13 Works

Data from: Hidden diversity in diatoms of Kenyan Lake Naivasha: a genetic approach detects temporal variation

Kathleen R. Stoof-Leichsenring, Laura S. Epp, Martin H. Trauth & Ralph Tiedemann
This study provides insights into the morphological and genetic diversity in diatoms occurring in core sediments from tropical lakes in Kenya. We developed a genetic survey technique specific for diatoms utilizing a short region (76-67 bp) of the ribulose-1,5-bisphosphate carboxylase/oxygenase large subunit (rbcL) gene as genetic barcode. Our analyses (i) validated the use of rbcL as a barcoding marker for diatoms, applied to sediment samples, (ii) showed a significant correlation between the results obtained by...

Data from: Islands in the ice: detecting past vegetation on Greenlandic nunataks using historical records and sedimentary ancient DNA meta-barcoding

Tina Jørgensen, Kurt H Kjær, James Haile, Morten Rasmussen, Sanne Boessenkool, Kenneth Andersen, Eric Coissac, Pierre Taberlet, Christian Brochmann, Ludovic Orlando, M. Thomas P. Gilbert & Eske Willerslev
Nunataks are isolated bedrocks protruding through ice sheets. They vary in age, but represent island environments in “oceans” of ice through which organism dispersals and replacements can be studied over time. The J.A.D. Jensen’s Nunataks at the southern Greenland ice sheet are the most isolated nunataks on the northern hemisphere - some 30 km from the nearest biological source. They constitute around 2 km2 of ice-free land that was established in the early Holocene. We...

Data from: A comparative study of ancient sedimentary DNA, pollen and macrofossils from permafrost sediments of northern Siberia reveals long-term vegetational stability

Tina Jørgensen, James Haile, Per Möller, Andrei Andreev, Sanne Boessenkool, Morten Rasmussen, Frank Kienast, Eric Coissac, Pierre Taberlet, Christian Brochmann, Nancy H. Bigelow, Kenneth Andersen, Ludovic Orlando, M. Thomas P. Gilbert & Eske Willerslev
Although ancient DNA from sediments (sedaDNA) has been used to investigate past ecosystems, the approach has never been directly compared to the traditional methods of pollen and macrofossil analysis. We conducted a comparative survey of 18 ancient permafrost samples spanning the Late Pleistocene (46–12.5 thousand years ago), from the Taymyr Peninsula in northern Siberia. The results show that pollen, macrofossils and sedaDNA are complementary rather than overlapping, and in combination reveal more detailed information on...

Data from: Inferring species networks from gene trees in high-polyploid North American and Hawaiian violets (Viola, Violaceae)

Thomas Marcussen, Kjetill S. Jakobsen, Jiří Danihelka, Harvey E. Ballard, Kim Blaxland, Anne K. Brysting & Bengt Oxelman
The phylogenies of allopolyploids take the shape of networks and cannot be adequately represented as bifurcating trees. Especially for high-polyploids (i.e., organisms with more than six sets of nuclear chromosomes), the signatures of gene homoeolog loss, deep coalescence and polyploidy may become confounded, with the result that gene trees may be congruent with more than one species network. Herein, we obtained the most parsimonious species network by objective comparison of competing scenarios involving polyploidization and...

Data from: Blocking human contaminant DNA during PCR allows amplification of rare mammal species from sedimentary ancient DNA

Sanne Boessenkool, Laura S. Epp, James Haile, Eva Bellemain, Mary Edwards, Eric Coissac, Eske Willerslev & Christian Brochmann
Analyses of degraded DNA are typically hampered by contamination, especially when employing universal primers such as commonly used in environmental DNA studies. In addition to false-positive results, the amplification of contaminant DNA may cause false-negative results due to competition, or bias, during the PCR. In this study, we test the utility of human-specific blocking primers in mammal diversity analyses of ancient permafrost samples from Siberia. Using quantitative PCR (qPCR) on human and mammoth DNA we...

Data from: The million-year wait for macroevolutionary bursts

Josef C Uyeda, Thomas F Hansen, Stevan J Arnold & Jason Pienaar
We lack a comprehensive understanding of evolutionary pattern and process because short-term and long-term data have rarely been combined into a single analytical framework. Here we test alternative models of phenotypic evolution using a dataset of unprecedented size and temporal span (nearly 8,000 data points). The data are body-size measurements taken from historical studies, the fossil record, and among-species comparative data representing mammals, squamates, and birds. By analyzing this unusually large dataset, we identify stochastic...

Data from: Interpreting the evolutionary regression: the interplay between observational and biological errors in phylogenetic comparative studies

Thomas F. Hansen & Krzysztof Bartoszek
Regressions of biological variables across species are rarely perfect. Usually there are residual deviations from the estimated model relationship, and such deviations commonly show a pattern of phylogenetic correlations indicating that they have biological causes. We discuss the origins and effects of phylogenetically correlated biological variation in regression studies. In particular, we discuss the interplay of biological deviations with deviations due to observational or measurement errors, which are also important in comparative studies based on...

Data from: Candidate genes for colour and vision exhibit signals of selection across the pied flycatcher (Ficedula hypoleuca) breeding range

Paula K. Lehtonen, Toni Laaksonen, Aleksandr V. Artemyev, Eugen Belskii, Paul R. Berg, Christiaan Both, Laura Buggiotti, Stanislav Bureš, Malcolm D. Burgess, Andrey V. Bushuev, Indrikis Krams, Juan Moreno, Marko Mägi, Andreas Nord, Jaime Potti, Pierre-Alain Ravussin, Glenn Peter Sætre, Paivi Sirkiä, Wolfgang Winkel & Craig R. Primmer
The role of natural selection in shaping adaptive trait differentiation in natural populations has long been recognized. Determining its molecular basis, however, remains a challenge. Here, we search for signals of selection in candidate genes for colour and its perception in a passerine bird. Pied flycatcher plumage varies geographically in both its structural and pigment-based properties. Both characteristics appear to be shaped by selection. A single-locus outlier test revealed two of fourteen loci to exhibit...

Data from: Hybrid speciation in sparrows I: phenotypic intermediacy, genetic admixture and barriers to gene flow

Jo S Hermansen, Stein A Sæther, Thomas Borge, Tore O Elgvin, Elin Hjelle & Glenn-Peter Sætre
Homoploid hybrid speciation is thought to require unusual circumstances to yield reproductive isolation from the parental species, and few examples are known from nature. Here we present genetic evidence for this mode of speciation in birds. Using Bayesian assignment analyses of 751 individuals genotyped for 14 unlinked, nuclear microsatellite loci, we show that the phenotypically intermediate Italian sparrow (Passer italiae) does not form a cluster of its own, but instead exhibits clear admixture (over its...

Data from: Positive feedback between ecological and reproductive character displacement in a young avian hybrid zone

Niclas Vallin, Amber M. Rice, Richard I. Bailey, Arild Husby & Anna Qvarnström
Character displacement can reduce costly interspecific interactions between young species. We investigated the mechanisms behind divergence in three key traits - breeding habitat choice, timing of breeding and plumage coloration - in Ficedula flycatchers. We found that male pied flycatchers became expelled from the preferred deciduous habitat into mixed forest as the superior competitor, collared flycatchers, increased in numbers. The peak in food abundance differs between habitats, and the spatial segregation was paralleled by an...

Data from: Species introduction promotes hybridization and introgression in Coregonus: is there sign of selection against hybrids?

Kimmo K Kahilainen, Kjartan Østbye, Chris Harrod, Takahito Shikano, Tommi Malinen & Juha Merilä
Species introductions are considered one of the major drivers of biodiversity loss via ecological interactions and genetic admixture with local fauna. We examined two well-recognized fish species, native whitefish (Coregonus lavaretus) and introduced vendace (C. albula), as well as their morphological hybrids in a single lake to test for selection against hybrids and backcrosses in the wild. A representative random subsample of 693 individuals (27.8%) was taken from the total catch of coregonids. This subsample...

Data from: Strong and consistent natural selection associated with armour reduction in sticklebacks

Arnaud Le Rouzic, Kjartan Østbye, Tom O. Klepaker, Thomas F. Hansen, Louis Bernatchez, Dolph Schluter & Leif Asbjørn Vøllestad
Measuring the strength of natural selection is tremendously important in evolutionary biology, but remains a challenging task. In this work, we analyse the characteristics of selection for a morphological change (lateral-plate reduction) in the threespine stickleback Gasterosteus aculeatus. Adaptation to freshwater, leading to the reduction or loss of the bony lateral armor, has indeed occurred in parallel on numerous occasions in this species. Completely-plated and low-plated sticklebacks were introduced into a pond, and the phenotypic...

Data from: Diversity patterns of uncultured Haptophytes unravelled by pyrosequencing in Naples Bay

Lucie Bittner, Angélique Gobet, Stéphane Audic, Sarah Romac, Elianne S. Egge, Sébastien Santini, Hiroyuki Ogata, Ian Probert, Bente Edvardsen & Colomban De Vargas
Haptophytes are a key phylum of marine protists, including ~300 described morphospecies and 80 morphogenera. We used 454 pyrosequencing on large subunit ribosomal DNA (LSU rDNA) fragments to assess the diversity from size-fractioned plankton samples collected in the Bay of Naples. One group-specific primer set targeting the LSU rDNA D1/D2 region was designed to amplify Haptophyte sequences from nucleic acid extracts (total DNA or RNA) of two size fractions (0.8–3 or 3–20 μm) and two...

Registration Year

  • 2011
    13

Resource Types

  • Dataset
    13

Affiliations

  • University of Oslo
    13
  • Natural History Museum
    3
  • French National Centre for Scientific Research
    3
  • Lund University
    2
  • University of Gothenburg
    2
  • University of Cologne
    1
  • Oregon State University
    1
  • North-West University
    1
  • Moscow State University
    1
  • Lehigh University
    1