68 Works

Sequence alignments for ITS, rpl16, and trnL-trnF

Lars Hedenäs
The two data files consist of sequence alignments in FASTA format. The file 'Distichium_alignment_ITS.txt' is the alignment used for the analysis resulting in the network in Fig. 1A in the paper and the file 'Distichium_alignment_3 markers.txt' is the alignment used for the analysis resulting in the network in Fig. 1B. The GenBank numbers corresponding with the sequence numbers can be found in Appendix 1 in the paper.

Differences in decompression of the high-pressure Cycladic Blueschist Unit (Naxos Island, Greece): what can inclusions tell us?

Alexandre Peillod , Jarosław Majka , Uwe Ring , Kirsten Drüppel , Clifford Patten , Andreas Karlsson , Adam Włodek & Elof Tehler
Determining the tectonic evolution and thermal structure of a tectonic unit that experiences a subduction-related pressure temperature (P-T) loop is challenging. Within a single unit, P-T conditions can vary from top to bottom which can be only revealed by detailed petrological work. We present micropetrological data of the middle section of the Cycladic Blueschist Unit (CBU) in Naxos, Greece, which indicate a different P-T loop than the top of the section. In the middle section,...

Phylogenomics of white-eyes, a ‘great speciator,’ reveals Indonesian archipelago as the center of lineage diversity

Chyi Yin Gwee, Kritika Garg, Balaji Chattopadhyay, Keren Sadanandan, Dewi Prawiradilaga, Martin Irestedt, Fu-Min Lei, Luke Bloch, Jessica Lee, Mohammad Irham, Tri Haryoko, Malcolm Soh, Kelvin Peh, Karen Rowe, Teuku Ferasyi, Shaoyuan Wu, Guinevere Wogan, Rauri Bowie & Frank Rheindt
Archipelagoes serve as important ‘natural laboratories’ which facilitate the study of island radiations and contribute to the understanding of evolutionary processes. The white-eye genus Zosterops is a classical example of a ‘great speciator’, comprising c. 100 species from across the Old World, most of them insular. We achieved an extensive geographic DNA sampling of Zosterops by using historical specimens and recently collected samples. Using over 700 genome-wide loci in conjunction with coalescent species tree methods...

Data from: Probing the ecology and climate of the Eocene Southern Ocean with sand tiger sharks Striatolamia macrota

Sora Kim, Sarah Zeichner, Albert Colman, Howie Scher, Jürgen Kriwet & Thomas Mörs
During the Eocene, the Earth climate system transitioned from greenhouse to icehouse conditions. Central to many explanations is the Southern Ocean—where tectonic configurations influenced oceanic gateways, ocean circulation reduced heat transport, and/or greenhouse gas declines prompted glaciation. To date, few studies have explored the implications of this climate transition on high latitude, marine vertebrates. Seymour Island near the Antarctic Peninsula preserves a rich, diverse fossil assemblage in the Tertiary Eocene La Meseta (TELM) Formation (Fm)....

Genomic signatures of rapid adaptive divergence in a tropical montane species

Per Ericson, Martin Irestedt & Yanhua Qu
This dataset contains data from a study described in the paper: Ericson, P.G.P., Irestedt, M., She, H., and Qu, Y. (2021) "Genomic signatures of rapid adaptive divergence in a tropical montane species". Biology Letters (in print). The study investigates allopatric divergence and selection in Archbold’s Bowerbird (Amblyornis papuensis), an iconic bird living in a tropical mountain region in New Guinea, using a novel chromosome-level genome and population genomic comparisons. Our results show that the two...

Data from: Early wasp plucks the flower: disparate extant diversity of sawfly superfamilies (Hymenoptera: 'Symphyta') may reflect asynchronous switching to angiosperm hosts

Tommi Nyman, Renske E. Onstein, Daniele Silvestro, Saskia Wutke, Andreas Taeger, Niklas Wahlberg, Stephan Blank & Tobias Malm
The insect order Hymenoptera originated during the Permian nearly 300 million years ago. Ancestrally herbivorous hymenopteran lineages today make up the paraphyletic suborder 'Symphyta,' which encompasses circa 8200 species with very diverse host-plant associations. We used phylogeny-based statistical analyses to explore drivers of diversity dynamics within the 'Symphyta,' with a particular focus on the hypothesis that diversification of herbivorous insects has been driven by the explosive radiation of angiosperms during and after the Cretaceous. Our...

Arrival dates of male and female willow warblers (Phylloscopus trochilus) to their breeding site in Sweden 1979-2016

Johanna Hedlund, Thord Fransson, Cecilia Kullberg, Jan-Olov Persson & Sven Jakobsson
Protandry is a widespread life-history phenomenon describing how males precede females at the site or state of reproduction. In migratory birds, protandry has important influence on individual fitness, the migratory syndrome and phenological response to climate change. Despite its significance, accurate analyses on the dynamics of protandry using data sets collected at the breeding site, are lacking. Basing our study on records collected daily, spanning a period of 38 years, we aim to investigate protandry...

Bayesian inference of ancestral host-parasite interactions under a phylogenetic model of host repertoire evolution

Mariana P. Braga, Michael J. Landis, Sören Nylin, Niklas Janz & Fredrik Ronquist
Intimate ecological interactions, such as those between parasites and their hosts, may persist over long time spans, coupling the evolutionary histories of the lineages involved. Most methods that reconstruct the coevolutionary history of such interactions make the simplifying assumption that parasites have a single host. Many methods also focus on congruence between host and parasite phylogenies, using cospeciation as the null model. However, there is an increasing body of evidence suggesting that the host ranges...

Ancient horse genomes reveal the timing and extent of dispersals across the Bering Land Bridge

Alisa Vershinina, Peter Heintzman, Duane Froese, Grant Zazula, Molly Cassatt-Johnstone, Love Dalén, Clio Der Sarkissian, Shelby Dunn, Luca Ermini, Cristina Gamba, Pamela Groves, Joshua Kapp, Daniel Mann, Andaine Seguin-Orlando, John Southon, Mathias Stiller, Matthew Wooller, Gennady Baryshnikov, Dmitry Gimranov, Eric Scott, Elizabeth Hall, Susan Hewitson, Irina Kirillova, Pavel Kosintsev, Fedor Shidlovsky … & Beth Shapiro
The Bering Land Bridge (BLB) last connected Eurasia and North America during the Pleistocene. Although the BLB would have enabled transfers of terrestrial biota in both directions, it also acted as an ecological filter whose permeability varied considerably over time. Here we explore the possible impacts of this ecological corridor on genetic diversity within, and connectivity among, populations of a once wide-ranging group, the caballine horses (Equus spp.). Using a panel of 187 mitochondrial and...

A “Dirty” Footprint: Soil macrofauna biodiversity and fertility in Amazonian Dark Earths and adjacent soils

Wilian C. Demetrio, Ana C. Conrado, Agno N. S. Acioli, Alexandre C. Ferreira, Marie L. C. Bartz, Samuel W. James, Elodie Silva, Lilianne S. Maia, Gilvan C. Martins, Rodrigo S. Macedo, David W. G. Stanton, Patrick Lavelle, Elena Velasquez, Anne Zangerlé, Rafaella Barbosa, Sandra C. Tapia‐Coral, Aleksander W. Muniz, Alessandra Santos, Talita Ferreira, Rodrigo F. Segalla, Thibaud Decaëns, Herlon S. Nadolny, Clara P. Peña‐Venegas, Cláudia M. B. F. Maia, Amarildo Pasini … & George G. Brown
Amazonian rainforests once thought to hold an innate pristine wilderness, are increasingly known to have been densely inhabited by populations showing a diverse and complex cultural background prior to European arrival. To what extent these societies impacted their landscape is unclear. Amazonian Dark Earths (ADEs) are fertile soils found throughout the Amazon Basin, created by pre-Columbian societies as a result of more sedentary habits. Much is known of the chemistry of these soils, yet their...

A genome-wide investigation of adaptations related to tool use behaviour in New Caledonian and Hawaiian crows

Nicolas Dussex, Verena E. Kutschera, R. Axel W. Wiberg, Darren Parker, Gavin Hunt, Russell D. Gray, Kim Rutherford, Abe Hideaki, Robert Fleischer, Christian Rutz, Michael G. Ritchie, Jochen B.W. Wolf & Neil J. Gemmell
GFF3 file with protein-coding gne predictions for the C. moneduloides de novo genome assembly (available at the National Center for Biotechnology Information (NCBI); assembly accession number: VRTO00000000), generated using the MAKER2 pipeline.

ITS and nrLSU DNA sequence data from four species of Coreomyces (Laboulbeniomycetes)

Henrik Sundberg, Åsa Kruys, Johannes Bergsten & Stefan Ekman
The genus Coreomyces (Laboulbeniaceae, Laboulbeniomycetes, Ascomycota) includes minute parasites on water boatmen (Corixidae, Hemiptera, Insecta). This taxonomic study is primarily based on freshly sampled corixids infected by Coreomyces from Sweden, although a few samples from Denmark and Turkey were also included. All records were verified using DNA sequence data from the internal transcribed spacer region and large subunit of the nuclear ribosomal DNA repeat region. We recognise four species, two of which are new to...

Data from: Megaphylogeny resolves global patterns of mushroom evolution

Torda Varga, Krisztina Krizsán, Csenge Földi, Bálint Dima, Marisol Sánchez-García, Santiago Sánchez-Ramírez, Gergely J. Szöllősi, János G. Szarkándi, Viktor Papp, László Albert, William Andreopoulos, Claudio Angelini, Vladimír Antonín, Kerrie W. Barry, Neale L. Bougher, Peter Buchanan, Bart Buyck, Viktória Bense, Pam Catcheside, Mansi Chovatia, Jerry Cooper, Wolfgang Dämon, Dennis Desjardin, Péter Finy, József Geml … & László G. Nagy
Mushroom-forming fungi (Agaricomycetes) have the greatest morphological diversity and complexity of any group of fungi. They have radiated into most niches and fulfill diverse roles in the ecosystem, including wood decomposers, pathogens or mycorrhizal mutualists. Despite the importance of mushroom-forming fungi, large-scale patterns of their evolutionary history are poorly known, in part due to the lack of a comprehensive and dated molecular phylogeny. Here, using multigene and genome-based data, we assemble a 5,284-species phylogenetic tree...

Data from: Extinctions, genetic erosion and conservation options for the black rhinoceros (Diceros bicornis)

Yoshan Moodley, Isa-Rita M. Russo, Desiré L. Dalton, Antoinette Kotzé, Shadrack Muya, Patricia Haubensak, Boglárka Bálint, Gopi K. Munimanda, Caroline Deimel, Andrea Setzer, Kara Dicks, Barbara Herzig-Straschil, Daniela C. Kalthoff, Hans R. Siegismund, Jan Robovský, Paul O’Donoghue & Michael W. Bruford
The black rhinoceros is again on the verge of extinction due to unsustainable poaching in its native range. Despite a wide historic distribution, the black rhinoceros was traditionally thought of as depauperate in genetic variation, and with very little known about its evolutionary history. This knowledge gap has hampered conservation efforts because hunting has dramatically reduced the species’ once continuous distribution, leaving five surviving gene pools of unknown genetic affinity. Here we examined the range-wide...

Data from: Three-dimensional preservation of cellular and subcellular structures reveal 1.6 billion-year-old probable crown-group red algae

Stefan Bengtson, Therese Sallstedt, Veneta Belivanova & Martin Whitehouse
The ~1.6 Ga Tirohan Dolomite of the Lower Vindhyan in central India contains phosphatized stromatolitic microbialites. We report from there uniquely well-preserved fossils interpreted as crown-group rhodophytes (red algae). The filamentous form Rafatazmia chitrakootensis n.gen, n.sp. has uniserial rows of large cells and grows through diffusely distributed septation. Each cell has a centrally suspended, conspicuous rhomboidal disk interpreted as a pyrenoid. The septa between the cells have central structures that may represent pit connections and...

Data from: Demographic inference from whole-genome and RAD sequencing data suggests alternating human impacts on goose populations since the last ice age

Jose Martin Pujolar, Love Dalén, Michael M. Hansen & Jesper Madsen
We investigated how population changes and fluctuations in the pink-footed goose might have been affected by climatic and anthropogenic factors. First, genomic data confirmed the existence of two separate populations: western (Iceland) and eastern (Svalbard/Denmark). Second, emographic inference suggests that the species survived the last glacial period as a single ancestral population with a low population size (100-1,000 individuals) that split into the current populations at the end of the Last Glacial Maximum with Iceland...

Data from: Synchrotron X-ray tomographic microscopy of fossil embryos

Philip C. J. Donoghue, Stefan Bengtson, Xi-Ping Dong, Neil J. Gostling, Therese Huldtgren, John A. Cunningham, Chongyu Yin, Zhao Yue, Fan Peng & Marco Stampanoni
Fossilized embryos from the late Neoproterozoic and earliest Phanerozoic have caused much excitement because they preserve the earliest stages of embryology of animals that represent the initial diversification of metazoans. However, the potential of this material has not been fully realized because of reliance on traditional, non-destructive methods that allow analysis of exposed surfaces only, and destructive methods that preserve only a single two-dimensional view of the interior of the specimen. Here, we have applied...

Data from: A total-evidence approach to dating with fossils, applied to the early radiation of the Hymenoptera

Fredrik Ronquist, Seraina Klopfstein, Lars Vilhelmsen, Susanne Schulmeister, Debra L. Murray & Alexandr P. Rasnitsyn
Phylogenies are usually dated by calibrating interior nodes against the fossil record. This relies on indirect methods that, in the worst case, misrepresent the fossil information. Here, we contrast such node dating with an approach that includes fossils along with the extant taxa in a Bayesian total-evidence analysis. As a test case, we focus on the early radiation of the Hymenoptera, mostly documented by poorly preserved impression fossils that are difficult to place phylogenetically. Specifically,...

Small shelly fossils and carbon isotopes from the early Cambrian (Stage 3-4) Mural Formation of western Laurentia

Christian B. Skovsted, Uwe Balthasar, Jakob Vinther & Erik Sperling
The extraordinary window of phosphatised and phosphatic Small Shelly Fossils (SSFs) during the early and middle Cambrian is an important testament to the radiation of biomineralising metazoans. While SSF are well known from most Cambrian palaeocontinents during this time interval, western Laurentia has relatively few SSF faunas. Here we describe a diverse SSF fauna from the early Cambrian (Stage 3-4) Mural Formation at three localities in Alberta and British Columbia, Canada, complemented by carbon isotope...

Messinian vegetation and climate of the intermontane Florina-Ptolemais-Servia Basin, NW Greece: How well do plant fossils reflect past environments?

Johannes Martin Bouchal, Tuncay H. Güner, Dimitrios Velitzelos, Evangelos Velitzelos & Thomas Denk
The late Miocene is marked by pronounced environmental changes and the appearance of strong temperature and precipitation seasonality. Although environmental heterogeneity is to be expected during this time, it is challenging to reconstruct palaeoenvironments using plant fossils. We investigated leaves and dispersed spores/pollen from 6.4–6 Ma strata in the intermontane Florina-Ptolemais-Servia Basin (FPS) of NW Greece. To assess how well plant fossils reflect the actual vegetation of the FPS, we assigned fossil-taxa to biomes providing...

UCE Phylogenomics resolves major relationships among Ectaheteromorph ants (Hymenoptera: Formicidae: Ectatomminae, Heteroponerinae): A new classification for the subfamilies and the description of a new genus

G P Camacho, W Franco, M G Branstetter, M R Pie, J T Longino, T R Schultz & R M Feitosa
Uncovering the evolutionary history of the subfamilies Ectatomminae and Heteroponerinae, or ectaheteromorphs, is key to understanding a major branch of the ant tree of life. Despite their diversity and ecological importance, phylogenetic relationships in the group have not been well explored. One particularly suitable tool for resolving phylogeny is the use of ultraconserved elements (UCEs), which have been shown to be ideal markers at a variety of evolutionary time scales. In the present study, we...

Increasing morphological disparity and decreasing optimality for jaw speed and strength during the radiation of jawed vertebrates

William Deakin, Philip Anderson, Wendy Den Boer, Thomas Smith, Jennifer Hill, Martin Rücklin, Philip Donoghue & Emily Rayfield
The Siluro-Devonian adaptive radiation of jawed vertebrates, which underpins almost all living vertebrate biodiversity, is characterised by the evolutionary innovation of the lower jaw. Multiple lines of evidence have suggested that the jaw evolved from a rostral gill arch, but when the jaw took on a feeding function remains unclear. We quantified the variety of form in the earliest jaws in the fossil record and , from which we generated a range of theoretical morphospacelogies...

Raw data of nine microsatellite read lengths for 655 Coregonus individuals from 18 populations

Thomas Mehner, Stefan Palm, Bo Delling, Juha Karjalainen & Jolanta Kielpinska
The dataset lists the diploid read lengths for nine microsatellites of 655 individuals of Coregonus fishes (Baltic and Siberian ciscoes, C. albula, C. fontanae, C. lucinensis, C. sardinella plus one C. maraena population) from 18 populations in Germany, Sweden, Finland, Poland and Russia. The nine microsatellites are BWF1, BWF2, Cisco126, Cisco157, Cisco90, Cocl23, Sfo23, Sfo8, Str73.

Data from: The fluctuating world of a tundra predator guild: bottom-up constraints overrule top-down species interactions in winter

Marianne Stoessel, Bodil Elmhagen, Mikael Vinka, Peter Hellström & Anders Angerbjörn
Global warming is predicted to change ecosystem functioning and structure in Arctic ecosystems by strengthening top-down species interactions, i.e. predation pressure on small herbivores and interference between predators. Yet, previous research is biased towards the summer season. Due to greater abiotic constraints, Arctic ecosystem characteristics might be more pronounced in winter. Here we test the hypothesis that top-down species interactions prevail over bottom-up effects in Scandinavian mountain tundra (Northern Sweden) where effects of climate warming...

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  • Swedish Museum of Natural History
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