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  • 1.
    Alavioon, Ghazal
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Hotzy, Cosima
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Nakhro, Khriezhanuo
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Rudolf, Sandra
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Scofield, Douglas
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Zajitschek, Susanne
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology. Spanish Natl Res Council, Donana Biol Stn, Seville 41092, Spain.
    Maklakov, Alex A
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology. Univ East Anglia, Sch Biol Sci, Norwich NR4 7TJ, Norfolk, England.
    Immler, Simone
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology. Univ East Anglia, Sch Biol Sci, Norwich NR4 7TJ, Norfolk, England.
    Haploid selection within a single ejaculate increases offspring fitness2017In: Proceedings of the National Academy of Sciences of the United States of America, ISSN 0027-8424, E-ISSN 1091-6490, no 30, p. 8053-8058Article in journal (Refereed)
    Abstract [en]

    An inescapable consequence of sex in eukaryotes is the evolution of a biphasic life cycle with alternating diploid and haploid phases. The occurrence of selection during the haploid phase can have far-reaching consequences for fundamental evolutionary processes including the rate of adaptation, the extent of inbreeding depression, and the load of deleterious mutations, as well as for applied research into fertilization technology. Although haploid selection is well established in plants, current dogma assumes that in animals, intact fertile sperm within a single ejaculate are equivalent at siring viable offspring. Using the zebrafish Danio rerio, we show that selection on phenotypic variation among intact fertile sperm within an ejaculate affects offspring fitness. Longer-lived sperm sired embryos with increased survival and a reduced number of apoptotic cells, and adult male offspring exhibited higher fitness. The effect on embryo viability was carried over into the second generation without further selection and was equally strong in both sexes. Sperm pools selected by motile phenotypes differed genetically at numerous sites throughout the genome. Our findings clearly link within-ejaculate variation in sperm phenotype to offspring fitness and sperm genotype in a vertebrate and have major implications for adaptive evolution.

  • 2.
    Burdon, Rosalie C. F.
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Junker, Robert R.
    Scofield, Douglas
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Parachnowitsch, Amy L.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Bacteria colonising Penstemon digitalis show volatile and tissue-specific responses to a natural concentration range of the floral volatile linalool2018In: Chemoecology, ISSN 0937-7409, E-ISSN 1423-0445, Vol. 28, no 1, p. 11-19Article in journal (Refereed)
  • 3. Catania, Francesco
    et al.
    Gao, Xiang
    Scofield, Douglas
    Endogenous Mechanisms for the Origins of Spliceosomal Introns2009In: Journal of Heredity, ISSN 0022-1503, E-ISSN 1465-7333, Vol. 100, no 5, p. 591-596Article in journal (Refereed)
    Abstract [en]

    Over 30 years since their discovery, the origin of spliceosomal introns remains uncertain. One nearly universally accepted hypothesis maintains that spliceosomal introns originated from self-splicing group-II introns that invaded the uninterrupted genes of the last eukaryotic common ancestor (LECA) and proliferated by “insertion” events. Although this is a possible explanation for the original presence of introns and splicing machinery, the emphasis on a high number of insertion events in the genome of the LECA neglects a considerable body of empirical evidence showing that spliceosomal introns can simply arise from coding or, more generally, nonintronic sequences within genes. After presenting a concise overview of some of the most common hypotheses and mechanisms for intron origin, we propose two further hypotheses that are broadly based on central cellular processes: 1) internal gene duplication and 2) the response to aberrant and fortuitously spliced transcripts. These two nonmutually exclusive hypotheses provide a powerful way to explain the establishment of spliceosomal introns in eukaryotes without invoking an exogenous source.

  • 4. Cossu, Rosa Maria
    et al.
    Casola, Claudio
    Giacomello, Stefania
    Vidalis, Amaryllis
    Scofield, Douglas G.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Zuccolo, Andrea
    LTR Retrotransposons Show Low Levels of Unequal Recombination and High Rates of Intraelement Gene Conversion in Large Plant Genomes2017In: Genome Biology and Evolution, ISSN 1759-6653, E-ISSN 1759-6653, Vol. 9, no 12, p. 3449-3462Article in journal (Refereed)
  • 5.
    Dahlö, Martin
    et al.
    Uppsala University, Science for Life Laboratory, SciLifeLab. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology.
    Scofield, Douglas
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Schaal, Wesley
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Pharmacy, Department of Pharmaceutical Biosciences. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Spjuth, Ola
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Pharmacy, Department of Pharmaceutical Biosciences. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Tracking the NGS revolution: managing life science research on shared high-performance computing clusters2018In: GigaScience, ISSN 2047-217X, E-ISSN 2047-217X, Vol. 7, no 5, article id giy028Article in journal (Refereed)
  • 6.
    Eiler, Alexander
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Mondav, Rhiannon
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Sinclair, Lucas
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Fernandez-Vidal, Leyden
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Scofield, Douglas G.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Schwientek, Patrick
    Martinez-Garcia, Manuel
    Torrents, David
    McMahon, Katherine D.
    Andersson, Siv G. E.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular Evolution. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Stepanauskas, Ramunas
    Woyke, Tanja
    Bertilsson, Stefan
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Tuning fresh: radiation through rewiring of central metabolism in streamlined bacteria2016In: The ISME Journal, ISSN 1751-7362, E-ISSN 1751-7370, Vol. 10, no 8, p. 1902-1914Article in journal (Refereed)
  • 7. Hong, Xin
    et al.
    Scofield, Douglas
    Lynch, Michael
    Intron size, abundance, and distribution within untranslated regions of genes2006In: Molecular biology and evolution, ISSN 0737-4038, E-ISSN 1537-1719, Vol. 23, no 12, p. 2392-2404Article in journal (Refereed)
    Abstract [en]

    Most research concerning the evolution of introns has largely considered introns within coding sequences (CDSs), without regard for introns located within untranslated regions (UTRs) of genes. Here, we directly determined intron size, abundance, and distribution in UTRs of genes using full-length cDNA libraries and complete genome sequences for four species,Arabidopsis thaliana, Drosophila melanogaster, human, and mouse. Overall intron occupancy (introns/exon kbp) is lower in 5′ UTRs than CDSs, but intron density (intron occupancy in regions containing introns) tends to be higher in 5′ UTRs than in CDSs. Introns in 5′ UTRs are roughly twice as large as introns in CDSs, and there is a sharp drop in intron size at the 5′ UTR-CDS boundary. We propose a mechanistic explanation for the existence of selection for larger intron size in 5′ UTRs, and outline several implications of this hypothesis. We found introns to be randomly distributed within 5′ UTRs, so long as a minimum required exon size was assumed. Introns in 3′ UTRs were much less abundant than in 5′ UTRs. Though this was expected for human and mouse that have intron-dependent nonsense-mediated decay (NMD) pathways that discourage the presence of introns within the 3′ UTR, it was also true for A. thaliana and D. melanogaster, which may lack intron-dependent NMD. Our findings have several implications for theories of intron evolution and genome evolution in general.

  • 8. Kaiser, Kristine
    et al.
    Scofield, Douglas G.
    Alloush, Menemsha
    Jones, Robin M.
    Marczak, Susanne
    Martineau, Katherine
    Oliva, Mark A.
    Narins, Peter M.
    When sounds collide: the effect of anthropogenic noise on a breeding assemblage of frogs in Belize, Central America2011In: Behaviour, ISSN 0005-7959, E-ISSN 1568-539X, Vol. 148, no 2, p. 215-232Article in journal (Refereed)
    Abstract [en]

    Many organisms depend on acoustic communication for myriad functions, and have evolved behaviours to minimize effects of naturally occurring acoustic interference. However, as habitats are subject to increased alteration, anthropogenic noise becomes unavoidable, and how animals overcome such interference is not well understood. In most ecosystems, only a subset of frog species is associated with disturbed habitats; the ability of these species to overcome exogenous noise suggests that habitat associations may be related to species' response to noise. We tested the hypothesis that frogs associated with largely undisturbed forest habitat would be less likely to increase call output in response to exogenous noise than would those associated with disturbed or open habitat. While this relationship was not significant, we found a slight trend supporting the hypothesis. We then asked whether anthropogenic noise affects chorus tenure at individual- or at chorus-levels. Male frogs exposed to anthropogenic noise decreased both the number of days present at the chorus and the nightly chorus duration relative to controls. Because females generally join choruses late at night to breed, the effects of noise shown here are likely to substantially decrease frog reproductive success; thus, the acoustic environment may play an important role in shaping population dynamics and in amphibian declines.

  • 9. Lynch, Michael
    et al.
    Hong, Xin
    Scofield, Douglas G.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    NMD and the evolution of eukaryotic gene structure2006In: Nonsense-Mediated mRNA Decay / [ed] Lynne E. Maquat, Landes Bioscience/Eurekah.com , 2006, p. 197-211Chapter in book (Refereed)
    Abstract [en]

    All cells are confronted with undesirable transcripts derived from mutant alleles, but the production of aberrant transcripts from otherwise normal DNA may be an even greater challenge. The substantial fraction of problematical transcripts containing premature termination codons (PTCs) are subject to elimination by the nonsense-mediated mRNA decay (NMD) pathway. Phylogenetic analysis suggests that NMD and the exon junction complex (EJC) upon which it depends in mammals (see chapter by Maquat) are ancient, raising the possibility of an early association of NMD with introns. This may help explain why introns were able to proliferate to an apparently considerable degree in the stem eukaryote, despite the mutational burden that introns impose upon their host genes. A long-term evolutionary asso- ciation between NMD and introns also provides a possible explanation for the nonrandom spatial distribution of introns in the genes of multicellular species and for an apparent slow- down (and possible stabilization) of intron colonization in modern species. Several lineages, all of which are nearly devoid of ancestral introns, appear to have lost NMD and the EJC, and these taxa have exceptionally simple genomic features that minimize the chances of producing erroneous transcripts. Validation of these ideas will require empirical work on the degree of coordination between NMD, the EJC, and the locations of introns in a wide array of genes distributed across diverse phylogenetic lineages. 

  • 10. Lynch, Michael
    et al.
    Scofield, Douglas
    Hong, Xin
    The evolution of transcription-initiation sites2005In: Molecular biology and evolution, ISSN 0737-4038, E-ISSN 1537-1719, Vol. 22, no 4, p. 1137-1146Article in journal (Refereed)
    Abstract [en]

    Unlike the situation in prokaryotes, most eukaryotic messenger RNAs contain a moderately long 5′ untranslated region (UTR). Such leader sequences impose a burden on eukaryotic genes by providing substrate for the mutational origin of premature translation-initiation codons, which generally result in defective proteins. To gain an insight into the expansion of 5′ UTRs in eukaryotic genomes, we present a simple null model in which the evolution of transcription-initiation sites is entirely driven by the stochastic mutational flux of core-promoter sequences and premature translation-initiation codons. This model yields results consistent with a variety of heretofore disconnected observations, including the form of length distributions of 5′ UTRs, the relatively low variance in UTR features among distantly related eukaryotes, the universal reliance on relatively simple core-promoter sequences, and the elevated density of introns in the 5′ UTR. We suggest that the reduced effective population sizes of most eukaryotes impose a population-genetic environment conducive to the movement of core promoters to random positions, subject to the constraint imposed by the upstream accumulation of premature translation-initiation codons. If this hypothesis is correct, then selection for gene-specific regulatory features need not be invoked to explain either the origin of lengthy eukaryotic 5′ UTRs or the 1,000-fold range of 5′-UTR lengths among genes within species. Nevertheless, once permanently established, expanded 5′ UTRs may have provided a novel substrate for the evolution of mechanisms for posttranscriptional regulation of eukaryotic gene expression. These results provide a further example of how an increase in the power of random genetic drift can passively promote the evolution of forms of gene architecture that ultimately facilitate the evolution of organismal complexity.

  • 11. Mortellaro, Steve
    et al.
    Barry, Mike
    Gann, George
    Zahina, John
    Channon, Sally
    Hilsenbeck, Charles
    Scofield, Douglas G.
    Wilder, George
    Wilhelm, Gerould
    Coefficients of Conservatism Values and the Floristic Quality Index for the vascular plants of south Florida2012In: Southeastern naturalist (Steuben, Me.), ISSN 1528-7092, E-ISSN 1938-5412, Vol. 11, no mo3, p. 1-62Article in journal (Refereed)
    Abstract [en]

    Since pre-European settlement, major alterations to the native landscape have been made, due largely to urban and agricultural developments. In south Florida, these activities have caused extensive degradation to native plant communities leaving remnant native lands. Therefore, the floristic quality of these native lands is changing, and a tool to assess their quality is needed. Assignment of coefficient of conservatism (C) values (ranging from 0 to 10) to each native plant within south Florida allows for the use of the floristic quality index (FQI), a tool to assess the quality of natural or remnant native plant communities. The coefficient of conservatism concept is based on two factors: 1) plants have various degrees of fidelity to specific habitats and their quality, and 2) plants have varying tolerances to disturbances and respond in various degrees. The establishment of C values and the use of the FQI eliminate subjectivity and provide a standardized method to evaluate the floristic condition of a site, which allows for comparisons between different sites and monitoring of sites over time. Non-native plants are not assigned conservatism coefficients values because they did not evolve in the native landscape. In south Florida (Florida Keys excluded), there are approximately 2226 plants, of which 64% (1434) are considered native and 36% (792) are considered non-native. Of the 1434 plants examined, only 94 native plants remained unranked, because the team did not have enough experience with the plant to confidently assign a C value. Approximately 33% of plants ranked fell into the ruderal categories (0–4), whereas 67% fell into obligate to natural areas categories (5–10). Once a thorough inventory of a site has been completed, a mean C value and FQI can be calculated.

  • 12. Omilian, Angela
    et al.
    Scofield, Douglas
    Lynch, Michael
    Intron presence-absence polymorphisms in Daphnia2008In: Molecular biology and evolution, ISSN 0737-4038, E-ISSN 1537-1719, Vol. 25, no 10, p. 2129-2139Article in journal (Refereed)
    Abstract [en]

    Here, we report 2 novel intron gains segregating in populations ofDaphnia pulex endemic to Oregon. These novel introns do not have an obvious source and are not present in any D. pulex populations outside Oregon, other species of Daphnia that we examined, or any other organism for which sequence data are available. Furthermore, the novel introns are both found in the same gene, a Rab GTPase (rab4), and they appear to differ in their insertion site by one base pair, providing some support to the proto-splice site hypothesis. The rarity of intron-gain polymorphisms is questioned as we discovered 2 events in an initial survey of only 6 nuclear loci in 36 Daphnia individuals. Neutrality tests failed to ascertain a clear selective effect for either intron insertion, and a significant difference in recombination rate was not observed in alleles that contain the novel intron insertion versus alleles lacking it. We conclude that one novel intron insertion segregating at high frequencies inDaphnia populations in Oregon is unlikely to be adaptive and may result from the reduced efficacy of selection in isolated populations of small effective size.

  • 13.
    Onuţ-Brännström, Ioana
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Benjamin, Mitchell
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Scofield, Douglas G.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Starri, Heiðmarsson
    Icelandic Institute of Natural History, Borgir Nordurslod, Iceland.
    Andersson, Martin G.I.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    Lindström, Eva S.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    Johannesson, Hanna
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Sharing of photobionts in sympatric populations of Thamnolia and Cetraria lichens: evidence from high-throughput sequencing2018In: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 8, article id 4406Article in journal (Refereed)
    Abstract [en]

    In this study, we explored the diversity of green algal symbionts (photobionts) in sympatric populations of the cosmopolitan lichen-forming fungi Thamnolia and Cetraria. We sequenced with both Sanger and Ion Torrent High-Throughput Sequencing technologies the photobiont ITS-region of 30 lichen thalli from two islands: Iceland and Öland. While Sanger recovered just one photobiont genotype from each thallus, the Ion Torrent data recovered 10–18 OTUs for each pool of 5 lichen thalli, suggesting that individual lichens can contain heterogeneous photobiont populations. Both methods showed evidence for photobiont sharing between Thamnolia and Cetraria on Iceland. In contrast, our data suggest that on Öland the two mycobionts associate with distinct photobiont communities, with few shared OTUs revealed by Ion Torrent sequencing. Furthermore, by comparing our sequences with public data, we identified closely related photobionts from geographically distant localities. Taken together, we suggest that the photobiont composition in Thamnolia and Cetraria results from both photobiont-mycobiont codispersal and local acquisition during mycobiont establishment and/or lichen growth. We hypothesize that this is a successful strategy for lichens to be flexible in the use of the most adapted photobiont for the environment.

  • 14. Schultz, Stewart T.
    et al.
    Scofield, Douglas
    Mutation Accumulation in Real Branches: Fitness Assays for Genomic Deleterious Mutation Rate and Effect in Large-Statured Plants2009In: American Naturalist, ISSN 0003-0147, E-ISSN 1537-5323, Vol. 174, no 2, p. 163-175Article in journal (Refereed)
    Abstract [en]

    The genomic deleterious mutation rate and mean effect are central to the biology and evolution of all species. Large‐statured plants, such as trees, are predicted to have high mutation rates due to mitotic mutation and the absence of a sheltered germ line, but their size and generation time has hindered genetic study. We develop and test approaches for estimating deleterious mutation rates and effects from viability comparisons within the canopy of large‐statured plants. Our methods, inspired by E. J. Klekowski, are a modification of the classic Bateman‐Mukai mutation‐accumulation experiment. Within a canopy, cell lineages accumulate mitotic mutations independently. Gametes or zygotes produced at more distal points by these cell lineages contain more mitotic mutations than those at basal locations, and within‐flower selfs contain more homozygous mutations than between‐flower selfs. The resulting viability differences allow demonstration of lethal mutation with experiments similar in size to assays of genetic load and allow estimates of the rate and effect of new mutations with moderate precision and bias similar to that of classic mutation‐accumulation experiments in small‐statured organisms. These methods open up new possibilities with the potential to provide valuable new insights into the evolutionary genetics of plants.

  • 15. Scofield, Douglas
    Medial pith cells per meter in twigs as a proxy for mitotic growth rate (Phi/m) in the apical meristem2006In: American Journal of Botany, ISSN 0002-9122, E-ISSN 1537-2197, Vol. 93, no 12, p. 1740-1747Article in journal (Refereed)
    Abstract [en]

    The Φ model for plant mating system evolution proposes a causal link between Φ, the number of mitoses that occur within a plant's lifetime from zygote to gamete production, and constraints on the evolution of inbreeding depression and thereby on the evolution of plant mating systems. Through its use of plant stature, the Φ model emphasizes the important role of morphology in creating developmental and genetic constraints on plant evolution. However, the estimation of Φ itself is likely to be extraordinarily complex. Here I describe a protocol for estimating Φ per meter linear growth by an apical meristem (Φ/m) using medial pith cells from mature internodes of twigs. While such cells are produced by the apical meristem, during internode elongation, these pith cells also undergo further mitoses, and thus their measurement can only approximate a “true” Φ/m via the application of a multiplier (the adjustment ratio) that partially corrects for the occurrence of cell divisions and cell growth beyond the apical meristem. I applied this method to Delonix regia(Caesalpiniaceae) and derived several adjustment ratios from the literature. Because variation in Φ/m can have profound evolutionary implications, I also examined interspecific and intraspecific variation as well as within-individual variation in Φ/m. Conifers apparently have lower Φ/m than do angiosperms, while 20% of the total variance in Φ/m for D. regia was found among individual trees, with the remainder found within trees. Given the large differences in stature between “high-Φ” plants such as trees and “low-Φ” plants such as herbs, these results support the idea that the total per-generation mutation rate for high-Φ plants is likely to be many times higher than that for low-Φ plants.

  • 16.
    Scofield, Douglas G.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    A definitive demonstration of fitness effects due to somatic mutation in a plant2014In: Heredity, ISSN 0018-067X, E-ISSN 1365-2540, Vol. 112, no 4, p. 361-362Article in journal (Other academic)
  • 17. Scofield, Douglas G.
    et al.
    Alfaro, Victor Ryan
    Sork, Victoria L.
    Grivet, Delphine
    Martinez, Edith
    Papp, Jeannette
    Pluess, Andrea R.
    Koenig, Walter D.
    Smouse, Peter E.
    Foraging patterns of acorn woodpeckers (Melanerpes formicivorus) on valley oak (Quercus lobata N,e) in two California oak savanna-woodlands2011In: Oecologia, ISSN 0029-8549, E-ISSN 1432-1939, Vol. 166, no 1, p. 187-196Article in journal (Refereed)
    Abstract [en]

    Landscape characteristics and social behavior can affect the foraging patterns of seed-dependent animals. We examine the movement of acorns from valley oak (Quercus lobata) trees to granaries maintained by acorn woodpeckers (Melanerpes formicivorus) in two California oak savanna-woodlands differing in the distribution of Q. lobata within each site. In 2004, we sampled Q. lobata acorns from 16 granaries at Sedgwick Reserve in Santa Barbara County and 18 granaries at Hastings Reserve in Monterey County. Sedgwick has lower site-wide density of Q. lobata than Hastings as well as different frequencies of otherQuercus species common to both sites. We found acorn woodpeckers foraged from fewer Q. lobata seed source trees (K g = 4.1 ± 0.5) at Sedgwick than at Hastings (K g = 7.6 ± 0.6) and from fewer effective seed sources (N em* = 2.00 and 5.78, respectively). The differences between sites are due to a greater number of incidental seed sources used per granary at Hastings than at Sedgwick. We also found very low levels of seed source sharing between adjacent granaries, indicating that territoriality is strong at both sites and that each social group forages on its own subset of trees. We discovered an interesting spatial pattern in the location of granaries. At Sedgwick, acorn woodpeckers situated their granaries within areas of higher-than-average tree density, while at Hastings, they placed them within areas of lower-than-average tree density, with the outcome that granaries at the two sites were located in areas of similar valley oak density. Our results illustrate that landscape characteristics might influence the number of trees visited by acorn woodpeckers and the locations of territories, while woodpecker social behavior, such as territoriality, shapes which trees are visited and whether they are shared with other social groups.

  • 18. Scofield, Douglas G.
    et al.
    Sork, Victoria L.
    Smouse, Peter E.
    Influence of acorn woodpecker social behaviour on transport of coast live oak (Quercus agrifolia) acorns in a southern California oak savanna2010In: Journal of Ecology, ISSN 0022-0477, E-ISSN 1365-2745, Vol. 98, no 3, p. 561-572Article in journal (Refereed)
    Abstract [en]

    1. Many plant species depend upon animals for seed dispersal, yet animals disperse seeds in pursuit of their own social and behavioural agendas. Animal social behaviour affects where and how they forage, so it must also shape patterns of seed dispersal.

    2. At Sedgwick Reserve, California, USA, we established a study population of Quercus agrifolia to determine patterns of acorn foraging by the acorn woodpecker (Melanerpes formicivorous). This cooperative breeder lives in social groups that defend territories surrounding arboreal seed caches (granaries), foraging communally within these territories.

    3. We genotyped pericarp tissue of 568 acorns, as well as 285 adult Q. agrifolia trees, including all adults within 150 m of 16 focal granaries. After quantifying genotyping error, we identified a genetically reliable subset of 524 acorns. We assigned a source tree to each acorn and estimated the number of seed sources per granary and seed source sharing among granaries.

    4. We found one to eight distinct seed-source genotypes per granary, and an effective source diversity ranging from 1.0 to 6.6 seed sources. Of all transport events, 96.5% involve source trees within 150 m of the granaries. For one granary, all sampled acorns were transported from five trees located more than 1.3 km away, with all source trees within 90 m of each other. No measure of seed-source diversity was associated with density of potential seed sources, and the pattern of acorn movement fits three traditional dispersal curves poorly.

    5. Woodpecker groups rarely collected acorns from overlapping sets of maternal sources. Some pairs of neighbouring granaries shared maternal sources, and we identify those that were probably maintained by the same woodpecker group.

    6.Synthesis. Territoriality of woodpecker groups restricts both the spatial area of foraging and the sharing of seed sources. This foraging behaviour limits distances and directions of acorn transport from oaks located within woodpecker territories. Dispersal agents with this type of social structure will create a high degree of local genetic structure. Extreme behavioural variations may result in anomalous long-distance dispersal events that increase genetic connectivity, but are likely to do so in an episodic and erratic fashion.

  • 19. Scofield, Douglas
    et al.
    Hong, Xin
    Lynch, Michael
    Position of the final intron in full-length transcripts: Determined by NMD?2007In: Molecular biology and evolution, ISSN 0737-4038, E-ISSN 1537-1719, Vol. 24, no 4, p. 896-899Article in journal (Refereed)
    Abstract [en]

    Nonsense-mediated decay (NMD) pathways for detection and degradation of transcripts containing premature termination (stop) codons (PTCs) are ubiquitous among the eukaryotes. NMD uses the presence of a second signal downstream of a termination codon to distinguish a PTC from a true stop codon. In mammals and perhaps other eukaryotes, the second signal is a protein complex closely associated with exon–exon junctions formed after removal of spliceosomal introns. A valid transcript in such species must have its 3′-most intron positioned so as not to serve as a second signal relative to the true stop. This requirement has been termed the “55-bp rule”, in reference to the position within the 3′ untranslated region (3′ UTR) of valid transcripts downstream of which introns should not be found. However, as more information has become available, it is apparent that the 55-bp rule still holds in species with NMD pathways, which are not intron dependent. To clarify the applicability of the 55-bp rule, we constructed a large database of 3′-most intron positions within full-length transcripts from 4 eukaryotes, 2 of which (human and mouse) use intron positions for NMD, 1 of which (Drosophila melanogaster) does not, and 1 of which (Arabidopsis thaliana) may not use intron positions. Surprisingly, we found intron numbers to be sharply reduced within 3′ UTRs in comparison to coding sequences starting immediately downstream of true stop, rather than 55 bp; this strong threshold existed for all 4 species. We suggest that a more general mechanism—higher rates of intron inclusion within 3′ UTRs—is better able to explain this threshold. We propose that 3′ UTRs are better able to tolerate loss of intron integrity than other gene regions, due to the generally greater length of conserved sequences important within 3′ UTR exons. This mechanism may also help to explain the roughly 3 times greater length of 3′ UTRs in comparison to 5′ UTRs.

  • 20. Scofield, Douglas
    et al.
    Lynch, Michael
    Evolutionary Diversification of the Sm Family of RNA-Associated Proteins2008In: Molecular biology and evolution, ISSN 0737-4038, E-ISSN 1537-1719, Vol. 25, no 11, p. 2255-2267Article in journal (Refereed)
    Abstract [en]

    The Sm family of proteins is closely associated with RNA metabolismthroughout all life. These proteins form homomorphic and heteromorphic rings consisting of six or seven subunits with a characteristic central pore, the presence of which is critical for binding U-rich regions of single-stranded RNA. Eubacteria and Archaea typically carry one or two forms ofSm proteins and assemble one homomorphic ring per Sm protein. Eukaryotes typically carry 16 or more Sm proteins that assemble to form heteromorphic rings which lie at the center of a number of critical RNA-associated small nuclear ribonucleoproteins (snRNPs). High Sm protein diversity and heteromorphic Sm rings are features stretching back to the origin of eukaryotes; very deep phylogenetic divisions among existing Smproteins indicate simultaneous evolution across essentially all existing eukaryotic life. Two basic forms of heteromorphic Sm rings are found in eukaryotes. Fixed Sm rings are highly stable and static and are assembled around an RNA cofactor. Flexible Sm rings also stabilize and chaperone RNA but assemble in the absence of an RNA substrate and, more significantly, associate with and dissociate from RNA substrates more freely than fixed rings. This suggests that the conformation of flexible Smrings might be modified in some specific manner to facilitate association and dissociation with RNA. Diversification of eukaryotic Sm proteins may have been initiated by gene transfers and/or genome clashes that accompanied the origin of the eukaryotic cell itself, with further diversification driven by a greater need for steric specificity within increasingly complex snRNPs.

  • 21. Scofield, Douglas
    et al.
    Schultz, Stewart
    Mitosis, stature and evolution of plant mating systems: low-Phi and high-Phi plants2006In: Proceedings of the Royal Society of London. Biological Sciences, ISSN 0962-8452, E-ISSN 1471-2954, Vol. 273, no 1584, p. 275-282Article in journal (Refereed)
    Abstract [en]

    There is a long-recognized association in plants between small stature and selfing, and large stature and outcrossing. Inbreeding depression is central to several hypotheses for this association, but differences in the evolutionary dynamics of inbreeding depression associated with differences in stature are rarely considered. Here, we propose and test the Phi model of plant mating system evolution, which assumes that the per-generation mutation rate of a plant is a function of the number of mitoses (Phi) that occur from zygote to gamete, and predicts fundamental differences between low-Phi (small-statured) and high-Phi (large-statured) plants in the outcomes of the joint evolution of outcrossing rate and inbreeding depression. Using a large dataset of published population genetic studies of angiosperms and conifers, we compute fitted values of inbreeding depression and deleterious mutation rates for small- and large-statured plants. Consistent with our Phi model, we find that populations of small-statured plants exhibit a range of mating systems, significantly lower mutation rates, and intermediate inbreeding depression, while large-statured plants exhibit very high mutation rates and the maximum inbreeding depression of unity. These results indicate that (i) inbred progeny typically observed in large-statured plant populations are completely lost prior to maturity in nearly all populations; (ii) evolutionary shifts from outcrossing to selfing are generally not possible in large-statured species, rather, large-statured species are more likely to evolve mating systems that avoid selfing such as self-incompatibility and dioecy; (iii) destabilization of the mating system-high selfing rate with high-inbreeding depression-might be a common occurrence in large-statured species; and (iv) large-statured species in fragmented populations might be at higher risk of extinction than previously thought. Our results help to unify and simplify a large and diverse field of research, and serve to emphasize the importance that developmental and genetic constraints play in the evolution of plant mating systems.

  • 22. Scofield, Douglas
    et al.
    Smouse, Peter E.
    Karubian, Jordan
    Sork, Victoria L.
    Use of Alpha, Beta, and Gamma Diversity Measures to Characterize Seed Dispersal by Animals2012In: American Naturalist, ISSN 0003-0147, E-ISSN 1537-5323, Vol. 180, no 6, p. 719-732Article in journal (Refereed)
    Abstract [en]

    Seed dispersal shapes ecological and evolutionary dynamics of plant populations. Here, we extend classical diversity measures to study the impact of disperser behavior on seed dispersal. We begin by extending our previous diversity structure approach, which partitioned seed source diversity within and among dispersal sites, into the more general framework of traditional diversity measures. This statistical approach allows an assessment of the extent to which foraging behavior shapes α and γ diversity, as well as the divergence in seed sources among dispersal sites, which we call δ. We also introduce tests to facilitate comparisons of diversity among dispersal sites and seed vectors and to compare overall diversity among sampled systems. We then apply these tools to investigate the diversity blend of parentage resulting from seed dispersal by two avian seed vectors with very different social and foraging behaviors: (1) acorn woodpeckers, transportingQuercus agrifolia acorns, and (2) long-wattled umbrellabirds, transporting Oenocarpus bataua palm nuts. Using these diversity and divergence measures, we test the hypothesis that different foraging behaviors generate distinctive diversity partitions for the two focal tree species. This approach provides a new tool for assessment of the impact of dispersal agents on the seed source structure of plant populations, which can be extended to include the impact of virtually any propagule vector for a range of systems.

  • 23. Smouse, Peter E.
    et al.
    Sork, Victoria L.
    Scofield, Douglas G.
    Grivet, Delphine
    Using Seedling and Pericarp Tissues to Determine Maternal Parentage of Dispersed Valley Oak Recruits2012In: Journal of Heredity, ISSN 0022-1503, E-ISSN 1465-7333, Vol. 103, no 2, p. 250-259Article in journal (Refereed)
    Abstract [en]

    The spatial pattern of established seedlings yields valuable information about variation in fecundity, dispersal, and spatial structure of distributed recruits, but separating maternal and paternal contributions in monoecious species has been hampered by the “2 parent” problem. It is now possible to determine the maternal parentage of established recruits with genetic assay of maternally derived tissues of the seed or fruit, but the DNA of weathered maternal tissues often yields unreliable genotypes, reducing the practical range of such assay. We develop a mixed assay of seedling and seed (pericarp) tissues and illustrate it with distributed recruits of California valley oak (Quercus lobata Née). Detailed analysis indicates correct maternal assignment rates of canopy patch recruits of 56% (seedling assay only) versus 94% (mixed assay). For open patch recruits, maternal assignment rates were less than 50% (seedling assay only) versus 91% (mixed assay). The strategy of choice is to use seedling genotypes to identify a small set of credible parental candidates and then deploy 3–4 well-chosen pericarp/endocarp loci to reduce that list to a single obvious maternal candidate. The increase in the number of recruits available for subsequent analysis is pronounced, increasing precision and statistical power for subsequent inference.

  • 24.
    Sork, Victoria L.
    et al.
    Univ Calif Los Angeles, Dept Ecol & Evolutionary Biol, Los Angeles, CA 90095 USA.;Univ Calif Los Angeles, Inst Environm & Sustainabil, Los Angeles, CA 90095 USA..
    Smouse, Peter E.
    Rutgers State Univ, Dept Ecol Evolut & Nat Resources, New Brunswick, NJ 08901 USA..
    Grivet, Delphine
    CIFOR Natl Inst Agr & Food Res & Technol, Ctr Forest Res, Dept Forest Ecol & Genet, Madrid, Spain..
    Scofield, Douglas G.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology. Univ Calif Los Angeles, Dept Ecol & Evolutionary Biol, Los Angeles, CA 90095 USA..
    Impact of asymmetric male and female gamete dispersal on allelic diversity and spatial genetic structure in valley oak (Quercus lobata Nee)2015In: Evolutionary Ecology, ISSN 0269-7653, E-ISSN 1573-8477, Vol. 29, no 6, p. 927-945Article in journal (Refereed)
    Abstract [en]

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

  • 25.
    Steige, Kim A.
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Laenen, Benjamin
    Reimegård, Johan
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular Evolution. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Scofield, Douglas G.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Slotte, Tanja
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Genomic analysis reveals major determinants of cis-regulatory variation in Capsella grandiflora2017In: Proceedings of the National Academy of Sciences of the United States of America, ISSN 0027-8424, E-ISSN 1091-6490, Vol. 114, no 5, p. 1087-1092Article in journal (Refereed)
  • 26.
    Steige, Kim A.
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Reimegård, Johan
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular Evolution. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Koenig, Daniel
    Max Planck Inst Dev Biol, Dept Mol Biol, Tubingen, Germany..
    Scofield, Douglas G.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Slotte, Tanja
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology. Stockholm Univ, Sci Life Lab, Dept Ecol Environm & Plant Sci, S-10691 Stockholm, Sweden..
    Cis-Regulatory Changes Associated with a Recent Mating System Shift and Floral Adaptation in Capsella2015In: Molecular biology and evolution, ISSN 0737-4038, E-ISSN 1537-1719, Vol. 32, no 10, p. 2501-2514Article in journal (Refereed)
    Abstract [en]

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

  • 27. Thompson, Pamela G.
    et al.
    Scofield, Douglas
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Sork, Victoria
    What seeds tell us about birds: A multi-year analysis of acorn woodpecker foraging movements2014In: Movement Ecology, E-ISSN 2051-3933, Vol. 2, p. 12-Article in journal (Refereed)
    Abstract [en]

    Background: Foraging movements of animals shape their efficiency in finding food and their exposure to the environment while doing so. Our goal was to test the optimal foraging theory prediction that territorial acorn woodpeckers (Melanerpes formicivorus) should forage closer to their ‘central place’ in years of high resource availability and further afield when resources are less available. We used genetic data on acorns stored in caching sites (granaries) and adult trees for two oak species (Quercus lobata and Quercus agrifolia) to track acorn movements across oak savanna habitat in central California. We also compared the patterns of trees these territorial bird groups foraged upon, examining the effective numbers of source trees represented within single granaries (α), the effective number of granaries (β), the diversity across all granaries (γ), and the overlap (ω) in source trees among different granaries, both within and across years.

    Results: In line with optimal foraging theory predictions, most bird groups foraged shorter distances in years with higher acorn abundance, although we found some exceptionally long distance foraging movements in high acorn crop years. The α-diversity values were significantly higher for Quercus lobata, but not for Quercus agrifolia, in years of high acorn production. We also found that different woodpecker family groups visited almost completely non-overlapping sets of source trees, and each particular group visited largely the same set of source trees from year to year, indicating strong territorial site fidelity.

    Conclusions: Acorn woodpeckers forage in a pattern consistent with optimal foraging theory, with a few fascinating exceptions of long distance movement. The number of trees they visit increases in years of high acorn availability, but the extra trees visited are mostly local. The territorial social behavior of the birds also restricts their movement patterns to a minimally overlapping subsets of trees, but the median movement distance appears to be shaped more by the availability of trees with acorns than by rigid territorial boundaries. 

  • 28.
    Urbina, Hector
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Scofield, Douglas G.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology. Uppsala Univ, Dept Informat Technol, Uppsala Multidisciplinary Ctr Adv Computat Sci, Box 137, S-75105 Uppsala, Sweden..
    Cafaro, Matias
    Univ Puerto Rico, Dept Biol, Mayaguez, PR 00681 USA..
    Rosling, Anna
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    DNA-metabarcoding uncovers the diversity of soil-inhabiting fungi in the tropical island of Puerto Rico2016In: Mycoscience, ISSN 1340-3540, E-ISSN 1618-2545, Vol. 57, no 3, p. 217-227Article in journal (Refereed)
    Abstract [en]

    Soil fungal communities in tropical regions remain poorly understood. In order to increase the knowledge of diversity of soil-inhabiting fungi, we extracted total DNA from top-organic soil collected in seven localities dominated by four major ecosystems in the tropical island of Puerto Rico. In order to comprehensively characterize the fungal community, we PCR-amplified the internal transcribed spacer 2 (ITS2) fungal barcode using newly designed degenerated primers and varying annealing temperatures to minimize primer bias. Sequencing results, obtained using Ion Torrent technology, comprised a total of 566,613 sequences after quality filtering. These sequences were clustered into 4140 molecular operational taxonomic units (MOTUs) after removing low frequency sequences and rarefaction to account for differences in read depth between samples. Our results demonstrate that soil fungal communities in Puerto Rico are structured by ecosystem. Ascomycota, followed by Basidiomycota, dominates the diversity of fungi in soil. Amongst Ascomycota, the recently described soil-inhabiting class Archaeorhizomycetes was present in all localities, and taxa in Archaeorhizomycetes were among the most commonly observed MOTUs. The Basidiomycota community was dominated by soil decomposers and ectomycorrhizal fungi with a distribution strongly affected by local variation to a greater degree than Ascomycota.

  • 29. Wang, Jing
    et al.
    Ding, Jihua
    Tan, Biyue
    Robinson, Kathryn M.
    Michelson, Ingrid H.
    Johansson, Anna
    Uppsala University, Science for Life Laboratory, SciLifeLab.
    Nystedt, Björn
    Uppsala University, Science for Life Laboratory, SciLifeLab.
    Scofield, Douglas G.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Nilsson, Ove
    Jansson, Stefan
    Street, Nathaniel R.
    Ingvarsson, Pär K.
    A major locus controls local adaptation and adaptive life history variation in a perennial plant2018In: Genome Biology, ISSN 1465-6906, E-ISSN 1474-760X, Vol. 19, article id 72Article in journal (Refereed)
  • 30. Wang, Jing
    et al.
    Scofield, Douglas G.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Street, Nathaniel R.
    Ingvarsson, Pär K.
    Variant calling using NGS data in European aspen (Populus tremula)2015In: Advances in the Understanding of Biological Sciences using Next Generation Sequencing (NGS) Approaches / [ed] Guarav Sablok, Sunil Kumar, Saneyoshi Ueno, Jimmy Kuo, Claudio Varotto, Springer, 2015Chapter in book (Refereed)
  • 31.
    Wang, Jing
    et al.
    Umea Univ, Umea Plant Sci Ctr, Dept Ecol & Environm Sci, SE-90187 Umea, Sweden..
    Street, Nathaniel R.
    Umea Univ, Umea Plant Sci Ctr, Dept Plant Physiol, SE-90187 Umea, Sweden..
    Scofield, Douglas G.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology. Umea Univ, Umea Plant Sci Ctr, Dept Ecol & Environm Sci, SE-90187 Umea, Sweden.;Uppsala Univ, Uppsala Multidisciplinary Ctr Adv Computat Sci, SE-75105 Uppsala, Sweden..
    Ingvarsson, Par K.
    Umea Univ, Umea Plant Sci Ctr, Dept Ecol & Environm Sci, SE-90187 Umea, Sweden..
    Natural Selection and Recombination Rate Variation Shape Nucleotide Polymorphism Across the Genomes of Three Related Populus Species2016In: Genetics, ISSN 0016-6731, E-ISSN 1943-2631, Vol. 202, no 3, p. 1185-1200Article in journal (Refereed)
    Abstract [en]

    A central aim of evolutionary genomics is to identify the relative roles that various evolutionary forces have played in generating and shaping genetic variation within and among species. Here we use whole-genome resequencing data to characterize and compare genome-wide patterns of nucleotide polymorphism, site frequency spectrum, and population-scaled recombination rates in three species of Populus: Populus tremula, P. tremuloides, and P. trichocarpa. We find that P. tremuloides has the highest level of genome-wide variation, skewed allele frequencies, and population-scaled recombination rates, whereas P. trichocarpa harbors the lowest. Our findings highlight multiple lines of evidence suggesting that natural selection, due to both purifying and positive selection, has widely shaped patterns of nucleotide polymorphism at linked neutral sites in all three species. Differences in effective population sizes and rates of recombination largely explain the disparate magnitudes and signatures of linked selection that we observe among species. The present work provides the first phylogenetic comparative study on a genome-wide scale in forest trees. This information will also improve our ability to understand how various evolutionary forces have interacted to influence genome evolution among related species.

  • 32.
    Wang, Jing
    et al.
    Umea Univ, Dept Ecol & Environm Sci, Umea, SE, Sweden..
    Street, Nathaniel R.
    Umea Univ, Dept Plant Physiol, Umea Plant Sci Ctr, S-90187 Umea, SE, Sweden..
    Scofield, Douglas G.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology. Umea Univ, Dept Ecol & Environm Sci, Umea, SE, Sweden..
    Ingvarsson, Par K.
    Umea Univ, Dept Ecol & Environm Sci, Umea, SE, Sweden..
    Variation in Linked Selection and Recombination Drive Genomic Divergence during Allopatric Speciation of European and American Aspens2016In: Molecular biology and evolution, ISSN 0737-4038, E-ISSN 1537-1719, Vol. 33, no 7, p. 1754-1767Article in journal (Refereed)
    Abstract [en]

    Despite the global economic and ecological importance of forest trees, the genomic basis of differential adaptation and speciation in tree species is still poorly understood. Populus tremula and Populus tremuloides are two of the most widespread tree species in the Northern Hemisphere. Using whole-genome re-sequencing data of 24 P. tremula and 22 P. tremuloides individuals, we find that the two species diverged similar to 2.2-3.1 million years ago, coinciding with the severing of the Bering land bridge and the onset of dramatic climatic oscillations during the Pleistocene. Both species have experienced substantial population expansions following long-term declines after species divergence. We detect widespread and heterogeneous genomic differentiation between species, and in accordance with the expectation of allopatric speciation, coalescent simulations suggest that neutral evolutionary processes can account for most of the observed patterns of genetic differentiation. However, there is an excess of regions exhibiting extreme differentiation relative to those expected under demographic simulations, which is indicative of the action of natural selection. Overall genetic differentiation is negatively associated with recombination rate in both species, providing strong support for a role of linked selection in generating the heterogeneous genomic landscape of differentiation between species. Finally, we identify a number of candidate regions and genes that may have been subject to positive and/or balancing selection during the speciation process.

  • 33. Zuccolo, Andrea
    et al.
    Scofield, Douglas G.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    De Paoli, Emanuele
    Morgante, Michele
    The Ty1-copia LTR retroelement family PARTC is highly conserved in conifers over 200 MY of evolution2015In: Gene, ISSN 0378-1119, E-ISSN 1879-0038, Vol. 568, no 1, p. 89-99Article in journal (Refereed)
    Abstract [en]

    Long Terminal Repeat retroelements (LTR-RTs) are a major component of many plant genomes. Although well studied and described in angiosperms, their features and dynamics are poorly understood in gymnosperms. Representative complete copies of a Ty1-copia element isolate in Picea abies and named PARTC were identified in six other conifer species (Picea glauca, Pinus sylvestris, Pinus taeda, Abies sibirica, Taxus baccata and Juniperus communis) covering more than 200 million years of evolution. Here we characterized the structure of this element, assessed its abundance across conifers, studied the modes and timing of its amplification, and evaluated the degree of conservation of its extant copies at nucleotide level over distant species. We demonstrated that the element is ancient, abundant, widespread and its paralogous copies are present in the genera Picea, Pinus and Abies as an LTR-RT family. The amplification leading to the extant copies of PARTC occurred over long evolutionary times spanning 10 s of MY and mostly took place after the speciation of the conifers analyzed. The level of conservation of PARTC is striking and may be explained by low substitution rates and limited removal mechanisms for LTR-RTs. These PARTC features and dynamics are representative of a more general scenario for LTR-RTs in gymnosperms quite different from that characterizing the vast majority of LTR-RT elements in angiosperms. (C) 2015 Elsevier B.V. All rights reserved.

1 - 33 of 33
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