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  • 1301.
    Pečnerová, Patrícia
    et al.
    Stockholms universitet, Naturvetenskapliga fakulteten, Zoologiska institutionen. Swedish Museum of Natural History, Sweden.
    Díez-Del-Molino, David
    Dussex, Nicolas
    Feuerborn, Tatiana
    von Seth, Johanna
    van der Plicht, Johannes
    Nikolskiy, Pavel
    Tikhonov, Alexei
    Vartanyan, Sergey
    Dalén, Love
    Genome-Based Sexing Provides Clues about Behavior and Social Structure in the Woolly Mammoth2017Inngår i: Current Biology, ISSN 0960-9822, E-ISSN 1879-0445, Vol. 27, nr 22, s. 3505-3510.e3Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    While present-day taxa are valuable proxies for understanding the biology of extinct species, it is also crucial to examine physical remains in order to obtain a more comprehensive view of their behavior, social structure, and life histories [1, 2]. For example, information on demographic parameters such as age distribution and sex ratios in fossil assemblages can be used to accurately infer socioecological patterns (e.g., [3]). Here we use genomic data to determine the sex of 98 woolly mammoth (Mammuthus primigenius) specimens in order to infer social and behavioral patterns in the last 60,000 years of the species' existence. We report a significant excess of males among the identified samples (69% versus 31%; p < 0.0002). We argue that this male bias among mammoth remains is best explained by males more often being caught in natural traps that favor preservation. Wehypothesize that this is a consequence of social structure in proboscideans, which is characterized by matriarchal hierarchy and sex segregation. Without the experience associated with living in a matriarchal family group, or a bachelor group with an experienced bull, young or solitary males may have been more prone to die in natural traps where good preservation is more likely.

  • 1302.
    Pečnerová, Patrícia
    et al.
    Stockholms universitet, Naturvetenskapliga fakulteten, Zoologiska institutionen. Swedish Museum of Natural History, Sweden.
    Díez-Del-Molino, David
    Palkopoulou, Eleftheria
    Skoglund, Pontus
    Tikhonov, Alexei
    Nikolskiy, Pavel
    Vartanyan, Sergey
    Dalén, Love
    Stockholms universitet, Naturvetenskapliga fakulteten, Zoologiska institutionen. Swedish Museum of Natural History, Sweden.
    Pre-extinction population dynamics and genome erosion in the woolly mammothManuskript (preprint) (Annet vitenskapelig)
  • 1303.
    Pečnerová, Patrícia
    et al.
    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; Harvard Medical School, Massachusetts.
    Wheat, Christopher W.
    Stockholms universitet, Naturvetenskapliga fakulteten, Zoologiska institutionen.
    Skoglund, Pontus
    Vartanyan, Sergey
    Tikhonov, Alexei
    Nikolskiy, Pavel
    van der Plicht, Johannes
    Díez-del-Molino, David
    Dalén, Love
    Mitogenome evolution in the last surviving woolly mammoth population reveals neutral and functional consequences of small population size2017Inngår i: Evolution Letters, ISSN 2056-3744, Vol. 1, nr 6, s. 292-303Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    The onset of the Holocene was associated with a global temperature increase, which led to a rise in sea levels and isolation of the last surviving population of woolly mammoths on Wrangel Island. Understanding what happened with the population's genetic diversity at the time of the isolation and during the ensuing 6000 years can help clarify the effects of bottlenecks and subsequent limited population sizes in species approaching extinction. Previous genetic studies have highlighted questions about how the Holocene Wrangel population was established and how the isolation event affected genetic diversity. Here, we generated high-quality mitogenomes from 21 radiocarbon-dated woolly mammoths to compare the ancestral large and genetically diverse Late Pleistocene Siberian population and the small Holocene Wrangel population. Our results indicate that mitogenome diversity was reduced to one single haplotype at the time of the isolation, and thus that the Holocene Wrangel Island population was established by a single maternal lineage. Moreover, we show that the ensuing small effective population size coincided with fixation of a nonsynonymous mutation, and a comparative analysis of mutation rates suggests that the evolutionary rate was accelerated in the Holocene population. These results suggest that isolation on Wrangel Island led to an increase in the frequency of deleterious genetic variation, and thus are consistent with the hypothesis that strong genetic drift in small populations leads to purifying selection being less effective in removing deleterious mutations.

  • 1304.
    Pilloud, Marin A.
    et al.
    Univ Nevada, Anthropol, Reno, NV, USA.
    Somel, Mehmet
    Middle East Tech Univ, Ankara, Turkey.
    Haddow, Scott D.
    Univ Bordeaux, PACEA UMR, Bordeaux, France.
    Knusel, Christopher J.
    Univ Bordeaux, PACEA UMR, Bordeaux, France.
    Larsen, Clark Spencer
    Ohio State Univ, Anthropol, Columbus, OH, USA.
    Ozbasaran, Mihriban
    Istanbul Univ, Archaeol Dept, Istanbul, Turkey.
    Erdal, Omur Dilek
    Hacettepe Univ, Dept Anthropol, Ankara, Turkey.
    Baird, Douglas
    Univ Liverpool, Dept Archaeol Class & Egyptol, Liverpool, Merseyside, England.
    Pearson, Jessica
    Univ Liverpool, Dept Archaeol Class & Egyptol, Liverpool, Merseyside, England.
    Gotherstrom, Anders
    Stockholm Univ, Dept Archaeol & Class Studies, Stockholm, Sweden.
    Stora, Jan
    Stockholm Univ, Dept Archaeol & Class Studies, Stockholm, Sweden.
    Jakobsson, Mattias
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för organismbiologi, Människans evolution.
    Kilinc, Gulsah Merve
    Middle East Tech Univ, Ankara, Turkey.
    Ozer, Fusun
    Middle East Tech Univ, Ankara, Turkey.
    Koptekin, Dilek
    Middle East Tech Univ, Ankara, Turkey.
    Dagtas, Nihan Dilsad
    Middle East Tech Univ, Ankara, Turkey.
    Mobility in Neolithic Central Anatolia: A Comparison of Dental Morphometrics and aDNA2017Inngår i: American Journal of Physical Anthropology, ISSN 0002-9483, E-ISSN 1096-8644, Vol. 162, nr S64, s. 316-316Artikkel i tidsskrift (Annet vitenskapelig)
  • 1305.
    Plomion, Christophe
    et al.
    Univ Bordeaux, BIOGECO, INRA, Cestas, France.
    Aury, Jean-Marc
    CEA, Genoscope, Inst Biol Francois Jacob, Evry, France.
    Amselem, Joelle
    Univ ParisSaclay, URGI, INRA, Versailles, France.
    Leroy, Thibault
    Univ Bordeaux, BIOGECO, INRA, Cestas, France.
    Murat, Florent
    INRA UCA, GDEC, Clermont Ferrand, France.
    Duplessis, Sebastien
    Univ Lorraine, IAM, INRA, Champenoux, France.
    Faye, Sebastien
    CEA, Genoscope, Inst Biol Francois Jacob, Evry, France.
    Francillonne, Nicolas
    Univ ParisSaclay, URGI, INRA, Versailles, France.
    Labadie, Karine
    CEA, Genoscope, Inst Biol Francois Jacob, Evry, France.
    Le Provost, Gregoire
    Univ Bordeaux, BIOGECO, INRA, Cestas, France.
    Lesur, Isabelle
    Univ Bordeaux, BIOGECO, INRA, Cestas, France;HelixVenture, Merignac, France.
    Bartholome, Jerome
    Univ Bordeaux, BIOGECO, INRA, Cestas, France.
    Faivre-Rampant, Patricia
    Univ Paris Saclay, INRA, US EPGV 1279, Evry, France.
    Kohler, Annegret
    Univ Lorraine, IAM, INRA, Champenoux, France.
    Leple, Jean-Charles
    INRA, BIOFORA, Orleans, France.
    Chantret, Nathalie
    Univ Montpellier, AGAP, CIRAD, INRA,Montpellier SupAgro, Montpellier, France.
    Chen, Jun
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Växtekologi och evolution. Uppsala universitet, Science for Life Laboratory, SciLifeLab.
    Dievart, Anne
    CIRAD, UMR AGAP, Montpellier, France;Univ Montpellier, CIRAD, INRA, Montpellier SupAgro, Montpellier, France.
    Alaeitabar, Tina
    Univ ParisSaclay, URGI, INRA, Versailles, France.
    Barbe, Valerie
    CEA, Genoscope, Inst Biol Francois Jacob, Evry, France.
    Belser, Caroline
    CEA, Genoscope, Inst Biol Francois Jacob, Evry, France.
    Berges, Helene
    INRA, CNRGV, Castanet Tolosan, France.
    Bodenes, Catherine
    Univ Bordeaux, BIOGECO, INRA, Cestas, France.
    Bogeat-Triboulot, Marie-Beatrice
    Univ Lorraine, UMR Silva, INRA, AgroPariTech, Nancy, France.
    Bouffaud, Marie-Lara
    UFZ Helmholtz Ctr Environm Res, Dept Soil Ecol, Halle, Germany.
    Brachi, Benjamin
    Univ Bordeaux, BIOGECO, INRA, Cestas, France.
    Chancerel, Emilie
    Univ Bordeaux, BIOGECO, INRA, Cestas, France.
    Cohen, David
    Univ Lorraine, UMR Silva, INRA, AgroPariTech, Nancy, France.
    Couloux, Arnaud
    CEA, Genoscope, Inst Biol Francois Jacob, Evry, France.
    Da Silva, Corinne
    CEA, Genoscope, Inst Biol Francois Jacob, Evry, France.
    Dossat, Carole
    CEA, Genoscope, Inst Biol Francois Jacob, Evry, France.
    Ehrenmann, Francois
    Univ Bordeaux, BIOGECO, INRA, Cestas, France.
    Gaspin, Christine
    INRA, Plateforme Bioinformat Toulouse Midi Pyrenees, Auzeville Castanet Tolos, Germany.
    Grima-Pettenati, Jacqueline
    Univ Toulouse, CNRS, UMR 5546, LRSV, Castanet Tolosan, France.
    Guichoux, Erwan
    Univ Bordeaux, BIOGECO, INRA, Cestas, France.
    Hecker, Arnaud
    Univ Lorraine, IAM, INRA, Champenoux, France.
    Herrmann, Sylvie
    German Ctr Integrat Res IDiv, Leipzig, Germany.
    Hugueney, Philippe
    Univ Strasbourg, SVQV, INRA, Colmar, France.
    Hummel, Irene
    Univ Lorraine, UMR Silva, INRA, AgroPariTech, Nancy, France.
    Klopp, Christophe
    INRA, Plateforme Bioinformat Toulouse Midi Pyrenees, Auzeville Castanet Tolos, Germany.
    Lalanne, Celine
    Univ Bordeaux, BIOGECO, INRA, Cestas, France.
    Lascoux, Martin
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Växtekologi och evolution. Uppsala universitet, Science for Life Laboratory, SciLifeLab.
    Lasserre, Eric
    Univ Perpignan, UMR 5096, Perpignan, France.
    Lemainque, Arnaud
    CEA, Genoscope, Inst Biol Francois Jacob, Evry, France.
    Desprez-Loustau, Marie-Laure
    Univ Bordeaux, BIOGECO, INRA, Cestas, France.
    Luyten, Isabelle
    Univ ParisSaclay, URGI, INRA, Versailles, France.
    Madoui, Mohammed-Amin
    CEA, Genoscope, Inst Biol Francois Jacob, Evry, France.
    Mangenot, Sophie
    CEA, Genoscope, Inst Biol Francois Jacob, Evry, France.
    Marchal, Clemence
    Univ Lorraine, IAM, INRA, Champenoux, France.
    Maumus, Florian
    Univ ParisSaclay, URGI, INRA, Versailles, France.
    Mercier, Jonathan
    CEA, Genoscope, Inst Biol Francois Jacob, Evry, France.
    Michotey, Celia
    Univ ParisSaclay, URGI, INRA, Versailles, France.
    Panaud, Olivier
    Univ Perpignan, UMR 5096, Perpignan, France.
    Picault, Nathalie
    Univ Perpignan, UMR 5096, Perpignan, France.
    Rouhier, Nicolas
    Univ Lorraine, IAM, INRA, Champenoux, France.
    Rue, Olivier
    INRA, Plateforme Bioinformat Toulouse Midi Pyrenees, Auzeville Castanet Tolos, Germany.
    Rustenholz, Camille
    Univ Strasbourg, SVQV, INRA, Colmar, France.
    Salin, Franck
    Univ Bordeaux, BIOGECO, INRA, Cestas, France.
    Soler, Marcal
    Univ Toulouse, CNRS, UMR 5546, LRSV, Castanet Tolosan, France;Univ Girona, Lab Suro, Girona, Spain.
    Tarkka, Mika
    UFZ Helmholtz Ctr Environm Res, Dept Soil Ecol, Halle, Germany.
    Velt, Amandine
    Univ Strasbourg, SVQV, INRA, Colmar, France.
    Zanne, Amy E.
    George Washington Univ, Dept Biol Sci, Washington, DC 20052 USA.
    Martin, Francis
    Univ Lorraine, IAM, INRA, Champenoux, France.
    Wincker, Patrick
    Univ Paris Saclay, Genom Metab, Genoscope, Inst Biol Francois Jacob,CEA,CNRS,Univ Evry, Evry, France.
    Quesneville, Hadi
    Univ ParisSaclay, URGI, INRA, Versailles, France.
    Kremer, Antoine
    Univ Bordeaux, BIOGECO, INRA, Cestas, France.
    Salse, Jerome
    INRA UCA, GDEC, Clermont Ferrand, France.
    Oak genome reveals facets of long lifespan2018Inngår i: NATURE PLANTS, ISSN 2055-026X, Vol. 4, nr 7, s. 440-452Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Oaks are an important part of our natural and cultural heritage. Not only are they ubiquitous in our most common landscapes' but they have also supplied human societies with invaluable services, including food and shelter, since prehistoric times(2). With 450 species spread throughout Asia, Europe and America(3), oaks constitute a critical global renewable resource. The longevity of oaks (several hundred years) probably underlies their emblematic cultural and historical importance. Such long-lived sessile organisms must persist in the face of a wide range of abiotic and biotic threats over their lifespans. We investigated the genomic features associated with such a long lifespan by sequencing, assembling and annotating the oak genome. We then used the growing number of whole-genome sequences for plants (including tree and herbaceous species) to investigate the parallel evolution of genomic characteristics potentially underpinning tree longevity. A further consequence of the long lifespan of trees is their accumulation of somatic mutations during mitotic divisions of stem cells present in the shoot apical meristems. Empirical(4) and modelling(5) approaches have shown that intra-organismal genetic heterogeneity can be selected for(6) and provides direct fitness benefits in the arms race with short-lived pests and pathogens through a patchwork of intra-organismal phenotypes(7). However, there is no clear proof that large-statured trees consist of a genetic mosaic of clonally distinct cell lineages within and between branches. Through this case study of oak, we demonstrate the accumulation and transmission of somatic mutations and the expansion of disease-resistance gene families in trees.

  • 1306.
    Podani, Janos
    et al.
    Eotvos Lorand Univ, Inst Biol, Dept Plant Systemat Ecol & Theoret Biol, Budapest, Hungary.;Hungarian Acad Sci, Ecol Res Grp, Budapest, Hungary..
    Morrison, David A.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för organismbiologi, Systematisk biologi.
    Categorizing ideas about systematics: alternative trees of trees, and related representations2017Inngår i: Rendiconti Lincei SCIENZE FISICHE E NATURALI, ISSN 2037-4631, E-ISSN 1720-0776, Vol. 28, nr 1, s. 191-202Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    This study is an attempt to expand a previous survey by Fisler and Lecointre (FL) for systematizing ideas on the use of the tree metaphor in classification, as expressed by various historically important figures in their writings. FL used a cladistic approach to analyze their data, as employed in biological classification. We supplement this analysis here using several methods of multivariate data exploration, producing a UPGMA dendrogram, a minimum spanning tree, a neighbor joining additive tree, a plexus graph, a phylogenetic network, and two multidimensional scaling ordinations of the same data used by FL. We confirm the validity of many of FL's smaller clusters of writings, and revealed a new 3-group categorization undetected by the previous study. These three groups largely correspond to Classifiers, who did not consider evolution for historical reasons or on purpose, Non-analytical evolutionists, who recognized evolution but with a more or less na < ve attitude towards the temporal change of life, and Modelers, with more explicit views on evolutionary processes, often applying objective mathematical tools for exploring the past and present of organismal diversity. Some scientists were difficult to assign to any group unambiguously, including J. W. von Goethe, who takes a unique position in the history of biology, and, to a lesser extent, E. Mayr and G. G. Simpson, the leaders of the gradist school of systematics. We argue that cladistic methods are insufficient by themselves, notably in situations where there are no obvious ancestor-descendant relationships underlying the development of the objects being analyzed.

  • 1307.
    Poelstra, Jelmer
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Evolutionsbiologi.
    The Genetics of Speciation and Colouration in Carrion and Hooded Crows2013Doktoravhandling, med artikler (Annet vitenskapelig)
    Abstract [en]

    A fundamental goal in biological research is to gain an understanding of the evolutionary processes and genetic elements that drive speciation. Genes responsible for reproductive isolation in young divergent lineages are particularly poorly known. In this thesis, the speciation genetics of carrion (Corvus (corone) corone) and hooded (C. (corone) cornix) crows were studied. These taxa differ strikingly in colouration and meet in a narrow hybrid zone in Europe, yet appear to be very similar genetically. A major component of reproductive isolation is social selection on colour differences.

    First, we investigated the genetic basis of plumage divergence between carrion and hooded crows using a candidate gene approach. Nucleotide divergence was confirmed to be low, while there was no evidence for any of the sequenced genes to be associated with colour differences.

    Second, we performed a simulation study to assess the performance of RNA-seq, a relatively novel approach that we later employed ourselves. We asked how variation in transcriptome complexity and bioinformatic workflow affected the accuracy of gene expression profiling. We generally found reassuring robustness and made a number of specific recommendations.

    Third, we compared the corticosterone stress response of carrion and hooded crows. In accordance with the hypothesis that the degree of melanization and physiological traits are correlated due to pleiotropy, we found a higher stress response in hooded crows, and detected possibly associated gene expression in pituitary.

    Fourth, we investigated genomic divergence by assembling a hooded crow reference genome followed by whole-genome resequencing of four European population samples. Northern European carrion crows were more similar to hooded crows than to Spanish carrion crows, pointing towards rampant introgression far beyond the hybrid zone. Nevertheless, several narrow genomic regions harboured high between-taxon divergence and were potentially associated with phenotypic traits.

    Fifth, we compared whole-transcriptome gene expression profiles between crows, focusing on skin with developing feathers. We used a design that allowed to differentiate between taxon-specific, colour-specific and body patterning effects. Widespread underexpression of genes in the melanogenesis pathway was associated with grey colour, and we detected several genes that may contribute to colour divergence in this system.

  • 1308.
    Poelstra, Jelmer W.
    et al.
    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.
    Wolf, Jochen
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Evolutionsbiologi.
    An extensive candidate gene approach to speciation: diversity, divergence and linkage disequilibrium in candidate pigmentation genes across the European crow hybrid zone2013Inngår i: Heredity, ISSN 0018-067X, E-ISSN 1365-2540, Vol. 111, nr 6, s. 467-473Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Colouration patterns have an important role in adaptation and speciation. The European crow system, in which all-black carrion crows and grey-coated hooded crows meet in a narrow hybrid zone, is a prominent example. The marked phenotypic difference is maintained by assortative mating in the absence of neutral genetic divergence, suggesting the presence of few pigmentation genes of major effect. We made use of the rich phenotypic and genetic resources in mammals and identified a comprehensive panel of 95 candidate pigmentation genes for birds. Based on functional annotation, we chose a subset of the most promising 37 candidates, for which we developed a marker system that demonstrably works across the avian phylogeny. In total, we sequenced 107 amplicons (~3 loci per gene, totalling 60 kb) in population samples of crows (n=23 for each taxon). Tajima’s D, Fu’s FS, DHEW and HKA (Hudson–Kreitman–Aguade) statistics revealed several amplicons that deviated from neutrality; however, none of these showed significantly elevated differentiation between the two taxa. Hence, colour divergence in this system may be mediated by uncharacterized pigmentation genes or regulatory regions outside genes. Alternatively, the observed high population recombination rate (4Ner~0.03), with overall linkage disequilibrium dropping rapidly within the order of few 100 bp, may compromise the power to detect causal loci with nearby markers. Our results add to the debate as to the utility of candidate gene approaches in relation to genomic features and the genetic architecture of the phenotypic trait in question.

  • 1309.
    Poelstra, Jelmer W.
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Evolutionsbiologi.
    Müller, Inge
    Max Planck Institute for Ornithology, Radolfzell.
    Vijay, Nagarjun
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Evolutionsbiologi.
    Baglione, Vittorio
    Universidad de Valladolid.
    Wolf, Jochen
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Evolutionsbiologi.
    Covariance between colouration, corticosterone response and gene expression patterns suggests pleiotropy in the melanocortin system in carrion and hooded crowsManuskript (preprint) (Annet vitenskapelig)
  • 1310.
    Poelstra, Jelmer W.
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Evolutionsbiologi.
    Vijay, Nagarjun
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Evolutionsbiologi.
    Bossu, Christen
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Evolutionsbiologi.
    Lantz, Henrik
    Uppsala universitet, Science for Life Laboratory, SciLifeLab.
    Ryll, Bettina
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för organismbiologi, Evolution och utvecklingsbiologi.
    Müller, Inge
    Max Planck Institute for Ornithology, Radolfzell.
    Baglione, Vittorio
    Universidad de Valladolid.
    Unneberg, Per
    Uppsala universitet, Science for Life Laboratory, SciLifeLab.
    Wikelski, Martin
    Max Planck Institute for Ornithology, Radolfzell.
    Grabherr, Manfred
    Uppsala universitet, Science for Life Laboratory, SciLifeLab.
    Wolf, Jochen
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Evolutionsbiologi.
    The architecture of genomic and phenotypic divergence across the European crow hybrid zoneManuskript (preprint) (Annet vitenskapelig)
  • 1311.
    Poelstra, Jelmer W.
    et al.
    Uppsala universitet, Science for Life Laboratory, SciLifeLab. Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Evolutionsbiologi.
    Vijay, Nagarjun
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Evolutionsbiologi. Uppsala universitet, Science for Life Laboratory, SciLifeLab.
    Bossu, Christen M.
    Uppsala universitet, Science for Life Laboratory, SciLifeLab. Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Evolutionsbiologi.
    Lantz, Henrik
    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, Beräknings- och systembiologi. Uppsala universitet, Science for Life Laboratory, SciLifeLab.
    Ryll, Bettina
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för organismbiologi, Evolution och utvecklingsbiologi.
    Mueller, I.
    Baglione, V.
    Unneberg, P.
    Wikelski, M.
    Grabherr, Manfred G.
    Uppsala universitet, Science for Life Laboratory, SciLifeLab. Uppsala universitet, Medicinska och farmaceutiska vetenskapsområdet, Medicinska fakulteten, Institutionen för medicinsk biokemi och mikrobiologi.
    Wolf, Jochen B. W.
    Uppsala universitet, Science for Life Laboratory, SciLifeLab. Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Evolutionsbiologi.
    The genomic landscape underlying phenotypic integrity in the face of gene flow in crows2014Inngår i: Science, ISSN 0036-8075, E-ISSN 1095-9203, Vol. 344, nr 6190, s. 1410-1414Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    The importance, extent, and mode of interspecific gene flow for the evolution of species has long been debated. Characterization of genomic differentiation in a classic example of hybridization between all-black carrion crows and gray-coated hooded crows identified genome-wide introgression extending far beyond the morphological hybrid zone. Gene expression divergence was concentrated in pigmentation genes expressed in gray versus black feather follicles. Only a small number of narrow genomic islands exhibited resistance to gene flow. One prominent genomic region (<2 megabases) harbored 81 of all 82 fixed differences (of 8.4 million single-nucleotide polymorphisms in total) linking genes involved in pigmentation and in visual perception-a genomic signal reflecting color-mediated prezygotic isolation. Thus, localized genomic selection can cause marked heterogeneity in introgression landscapes while maintaining phenotypic divergence.

  • 1312.
    Poelstra, Jelmer W.
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Evolutionsbiologi.
    Vijay, Nagarjun
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Evolutionsbiologi.
    Müller, Inge
    Max Planck Institute for Ornithology, Radolfzell.
    Ryll, Bettina
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för organismbiologi, Evolution och utvecklingsbiologi.
    Baglione, Vittorio
    Universidad de Valladolid.
    Wikelski, Martin
    Max Planck Institute for Ornithology, Radolfzell.
    Wolf, Jochen
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Evolutionsbiologi.
    The genetics of colouration patterning and divergence in carrion and hooded crows as inferred from transcriptome-wide gene expression profilesManuskript (preprint) (Annet vitenskapelig)
  • 1313. Polasky, Stephen
    et al.
    Carpenter, Stephen R.
    Center for Limnology, University of Wisconsin, Madison.
    Folke, Carl
    Stockholms universitet, Stockholm Resilience Centre.
    Keeler, Bonnie
    Institute on the Environment, University of Minnesota.
    Decision-making under great uncertainty: environmental management in an era of global change2011Inngår i: Trends in Ecology and Evolution, Vol. 26, nr 8, s. 398-404Artikkel, forskningsoversikt (Fagfellevurdert)
  • 1314.
    Ponstein, Jasper
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Geovetenskapliga sektionen, Institutionen för geovetenskaper.
    Evolution of the Vascular Pattern in Mammals: Using Synchrotron Imaging to Visualise Hidden 3D Structures2017Independent thesis Advanced level (degree of Master (Two Years)), 20 poäng / 30 hpOppgave
    Abstract [en]

    The morphology and histology of long bones are important tools for understanding tetrapod locomotion and growth. In mammals, the epiphyses of long bones ossify from a secondary centre of ossification. The consensus is that vascular canals are closely tied to the formation of these centres. However, the epiphyseal vascular organisation differs significantly between each major clade of mammals: Eutheria, Metatheria and Monotremata. Previous studies on the distribution of canals mainly examined 2D thinsections, which has led to inaccurate interpretations of their three-dimensionality. This study uses propagation phase-contrast X-ray microtomography to visualise the epiphyseal vascularisation of humeri from the eutherian Dasypus novemcinctus, the metatherian Didelphis marsupialis and the monotreme Tachyglossus aculeatus in 3D, to update on the known variability in extant mammals. Additionally, humeri from two stem-mammals, Galesaurus planiceps and Morganucodon sp., are included to infer the ancestral condition for Mammalia. Two types of canals are considered; piercing canals that pierce through the metaphysis, and cartilage canals that are connected to the perichondrium. Cartilage canals are reported in D. marsupialis, where these were previously thought to be absent. Traces of cartilage canals are also found in Morganucodon sp. Both fossil taxa exhibit piercing canals, as in monotremes and eutherians, although the canals are more numerous in the fossils. The distribution of cartilage canals therefore is wider than previously assumed. This new fossil data shows that both types of canals have evolved within the mammalian stem-group, thereby suggesting that the process involving both types of canals for ossifying epiphyses is relatively ancient.

    Fulltekst tilgjengelig fra 2020-06-21 15:34
  • 1315.
    Pontarp, Mikael
    et al.
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för ekologi, miljö och geovetenskap. Univ Zurich, Dept Evolutionary Biol & Environm Studies, Winterthurerstr 190, CH-8057 Zurich, Switzerland.
    Petchey, Owen L.
    Community trait overdispersion due to trophic interactions: concerns for assembly process inference2016Inngår i: Proceedings of the Royal Society of London. Biological Sciences, ISSN 0962-8452, E-ISSN 1471-2954, Vol. 283, nr 1840, artikkel-id 20161729Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    The expected link between competitive exclusion and community trait over-dispersion has been used to infer competition in local communities, and trait clustering has been interpreted as habitat filtering. Such community assembly process inference has received criticism for ignoring trophic interactions, as competition and trophic interactions might create similar trait patterns. While other theoretical studies have generally demonstrated the importance of predation for coexistence, ours provides the first quantitative demonstration of such effects on assembly process inference, using a trait-based ecological model to simulate the assembly of a competitive primary consumer community with and without the influence of trophic interactions. We quantified and contrasted trait dispersion/clustering of the competitive communities with the absence and presence of secondary consumers. Trophic interactions most often decreased trait clustering (i.e. increased dispersion) in the competitive communities due to evenly distributed invasions of secondary consumers and subsequent competitor extinctions over trait space. Furthermore, effects of trophic interactions were somewhat dependent on model parameters and clustering metric. These effects create considerable problems for process inference from trait distributions; one potential solution is to use more process-based and inclusive models in inference.

  • 1316.
    Pontarp, Mikael
    et al.
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för ekologi, miljö och geovetenskap. Department of Evolutionary Biology and Environmental Studies, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland.
    Petchey, Owen L.
    Ecological opportunity and predator-prey interactions: linking eco-evolutionary processes and diversification in adaptive radiations2018Inngår i: Proceedings of the Royal Society of London. Biological Sciences, ISSN 0962-8452, E-ISSN 1471-2954, Vol. 285, nr 1874, artikkel-id 20172550Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Much of life's diversity has arisen through ecological opportunity and adaptive radiations, but the mechanistic underpinning of such diversification is not fully understood. Competition and predation can affect adaptive radiations, but contrasting theoretical and empirical results show that they can both promote and interrupt diversification. A mechanistic understanding of the link between microevolutionary processes and macroevolutionary patterns is thus needed, especially in trophic communities. Here, we use a trait-based eco-evolutionary model to investigate the mechanisms linking competition, predation and adaptive radiations. By combining available micro-evolutionary theory and simulations of adaptive radiations we show that intraspecific competition is crucial for diversification as it induces disruptive selection, in particular in early phases of radiation. The diversification rate is however decreased in later phases owing to interspecific competition as niche availability, and population sizes are decreased. We provide new insight into how predation tends to have a negative effect on prey diversification through decreased population sizes, decreased disruptive selection and through the exclusion of prey from parts of niche space. The seemingly disparate effects of competition and predation on adaptive radiations, listed in the literature, may thus be acting and interacting in the same adaptive radiation at different relative strength as the radiation progresses.

  • 1317.
    Postma, Froukje M.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Växtekologi och evolution.
    Selection during Early Life Stages and Local Adaptation in Arabidopsis thaliana2016Doktoravhandling, med artikler (Annet vitenskapelig)
    Abstract [en]

    Organisms are often adapted to their local environment, but the role of early life stages in adaptive differentiation among populations remains poorly known. The aim of my thesis was to investigate the contribution of early life stages to the magnitude and genetic basis of local adaptation, and to identify the underlying adaptive traits. For this, I used two natural populations of the annual plant Arabidopsis thaliana from Italy and Sweden, and a Recombinant Inbred Line (RIL) population derived from a cross between these populations. By combining greenhouse and field experiments, Quantitative Trait Loci (QTL) mapping, and path analysis, I examined (1) the genetic basis of seed dormancy, (2) the contribution of differential seedling establishment to local adaptation, (3) among-year variation in selection during seedling establishment, (4) direct and indirect effects of seed dormancy and timing of germination on fitness, and (5) the adaptive value of the seed bank.

    I found that both the level and the genetic basis of seed dormancy were affected by the maternal environment. One major-effect QTL was identified in all maternal environments, which overlaps with the dormancy gene DELAY OF GERMINATION 1 (DOG1).

    Selection through seedling establishment success contributed strongly to local adaptation and genetic tradeoffs, and varied among years. Variation in seedling establishment and overall fitness among RILs could be explained by genetically based differences in seed dormancy and timing of germination. Seed dormancy affected fitness throughout the life cycle, by affecting the proportion of germinated seeds, and indirectly via effects on timing of germination, plant size and flowering time.

    My results suggest that a considerable portion of A. thaliana seeds enter the seed bank. I found genetic differences in dormancy cycling behaviour between the two populations, which could contribute to local adaptation. The value of a seed bank should be higher at the Swedish study site than at the Italian study site due to lower rate of seed mortality in the soil.

    Overall, the results of this thesis demonstrate that early life stages contribute strongly to both the magnitude and the genetics of local adaptation.

  • 1318.
    Postma, Froukje M.
    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.
    Among-year variation in selection during early life stages and the genetic basis of fitness in Arabidopsis thaliana2018Inngår i: Molecular Ecology, ISSN 0962-1083, E-ISSN 1365-294X, Vol. 27, nr 11, s. 2498-2511Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Incomplete information regarding both selection regimes and the genetic basis of fitness limits our understanding of adaptive evolution. Among-year variation in the genetic basis of fitness is rarely quantified, and estimates of selection are typically based on single components of fitness, thus potentially missing conflicting selection acting during other life-history stages. Here, we examined among-year variation in selection on a key life-history trait and the genetic basis of fitness covering the whole life cycle in the annual plant Arabidopsis thaliana. We planted freshly matured seeds of >200 recombinant inbred lines (RILs) derived from a cross between two locally adapted populations (Italy and Sweden), and both parental genotypes at the native site of the Swedish population in three consecutive years. We quantified selection against the nonlocal Italian genotype, mapped quantitative trait loci (QTL) for fitness and its components, and quantified selection on timing of germination during different life stages. In all 3years, the local Swedish genotype outperformed the nonlocal Italian genotype. However, both the contribution of early life stages to relative fitness, and the effects of fitness QTL varied among years. Timing of germination was under conflicting selection through seedling establishment vs. adult survival and fecundity, and both the direction and magnitude of net selection varied among years. Our results demonstrate that selection during early life stages and the genetic basis of fitness can vary markedly among years, emphasizing the need for multiyear studies considering the whole life cycle for a full understanding of natural selection and mechanisms maintaining local adaptation.

  • 1319.
    Postma, Froukje M.
    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.
    Early life stages contribute strongly to local adaptation in Arabidopsis thaliana2016Inngår i: Proceedings of the National Academy of Sciences of the United States of America, ISSN 0027-8424, E-ISSN 1091-6490, Vol. 113, nr 27, s. 7590-7595Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    The magnitude and genetic basis of local adaptation is of fundamental interest in evolutionary biology. However, field experiments usually do not consider early life stages, and therefore may underestimate local adaptation and miss genetically based tradeoffs. We examined the contribution of differences in seedling establishment to adaptive differentiation and the genetic architecture of local adaptation using recombinant inbred lines (RIL) derived from a cross between two locally adapted populations (Italy and Sweden) of the annual plant Arabidopsis thaliana. We planted freshly matured, dormant seeds (> 180 000) representing >200 RILs at the native field sites of the parental genotypes, estimated the strength of selection during different life stages, mapped quantitative trait loci (QTL) for fitness and its components, and quantified selection on seed dormancy. We found that selection during the seedling establishment phase contributed strongly to the fitness advantage of the local genotype at both sites. With one exception, local alleles of the eight distinct establishment QTL were favored. The major QTL for establishment and total fitness showed evidence of a fitness tradeoff and was located in the same region as the major seed dormancy QTL and the dormancy gene DELAY OF GERMINATION 1 (DOG1). RIL seed dormancy could explain variation in seedling establishment and fitness across the life cycle. Our results demonstrate that genetically based differences in traits affecting performance during early life stages can contribute strongly to adaptive differentiation and genetic tradeoffs, and should be considered for a full understanding of the ecology and genetics of local adaptation.

  • 1320.
    Postma, Froukje M.
    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.
    Maternal environment affects the genetic basis of seed dormancy in Arabidopsis thaliana2015Inngår i: Molecular Ecology, ISSN 0962-1083, E-ISSN 1365-294X, Vol. 24, nr 4, s. 785-797Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    The genetic basis of seed dormancy, a key life history trait important for adaptive evolution in plant populations, has yet been studied only using seeds produced under controlled conditions in greenhouse environments. However, dormancy is strongly affected by maternal environmental conditions, and interactions between seed genotype and maternal environment have been reported. Consequently, the genetic basis of dormancy of seeds produced under natural field conditions remains unclear. We examined the effect of maternal environment on the genetic architecture of seed dormancy using a recombinant inbred line (RIL) population derived from a cross between two locally adapted populations of Arabidopsis thaliana from Italy and Sweden. We mapped quantitative trait loci (QTL) for dormancy of seeds produced in the greenhouse and at the native field sites of the parental genotypes. The Italian genotype produced seeds with stronger dormancy at fruit maturation than did the Swedish genotype in all three environments, and the maternal field environments induced higher dormancy levels compared to the greenhouse environment in both genotypes. Across the three maternal environments, a total of nine dormancy QTL were detected, three of which were only detected among seeds matured in the field, and six of which showed significant QTLxmaternal environment interactions. One QTL had a large effect on dormancy across all three environments and colocalized with the candidate gene DOG1. Our results demonstrate the importance of studying the genetic basis of putatively adaptive traits under relevant conditions.

  • 1321.
    Prentice, Honor C
    et al.
    Department of Biology, Lund University.
    Li, Yuan
    Department of Biology, Lund University.
    Lönn, Mikael
    Södertörns högskola, Institutionen för naturvetenskap, miljö och teknik, Miljövetenskap.
    Tunlid, Anders
    Department of Biology, Lund University.
    Ghatnekar, Lena
    Department of Biology, Lund University.
    A horizontally transferred nuclear gene is associated with microhabitat variation in a natural plant population2015Inngår i: Proceedings of the Royal Society of London. Biological Sciences, ISSN 0962-8452, E-ISSN 1471-2954, Vol. 282, nr 1821, artikkel-id 20152453Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Horizontal gene transfer involves the non-sexual interspecific transmission of genetic material. Even if they are initially functional, horizontally transferred genes are expected to deteriorate into non-expressed pseudogenes, unless they become adaptively relevant in the recipient organism. However, little is known about the distributions of natural transgenes within wild species or the adaptive significance of natural transgenes within wild populations. Here, we examine the distribution of a natural plant-to-plant nuclear transgene in relation to environmental variation within a wild population. Festuca ovina is polymorphic for an extra (second) expressed copy of the nuclear gene (PgiC) encoding cytosolic phosphoglucose isomerase, with the extra PgiC locus having been acquired horizontally from the distantly related grass genus Poa. We investigated variation at PgiC in samples of F. ovina from a fine-scale, repeating patchwork of grassland microhabitats, replicated within spatially separated sites. Even after accounting for spatial effects, the distributions of F. ovina individuals carrying the additional PgiC locus, and one of the enzyme products encoded by the locus, are significantly associated with fine-scale habitat variation. Our results suggest that the PgiC transgene contributes, together with the unlinked 'native' PgiC locus, to local adaptation to a fine-scale mosaic of edaphic and biotic grassland microhabitats.

  • 1322.
    Prentice, Honor C
    et al.
    Department of Biology, Lund University.
    Li, Yuan
    Department of Biology, Lund University.
    Lönn, Mikael
    Södertörns högskola, Miljövetenskap.
    Tunlid, Anders
    Department of Biology, Lund University.
    Ghatnekar, Lena
    Department of Biology, Lund University.
    A horizontally transferred nuclear gene is associated with microhabitat variationin a natural plant population2015Inngår i: Proceedings of the Royal Society of London. Biological Sciences, ISSN 0962-8452, E-ISSN 1471-2954, Vol. 282, nr 1821, artikkel-id 20152453Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Horizontal gene transfer involves the non-sexual interspecific transmission of genetic material. Even if they are initially functional, horizontally transferred genes are expected to deteriorate into non-expressed pseudogenes, unless they become adaptively relevant in the recipient organism. However, little is known about the distributions of natural transgenes within wild species or the adaptive significance of natural transgenes within wild populations. Here, we examine the distribution of a natural plant-to-plant nuclear transgene in relation to environmental variation within a wild population. Festuca ovina is polymorphic for an extra (second) expressed copy of the nuclear gene (PgiC) encoding cytosolic phosphoglucose isomerase, with the extra PgiC locus having been acquired horizontally from the distantly related grass genus Poa. We investigated variation at PgiC in samples of F. ovina from a fine-scale, repeating patchwork of grassland microhabitats, replicated within spatially separated sites. Even after accounting for spatial effects, the distributions of F. ovina individuals carrying the additional PgiC locus, and one of the enzyme products encoded by the locus, are significantly associated with fine-scale habitat variation. Our results suggest that the PgiC transgene contributes, together with the unlinked 'native' PgiC locus, to local adaptation to a fine-scale mosaic of edaphic and biotic grassland microhabitats.

  • 1323. Price, Trevor D.
    et al.
    Hooper, Daniel M.
    Buchanan, Caitlyn D.
    Johansson, Ulf S.
    Naturhistoriska riksmuseet, Enheten för zoologi.
    Tietze, D. Thomas
    Alström, Per
    Olsson, Urban
    Ghosh-Harihar, Mousumi
    Ishtiaq, Farah
    Gupta, Sandeep K.
    Martens, Jochen
    Harr, Bettina
    Singh, Pratap
    Mohan, Dhananjai
    Niche filling slows the diversification of Himalayan songbirds2014Inngår i: Nature, ISSN 0028-0836, E-ISSN 1476-4687, Vol. 509, s. 222-225Artikkel i tidsskrift (Fagfellevurdert)
  • 1324.
    Promerová, Marta
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Evolutionsbiologi. Max Planck Inst Sci Human Hist, Dept Archaeogenet, Jena, Germany..
    Alavioon, Ghazal
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Evolutionsbiologi.
    Tusso Gomez, Sergio
    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. Friedrich Schiller Univ Jena, Dept Populat Ecol, Jena, Germany..
    Immler, Simone
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Evolutionsbiologi.
    No evidence for MHC class II-based non-random mating at the gametic haplotype in Atlantic salmon2017Inngår i: Heredity, ISSN 0018-067X, E-ISSN 1365-2540, Vol. 118, nr 6, s. 563-567Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Genes of the major histocompatibility complex (MHC) are a likely target of mate choice because of their role in inbreeding avoidance and potential benefits for offspring immunocompetence. Evidence for female choice for complementary MHC alleles among competing males exists both for the pre- and the postmating stages. However, it remains unclear whether the latter may involve non-random fusion of gametes depending on gametic haplotypes resulting in transmission ratio distortion or non-random sequence divergence among fused gametes. We tested whether non-random gametic fusion of MHC-II haplotypes occurs in Atlantic salmon Salmo salar. We performed in vitro fertilizations that excluded interindividual sperm competition using a split family design with large clutch sample sizes to test for a possible role of the gametic haplotype in mate choice. We sequenced two MHC-II loci in 50 embryos per clutch to assess allelic frequencies and sequence divergence. We found no evidence for transmission ratio distortion at two linked MHC-II loci, nor for non-random gamete fusion with respect to MHC-II alleles. Our findings suggest that the gametic MHC-II haplotypes play no role in gamete association in Atlantic salmon and that earlier findings of MHC-based mate choice most likely reflect choice among diploid genotypes. We discuss possible explanations for these findings and how they differ from findings in mammals.

  • 1325.
    Puckett, Emily E.
    et al.
    Fordham Univ, Biol Field Stn, Louis Calder Ctr, Armonk, NY 10504 USA.
    Park, Jane
    Fordham Univ, Biol Field Stn, Louis Calder Ctr, Armonk, NY 10504 USA.
    Combs, Matthew
    Fordham Univ, Biol Field Stn, Louis Calder Ctr, Armonk, NY 10504 USA.
    Blum, Michael J.
    Tulane Univ, Xavier Ctr Bioenvironm Res, New Orleans, LA 70112 USA.
    Bryant, Juliet E.
    Univ Oxford, Clin Res Unit, Hanoi, Vietnam.
    Caccone, Adalgisa
    Yale Univ, Dept Ecol & Evolutionary Biol, POB 208106, New Haven, CT 06520 USA.
    Costa, Federico
    Univ Fed Bahia, Inst Saude Colet, Salvador, BA, Brazil.
    Denium, Eva E.
    Univ Edinburgh, Inst Evolutionary Biol, Ashworth Labs, Charlotte Auerbach Rd, Edinburgh EH9 3FL, Midlothian, Scotland; Wageningen Univ, Math & Stat Methods Grp, Droevendaalsesteeg 1, NL-6708 PB Wageningen, Netherlands.
    Esther, Alexandra
    Fed Res Ctr Cultivated Plants, Inst Plant Protect Hort & Forests, Vertebrate Res, Julius Kuhn Inst, Munster, Germany.
    Himsworth, Chelsea G.
    British Columbia Minist Agr, Anim Hlth Ctr, 1767 Angus Campbell Rd, Abbotsford, BC V3G 2M3, Canada.
    Keightley, Peter D.
    Univ Edinburgh, Inst Evolutionary Biol, Ashworth Labs, Charlotte Auerbach Rd, Edinburgh EH9 3FL, Midlothian, Scotland.
    Ko, Albert
    Yale Univ, Lab Epidemiol & Publ Hlth, New Haven, CT USA.
    Lundkvist, Åke
    Uppsala universitet, Medicinska och farmaceutiska vetenskapsområdet, Medicinska fakulteten, Institutionen för medicinsk biokemi och mikrobiologi.
    McElhinney, Lorraine M.
    APHA, Wildlife Zoonoses & Vector Borne Dis Res Grp, Woodham Lane, New Haw, Surrey, England.
    Morand, Serge
    Ctr Infectiol Christophe Merieux Laos, CNRS CIRAD, Viangchan, Laos.
    Robins, Judith
    Univ Auckland, Dept Anthropol, Private Bag 92019, Auckland, New Zealand; Univ Auckland, Sch Biol Sci, Private Bag 92019, Auckland, New Zealand.
    Russell, James
    Univ Auckland, Sch Biol Sci, Private Bag 92019, Auckland, New Zealand; Univ Auckland, Dept Stat, Private Bag 92019, Auckland, New Zealand.
    Strand, Tanja M.
    Uppsala universitet, Medicinska och farmaceutiska vetenskapsområdet, Medicinska fakulteten, Institutionen för medicinsk biokemi och mikrobiologi.
    Suarez, Olga
    Univ Buenos Aires, EGE Fac Ciencias Exactas & Nat, IEGEBA CONICET, Lab Ecol Roedores Urbanos, Pabellon 2,Ciudad Univ,C1428EHA, Buenos Aires, DF, Argentina.
    Yon, Lisa
    Univ Nottingham, Sch Vet Med & Sci, Sutton Bonington Campus, Loughborough LE12 5RD, Leics, England.
    Munshi-South, Jason
    Fordham Univ, Biol Field Stn, Louis Calder Ctr, Armonk, NY 10504 USA.
    Global population divergence and admixture of the brown rat (Rattus norvegicus)2016Inngår i: Proceedings of the Royal Society of London. Biological Sciences, ISSN 0962-8452, E-ISSN 1471-2954, Vol. 283, nr 1841, artikkel-id 20161762Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Native to China and Mongolia, the brown rat (Rattus norvegicus) now enjoys a worldwide distribution. While black rats and the house mouse tracked the regional development of human agricultural settlements, brown rats did not appear in Europe until the 1500s, suggesting their range expansion was a response to relatively recent increases in global trade. We inferred the global phylogeography of brown rats using 32 k SNPs, and detected 13 evolutionary clusters within five expansion routes. One cluster arose following a southward expansion into Southeast Asia. Three additional clusters arose from two independent eastward expansions: one expansion from Russia to the Aleutian Archipelago, and a second to western North America. Westward expansion resulted in the colonization of Europe from which subsequent rapid colonization of Africa, the Americas and Australasia occurred, and multiple evolutionary clusters were detected. An astonishing degree of fine-grained clustering between and within sampling sites underscored the extent to which urban heterogeneity shaped genetic structure of commensal rodents. Surprisingly, few individuals were recent migrants, suggesting that recruitment into established populations is limited. Understanding the global population structure of R. norvegicus offers novel perspectives on the forces driving the spread of zoonotic disease, and aids in development of rat eradication programmes.

  • 1326.
    Puentes, Adriana
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Växtekologi och evolution.
    Plant-Herbivore Interactions and Evolutionary Potential of Natural Arabidopsis lyrata Populations2012Doktoravhandling, med artikler (Annet vitenskapelig)
    Abstract [en]

    In this thesis, I combined field, greenhouse and common-garden experiments to examine the ecological and evolutionary consequences of plant-herbivore interactions and the genetic architecture of fitness-related traits in the insect-pollinated, self-incompatible, perennial herb Arabidopsis lyrata. More specifically, I examined (1) whether damage to leaves and inflorescences affects plant fitness non-additively, (2) whether trichome production is associated with a cost in terms of reduced tolerance to leaf and inflorescence damage, (3) whether young plant resistance to a specialist insect herbivore varies among populations, and (4) whether the evolution of flowering time, floral display and rosette size is constrained by lack of genetic variation or by genetic correlations among traits.

    A two-year field experiment in a Swedish population showed that damage to rosette leaves and to inflorescences can affect both current and future plant performance of A. lyrata, and that effects on some fitness components are non-additive. A two-year field experiment in another Swedish population indicated that trichome-producing plants are not less tolerant than glabrous plants to leaf and inflorescence damage. In a greenhouse experiment, acceptability of young plants (5-6 weeks old) to ovipositing females and damage received by Plutella xylostella larvae varied considerably among twelve A. lyrata populations. Both oviposition and leaf damage were positively correlated with rosette size, but trichome density in the trichome-producing morph was apparently too low at this developmental stage to influence resistance to P. xylostella. In a common-garden experiment, flowering time, floral display and rosette size varied among four Scandinavian A. lyrata populations, and displayed significant additive genetic variation in some populations. Yet, strong genetic correlations between flowering start and number of flowers, and between petal length and petal width suggest that these traits may not evolve independently.

    Taken together, the results indicate the need to consider possible long-term and non-additive effects of herbivore damage to different plant parts, that there is no trade-off between trichome production and tolerance to herbivory, that the importance of morphological defenses against herbivory may change through plant ontogeny, and that considerable genetic variation for traits such as flowering time and floral display can be maintained in natural plant populations.

  • 1327.
    Puentes, Adriana
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Växtekologi och evolution. Swedish Univ Agr Sci, Dept Ecol, SE-75007 Uppsala, Sweden..
    Granath, Gustaf
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Växtekologi och evolution. Swedish Univ Agr Sci, Dept Ecol, SE-75007 Uppsala, Sweden..
    Ågren, Jon
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Växtekologi och evolution.
    Similarity in G matrix structure among natural populations of Arabidopsis lyrata2016Inngår i: Evolution, ISSN 0014-3820, E-ISSN 1558-5646, Vol. 70, nr 10, s. 2370-2386Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Understanding the stability of the G matrix in natural populations is fundamental for predicting evolutionary trajectories; yet, the extent of its spatial variation and how this impacts responses to selection remain open questions. With a nested paternal half-sib crossing design and plants grown in a field experiment, we examined differences in the genetic architecture of flowering time, floral display, and plant size among four Scandinavian populations of Arabidopsis lyrata. Using a multivariate Bayesian framework, we compared the size, shape, and orientation of G matrices and assessed their potential to facilitate or constrain trait evolution. Flowering time, floral display and rosette size varied among populations and significant additive genetic variation within populations indicated potential to evolve in response to selection. Yet, some characters, including flowering start and number of flowers, may not evolve independently because of genetic correlations. Using a multivariate framework, we found few differences in the genetic architecture of traits among populations. G matrices varied mostly in size rather than shape or orientation. Differences in multivariate responses to selection predicted from differences in G were small, suggesting overall matrix similarity and shared constraints to trait evolution among populations.

  • 1328.
    Puentes, Adriana
    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.
    Genetic variation and covariation in flowering time, floral display and rosette size in four Scandinavian Arabidopsis lyrata populationsManuskript (preprint) (Annet vitenskapelig)
    Abstract [en]

    Levels of additive genetic variation and patterns of genetic correlations among traits influence evolutionary trajectories of traits in natural populations and among-population differentiation. With a nested paternal half-sib crossing design we examined the genetic architecture of flowering time, floral display and rosette size in four Scandinavian populations of the perennial herb Arabidopsis lyrata grown in a common-garden experiment in the Swedish native range. We specifically asked whether these traits vary genetically among populations, whether response to selection is constrained by lack of genetic variation or by genetic covariances among traits, and whether there is evidence of a trade-off between allocation to reproduction and vegetative growth, or between the number and size of flowers produced. The characters examined varied genetically among populations and displayed significant additive genetic variation in some populations. A strong negative genetic correlation between flowering start and number of flowers, and a strong positive correlation between petal length and width indicated that these pairs of traits do not evolve independently in some populations. G-matrices varied among populations suggesting that genetic (co)variances have evolved locally. There was no evidence of a trade-off between allocation to reproduction and vegetative growth or between the number and size of flowers, indicating that variation in resource acquisition was larger than variation in relative allocation to these different functions. 

  • 1329.
    Pålsson, Aksel
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för biologisk grundutbildning.
    Genflöde, hybridisering och sympatrisk artbildning - med strandsnäcka som exempel2014Independent thesis Basic level (degree of Bachelor), 10 poäng / 15 hpOppgave
    Abstract [sv]

    Det finns idag en mängd olika artbegrepp men inget universellt som fungerar för alla organismer. Det mest använda är det biologiska artbegreppet som innebär att en art är en population organismer som är reproduktivt isolerade från andra populationer. De evolutionära processerna som leder till bildandet av nya arter delas upp beroende på vilken geografisk skala de utspelar sig i. Den allopatriska modellen som är den mest vedertagna innebär att geografiskt isolerade populationer med tiden ackumulerar genetiska, morfologiska eller beteendemässiga differentieringar till den grad att populationerna kan betraktas som olika arter. Sympatrisk artbildning är när artbildning sker inom ett och samma geografiska område, alltså utan geografisk isolering. Denna modell har länge varit omdebatterad men bevisen för den, både teoretiska och praktiska, ökar ständigt. Reproduktionsbarriärer är biologiska karaktärer som hindrar genflöde mellan populationer och delas upp i prezygotiska och postzygotiska. Hybridisering mellan närbesläktade arter eller divergerande ekotyper inom samma art kan leda till uppkomsten av hybridzoner. Ett exempel på det är den vivipara standsnäckan som är en art som ofta bildar två skilda ekotyper med en hybridzon mellan ekotypernas respektive mikrohabitat. Ett mikrohabitat är ett litet habitat inom ett större, i det här fallet är det den övre och lägre kustnivån. Den vivipara strandsnäckan beskrivs ofta som ett exempel av begynnande sympatrisk artbildning driven av det naturliga urvalet. Det pågår mycket forskning angående de här snäckornas differentiering och om vilka faktorer det är som ligger bakom. Snäckans två ekotyper är delvis reproduktivt isolerade men vad som kommer hända i framtiden, ifall de reproduktiva barriärerna mellan ekotyperna kommer fullbordas och ekotyperna kommer bli olika arter är okänt. Det råder idag ingen konsensus om vilka faktorer som är de mest betydelsefulla för upprätthållandet av divergensen. Det nuvarande läget tyder dock på att det är yttre miljöfaktorer (exogena faktorer) är de starkaste i det här fallet. Detta eftersom att olika ekotyper har olika fitness i olika habitat vilket är en exogen selektionsmekanism.

  • 1330.
    Qiao, Tuo
    et al.
    Chinese Acad Sci, Inst Vertebrate Paleontol & Paleoanthropol, Key Lab Vertebrate Evolut & Human Origins, Beijing, Peoples R China..
    King, Benedict
    Flinders Univ S Australia, Sch Biol Sci, Adelaide, SA, Australia..
    Long, John A.
    Flinders Univ S Australia, Sch Biol Sci, Adelaide, SA, Australia..
    Ahlberg, Per E.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för organismbiologi, Evolution och utvecklingsbiologi.
    Zhu, Min
    Chinese Acad Sci, Inst Vertebrate Paleontol & Paleoanthropol, Key Lab Vertebrate Evolut & Human Origins, Beijing, Peoples R China..
    Early Gnathostome Phylogeny Revisited: Multiple Method Consensus2016Inngår i: PLoS ONE, ISSN 1932-6203, E-ISSN 1932-6203, Vol. 11, nr 9, artikkel-id e0163157Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    A series of recent studies recovered consistent phylogenetic scenarios of jawed vertebrates, such as the paraphyly of placoderms with respect to crown gnathostomes, and antiarchs as the sister group of all other jawed vertebrates. However, some of the phylogenetic relationships within the group have remained controversial, such as the positions of Entelognathus, ptyctodontids, and the Guiyu-lineage that comprises Guiyu, Psarolepis and Achoania. The revision of the dataset in a recent study reveals a modified phylogenetic hypothesis, which shows that some of these phylogenetic conflicts were sourced from a few inadvertent miscodings. The interrelationships of early gnathostomes are addressed based on a combined new dataset with 103 taxa and 335 characters, which is the most comprehensive morphological dataset constructed to date. This dataset is investigated in a phylogenetic context using maximum parsimony (MP), Bayesian inference (BI) and maximum likelihood (ML) approaches in an attempt to explore the consensus and incongruence between the hypotheses of early gnathostome interrelationships recovered from different methods. Our findings consistently corroborate the paraphyly of placoderms, all 'acanthodians' as a paraphyletic stem group of chondrichthyans, Entelognathus as a stem gnathostome, and the Guiyu-lineage as stem sarcopterygians. The incongruence using different methods is less significant than the consensus, and mainly relates to the positions of the placoderm Wuttagoonaspis, the stem chondrichthyan Ramirosuarezia, and the stem osteichthyan Lophosteus D the taxa that are either poorly known or highly specialized in character complement. Given that the different performances of each phylogenetic approach, our study provides an empirical case that the multiple phylogenetic analyses of morphological data are mutually complementary rather than redundant.

  • 1331. Qiu, Suo
    et al.
    Zeng, Kai
    Slotte, Tanja
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Evolutionsbiologi.
    Wright, Stephen
    Charlesworth, Deborah
    Reduced Efficacy of Natural Selection on Codon Usage Bias in Selfing Arabidopsis and Capsella Species2011Inngår i: Genome Biology and Evolution, ISSN 1759-6653, E-ISSN 1759-6653, Vol. 3, s. 868-880Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Population genetic theory predicts that the efficacy of natural selection in a self-fertilizing species should be lower than its outcrossing relatives because of the reduction in the effective population size (N(e)) in the former brought about by inbreeding. However, previous analyses comparing Arabidopsis thaliana (selfer) with A. lyrata (outcrosser) have not found conclusive support for this prediction. In this study, we addressed this issue by examining silent site polymorphisms (synonymous and intronic), which are expected to be informative about changes in N(e). Two comparisons were made: A. thaliana versus A. lyrata and Capsella rubella (selfer) versus C. grandiflora (outcrosser). Extensive polymorphism data sets were obtained by compiling published data from the literature and by sequencing 354 exon loci in C. rubella and 89 additional loci in C. grandiflora. To extract information from the data effectively for studying these questions, we extended two recently developed models in order to investigate detailed selective differences between synonymous codons, mutational biases, and biased gene conversion (BGC), taking into account the effects of recent changes in population size. We found evidence that selection on synonymous codons is significantly weaker in the selfers compared with the outcrossers and that this difference cannot be fully accounted for by mutational biases or BGC.

  • 1332.
    Qu, Qingming
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för organismbiologi, Evolution och utvecklingsbiologi.
    3D Histological Architecture And Ontogeny In Two Early Osteichthyan Scales: the Origin Of Cosmine And A Reconsideration Of The Phylogenetic Application Of Paleohistology Data2013Konferansepaper (Annet vitenskapelig)
    Abstract [en]

    The histology of early osteichthyan scales have been extensively studied using thin sections and acid-etched ground surfaces, and it is known that these rhombic scales are composed of multiple odontodes (tooth-like denticles) in the crown and bony tissues in the base. However, the 2D nature of the ground sections does not allow us to know the 3D morphology and distribution of the odontodes, which contain the ontogenetic history of the scales. To compensate the traditional study based on ground sections, we used Propagation phase contrast X-ray Synchrotron microtomography (PPC-SRµCT) to examine body scales of two early osteichthyans Andreolepis and Psarolepis, both of which are important taxa to understand the origin of osteichthyan crown group.

     

    The reconstructed 3D models of the histological architecture provide novel data of the ontogenetic history of the scales. The crown of Andreolepis scale is constructed two distinct type of growth patterns: a linear polarized pattern in the initial stage and a gap-filling pattern in the later stage. In the crown of Psarolepis scale the second odontode is most peculiar, with a the enamel covering penetrated by several pores, while the primordia odontode is almost morphologically identical with that of Andreolepis scale. A developmental shift following the formation of the primordia odontode may be the key step of the evolution of cosmoid scales, and Psarolepis scale is explained as a transitional form between the Andreolepis-type scale and the typical cosmoid scales in more derived sarcopterygians such as Osteolepis. Comparison of the entire canal system among Andreolepis, Psarolepis and more derived sarcopterygians show that the pore-canal system and cosmine-like construction are already present in Psarolepis scales, although the construction is different from typical cosmine as in Osteolepis. A stepwise scenario of the origin of pore-canal system and cosmine is proposed according to the new data.

     

    New characters are composed based on the in situ 3D data and could be incorporated into phylogenetic analysis in the future when more taxa have been studied using similar imaging method and 3D histology obtained. The 3D histology study of skeletal fossils using PPC-SRµCT could provide more informative and reliable phylogenetic data.

  • 1333.
    Qu, Qingming
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för organismbiologi.
    Three-dimensional Virtual Histology of Early Vertebrate Scales Revealed by Synchrotron X-ray Phase-contrast Microtomography2015Doktoravhandling, med artikler (Annet vitenskapelig)
    Abstract [en]

    Vertebrate hard tissues first appeared in the dermal skeletons of early jawless vertebrates (ostracoderms) and were further modified in the earliest jawed vertebrates. Fortunately, histological information is usually preserved in these early vertebrate fossils and has thus been studied for more than a century, done so by examining thin sections, which provide general information about the specific features of vertebrate hard tissues in their earliest forms. Recent progress in synchrotron X-ray microtomography technology has caused a revolution in imaging methods used to study the dermal skeletons of early vertebrates. Virtual thin sections obtained in this manner can be used to reconstruct the internal structures of dermal skeletons in three-dimensions (3D), such as vasculature, buried odontodes (tooth-like unites) and osteocytes. Several body scales of early vertebrates have been examined using this imaging method and in situ 3D models of internal structures are created. Andreolepis (an early osteichthyan) scale shows linear growth pattern of odontodes in early developmental stage, which is not observable in traditional thin sections. The scale of another early osteichthyan Psarolepis was studied in the same way. Comparison between Andreolepis and Psarolepis shows that cosmine, a tissue complex in dermal skeleton of early sarcopterygians, originated by a developmental change of odontode shape. Two scales of osteostracans, a group of extinct jawless vertebrates, were studied in 3D and more details have been revealed in comparison to previous results based solely on 2D thin sections. 3D data enables us to compare the vasculature and canal system in different taxa in great detail, which forms the basis of formulating primary homology hypothesis and phylogenetic characters.

    The new data resulting from this study suggests that vertebrate fossils have preserved much more histological information than we currently appreciate, and provide a new data source of microanatomical structures inside the fossils that can contribute new characters for phylogenetic analysis of early jawed vertebrates.

  • 1334.
    Qu, Qingming
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för organismbiologi.
    Blom, Henning
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för organismbiologi, Evolution och utvecklingsbiologi.
    Sanchez, Sophie
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för organismbiologi, Evolution och utvecklingsbiologi.
    Ahlberg, Per
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för organismbiologi, Evolution och utvecklingsbiologi.
    Three-dimensional virtual histology of silurian osteostracan scales revealed by synchrotron radiation microtomography2015Inngår i: Journal of morphology (1931. Print), ISSN 0362-2525, E-ISSN 1097-4687, Vol. 276, nr 8, s. 873-888Artikkel i tidsskrift (Fagfellevurdert)
  • 1335.
    Qu, Qingming
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för organismbiologi.
    Haitina, Tatjana
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för organismbiologi, Evolution och utvecklingsbiologi.
    Zhu, Min
    Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences.
    Ahlberg, Per Erik
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för organismbiologi, Evolution och utvecklingsbiologi.
    New genomic and fossil data illuminate the origin of enamel2015Inngår i: Nature, ISSN 0028-0836, E-ISSN 1476-4687, Vol. 526, nr 7571, s. 108-120Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Enamel, the hardest vertebrate tissue, covers the teeth of almost all sarcopterygians (lobe-finned bony fishes and tetrapods) as well as the scales and dermal bones of many fossil lobe-fins(1-5). Enamel deposition requires an organic matrix containing the unique enamel matrix proteins (EMPs) amelogenin (AMEL), enamelin (ENAM) and ameloblastin (AMBN)(6). Chondrichthyans (cartilaginous fishes) lack both enamel and EMP genes(7,8). Many fossil and a few living non-teleost actinopterygians (ray-finned bony fishes) such as the gar, Lepisosteus, have scales and dermal bones covered with a proposed enamel homologue called ganoine(1,9). However, no gene or transcript data for EMPs have been described from actinopterygians(10,11). Here we show that Psarolepis romeri, a bony fish from the the Early Devonian period, combines enamel-covered dermal odontodes on scales and skull bones with teeth of naked dentine, and that Lepisosteus oculatus (the spotted gar) has enam andambn genes that are expressed in the skin, probably associated with ganoine formation. The genetic evidence strengthens the hypothesis that ganoine is homologous with enamel. The fossil evidence, further supported by the Silurian bony fish Andreolepis, which has enamel-covered scales but teeth and odontodes on its dermal bones made of naked dentine(12-16), indicates that this tissue originated on the dermal skeleton, probably on the scales. It subsequently underwent heterotopic expansion across two highly conserved patterning boundaries (scales/head-shoulder and dermal/oral) within the odontode skeleton.

  • 1336.
    Qu, Qingming
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för organismbiologi, Evolution och utvecklingsbiologi.
    Sanchez, Sophie
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för organismbiologi, Evolution och utvecklingsbiologi. Uppsala universitet, Science for Life Laboratory, SciLifeLab. European Synchrotron Radiat Facil, 71 Ave Martyrs, F-38043 Grenoble 09, France.
    Zhu, Min
    Chinese Acad Sci, Inst Vertebrate Paleontol & Paleoanthropol, Key Lab Vertebrate Evolut & Human Origins, Xiwaidajie 142, Beijing 100044, Peoples R China.
    Blom, Henning
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för organismbiologi, Evolution och utvecklingsbiologi.
    Ahlberg, Per E
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för organismbiologi, Evolution och utvecklingsbiologi. Uppsala universitet, Science for Life Laboratory, SciLifeLab.
    The origin of novel features by changes in developmental mechanisms: ontogeny and three-dimensional microanatomy of polyodontode scales of two early osteichthyans2017Inngår i: Biological Reviews, ISSN 1464-7931, E-ISSN 1469-185X, Vol. 92, nr 2, s. 1189-1212Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Recent advances in synchrotron imaging allow us to study the three-dimensional (3D) histology of vertebrate fossils, including microfossils (e.g. teeth and scales) of early jawed vertebrates. These microfossils can often be scanned at submicron resolution (<1 µm) because of their small size. The resulting voxel (3D pixel) stacks can be processed into virtual thin sections revealing almost every internal detail of the samples, comparable to traditional thin sections. In addition, 3D models of the internal microanatomical structures, such as embedded odontodes and vasculature, can be assembled and examined in situ. Scales of two early osteichthyans, Psarolepis romeri from the Early Devonian of China and Andreolepis hedei from the Late Silurian of Sweden, were scanned using propagation phase-contrast synchrotron X-ray microtomography (PPC-SRµCT), and 3D models of internal canal systems and buried odontodes were created from the scans. Based on these new data, we review the evolutionary origin of cosmine and its associated pore-canal system, which has been long recognized as a synapomorphy of sarcopterygians. The first odontode that appeared during growth shows almost identical morphology in the two scales, but the second odontode of the Psarolepis scale shows a distinctive morphology with several pores on the surface. It is suggested that a shift from ridge-like odontode to pore-bearing odontode was the key step in the origin of cosmine, which was then elaborated further in more-derived sarcopterygians. We perform a detailed comparison between the two scales and propose a primary homology framework to generate microanatomical characters, which can be used in the phylogenetic analysis of early osteichthyans when more 3D data become available. Our results highlight the importance of 3D data for the study of histology and ontogeny of the dermal skeleton of early jawed vertebrates, especially scales of the polyodontode type. The traditional microvertebrate collection is not only useful for biostratigraphic studies, but also preserves invaluable biological information about the growth of vertebrate hard tissues. Today, we are only beginning to understand the biological meaning of the new 3D data. The increasing availability of such data will enable, and indeed require, a complete revision of traditional palaeohistological studies on early vertebrates.

  • 1337.
    Qu, Qingming
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för organismbiologi.
    Sanchez, Sophie
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för organismbiologi, Evolution och utvecklingsbiologi.
    Zhu, Min
    Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences.
    Blom, Henning
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för organismbiologi, Evolution och utvecklingsbiologi.
    Tafforeau, Paul
    European Synchrotron Radiation Facility.
    Ahlberg, Per
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för organismbiologi, Evolution och utvecklingsbiologi.
    The origin of novel features by changes in developmental mechanisms: a 3D virtual paleohistology study on polyodontode scales of primitive osteichthyans2015Manuskript (preprint) (Annet vitenskapelig)
  • 1338.
    Qu, Yanhua
    et al.
    Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China.
    Ericson, Per G P
    Naturhistoriska riksmuseet, Forskningsavdelningen centralt.
    Lei, Fu Min
    Li, Shou Hsien
    Postglacial colonization of the Tibetan plateau inferred from the matrilineal genetic structure of the endemic red-necked snow finch, Pyrgilauda ruficollis.2005Inngår i: Molecular Ecology, ISSN 0962-1083, E-ISSN 1365-294X, Vol. 14, nr 6, s. 1767-81Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Most phylogeographical studies of postglacial colonization focus on high latitude locations in the Northern Hemisphere. Here, we studied the phylogeographical structure of the red-necked snow finch Pyrgilauda ruficollis, an endemic species of the Tibetan plateau. We analysed 879 base pairs (bp) of the mitochondrial cytochrome b gene and 529 bp of the control region in 41 birds from four regional groups separated by mountain ranges. We detected 34 haplotypes, 31 of which occurred in a single individual and only three of which were shared among sampling sites within regional groups or among regional groups. Haplotype diversity was high (h = 0.94); nucleotide diversity was low (eth = 0.00415) and genetic differentiation was virtually non-existent. Analyses of mismatch distributions and geographically nested clades yielded results consistent with contiguous range expansion, and the expansion times were estimated as 0.07-0.19 million years ago (Ma). Our results suggest that P. ruficollis colonized the Tibetan plateau after the extensive glacial period (0.5-0.175 Ma), expanding from the eastern margin towards the inner plateau. Thus, in contrast to many of the post-glacial phylogeographical structures known at high latitudes, this colonization occurred without matrilineal population structuring. This might be due to the short glacial cycles typical of the Tibetan plateau, adaptation of P. ruficollis to cold conditions, or refugia and colonized habitat being semicontinuous and thus promoting population mixing.

  • 1339.
    Qu, Yanhua
    et al.
    Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China.
    Ericson, Per G P
    Naturhistoriska riksmuseet, Forskningsavdelningen centralt.
    Lei, Fumin
    Gebauer, Axel
    Kaiser, Martin
    Helbig, Andreas J
    Molecular phylogenetic relationship of snow finch complex (genera Montifringilla, Pyrgilauda, and Onychostruthus) from the Tibetan plateau.2006Inngår i: Molecular Phylogenetics and Evolution, ISSN 1055-7903, E-ISSN 1095-9513, Vol. 40, nr 1, s. 218-26Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    The snow finch complex (Montifringilla, Pyrgilauda, and Onychostruthus) has its center of distribution on the Tibetan plateau, with six out of seven species in the genera occurring there. Phylogenetic relationships among these six species of three genera have been studied based on DNA sequence data obtained from the mitochondrial cytochrome b gene and the nuclear myoglobin gene. The results support monophyly of the snow finch complex group and three major evolutionary lineages are recognized. The first clade consists of ruficollis, blanfordi, and davidiana. These three taxa are sometimes placed in their own genus, Pyrgilauda, and the DNA data supports this. The three taxa nivalis, henrici, and adamsi have traditionally been placed in the genus Montifringilla, and they group together strongly in the present analysis. The results further suggest that nivalis and adamsi are more closely related to each other than are nivalis and henrici, despite that the latter two are often regarded as conspecific. The third distinct lineage within the snow finch complex consists of taczanowskii, which has been placed its own genus, Onychostruthus. This taxon has a basal position in the phylogenetic tree and is sister to all other snow finches. We estimated that taczanowskii split from the other taxa between 2 and 2.5 mya, i.e., about the time for the most recent uplift of the Tibetan plateau, "the Tibet movement", 3.6-1.7 mya. Cladogenesis within the Montifringilla and Pyrgilauda clades seems to be contemporary with the second phase of "Tibet movement" at 2.5 mya and the third phase at 1.7 mya and "Kunhuang movement" in 1.5-0.6 mya. The dramatic climatic and ecological changes following from the uplift of the Tibetan plateau, together with the cyclic contraction and expansion of suitable habitats during the Pleistocene, are probably the most important factors for the cladogenesis in snow finch complex.

  • 1340.
    Qu, Yanhua
    et al.
    Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China.
    Ericson, Per G P
    Naturhistoriska riksmuseet, Forskningsavdelningen centralt.
    Quan, Qing
    Song, Gang
    Zhang, Ruiying
    Gao, Bin
    Lei, Fumin
    Long-term isolation and stability explain high genetic diversity in the Eastern Himalaya.2014Inngår i: Molecular Ecology, ISSN 0962-1083, E-ISSN 1365-294X, Vol. 23, nr 3, s. 705-20Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    China's Southwest Mountainous Region in Eastern Himalaya is a ‘biodiversity hotspot’ of global interest for conservation. Yet little is known about what has driven this unique diversity. The dramatic topography of the Southwest Mountainous Region resulting from the tectonic uplift during the late Pliocene leads to dramatic ecological stratification, which creates physical barriers to migration and isolates organisms into different subregions and mountain systems. This agrees with the observation that the phylogeographical patterns found in four species of birds (Alcippe morrisonia, Stachyridopsis ruficeps, Parus monticolus and Aegithalos concinnus) distributed in this region are characterized by deep splits between lineages that coalesce between 0.8 and 2.1 Ma. Unlike other regions at this latitude, the Southwest Mountainous Region was largely unaffected by the Pleistocene glaciations. Genetically isolated populations of these birds could thus be maintained throughout the Pleistocene in these rather stable montane environments. In comparison, we found radically different phylogeographical patterns in populations of the same four species distributed in the adjacent lowland, the Central China region. This region has a distinctly different geological history with dramatic, climate-induced shifts in vegetation during the Pleistocene. Here, we found a considerably less geographical structure in the genetic variation and a much younger coalescence time (0.3-0.7 Ma). We also found evidence of genetic bottlenecks during the glacial periods and gene flow during the interglacial expansions. We conclude that the high genetic diversity in the Southwest Mountainous Region results from a long-term in situ diversification within these evolutionary isolated and environment stable montane habitats.

  • 1341.
    Qu, Yanhua
    et al.
    Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China.
    Song, Gang
    Gao, Bin
    Quan, Qing
    Ericson, Per G P
    Naturhistoriska riksmuseet, Forskningsavdelningen centralt.
    Lei, Fumin
    The influence of geological events on the endemism of East Asian birds studied through comparative phylogeography2015Inngår i: Journal of Biogeography, ISSN 0305-0270, E-ISSN 1365-2699, Vol. 42, nr 1, s. 179-192Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Aim: East Asia is known for its exceptionally high biological diversity and endemism. Various geological and climatic events during the Pliocene and Pleistocene have been invoked to explain this high endemism, and these processes have had different impacts on different organisms. Herein, we investigate the relative role of these historical processes in the genetic evidence for endemism of intraspecific lineages of two East Asian species: the grey-cheeked fulvetta (Alcippe morrisonia) and the red-headed tree babbler (Stachyridopsis ruficeps).

    Location: East Asia.

    Methods: We studied the genetic structure based on mitochondrial and nuclear DNA and evaluated the phylogeographical lineages using coalescent species tree approaches. The influences of different historical processes on diversification among phylogeographical lineages were analysed using coalescent models. We tested correlations between ecological divergence and phylogeographical splits.

    Results: The genetic structure analysis and species tree estimation revealed three deeply divergent lineages within both species. One lineage is endemic to the mountains of Southwest China and the other to Taiwan. Coalescent simulations suggested that lineage diversification mostly occurred during the late Pliocene. Within this time frame, uplift of the mountains of Southwest China and formation of the island of Taiwan are geological events consistent with the geographical isolation and ecological niche divergence of these phylogeographical lineages.

    Main conclusions: Our results suggest that the main driver of avian endemism in East Asia was the formation of new montane and island habitats following the uplift of the mountains of Southwest China and formation of the island of Taiwan in the Pliocene. However, the populations in the two regions were affected differently by the climatic oscillations during the Pleistocene. The mountains of Southwest China were climatically stable during glaciations,allowing populations to persist throughout the Pleistocene and maintain their genetic uniqueness. In contrast, glaciations resulted in lowered sea levels, allowing dispersal between the island of Taiwan and mainland China, thus obscuring the genetic endemism of the Taiwanese populations.

  • 1342.
    Qu, Yanhua
    et al.
    Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China.
    Tian, Shilin
    Han, Nanjian
    Zhao, Hongwei
    Gao, Bin
    Fu, Jun
    Cheng, Yalin
    Song, Gang
    Ericson, Per G P
    Naturhistoriska riksmuseet, Forskningsavdelningen centralt.
    Zhang, Yong E.
    Wang, Dawei
    Quan, Qing
    Jiang, Zhi
    Li, Ruiquang
    Lei, Fumin
    Genetic responses to seasonalvariation in altitudinal stress: whole-genome resequencing ofgreat tit in eastern Himalayas2015Inngår i: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 5, artikkel-id 14256Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Species that undertake altitudinal migrations are exposed to a considerable seasonal variationin oxygen levels and temperature. How they cope with this was studied in a population of greattit (Parus major) that breeds at high elevations and winters at lower elevations in the easternHimalayas. Comparison of population genomics of high altitudinal great tits and those living inlowlands revealed an accelerated genetic selection for carbohydrate energy metabolism (aminosugar, nucleotide sugar metabolism and insulin signaling pathways) and hypoxia response (PI3K-akt,mTOR and MAPK signaling pathways) in the high altitudinal population. The PI3K-akt, mTOR andMAPK pathways modulate the hypoxia-inducible factors, HIF-1α and VEGF protein expression thusindirectly regulate hypoxia induced angiogenesis, erythropoiesis and vasodilatation. The strategiesobserved in high altitudinal great tits differ from those described in a closely related species onthe Tibetan Plateau, the sedentary ground tit (Parus humilis). This species has enhanced selectionin lipid-specific metabolic pathways and hypoxia-inducible factor pathway (HIF-1). Comparativepopulation genomics also revealed selection for larger body size in high altitudinal great tits.

  • 1343.
    Qu, Yanhua
    et al.
    Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China.
    Zhao, Hongwei
    Han, Naijian
    Zhou, Guangyu
    Song, Gang
    Gao, Bin
    Tian, Shilin
    Zhang, Jinbo
    Zhang, Ruiying
    Meng, Xuehong
    Zhang, Yuan
    Zhang, Yong
    Zhu, Xiaojia
    Wang, Wenjuan
    Lambert, David
    Ericson, Per G P
    Naturhistoriska riksmuseet, Forskningsavdelningen centralt.
    Subramanian, Sankar
    Yeung, Carol
    Zhu, Hongmei
    Jiang, Zhi
    Li, Ruiqiang
    Lei, Fumin
    Ground tit genome reveals avian adaptation to living at high altitudes in the Tibetan plateau.2013Inngår i: Nature communications, ISSN 2041-1723, Vol. 4, s. 2071-Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    The ground tit (Parus humilis) is endemic to the Tibetan plateau. It is a member of family Paridae but it was long thought to be related to the ground jays because of their morphological similarities. Here we present the ground tit's genome and re-sequence two tits and one ground jay, to clarify this controversially taxonomic status and uncover its genetic adaptations to the Tibetan plateau. Our results show that ground tit groups with two tits and it diverges from them between 7.7 and 9.9 Mya. Compared with other avian genomes, ground tit shows expansion in genes linked to energy metabolism and contractions in genes involved in immune and olfactory perception. We also found positively selected and rapidly evolving genes in hypoxia response and skeletal development. These results indicated that ground tit evolves basic strategies and 'tit-to-jay' change for coping with the life in an extreme environment.

  • 1344.
    Qvarnström, Anna
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Zooekologi.
    Rudh, Andreas
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Zooekologi.
    Edström, Torkel
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Zooekologi.
    Ödeen, Anders
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Zooekologi.
    Lovlie, Hanne
    Tullberg, Birgitta S.
    Coarse Dark Patterning Functionally Constrains Adaptive Shifts from Aposematism to Crypsis in Strawberry Poison Frogs2014Inngår i: Evolution, ISSN 0014-3820, E-ISSN 1558-5646, Vol. 68, nr 10, s. 2793-2803Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Ecological specialization often requires tight coevolution of several traits, which may constrain future evolutionary pathways and make species more prone to extinction. Aposematism and crypsis represent two specialized adaptations to avoid predation. We tested whether the combined effects of color and pattern on prey conspicuousness functionally constrain or facilitate shifts between these two adaptations. We combined data from 17 natural populations of strawberry poison frogs, Oophaga pumilio with an experimental approach using digitalized images of frogs and chickens as predators. We show that bright coloration often co-occurs with coarse patterning among the natural populations. Dull green frogs with coarse patterning are rare in nature but in the experiment they were as easily detected as bright red frogs suggesting that this trait combination represents a transient evolutionary state toward aposematism. Hence, a gain of either bright color or coarse patterning leads to conspicuousness, but a transition back to crypsis would be functionally constrained in populations with both bright color and coarse patterning by requiring simultaneous changes in two traits. Thus, populations (or species) signaling aposematism by conspicuous color should be less likely to face an evolutionary dead end and more likely to radiate than populations with both conspicuous color and coarse patterning.

  • 1345.
    Qvarnström, Anna
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Zooekologi.
    Ålund, Murielle
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Zooekologi.
    McFarlane, Eryn S.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Zooekologi.
    Sirkiä, Päivi M.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Zooekologi.
    Climate adaptation and speciation: particular focus on reproductive barriers in Ficedula flycatchers2015Inngår i: Evolutionary Applications, ISSN 1752-4571, E-ISSN 1752-4571, Vol. 9, nr 1, s. 119-134Artikkel, forskningsoversikt (Fagfellevurdert)
    Abstract [en]

    Climate adaptation is surprisingly rarely reported as a cause for the build-up of reproductive isolation between diverging populations. In this review, we summarize evidence for effects of climate adaptation on pre- and postzygotic isolation between emerging species with a particular focus on pied (Ficedula hypoleuca) and collared (Ficedula albicollis) flycatchers as a model for research on speciation. Effects of climate adaptation on prezygotic isolation or extrinsic selection against hybrids have been documented in several taxa, but the combined action of climate adaptation and sexual selection is particularly well explored in Ficedula flycatchers. There is a general lack of evidence for divergent climate adaptation causing intrinsic postzygotic isolation. However, we argue that the profound effects of divergence in climate adaptation on the whole biochemical machinery of organisms and hence many underlying genes should increase the likelihood of genetic incompatibilities arising as side effects. Fast temperature-dependent co-evolution between mitochondrial and nuclear genomes may be particularly likely to lead to hybrid sterility. Thus, how climate adaptation relates to reproductive isolation is best explored in relation to fast-evolving barriers to gene flow, while more research on later stages of divergence is needed to achieve a complete understanding of climate-driven speciation.

  • 1346.
    Qvarnström, Martin
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Geovetenskapliga sektionen, Institutionen för geovetenskaper.
    Palaeoenvironments of the Earliest (Middle Devonian) Tetrapod Trackways from the Holy Cross Mountains, Poland;Locomotion in a Terrestrial Setting?2015Independent thesis Advanced level (degree of Master (Two Years)), 30 poäng / 45 hpOppgave
    Abstract [en]

    The palaeoenvironment from which early tetrapods emerged is crucial to comprehend in order to understand the mechanisms that drove and allowed the terrestrialization of vertebrates; one of the most important evolutionary ‘events’ in the history of animals. Nevertheless, much of the terrestrialization is shrouded in obscurity, inter alia, due to scarcity of early tetrapods in the fossil record. Each new discovery of anything linked to vertebrate terrestrialization is therefore of great importance. Here, I present new detailed analyses of the palaeoenvironmental conditions at the time of formation of the earliest (early Middle Devonian) tetrapod trackways found in the Zachełmie Quarry in the Holy Cross Mountains of southern Poland. The trackways are found in three horizons in a clay-rich dolomitic succession represented by the Lower Complex of the Wojciechowice Formation. This Lower Complex is composed of short shallowing upward sequences that often terminate with desiccation cracks and/or paleosols. Vertically fluctuating δ18O values in the complex suggest multiple episodes of closed hydrological systems. A model of ephemeral to perennial lakes in a terrestrial setting is therefore proposed. Such environment is in concordance with evidence of scarce bioturbation and a flourish of microbial communities that, in contrast to a normal marine setting, most likely represent an ecologically stressed ecosystem. Furthermore: non-marine rare earth element (REE) signals, desiccation events, fossils of green algae (charophytes), paleosol development, low energy cyclic deposits and general lack of marine taxa in the body and trace fossil records in this complex firmly establishes the interpretation of palustrine carbonates formed in a lacustrine-like setting. However, in the lower part of the complex, some highly fractioned marine fossils occur. These are suggested to have been transported during wash-up events which temporally places the setting in marine proximity. Seasons of monsoonal rainfall resulted in erosion and influx of detrital grains which is evidenced by fine planar lamination (of seasonal cyclicity) in most of the sediments and occasional occurrence of blackened clasts (and rain-drop imprints).Thus, none of the pre-existing palaeoenvironmental hypotheses of tetrapod emergence are in full concordance with the data from the Zachełmie Quarry. Instead, a new palaeoenvironment is proposed for the earliest tetrapods: schizohaline ephermal to perennial lakes with periodic desiccation. This infers that already in the early Middle Devonian, tetrapods had conquered the terrestrial realm and were perhaps already capable of terrestrial locomotion over quite substantial distances.

  • 1347.
    Qvarnström, Martin
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för organismbiologi, Evolution och utvecklingsbiologi.
    Niedzwiedzki, Grzegorz
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för organismbiologi, Evolution och utvecklingsbiologi.
    Zigaite, Zivile
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för organismbiologi, Evolution och utvecklingsbiologi.
    Vertebrate coprolites (fossil faeces): An underexplored Konservat-Lagerstatte2016Inngår i: Earth-Science Reviews, ISSN 0012-8252, E-ISSN 1872-6828, Vol. 162, s. 44-57Artikkel, forskningsoversikt (Fagfellevurdert)
    Abstract [en]

    Fossilized soft tissues of animals (e.g. muscles, hair and feathers) are valuable sources of palaeobiological information, but a poor preservation potential makes them undesirably scarce in the fossil record. The aim of this review is to summarize main findings, current progress and the analytical constraints of detecting fossilized soft tissues in coprolites from, mainly, freshwater and terrestrial carnivorous vertebrates. We conclude that soft-tissue inclusions in coprolites are sources of two important lines of information: the fossils can be put in a direct palaeoecological context, and characters of extinct taxa are more likely preserved in the phosphate-rich taphonomic microenvironment of coprolites than elsewhere. As a result, it is possible to unravel the deep-time origins of host-parasite relations, to understand ancient trophic food webs and detect new soft-tissue characters of different animal groups. Examples of the latter include muscle tissues from a tyrannosaurid prey, tapeworm eggs (including a developing embryo) in a Permian shark coprolite, as well as hair from multituberculates and, probably, from stem-mammals (Therapsids). Additionally, the use of coprolites in an archaeological context is briefly reviewed with focus on key aspects that may become implemented in studies of pre-Quaternary specimens as well. In summary, there is a wide range of information that can be extracted from coprolites, which has not yet been fully explored in palaeontological studies.

  • 1348.
    Qvarnström, Martin
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för organismbiologi, Evolution och utvecklingsbiologi.
    Szrek, Piotr
    Natl Res Inst, Polish Geol Inst, Rakowiecka 4 St, PL-00075 Warsaw, Poland..
    Ahlberg, Per E.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för organismbiologi, Evolution och utvecklingsbiologi.
    Niedzwiedzki, Grzegorz
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för organismbiologi, Evolution och utvecklingsbiologi.
    Non-marine palaeoenvironment associated to the earliest tetrapod tracks2018Inngår i: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 8, artikkel-id 1074Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Opinions differ on whether the evolution of tetrapods (limbed vertebrates) from lobe-finned fishes was directly linked to terrestrialization. The earliest known tetrapod fossils, from the Middle Devonian (approximately 390 million years old) of Zachelmie Quarry in Poland, are trackways made by limbs with digits; they document a direct environmental association and thus have the potential to help answer this question. However, the tetrapod identity of the tracks has recently been challenged, despite their well-preserved morphology, on account of their great age and supposedly shallow marine (intertidal or lagoonal) depositional environment. Here we present a new palaeoenvironmental interpretation of the track-bearing interval from Zachelmie, showing that it represents a succession of ephemeral lakes with a restricted and non-marine biota, rather than a marginal marine environment as originally thought. This context suggests that the trackmaker was capable of terrestrial locomotion, consistent with the appendage morphology recorded by the footprints, and thus provides additional support for a tetrapod identification.

  • 1349.
    Radosavljevic, Sonja
    Linköpings universitet, Matematiska institutionen, Matematik och tillämpad matematik. Linköpings universitet, Tekniska fakulteten.
    Permanence of age-structured populations in a spatio-temporal variable environment2016Doktoravhandling, med artikler (Annet vitenskapelig)
    Abstract [en]

    It is widely recognized that various biotic and abiotic factors cause changes in the size of a population and its age distribution. Population structure, intra-specific competition, temporal variability and spatial heterogeneity are identified as the most important factors that, alone or in combination, influence population dynamics. Despite being well-known, these factors are difficult to study, both theoretically and empirically. However, in an increasingly variable world, permanence of a growing number of species is threatened by climate changes, habitat fragmentation or reduced habitat quality. For purposes of conservation of species and land management, it is crucially important to have a good analysis of population dynamics, which will increase our theoretical knowledge and provide practical guidelines.

    One way to address the problem of population dynamics is to use mathematical models. The choice of a model depends on what we want to study or what we aim to achieve. For an extensive theoretical study of population processes and for obtaining qualitative results about population growth or decline, analytical models with various level of complexity are used. The competing interests of realism and solvability of the model are always present. This means that, on one hand, we always aim to make a model that will truthfully reflect reality, while on the other hand, we need to keep the model mathematically solvable. This prompts us to carefully choose the most prominent ecological factors relevant to the problem at hand and to incorporate them into a model. Ideally, the results give new insights into population processes and complex interactions between the mentioned factors and population dynamics.

    The objective of the thesis is to formulate, analyze, and apply various mathematical models of population dynamics. We begin with a classical linear age-structured model and gradually add temporal variability, intra-specific competition and spatial heterogeneity. In this way, every subsequent model is more realistic and complex than the previous one. We prove existence and uniqueness of a nonnegative solution to each boundary-initial problem, and continue with investigation of the large time behavior of the solution.

    In the ecological terms, we are establishing conditions under which a population can persist in a certain environment. Since our aim is a qualitative analysis of a solution, we often examine upper and lower bounds of a solution. Their importance is in the fact that they are obtained analytically and parameters in their expression have biological meaning. Thus, instead of analyzing an exact solution (which often proves to be difficult), we analyze the corresponding upper and lower solutions.

    We apply our models to demonstrate the influence of seasonal changes (or some other periodic temporal variation) and spatial structure of the habitat on population persistence. This is particularly important in explaining behavior of migratory birds or populations that inhabits several patches, some of which are of low quality. Our results extend the previously obtained results in some aspects and point out that all factors (age structure, density dependence, spatio-temporal variability) need to be considered when setting up a population model and predicting population growth.

  • 1350.
    Raff, Elizabeth C.
    et al.
    Department of Biology and Indiana Molecular Biology Institute, Indiana University, Bloomington, IN .
    Schollaert, Kaila L.
    Department of Biology and Indiana Molecular Biology Institute, Indiana University, Bloomington, IN .
    Nelson, David E.
    Department of Biology and Indiana Molecular Biology Institute, Indiana University, Bloomington, IN .
    Donoghue, Philip C. J.
    Department of Earth Sciences, University of Bristol, Bristol BS8 1RJ, United Kingdom.
    Thomas, Ceri-Wyn
    Department of Earth Sciences, University of Bristol, Bristol BS8 1RJ, United Kingdom.
    Turner, F. Rudolf
    Department of Biology and Indiana Molecular Biology Institute, Indiana University, Bloomington, IN .
    Stein, Barry D.
    Department of Biology and Indiana Molecular Biology Institute, Indiana University, Bloomington, IN .
    Dong, Xiping
    Department of Earth and Space Sciences, Peking University, Beijing 100871, Peoples Republic of China.
    Bengtson, Stefan
    Department of Palaeozoology, Swedish Museum of Natural History, SE-104 05 Stockholm, Sweden.
    Huldtgren, Therese
    Department of Geology and Geochemistry, Stockholm University, SE-106 91 Stockholm, Sweden.
    Embryo fossilization is a biological process mediated by microbial biofilms2008Inngår i: Proceedings of the National Academy of Sciences, Vol. 105, nr 49, s. 19360-19365Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Fossilized embryos with extraordinary cellular preservation appear in the Late Neoproterozoic and Cambrian, coincident with the appearance of animal body fossils. It has been hypothesized that microbial processes are responsible for preservation and mineralization of organic tissues. However, the actions of microbes in preservation of embryos have not been demonstrated experimentally. Here, we show that bacterial biofilms assemble rapidly in dead marine embryos and form remarkable pseudomorphs in which the bacterial biofilm replaces and exquisitely models details of cellular organization and structure. The experimental model was the decay of cleavage stage embryos similar in size and morphology to fossil embryos. The data show that embryo preservation takes place in 3 distinct steps: (i) blockage of autolysis by reducing or anaerobic conditions, (ii) rapid formation of microbial biofilms that consume the embryo but form a replica that retains cell organization and morphology, and (iii) bacterially catalyzed mineralization. Major bacterial taxa in embryo decay biofilms were identified by using 16S rDNA sequencing. Decay processes were similar in different taphonomic conditions, but the composition of bacterial populations depended on specific conditions. Experimental taphonomy generates preservation states similar to those in fossil embryos. The data show how fossilization of soft tissues in sediments can be mediated by bacterial replacement and mineralization, providing a foundation for experimentally creating biofilms from defined microbial species to model fossilization as a biological process.

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