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  • 1551.
    Svensson, P. Andreas
    et al.
    Monash Univ, Sch Biol Sci, Clayton, Vic 3800, Australia.
    Lehtonen, T. K.
    Monash Univ, Sch Biol Sci, Clayton, Vic 3800, Australia.
    Wong, B. B. M.
    Monash Univ, Sch Biol Sci, Clayton, Vic 3800, Australia.
    The interval between sexual encounters affects male courtship tactics in a desert-dwelling fish2010Inngår i: Behavioral Ecology and Sociobiology, ISSN 0340-5443, E-ISSN 1432-0762, Vol. 64, nr 2, s. 1967-1970Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Courtship displays are often important in determining male mating success but can also be costly. Thus, instead of courting females indiscriminately, males might be expected to adjust their signalling effort strategically. Theory, however, predicts that such adjustments should depend on the rate with which males encounter females, a prediction that has been subject to very little empirical testing. Here, we investigate the effects of female encounter rate on male courtship intensity by manipulating the time interval between sequential presentations of large (high quality) and small (low quality) females in a fish, the Australian desert goby Chlamydogobius eremius. Males that were presented with a small female immediately after a large female reduced their courtship intensity significantly. However, males courted large and small females with equal intensity if the interval between the sequential presentations was longer. Our results suggest that mate encounter rate is an important factor shaping male reproductive decisions and, consequently, the evolutionary potential of sexual selection.

  • 1552.
    Svensson, P. Andreas
    et al.
    Linnéuniversitetet, Fakultetsnämnden för naturvetenskap och teknik, Institutionen för naturvetenskap, NV.
    Lehtonen, Topi K.
    Wong, Bob B. M.
    A high aggression strategy for smaller males2012Konferansepaper (Fagfellevurdert)
    Abstract [en]

    Male-male conflict is common among animals, but questions remain as to when, how and by whom aggression should be initiated. Factors that affect agonistic strategies include residency, the value of the contested resource and the fighting ability of the contestants. Game-theoretical models often assume that strategies for aggression are conditional and shaped by mutual assessment. We quantified aggression in a fish, the Australian desert goby, <i>Chlamydogobius eremius</i>, by exposing nest-holding males to male intruders. The perceived value of the resource (the nest) was manipulated by exposing half of the residents to sexually receptive females before the trial. We found resident male aggression to be unaffected by perceived mating opportunities. It was also unaffected by the size of the intruder. Instead, aggression was related the residents' own size, namely, smaller males attacked sooner and with greater intensity than larger males. Thus, contrary to theory, resident desert goby males appeared to have set strategies for initiating aggression. Rather than viewing high aggression in small males as a paradox (i.e. the Napoleon effect), we suggest that small individuals may benefit from attacking early, before an intruder has time to assess the resident and/or the resource.

  • 1553.
    Svensson, P. Andreas
    et al.
    Linnéuniversitetet, Fakultetsnämnden för naturvetenskap och teknik, Institutionen för naturvetenskap, NV. Monash University, Australia.
    Lehtonen, Topi K.
    Monash University, Australia ; University of Turku, Finland.
    Wong, Bob B. M.
    Monash University, Australia.
    A high aggression strategy for smaller males2012Inngår i: PLoS ONE, ISSN 1932-6203, E-ISSN 1932-6203, Vol. 7, nr 8, artikkel-id e43121Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Male-male conflict is common among animals, but questions remain as to when, how and by whom aggression should be initiated. Factors that affect agonistic strategies include residency, the value of the contested resource and the fighting ability of the two contestants. We quantified initiation of aggression in a fish, the desert goby, Chlamydogobius eremius, by exposing nest-holding males to a male intruder. The perceived value of the resource ( the nest) was manipulated by exposing half of the residents to sexually receptive females for two days before the trial. Resident male aggression, however, was unaffected by perceived mating opportunities. It was also unaffected by the absolute and relative size of the intruder. Instead resident aggression was negatively related to resident male size. In particular, smaller residents attacked sooner and with greater intensity compared to larger residents. These results suggest that resident desert goby males used set, rather than conditional, strategies for initiating aggression. If intruders are more likely to flee than retaliate, small males may benefit from attacking intruders before these have had an opportunity to assess the resident and/or the resource.

  • 1554.
    Svensson, P. Andreas
    et al.
    Linnéuniversitetet, Fakultetsnämnden för naturvetenskap och teknik, Institutionen för naturvetenskap, NV.
    Nilsson-Sköld, Helen
    University of Gothenburg.
    Skin biopsies as tools to measure fish coloration and colour change2011Inngår i: Skin Biopsy - Perspectives / [ed] Uday Khopkar, InTech, 2011Kapittel i bok, del av antologi (Annet vitenskapelig)
  • 1555.
    Svensson, P. Andreas
    et al.
    Department of Biology, Norwegian University of Science and Technology, N-7491 Trondheim, Norway.
    Pélabon, C.
    Blount, J. D.
    Forsgren, E.
    Bjerkeng, B.
    Amundsen, T.
    Temporal variability in a multicomponent trait: nuptial coloration of female two-spotted gobies2009Inngår i: Behavioral Ecology, ISSN 1045-2249, E-ISSN 1465-7279, Vol. 20, nr 2, s. 346-353Artikkel i tidsskrift (Fagfellevurdert)
  • 1556. Svensson, P. Andreas
    et al.
    Pélabon, C.
    Blount, J. D.
    Surai, P. F.
    Amundsen, T.
    Does female nuptial coloration reflect egg carotenoids and clutch quality in the two-spotted goby (Gobiusculus flavescens, Gobiidae)?2006Inngår i: Functional Ecology, ISSN 0269-8463, E-ISSN 1365-2435, Vol. 20, s. 689-698Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    1. Carotenoid based ornamentation has often been suggested to signal mate quality and species with such ornaments have frequently been used in studies of sexual selection. 2. FemaleGobiusculus flavescens(two-spotted goby) develop colourful orange bellies during the breeding season. Belly coloration varies among mature females, and previous work has shown nest holding males to prefer females with more colourful bellies. Since males invest heavily in offspring during incubation, the evolution of this preference can be explained if colourful females provide males with eggs of higher quality. 3. We tested this hypothesis by allowing males to spawn with 'colourful' and 'drab' females and comparing parameters including egg carotenoid concentration, clutch size, hatchability and larval viability between groups. We also investigated relationships between egg carotenoid concentration and clutch quality parameters. 4. Eggs from colourful females had higher concentrations of total carotenoids than eggs from drab females. Colourful females produced slightly larger clutches, but no measure of offspring quality differed between the two groups. Belly coloration quantified in photographs prior to spawning was a good predictor of egg carotenoid concentration, but there were no significant relationships between egg carotenoids and the measures of clutch quality. Females with high levels of egg carotenoids spawned slightly earlier, however, possibly because they were more ready to spawn or because of male mate choice. 5. We found that colourful females provided males with slightly larger clutches and eggs that contained more carotenoids, but despite this, the offspring were not of higher quality. Our results call into question the generality of a causal link between egg carotenoids and offspring quality.

  • 1557.
    Svensson, P. Andreas
    et al.
    Monash University, Australia.
    Wong, B. B. M.
    Monash University, Australia.
    Carotenoid-based signals in behavioural ecology: a review2011Inngår i: Behaviour, ISSN 0005-7959, E-ISSN 1568-539X, Vol. 148, nr 2, s. 131-189Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Carotenoids are among the most prevalent pigments used in animal signals and are also important for a range of physiological functions. These concomitant roles havemade carotenoidbased signals a popular topic in behavioural ecology while also causing confusion and controversy. After a thorough background, we review the many pitfalls, caveats and seemingly contradictory conclusions that can result from not fully appreciating the complex nature of carotenoid function. Current controversies may be resolved through a more careful regard of this complexity, and of the immense taxonomic variability of carotenoid metabolism. Studies investigating the physiological trade-offs between ornamental and physiological uses of carotenoids have yielded inconsistent results. However, in many studies, homeostatic regulation of immune and antioxidant systems may have obscured the effects of carotenoid supplementation. We highlight how carefully designed experiments can overcome such complications. There is also a need to investigate factors other than physiological trade-offs (such as predation risk and social interactions) as these, too, may shape the expression of carotenoidbased signals.Moreover, the processes limiting signal expression individuals are likely different from those operating over evolutionary time-scales. Future research should give greater attention to carotenoid pigmentation outside the area of sexual selection, and to taxa other than fishes and birds.

  • 1558.
    Sverrisdóttir, Oddný Ósk
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Evolutionsbiologi.
    Daskalaki, Evangelia
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Evolutionsbiologi.
    Skoglund, Pontus
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Evolutionsbiologi.
    Valdiosera, Cristina E.
    La Trobe University.
    Carretero, José M.
    Facultad de Humanidades, Departamento Históricas y Geografía.
    Arsuaga Ferreras, Juan Luis
    Facultad de Ciencias Geológicas.
    Jakobsson, Mattias
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Evolutionsbiologi.
    Götherström, Anders
    Stockholm University.
    A late Neolithic Iberian farmer exhibits genetic affinity to Neolithic Scandinavian farmers and a Bronze Age central European  farmerManuskript (preprint) (Annet vitenskapelig)
  • 1559.
    Symons, N.
    et al.
    Monash Univ, Sch Biol Sci, Melbourne, Vic 3004, Australia .
    Svensson, P. Andreas
    Monash Univ, Sch Biol Sci, Melbourne, Vic 3004, Australia .
    Wong, B. B. M.
    Monash Univ, Sch Biol Sci, Melbourne, Vic 3004, Australia .
    Do Male Desert Gobies Compromise Offspring Care to Attract Additional Mating Opportunities?2011Inngår i: PLoS ONE, ISSN 1932-6203, E-ISSN 1932-6203, Vol. 6, nr 6, s. e20576-Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Males often play a critical role in offspring care but the time and energy invested in looking after young can potentially limit their ability to seek out additional mating opportunities. Recent studies, however, suggest that a conflict between male parental effort and mating effort may not always be inevitable, especially if breeding occurs near the nest, or if parental behaviours are under sexual selection. Accordingly, we set out to experimentally investigate male care and courtship in the desert goby Chlamydogobius eremius, a nest-guarding fish with exclusive paternal care. Despite courtship occurring near the nest, we found that when egg-tending males were given the opportunity to attract additional females, they fanned their eggs less often, engaged in shorter fanning bouts, and spent more of their time outside their nests courting. Our findings highlight the importance of understanding the circumstances under which reproductive tradeoffs are expected to occur and how these, in turn, operate to influence male reproductive decisions.

  • 1560. Szrek, Piotr
    et al.
    Dec, Marek
    Niedzwiedzki, Grzegorz
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för organismbiologi, Evolution och utvecklingsbiologi.
    The first placoderm fish from the Lower Devonian of Poland2015Inngår i: Journal of Vertebrate Paleontology, ISSN 0272-4634, E-ISSN 1937-2809, Vol. 35, nr 3, artikkel-id e930471Artikkel i tidsskrift (Fagfellevurdert)
  • 1561.
    Szrek, Piotr
    et al.
    Polish Geol Inst, Natl Res Inst, Rakowiecka 4 St, PL-00075 Warsaw, Poland. Polish Geol Inst, Natl Res Inst, Holy Cross Mt Branch, Zgoda 21 St, PL-00075 Kielce, Poland..
    Salwa, Sylwester
    Holy Cross Mountains Branch of the Polish Geological Institute—National Research Institute, Zgoda 21 Street, 00-075 Kielce, Poland.
    Niedzwiedzki, Grzegorz
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för organismbiologi, Evolution och utvecklingsbiologi.
    Dec, Marek
    Polish Acad Sci, Inst Paleobiol, Twarda 51-55, PL-00818 Warsaw, Poland..
    Ahlberg, Per E.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för organismbiologi, Evolution och utvecklingsbiologi.
    Uchman, Alfred
    Jagiellonian Univ, Inst Geol Sci, Oleandry 2a, PL-30063 Krakow, Poland..
    A glimpse of a fish face: An exceptional fish feeding trace fossil from the Lower Devonian of the Holy Cross Mountains, Poland2016Inngår i: Palaeogeography, Palaeoclimatology, Palaeoecology, ISSN 0031-0182, E-ISSN 1872-616X, Vol. 454, s. 113-124Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    An exceptionally well-preserved assemblage of numerous invertebrate and vertebrate trace fossils is described from the Lower Devonian of the Holy Cross Mountains, southern Poland. Two trace-bearing horizons occur in the shallow-marine sequence that is exposed in a small outcrop near Ujazd village. One of the trace fossils is preserved as a bilobate, generally elliptical, epichnial pit is described as Osculichnus tarnowskae isp. nov. and interpreted as a unique example of praedichnia. Neoichnologic experiments and observations indicate that the ichnogenus Osculichnus was produced by feeding fish. The fish producing O. tarnowskae probably hunted bivalves, polychaetes and arthropods, which are represented by invertebrate trace fossils in the same horizons. The overall shape and morphological details of O. tarnowskae suggest that it was made by a lungfish broadly similar to Dipnorhynchus. The trace provides the first direct evidence for Devonian lungfish feeding behaviour, as well as the first record of three-dimensional soft-tissue morphology of the snout area of an Emsian representative of this group. The trace fossils from Ujazd provide new insight into the palaeoecology and taphonomy of the Lower Devonian of the Holy Cross Mountains.

  • 1562.
    Sällman Almén, Markus
    Uppsala universitet, Medicinska och farmaceutiska vetenskapsområdet, Medicinska fakulteten, Institutionen för neurovetenskap, Funktionell farmakologi.
    The Membrane Proteome: Evolution, Characteristics and Classification2012Doktoravhandling, med artikler (Annet vitenskapelig)
    Abstract [en]

    Membrane proteins are found in all kingdoms of life and are essential for cellular interactions with the environment. Although a large research effort have been put into this group many membrane proteins remains uncharacterized, both in terms of function and evolutionary history. We have estimated the component of α-helical membrane proteins within the human proteome; the membrane proteome. We found that the human membrane proteome make up 27% of all protein, which we could classify the majority of into 234 families and further into three major functional groups: receptors, transporters or enzymes. We extended this analysis by determining the membrane proteome of 24 organisms that covers all major groups of eukaryotes. This comprehensive membrane protein catalog of over 100,000 proteins was utilized to determine the evolutionary history of all membrane protein families throughout eukaryotes.  We also investigated the evolutionary history across eukaryotes of the antiviral Interferon induced transmembrane proteins (IFITM) and the G protein-coupled receptor (GPCR) superfamily in detail.  We identified ten novel human homologs to the IFITM proteins, which together with the known IFITMs forms a family that we call the Dispanins. Using phylogenetic analysis we show that the Dispanins first emerged in eukaryotes in a common ancestor of choanoflagellates and animals, and that the family later expanded in vertebrates into four subfamilies. The GPCR superfamily was mined across eukaryotic species and we present evidence for a common origin for four of the five main human GPCR families; Rhodopsin, Frizzled, Adhesion and Secretin in the cAMP receptor family that was found in non-metazoans and invertebrates, but has been lost in vertebrates. Here we present the first accurate estimation of the human proteome together with comprehensive functional and evolutionary classification and extend it to organisms that represents all major eukaryotic groups. Moreover, we identify a novel protein family, the Dispanins, which has an evolutionary history that has been formed by horizontal gene transfer from bacteria followed by expansions in the animal lineage. We also study the evolution of the GPCR superfamily throughout eukaryotic evolution and provide a comprehensive model of the evolution and relationship of these receptors.

  • 1563.
    Sällman Almén, Markus
    et al.
    Uppsala universitet, Medicinska och farmaceutiska vetenskapsområdet, Medicinska fakulteten, Institutionen för neurovetenskap, Funktionell farmakologi.
    Fredriksson, Robert
    Uppsala universitet, Medicinska och farmaceutiska vetenskapsområdet, Medicinska fakulteten, Institutionen för neurovetenskap, Funktionell farmakologi.
    Schiöth, Helgi
    Uppsala universitet, Medicinska och farmaceutiska vetenskapsområdet, Medicinska fakulteten, Institutionen för neurovetenskap, Funktionell farmakologi.
    Evolution and characteristics of the membrane proteomeManuskript (preprint) (Annet vitenskapelig)
    Abstract [en]

    Membrane proteins are found in all kingdoms of life and have a diverse set of functions and occupy key roles in many biological systems.  The majority of integral membrane proteins span the membrane with one or more transmembrane alpha helices, which both anchors the protein in the membrane and is crucial for their role in cell-cell interactions and signaling over the membrane. Herein, we have determined all alpha helical transmembrane proteins from 24 complete eukaryotic proteomes, which spans the four eukaryotic super groups chromalveolates, plants, excavates and unikonts. Hence, for the first time we are able to investigate the evolutionary history of the membrane proteome. In total we identify 100 955 membrane proteins among the more than 400 000 investigated proteins. We are able to place 91% of the membrane proteins into candidate families using Markov clustering based on sequence similarity and Pfam protein family affiliation. We provide evidence that most of the transporter and enzyme family repertoire of present eukaryotes was present already in the last common ancestor of all eukaryotes. Moreover, we discuss the functional nature of loss and gain of membrane protein families across eukaryotes and provide a comprehensive resource of the evolutionary history of the human membrane proteome.

  • 1564.
    Söderberg, Axel
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för biologisk grundutbildning.
    Song recognition in nestling Ficedula Flycatchers2016Independent thesis Basic level (degree of Bachelor), 20 poäng / 30 hpOppgave
  • 1565.
    Sörlin, Sverker
    KTH, Skolan för arkitektur och samhällsbyggnad (ABE), Filosofi och teknikhistoria, Teknik- och vetenskapshistoria.
    Darwins On the Origin of Species 150 år 20092008Annet (Annet (populærvitenskap, debatt, mm))
  • 1566.
    Sörlin, Sverker
    KTH, Skolan för arkitektur och samhällsbyggnad (ABE), Filosofi och teknikhistoria, Teknik- och vetenskapshistoria (bytt namn 20120201).
    Oskulden före Darwin: Harriet från Galápagos död2006Inngår i: Dagens nyheter, ISSN 1101-2447, nr 2006-06-27Artikkel i tidsskrift (Annet (populærvitenskap, debatt, mm))
  • 1567.
    Takahashi, Daisuke
    et al.
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för matematik och matematisk statistik.
    Yamanaka, Takehiko
    Sudo, Masaaki
    Andow, David A.
    Is a larger refuge always better?: Dispersal and dose in pesticide resistance evolution2017Inngår i: Evolution, ISSN 0014-3820, E-ISSN 1558-5646, Vol. 71, nr 6, s. 1494-1503Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    The evolution of resistance against pesticides is an important problem of modern agriculture. The high-dose/refuge strategy, which divides the landscape into treated and nontreated (refuge) patches, has proven effective at delaying resistance evolution. However, theoretical understanding is still incomplete, especially for combinations of limited dispersal and partially recessive resistance. We reformulate a two-patch model based on the Comins model and derive a simple quadratic approximation to analyze the effects of limited dispersal, refuge size, and dominance for high efficacy treatments on the rate of evolution. When a small but substantial number of heterozygotes can survive in the treated patch, a larger refuge always reduces the rate of resistance evolution. However, when dominance is small enough, the evolutionary dynamics in the refuge population, which is indirectly driven by migrants from the treated patch, mainly describes the resistance evolution in the landscape. In this case, for small refuges, increasing the refuge size will increase the rate of resistance evolution. Our analysis distils major driving forces from the model, and can provide a framework for understanding directional selection in source-sink environments.

  • 1568.
    Talavera, David
    et al.
    Univ Manchester, Fac Life Sci, Manchester, Lancs, England..
    Lovell, Simon C.
    Univ Manchester, Fac Life Sci, Manchester, Lancs, England..
    Whelan, Simon
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Evolutionsbiologi. Univ Manchester, Fac Life Sci, Manchester, Lancs, England..
    Covariation Is a Poor Measure of Molecular Coevolution2015Inngår i: Molecular biology and evolution, ISSN 0737-4038, E-ISSN 1537-1719, Vol. 32, nr 9, s. 2456-2468Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Recent developments in the analysis of amino acid covariation are leading to breakthroughs in protein structure prediction, protein design, and prediction of the interactome. It is assumed that observed patterns of covariation are caused by molecular coevolution, where substitutions at one site affect the evolutionary forces acting at neighboring sites. Our theoretical and empirical results cast doubt on this assumption. We demonstrate that the strongest coevolutionary signal is a decrease in evolutionary rate and that unfeasibly long times are required to produce coordinated substitutions. We find that covarying substitutions are mostly found on different branches of the phylogenetic tree, indicating that they are independent events that may or may not be attributable to coevolution. These observations undermine the hypothesis that molecular coevolution is the primary cause of the covariation signal. In contrast, we find that the pairs of residues with the strongest covariation signal tend to have low evolutionary rates, and that it is this low rate that gives rise to the covariation signal. Slowly evolving residue pairs are disproportionately located in the protein's core, which explains covariation methods' ability to detect pairs of residues that are close in three dimensions. These observations lead us to propose the "coevolution paradox": The strength of coevolution required to cause coordinated changes means the evolutionary rate is so low that such changes are highly unlikely to occur. As modern covariation methods may lead to breakthroughs in structural genomics, it is critical to recognize their biases and limitations.

  • 1569.
    Talla, Venkat
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Evolutionsbiologi. Uppsala University.
    Speciation genetics of recently diverged species: 2018Doktoravhandling, med artikler (Annet vitenskapelig)
    Abstract [en]

    Species differentiation can be a consequence of evolutionary forces including natural selection and random genetic drift. Patterns of genomic differentiation vary across the tree of life. This variation seems to be dependent on, for example, differences in genomic architecture and molecular mechanisms. However, the knowledge we currently possess, both regarding the processes driving speciation and the resulting genomic signatures, is from a very small subset of the overall biodiversity that resides on the planet. Therefore, characterization of the architecture of genomic divergence from more organism groups will be important to understand the effects of molecular mechanisms and evolutionary forces driving divergence between lineages. Hence it has not been possible to come to a consensus on the relative importance of genetic drift and natural selection on divergence processes in general. In this thesis, I use genomic approaches to investigate the forces underlying species and population differentiation in the European cryptic wood white butterflies (Leptidea sinapisL. reali and L. juvernica) and two closely related bird species, the chiffchaff (Phylloscopus collybita abietinus) and the Siberian chiffchaff (P. tristis). Both these groups contain recently diverged species, a prerequisite for investigating initial differentiation processes. However, the study systems also differ in several respects, allowing for applying distinct approaches to understand the divergence process in each system.

    In summary, by applying a suite of genomic approaches, my thesis work gives novel insights into the speciation history of wood whites and chiffchaff. I identify candidate genes for local adaptation in both systems and concludes that genome differentiation in wood white butterflies have been driven by a combination of random genetic drift and week directional selection in allopatry. In the chiffchaff, the general differentiation landscape seems to have been shaped by recurrent background selection (and potentially selective sweeps), likely as a consequence of regional variation in the recombination rate which has also been observed in other genome-scans in birds. Potentially, some of the highly differentiated regions contain barriers to gene-flow as these regions are still present in sympatry, where species exchange genetic material at a high rate.

  • 1570.
    Talla, Venkat
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Evolutionsbiologi.
    Kalsoom, Faheema
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Evolutionsbiologi.
    Shipilina, Daria
    Lomonosov Moscow State Univ, Dept Vertebrate Zool, Moscow 119991, Russia..
    Marova, Irina
    Lomonosov Moscow State Univ, Dept Vertebrate Zool, Moscow 119991, Russia..
    Backström, Niclas
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Evolutionsbiologi.
    Heterogeneous Patterns of Genetic Diversity and Differentiation in European and Siberian Chiffchaff (Phylloscopus collybita abietinus/P. tristis)2017Inngår i: G3: Genes, Genomes, Genetics, ISSN 2160-1836, E-ISSN 2160-1836, Vol. 7, nr 12, s. 3983-3998Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Identification of candidate genes for trait variation in diverging lineages and characterization of mechanistic underpinnings of genome differentiation are key steps toward understanding the processes underlying the formation of new species. Hybrid zones provide a valuable resource for such investigations, since they allow us to study how genomes evolve as species exchange genetic material and to associate particular genetic regions with phenotypic traits of interest. Here, we use whole-genome resequencing of both allopatric and hybridizing populations of the European (Phylloscopus collybita abietinus) and the Siberian chiffchaff (P. tristis)-two recently diverged species which differ in morphology, plumage, song, habitat, and migration-to quantify the regional variation in genome-wide genetic diversity and differentiation, and to identify candidate regions for trait variation. We find that the levels of diversity, differentiation, and divergence are highly heterogeneous, with significantly reduced global differentiation, and more pronounced differentiation peaks in sympatry than in allopatry. This pattern is consistent with regional differences in effective population size and recurrent background selection or selective sweeps reducing the genetic diversity in specific regions prior to lineage divergence, but the data also suggest that post-divergence selection has resulted in increased differentiation and fixed differences in specific regions. We find that hybridization and backcrossing is common in sympatry, and that phenotype is a poor predictor of the genomic composition of sympatric birds. The combination of a differentiation scan approach with identification of fixed differences pinpoint a handful of candidate regions that might be important for trait variation between the two species.

  • 1571.
    Talla, Venkat
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Evolutionsbiologi.
    Suh, Alexander
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Evolutionsbiologi.
    Kalsoom, Faheema
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Evolutionsbiologi.
    Dinca, Vlad
    Inst Biol Evolut CSIC UPF, Anim Biodivers & Evolut Program, Barcelona, Spain..
    Vila, Roger
    Inst Biol Evolut CSIC UPF, Anim Biodivers & Evolut Program, Barcelona, Spain..
    Friberg, Magne
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Växtekologi och evolution.
    Wiklund, Christer
    Stockholm Univ, Div Ecol, Dept Zool, Stockholm, Sweden..
    Backström, Niclas
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Evolutionsbiologi.
    Rapid Increase in Genome Size as a Consequence of Transposable Element Hyperactivity in Wood-White (Leptidea) Butterflies2017Inngår i: Genome Biology and Evolution, ISSN 1759-6653, E-ISSN 1759-6653, Vol. 9, nr 10, s. 2491-2505Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Characterizing and quantifying genome size variation among organisms and understanding if genome size evolves as a consequence of adaptive or stochastic processes have been long-standing goals in evolutionary biology. Here, we investigate genome size variation and association with transposable elements (TEs) across lepidopteran lineages using a novel genome assembly of the common wood-white (Leptidea sinapis) and population re-sequencing data from both L. sinapis and the closely related L. reali and L. juvernica together with 12 previously available lepidopteran genome assemblies. A phylogenetic analysis confirms established relationships among species, but identifies previously unknown intraspecific structure within Leptidea lineages. The genome assembly of L. sinapis is one of the largest of any lepidopteran taxon so far (643Mb) and genome size is correlated with abundance of TEs, both in Lepidoptera in general and within Leptidea where L. juvernica from Kazakhstan has considerably larger genome size than any other Leptidea population. Specific TE subclasses have been active in different Lepidoptera lineages with a pronounced expansion of predominantly LINEs, DNA elements, and unclassified TEs in the Leptidea lineage after the split from other Pieridae. The rate of genome expansion in Leptidea in general has been in the range of four Mb/Million year (My), with an increase in a particular L. juvernica population to 72Mb/My. The considerable differences in accumulation rates of specific TE classes in different lineages indicate that TE activity plays a major role in genome size evolution in butterflies and moths.

  • 1572.
    Tamarit, Daniel
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för cell- och molekylärbiologi, Molekylär evolution.
    Evolution of symbiotic lineages and the origin of new traits2016Doktoravhandling, med artikler (Annet vitenskapelig)
    Abstract [en]

    This thesis focuses on the genomic study of symbionts of two different groups of hymenopterans: bees and ants. Both groups of insects have major ecological impact, and investigating their microbiomes increases our understanding of their health, diversity and evolution.

    The study of the bee gut microbiome, including members of Lactobacillus and Bifidobacterium, revealed genomic processes related to the adaptation to the gut environment, such as the expansion of genes for carbohydrate metabolism and the acquisition of genes for interaction with the host. A broader genomic study of these genera demonstrated that some lineages evolve under strong and opposite substitution biases, leading to extreme GC content values. A comparison of codon usage patterns in these groups revealed ongoing shifts of optimal codons.

    In a separate study we analysed the genomes of several strains of Lactobacillus kunkeei, which inhabits the honey stomach of bees but is not found in their gut. We observed signatures of genome reduction and suggested candidate genes for host-interaction processes. We discovered a novel type of genome architecture where genes for metabolic functions are located in one half of the genome, whereas genes for information processes are located in the other half. This genome organization was also found in other Lactobacillus species, indicating that it was an ancestral feature that has since been retained. We suggest mechanisms and selective forces that may cause the observed organization, and describe processes leading to its loss in several lineages independently.

    We also studied the genome of a species of Rhizobiales bacteria found in ants. We discuss its metabolic capabilities and suggest scenarios for how it may affect the ants’ lifestyle. This genome contained a region with homology to the Bartonella gene transfer agent (GTA), which is a domesticated bacteriophage used to transfer bacterial DNA between cells. We propose that its unique behaviour as a specialist GTA, preferentially transferring host-interaction factors, originated from a generalist GTA that transferred random segments of chromosomal DNA.

    These bioinformatic analyses of previously uncharacterized bacterial lineages have increased our understanding of their physiology and evolution and provided answers to old and new questions in fundamental microbiology.

  • 1573.
    Tamarit, Daniel
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för cell- och molekylärbiologi, Molekylär evolution.
    Dyrhage, Karl
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för cell- och molekylärbiologi, Molekylär evolution.
    Edblom, Johan
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för cell- och molekylärbiologi, Molekylär evolution.
    Ås, Joel
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för cell- och molekylärbiologi, Molekylär evolution.
    Andersson, Siv G. E.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för cell- och molekylärbiologi, Molekylär evolution.
    Functionally structured genome architectures in Lactobacillus – insights into their variability and evolutionManuskript (preprint) (Annet vitenskapelig)
    Abstract [en]

    Bacterial genome architectures evolve in response to selective pressures on the interplay between replication and gene expression. Several genomes contain a higher fraction of genes coding for proteins involved in information processes near the origin of replication, which is thought to be due to selection for rapid growth. We recently described a novel type of genome architecture in Lactobacillus kunkeei (Tamarit, et al. 2015). In this genome, vertically inherited genes encoding proteins with roles in translation and replication have accumulated in the chromosomal half surrounding the terminus of replication, while species-specific genes, and genes encoding proteins with metabolic and transport functions have accumulated in the chromosomal half around the origin of replication. Here, we show that this pattern is present also in the closest relatives of L. kunkeei, and similar but not identical biased genome architectures are present in other groups within the Lactobacillaceae. Thus, the biased genome structure in L. kunkeei has emerged from an ancestral clustering of vertically inherited genes around the terminus of replication, while horizontally acquired genes have been inserted near the origin of replication. The genome bias has been lost independently in several groups due to insertions of mobile elements near the terminus of replication and/or major genome rearrangements. We propose chromosomal structuring in macrodomains in the Lactobacillaceae, and suggest that further exploration of its functional consequences and generality will provide valuable insights into the forces that shape genome organization in bacteria. 

  • 1574.
    Tamarit, Daniel
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för cell- och molekylärbiologi, Molekylär evolution.
    Ellegaard, Kirsten Maren
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för cell- och molekylärbiologi, Molekylär evolution.
    Wikander, Johan
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för cell- och molekylärbiologi, Molekylär evolution.
    Olofsson, Tobias
    Lund University.
    Vásquez, Alejandra
    Lund University.
    Andersson, Siv
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för cell- och molekylärbiologi, Molekylär evolution.
    Comparative Genomics of Lactobacillus kunkeii indicates Selection for Rapid Growth in the BeebreadManuskript (preprint) (Annet vitenskapelig)
  • 1575.
    Tamarit, Daniel
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för cell- och molekylärbiologi, Molekylär evolution. Uppsala universitet, Science for Life Laboratory, SciLifeLab.
    Neuvonen, Minna M.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för cell- och molekylärbiologi, Molekylär evolution. Uppsala universitet, Science for Life Laboratory, SciLifeLab.
    Engel, Philipp
    University of Lausanne.
    Guy, Lionel
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för cell- och molekylärbiologi, Molekylär evolution. Uppsala universitet, Science for Life Laboratory, SciLifeLab. Uppsala universitet, Medicinska och farmaceutiska vetenskapsområdet, Medicinska fakulteten, Institutionen för medicinsk biokemi och mikrobiologi.
    Andersson, Siv G. E.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för cell- och molekylärbiologi, Molekylär evolution. Uppsala universitet, Science for Life Laboratory, SciLifeLab.
    Origin and evolution of the Bartonella Gene Transfer Agent2018Inngår i: Molecular biology and evolution, ISSN 0737-4038, E-ISSN 1537-1719, Vol. 35, nr 2, s. 451-464Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Gene transfer agents (GTAs) are domesticated bacteriophages that have evolved into molecular machines for the transferof bacterial DNA. Despite their widespread nature and their biological implications, the mechanisms and selective forcesthat drive the emergence of GTAs are still poorly understood. Two GTAs have been identifiedintheAlphaproteobacteria:the RcGTA, which is widely distributed in a broad range of species; and the BaGTA, which has a restricted host range thatincludes vector-borne intracellular bacteria of the genusBartonella. The RcGTA packages chromosomal DNA randomly,whereas the BaGTA particles contain a relatively higher fraction of genes for host interaction factors that are amplifiedfrom a nearby phage-derived origin of replication. In this study, we compare the BaGTA genes with homologous bac-teriophage genes identified in the genomes ofBartonellaspecies and close relatives. Unlike the BaGTA, the prophagegenes are neither present in all species, nor inserted into homologous genomic sites. Phylogenetic inferences and sub-stitution frequency analyses confirm codivergence of the BaGTA with the host genome, as opposed to multiple integra-tion and recombination events in the prophages. Furthermore, the organizationof segments flanking the BaGTA differsfrom that of the prophages by a few rearrangement events,which have abolished the normal coordination betweenphage genome replication and phage gene expression. Based on the results of our comparative analysis, we propose amodel for how a prophage may be transformed into a GTA that transfers amplified bacterial DNA segments.

  • 1576. Tamas, I
    et al.
    Klasson, L M
    Sandström, J P
    Andersson, S G
    Mutualists and parasites: how to paint yourself into a (metabolic) corner.2001Inngår i: FEBS Letters, ISSN 0014-5793, E-ISSN 1873-3468, Vol. 498, nr 2-3, s. 135-9Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Eukaryotes have developed an elaborate series of interactions with bacteria that enter their bodies and/or cells. Genome evolution of symbiotic and parasitic bacteria multiplying inside eukaryotic cells results in both convergent and divergent changes. The genome sequences of the symbiotic bacteria of aphids, Buchnera aphidicola, and the parasitic bacteria of body louse and humans, Rickettsia prowazekii, provide insights into these processes. Convergent genome characteristics include reduction in genome sizes and lowered G+C content values. Divergent evolution was recorded for amino acid and cell wall biosynthetic genes. The presence of pseudogenes in both genomes provides examples of recent gene inactivation events and offers clues to the process of genome deterioration and host-cell adaptation.

  • 1577. Tamas, Ivica
    et al.
    Klasson, Lisa
    Canbäck, Björn
    Näslund, A Kristina
    Eriksson, Ann-Sofie
    Wernegreen, Jennifer J
    Sandström, Jonas P
    Moran, Nancy A
    Andersson, Siv G E
    50 million years of genomic stasis in endosymbiotic bacteria.2002Inngår i: Science, ISSN 0036-8075, E-ISSN 1095-9203, Vol. 296, nr 5577, s. 2376-9Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Comparison of two fully sequenced genomes of Buchnera aphidicola, the obligate endosymbionts of aphids, reveals the most extreme genome stability to date: no chromosome rearrangements or gene acquisitions have occurred in the past 50 to 70 million years, despite substantial sequence evolution and the inactivation and loss of individual genes. In contrast, the genomes of their closest free-living relatives, Escherichia coli and Salmonella spp., are more than 2000-fold more labile in content and gene order. The genomic stasis of B. aphidicola, likely attributable to the loss of phages, repeated sequences, and recA, indicates that B. aphidicola is no longer a source of ecological innovation for its hosts.

  • 1578.
    Tamas, Ivica
    et al.
    Uppsala University ; Stockholm University.
    Wernegreen, Jennifer J
    Marine Biological Laboratory, USA.
    Nystedt, Björn
    Uppsala University.
    Kauppinen, Seth N
    Marine Biological Laboratory, USA.
    Darby, Alistair C
    Uppsala University.
    Gomez-Valero, Laura
    Uppsala University.
    Lundin, Daniel
    Stockholm University.
    Poole, Anthony M
    Stockholm University.
    Andersson, Siv G E
    Uppsala University.
    Endosymbiont gene functions impaired and rescued by polymerase infidelity at poly(A) tracts2008Inngår i: Proceedings of the National Academy of Sciences of the United States of America, ISSN 0027-8424, E-ISSN 1091-6490, Vol. 105, nr 39, s. 14934-9Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Among host-dependent bacteria that have evolved by extreme reductive genome evolution, long-term bacterial endosymbionts of insects have the smallest (160-790 kb) and most A + T-rich (>70%) bacterial genomes known to date. These genomes are riddled with poly(A) tracts, and 5-50% of genes contain tracts of 10 As or more. Here, we demonstrate transcriptional slippage at poly(A) tracts within genes of Buchnera aphidicola associated with aphids and Blochmannia pennsylvanicus associated with ants. Several tracts contain single frameshift deletions; these apparent pseudogenes showed patterns of constraint consistent with purifying selection on the encoded proteins. Transcriptional slippage yielded a heterogeneous population of transcripts with variable numbers of As in the tract. Across several frameshifted genes, including B. aphidicola cell wall biosynthesis genes and a B. pennsylvanicus histidine biosynthesis gene, 12-50% of transcripts contained corrected reading frames that could potentially yield full-length proteins. In situ immunostaining confirmed the production of the cell wall biosynthetic enzyme UDP-N-acetylmuramyl pentapeptide synthase encoded by the frameshifted murF gene. Simulation studies indicated an overrepresentation of poly(A) tracts in endosymbiont genomes relative to other A + T-rich bacterial genomes. Polymerase infidelity at poly(A) tracts rescues the functionality of genes with frameshift mutations and, conversely, reduces the efficiency of expression for in-frame genes carrying poly(A) regions. These features of homopolymeric tracts could be exploited to manipulate gene expression in small synthetic genomes.

  • 1579.
    Tan, Biyue
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för ekologi, miljö och geovetenskap. Stora Enso AB.
    Genomic selection and genome-wide association studies to dissect quantitative traits in forest trees2018Doktoravhandling, med artikler (Annet vitenskapelig)
    Abstract [en]

    The convergence of quantitative genetics of complex traits with genomic technologies is quickly becoming an innovative approach to explore fundamental genetic questions and also have practical consequences for implementations in tree breeding. In this thesis, I used genomic selection and genome-wide association studies (GWAS) to dissect the genetic basis of quantitative traits, i.e. growth, phenology and wood property traits. I also assessed the importance of dominance and epistatic effects in hybrid Eucalyptus. Both dominance and epistasis are important in hybrids, as they are the likely contributing to the genetic basis of heterosis. To successfully implement genomic selection models, several important factors have to be considered. I found that for a good model establishment, both the size and composition of the training population, as well as the number of SNPs to be important considered. Based on the optimal models, additive, dominance and epistasis genetic effects of growth and wood traits have been estimated to evaluate genetic parameters and how these influence the prediction accuracy, which can be used in selecting elite breeding individuals or clones. I also addressed the advantage of genotyping-based analyses by showing that we could accurately correct pedigree information errors. More importantly, genotyping-based analyses capture both Mendelian segregation variation within full-sib families and cryptic genetic links through unknown common ancestors, which are not available from traditional pedigree data. GWAS were used to analyse growth and phenology related traits. Using a single-trait GWAS method, we identified a region strongly associated with the timing of bud set in Populus tremula, a trait with high heritability. For the growth related traits, we found that a multi-traits GWAS approach was more powerful than single-trait analyses as it identified more associated SNPs in hybrid Eucalyptus. Moreover, many more novel associated SNPs were identified from considering over-dominance effects in the GWAS analyses. After annotating the associated SNPs I show that these functional candidate genes were related to growth and responding to abiotic and biotic stress. In summary, the results of genomic selection and GWAS provided a deeper understanding of the genetic backgrounds of quantitative traits in forest trees.

  • 1580.
    Tan, Biyue
    et al.
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC). Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för ekologi, miljö och geovetenskap. Biomaterials Division, Stora Enso AB, Nacka SE-13104, Sweden.
    Grattapaglia, Dario
    Martins, Gustavo Salgado
    Ferreira, Karina Zamprogno
    Sundberg, Björn
    Ingvarsson, Pär K.
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC). Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för ekologi, miljö och geovetenskap.
    Evaluating the accuracy of genomic prediction of growth and wood traits in two Eucalyptus species and their F-1 hybrids2017Inngår i: BMC Plant Biology, ISSN 1471-2229, E-ISSN 1471-2229, Vol. 17, artikkel-id 110Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Background: Genomic prediction is a genomics assisted breeding methodology that can increase genetic gains by accelerating the breeding cycle and potentially improving the accuracy of breeding values. In this study, we use 41,304 informative SNPs genotyped in a Eucalyptus breeding population involving 90 E. grandis and 78 E. urophylla parents and their 949 F-1 hybrids to develop genomic prediction models for eight phenotypic traits-basic density and pulp yield, circumference at breast height and height and tree volume scored at age three and six years. We assessed the impact of different genomic prediction methods, the composition and size of the training and validation set and the number and genomic location of SNPs on the predictive ability (PA). Results: Heritabilities estimated using the realized genomic relationship matrix (GRM) were considerably higher than estimates based on the expected pedigree, mainly due to inconsistencies in the expected pedigree that were readily corrected by the GRM. Moreover, the GRM more precisely capture Mendelian sampling among related individuals, such that the genetic covariance was based on the true proportion of the genome shared between individuals. PA improved considerably when increasing the size of the training set and by enhancing relatedness to the validation set. Prediction models trained on pure species parents could not predict well in F-1 hybrids, indicating that model training has to be carried out in hybrid populations if one is to predict in hybrid selection candidates. The different genomic prediction methods provided similar results for all traits, therefore either GBLUP or rrBLUP represents better compromises between computational time and prediction efficiency. Only slight improvement was observed in PA when more than 5000 SNPs were used for all traits. Using SNPs in intergenic regions provided slightly better PA than using SNPs sampled exclusively in genic regions. Conclusions: The size and composition of the training set and number of SNPs used are the two most important factors for model prediction, compared to the statistical methods and the genomic location of SNPs. Furthermore, training the prediction model based on pure parental species only provide limited ability to predict traits in interspecific hybrids. Our results provide additional promising perspectives for the implementation of genomic prediction in Eucalyptus breeding programs by the selection of interspecific hybrids.

  • 1581.
    Tavares, Valeria da C.
    et al.
    Univ Fed Minas Gerais, Inst Ciencias Biol, Dept Zool, Belo Horizonte, MG, Brazil.;UEMG, Dept Ciencias Biol, Ibirite, MG, Brazil..
    Warsi, Omar M.
    Uppsala universitet, Medicinska och farmaceutiska vetenskapsområdet, Medicinska fakulteten, Institutionen för medicinsk biokemi och mikrobiologi. SUNY Stony Brook, Dept Ecol & Evolut, Stony Brook, NY 11794 USA..
    Balseiro, Fernando
    Minist Ciencia Tecnol & Medio Ambiente, Inst Ecol & Sistemat, Div Colecc Zool, Havana, Cuba..
    Mancina, Carlos A.
    CITMA, Inst Ecol & Sistemat, Div Zool, Havana, Cuba..
    Davalos, Liliana M.
    SUNY Stony Brook, Dept Ecol & Evolut, Stony Brook, NY 11794 USA.;SUNY Stony Brook, Sch Marine & Atmospher Sci, Consortium Interdisciplinary Environm Res, Stony Brook, NY 11794 USA..
    Out of the Antilles: Fossil phylogenies support reverse colonization of bats to South America2018Inngår i: Journal of Biogeography, ISSN 0305-0270, E-ISSN 1365-2699, Vol. 45, nr 4, s. 859-873Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Aim: Previous phylogenies of extant short-faced bats (Chiroptera: Stenodermatina) supported either two colonization events from the mainland to the Antilles, or reverse colonization, but lacked both fossil data and statistical modelling of biogeography. Recent multi-locus phylogenies of noctilionoid bats and likelihood modelling of ancestral ranges support a continental origin for the clade. We include all known extinct and extant stenodermatina species and apply statistical modelling to test competing biogeographical hypotheses. Location: The Neotropics, including the Antilles. Methods: We combined mitochondrial and nuclear sequences with 302 new morphological characters to infer phylogenies. Bayesian tip-dating analyses applied codon models to protein-coding genes, with relaxed molecular clocks fitting a compound Poisson process. The combined maximum clade credibility tree was used in comparisons of alternative biogeographical models. Results: The new phylogenies support the fossil Cubanycteris silvai as sister to all extant species of short-faced bats. Among Artibeus (the sister group to short-faced bats), the Antillean fossil A. anthonyi has distinctive characters and is nested within the subgenus Artibeus. The common ancestor of all short-faced bats is inferred to be Antillean, as a mainland origin is unlikely. Founder-event speciation is the most probable process explaining the distribution of these highly divergent fossil lineages. Main conclusions: Dated, character-based phylogenies of fossil species are indispensable for biogeographical inference: without fossils, biogeographical analyses find a mainland origin for short-faced bats. The rate of founder speciation in this clade is twice as high as the estimate from noctilionoids in general, highlighting the role of founder events in the diversification of island taxa. Although rare, reverse colonization contributes key species to continental communities. Short-faced bats, including Cubanycteris, share biomechanical adaptations for a strong bite conferring access to harder figs. We hypothesize these adaptations and characters related to roosting ecology enabled ancestral lineages to successfully establish and diversify on the mainland.

  • 1582. Tedersoo, Leho
    et al.
    Bahram, Mohammad
    Ryberg, Martin
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för organismbiologi, Systematisk biologi.
    Otsing, Eveli
    Koljalg, Urmas
    Abarenkov, Kessy
    Global biogeography of the ectomycorrhizal/sebacina lineage (Fungi, Sebacinales) as revealed from comparative phylogenetic analyses2014Inngår i: Molecular Ecology, ISSN 0962-1083, E-ISSN 1365-294X, Vol. 23, nr 16, s. 4168-4183Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Compared with plants and animals, large-scale biogeographic patterns of microbes including fungi are poorly understood. By the use of a comparative phylogenetic approach and ancestral state reconstructions, we addressed the global biogeography, rate of evolution and evolutionary origin of the widely distributed ectomycorrhizal (EcM) /sebacina lineage that forms a large proportion of the Sebacinales order. We downloaded all publicly available internal transcribed spacer (ITS) sequences and metadata and supplemented sequence information from three genes to construct dated phylogenies and test biogeographic hypotheses. The /sebacina lineage evolved 45-57Myr ago that groups it with relatively young EcM taxa in other studies. The most parsimonious origin for /sebacina is inferred to be North American temperate coniferous forests. Among biogeographic traits, region and biome exhibited stronger phylogenetic signal than host family. Consistent with the resource availability (environmental energy) hypothesis, the ITS region is evolving at a faster rate in tropical than nontropical regions. Most biogeographic regions exhibited substantial phylogenetic clustering suggesting a strong impact of dispersal limitation over a large geographic scale. In northern Holarctic regions, however, phylogenetic distances and phylogenetic grouping of isolates indicate multiple recent dispersal events.

  • 1583.
    Tedersoo, Leho
    et al.
    Univ Tartu, Nat Hist Museum, 14a Ravila, EE-50411 Tartu, Estonia;Univ Tartu, Inst Ecol & Earth Sci, 14a Ravila, EE-50411 Tartu, Estonia;Estonian Young Acad Sci, 6 Kohtu, Tallinn, Estonia.
    Sanchez-Ramirez, Santiago
    Univ Toronto, Dept Ecol & Evolutionary Biol, 25 Willcocks St, Toronto, ON M5S 3B2, Canada.
    Koljalg, Urmas
    Univ Tartu, Inst Ecol & Earth Sci, 14a Ravila, EE-50411 Tartu, Estonia.
    Bahram, Mohammad
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för organismbiologi, Systematisk biologi. Estonian Young Acad Sci, 6 Kohtu, Tallinn, Estonia.
    Doring, Markus
    Global Biodivers Informat Facil, Copenhagen, Denmark.
    Schigel, Dmitry
    Global Biodivers Informat Facil, Copenhagen, Denmark;Univ Helsinki, Dept Biosci, Helsinki, Finland.
    May, Tom
    Royal Bot Gardens Victoria, Birdwood Ave, Melbourne, Vic 3004, Australia.
    Ryberg, Martin
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för organismbiologi, Systematisk biologi.
    Abarenkov, Kessy
    Univ Tartu, Nat Hist Museum, 14a Ravila, EE-50411 Tartu, Estonia.
    High-level classification of the Fungi and a tool for evolutionary ecological analyses2018Inngår i: Fungal diversity, ISSN 1560-2745, E-ISSN 1878-9129, Vol. 90, nr 1, s. 135-159Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    High-throughput sequencing studies generate vast amounts of taxonomic data. Evolutionary ecological hypotheses of the recovered taxa and Species Hypotheses are difficult to test due to problems with alignments and the lack of a phylogenetic backbone. We propose an updated phylum-and class-level fungal classification accounting for monophyly and divergence time so that the main taxonomic ranks are more informative. Based on phylogenies and divergence time estimates, we adopt phylum rank to Aphelidiomycota, Basidiobolomycota, Calcarisporiellomycota, Glomeromycota, Entomophthoromycota, Entorrhizomycota, Kickxellomycota, Monoblepharomycota, Mortierellomycota and Olpidiomycota. We accept nine subkingdoms to accommodate these 18 phyla. We consider the kingdom Nucleariae (phyla Nuclearida and Fonticulida) as a sister group to the Fungi. We also introduce a perl script and a newick-formatted classification backbone for assigning Species Hypotheses into a hierarchical taxonomic framework, using this or any other classification system. We provide an example of testing evolutionary ecological hypotheses based on a global soil fungal data set.

  • 1584. Tegelström, Håkan
    et al.
    Wyöni, Per-Ivan
    Gelter, Hans
    Jaarola, Maarit
    Concordant divergence in proteins and mitochondrial DNA between two vole species in the genus Clethrionomys1988Inngår i: Biochemical Genetics, ISSN 0006-2928, E-ISSN 1573-4927, Vol. 26, nr 3-4, s. 223-237Artikkel i tidsskrift (Fagfellevurdert)
  • 1585.
    Thibert-Plante, Xavier
    et al.
    National Institute for Mathematical and Biological Synthesis, University of Tennessee, Knoxville, TN, USA and Department of Ecology and Genetics, Uppsala University, Uppsala, Sweden.
    Gavrilets, Sergey
    National Institute for Mathematical and Biological Synthesis, University of Tennessee, Knoxville, TN, USA and Department of Ecology and Evolutionary Biology and Department of Mathematics, University of Tennessee, Knoxville, TN, USA .
    Evolution of mate choice and the so-called magic traits in ecological speciation2013Inngår i: Ecology Letters, ISSN 1461-023X, E-ISSN 1461-0248, Vol. 16, nr 8, s. 1004-1013Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Non-random mating provides multiple evolutionary benefits and can result in speciation. Biological organisms are characterised by a myriad of different traits, many of which can serve as mating cues. We consider multiple mechanisms of non-random mating simultaneously within a unified modelling framework in an attempt to understand better which are more likely to evolve in natural populations going through the process of local adaptation and ecological speciation. We show that certain traits that are under direct natural selection are more likely to be co-opted as mating cues, leading to the appearance of magic traits (i.e. phenotypic traits involved in both local adaptation and mating decisions). Multiple mechanisms of non-random mating can interact so that trait co-evolution enables the evolution of non-random mating mechanisms that would not evolve alone. The presence of magic traits may suggest that ecological selection was acting during the origin of new species.

  • 1586.
    Thibert-Plante, Xavier
    et al.
    Redpath Museum and Department of Biology, McGill University, Montréal, QC, Canada and National Institute for Mathematical and Biological Synthesis, University of Tennessee, Knoxville, TN, USA.
    Hendry, A. P.
    Redpath Museum and Department of Biology, McGill University, Montréal, QC, Canada.
    Factors influencing progress toward sympatric speciation2011Inngår i: Journal of Evolutionary Biology, ISSN 1010-061X, E-ISSN 1420-9101, Vol. 24, nr 10, s. 2186-2196Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Many factors could influence progress towards sympatric speciation. Some of the potentially important ones include competition, mate choice and the degree to which alternative sympatric environments (resources) are discrete. What is not well understood is the relative importance of these different factors, as well as interactions among them. We use an individual-based numerical model to investigate the possibilities. Mate choice was modelled as the degree to which male foraging traits influence female mate choice. Competition was modelled as the degree to which individuals with different phenotypes compete for portions of the resource distribution. Discreteness of the environment was modelled as the degree of bimodality of the underlying resource distribution. We find that strong mate choice was necessary, but not sufficient, to cause sympatric speciation. In addition, sympatric speciation was most likely when the resource distribution was strongly bimodal and when competition among different phenotypes was intermediate. Even under these ideal conditions, however, sympatric speciation occurred only a fraction of the time. Sympatric speciation owing to competition on unimodal resource distributions was also possible, but much less common. In all cases, stochasticity played an important role in determining progress towards sympatric speciation, as evidenced by variation in outcomes among replicate simulations for a given set of parameter values. Overall, we conclude that the nature of competition is much less important for sympatric speciation than is the nature of mate choice and the underlying resource distribution. We argue that an increased understanding of the promoters and inhibitors of sympatric speciation is best achieved through models that simultaneously evaluate multiple potential factors.

  • 1587.
    Thibert-Plante, Xavier
    et al.
    Redpath Museum and Department of Biology, McGill University, Montreal, QC, Canada.
    Hendry, A. P.
    Redpath Museum and Department of Biology, McGill University, Montréal, QC, Canada.
    Five questions on ecological speciation addressed with individual-based simulations2009Inngår i: Journal of Evolutionary Biology, ISSN 1010-061X, E-ISSN 1420-9101, Vol. 22, nr 1, s. 109-123Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    We use an individual-based simulation model to investigate factors influencing progress toward ecological speciation. We find that environmental differences can quickly lead to the evolution of substantial reproductive barriers between a population colonizing a new environment and the ancestral population in the old environment. Natural selection against immigrants and hybrids was a major contributor to this isolation, but the evolution of sexual preference was also important. Increasing dispersal had both positive and negative effects on population size in the new environment and had positive effects on natural selection against immigrants and hybrids. Genetic divergence at unlinked, neutral genetic markers was low, except when environmental differences were large and sexual preference was present. Our results highlight the importance of divergent selection and adaptive divergence for ecological speciation. At the same time, they reveal several interesting nonlinearities in interactions between environmental differences, sexual preference, dispersal and population size.

  • 1588.
    Thibert-Plante, Xavier
    et al.
    Redpath Museum and Department of Biology, McGill University, Montre´al, QC, Canada.
    Hendry, A. P.
    Redpath Museum and Department of Biology, McGill University, Montre´al, QC, Canada.
    The consequences of phenotypic plasticity for ecological speciation2011Inngår i: Journal of Evolutionary Biology, ISSN 1010-061X, E-ISSN 1420-9101, Vol. 24, nr 2, s. 326-342Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    We use an individual-based numerical simulation to study the effects of phenotypic plasticity on ecological speciation. We find that adaptive plasticity evolves readily in the presence of dispersal between populations from different ecological environments. This plasticity promotes the colonization of new environments but reduces genetic divergence between them. We also find that the evolution of plasticity can either enhance or degrade the potential for divergent selection to form reproductive barriers. Of particular importance here is the timing of plasticity in relation to the timing of dispersal. If plasticity is expressed after dispersal, reproductive barriers are generally weaker because plasticity allows migrants to be better suited for their new environment. If plasticity is expressed before dispersal, reproductive barriers are either unaffected or enhanced. Among the potential reproductive barriers we considered, natural selection against migrants was the most important, primarily because it was the earliest-acting barrier. Accordingly, plasticity had a much greater effect on natural selection against migrants than on sexual selection against migrants or on natural and sexual selection against hybrids. In general, phenotypic plasticity can strongly alter the process of ecological speciation and should be considered when studying the evolution of reproductive barriers.

  • 1589.
    Thibert-Plante, Xavier
    et al.
    Redpath Museum and Department of Biology, 859 Sherbrooke St. West, McGill University, Montréal, QC, Canada H3A 2K6.
    Hendry, Andrew P.
    Redpath Museum and Department of Biology, 859 Sherbrooke St. West, McGill University, Montréal, QC, Canada H3A 2K6.
    When can ecological speciation be detected with neutral loci?2010Inngår i: Molecular Ecology, ISSN 0962-1083, E-ISSN 1365-294X, Vol. 19, nr 11, s. 2301-2314Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    It is not yet clear under what conditions empirical studies can reliably detect progress toward ecological speciation through the analysis of allelic variation at neutral loci. We use a simulation approach to investigate the range of parameter space under which such detection is, and is not, likely. We specifically test for the conditions under which divergent natural selection can cause a ‘generalized barrier to gene flow’ that is present across the genome. Our individual-based numerical simulations focus on how population divergence at neutral loci varies in relation to recombination rate with a selected locus, divergent selection on that locus, migration rate and population size. We specifically test whether genetic differences at neutral markers are greater between populations in different environments than between populations in similar environments. We find that this expected signature of ecological speciation can be detected under part of the parameter space, most consistently when divergent selection is strong and migration is intermediate. By contrast, the expected signature of ecological speciation is not reliably detected when divergent selection is weak or migration is low or high. These findings provide insights into the strengths and weaknesses of using neutral markers to infer ecological speciation in natural systems.

  • 1590.
    Thibert-Plante, Xavier
    et al.
    Redpath Museum and Department of Biology, McGill University, Montréal, Québec, Canada.
    Parrott, Lael
    Complex Systems Laboratory, Département de Géographie, Université de Montréal, Montréal, Québec, Canada.
    Prisoner’s dilemma and clusters on small-world networks2007Inngår i: Complexity, ISSN 1076-2787, E-ISSN 1099-0526, Vol. 12, nr 6, s. 22-36Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    The structure of interaction plays an important role in the outcome of evolutionary games. This study investigates the evolution of stochastic strategies of the prisoner's dilemma played on structures ranging from lattices to small world networks. Strategies and payoffs are analyzed as a function of the network characteristics of the node they are playing on. Nodes with lattice-like neighborhoods tend to perform better than the nodes modified during the rewiring process of the construction of the small-world network.

  • 1591.
    Thompson, John N.
    et al.
    Univ Calif Santa Cruz, Dept Ecol & Evolutionary Biol, Santa Cruz, CA 95064 USA..
    Schwind, Christopher
    Univ Calif Santa Cruz, Dept Ecol & Evolutionary Biol, Santa Cruz, CA 95064 USA..
    Friberg, Magne
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Växtekologi och evolution.
    Diversification of Trait Combinations in Coevolving Plant and Insect Lineages2017Inngår i: American Naturalist, ISSN 0003-0147, E-ISSN 1537-5323, Vol. 190, nr 2, s. 171-184Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Closely related species often have similar traits and sometimes interact with the same species. A crucial problem in evolutionary ecology is therefore to understand how coevolving species diverge when they interact with a set of closely related species from another lineage rather than with a single species. We evaluated geographic differences in the floral morphology of all woodland star plant species (Lithophragma, Saxifragaceae) that are pollinated by Greya (Prodoxidae) moths. Flowers of each woodland star species differed depending on whether plants interact locally with one, two, or no pollinating moth species. Plants of one species grown in six different environments showed few differences in floral traits, suggesting that the geographic differences are not due significantly to trait plasticity. Greya moth populations also showed significant geographic divergence in morphology, depending on the local host and on whether the moth species co-occurred locally. Divergence in the plants and the moths involved shifts in combinations of partially correlated traits, rather than any one trait. The results indicate that the geographic mosaic of coevolution can be amplified as coevolving lineages diversify into separate species and come together in different combinations in different ecosystems.

  • 1592. Thompson, John N.
    et al.
    Schwind, Christopher
    Guimaraes, Paulo R
    Friberg, Magne
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Växtekologi och evolution.
    Diversification through multi-trait evolution in a coevolving interaction2013Inngår i: Proceedings of the National Academy of Sciences of the United States of America, ISSN 0027-8424, E-ISSN 1091-6490, Vol. 110, nr 28, s. 11487-11492Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Mutualisms between species are interactions in which reciprocal exploitation results in outcomes that are mutually beneficial. This reciprocal exploitation is evident in the more than a thousand plant species that are pollinated exclusively by insects specialized to lay their eggs in the flowers they pollinate. By pollinating each flower in which she lays eggs, an insect guarantees that her larval offspring have developing seeds on which to feed, whereas the plant gains a specialized pollinator at the cost of some seeds. These mutualisms are often reciprocally obligate, potentially driving not only ongoing coadaptation but also diversification. The lack of known intermediate stages in most of these mutualisms, however, makes it difficult to understand whether these interactions could have begun to diversify even before they became reciprocally obligate. Experimental studies of the incompletely obligate interactions between woodland star (Lithophragma; Saxifragaceae) plants and their pollinating floral parasites in the moth genus Greya (Prodoxidae) show that, as these lineages have diversified, the moths and plants have evolved in ways that maintain effective oviposition and pollination. Experimental assessment of pollination in divergent species and quantitative evaluation of time-lapse photographic sequences of pollination viewed on surgically manipulated flowers show that various combinations of traits are possible for maintaining the mutualism. The results suggest that at least some forms of mutualism can persist and even diversify when the interaction is not reciprocally obligate.

  • 1593.
    Thulin, Mats
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för organismbiologi, Systematisk biologi.
    Moore, Abigail J.
    Brown Univ, Dept Ecol & Evolutionary Biol, 80 Waterman St,Box G-W, Providence, RI 02912 USA..
    El-Seedi, Hesham
    Uppsala universitet, Medicinska och farmaceutiska vetenskapsområdet, Farmaceutiska fakulteten, Institutionen för läkemedelskemi, Avdelningen för farmakognosi. Univ Malaya, Dept Chem, Kuala Lumpur 50603, Malaysia..
    Larsson, Anders
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för organismbiologi, Systematisk biologi.
    Christin, Pascal-Antoine
    Univ Sheffield, Dept Anim & Plant Sci, Western Bank, Sheffield S10 2TN, S Yorkshire, England..
    Edwards, Erika J.
    Brown Univ, Dept Ecol & Evolutionary Biol, 80 Waterman St,Box G-W, Providence, RI 02912 USA..
    Phylogeny and generic delimitation in Molluginaceae, new pigment data in Caryophyllales, and the new family Corbichoniaceae2016Inngår i: Taxon, ISSN 0040-0262, E-ISSN 1996-8175, Vol. 65, nr 4, s. 775-793Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    The circumscription of Molluginaceae has changed radically in recent years, with Corbichonia being moved to Lophiocarpaceae, Limeum to Limeaceae, Macarthuria to Macarthuriaceae and all species of Hypertelis, except the type, to Kewa in Kewaceae. In a broad analysis of core Caryophyllales using plastid trnK-matK and rbcL, sequences, the position of Molluginaceae in a strict sense as sister to the Portulacineae Glade is corroborated, as are the positions of Corbichonia, Limeum and Kewa outside the family. The phylogeny of Molluginaceae is reconstructed based on trnK-matK and nuclear ITS sequences of about half of the currently recognized species in the family and with representatives from all recognized genera. Mollugo is found to be polyphyletic and a new taxonomy for the family with 11 genera is proposed. Mollugo in its new restricted sense is a mainly American genus of about 15 species, including M. ulei comb. nov., previously placed in the monotypic Glischrothamnus. The Australian and Asian genus Trigastrotheca is resurrected for T. molluginea, T. pentaphylla comb. nov. and T. stricta comb. nov. The name Paramollugo nom. nov. is proposed for the Mollugo nudicaulis group and the combinations P. angustifolia comb. nov., P. cuneifolia comb. nov., P. decandra comb. nov., P. deltoidea comb. nov., P. navassensis comb. nov. and P. nudicaulis comb. nov. are made. Hypertelis is expanded to include, besides the type H. spergulacea, also H. cerviana comb. nov., H. fragilis comb. nov., H. umbellata comb. nov. and H. walteri comb. nov. In Pharnaceum, the new combination P. namaquense comb. nov. is made, Hypertelis longifolia is treated as a synonym of P. lineare and Mollugo tenella as a synonym of P. subtile. Corbichonia is proposed to be treated as a family of its own, Corbichoniaceae fam. nov. Several names are lectotypified, including the Linnaean Mollugo pentaphylla and M stricta. An anthocyanin is reported for the first time from Simmondsiaceae. The detection of anthocyanins in members of Kewaceae and Molluginaceae agree with previous reports and corroborate the view that these families represent reversals from betalains to anthocyanins. The report of an anthocyanin in Limeaceae, previously regarded as unpigmented, apparently represents a newly detected reversal from betalains to anthocyanins in this family.

  • 1594.
    Thunga, Venkata Raghava Pavankumar
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för biologisk grundutbildning.
    Nucleotide diversity and Linkage disequilibrium in Norway spruce (Picea abies)2014Independent thesis Advanced level (degree of Master (Two Years)), 30 poäng / 45 hpOppgave
    Abstract [en]

    Pattern of Linkage Disequilibrium (LD) is a major factor largely determining the power of association mapping studies. Along with nucleotide diversities and DNA polymorphism, knowledge of patterns of LD along the genome needs to be to known to effectively design association mapping studies. In this study, patterns of nucleotide diversity, population structure, LD was estimated in Norway spruce (Picea abies). The data used for this were 23 nuclear loci sequenced in around 90 individuals originating from natural populations of Norway spruce throughout the current distribution range in Sweden and Finland. The observed levels of nucleotide diversity are variable among loci varying between 0.002 and 0.008 if measured by average pairwise nucleotide diversity. Despite the samples stretching large part of Finland and Sweden there were no evidence for strong population structure. As in earlier studies LD decays fast with distance and the average pattern of the squared correlation of allele frequencies drops to less than 0.2 within 100bp. In order to put the data in perspective previously generated data sets were re-analyzed and compared to the inferred results. 

  • 1595.
    Thuy, Ben
    et al.
    Geoscience Centre, University of Göttingen.
    Kiel, Steffen
    Geoscience Center, Göttingen.
    Dulai, Alfred
    Gale, Andy S.
    University of Portsmouth, UK.
    Kroh, Andreas
    Natural History Museum, Vienna.
    Lord, Alan S.
    Numberger-Thuy, Lea
    Stöhr, Sabine
    Naturhistoriska riksmuseet, Enheten för zoologi.
    Wisshak, Max
    First glimpse into Lower Jurassic deep-sea biodiversity: in situ diversification and resilience against extinction2014Inngår i: Proceedings of the Royal Society of London. Biological Sciences, ISSN 0962-8452, E-ISSN 1471-2954, Vol. 281, artikkel-id 20132624Artikkel i tidsskrift (Fagfellevurdert)
  • 1596.
    Tibblin, Petter
    Linnéuniversitetet, Institutionen för biologi och miljö (BOM).
    Migratory behaviour and adaptive divergence in life-history traits of pike (Esox lucius)2015Doktoravhandling, med artikler (Annet vitenskapelig)
    Abstract [en]

    Population divergence shaped by natural selection is central to evolutionary ecology research and has been in focus since Darwin formulated “The origin of species”. Still, the process of adaptive divergence among sympatric populations is poorly understood. In this thesis I studied patterns of adaptive divergence among subpopulations of pike (Esox lucius) that are sympatric in the Baltic Sea but become short-term allopatric during spawning and initial juvenile growth in freshwater streams. I also examined causes and consequences of phenotypic variation among individuals within subpopulations to evaluate the contribution of natural selection to population divergence.

     

    I first investigated homing behaviour and population structures of pike to assess the potential for adaptive divergence among sympatric pike that migrate to spawn in different streams. Mark-recapture data suggested that migrating pike displayed homing behaviour and repeatedly returned to the same stream. Analyses of microsatellite data revealed partial reproductive isolation among subpopulations spawning in different streams. These subpopulations, however, were truly sympatric during the life-stage spent in the Baltic Sea.

     

    To address whether short-term allopatry has resulted in adaptive divergence among sympatric subpopulations I combined observational, experimental and molecular approaches. Observational data showed that subpopulations differed in morphological and life-history traits and common-garden experiments suggested that differences were, at least in part, genetically based. Moreover, QST-FST comparisons indicated that genetically based phenotypic differences has been driven by divergent selection, and a reciprocal translocation experiment showed that phenotypic variation represented local adaptations to spawning habitats. Finally, longitudinal and cross-sectional comparisons among individuals revealed associations between phenotypes, performance and fitness components.

     

    In conclusion, my thesis illustrates how short-term allopatry due to migratory behaviour can result in adaptive divergence among sympatric subpopulations. These findings advance the understanding of evolutionary processes at the finest spatiotemporal scale and illustrate that local adaptations can arise in environments with high connectivity.  The results also emphasise that fine spatial scale population structures must be taken into consideration in management and conservation of biodiversity in the Baltic Sea.

  • 1597.
    Tibblin, Petter
    Linnéuniversitetet, Fakulteten för Hälso- och livsvetenskap (FHL), Institutionen för biologi och miljö (BOM).
    Migratory behaviour and adaptive divergence in life-history traits of pike (Esox lucius)2015Doktoravhandling, med artikler (Annet vitenskapelig)
    Abstract [en]

    Population divergence shaped by natural selection is central to evolutionary ecology research and has been in focus since Darwin formulated “The origin of species”. Still, the process of adaptive divergence among sympatric populations is poorly understood. In this thesis I studied patterns of adaptive divergence among subpopulations of pike (Esox lucius) that are sympatric in the Baltic Sea but become short-term allopatric during spawning and initial juvenile growth in freshwater streams. I also examined causes and consequences of phenotypic variation among individuals within subpopulations to evaluate the contribution of natural selection to population divergence.

     

    I first investigated homing behaviour and population structures of pike to assess the potential for adaptive divergence among sympatric pike that migrate to spawn in different streams. Mark-recapture data suggested that migrating pike displayed homing behaviour and repeatedly returned to the same stream. Analyses of microsatellite data revealed partial reproductive isolation among subpopulations spawning in different streams. These subpopulations, however, were truly sympatric during the life-stage spent in the Baltic Sea.

     

    To address whether short-term allopatry has resulted in adaptive divergence among sympatric subpopulations I combined observational, experimental and molecular approaches. Observational data showed that subpopulations differed in morphological and life-history traits and common-garden experiments suggested that differences were, at least in part, genetically based. Moreover, QST-FST comparisons indicated that genetically based phenotypic differences has been driven by divergent selection, and a reciprocal translocation experiment showed that phenotypic variation represented local adaptations to spawning habitats. Finally, longitudinal and cross-sectional comparisons among individuals revealed associations between phenotypes, performance and fitness components.

     

    In conclusion, my thesis illustrates how short-term allopatry due to migratory behaviour can result in adaptive divergence among sympatric subpopulations. These findings advance the understanding of evolutionary processes at the finest spatiotemporal scale and illustrate that local adaptations can arise in environments with high connectivity.  The results also emphasise that fine spatial scale population structures must be taken into consideration in management and conservation of biodiversity in the Baltic Sea.

  • 1598.
    Tibblin, Petter
    et al.
    Linnéuniversitetet, Institutionen för biologi och miljö (BOM).
    Berggren, Hanna
    Linnéuniversitetet, Institutionen för biologi och miljö (BOM).
    Nordahl, Oscar
    Linnéuniversitetet, Institutionen för biologi och miljö (BOM).
    Larsson, Per
    Linnéuniversitetet, Institutionen för biologi och miljö (BOM).
    Forsman, Anders
    Linnéuniversitetet, Institutionen för biologi och miljö (BOM).
    Causes and consequences of intra-specific variation in vertebral number2016Inngår i: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 6, artikkel-id 26372Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Intraspecific variation in vertebral number is taxonomically widespread. Much scientific attention hasbeen directed towards understanding patterns of variation in vertebral number among individualsand between populations, particularly across large spatial scales and in structured environments.However, the relative role of genes, plasticity, selection, and drift as drivers of individual variation andpopulation differentiation remains unknown for most systems. Here, we report on patterns, causesand consequences of variation in vertebral number among and within sympatric subpopulations ofpike (Esox lucius). Vertebral number differed among subpopulations, and common garden experimentsindicated that this reflected genetic differences. A QST-FST comparison suggested that populationdifferences represented local adaptations driven by divergent selection. Associations with fitness traitsfurther indicated that vertebral counts were influenced both by stabilizing and directional selectionwithin populations. Overall, our study enhances the understanding of adaptive variation, which iscritical for the maintenance of intraspecific diversity and species conservation.

  • 1599.
    Tibblin, Petter
    et al.
    Linnéuniversitetet, Fakulteten för Hälso- och livsvetenskap (FHL), Institutionen för biologi och miljö (BOM).
    Berggren, Hanna
    Linnéuniversitetet, Fakulteten för Hälso- och livsvetenskap (FHL), Institutionen för biologi och miljö (BOM).
    Nordahl, Oscar
    Linnéuniversitetet, Fakulteten för Hälso- och livsvetenskap (FHL), Institutionen för biologi och miljö (BOM).
    Larsson, Per
    Linnéuniversitetet, Fakulteten för Hälso- och livsvetenskap (FHL), Institutionen för biologi och miljö (BOM).
    Forsman, Anders
    Linnéuniversitetet, Fakulteten för Hälso- och livsvetenskap (FHL), Institutionen för biologi och miljö (BOM).
    Causes and consequences of intra-specific variation in vertebral number2016Inngår i: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 6, artikkel-id 26372Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Intraspecific variation in vertebral number is taxonomically widespread. Much scientific attention hasbeen directed towards understanding patterns of variation in vertebral number among individualsand between populations, particularly across large spatial scales and in structured environments.However, the relative role of genes, plasticity, selection, and drift as drivers of individual variation andpopulation differentiation remains unknown for most systems. Here, we report on patterns, causesand consequences of variation in vertebral number among and within sympatric subpopulations ofpike (Esox lucius). Vertebral number differed among subpopulations, and common garden experimentsindicated that this reflected genetic differences. A QST-FST comparison suggested that populationdifferences represented local adaptations driven by divergent selection. Associations with fitness traitsfurther indicated that vertebral counts were influenced both by stabilizing and directional selectionwithin populations. Overall, our study enhances the understanding of adaptive variation, which iscritical for the maintenance of intraspecific diversity and species conservation.

  • 1600.
    Tibblin, Petter
    et al.
    Linnéuniversitetet, Fakulteten för Hälso- och livsvetenskap (FHL), Institutionen för biologi och miljö (BOM).
    Forsman, Anders
    Linnéuniversitetet, Fakulteten för Hälso- och livsvetenskap (FHL), Institutionen för biologi och miljö (BOM).
    Koch-Schmidt, Per
    Linnéuniversitetet, Fakulteten för Hälso- och livsvetenskap (FHL), Institutionen för biologi och miljö (BOM).
    Nordahl, Oscar
    Linnéuniversitetet, Fakulteten för Hälso- och livsvetenskap (FHL), Institutionen för biologi och miljö (BOM).
    Johannessen, Peter
    Linnéuniversitetet, Fakulteten för Hälso- och livsvetenskap (FHL), Institutionen för biologi och miljö (BOM).
    Nilsson, Jonas
    Linnéuniversitetet, Fakulteten för Hälso- och livsvetenskap (FHL), Institutionen för biologi och miljö (BOM).
    Larsson, Per
    Linnéuniversitetet, Fakulteten för Hälso- och livsvetenskap (FHL), Institutionen för biologi och miljö (BOM).
    Evolutionary divergence of adult body size and juvenile growth in sympatric subpopulations of a top predator in aquatic ecosystems2015Inngår i: American Naturalist, ISSN 0003-0147, E-ISSN 1537-5323, Vol. 186, nr 1, s. 98-110Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Evolutionary theory predicts that different selective regimes may contribute to divergent evolution of body size and growth rate among populations, but most studies have focused on allopatric populations. Here, we studied five sympatric subpopulations of anadromous northern pike (Esox lucius) in the Baltic Sea subjected to allopatric habitats for a short period of their life cycle due to homing behavior. We report differences in adult body size among subpopulations that were in part due to variation in growth rate. Body size of emigrating juveniles also differed among subpopulations, and differences remained when individuals were reared in a common environment, thus indicating evolutionary divergence among subpopulations. Furthermore, a QST-FST comparison indicated that differences had evolved due to divergent selection rather than genetic drift, possibly in response to differences in selective mortality among spawning habitats during the allopatric life stage. Adult and juvenile size were negatively correlated across subpopulations, and reconstruction of growth trajectories of adult fishes suggested that body size differences developed gradually and became accentuated throughout the first years of life. These results represent rare evidence that sympatric subpopulations can evolve differences in key life-history traits despite being subjected to allopatric habitats during only a very short fraction of their life.

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