species.

  • 1310.
    Skoglund, Pontus
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Evolutionsbiologi.
    Reconstructing the Human Past using Ancient and Modern Genomes2013Doktoravhandling, med artikler (Annet vitenskapelig)
    Abstract [en]

    The study of DNA variation is one of the most promising avenues for learning about the evolutionary and historical past of humans and other species. However, the difficulty associated with obtaining DNA directly from ancient remains have for long kept genomic studies of population history trapped in time; confined to interpreting patterns of modern-day variation without direct historical observations. In this thesis, I outline new approaches for the retrieval, analysis and interpretation of large-scale genomic data from ancient populations, including solutions to overcome problems associated with limited genome coverage, modern-day contamination, temporal differences between samples, and post-mortem DNA damage. I integrate large-scale genomic data sets from ancient remains with modern-day variation to trace the human past; from traits targeted by natural selection in the early ancestors of anatomically modern humans, to their descendants' interbreeding with archaic populations in Eurasia and the spread of agriculture in Europe and Africa. By first reconstructing the earliest population diversification events of early modern humans using a novel large-scale genomic data set from Khoe-San populations in southern Africa, I devise a new approach to search for genomic patterns of selective sweeps in ancestral populations and report evidence for skeletal development as a major target of selection during the emergence of early modern humans. Comparing publicly available genomes from archaic humans, I further find that the distribution of archaic human ancestry in Eurasia is more complex than previously thought. In the first direct genomic study of population structure in prehistoric populations, I demonstrate that individuals associated with farming- and hunter-gatherer complexes in Neolithic Scandinavia were strongly genetically differentiated, and direct comparisons with modern-day populations as well as other prehistoric individuals from Southern Europe suggest that this structure originated from Northward expansion of Neolithic farming populations. Finally, I develop a bioinformatic approach for removing modern-day contamination from large-scale ancient DNA sequencing data, and use this method to reconstruct the complete mitochondrial genome sequence of a Siberian Neandertal that is affected by substantial modern-day contamination.

  • 1311.
    Skoglund, Pontus
    et al.
    Stockholms universitet, Humanistiska fakulteten, Institutionen för arkeologi och antikens kultur. Harvard Medical School, USA; Broad Institute of Harvard and MIT, USA.
    Ersmark, Erik
    Stockholms universitet, Naturvetenskapliga fakulteten, Zoologiska institutionen. Swedish Museum of Natural History, Sweden.
    Palkopoulou, Eleftheria
    Stockholms universitet, Naturvetenskapliga fakulteten, Zoologiska institutionen. Swedish Museum of Natural History, Sweden.
    Dalen, Love
    Ancient Wolf Genome Reveals an Early Divergence of Domestic Dog Ancestors and Admixture into High-Latitude Breeds2015Inngår i: Current Biology, ISSN 0960-9822, E-ISSN 1879-0445, Vol. 25, nr 11, s. 1515-1519Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    The origin of domestic dogs is poorly understood [1-15], with suggested evidence of dog-like features in fossils that predate the Last Glacial Maximum [6, 9, 10, 14, 16] conflicting with genetic estimates of a more recent divergence between dogs and worldwide wolf populations [13, 15, 17-19]. Here, we present a draft genome sequence from a 35,000 year-old wolf from the Taimyr Peninsula in northern Siberia. We find that this individual belonged to a population that diverged from the common ancestor of present-day wolves and dogs very close in time to the appearance of the domestic dog lineage. We use the directly dated ancient wolf genome to recalibrate the molecular timescale of wolves and dogs and find that the mutation rate is substantially slower than assumed by most previous studies, suggesting that the ancestors of dogs were separated from present-day wolves before the Last Glacial Maximum. We also find evidence of introgression from the archaic Taimyr wolf lineage into present-day dog breeds from northeast Siberia and Greenland, contributing between 1.4% and 27.3% of their ancestry. This demonstrates that the ancestry of present-day dogs is derived from multiple regional wolf populations.

  • 1312.
    Skoglund, Pontus
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Evolutionsbiologi. Uppsala universitet, Science for Life Laboratory, SciLifeLab.
    Jakobsson, Mattias
    Uppsala universitet, Science for Life Laboratory, SciLifeLab. Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Evolutionsbiologi.
    Archaic human ancestry in East Asia2011Inngår i: Proceedings of the National Academy of Sciences of the United States of America, ISSN 0027-8424, E-ISSN 1091-6490, Vol. 108, nr 45, s. 18301-18306Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Recent studies of ancient genomes have suggested that gene flow from archaic hominin groups to the ancestors of modern humans occurred on two separate occasions during the modern human expansion out of Africa. At the same time, decreasing levels of human genetic diversity have been found at increasing distance from Africa as a consequence of human expansion out of Africa. We analyzed the signal of archaic ancestry in modern human populations, and we investigated how serial founder models of human expansion affect the signal of archaic ancestry using simulations. For descendants of an archaic admixture event, we show that genetic drift coupled with ascertainment bias for common alleles can cause artificial but largely predictable differences in similarity to archaic genomes. In genotype data from non-Africans, this effect results in a biased genetic similarity to Neandertals with increasing distance from Africa. However, in addition to the previously reported gene flow between Neandertals and non-Africans as well as gene flow between an archaic human population from Siberia ("Denisovans") and Oceanians, we found a significant affinity between East Asians, particularly Southeast Asians, and the Denisovagenome-a pattern that is not expected under a model of solely Neandertal admixture in the ancestry of East Asians. These results suggest admixture between Denisovans or a Denisova-related population and the ancestors of East Asians, and that the history of anatomically modern and archaic humans might be more complex than previously proposed.

  • 1313.
    Skoglund, Pontus
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Evolutionsbiologi.
    Malmstrom, Helena
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Evolutionsbiologi.
    Omrak, Ayca
    Raghavan, Maanasa
    Valdiosera, Cristina
    Günther, Torsten
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Evolutionsbiologi.
    Hall, Per
    Tambets, Kristiina
    Parik, Jueri
    Sjogren, Karl-Goran
    Apel, Jan
    Willerslev, Eske
    Stora, Jan
    Gotherstrom, Anders
    Jakobsson, Mattias
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Evolutionsbiologi. Uppsala universitet, Science for Life Laboratory, SciLifeLab.
    Genomic Diversity and Admixture Differs for Stone-Age Scandinavian Foragers and Farmers2014Inngår i: Science, ISSN 0036-8075, E-ISSN 1095-9203, Vol. 344, nr 6185, s. 747-750Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Prehistoric population structure associated with the transition to an agricultural lifestyle in Europe remains a contentious idea. Population-genomic data from 11 Scandinavian Stone Age human remains suggest that hunter-gatherers had lower genetic diversity than that of farmers. Despite their close geographical proximity, the genetic differentiation between the two Stone Age groups was greater than that observed among extant European populations. Additionally, the Scandinavian Neolithic farmers exhibited a greater degree of hunter-gatherer-related admixture than that of the Tyrolean Iceman, who also originated from a farming context. In contrast, Scandinavian hunter-gatherers displayed no significant evidence of introgression from farmers. Our findings suggest that Stone Age foraging groups were historically in low numbers, likely owing to oscillating living conditions or restricted carrying capacity, and that they were partially incorporated into expanding farming groups.

  • 1314. Sköld, H. N.
    et al.
    Amundsen, T.
    Svensson, P. Andreas
    Mayer, I.
    Bjelvenmark, J.
    Forsgren, E.
    Hormonal regulation of female nuptial coloration in a fish2008Inngår i: Hormones and Behavior, ISSN 0018-506X, E-ISSN 1095-6867, Vol. 54, nr 4, s. 549-556Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Physiological color change in camouflage and mating is widespread among fishes, but little is known about the regulation of such temporal changes in nuptial coloration and particularly concerning female coloration. To better understand regulation of nuptial coloration we investigated physiological color change in female two-spotted gobies (Gobiusculus flavescens). Females of this species develop an orange belly that acts as an ornament. The orange color is caused by the color of the gonads combined with the chromathophore based pigmentation and transparency of the skin. Often during courtship and female-female competition, a rapid increase in orange coloration, in combination with lighter sides and back that increases skin and body transparency, gives the belly an intense 'glowing' appearance. To understand how this increased orange coloration can be regulated we analysed chromatic and transparency effects of neurohumoral agents on abdominal skin biopsies in vitro. We found prolactin and alpha-melanocyte stimulating hormone (MSH) to increase orange coloration of the skin. By contrast, melatonin and noradrenaline increased skin transparency, but had a negative effect on orange coloration. However, mixtures of melatonin and MSH, or melatonin and prolactin, increased both orange coloration and transparency. This effect mimics the chromatic 'glow' effect that commonly takes place during courtship and intra sexual aggression. Notably, not only epidermal chromatophores but also internal chromatophores lining the peritoneum responded to hormone treatments. There were no chromatic effects of the sex steroids 17 beta-estradiol, testosterone or 11-ketotestosterone. We hypothesize that similar modulation of nuptial coloration by multiple hormones may be widespread in nature. (C) 2008 Elsevier Inc. All rights reserved.

  • 1315.
    Sletvold, Nina
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Växtekologi och evolution.
    Trunschke, Judith
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Växtekologi och evolution.
    Smit, Mart
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Växtekologi och evolution.
    Verbeek, Jeffrey
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Växtekologi och evolution.
    Ågren, Jon
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Växtekologi och evolution.
    Strong pollinator-mediated selection for increased flower brightness and contrast in a deceptive orchid2016Inngår i: Evolution, ISSN 0014-3820, E-ISSN 1558-5646, Vol. 70, nr 3, s. 716-724Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Contrasting flower color patterns that putatively attract or direct pollinators toward a reward are common among angiosperms. In the deceptive orchid Anacamptis morio, the lower petal, which makes up most of the floral display, has a light central patch with dark markings. Within populations, there is pronounced variation in petal brightness, patch size, amount of dark markings, and contrast between patch and petal margin. We tested whether pollinators mediate selection on these color traits and on morphology (plant height, number of flowers, corolla size, spur length), and whether selection is consistent with facilitated or negative frequency-dependent pollination. Pollinators mediated strong selection for increased petal brightness (Delta beta(poll) = 0.42) and contrast (Delta beta(poll) = 0.51). Pollinators also tended to mediate stabilizing selection on brightness (Delta gamma(poll) = -0.27, n.s.) favoring the most common phenotype in the population. Selection for reduced petal brightness among hand-pollinated plants indicated a fitness cost associated with brightness. The results demonstrate that flower color traits influence pollination success and seed production in A. morio, indicating that they affect attractiveness to pollinators, efficiency of pollen transfer, or both. The documented selection is consistent with facilitated pollination and selection for color convergence toward cooccurring rewarding species.

  • 1316.
    Sletvold, Nina
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Växtekologi och evolution.
    Ågren, Jon
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Växtekologi och evolution. Uppsala Univ, EBC, Dept Ecol & Genet, Plant Ecol & Evolut, SE-75236 Uppsala, Sweden..
    Nonlinear costs of reproduction in a long-lived plant2015Inngår i: Journal of Ecology, ISSN 0022-0477, E-ISSN 1365-2745, Vol. 103, nr 5, s. 1205-1213Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    A trade-off between current reproduction and future performance is a key component of life-history theory, but the shape of this trade-off for any specific fitness component remains elusive. We induced three to five levels of reproductive effort (RE) by manipulating fruit set of a long-lived orchid in two populations that differed in the length of the growing season and local climate and examined survival, size and fecundity the following year. Natural fruit set was 72% higher in the long-season population, but was not associated with a significant survival cost in any population. Survival decreased linearly with experimentally increased RE in the short-season population. In both populations, natural RE incurred growth and fecundity costs, and growth costs increased nonlinearly with diminishing costs at high RE. Fecundity costs increased linearly with RE in the long-season population, but nonlinearly with diminishing costs at high RE in the other. The results demonstrate that the shape of the cost function may be nonlinear with context-dependent intercept, slope and curvature. They are consistent with the prediction that survival costs appear only when RE exceeds natural levels, while growth and fecundity costs are evident at natural RE.Synthesis. We suggest that studies inducing multiple levels of RE are required to understand life-history trade-offs and their context dependence. This kind of information is fundamental for an understanding of the link between environmental heterogeneity, adaptive differentiation and life-history evolution.

  • 1317.
    Sletvold, Nina
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Växtekologi och evolution.
    Ågren, Jon
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Växtekologi och evolution.
    There is More to Pollinator-Mediated Selection than Pollen Limitation2014Inngår i: Evolution, ISSN 0014-3820, E-ISSN 1558-5646, Vol. 68, nr 7, s. 1907-1918Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Spatial variation in pollinator-mediated selection (Delta beta(poll)) is a major driver of floral diversification, but we lack a quantitative understanding of its link to pollen limitation (PL) and net selection on floral traits. For 2-5 years, we quantified Delta beta(poll) on floral traits in two populations each of two orchid species differing in PL. In both species, spatiotemporal variation in Delta beta(poll) explained much of the variation in net selection. Selection was consistently stronger and the proportion that was pollinator-mediated was higher in the severely pollen-limited deceptive species than in the rewarding species. Within species, variation in PL could not explain variation in Delta beta(poll) for any trait, indicating that factors influencing the functional relationship between trait variation and pollination success govern a major part of the observed variation in Delta beta(poll). Separating the effects of variation in mean interaction intensity and in the functional significance of traits will be necessary to understand spatiotemporal variation in selection exerted by the biotic environment.

  • 1318.
    Slove, Jessica
    et al.
    Stockholms universitet, Naturvetenskapliga fakulteten, Zoologiska institutionen.
    Eriksson, Torsten
    Department of Biodiversity informatics, Swedish Museum of Natural History.
    Nylin, Sören
    Stockholms universitet, Naturvetenskapliga fakulteten, Zoologiska institutionen.
    Janz, Niklas
    Stockholms universitet, Naturvetenskapliga fakulteten, Zoologiska institutionen.
    Exploring a complex trait - the effect of larval feeding ability and unequal transition costs on the dynamics ofhost range evolution in two groups of related butterfliesManuskript (preprint) (Annet vitenskapelig)
    Abstract [en]

    Host plant use is a complex trait, better described as the combined outcome of many interrelated traits, such as female preference and larval ability to feed, grow and survive. The necessary co-adaptation of these traits would suggest that the host shifts should be difficult to accomplish. Still, even though a large-scale conservatism can be seen in most groups, frequent changes in host use are not uncommon, suggesting that under some circumstances adding new plants to the range might not be as difficult as one might expect. In a case study on two closelyr elated butterfly genera, we investigate the effect of unequal transition costs and of including available data on larval feeding ability as well as plants used in the field, and describe and compare the dynamics of host range evolution in these groups. We find that apparent independent colonisations are in many cases likely to be the result of non-independent processes such as multiple losses, recolonisation or parallel colonisations following some preadaptation. Host plants shifts and range expansions are likely important drivers of the exceptional diversity of herbivorousinsects. A better understanding of the dynamics of host range evolution will improve our understanding of the source of this diversity.

  • 1319.
    Smeds, Linnea
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Evolutionsbiologi.
    Kawakami, Takeshi
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Evolutionsbiologi.
    Burri, Reto
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Evolutionsbiologi.
    Bolivar, Paulina
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Evolutionsbiologi.
    Husby, Arild
    Qvarnström, Anna
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Zooekologi.
    Uebbing, Severin
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Evolutionsbiologi.
    Ellegren, Hans
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Evolutionsbiologi.
    Genomic identification and characterization of the pseudoautosomal region in highly differentiated avian sex chromosomes2014Inngår i: Nature Communications, ISSN 2041-1723, E-ISSN 2041-1723, Vol. 5, s. 5448-Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    The molecular characteristics of the pseudoautosomal region (PAR) of sex chromosomes remain elusive. Despite significant genome-sequencing efforts, the PAR of highly differentiated avian sex chromosomes remains to be identified. Here we use linkage analysis together with whole-genome re-sequencing to uncover the 630-kb PAR of an ecological model species, the collared flycatcher. The PAR contains 22 protein-coding genes and is GC rich. The genetic length is 64cM in female meiosis, consistent with an obligate crossing-over event. Recombination is concentrated to a hotspot region, with an extreme rate of > 700 cM/Mb in a 67-kb segment. We find no signatures of sexual antagonism and propose that sexual antagonism may have limited influence on PAR sequences when sex chromosomes are nearly fully differentiated and when a recombination hotspot region is located close to the PAR boundary. Our results demonstrate that a very small PAR suffices to ensure homologous recombination and proper segregation of sex chromosomes during meiosis.

  • 1320.
    Smeds, Linnea
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Evolutionsbiologi.
    Qvarnström, Anna
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Zooekologi.
    Ellegren, Hans
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Evolutionsbiologi.
    Direct estimate of the rate of germline mutation in a bird2016Inngår i: Genome Research, ISSN 1088-9051, E-ISSN 1549-5469, Vol. 26, nr 9, s. 1211-1218Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    The fidelity of DNA replication together with repair mechanisms ensure that the genetic material is properly copied from one generation to another. However, on extremely rare occasions when damages to DNA or replication errors are not repaired, germline mutations can be transmitted to the next generation. Because of the rarity of these events, studying the rate at which new mutations arise across organisms has been a great challenge, especially in multicellular nonmodel organisms with large genomes. We sequenced the genomes of 11 birds from a three-generation pedigree of the collared flycatcher (Ficedula albicollis) and used highly stringent bioinformatic criteria for mutation detection and used several procedures to validate mutations, including following the stable inheritance of new mutations to subsequent generations. We identified 55 de novo mutations with a 10-fold enrichment of mutations at CpG sites and with only a modest male mutation bias. The estimated rate of mutation per site per generation was 4.6 x 10(-9), which corresponds to 2.3 x 10(-9) mutations per site per year. Compared to mammals, this is similar to mouse but about half of that reported for humans, which may be due to the higher frequency of male mutations in humans. We confirm that mutation rate scales positively with genome size and that there is a strong negative relationship between mutation rate and effective population size, in line with the drift-barrier hypothesis. Our study illustrates that it should be feasible to obtain direct estimates of the rate of mutation in essentially any organism from which family material can be obtained.

  • 1321. Smith, Felisa A
    et al.
    Boyer, Alison G
    Brown, James H
    Costa, Daniel P
    Dayan, Tamar
    Ernest, SK Morgan
    Evans, Alistair R
    Fortelius, Mikael
    Gittleman, John L
    Hamilton, Marcus J
    Harding, Larisa E
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för ekologi, miljö och geovetenskap.
    Lintulaakso, Kari
    Lyons, S Kathleen
    McCain, Christy
    Okie, Jordan G
    Saarinen, Juha J
    Sibly, Richard M
    Stephens, Patrick R
    Theodor, Jessica
    Uhen, Mark D
    The evolution of maximum body size of terrestrial mammals2010Inngår i: Science, ISSN 0036-8075, E-ISSN 1095-9203, Vol. 330, nr 6008, s. 1216-1219Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    The extinction of dinosaurs at the Cretaceous/Paleogene (K/Pg) boundary was the seminal event that opened the door for the subsequent diversification of terrestrial mammals. Our compilation of maximum body size at the ordinal level by sub-epoch shows a near-exponential increase after the K/Pg. On each continent, the maximum size of mammals leveled off after 40 million years ago and thereafter remained approximately constant. There was remarkable congruence in the rate, trajectory, and upper limit across continents, orders, and trophic guilds, despite differences in geological and climatic history, turnover of lineages, and ecological variation. Our analysis suggests that although the primary driver for the evolution of giant mammals was diversification to fill ecological niches, environmental temperature and land area may have ultimately constrained the maximum size achieved.

  • 1322.
    Sniegula, Szymon
    et al.
    Polish Acad Sci, Inst Nat Conservat, Dept Ecosyst Conservat, Al Mickiewicza 33, PL-31120 Krakow, Poland..
    Golab, Maria J.
    Polish Acad Sci, Inst Nat Conservat, Dept Ecosyst Conservat, Al Mickiewicza 33, PL-31120 Krakow, Poland..
    Johansson, Frank
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Zooekologi.
    Cannibalism and activity rate in larval damselflies increase along a latitudinal gradient as a consequence of time constraints2017Inngår i: BMC Evolutionary Biology, ISSN 1471-2148, E-ISSN 1471-2148, Vol. 17, artikkel-id 167Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Background: Predation is ubiquitous in nature. One form of predation is cannibalism, which is affected by many factors such as size structure and resource density. However, cannibalism may also be influenced by abiotic factors such as seasonal time constraints. Since time constraints are greater at high latitudes, cannibalism could be stronger at such latitudes, but we know next to nothing about latitudinal variation in cannibalism. In this study, we examined cannibalism and activity in larvae of the damselfly Lestes sponsa along a latitudinal gradient across Europe. We did this by raising larvae from the egg stage at different temperatures and photoperiods corresponding to different latitudes. Results: We found that the more seasonally time-constrained populations in northern latitudes and individuals subjected to greater seasonal time constraints exhibited a higher level of cannibalism. We also found that activity was higher at north latitude conditions, and thus correlated with cannibalism, suggesting that this behaviour mediates higher levels of cannibalism in time-constrained animals. Conclusions: Our results go counter to the classical latitude-predation pattern which predicts higher predation at lower latitudes, since we found that predation was stronger at higher latitudes. The differences in cannibalism might have implications for population dynamics along the latitudinal gradients, but further experiments are needed to explore this.

  • 1323. Sniegula, Szymon
    et al.
    Nilsson-Örtman, Viktor
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för ekologi, miljö och geovetenskap.
    Johansson, Frank
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för ekologi, miljö och geovetenskap.
    Growth Pattern Responses to Photoperiod across Latitudes in a Northern Damselfly2012Inngår i: PLoS ONE, ISSN 1932-6203, E-ISSN 1932-6203, Vol. 7, nr 9, s. e46024-Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Background: Latitudinal clines in temperature and seasonality impose strong seasonal constraints on ectotherms. Studies of population differentiation in phenotypic plasticity of life history traits along latitudinal gradients are important for understanding how organisms have adapted to seasonal environments and predict how they respond to climate changes. Such studies have been scarce for species with a northern distribution. Methodology/Principle Finding: Larvae of the northern damselfly Coenagrion johanssoni originating from semivoltine central, partivoltine northern, and partivoltine northernmost Swedish populations were reared in the laboratory. To investigate whether larvae use photoperiodic cues to induce compensatory growth along this latitudinal gradient, larvae were reared under two different photoperiods corresponding to a northern and southern latitude. In addition, field adult size was assessed to test the strength of possible compensatory growth mechanisms under natural conditions and hatchling size was measured to test for maternal effects. We hypothesized that populations originating from lower latitudes would be more time constrained than high-latitude populations because they have a shorter life cycle. The results showed that low-latitude populations had higher growth rates in summer/fall. In general northern photoperiods induced higher growth rates, but this plastic response to photoperiod was strongest in the southernmost populations and negligible in the northernmost population. During spring, central populations grew faster under the southern rather than the northern photoperiod. On the other hand, northern and northernmost populations did not differ between each other and grew faster in the northern rather than in the southern photoperiod. Field sampled adults did not differ in size across the studied regions. Conclusion/Significance: We found a significant differentiation in growth rate across latitudes and latitudinal difference in growth rate response to photoperiod. Importantly, growth responses measured at a single larval developmental stage in one season may not always generalize to other developmental stages or seasons.

  • 1324. Sniegula, Szymon
    et al.
    Prus, Monika A.
    Golab, Maria J.
    Outomuro, David
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Zooekologi.
    Do males with higher mating success invest more in armaments?: An across-populations study in damselflies2017Inngår i: Ecological Entomology, ISSN 0307-6946, E-ISSN 1365-2311, Vol. 42, nr 4, s. 526-530Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    1. Males with higher mating success would be expected to invest more in traits that facilitate mating, leading to steeper allometry of those traits with respect to body size. Across-population studies following latitudinal variation in male mating success are an excellent study system to address this question.

    2. Males of the damselfly Lestes sponsa were used to investigate whether the allometric patterns of the length and width of the anal appendages, used for grasping the female prior tomating, corresponded to male mating success. Across a large latitudinal gradient, it was hypothesised that there is a larger investment in the grasping apparatus, i.e. a steeper allometric slope, following higher mating success.

    3. Behavioural observations in field enclosures showed the highest mating success at high latitude, while there were no significant differences in mating success between the central and low latitudes. Positive allometry was found for the length of the anal appendages in high-latitude males, while central-and low-latitude males showed no significant regressions of the traits on body size.

    4. These results partially support the hypothesis, as high-latitude, more successful males invested more in the length ( but not the width) of the grasping apparatus than did central-and low-latitude males. Therefore, higher mating success might be facilitated by larger investment in armaments. Intraspecific studies on allometric patterns of traits that participate in mating success might offer new insights into the role of those traits in the reproductive behaviour of a species.

  • 1325.
    Sokolovskis, Kristaps
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för biologisk grundutbildning. Lund University, MEEL, Bensch group.
    Genetics of bird migration: Study on East Siberian willow warblers (Phylloscopus trochilus)2017Independent thesis Advanced level (degree of Master (Two Years)), 30 poäng / 45 hpOppgave
    Abstract [en]

    Seasonal long-distance bird migration between wintering and breeding grounds is oneof the most remarkable phenomena in the history of life on earth. Migration strategies androutes vary greatly. Some birds migrate in social groups whilst others migrate alone at night,some cross few hundreds of km whilst others cover thousands of km. Avian migration has beenstudied extensively nevertheless numerous important questions remain unanswered. This studyaims to contribute to the understanding of the genetic basis of the innate migratory program ofa common songbird.From results of classical crossbreeding and orientation experiments with captiveblackcaps (Sylvia atricapilla) we can be sure that songbird migration directions as well asdurations are traits that are being inherited genetically and most likely have a multi-locusgenetic architecture. The chosen model species for my project is the willow warbler(Phylloscopus trochilus), one of the most common leaf warblers in the Palearctic. The willowwarbler has a continuous breeding distribution from the coast of the Atlantic to the coast ofPacific. They overwinter in sub-Saharan Africa. Three subspecies have been recognized: P. t.trochilus (breeding in central/western Europe and migrating SSW to western Africa), P. t.acredula (breeding in northern and eastern Europe, migrating SSE to east and south Africa)and P. t. yakutensis (breeding east of Ural Mountains, presumably migrating to SouthernAfrica). Morphological differences across the willow warbler subspecies are subtle and it has

    been previously shown that genome wide FST is close to zero. The low level of neutral back-ground divergence offers a good system for studying the genetics of passerine migration. This

    report contributes with novel data on phenotypes and genotypes of the subspecies yakutensisstudied at Chaun river delta, at the very eastern range limit of the species. As a proxy for thewintering location of yakutensis I used C and N stable isotope signatures from winter grownfeathers and inferred wintering range to be in Southern Africa. I genotyped 36 yakutensis fromChaun on four nuclear markers, of which three are located on the only divergent regions thatdiffers between the migratory phenotypes in Europe + CLOCK gene (a candidate for timing ofmigration). Analyzes revealed that yakutensis, despite strong differences in migration direction,distance, timing and wintering ground location cannot be separated from acredula genetically.

    Fulltekst tilgjengelig fra 2018-12-31 09:07
  • 1326. Soliani, Carolina
    et al.
    Tsuda, Yoshiaki
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Växtekologi och evolution.
    Bagnoli, Francesca
    Gallo, Leonardo A.
    Vendramin, Giovanni G.
    Marchelli, Paula
    Halfway encounters: Meeting points of colonization routes among the southern beeches Nothofagus pumilio and N. antarctica2015Inngår i: Molecular Phylogenetics and Evolution, ISSN 1055-7903, E-ISSN 1095-9513, Vol. 85, s. 197-207Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    The Patagonian region is characterized by a complex biogeographic history, with evidence of deep phylogeographic breaks shared among species. Of particular interest to conservation is the nature of colonization and settlement patterns after the last glacial period, including the detection of secondary contact between different lineages and/or hybridization among related species around phylogeographic breaks. Here we studied population demography and past hybridization of two widespread tree species endemic to South America, Nothofagus pumilio and N. antarctica. Using 8 nuclear microsatellites we genotyped 41 populations of both species. Genetic variation and structure across the geographic region were evaluated within and among species and the past demographic history of hybridization between the two species was inferred using Approximate Bayesian Computation (ABC). Northern and southern lineages were identified in each species, and Bayesian clustering revealed their convergence at mid latitudes (42 degrees S). Spatial genetic structure (SGS) also indicated the existence of a genetic discontinuity at these latitudes, which is in agreement with previous data from maternal DNA markers. Several populations around 42-44 degrees S presented high levels of genetic diversity with a decrease toward southern populations. Even though the species are clearly differentiated (G'(ST) = 0.335), admixed gene pools were observed in both species. Two independent runs of ABC suggested that inter species admixture-like patterns occurred within the timescale of the Last Glacial Maximum (around 20,000 BP). We also provide evidences of recent and bi-directional hybridization/introgression between the two Nothofagus species and describe features of the populations demography in the past. The settlement of a secondary contact zone in Nothofagus species around 42-44 degrees S coincides with the phylogeographic breaks and hotspots of genetic diversity found in other plant and animal species in Patagonia, highlighting its importance as reservoir of diversity. The characterization of the population history of native species can contribute substantially to long-term conservation and management policies.

  • 1327.
    Sorato, Enrico
    et al.
    Linköpings universitet, Institutionen för fysik, kemi och biologi. Linköpings universitet, Tekniska fakulteten. Macquarie University, Australia.
    Griffith, Simon C.
    Macquarie University, Australia; University of New South Wales, Australia.
    Russell, Andy F.
    University of New South Wales, Australia; University of Exeter, England.
    The price of associating with breeders in the cooperatively breeding chestnut-crowned babbler: foraging constraints, survival and sociality2016Inngår i: Journal of Animal Ecology, ISSN 0021-8790, E-ISSN 1365-2656, Vol. 85, nr 5, s. 1340-1351Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    1. Understanding the costs of living with breeders might offer new insights into the factors that counter evolutionary transitions from selfish individuals to cooperative societies. While selection on early dispersal is well understood, it is less clear whether costs are also associated with remaining with family members during subsequent breeding, a prerequisite to the evolution of kin-based cooperation. 2. We propose and test the hypothesis that living in groups containing breeders is costly and that such costs are exacerbated by increasing group size. For example, in group-living central- place foragers, group members might suffer from resource depletion when foraging in a restricted area during breeding and significant costs of repeatedly travelling between foraging patches and the site of offspring. 3. Using the cooperatively breeding chestnut-crowned babbler (Pomatostomus ruficeps), for which grouping during breeding is obligatory, we show that reproduction is associated with substantially reduced foraging areas and evidence of resource depletion, particularly in larger groups. Such effects largely persisted from the onset of incubation through to offspring independence 4-5 months later. All group members, irrespective of their breeder or helper status, lost significant body mass over this period, and, in males, mass loss was associated with reduced interannual survival. 4. Although babblers are constrained from living outside of breeding groups due to high risks of predation and the poor success of breeding without helpers, we suggest that the effects we describe may generally select against group living during breeding attempts in species where constraints to independent breeding and costs of dispersal are less acute.

  • 1328.
    Sorenson, Michael D
    et al.
    University of Michigan, Museum of Zoology and Department of Biology.
    Ast, Jennifer C
    University of Michigan, Museum of Zoology and Department of Biology.
    Dimcheff, Derek E
    University of Michigan, Museum of Zoology and Department of Biology.
    Yuri, Tamaki
    University of Michigan, Museum of Zoology and Department of Biology.
    Mindell, David P
    University of Michigan, Museum of Zoology and Department of Biology.
    Primers for a PCR-based approach to mitochondrial genome sequencing in birds and other vertebrates1999Inngår i: Molecular Phylogenetics and Evolution, ISSN 1055-7903, E-ISSN 1095-9513, Vol. 12, s. 105-114Artikkel i tidsskrift (Fagfellevurdert)
  • 1329.
    Sork, Victoria L.
    et al.
    Univ Calif Los Angeles, Dept Ecol & Evolutionary Biol, Los Angeles, CA 90095 USA.;Univ Calif Los Angeles, Inst Environm & Sustainabil, Los Angeles, CA 90095 USA..
    Smouse, Peter E.
    Rutgers State Univ, Dept Ecol Evolut & Nat Resources, New Brunswick, NJ 08901 USA..
    Grivet, Delphine
    CIFOR Natl Inst Agr & Food Res & Technol, Ctr Forest Res, Dept Forest Ecol & Genet, Madrid, Spain..
    Scofield, Douglas G.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Evolutionsbiologi. Univ Calif Los Angeles, Dept Ecol & Evolutionary Biol, Los Angeles, CA 90095 USA..
    Impact of asymmetric male and female gamete dispersal on allelic diversity and spatial genetic structure in valley oak (Quercus lobata Nee)2015Inngår i: Evolutionary Ecology, ISSN 0269-7653, E-ISSN 1573-8477, Vol. 29, nr 6, s. 927-945Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    The distribution and abundance of genetic diversity in plant populations is initiated by sexually asymmetric propagule dispersal through pollen and seeds. Because these processes occur serially, it is not transparent how each contributes to subsequent patterns of genetic diversity. Using combined seedling/seed coat assay for naturally distributed seedlings of Quercus lobata N,e, we extracted male and female gametic genotypes, and then assessed (wind-vectored) paternal and (gravity- and animal-vectored) maternal contributions to spatially distributed allelic diversity. We evaluated 200 naturally recruited seedlings from 4 open patches away from any adult canopies (denoted 'open'), and 174 seedlings from 14 patches immediately beneath adult canopies (denoted 'canopy'). The open patches included 19 % long distant dispersal events of > 1 km while the canopy patches contained seedlings from one tree overhead. For each patch type, we partitioned average allelic diversity for six microsatellite loci for the whole study site (gamma) into separate within-patch (alpha) and among-patch (beta) components, translated into among-patch divergence (delta). We found that alpha-diversity resulting from seed dispersal was much less than that from pollen dispersal in both patch types, while total gamma-diversity across the site was similar. Divergence (delta) among canopy patches was significantly greater than delta among open patches. We then evaluated spatial genetic autocorrelation (kinship) patterns for both open and canopy strata, separately for male and female gametes. Female gametes showed sharply declining kinship with increasing distance for canopy patches and modestly for open patches. In sharp contrast, male gametes from both patches showed only subtle decline of kinship, but seedlings still showed significant structure across patch types. On balance, sexual asymmetry in propagule dispersal shapes both the abundance and distribution of allelic diversity, with pollen dispersal promoting overall diversity but reducing spatial structure, but seed-dispersal reduces overall diversity and markedly increases spatial genetic structure.

  • 1330.
    Sotero-Caio, Cibele G.
    et al.
    Texas Tech Univ, Dept Biol Sci, Lubbock, TX 79409 USA..
    Platt, Roy N., II
    Texas Tech Univ, Dept Biol Sci, Lubbock, TX 79409 USA..
    Suh, Alexander
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Evolutionsbiologi.
    Ray, David A.
    Texas Tech Univ, Dept Biol Sci, Lubbock, TX 79409 USA..
    Evolution and Diversity of Transposable Elements in Vertebrate Genomes2017Inngår i: Genome Biology and Evolution, ISSN 1759-6653, E-ISSN 1759-6653, Vol. 9, nr 1, s. 161-177Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Transposable elements (TEs) are selfish genetic elements that mobilize in genomes via transposition or retrotransposition and often make up large fractions of vertebrate genomes. Here, we review the current understanding of vertebrate TE diversity and evolution in the context of recent advances in genome sequencing and assembly techniques. TEs make up 4-60% of assembled vertebrate genomes, and deeply branching lineages such as ray-finned fishes and amphibians generally exhibit a higher TE diversity than the more recent radiations of birds and mammals. Furthermore, the list of taxa with exceptional TE landscapes is growing. We emphasize that the current bottleneck in genome analyses lies in the proper annotation of TEs and provide examples where superficial analyses led to misleading conclusions about genomeevolution. Finally, recent advances in long-read sequencing will soon permit access to TE-rich genomic regions that previously resisted assembly including the gigantic, TE-rich genomes of salamanders and lungfishes.

  • 1331.
    Spagopoulou, Foteini
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Zooekologi.
    Blom, Mozes P. K.
    Dept. of Bioinformatics and Genetics, Naturhistoriska Riksmuseet.
    Digest: Life history evolution in Darwin's dream ponds2018Inngår i: Evolution, ISSN 0014-3820, E-ISSN 1558-5646Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Can variation in sex‐specific parental investment lead to sexual dimorphism in immune response? Keller et al. (2018) measured immune cell parameters, expression of candidate genes and composition of buccal microbiota in mouthbrooding cichlid species from Lake Tanganyika that show either maternal or biparental care. They found that maternal mouthbrooding species have increased sexual dimorphism in immune parameters, while biparental mouthbrooders exhibit an upregulated adaptive immune response, suggesting resource allocation shifts between parental investment and the immune system.

    Fulltekst tilgjengelig fra 2019-04-01 00:00
  • 1332.
    Spagopoulou, Foteini
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Zooekologi.
    Hooper, Amy
    Evolution and Ecology Research Centre, University of New South Wales.
    Wylde, Zacharia
    Evolution and Ecology Research Centre, University of New South Wales.
    Bonduriansky, Russel
    Evolution and Ecology Research Centre, University of New South Wales.
    Maklakov, Alexei
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Zooekologi.
    Early-life parental diet effects on ageing depend on the sex of parents and their offspringManuskript (preprint) (Annet vitenskapelig)
  • 1333.
    Spagopoulou, Foteini
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Zooekologi.
    Teplitsky, Celine
    Centre D'Ecologie Fonctionelle & Evolutive.
    Gustafsson, Lars
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Zooekologi.
    Maklakov, Alexei
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Zooekologi.
    “Silver-spoon” natal conditions increase early-life fitness but accelerate reproductive ageing in a wild birdManuskript (preprint) (Annet vitenskapelig)
    Abstract [en]

    Early-life conditions can have long-lasting effects and organisms that experience a poor start in life are often expected to age at a faster rate. Alternatively, individuals raised in high-quality environments can overinvest in early-reproduction resulting in rapid ageing. Here we use long-term experimental manipulation of early-life conditions in a natural population of collared flycatchers (Ficedula albicollis), to show that females raised in a low-competition environment have higher early-life reproduction but lower late-life reproduction than females raised in high-competition environment. We experimentally created either artificially increased (high-competition) or reduced (low-competition) broods. Reproductive success of high-competition females peaked in late-life, when low-competition females were already in steep reproductive decline and suffered from higher mortality rate. Our results demonstrate that “silver spoon” effects can increase female early-life performance at the cost of faster reproductive ageing and increased late-life mortality. These findings support the evolutionary theory of ageing and show that early-life environmental conditions shape reproductive and demographic ageing in nature.

  • 1334.
    Spang, Anja
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för cell- och molekylärbiologi, Molekylär evolution. Uppsala universitet, Science for Life Laboratory, SciLifeLab.
    Caceres, Eva F.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för cell- och molekylärbiologi, Molekylär evolution. Uppsala universitet, Science for Life Laboratory, SciLifeLab.
    Ettema, Thijs J. G.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för cell- och molekylärbiologi, Molekylär evolution. Uppsala universitet, Science for Life Laboratory, SciLifeLab.
    Genomic exploration of the diversity, ecology, and evolution of the archaeal domain of life.2017Inngår i: Science, ISSN 0036-8075, E-ISSN 1095-9203, Vol. 357, nr 6351, artikkel-id eaaf3883Artikkel, forskningsoversikt (Fagfellevurdert)
    Abstract [en]

    About 40 years ago, Archaea were recognized as a major prokaryotic domain of life besides Bacteria. Recently, cultivation-independent sequencing methods have produced a wealth of genomic data for previously unidentified archaeal lineages, several of which appear to represent newly revealed branches in the tree of life. Analyses of some recently obtained genomes have uncovered previously unknown metabolic traits and provided insights into the evolution of archaea and their relationship to eukaryotes. On the basis of our current understanding, much archaeal diversity still defies genomic exploration. Efforts to obtain and study genomes and enrichment cultures of uncultivated microbial lineages will likely further expand our knowledge about archaeal phylogenetic and metabolic diversity and their cell biology and ecological function.

  • 1335.
    Spang, Anja
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för cell- och molekylärbiologi, Molekylär evolution. Uppsala universitet, Science for Life Laboratory, SciLifeLab.
    Ettema, Thijs J. G.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för cell- och molekylärbiologi, Molekylär evolution. Uppsala universitet, Science for Life Laboratory, SciLifeLab.
    Archaeal evolution: The methanogenic roots of Archaea2017Inngår i: Nature Microbiology, E-ISSN 2058-5276, Vol. 2, artikkel-id 17109Artikkel i tidsskrift (Annet vitenskapelig)
  • 1336.
    Spang, Anja
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för cell- och molekylärbiologi, Molekylär evolution. Uppsala universitet, Science for Life Laboratory, SciLifeLab.
    Saw, Jimmy H.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för cell- och molekylärbiologi, Molekylär evolution. Uppsala universitet, Science for Life Laboratory, SciLifeLab.
    Jorgensen, Steffen L.
    Zaremba-Niedzwiedzka, Katarzyna
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för cell- och molekylärbiologi, Molekylär evolution. Uppsala universitet, Science for Life Laboratory, SciLifeLab.
    Martijn, Joran
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för cell- och molekylärbiologi, Molekylär evolution. Uppsala universitet, Science for Life Laboratory, SciLifeLab.
    Lind, Anders E.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för cell- och molekylärbiologi, Molekylär evolution. Uppsala universitet, Science for Life Laboratory, SciLifeLab.
    van Eijk, Roel
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för cell- och molekylärbiologi, Molekylär evolution. Uppsala universitet, Science for Life Laboratory, SciLifeLab.
    Schleper, Christa
    Guy, Lionel
    Uppsala universitet, Medicinska och farmaceutiska vetenskapsområdet, Medicinska fakulteten, Institutionen för medicinsk biokemi och mikrobiologi. Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för cell- och molekylärbiologi, Molekylär evolution. Uppsala universitet, Science for Life Laboratory, SciLifeLab.
    Ettema, Thijs J. G.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för cell- och molekylärbiologi, Molekylär evolution. Uppsala universitet, Science for Life Laboratory, SciLifeLab.
    Complex archaea that bridge the gap between prokaryotes and eukaryotes2015Inngår i: Nature, ISSN 0028-0836, E-ISSN 1476-4687, Vol. 521, nr 7551, s. 173-179Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    The origin of the eukaryotic cell remains one of the most contentious puzzles in modern biology. Recent studies have provided support for the emergence of the eukaryotic host cell from within the archaeal domain of life, but the identity and nature of the putative archaeal ancestor remain a subject of debate. Here we describe the discovery of 'Lokiarchaeota', a novel candidate archaeal phylum, which forms a monophyletic group with eukaryotes in phylogenomic analyses, and whose genomes encode an expanded repertoire of eukaryotic signature proteins that are suggestive of sophisticated membrane remodelling capabilities. Our results provide strong support for hypotheses in which the eukaryotic host evolved from a bona fide archaeon, and demonstrate that many components that underpin eukaryote-specific features were already present in that ancestor. This provided the host with a rich genomic 'starter-kit' to support the increase in the cellular and genomic complexity that is characteristic of eukaryotes.

  • 1337. Stadler, Tanja
    et al.
    Bokma, Folmer
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för ekologi, miljö och geovetenskap.
    Estimating Speciation and Extinction Rates for Phylogenies of Higher Taxa2013Inngår i: Systematic Biology, ISSN 1063-5157, E-ISSN 1076-836X, Vol. 62, nr 2, s. 220-230Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Speciation and extinction rates can be estimated from molecular phylogenies. Recently, a number of methods have been published showing that these rates can be estimated even if the phylogeny is incomplete, that is, if not all extant species are included. We show that the accuracy of such methods strongly depends on making the correct assumptions about how the sampling process was performed. We focus on phylogenies that are incomplete because some subclades (e.g., genera and families) are each represented as a single lineage. We show that previous methods implicitly assumed that such subclades are defined by randomly (or in an extreme deterministic way) choosing the edges that define the subclades from the complete species phylogeny. We show that these methods produce biased results if higher taxa are defined in a different manner. We introduce strict higher level phylogenies where subclades are defined so that the phylogeny is fully resolved from its origin to time x(cut), and fully unresolved thereafter, so that for all subclades, stem age > x(cut) > crown age. We present estimates of speciation and extinction rates from a phylogeny of birds in which this subclade definition was applied. However, for most higher level phylogenies in the literature, it is unclear how higher taxa were defined, but often such phylogenies can be easily transformed into strict higher level phylogenies, as we illustrate by estimating speciation and extinction rates from a near-complete but only partly resolved species-level phylogeny of mammals. The accuracy of our methods is verified using simulations.

  • 1338. Stadler, Tanja
    et al.
    Rabosky, Daniel L.
    Ricklefs, Robert E.
    Bokma, Folmer
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för ekologi, miljö och geovetenskap.
    On age and species richness of higher taxa2014Inngår i: American Naturalist, ISSN 0003-0147, E-ISSN 1537-5323, Vol. 184, nr 4, s. 447-455Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Many studies have tried to identify factors that explain differences in numbers of species between clades against the background assumption that older clades contain more species because they have had more time for diversity to accumulate. The finding in several recent studies that species richness of clades is decoupled from stem age has been interpreted as evidence for ecological limits to species richness. Here we demonstrate that the absence of a positive age-diversity relationship, or even a negative relationship, may also occur when taxa are defined based on time or some correlate of time such as genetic distance or perhaps morphological distinctness. Thus, inferring underlying processes from distributions of species across higher taxa requires caution concerning the way in which higher taxa are defined. When this definition is unclear, crown age is superior to stem age as a measure of clade age.

  • 1339.
    Steige, Kim A.
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Evolutionsbiologi.
    Reimegård, Johan
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för cell- och molekylärbiologi, Molekylär evolution. Uppsala universitet, Science for Life Laboratory, SciLifeLab.
    Koenig, Daniel
    Max Planck Inst Dev Biol, Dept Mol Biol, Tubingen, Germany..
    Scofield, Douglas G.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Evolutionsbiologi.
    Slotte, Tanja
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Evolutionsbiologi. Stockholm Univ, Sci Life Lab, Dept Ecol Environm & Plant Sci, S-10691 Stockholm, Sweden..
    Cis-Regulatory Changes Associated with a Recent Mating System Shift and Floral Adaptation in Capsella2015Inngår i: Molecular biology and evolution, ISSN 0737-4038, E-ISSN 1537-1719, Vol. 32, nr 10, s. 2501-2514Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    The selfing syndrome constitutes a suite of floral and reproductive trait changes that have evolved repeatedly across many evolutionary lineages in response to the shift to selfing. Convergent evolution of the selfing syndrome suggests that these changes are adaptive, yet our understanding of the detailed molecular genetic basis of the selfing syndrome remains limited. Here, we investigate the role of cis-regulatory changes during the recent evolution of the selfing syndrome in Capsella rubella, which split from the outcrosser Capsella grandiflora less than 200 ka. We assess allele-specific expression (ASE) in leaves and flower buds at a total of 18,452 genes in three interspecific F1 C. grandiflora x C. rubella hybrids. Using a hierarchical Bayesian approach that accounts for technical variation using genomic reads, we find evidence for extensive cis-regulatory changes. On average, 44% of the assayed genes show evidence of ASE; however, only 6% show strong allelic expression biases. Flower buds, but not leaves, show an enrichment of cis-regulatory changes in genomic regions responsible for floral and reproductive trait divergence between C. rubella and C. grandiflora. We further detected an excess of heterozygous transposable element (TE) insertions near genes with ASE, and TE insertions targeted by uniquely mapping 24-nt small RNAs were associated with reduced expression of nearby genes. Our results suggest that cis-regulatory changes have been important during the recent adaptive floral evolution in Capsella and that differences in TE dynamics between selfing and outcrossing species could be important for rapid regulatory divergence in association with mating system shifts.

  • 1340.
    Stenberg, Per
    et al.
    Umeå universitet, Medicinska fakulteten, Institutionen för molekylärbiologi (Medicinska fakulteten). Umeå universitet, Medicinska fakulteten, Umeå centrum för molekylär patogenes (UCMP) (Medicinska fakulteten).
    Saura, Anssi
    Umeå universitet, Medicinska fakulteten, Institutionen för molekylärbiologi (Medicinska fakulteten).
    Cytology of Asexual Animals2009Inngår i: Lost Sex: The Evolutionary Biology of Parthenogenesis / [ed] Isa Schön, Koen Martens, Peter Dijk, Dordrecht: Springer Netherlands, 2009, s. 63-74Kapittel i bok, del av antologi (Annet vitenskapelig)
    Abstract [en]

    We review the cytological mechanisms underlying asexual reproduction, i.e. reproduction without fertilization, in animals. Asexuality or parthenogenesis has evolved many times and the cytological mechanisms to restore the parental chromosome number can vary between and even within species. In automictic or meiotic parthenogenesis, meiosis takes place but the chromosomal constitution of the mother is restored through one or several different mechanisms. Some of these mechanisms enforce homozygosity at all loci while some other mechanisms pass the genome of the mother intact to the offspring. In apomictic or mitotic parthenogenesis the eggs are formed through what is essentially a set of mitoses. Polyploidy, is in general incompatible with chromosomal sex determination and is a rare condition in animals. However, many asexual and hermaphroditic forms are polyploid to various degrees. Polyploidy is divided into allo- and autopolyploidy. In the former mode the chromosome sets are derived from two or more different species while in autopolyploidy the multiplication has taken place within one species. We discuss the evolutionary consequences of the different cytological mechanisms involved in asexual reproduction.

  • 1341.
    Stewart, Joshua D.
    et al.
    University of California, USA ; The Manta Trust, UK.
    Beale, Calvin S.
    Misool Manta Project, Indonesia.
    Fernando, Daniel
    Linnéuniversitetet, Fakulteten för Hälso- och livsvetenskap (FHL), Institutionen för biologi och miljö (BOM). The Manta Trust, UK ; Blue Resources, Sri Lanka.
    Sianipar, Abraham B.
    Conservation International, Indonesia.
    Burton, Ronald S.
    University of California, USA.
    Semmens, Brice X.
    University of California, USA.
    Aburto-Oropeza, Octavio
    University of California, USA.
    Spatial ecology and conservation of Manta birostris in the Indo-Pacific2016Inngår i: Biological Conservation, ISSN 0006-3207, E-ISSN 1873-2917, Vol. 200, s. 178-183Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Information on the movements and population connectivity of the oceanic manta ray (Manta birostris) is scarce. The species has been anecdotally classified as a highly migratory species based on the pelagic habitats it often occupies, and migratory behavior exhibited by similar species. As a result, in the absence of ecological data, population declines in oceanic manta have been addressed primarily with international-scale management and conservation efforts. Using a combination of satellite telemetry, stable isotope and genetic analyses we demonstrate that, contrary to previous assumptions, the species appears to exhibit restricted movements and fine-scale population structure. M. birostris tagged at four sites in the Indo-Pacific exhibited no long-range migratory movements and had non-overlapping geographic ranges. Using genetic and isotopic analysis, we demonstrate that the observed movements and population structure persist on multi-year and generational time scales. These data provide the first insights into the long-term movements and population structure of oceanic manta rays, and suggest that bottom-up, local or regional approaches to managing oceanic mantas could prove more effective than existing, international-scale management strategies. This case study highlights the importance of matching the scales at which management and relevant ecological processes occur to facilitate the effective conservation of threatened species.

  • 1342.
    Stocks, Michael
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Växtekologi och evolution.
    Neutral and Adaptive Processes Shaping Genetic Variation in Spruce Species2013Doktoravhandling, med artikler (Annet vitenskapelig)
    Abstract [en]

    Population genetic analyses can provide information about both neutral and selective evolutionary processes shaping genetic variation. In this thesis, extensive population genetic methods were used to make inferences about genetic drift and selection in spruce species. In paper I we studied four species from the Qinghai-Tibetan Plateau (QTP): Picea likiangensis, P. purpurea, P. wilsonii and P. schrenkiana. Big differences in estimates of genetic diversity and Ne were observed in the more restricted species, P. schrenkiana, and the other more widely distributed species. Furthermore, P. purpurea appears to be a hybrid between P. likiangensis and P. wilsonii. In paper II we used Approximate Bayesian Computation (ABC) to find that the data support a drastic reduction of Ne in Taiwan spruce around 300-500 kya, in line with evidence from the pollen records. The split from P. wilsonii was dated to between 4-8 mya, around the time that Taiwan was formed. These analyses relied on a small sample size, and so in Paper III we investigated the impact of small datasets on the power to distinguish between models in ABC. We found that when genetic diversity is low there is little power to distinguish between simple coalescent models and this can determine the number of samples and loci required.

    In paper IV we studied the relative importance of genetic drift and selection in four spruce species with differing Ne: P. abies, P. glauca, P. jezoensis and P. breweriana. P. breweriana, which has a low Ne, exhibits a low fraction of adaptive substitutions, while P. abies has high Ne and a high fraction of adaptive substitutions. The other two spruce, however, do not support this suggesting other factors a more important. In paper V we find that several SNPs correlate with both a key adaptive trait (budset) and latitude. The expression of one in particular (PoFTL2) correlates with budset and was previously indentified in P. abies. These studies have helped characterise the importance of different population genetic processes in shaping genetic variation in spruce species and has laid some solid groundwork for future studies of spruce.

  • 1343.
    Stocks, Michael
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Växtekologi och evolution.
    Chen, Jun
    Institut fur Populationsgenetik, Wien.
    Källman, Thomas
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Växtekologi och evolution.
    Bousquet, Jean
    Universite Laval, Quebec.
    Lascoux, Martin
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Växtekologi och evolution.
    Molecular adaptation in spruce speciesManuskript (preprint) (Annet vitenskapelig)
  • 1344.
    Stocks, Michael
    et al.
    University of Sheffield, Sheffield, United Kingdom; Department of Plant Ecology and Evolution, Uppsala University, Uppsala, Sweden.
    Dean, Rebecca
    Uppsala University, Uppsala, Sweden; Department of Genetics, Evolution and Environment, University College London, London, United Kingdom.
    Rogell, Björn
    Department of Animal Ecology, Uppsala University, Uppsala, Sweden; Department of Zoology, Stockholm University, Stockholm, Sweden.
    Friberg, Urban
    Linköpings universitet, Institutionen för fysik, kemi och biologi, Biologi. Linköpings universitet, Tekniska högskolan. Department of Evolutionary Biology, Uppsala University, Uppsala, Sweden.
    Sex-specific Trans-regulatory Variation on the Drosophila melanogaster X Chromosome2015Inngår i: PLoS Genetics, ISSN 1553-7390, E-ISSN 1553-7404, Vol. 11, nr 2, s. 1-19, artikkel-id e1005015Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    The X chromosome constitutes a unique genomic environment because it is present in onecopy in males, but two copies in females. This simple fact has motivated several theoreticalpredictions with respect to how standing genetic variation on the X chromosome should differfrom the autosomes. Unmasked expression of deleterious mutations in males and alower census size are expected to reduce variation, while allelic variants with sexually antagonisticeffects, and potentially those with a sex-specific effect, could accumulate on theX chromosome and contribute to increased genetic variation. In addition, incomplete dosagecompensation of the X chromosome could potentially dampen the male-specific effectsof random mutations, and promote the accumulation of X-linked alleles with sexually dimorphicphenotypic effects. Here we test both the amount and the type of genetic variation onthe X chromosome within a population of Drosophila melanogaster, by comparing the proportionof X linked and autosomal trans-regulatory SNPs with a sexually concordant anddiscordant effect on gene expression. We find that the X chromosome is depleted for SNPswith a sexually concordant effect, but hosts comparatively more SNPs with a sexually discordanteffect. Interestingly, the contrasting results for SNPs with sexually concordant anddiscordant effects are driven by SNPs with a larger influence on expression in females thanexpression in males. Furthermore, the distribution of these SNPs is shifted towards regionswhere dosage compensation is predicted to be less complete. These results suggest thatintrinsic properties of dosage compensation influence either the accumulation of differenttypes of trans-factors and/or their propensity to accumulate mutations. Our findings documenta potential mechanistic basis for sex-specific genetic variation, and identify the X as areservoir for sexually dimorphic phenotypic variation. These results have general implicationsfor X chromosome evolution, as well as the genetic basis of sex-specificevolutionary change.

  • 1345.
    Stocks, Michael
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Växtekologi och evolution.
    Siol, Mathieu
    Institut National de la Recherche Agronomique (INRA), UMR Agroecologie, Dijon.
    Lascoux, Martin
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Växtekologi och evolution.
    De Mita, Stéphane
    Institut National de la Recherche Agronomique (INRA), UMR Interactions Arbres-Microorganismes, Nancy.
    Amount of information needed for model choice in Approximate Bayesian Computation2014Inngår i: PLoS ONE, ISSN 1932-6203, E-ISSN 1932-6203, Vol. 9, nr 6, s. e99581-Artikkel i tidsskrift (Annet vitenskapelig)
    Abstract [en]

    Approximate Bayesian Computation (ABC) has become a popular technique in evolutionary genetics for elucidating population structure and history due to its flexibility. The statistical inference framework has benefited from significant progress in recent years. In population genetics, however, its outcome depends heavily on the amount of information in the dataset, whether that be the level of genetic variation or the number of samples and loci. Here we look at the power to reject a simple constant population size coalescent model in favor of a bottleneck model in datasets of varying quality. Not only is this power dependent on the number of samples and loci, but it also depends strongly on the level of nucleotide diversity in the observed dataset. Whilst overall model choice in an ABC setting is fairly powerful and quite conservative with regard to false positives, detecting weaker bottlenecks is problematic in smaller or less genetically diverse datasets and limits the inferences possible in non-model organism where the amount of information regarding the two models is often limited. Our results show it is important to consider these limitations when performing an ABC analysis and that studies should perform simulations based on the size and nature of the dataset in order to fully assess the power of the study.

  • 1346.
    Strand, Tanja
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Populationsbiologi och naturvårdsbiologi.
    European Black Grouse: MHC Genetic Diversity and Population Structure2011Doktoravhandling, med artikler (Annet vitenskapelig)
    Abstract [en]

    Black grouse Tetrao tetrix is a bird species composed of large, continuous as well as severely reduced and fragmented populations, making it an optimal species to investigate how genetic diversity is affected by habitat fragmentation. I have focused on genetic diversity in the Major Histocompatibility Complex (MHC) to measure the ability of the black grouse to respond to environmental changes.

    I partly characterized MHC class II in black grouse and found striking similarities with chicken MHC class II. I demonstrated that black grouse possess a similar compact MHC as chicken with few MHC class II B (BLB) and Y (YLB) loci. I did not find evidence of balancing selection in YLB so I concentrated further studies on BLB.

    I developed a PCR-based screening method for amplifying and separating expressed BLB alleles in European black grouse populations. Small fragmented populations had lost neutral genetic diversity (based on microsatellites and SNPs) compared to samples from the historical distribution and contemporary large populations. There was also a trend, albeit less pronounced, for reduced MHC diversity in these populations. Neutral markers in small isolated populations were affected by increased levels of genetic drift and were therefore genetically differentiated compared to other populations. MHC markers on the other hand, were not subjected to genetic drift to the same extent probably due a long historic process of balancing selection.

    Inferences of heterozygosity and evolutionary patterns as well as detailed correlations to reproductive success and diseases cannot be performed until MHC can be amplified in a locus-specific manner. Therefore, I developed a single locus sequence-based typing method for independently amplifying MHC class II B loci (BLB1 and BLB2). I found that BLB1 and BLB2 were duplicated in a common ancestor to chickens and black grouse and that these loci are subjected to homogenizing concerted evolution due to inter-genetic exchange between loci after species divergence.  I could also verify that both BLB1 and BLB2 were transcribed in black grouse and under balancing selection.

    This collection of work has significance for future conservation of black grouse as well as research and management of zoonotic diseases.

  • 1347.
    Strand, Tanja
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Populationsbiologi och naturvårdsbiologi.
    Segelbacher, Gernot
    Dept Wildlife Ecology and Management, University Freiburg.
    Quintela, Maria
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Zooekologi. Dept of Animal Biology, Plant Biology and Ecology, Faculty of Science, University of A Coruña.
    Xiao, Lyngyun
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Zooekologi.
    Axelsson, Tomas
    Uppsala universitet, Medicinska och farmaceutiska vetenskapsområdet, Medicinska fakulteten.
    Höglund, Jacob
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och evolution, Populationsbiologi och naturvårdsbiologi.
    Can balancing selection on MHC loci counteract genetic drift in small fragmented populations of black grouse?2012Inngår i: Ecology and Evolution, ISSN 2045-7758, E-ISSN 2045-7758, Vol. 2, nr 2, s. 341-353Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    The ability of natural populations to adapt to new environmental conditions is crucial for their survival and partly determined by the standing genetic variation in each population. Populations with higher genetic diversity are more likely to contain individuals that are better adapted to new circumstances than populations with lower genetic diversity. Here we use both neutral and MHC markers to test whether small and highly fragmented populations hold lower genetic diversity than large ones. We use black grouse as it is distributed across Europe and found in populations with varying degrees of isolation and size. We sampled eleven different populations; five continuous, three isolated and three small and isolated. We tested patterns of genetic variation in these populations using three different types of genetic markers: nine microsatellites and 21 SNPs (Single Nucleotide Polymorphisms) which both were found to be neutral, and two functional MHC (Major Histocompatibility Complex) genes that are presumably under selection. The small isolated populations displayed significantly lower neutral genetic diversity compared to continuous populations. A similar trend, but not as pronounced, was found for genotypes at MHC class II loci. Populations were less divergent at MHC genes compared to neutral markers. Measures of genetic diversity and population genetic structure were positively correlated among microsatellites and SNPs, but none of them were correlated to MHC when comparing all populations. Our results suggest that balancing selection at MHC loci does not counteract the power of genetic drift when populations get small and fragmented. 

  • 1348.
    Strand, Tanja
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Populationsbiologi och naturvårdsbiologi.
    Wang, Biao
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Populationsbiologi och naturvårdsbiologi.
    Meyer-Lucht, Yvonne
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Populationsbiologi och naturvårdsbiologi.
    Höglund, Jacob
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och evolution, Populationsbiologi och naturvårdsbiologi.
    Evolutionary history of black grouse BLB1 and BLB2 revealed through single locus sequence-based typingManuskript (preprint) (Annet vitenskapelig)
  • 1349.
    Strand, Tanja
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och evolution, Populationsbiologi och naturvårdsbiologi.
    Westerdahl, Helena
    Höglund, Jacob
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och evolution, Populationsbiologi och naturvårdsbiologi.
    Alatalo, Rauno V.
    Siitari, Heli
    The MHC class II of the Black grouse (Tetrao tetrix) consists of low numbers of B and Y genes with variable diversity and expression2007Inngår i: Immunogenetics, ISSN 0093-7711, E-ISSN 1432-1211, Vol. 59, nr 9, s. 725-734Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    We found that the Black grouse (Tetrao tetrix) possess low numbers of Mhc class II B (BLB) and Y (YLB) genes with variable diversity and expression. We have therefore shown, for the first time, that another bird species (in this case, a wild lek-breeding galliform) shares several features of the simple Mhc of the domestic chicken (Gallus gallus). The Black grouse BLB genes showed the same level of polymorphism that has been reported in chicken, and we also found indications of balancing selection in the peptide-binding regions. The YLB genes were less variable than the BLB genes, also in accordance with earlier studies in chicken, although their functional significance still remains obscure. We hypothesize that the YLB genes could have been under purifying selection, just as the mammal Mhc-E gene cluster.

  • 1350.
    Strassert, Jürgen F H
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för organismbiologi, Systematisk biologi. Uppsala universitet, Science for Life Laboratory, SciLifeLab. Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada.
    Karnkowska, Anna
    Hehenberger, Elisabeth
    del Campo, Javier
    Kolisko, Martin
    Okamot, Noriko
    Burki, Fabien
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för organismbiologi, Systematisk biologi. Uppsala universitet, Science for Life Laboratory, SciLifeLab. Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada.
    Janouškovec, Jan
    Poirier, Camille
    Leonard, Guy
    Hallam, Steven J
    Richards, Thomas A
    Worden, Alexandra Z
    Santoro, Alyson E
    Keeling, Patrick J
    Single cell genomics of uncultured marine alveolates shows paraphyly of basal dinoflagellates2018Inngår i: The ISME Journal, ISSN 1751-7362, E-ISSN 1751-7370, Vol. 12, s. 304-308Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Marine alveolates (MALVs) are diverse and widespread early-branching dinoflagellates, but most knowledge of the group comes from a few cultured species that are generally not abundant in natural samples, or from diversity analyses of PCR-based environmental SSU rRNA gene sequences. To more broadly examine MALV genomes, we generated single cell genome sequences from seven individually isolated cells. Genes expected of heterotrophic eukaryotes were found, with interesting exceptions like presence of proteorhodopsin and vacuolar H+-pyrophosphatase. Phylogenetic analysis of concatenated SSU and LSU rRNA gene sequences provided strong support for the paraphyly of MALV lineages. Dinoflagellate viral nucleoproteins were found only in MALV groups that branched as sister to dinokaryotes. Our findings indicate that multiple independent origins of several characteristics early in dinoflagellate evolution, such as a parasitic life style, underlie the environmental diversity of MALVs, and suggest they have more varied trophic modes than previously thought.

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