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  • 101.
    Lindenfors, Patrik
    et al.
    Stockholm University, Faculty of Science, Department of Zoology, Animal Ecology. Stockholm University, Faculty of Humanities, Centre for the Study of Cultural Evolution.
    Jansson, Fredrik
    Stockholm University, Faculty of Humanities, Centre for the Study of Cultural Evolution.
    Sandberg, Mikael
    Stockholm University, Faculty of Humanities, Centre for the Study of Cultural Evolution.
    The cultural evolution of democracy: saltational changes in a political regime landscape2011In: PLoS ONE, ISSN 1932-6203, E-ISSN 1932-6203, Vol. 6, no 11, p. e28270-Article in journal (Refereed)
    Abstract [en]

    Transitions to democracy are most often considered the outcome of historical modernization processes. Socio-economicchanges, such as increases in per capita GNP, education levels, urbanization and communication, have traditionally been found to be correlates or ‘requisites’ of democratic reform. However, transition times and the number of reform steps havenot been studied comprehensively. Here we show that historically, transitions to democracy have mainly occurred throughrapid leaps rather than slow and incremental transition steps, with a median time from autocracy to democracy of 2.4 years,and overnight in the reverse direction. Our results show that autocracy and democracy have acted as peaks in an evolutionary landscape of possible modes of institutional arrangements. Only scarcely have there been slow incremental transitions. We discuss our results in relation to the application of phylogenetic comparative methods in cultural evolutionand point out that the evolving unit in this system is the institutional arrangement, not the individual country which isinstead better regarded as the ‘host’ for the political system.

  • 102.
    Lindenfors, Patrik
    et al.
    Stockholm University, Faculty of Science, Department of Zoology, Animal Ecology. Stockholm University, Faculty of Humanities, Centre for the Study of Cultural Evolution.
    Tullberg, Birgitta
    Stockholm University, Faculty of Science, Department of Zoology, Animal Ecology.
    Evolutionary aspects of aggression: the importance of sexual selection2011In: Aggression / [ed] Robert Huber, Danika L. Bannasch, Patricia Brennan, San Diego: Academic Press, 2011, p. 7-22Chapter in book (Refereed)
    Abstract [en]

    Aggressive behaviors in animals, for example, threat, attack, and defense, arecommonly related to competition over resources, competition over matingopportunities, or fights for survival. In this chapter, we focus on aggressivecompetition over mating opportunities, since this competition explains muchof the distribution of weaponry and large body size, but also because this type ofcompetition sheds light on the sex skew in the use of violence in mammals,including humans. Darwin (1871) termed this type of natural selection, wheredifferences in reproductive success are caused by competition over mates, sexualselection. Not all species have a pronounced competition over mates, however.Instead, this aspect of sociality is ultimately determined by ecological factors. 

    In species where competition over mates is rampant, this has evolutionary effectson weaponry and body size such that males commonly bear more vicious weaponsand are larger than females. A review of sexual selection in mammals reveals howcommon aggressive competition over mating opportunities is in this group.Nearly half of all mammal species exhibit male-biased sexual size dimorphism,a pattern that is clearly linked to sexual selection. Sexual selection is alsocommon in primates, where it has left clear historical imprints in body massdifferences, in weaponry differences (canines), and also in brain structure differences.However, when comparing humans to our closest living primate relatives,it is clear that the degree of male sexual competition has decreased in thehominid lineage. Nevertheless, our species displays dimorphism, polygyny, andsex-specific use of violence typical of a sexually selected mammal. Understandingthe biological background of aggressive behaviors is fundamental to understandinghuman aggression.

  • 103.
    Lledó, María Dolores
    et al.
    Royal Botanic Gardens, Kew, UK.
    Karis, Per Ola
    Stockholm University, Faculty of Science, Department of Botany.
    Crespo, Manuel B.
    Universidad de Alicante, Spain.
    Fay, Michael F.
    Royal Botanic Gardens, Kew, UK.
    Chase, Mark W.
    Royal Botanic Gardens, Kew, UK.
    Endemism and evolution in Macaronesian and Mediterranean Limonium taxa2011In: The biology of island floras / [ed] David Bramwell & Juli Caujapé-Castells, Cambridge University Press, 2011, p. 325-337Chapter in book (Other academic)
    Abstract [en]

    The study of plant speciation on oceanic islands has improved enormously with the help of molecular systematics. Studies have targeted groups present on both the mainland and islands with the aim of understanding plant migration and evolution in isolation. In addition, relatively young volcanic islands give the opportunity to place the evolutionary process in a time frame, by dating molecular trees according to the age of the islands or by relying on the fossil record. Molecular phylogenetics can also be valuable in helping to reconstruct character evolution and understand the syndrome of characters diagnosing oceanic species.

    Frontmatter:

    •  Read PDF

    pp. i-ivContents:

    •  Read PDF

    pp. v-viiContributors:

    •  Read PDF

    pp. viii-xiiPreface:

    •  Read PDF

    pp. xiii-xvi1 - Introduction: islands and plants:

    •  Read PDF

    By David Bramwellpp. 1-102 - The reproductive biology of island plants:

    •  Read PDF

    By Daniel J. Crawford, Gregory J. Anderson and Gabriel Bernardellopp. 11-363 - Spatial methodologies in historical biogeography of islands:

    •  Read PDF

    By Paula Posadas, Jorge V. Crisci and Liliana Katinaspp. 37-564 - Origin and evolution of Hawaiian endemics: new patterns revealed by molecular phylogenetic studies:

    •  Read PDF

    By Sterling C. Keeley and Vicki A. Funkpp. 57-885 - Origins and evolution of Galapagos endemic vascular plants:

    •  Read PDF

    By Alan Tye and Javier Francisco-Ortegapp. 89-1536 - The plants of the Caribbean islands: a review of the biogeography, diversity and conservation of a storm-battered biodiversity hotspot:

    •  Read PDF

    By Michael Maunder et al.pp. 154-1787 - The biogeography of Madagascar palms:

    •  Read PDF

    By John Dransfield and Mijoro Rakotoarinivopp. 179-1968 - Evolution and

  • 104.
    Løvlie, Hanne
    et al.
    Stockholm University, Faculty of Science, Department of Zoology. University of Oxford, England.
    Gillingham, Mark A. F.
    Worley, Kirsty
    Pizzari, Tommaso
    Richardson, David S.
    Cryptic female choice favours sperm from major histocompatibility complex-dissimilar males2013In: Proceedings of the Royal Society of London. Biological Sciences, ISSN 0962-8452, E-ISSN 1471-2954, Vol. 280, no 1769, article id 20131296Article in journal (Refereed)
    Abstract [en]

    Cryptic female choice may enable polyandrous females to avoid inbreeding or bias offspring variability at key loci after mating. However, the role of these genetic benefits in cryptic female choice remains poorly understood. Female red junglefowl, Gallus gallus, bias sperm use in favour of unrelated males. Here, we experimentally investigate whether this bias is driven by relatedness per se, or by similarity at the major histocompatibility complex (MHC), genes central to vertebrate acquired immunity, where polymorphism is critical to an individual's ability to combat pathogens. Through experimentally controlled natural matings, we confirm that selection against related males' sperm occurs within the female reproductive tract but demonstrate that this is more accurately predicted by MHC similarity: controlling for relatedness per se, more sperm reached the eggs when partners were MHC-dissimilar. Importantly, this effect appeared largely owing to similarity at a single MHC locus (class I minor). Further, the effect of MHC similarity was lost following artificial insemination, suggesting that male phenotypic cues might be required for females to select sperm differentially. These results indicate that postmating mechanisms that reduce inbreeding may do so as a consequence of more specific strategies of cryptic female choice promoting MHC diversity in offspring.

  • 105.
    Maklakov, Alexei
    et al.
    Uppsala Universitet.
    Immler, Simone
    Uppsala Universitet.
    Gonzalez-Voyer, Alejandro
    Rönn, Johanna
    Uppsala universitet.
    Kolm, Niclas
    Brains and the city: big-brained passerine birds succeed in urban environments2011In: Biology Letters, ISSN 1744-9561, E-ISSN 1744-957X, Vol. 7, no 5, p. 730-732Article in journal (Refereed)
    Abstract [en]

    Urban regions are among the most human-altered environments on Earth and they are poised for rapid expansion following population growth and migration. Identifying the biological traits that determine which species are likely to succeed in urbanized habitats is important for predicting global trends in biodiversity. We provide the first evidence for the intuitive yet untested hypothesis that relative brain size is a key factor predisposing animals to successful establishment in cities. We apply phylogenetic mixed modelling in a Bayesian framework to show that passerine species that succeed in colonizing at least one of 12 European cities are more likely to belong to big-brained lineages than species avoiding these urban areas. These data support findings linking relative brain size with the ability to persist in novel and changing environments in vertebrate populations, and have important implications for our understanding of recent trends in biodiversity.

  • 106. Masahito, Tsuboi
    et al.
    van der Bijl, Wouter
    Stockholm University, Faculty of Science, Department of Zoology.
    Kopperud, Bjørn Tore
    Erritzøe, Johannes
    Voje, Kjetil L.
    Kotrschal, Alexander
    Stockholm University, Faculty of Science, Department of Zoology.
    Yopak, Kara E.
    Collin, Shaun P.
    Hansen, Thomas F.
    Iwaniuk, Andrew
    Kolm, Niclas
    Stockholm University, Faculty of Science, Department of Zoology.
    Breakdown of brain-body allometry and the exceptional encephalization of mammals and birdsManuscript (preprint) (Other academic)
  • 107. Mayer, Georg
    et al.
    Hering, Lars
    Stosch, Juliane M.
    Stevenson, Paul A.
    Dircksen, Heinrich
    Stockholm University, Faculty of Science, Department of Zoology, Functional Morphology.
    Evolution of pigment-dispersing factor neuropeptides in panarthropoda: Insights from onychophora (Velvet Worms) and tardigrada (Water Bears)2015In: Journal of Comparative Neurology, ISSN 0021-9967, E-ISSN 1096-9861, Vol. 523, no 13, p. 1865-1885Article in journal (Refereed)
    Abstract [en]

    Pigment-dispersing factor (PDF) denotes a conserved family of homologous neuropeptides present in several invertebrate groups, including mollusks, nematodes, insects and crustaceans (referred to here as pigment-dispersing hormone, PDH). Regarding their encoding genes (pdf, pdh), insects possess only one, nematodes two, and decapod crustaceans up to three, but their phylogenetic relationship is unknown. To shed light on the origin and diversification of pdf/pdh homologs in Panarthropoda (Onychophora + Tardigrada + Arthropoda) and other molting animals (Ecdysozoa), we analyzed the transcriptomes of five distantly related onychophorans and a representative tardigrade and searched for putative pdf homologs in publically available genomes of other protostomes. This revealed only one pdf homolog in several mollusk and annelid species, two in Onychophora, Priapulida and Nematoda, and three in Tardigrada. Phylogenetic analyses suggest that the last common ancestor of Panarthropoda possessed two pdf homologs, one of which was lost in the arthropod or arthropod/tardigrade lineage, followed by subsequent duplications of the remaining homolog in some taxa. Immunolocalization of PDF-like peptides in six onychophoran species, using a broadly reactive antibody that recognizes PDF/PDH peptides in numerous species, revealed an elaborate system of neurons and fibers in their central and peripheral nervous systems. Large varicose projections in the heart suggest that the PDF neuropeptides functioned as both circulating hormones and locally released transmitters in the last common ancestor of Onychophora and Arthropoda. The lack of PDF-like immunoreactive somata associated with the onychophoran optic ganglion conforms to the hypothesis that onychophoran eyes are homologous to the arthropod median ocelli.

  • 108. McDade, Lucinda A.
    et al.
    Daniel, Thomas F.
    Kiel, Carrie A.
    Borg, Agneta Julia
    Stockholm University, Faculty of Science, Department of Botany.
    Phylogenetic placement, delimitation, and relationships among genera of the enigmatic Nelsonioideae (Lamiales: Acanthaceae)2012In: Taxon, ISSN 0040-0262, E-ISSN 1996-8175, Vol. 61, no 3, p. 637-651Article in journal (Refereed)
    Abstract [en]

    We took a two-tiered approach to test monophyly of Nelsonioideae and place the group within Lamiales, and to determine relationships among taxa within the group. Phylogenetic analysis of a molecular dataset (ndhF+trnL-F) for a broad sample of Lamiales supports monophyly of Nelsonioideae and places the clade with strong support as sister to a lineage composed of all other plants treated as Acanthaceae (Avicennia, Thunbergioideae, Acanthoideae). We propose to treat this entire group as Acanthaceae s.l. and hypothesize that indurate, explosively dehiscent capsules are a synapomorphy for the family, albeit with autapomorphic fruit types in Avicennia and Mendoncia. These results further support monophyly of family-level groups that have emerged from recent studies of Lamiales but are largely unsuccessful in resolving relationships among these groups, as also encountered by other workers. Our results contradict some aspects of relationships that have seemed resolved by earlier studies, notably among Byblidaceae, Scrophulariaceae, Thomandersia, and other Lamiales. Among Nelsonioideae, analysis of sequence data from rapidly evolving genic regions (trnS-G, ndhF-rpl32+rpl32-trnL((UAG)), nrITS) and a larger sample of nelsonioids (i.e., all genera and multiple taxa to represent the diversity of species-rich genera) indicates that Nelsonia and Elytraria are monophyletic with strong support, but with only moderate support for Nelsonia as the first branching clade and Elytraria sister to the remaining nelsonioids. An African clade comprising monospecific Saintpauliopsis sister to Anisosepalum (two of three species sampled) is sister to a clade that includes all sampled members of pantropical Staurogyne plus New World Gynocraterium and Asian Ophiorrhiziphyllon. Gynocraterium is sister to all sampled members of New World Staurogyne; this last clade is sister to a clade comprising the other sampled Staurogyne plus Ophiorrhiziphyllon, which is nested among Asian Staurogyne. The taxonomic implications of these patterns of relationship are discussed. Our results suggest that Nelsonioideae have a complex history of inter-continental dispersals compared to other lineages of Acanthaceae of similar to much larger size in terms of number of species, making it an interesting group for biogeographic study.

  • 109. Mellows, Andrew
    et al.
    Barnett, Ross
    Dalen, Love
    Sandoval Castellanos, Edson
    Stockholm University, Faculty of Science, Department of Zoology, Systematic Zoology.
    Linderholm, Anna
    McGovern, Thomas H.
    Church, Mike J.
    Larson, Greger
    The impact of past climate change on genetic variation and population connectivity in the Icelandic arctic fox2012In: Proceedings of the Royal Society of London. Biological Sciences, ISSN 0962-8452, E-ISSN 1471-2954, Vol. 279, no 1747, p. 4568-4573Article in journal (Refereed)
    Abstract [en]

    Previous studies have suggested that the presence of sea ice is an important factor in facilitating migration and determining the degree of genetic isolation among contemporary arctic fox populations. Because the extent of sea ice is dependent upon global temperatures, periods of significant cooling would have had a major impact on fox population connectivity and genetic variation. We tested this hypothesis by extracting and sequencing mitochondrial control region sequences from 17 arctic foxes excavated from two late-ninth-century to twelfth-century AD archaeological sites in northeast Iceland, both of which predate the Little Ice Age (approx. sixteenth to nineteenth century). Despite the fact that five haplotypes have been observed in modern Icelandic foxes, a single haplotype was shared among all of the ancient individuals. Results from simulations within an approximate Bayesian computation framework suggest that the rapid increase in Icelandic arctic fox haplotype diversity can only be explained by sea-ice-mediated fox immigration facilitated by the Little Ice Age.

  • 110. Mendez, Martin
    et al.
    Jefferson, Thomas A.
    Kolokotronis, Sergios-Orestis
    Kruetzen, Michael
    Parra, Guido J.
    Collins, Tim
    Minton, Giana
    Baldwin, Robert
    Berggren, Per
    Särnblad, Anna
    Stockholm University, Faculty of Science, Department of Zoology.
    Amir, Omar A.
    Peddemors, Vic M.
    Karczmarski, Leszek
    Guissamulo, Almeida
    Smith, Brian
    Sutaria, Dipani
    Amato, George
    Rosenbaum, Howard C.
    Integrating multiple lines of evidence to better understand the evolutionary divergence of humpback dolphins along their entire distribution range: a new dolphin species in Australian waters?2013In: Molecular Ecology, ISSN 0962-1083, E-ISSN 1365-294X, Vol. 22, no 23, p. 5936-5948Article in journal (Refereed)
    Abstract [en]

    The conservation of humpback dolphins, distributed in coastal waters of the Indo-West Pacific and eastern Atlantic Oceans, has been hindered by a lack of understanding about the number of species in the genus (Sousa) and their population structure. To address this issue, we present a combined analysis of genetic and morphologic data collected from beach-cast, remote-biopsied and museum specimens from throughout the known Sousa range. We extracted genetic sequence data from 235 samples from extant populations and explored the mitochondrial control region and four nuclear introns through phylogenetic, population-level and population aggregation frameworks. In addition, 180 cranial specimens from the same geographical regions allowed comparisons of 24 morphological characters through multivariate analyses. The genetic and morphological data showed significant and concordant patterns of geographical segregation, which are typical for the kind of demographic isolation displayed by species units, across the Sousa genus distribution range. Based on our combined genetic and morphological analyses, there is convincing evidence for at least four species within the genus (S.teuszii in the Atlantic off West Africa, S.plumbea in the central and western Indian Ocean, S.chinensis in the eastern Indian and West Pacific Oceans, and a new as-yet-unnamed species off northern Australia).

  • 111.
    Metz, Hans
    et al.
    Leiden University.
    Leimar, Olof
    Stockholm University, Faculty of Science, Department of Zoology.
    A simple fitness proxy for structured populations with continuous traits, with case studies on the evolution of haplo-diploids and genetic dimorphisms2011In: Journal of Biological Dynamics, ISSN 1751-3758, E-ISSN 1751-3766, Vol. 5, no 2, p. 163-190Article in journal (Refereed)
    Abstract [en]

    For structured populations in equilibrium with everybody born equal ln(R0) is a useful fitness proxy for ESS and most adaptive dynamics calculations, with R0 the average lifetime number of offspring in the clonal and haploid cases, and half the average lifetime number of offspring fathered or mothered for Mendelian diploids. When individuals have variable birth states, as is e.g. the case in spatial models, R0 is itself an eigenvalue, which usually cannot be expressed explicitly in the trait vectors under consideration. In that case Q(Y | X ) := - det (I - L(Y | X )) can often be used as fitness proxy, with L the next-generation matrix for a potential mutant characterised by the trait vector Y in the (constant) environment engendered by a resident characterised by X . If the trait space is connected, global univadability can be determined from it. Moreover it can be used in all the usual local calculations like the determination of evolutionarily singular trait vectors and their local invadability and attractivity.

    We conclude with three extended case studies demonstrating the usefulness of Q: the calculation of ESSes under haplo-diploid genetics (I), of Evolutionarily Steady genetic Dimorphisms with a priori proportionality of macro- and micro-gametic outputs (an assumption that is generally made but the fulfilment of which is a priori highly exceptional) (II), and of ESDs without such proportionality (III). These case studies should also have some interest in their own right for the spelled out calculation recipes and their underlying modelling methodology. 

  • 112. Neel, M. C.
    et al.
    McKelvey, K.
    Ryman, Nils
    Stockholm University, Faculty of Science, Department of Zoology.
    Lloyd, M. W.
    Bull, R. Short
    Allendorf, F. W.
    Schwartz, M. K.
    Waples, R. S.
    Estimation of effective population size in continuously distributed populations: there goes the neighborhood2013In: Heredity, ISSN 0018-067X, E-ISSN 1365-2540, Vol. 111, no 3, p. 189-199Article in journal (Refereed)
    Abstract [en]

    Use of genetic methods to estimate effective population size (N-e) is rapidly increasing, but all approaches make simplifying assumptions unlikely to be met in real populations. In particular, all assume a single, unstructured population, and none has been evaluated for use with continuously distributed species. We simulated continuous populations with local mating structure, as envisioned by Wright's concept of neighborhood size (NS), and evaluated performance of a single-sample estimator based on linkage disequilibrium (LD), which provides an estimate of the effective number of parents that produced the sample (N-b). Results illustrate the interacting effects of two phenomena, drift and mixture, that contribute to LD. Samples from areas equal to or smaller than a breeding window produced estimates close to the NS. As the sampling window increased in size to encompass multiple genetic neighborhoods, mixture LD from a two-locus Wahlund effect overwhelmed the reduction in drift LD from incorporating offspring from more parents. As a consequence, (N) over cap (b) never approached the global N-e, even when the geographic scale of sampling was large. Results indicate that caution is needed in applying standard methods for estimating effective size to continuously distributed populations.

  • 113.
    Neethiraj, Ramprasad
    Stockholm University, Faculty of Science, Department of Zoology.
    Advances in studying the role of genetic divergence and recombination in adaptation in non-model species2019Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    Understanding the role of genetic divergence and recombination in adaptation is crucial to understanding the evolutionary potential of species since they can directly affect the levels of genetic variation present within populations or species. Genetic variation in the functional parts of the genome such as exons or regulatory regions is the raw material for evolution, because natural selection can only operate on phenotypic variation already present in the population. When natural selection acts on a phenotype, it usually results in reduction in the levels of genetic variation at the causal loci, and the surrounding linked loci, due to recombination dynamics (i.e. linkage); the degree to which natural selection influences the genetic differentiation in the linked regions depends on the local recombination rates.

    Studies investigating the role of genetic divergence and recombination are common in model species such as Drosophila melanogaster. Only recently have genomic tools allowed us to start investigating their role in shaping genetic variation in non-model species. This thesis adds to the growing research in that domain. In this thesis, I have asked a diverse set of questions to understand the role of genetic divergence and recombination in adaptation in non-model species, with a focus on Lepidoptera.

    First, how do we identify causal genetic variation causing adaptive phenotypes? This question is fundamental to evolutionary biology and addressing it requires a well-assembled genome, the generation of which is a cost, labor, and time intensive task. In paper I, I present a tool, MESPA, that stitches together exonic sequences in fragmented assemblies to produce high-quality gene models. These high-quality gene models can be used by researchers in the downstream analyses, providing genomic insights for a fraction of cost of a high quality genome. 

    Second, what does the pattern of recombination rate look like in chromosomes that lack centromeres (i.e.holocentric chromosomes)? In paper II, I compare the recombination landscape and the patterns of nucleotide diversity in three Lepidotera with holocentric chromosomes, Pieris napi, Bombyx mandarina, and Bombyx mori, with a monocentric species. Our results show that on average these three Lepidoptera have high rates of recombination across the vast majority of their genome. Our results also suggest that given similar effective population sizes, these species are likely to harbor more genetic diversity compared to monocentric species, which has important evolutionary consequences for these species.

    Third, what is the potential for parallelism at the genetic level in convergent melanic phenotypes? In paper III, I investigated the genetic basis of the female-limited melanic phenotype in the green-veined white (Pieris napi) butterfly, and found a 20kb region, approximately 50kb from the gene cortex, associated with this trait. This gene has been implicated in melanic phenotypes in other Lepidoptera that diverged from Pieris approximately 100my, indicating very high predictability for this trait.

    Finally, what is the role of cis-regulatory variation in local adaptation? In paper IV, I analyzed the relationship between allele specific expression (ASE) and genetic divergence (FST) in the F1 hybrids of Pieris napi napi and Pieris napi adalwinda. I show that intersecting results from ASE with FST is a powerful approach to identify genes involved in local adaptation.

  • 114.
    Neethiraj, Ramprasad
    et al.
    Stockholm University, Faculty of Science, Department of Zoology.
    de la Paz Celorio-Mancera, Maria
    Stockholm University, Faculty of Science, Department of Zoology.
    Nylin, Sören
    Stockholm University, Faculty of Science, Department of Zoology.
    Wheat, Christopher
    Stockholm University, Faculty of Science, Department of Zoology.
    Investigating cis-regulatory variation within and between populations reveals significant enrichment of genes in central metabolismManuscript (preprint) (Other academic)
  • 115.
    Neethiraj, Ramprasad
    et al.
    Stockholm University, Faculty of Science, Department of Zoology.
    Nylin, Sören
    Stockholm University, Faculty of Science, Department of Zoology.
    Wheat, Christopher
    Stockholm University, Faculty of Science, Department of Zoology.
    Holocentric chromosomes facilitate recombination and genetic variation in LepidopteraManuscript (preprint) (Other academic)
  • 116.
    Neethiraj, Ramprasad
    et al.
    Stockholm University, Faculty of Science, Department of Zoology.
    Pruisscher, Peter
    Stockholm University, Faculty of Science, Department of Zoology.
    Pruisscher Keehnen, Naomi
    Stockholm University, Faculty of Science, Department of Zoology.
    Woronik, Alyssa
    Gotthard, Karl
    Stockholm University, Faculty of Science, Department of Zoology.
    Nylin, Sören
    Stockholm University, Faculty of Science, Department of Zoology.
    Wheat, Christopher
    Stockholm University, Faculty of Science, Department of Zoology.
    A dark melanic morph of Pieris napi shares its origins with other dark morphs of LepidopteraManuscript (preprint) (Other academic)
  • 117.
    Norberg, Ulf
    et al.
    Stockholm University, Faculty of Science, Department of Zoology.
    Enfjäll, Karin
    Stockholm University, Faculty of Science, Department of Zoology.
    Leimar, Olof
    Stockholm University, Faculty of Science, Department of Zoology.
    Habitat exploration in butterflies - an outdoor cage experiment2002In: Evolutionary ecology, Vol. 16, p. 1-14Article in journal (Refereed)
  • 118.
    Norberg, Ulf
    et al.
    Stockholm University, Faculty of Science, Department of Zoology, Ethology.
    Leimar, Olof
    Stockholm University, Faculty of Science, Department of Zoology, Ethology.
    Spatial and temporal variation in flight morphology in the butterfly Melitaea cixia (Lepidoptera: Nymphalidae)2002In: Biological Journal of the Linnean Society, ISSN 0024-4066, E-ISSN 1095-8312, Vol. 77, p. 445-453Article in journal (Refereed)
  • 119.
    Norbäck Ivarsson, Lena
    Stockholm University, Faculty of Science, Department of Ecology, Environment and Plant Sciences.
    Pollen morphology in Ephedra (Gnetales) and implications for understanding fossil ephedroid pollen from the Tibetan Plateau, using a phylogenetic approach2013Independent thesis Advanced level (degree of Master (Two Years)), 30 credits / 45 HE creditsStudent thesis
  • 120.
    Nylin, Sören
    et al.
    Stockholm University, Faculty of Science, Department of Zoology.
    Slove, Jessica
    Stockholm University, Faculty of Science, Department of Zoology.
    Janz, Niklas
    Stockholm University, Faculty of Science, Department of Zoology.
    Host range oscillations in nymphalid butterflies: a phylogenetic investigationManuscript (preprint) (Other academic)
    Abstract [en]

    It has been suggested that phenotypic plasticity is a major factor in the diversification of life, and that variation in host range in phytophagous insects is a good model for investigating this claim. We explore the use of angiosperm plants as hosts for nymphalid butterflies, and in particular the evidence for past oscillations in host range and how they are linked to host shifts and diversification. At the level of orders of plants, a relatively simple pattern of host use emerges, despite the 100 million years of history of the family Nymphalidae. The ancestral host order was very likely Rosales. Later, major host shifts occurred to Gentianales (and even later Solanales) in the Danainae; to Arecales (and even later Poales) in the ”satyrines”; to Malpighiales as the main host order in the ”heliconiines”; and to Lamiales within Nymphalinae. We review the evidence that these host shifts and the accompanying diversifications were associated with transient polyphagous stages, as suggested by the ”oscillation hypothesis” of Janz & Nylin. In addition, we investigate all currently polyphagous nymphalid species (in terms of feeding on more than one host order) and demonstrate that the state of polyphagy is rare and has a weak phylogenetic signal and a very apical distribution in the phylogeny; we argue that these are signs of its transient nature. We contrast our results with data from the bark beetles Dendroctonus, where a more specialized host use is instead the apical state, and suggest that this is simply a stage during a single oscillation when host range is decreasing.

  • 121.
    Nyström, Veronica
    et al.
    Stockholm University, Faculty of Science, Department of Zoology.
    Humphrey, Joanne
    Skoglund, Pontus
    McKeown, Niall J.
    Vartanyan, Sergey
    Shaw, Paul W.
    Lidén, Kerstin
    Stockholm University, Faculty of Humanities, Department of Archaeology and Classical Studies, Archaeological Research Laboratory.
    Jakobsson, Mattias
    Barnes, Ian
    Angerbjörn, Anders
    Stockholm University, Faculty of Science, Department of Zoology.
    Lister, Adrian
    Dalen, Love
    Microsatellite genotyping reveals end-Pleistocene decline in mammoth autosomal genetic variation2012In: Molecular Ecology, ISSN 0962-1083, E-ISSN 1365-294X, Vol. 21, no 14, p. 3391-3402Article in journal (Refereed)
    Abstract [en]

    The last glaciation was a dynamic period with strong impact on the demography of many species and populations. In recent years, mitochondrial DNA sequences retrieved from radiocarbon-dated remains have provided novel insights into the history of Late Pleistocene populations. However, genotyping of loci from the nuclear genome may provide enhanced resolution of population-level changes. Here, we use four autosomal microsatellite DNA markers to investigate the demographic history of woolly mammoths (Mammuthus primigenius) in north-eastern Siberia from before 60 000 years ago up until the species final disappearance c. 4000 years ago. We identified two genetic groups, implying a marked temporal genetic differentiation between samples with radiocarbon ages older than 12 thousand radiocarbon years before present (ka) and those younger than 9 ka. Simulation-based analysis indicates that this dramatic change in genetic composition, which included a decrease in individual heterozygosity of approximately 30%, was due to a multifold reduction in effective population size. A corresponding reduction in genetic variation was also detected in the mitochondrial DNA, where about 65% of the diversity was lost. We observed no further loss in genetic variation during the Holocene, which suggests a rapid final extinction event.

  • 122.
    Olofsson, Martin
    et al.
    Stockholm University, Faculty of Science, Department of Zoology.
    Jakobsson, Sven
    Stockholm University, Faculty of Science, Department of Zoology.
    Wiklund, Christer
    Stockholm University, Faculty of Science, Department of Zoology.
    Bird attacks on a butterfly with marginal eyespots and the role of prey concealment against the background2013In: Biological Journal of the Linnean Society, ISSN 0024-4066, E-ISSN 1095-8312, Vol. 109, no 2, p. 290-297Article in journal (Refereed)
    Abstract [en]

    Small eyespots on butterflies have long been thought to deflect attacks, and birds are the presumptive drivers selecting for these patterns; however, evidence of this function is still ambiguous. Marginal eyespots typically consist of a UV-reflective white pupil, surrounded by one black and one yellowish ring. We have recently shown that Cyanistes caeruleus (blue tits) attack such eyespots, but only under low light intensities with accentuated UV levels: the increased salience of the eyespots relative to the rest of the butterfly probably explains this result. Possibly the background against which the butterfly is concealed may deceive birds to make similar errors. We therefore presented speckled wood butterflies decorated with eyespots (or controls without eyespots) to C.caeruleus against two backgrounds: oak and birch bark. Our results show that: (1) eyespots, independent of background, were effective in deflecting attacks; (2) the time elapsed between a bird landing and the attack was interactively dependent on the background and whether the butterfly bore an eyespot; and (3) the speed at which a butterfly was attacked predicted the outcome, with faster birds being more prone to errors than slower birds. This underscores a speedaccuracy trade-off in the predators, and that background plays a role in the defensive qualities of marginal eyespots.(c) 2013 The Linnean Society of London, Biological Journal of the Linnean Society, 2013, 109, 290297.

  • 123.
    Olsen, Morten Tange
    et al.
    Stockholm University, Faculty of Science, Department of Genetics, Microbiology and Toxicology.
    Bérubé, Martine
    Stockholm University, Faculty of Science, Department of Genetics, Microbiology and Toxicology.
    Robbins, Jooke
    Palsbøll, Per
    Stockholm University, Faculty of Science, Department of Genetics, Microbiology and Toxicology.
    Empirical evaluation of humpback whale telomere length estimates; quality control and factors causing variability in the singleplex and multiplex qPCR methodsIn: BMC Genetics, ISSN 1471-2156, E-ISSN 1471-2156Article in journal (Other academic)
  • 124.
    Olsen, Morten Tange
    et al.
    Stockholm University, Faculty of Science, Department of Genetics, Microbiology and Toxicology.
    Pampoulie, Christophe
    Danielsdottir, Anna
    Lidh, Emmelie
    Bérubé, Martine
    Stockholm University, Faculty of Science, Department of Genetics, Microbiology and Toxicology.
    Vikingsson, Gisli
    Palsbøll, Per
    Stockholm University, Faculty of Science, Department of Genetics, Microbiology and Toxicology.
    Nucleotide variation at MDH-1 and MPI in North Atlantic fin whales (Balaenoptera physalus) indicate that allozyme variation reflects phenotypic plasticity and not population genetic structureIn: Molecular EcologyArticle in journal (Other academic)
  • 125.
    Olsen, Morten Tange
    et al.
    Stockholm University, Faculty of Science, Department of Genetics, Microbiology and Toxicology.
    Robbins, Jooke
    Bérubé, Martine
    Stockholm University, Faculty of Science, Department of Genetics, Microbiology and Toxicology.
    Palsbøll, Per
    Stockholm University, Faculty of Science, Department of Genetics, Microbiology and Toxicology.
    Sex-specific costs of reproduction in a long-lived mammal; the humpback whaleManuscript (preprint) (Other academic)
  • 126.
    Olsen, Morten Tange
    et al.
    Stockholm University, Faculty of Science, Department of Genetics, Microbiology and Toxicology.
    Robbins, Jooke
    Bérubé, Martine
    Stockholm University, Faculty of Science, Department of Genetics, Microbiology and Toxicology.
    Palsbøll, Per
    Stockholm University, Faculty of Science, Department of Genetics, Microbiology and Toxicology.
    Telomeres as proxies for cetacean age and life historiesManuscript (preprint) (Other academic)
  • 127.
    Olsen, Morten Tange
    et al.
    Stockholm University, Faculty of Science, Department of Genetics, Microbiology and Toxicology.
    Volny, Veronica Hirsh
    Berube, Martine
    Stockholm University, Faculty of Science, Department of Genetics, Microbiology and Toxicology.
    Dietz, Rune
    Lydersen, Christian
    Kovacs, Kit M.
    Dodd, Richard S.
    Palsbøll, Per
    Stockholm University, Faculty of Science, Department of Genetics, Microbiology and Toxicology.
    A simple route to single-nucleotide polymorphisms in a nonmodel species: identification and characterization of SNPs in the Artic ringed seal (Pusa hispida hispida)2011In: Molecular Ecology Resources, ISSN 1755-098X, E-ISSN 1755-0998, Vol. 11, p. 9-19Article in journal (Refereed)
    Abstract [en]

    Although single-nucleotide polymorphisms (SNPs) have become the marker of choice in the field of human genetics, these markers are only slowly emerging in ecological, evolutionary and conservation genetic analyses of nonmodel species. This is partly because of difficulties associated with the discovery and characterization of SNP markers. Herein, we adopted a simple straightforward approach to identifying SNPs, based on screening of a random genomic library. In total, we identified 768 SNPs in the ringed seal, Pusa hispida hispida, in samples from Greenland and Svalbard. Using three seal samples, SNPs were discovered at a rate of one SNP per 402 bp, whereas re-sequencing of 96 seals increased the density to one SNP per 29 bp. Although applicable to any species of interest, the approach is especially well suited for SNP discovery in nonmodel organisms and is easily implemented in any standard genetics laboratory, circumventing the need for prior genomic data and use of next-generation sequencing facilities.

  • 128. Ord, Terry
    et al.
    Klomp, Danielle
    Garcia-Porta, Joan
    Hagman, Mattias
    University of New South Wales, Kensington, Australia.
    Repeated evolution of exaggerated dewlaps and other throat morphology in lizards.2015In: Journal of Evolutionary Biology, ISSN 1010-061X, E-ISSN 1420-9101, Vol. 28, p. 1948-1964Article in journal (Refereed)
    Abstract [en]

    The existence of elaborate ornamental structures in males is often assumed to reflect the outcome of female mate choice for showy males. However, female mate choice appears weak in many iguanian lizards, but males still exhibit an array of ornament-like structures around the throat. We performed a phylogenetic comparative study to assess whether these structures have originated in response to male–male competition or the need for improved signal efficiency in visually difficult environments. We found little evidence for the influence of male–male competition. Instead, forest species were more likely to exhibit colourful throat appendages than species living in open habitats, suggesting selection for signal efficiency. On at least three independent occasions, throat ornamentation has become further elaborated into a large, conspicuously coloured moving dewlap. Although the function of the dewlap is convergent, the underlying hyoid apparatus has evolved very differently, revealing the same adaptive outcome has been achieved through multiple evolutionary trajectories. More generally, our findings highlight that extravagant, ornament-like morphology can evolve in males without the direct influence of female mate choice and that failure to consider alternative hypotheses for the evolution of these structures can obscure the true origins of signal diversity among closely related taxa.

  • 129.
    Pečnerová, Patrícia
    Stockholm University, Faculty of Science, Department of Zoology. Swedish Museum of Natural History.
    Genomic analysis of the process leading up to the extinction of the woolly mammoth2018Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    Species worldwide are subject to contractions in both abundance and geographical range, and their persistence in a changing environment may thus depend on the ability to survive in small and fragmented populations. Despite the urgent need to understand how extinction works, our knowledge of pre-extinction genetic processes is limited because techniques allowing population and conservation genomics to be studied in wild threatened populations have become available only recently. In this thesis, I used the last surviving population of the woolly mammoth (Mammuthus primigenius) as a model for studying pre-extinction population dynamics. I used ancient DNA as a tool to study microevolutionary processes in real time, analysing genetic changes in response to environmental shifts at the end of the last Ice Age and exploring impacts of genetic drift and inbreeding as woolly mammoths became isolated on Wrangel Island and survived for 6000 years at small population size. Using mitochondrial genomes, I found evidence of a founder effect that decreased the maternal diversity to a single lineage at the time when mammoths became trapped on Wrangel Island (~10,500 years ago). Moreover, a two- to three-fold higher mitochondrial mutation rate in Holocene and a fixed, potentially detrimental mutation in the ATP6 gene encoding for one of the key enzymes of the oxidative phosphorylation pathway, is consistent with the hypothesis that selection is less effective in removing deleterious mutations in small populations. A loss of diversity was also observed in an immunity gene that belongs to the major histocompatibility complex (MHC), even though the MHC is considered to be under balancing selection. Low-coverage genomic data was analysed in order to estimate endogenous DNA content and molecular sex of the mammoth samples. The observation of a male bias (69%) in the sex ratio led to the conclusion that male mammoths were more likely to die in a way that ensured good preservation. Another potential way of getting information about life history strategies of extinct species, which was explored here, is by measuring testosterone levels in mammoth hair shafts in connection with molecular sex inference. Finally, given that previous estimates have suggested a very small Holocene effective population size on Wrangel Island and thus that the population may have been too small to avoid genome erosion, four mammoths were sequenced to a high coverage in order to look for genomic consequences of small population size. When compared to mammoths from the Pleistocene mainland population, Wrangel Island mammoths had lower levels of genome-wide diversity and had a higher proportion of their genomes allocated in runs of homozygosity, which are large fragments completely depleted of diversity. Importantly, genome erosion appears to have accelerated in the last ten generations before the extinction, resulting in the last known woolly mammoth having almost 40% of its genome without any genetic diversity. Overall, these results highlight how genetic drift and inbreeding triggered genomic deterioration in the last surviving woolly mammoth population. Although Wrangel Island was a refugium, where mammoths survived for thousands of years after the last Ice Age, and the causal factors of the final extinction are not yet clear, isolation and small population size without any possibility of new gene flow may have contributed to reduced fitness, and thus to extinction. 

  • 130.
    Pečnerová, Patrícia
    et al.
    Stockholm University, Faculty of Science, Department of Zoology. 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 Mammoth2017In: Current Biology, ISSN 0960-9822, E-ISSN 1879-0445, Vol. 27, no 22, p. 3505-3510.e3Article in journal (Refereed)
    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.

  • 131.
    Pečnerová, Patrícia
    et al.
    Stockholm University, Faculty of Science, Department of Zoology. Swedish Museum of Natural History, Sweden.
    Díez-Del-Molino, David
    Palkopoulou, Eleftheria
    Skoglund, Pontus
    Tikhonov, Alexei
    Nikolskiy, Pavel
    Vartanyan, Sergey
    Dalén, Love
    Stockholm University, Faculty of Science, Department of Zoology. Swedish Museum of Natural History, Sweden.
    Pre-extinction population dynamics and genome erosion in the woolly mammothManuscript (preprint) (Other academic)
  • 132.
    Pečnerová, Patrícia
    et al.
    Stockholm University, Faculty of Science, Department of Zoology. Swedish Museum of Natural History, Sweden.
    Palkopoulou, Eleftheria
    Stockholm University, Faculty of Science, Department of Zoology. Swedish Museum of Natural History, Sweden; Harvard Medical School, Massachusetts.
    Wheat, Christopher W.
    Stockholm University, Faculty of Science, Department of Zoology.
    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 size2017In: Evolution Letters, ISSN 2056-3744, Vol. 1, no 6, p. 292-303Article in journal (Refereed)
    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.

  • 133. Polasky, Stephen
    et al.
    Carpenter, Stephen R.
    Center for Limnology, University of Wisconsin, Madison.
    Folke, Carl
    Stockholm University, Stockholm Resilience Centre.
    Keeler, Bonnie
    Institute on the Environment, University of Minnesota.
    Decision-making under great uncertainty: environmental management in an era of global change2011In: Trends in Ecology and Evolution, Vol. 26, no 8, p. 398-404Article, review/survey (Refereed)
  • 134.
    Pruisscher, Peter
    Stockholm University, Faculty of Science, Department of Zoology.
    Functional genomics of diapause in two temperate butterflies2019Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    Natural selection will act on a given phenotype to maximize fitness in a particular environment, even if this would result in reduced fitness in other environments. In insects some of the strongest selection pressures act on timing life cycles to seasonal variation in environmental conditions, in order to maximize growth, reproduction, and to anticipate the onset of winter. Many temperate insects survive winter by entering a pre-programmed state of developmental arrest, called diapause. The decision to induce diapause is predominantly based on measuring day length. Populations have adapted to latitudinal variation in photoperiod, thereby synchronizing with local seasonal variation. However, there is no general understanding of the genetic basis for controlling diapause induction, maintenance and termination. In this thesis I aimed to gain a better understanding of the genetic basis underlying variation in the induction decision, as well as to gain insights into gene expression changes during diapause in temperate butterflies.

     

    I started by revealing local adaptation in the photoperiodic response of two divergent populations of Pieris napi (Paper I). I found that variation in diapause induction among populations of both P. napi and Pararge aegeria showed strong sex-linked inheritance in inter-population crosses (Paper I and II). The genome-wide variation across populations was relatively low in both species. However, there was strong divergence in genomic regions containing the circadian clock genes timeless and period in P. aegeria, and period, cycle, and clock in P. napi. The genetic variation in these specific regions segregated between diapausing and direct developing individuals of inter-population crosses, showing that allelic variation at few genes with known functions in the circadian clock correlated to variation in diapause induction (Paper II and III).

     

    Furthermore, I investigated the transcriptional dynamics in two tissues (head and abdomen) during diapause (Paper IV). Already at the first day of pupal development there are on average 409 differentially expressed genes (DEG) each up and down regulated between the direct development and diapause pathways, and this increases dramatically across these formative stages to an average of 2695. Moreover, gene expression is highly dynamic during diapause, showing more than 2600 DEG’s in the first month of diapause development, but only 20 DEG’s in the third month. Moreover, gene expression is independent of environmental conditions, revealing a pre-programmed transcriptional landscape that is active during the winter. Still, adults emerging from either the direct or diapause pathways do not show large transcriptomic differences, suggesting the adult phenotype is strongly canalized.

     

    Thus, by integrating whole-genome scans with targeted genotyping and bulk-segregant analyses in population crosses, I demonstrate that adaptive variation in seasonal life cycle regulation in the two butterflies P. napi and P. aegeria both converge on genes of the circadian clock, suggesting convergent evolution in these distantly related butterflies.

    Moreover, the diapause program is a dynamic process with a distinct transcriptional profile in comparison to direct development, showing that on a transcriptome level diapause development and direct development are two distinct developmental strategies.

  • 135.
    Pruisscher, Peter
    et al.
    Stockholm University, Faculty of Science, Department of Zoology.
    Lehmann, Philipp
    Stockholm University, Faculty of Science, Department of Zoology.
    de la Paz Celorio-Mancera, Maria
    Stockholm University, Faculty of Science, Department of Zoology.
    Nylin, Sören
    Stockholm University, Faculty of Science, Department of Zoology.
    Gotthard, Karl
    Stockholm University, Faculty of Science, Department of Zoology.
    Wheat, Christopher
    Stockholm University, Faculty of Science, Department of Zoology.
    Transcriptomic profiling of pupal diapause in the butterfly Pieris napiManuscript (preprint) (Other academic)
    Abstract [en]

    Diapause is a common means of overwintering among insects that is characterized by arrested development and increased tolerance to stress and cold. Diapause is a vital aspect of life cycle timing, and while the expression of specific candidate genes during diapause have been investigated, there is no general understanding of the dynamics of the transcriptional landscape as a whole during the extended diapause phenotype. Here we performed a time-course experiment using RNA-Seq on the head and abdomen in the butterfly Pieris napi. In both body parts, comparing diapause and directly developing siblings, differentially expressed genes are detected from the first day of pupal development and onwards, varying dramatically across these formative stages. During diapause there are strong gene expression dynamics independent of environmental conditions, revealing a pre-programmed transcriptional landscape that is active during the winter. Different biological processes appear to be active in the two body parts. Still, adults emerging from either the direct or diapause pathways do not show large transcriptomic differences, suggesting the adult phenotype is strongly canalized.

  • 136.
    Pruisscher, Peter
    et al.
    Stockholm University, Faculty of Science, Department of Zoology.
    Nylin, Sören
    Stockholm University, Faculty of Science, Department of Zoology.
    Wheat, Christopher
    Stockholm University, Faculty of Science, Department of Zoology.
    Gotthard, Karl
    Stockholm University, Faculty of Science, Department of Zoology.
    A chromosomal block containing clock genes associates with variation in diapause inductionManuscript (preprint) (Other academic)
    Abstract [en]

    Developmental plasticity describes the capacity of individuals with the same genotype to induce permanent change in a phenotype depending on a specific external input. One well-studied example of adaptive developmental plasticity is the induction of facultative diapause in insects. Studies investigating the inheritance of diapause induction have suggested diverse genetic backgrounds. However, only few studies have performed unbiased genome scans to identify genes affecting the induction decision. Here we perform an unbiased whole genome scan to identify divergence between two populations that differ in their propensity to diapause, finding low divergence between these populations. We then investigate genetic differences between diapausing and directly developing siblings from backcrosses of these populations that revealed one particular region of divergence. This region is located on the Z-chromosome and contained three circadian clock genes, cyc_2, clock, and per. The results from this study help understand the genetic basis that is underlying plasticity.

  • 137. Rakotoarivelo, Fanny P.
    et al.
    Razafimandimbison, Sylvain G.
    Stockholm University, Faculty of Science, The Bergius Botanical Garden Museum.
    Mallet, Bertrand
    Faliniaina, Lucien
    Pailler, Thierry
    Molecular systematics and evolutionary trends and relationships in the genus Jumellea (Orchidaceae): Implications for its species limits2012In: Taxon, ISSN 0040-0262, E-ISSN 1996-8175, Vol. 61, no 3, p. 534-544Article in journal (Refereed)
    Abstract [en]

    Jumellea is an orchid genus centered on Madagascar but also occurs on some of the neighboring oceanic islands (the Mascarenes and Comoros) and in southern and eastern Africa. Prior to our study the genus contained ca. 55 morphologically distinct species, of which six are found in the Comoros (three endemic, three shared with Madagascar), nine in the Mascarenes (four endemic, four shared with Madagascar), two in southern and eastern Africa (both endemic), and 41 species endemic to Madagascar. We perform Bayesian and parsimony phylogenetic analyses of Jumellea based on combined chloroplast (matK, trnL-F, rps16, ycf1) and nuclear (nrITS) data from 60 specimens representing 47 species, four subspecies, and two varieties of Jumellea: (1) to assess the phylogenetic value of growth form, leaf, bract and lip shape, and spur length, presently used for recognizing informal groups within the genus; and (2) to test the monophyly of some variable species (e.g., J. gracilipes, J. lignosa). We find no support for the informal groups of Jumellea, as all the characters tested are evolutionarily labile. Jumellea lignosa (comprising J. lignosa subsp. lignosa, subsp. tenuibracteata, subsp. actuissima, and subsp. latilabia) is not monophyletic unless subsp. tenuibracteata is excluded. Jumellea gracilipes s.l. (including J. ambongensis, J. imerinensis, and J. unguicularis) is polyphyletic. As a result, we resurrect these three latter species, and recognize J. lignosa subsp. tenuibracteata at species level. Furthermore, we propose new circumscriptions for the following species: the Comorian J. arachnantha (including the Malagasy J. sagittata); the Reunionese J. exilis (including the Malagasy J. flavescens); the Reunionese J. recta (including the Malagasy Jumellea sp. I); the Reunionese J. recurva (including the Malagasy J. pandurata); and the Reunionese J. stenophylla (including the Malagasy J. gracilipes 2 and 3). Finally, Jumellea arborescens and J. maxillarioides are recorded from Madagascar and the Comoros. Finally, the number of species of Jumellea has now increased from 55 to 57: seven species in the Comoros (four shared with Madagascar), nine species in the Mascarenes (four shared with Madagascar), two species in Africa, and 39 species, three subspecies, and two varieties restricted to Madagascar.

  • 138.
    Razafimandimbison, Sylvain G.
    et al.
    Stockholm University, Faculty of Science, Department of Botany.
    Kainulainen, Kent
    Stockholm University, Faculty of Science, Department of Botany.
    Wong, Khoon M.
    Beaver, Katy
    Bremer, Birgitta
    Stockholm University, Faculty of Science, Department of Botany.
    Molecular support for a basal grade of morphologically distinct, monotypic genera in the species-rich Vanguerieae alliance (Rubiaceae, Ixoroideae): Its systematic and conservation implications2011In: Taxon, ISSN 0040-0262, E-ISSN 1996-8175, Vol. 60, no 4, p. 941-952Article in journal (Refereed)
    Abstract [en]

    Many monotypic genera with unique apomorphic characters have been difficult to place in the morphology-based classifications of the coffee family (Rubiaceae). We rigorously assessed the subfamilial phylogenetic position and generic status of three enigmatic genera, the Seychellois Glionnetia, the Southeast Asian Jackiopsis, and the Chinese Trailliaedoxa within Rubiaceae, using sequence data of four plastid markers (ndhF, rbcL, rps16, trnT-F). The present study provides molecular phylogenetic support for positions of these genera in the subfamily Ixoroideae, and reveals the presence of a basal grade of morphologically distinct, monotypic genera (Crossopteryx,Jackiopsis,Scyphiphora,Trailliaedoxa, and Glionnetia, respectively) in the species-rich Vanguerieae alliance. These five genera may represent sole representatives of their respective lineages and therefore may carry unique genetic information. Their conservation status was assessed, applying the criteria set in IUCN Red List Categories. We consider Glionnetia and Jackiopsis Endangered. Scyphiphora is recognized as Near Threatened despite its extensive range and Crossopteryx as Least Concern. Trailliaedoxa is poorly known (Data Deficient). Finally, the generic status of Glionnetia,Jackiopsis, and Trailliaedoxa and the monogeneric tribe Jackieae as defined by Ridsdale are supported.

  • 139. Reber, A
    et al.
    Purcell, J
    Buechel, S D
    Buri, P
    Chapuisat, M
    The expression and impact of antifungal grooming in ants.2011In: Journal of Evolutionary Biology, ISSN 1010-061X, E-ISSN 1420-9101, Vol. 24, no 5, p. 954-64Article in journal (Refereed)
    Abstract [en]

    Parasites can cause extensive damage to animal societies in which many related individuals frequently interact. In response, social animals have evolved diverse individual and collective defences. Here, we measured the expression and efficiency of self-grooming and allo-grooming when workers of the ant Formica selysi were contaminated with spores of the fungal entomopathogen Metarhizium anisopliae. The amount of self-grooming increased in the presence of fungal spores, which shows that the ants are able to detect the risk of infection. In contrast, the amount of allo-grooming did not depend on fungal contamination. Workers groomed all nestmate workers that were re-introduced into their groups. The amount of allo-grooming towards noncontaminated individuals was higher when the group had been previously exposed to the pathogen. Allo-grooming decreased the number of fungal spores on the surface of contaminated workers, but did not prevent infection in the conditions tested (high dose of spores and late allo-grooming). The rate of disease transmission to groomers and other nestmates was extremely low. The systematic allo-grooming of all individuals returning to the colony, be they contaminated or not, is probably a simple but robust prophylactic defence preventing the spread of fungal diseases in insect societies.

  • 140. Ritchie, Euan G.
    et al.
    Elmhagen, Bodil
    Stockholm University, Faculty of Science, Department of Zoology.
    Glen, Alistair S.
    Letnic, Mike
    Ludwig, Gilbert
    McDonald, Robbie A.
    Ecosystem restoration with teeth: what role for predators?2012In: Trends in Ecology & Evolution, ISSN 0169-5347, E-ISSN 1872-8383, Vol. 27, no 5, p. 265-271Article in journal (Refereed)
    Abstract [en]

    Recent advances highlight the potential for predators to restore ecosystems and confer resilience against globally threatening processes, including climate change and biological invasions. However, releasing the ecological benefits of predators entails significant challenges. Here, we discuss the economic, environmental and social considerations affecting predator-driven ecological restoration programmes, and suggest approaches for reducing the undesirable impacts of predators. Because the roles of predators are context dependent, we argue for increased emphasis on predator functionality in ecosystems and less on the identities and origins of species and genotypes. We emphasise that insufficient attention is currently given to the importance of variation in the social structures and behaviours of predators in influencing the dynamics of trophic interactions. Lastly, we outline experiments specifically designed to clarify the ecological roles of predators and their potential utility in ecosystem restoration.

  • 141. Ronquist, Fredrik
    et al.
    Teslenko, Maxim
    van der Mark, Paul
    Ayres, Daniel L.
    Darling, Aaron
    Höhna, Sebastian
    Stockholm University, Faculty of Science, Department of Mathematics.
    Larget, Bret
    Liu, Liang
    Suchard, Marc A.
    Huelsenbeck, John P.
    MrBayes 3.2: Efficient Bayesian Phylogenetic Inference and Model Choice Across a Large Model Space2012In: Systematic Biology, ISSN 1063-5157, E-ISSN 1076-836X, Vol. 61, no 3, p. 539-542Article in journal (Refereed)
    Abstract [en]

    Since its introduction in 2001, MrBayes has grown in popularity as a software package for Bayesian phylogenetic inference using Markov chain Monte Carlo (MCMC) methods. With this note, we announce the release of version 3.2, a major upgrade to the latest official release presented in 2003. The new version provides convergence diagnostics and allows multiple analyses to be run in parallel with convergence progress monitored on the fly. The introduction of new proposals and automatic optimization of tuning parameters has improved convergence for many problems. The new version also sports significantly faster likelihood calculations through streaming single-instruction-multiple-data extensions (SSE) and support of the BEAGLE library, allowing likelihood calculations to be delegated to graphics processing units (GPUs) on compatible hardware. Speedup factors range from around 2 with SSE code to more than 50 with BEAGLE for codon problems. Checkpointing across all models allows long runs to be completed even when an analysis is prematurely terminated. New models include relaxed clocks, dating, model averaging across time-reversible substitution models, and support for hard, negative, and partial (backbone) tree constraints. Inference of species trees from gene trees is supported by full incorporation of the Bayesian estimation of species trees (BEST) algorithms. Marginal model likelihoods for Bayes factor tests can be estimated accurately across the entire model space using the stepping stone method. The new version provides more output options than previously, including samples of ancestral states, site rates, site d(N)/d(S) rations, branch rates, and node dates. A wide range of statistics on tree parameters can also be output for visualization in FigTree and compatible software.

  • 142.
    Rydin, Catarina
    Stockholm University, Faculty of Science, Department of Ecology, Environment and Plant Sciences.
    Gnetales – ett litet fönster mot en svunnen värld2018In: Svensk Botanisk Tidskrift, ISSN 0039-646X, Vol. 112, no 1, p. 4-21Article in journal (Refereed)
    Abstract [en]

    The Gnetales – a small window onto a lost world

    The Gnetales share a number of similarities with angiosperms and were, based on their morphology, viewed as the angiosperms’ closest living relatives. Molecular data refute this hypothesis and indicate instead that the Gnetales are misunderstood conifers. Regardless, the Gnetales are immensely interesting survivors of an ancient past. They radiated during the Early Cretaceous and extant species constitute only a small fraction of a much greater historical diversity. Structure and function of extant species are often considered odd, enigmatic and difficult to understand. Among the oddities of the Gnetales are the morphologically unique Welwitschia, with close relatives only known as fossils of the Early Cretaceous, and the discovery of moonlight pollination in Ephedra foeminea. The Gnetales continue to attract scientists’ attention, decade after decade, perhaps because they form a tiny window through which we are allowed a glimpse of long gone ecosystems.

  • 143.
    Sangster, George
    Stockholm University, Faculty of Science, Department of Zoology, Systematic Zoology.
    Review of: Festschrift for Ned Johnson: Geographic variation and evolution in birds by C Cicero and J V Remsen.2008In: Ibis, ISSN 0019-1019, E-ISSN 1474-919X, Vol. 150, p. 843-Article, book review (Other academic)
  • 144.
    Sangster, George
    Stockholm University, Faculty of Science, Department of Zoology, Systematic Zoology.
    The ring species concept revisitedManuscript (preprint) (Other academic)
    Abstract [en]

    Ring species may offer important insights into the role of isolation by distance in speciation. In recent years, the study of ring species has been revigorated by the application of phylogeographic methods. The concept of ring species, however, has received little attention since its original formulation in the first half of the twentieth century. A review of the two best-documented cases of putative ring species suggests that different evolutionary patterns have been referred to by the term ‘ring species’. These putative ring species share a circular colonization pattern but have fundamentally different evolutionary histories and patterns of geographic variation. Because these patterns cannot be explained by a single evolutionary model, a terminological distinction is warranted. It is suggested that the term ‘ring species’ be restricted to taxa which form a single evolutionary unit and in which the end-points have diverged as a result of isolation by distance. The new evolutionary term ‘taxon chain’ is suggested for a clade consisting of multiple evolutionary units separated by secondary contact zones. The study of ring species and taxon chains requires an integrative approach, including the description of geographic variation, phylogeographic study of historical divergence, assessment of gene flow, and study of interactions in contact zones.

  • 145.
    Sangster, George
    et al.
    Stockholm University, Faculty of Science, Department of Zoology, Systematic Zoology. Swedish Museum of Natural History.
    Collinson, J. Martin
    Crochet, Pierre-Andre
    Knox, Alan G.
    Parkin, David T.
    Votier, Stephen C.
    Taxonomic recommendations for Western Palearcticbirds: ninth report2013In: Ibis, ISSN 0019-1019, E-ISSN 1474-919X, Vol. 155, no 4, p. 898-907Article in journal (Other academic)
  • 146. Sanudo-Restrepo, Claudia P.
    et al.
    Dinca, Vlad
    Stockholm University, Faculty of Science, Department of Zoology.
    Talavera, Gerard
    Vila, Roger
    Biogeography and systematics of Aricia butterflies (Lepidoptera, Lycaenidae)2013In: Molecular Phylogenetics and Evolution, ISSN 1055-7903, E-ISSN 1095-9513, Vol. 66, no 1, p. 369-379Article in journal (Refereed)
    Abstract [en]

    Butterflies of the Aricia species group represent a paradigm of unresolved taxonomy, both at the genus and species levels. We studied phylogenetic relationships, biogeography, and systematics based on genetic - nuclear and mitochondrial - and morphometric - external (wings) and internal (genitalia) data. We show that Aricia is a monophyletic genus comprising the taxa Pseudoaricia, Ultraaricia and Umpria, which are here considered junior synonyms of Aricia. The taxa allous, inhonora, issekutzi, mandzhuriana, myrmecias and transalaica, which have often been raised to species rank, are shown to probably represent subspecies or synonyms. We show that montensis is likely a good species that is sister to all A. artaxerxes populations across the Palearctic region. The species A. anteros and A. morronensis are shown to display deep intraspecific divergences and they may harbor cryptic species. We also discovered that A. cramera and A. agestis exhibit a pattern of mutual exclusion on islands, and a parapatric distribution in mainland with a narrow contact zone where potential hybrids were detected. The lack of a prezygotic barrier that prevents their coexistence could explain this phenomenon. This study will hopefully contribute to the stability of the systematics of Aricia, a group with potential for the study of the link between speciation and biogeography.

  • 147.
    Schwander, Tanja
    et al.
    University of Groningen.
    Leimar, Olof
    Stockholm University, Faculty of Science, Department of Zoology.
    Genes as leaders and followers in evolution2011In: Trends in Ecology & Evolution, ISSN 0169-5347, E-ISSN 1872-8383, Vol. 26, no 3, p. 143-151Article, review/survey (Refereed)
    Abstract [en]

    A major question for the study of phenotypic evolution is whether intra- and interspecific diversity originates directly from genetic variation, or instead, as plastic responses to environmental influences initially, followed later by genetic change. In species with discrete alternative phenotypes, evolutionary sequences can be inferred from transitions between environmental and genetic phenotype control, and from losses of phenotypic alternatives. From the available evidence, sequences appear equally probable to start with genetic polymorphism as with polyphenism, with a possible dominance of one or the other for specific trait types. We argue in this review that to evaluate the prevalence of each route, an investigation of both genetic and environmental cues for phenotype determination in several related rather than in isolated species is required.

  • 148.
    Schwander, Tanja
    et al.
    University of Groningen.
    Leimar, Olof
    Stockholm University, Faculty of Science, Department of Zoology.
    The evolution of novel cues for ancestral phenotypes2011In: Trends in Ecology & Evolution, ISSN 0169-5347, E-ISSN 1872-8383, Vol. 26, no 9, p. 436-437Article in journal (Refereed)
  • 149.
    Schäpers, Alexander
    Stockholm University, Faculty of Science, Department of Zoology.
    Evolutionary and mechanistic aspects of insect host plant preference2016Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    Plant feeding insects comprise about 25% of all animal species on earth and play an important role in all ecosystems. Although we understand that their association with plants is a key-factor driving the diversification in this group, we still have large gaps in our knowledge of the underlying processes of this relationship. Female choice of host plant is an important event in the insect life-cycle, as it is a major determinant of the larval food plant. In this Thesis I studied different aspects of insect host plant choice and used butterflies from the family Nymphalidae as my study system. I found that butterflies have a well developed olfactory system and that they use odors when searching for food or host plants. However, the information obtained from the odor of host plants does not seem to be sufficient for the studied species to make a distinction between plants of different qualities. Interestingly, even when in full contact with the leaf they do not make optimal decisions. I show for example that a sub-optimal female choice may be mitigated by larval ability to cope with unfavorable situations. Moreover, species that utilize a broader set of host plants may not be very well adapted to all the hosts they use, but at the same time they may survive in areas where there is only a subset of the plants available. Lastly, differences in the evolution of life-history traits between species can account for differences in how each species realizes its lifestyle. Thus, by incorporating findings on mechanisms of host plant choice with the ecological and evolutionary context of a species, our ability to explain the dynamics of host plant choice and insect-plant interactions can be improved.

  • 150.
    Schäpers, Alexander
    et al.
    Stockholm University, Faculty of Science, Department of Zoology.
    Petrén, Hampus
    Wheat, Christopher W.
    Stockholm University, Faculty of Science, Department of Zoology.
    Wiklund, Christer
    Stockholm University, Faculty of Science, Department of Zoology.
    Friberg, Magne
    Female fecundity variation affects reproducibility of experiments on host plant preference and acceptance in a phytophagous insect2017In: Proceedings of the Royal Society of London. Biological Sciences, ISSN 0962-8452, E-ISSN 1471-2954, Vol. 284, no 1849, article id 20162643Article in journal (Refereed)
    Abstract [en]

    Reproducibility is a scientific cornerstone. Many recent studies, however, describe a reproducibility crisis and call for assessments of reproducibility across scientific domains. Here, we explore the reproducibility of a classic ecological experiment—that of assessing female host plant preference and acceptance in phytophagous insects, a group in which host specialization is a key driver of diversification. We exposed multiple cohorts of Pieris napi butterflies from the same population to traditional host acceptance and preference tests on three Brassicaceae host species. Whereas the host plant rank order was highly reproducible, the propensity to oviposit on low-ranked hosts varied significantly even among cohorts exposed to similar conditions. Much variation could be attributed to among-cohort variation in female fecundity, a trait strongly correlated both to female size and to the size of the nuptial gift a female receives during mating. Small males provide small spermatophores, and in our experiment small females that mated with small males had a disproportionally low propensity to oviposit on low-ranked hosts. Hence, our results provide empirical support to the theoretical prediction that female host utilization is strongly affected by non-genetic, environmental variation, and that such variation can affect the reproducibility of ecological experiments even under seemingly identical conditions.

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