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  • 1. Bakker, Freek T
    et al.
    Antonelli, Alexandre
    Clarke, Julia A
    Cook, Joseph A
    Edwards, Scott V
    Ericson, Per G P
    Naturhistoriska riksmuseet, Enheten för bioinformatik och genetik.
    Faurby, Søren
    Ferrand, Nuno
    Gelang, Magnus
    Gillespie, Rosemary G
    Irestedt, Martin
    Lundin, Kennet
    Larsson, Ellen
    Matos-Maravi­, Pavel
    Muller, Johannes
    von Proschwitz, Ted
    Roderick, George K
    Schliep, Alexander
    Wahlberg, Niklas
    Wiedenhoeft, John
    Källersjö, Mari
    The Global Museum: natural history collections and the future of evolutionary science and public education2020Inngår i: PeerJ, E-ISSN 2167-8359, ISSN 2167-8359, Vol. 8, artikkel-id e8225Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Natural history museums are unique spaces for interdisciplinary research and educational innovation. Through extensive exhibits and public programming and by hosting rich communities of amateurs, students, and researchers at all stages of their careers, they can provide a place-based window to focus on integration of science and discovery, as well as a locus for community engagement. At the same time, like a synthesis radio telescope, when joined together through emerging digital resources, the global community of museums (the 'Global Museum') is more than the sum of its parts, allowing insights and answers to diverse biological, environmental, and societal questions at the global scale, across eons of time, and spanning vast diversity across the Tree of Life. We argue that, whereas natural history collections and museums began with a focus on describing the diversity and peculiarities of species on Earth, they are now increasingly leveraged in new ways that significantly expand their impact and relevance. These new directions include the possibility to ask new, often interdisciplinary questions in basic and applied science, such as in biomimetic design, and by contributing to solutions to climate change, global health and food security challenges. As institutions, they have long been incubators for cutting-edge research in biology while simultaneously providing core infrastructure for research on present and future societal needs. Here we explore how the intersection between pressing issues in environmental and human health and rapid technological innovation have reinforced the relevance of museum collections. We do this by providing examples as food for thought for both the broader academic community and museum scientists on the evolving role of museums. We also identify challenges to the realization of the full potential of natural history collections and the Global Museum to science and society and discuss the critical need to grow these collections. We then focus on mapping and modelling of museum data (including place-based approaches and discovery), and explore the main projects, platforms and databases enabling this growth. Finally, we aim to improve relevant protocols for the long-term storage of specimens and tissues, ensuring proper connection with tomorrow's technologies and hence further increasing the relevance of natural history museums.

    Fulltekst (pdf)
    fulltext
  • 2.
    Bomfleur, Benjamin
    et al.
    Naturhistoriska riksmuseet, Enheten för paleobiologi. Westfälische Wilhelms-Universität Münster.
    Grimm, Guido
    Department fu¨r Pala¨ontologie, Universita¨t Wien, Wien, Austria.
    McLoughlin, Stephen
    Naturhistoriska riksmuseet, Enheten för paleobiologi.
    The fossil Osmundales (Royal Ferns)—a phylogenetic network analysis, revised taxonomy, and evolutionary classification of anatomically preserved trunks and rhizomes2017Inngår i: PeerJ, E-ISSN 2167-8359, Vol. 5, artikkel-id e3433Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    The Osmundales (Royal Fern order) originated in the late Paleozoic and is the most ancient surviving lineage of leptosporangiate ferns. In contrast to its low diversity today (less than 20 species in six genera), it has the richest fossil record of any extant group of ferns. The structurally preserved trunks and rhizomes alone are referable to more than 100 fossil species that are classified in up to 20 genera, four subfamilies, and two families. This diverse fossil record constitutes an exceptional source of information on the evolutionary history of the group from the Permian to the present. However, inconsistent terminology, varying formats of description, and the general lack of a uniform taxonomic concept renders this wealth of information poorly accessible. To this end, we provide a comprehensive review of the diversity of structural features of osmundalean axes under a standardized, descriptive terminology. A novel morphological character matrix with 45 anatomical characters scored for 15 extant species and for 114 fossil operational units (species or specimens) is analysed using networks in order to establish systematic relationships among fossil and extant Osmundales rooted in axis anatomy. The results lead us to propose an evolutionary classification for fossil Osmundales and a revised, standardized taxonomy for all taxa down to the rank of (sub)genus. We introduce several nomenclatural novelties: (1) a new subfamily Itopsidemoideae (Guaireaceae) is established to contain Itopsidema, Donwelliacaulis, and Tiania; (2) the thamnopteroid genera Zalesskya, Iegosigopteris, and Petcheropteris are all considered synonymous with Thamnopteris; (3) 12 species of Millerocaulis and Ashicaulis are assigned to modern genera (tribe Osmundeae); (4) the hitherto enigmatic Aurealcaulis is identified as an extinct subgenus of Plenasium; and (5) the poorly known Osmundites tuhajkulensis is assigned to Millerocaulis. In addition, we consider Millerocaulis stipabonettiorum a possible member of Palaeosmunda and Millerocaulis estipularis as probably constituting the earliest representative of the (Todea-)Leptopteris lineage (subtribe Todeinae) of modern Osmundoideae.

    Fulltekst (pdf)
    fulltext
  • 3.
    Malm, Tobias
    et al.
    Naturhistoriska riksmuseet, Enheten för zoologi.
    Rota, Jadranka
    Department of Biology, Lund University, Lund, Sweden.
    Chazot, Nicolas
    Department of Biology, Lund University, Lund, Sweden.
    Peña, Carlos
    HipLead, San Francisco, CA, United States of America.
    Wahlberg, Niklas
    Department of Biology, Lund University, Lund, Sweden.
    A simple method for data partitioning based on relative evolutionary rates2018Inngår i: PeerJ, E-ISSN 2167-8359, s. 1-21, artikkel-id 6:e5498Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Background. Multiple studies have demonstrated that partitioning of molecular datasets is important in model-based phylogenetic analyses. Commonly, partitioning is done a priori based on some known properties of sequence evolution, e.g. differences in rate of evolution among codon positions of a protein-coding gene. Here we propose a new method for data partitioning based on relative evolutionary rates of the sites in the alignment of the dataset being analysed. The rates are inferred using the previously published Tree Independent Generation of Evolutionary Rates (TIGER), and the partitioning is conducted using our novel python script RatePartitions. We conducted simulations to assess the performance of our new method, and we applied it to eight published multi-locus phylogenetic datasets, representing different taxonomic ranks within the insect order Lepidoptera (butterflies and moths) and one phylogenomic dataset, which included ultra-conserved elements as well as introns.

    Methods. We used TIGER-rates to generate relative evolutionary rates for all sites in the alignments. Then, using RatePartitions, we partitioned the data into partitions based on their relative evolutionary rate. RatePartitions applies a simple formula that ensures a distribution of sites into partitions following the distribution of rates of the characters from the full dataset. This ensures that the invariable sites are placed in a partition with slowly evolving sites, avoiding the pitfalls of previously used methods, such as kmeans. Different partitioning strategies were evaluated using BIC scores as calculated by PartitionFinder.

    Results. Simulations did not highlight any misbehaviour of our partitioning approach, even under difficult parameter conditions or missing data. In all eight phylogenetic datasets, partitioning using TIGER-rates and RatePartitions was significantly better as measured by the BIC scores than other partitioning strategies, such as the commonly used partitioning by gene and codon position. We compared the resulting topologies and node support for these eight datasets as well as for the phylogenomic dataset.

    Discussion. We developed a new method of partitioning phylogenetic datasets without using any prior knowledge (e.g. DNA sequence evolution). This method is entirely based on the properties of the data being analysed and can be applied to DNA sequences (protein-coding, introns, ultra-conserved elements), protein sequences, as well as morphological characters. A likely explanation for why our method performs better than other tested partitioning strategies is that it accounts for the heterogeneity in the data to a much greater extent than when data are simply subdivided based on prior knowledge.

    Fulltekst (pdf)
    fulltext
  • 4.
    Marquina, Daniel
    et al.
    Naturhistoriska riksmuseet, Enheten för bioinformatik och genetik.
    Buczek, Mateusz
    Institute of Environmental Sciences, Faculty of Biology, Jagiellonian University, Krakow, Poland.
    Ronquist, Fredrik
    Naturhistoriska riksmuseet, Enheten för bioinformatik och genetik.
    Łukasik, Piotr
    Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden;Institute of Environmental Sciences, Faculty of Biology, Jagiellonian University, Krakow, Poland.
    The effect of ethanol concentration on the morphological and molecular preservation of insects for biodiversity studies2021Inngår i: PeerJ, E-ISSN 2167-8359, Vol. 9, s. e10799-e10799, artikkel-id e10799Artikkel i tidsskrift (Fagfellevurdert)
  • 5.
    Rowan, John
    et al.
    Department of Anthropology, University at Albany, Albany, New York, United States.
    Lazagabaster, Ignacio A.
    Museum für Naturkunde, Berlin, Germany.
    Campisano, Christopher J.
    Institute of Human Origins, School of Human Evolution and Social Change, Arizona State University, Tempe, Arizona, United States.
    Bibi, Faysal
    Museum für Naturkunde, Berlin, Germany.
    Bobe, René
    Primate Models for Behavioural Evolution, Institute of Cognitive and Evolutionary Anthropology, School of Anthropology, University of Oxford, Oxford, United Kingdom;Gorongosa National Park, Sofala, Mozambique;Interdisciplinary Center for Archaeology and Evolution of Human Behavior (ICArEHB), Universidade do Algarve, Faro, Portugal.
    Boisserie, Jean-Renaud
    Laboratoire Paléontologie Évolution Paléoécosystèmes Paléoprimatologie, Université de Poitiers, Poitiers, France;Centre Français des Etudes Ethiopiennes (CNRS and Ministère des Affaires Etrangères, Ambassade de France, Ethiopia), Addis Ababa, Ethiopia.
    Frost, Stephen R.
    Department of Anthropology, University of Oregon, Eugene, Oregon, United States.
    Getachew, Tomas
    Laboratoire Paléontologie Évolution Paléoécosystèmes Paléoprimatologie, Université de Poitiers, Poitiers, France;Authority for Research and Conservation of Cultural Heritage, Addis Ababa, Ethiopia.
    Gilbert, Christopher C.
    Department of Anthropology, City University of New York, Hunter College, New York, United States;New York Consortium in Evolutionary Primatology (NYCEP), New York, United States.
    Lewis, Margaret E.
    Biology Program, School of Natural Sciences and Mathematics, Stockton University, Galloway, New Jersey, United States.
    Melaku, Sahleselasie
    Authority for Research and Conservation of Cultural Heritage, Addis Ababa, Ethiopia;Paleoanthropology and Paleoenvironment Program, Addis Ababa University, Addis Ababa, Ethiopia.
    Scott, Eric
    Cogstone Resource Management Inc, Orange, California, United States;Department of Biology, California State University, San Bernardino, San Bernardino, California, United States.
    Souron, Antoine
    PACEA, Université Bordeaux, Bordeaux, France.
    Werdelin, Lars
    Naturhistoriska riksmuseet, Enheten för paleobiologi.
    Kimbel, William H.
    Institute of Human Origins, School of Human Evolution and Social Change, Arizona State University, Tempe, Arizona, United States.
    Reed, Kaye E.
    Institute of Human Origins, School of Human Evolution and Social Change, Arizona State University, Tempe, Arizona, United States.
    Early Pleistocene large mammals from Maka’amitalu, Hadar, lower Awash Valley, Ethiopia2022Inngår i: PeerJ, E-ISSN 2167-8359, Vol. 10, s. e13210-e13210, artikkel-id e13210Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    The Early Pleistocene was a critical time period in the evolution of eastern African

    mammal faunas, but fossil assemblages sampling this interval are poorly known from

    Ethiopia’s Afar Depression. Field work by the Hadar Research Project in the

    Busidima Formation exposures (~2.7–0.8 Ma) of Hadar in the lower Awash Valley,

    resulted in the recovery of an early Homo maxilla (A.L. 666-1) with associated stone

    tools and fauna from the Maka’amitalu basin in the 1990s. These assemblages are

    dated to ~2.35 Ma by the Bouroukie Tuff 3 (BKT-3). Continued work by the Hadar

    Research Project over the last two decades has greatly expanded the faunal collection.

    Here, we provide a comprehensive account of the Maka’amitalu large mammals

    (Artiodactyla, Carnivora, Perissodactyla, Primates, and Proboscidea) and discuss

    their paleoecological and biochronological significance. The size of the Maka’amitalu 

    assemblage is small compared to those from the Hadar Formation (3.45–2.95 Ma)

    and Ledi-Geraru (2.8–2.6 Ma) but includes at least 20 taxa. Bovids, suids, and

    Theropithecus are common in terms of both species richness and abundance, whereas

    carnivorans, equids, and megaherbivores are rare. While the taxonomic composition

    of the Maka’amitalu fauna indicates significant species turnover from the Hadar

    Formation and Ledi-Geraru deposits, turnover seems to have occurred at a constant

    rate through time as taxonomic dissimilarity between adjacent fossil assemblages is

    strongly predicted by their age difference. A similar pattern characterizes functional

    ecological turnover, with only subtle changes in dietary proportions, body size

    proportions, and bovid abundances across the composite lower Awash sequence.

    Biochronological comparisons with other sites in eastern Africa suggest that the taxa

    recovered from the Maka’amitalu are broadly consistent with the reported age of the

    BKT-3 tuff. Considering the age of BKT-3 and biochronology, a range of 2.4–1.9 Ma

    is most likely for the faunal assemblage.

    Fulltekst (pdf)
    fulltext
  • 6. Simeone, Marco C.
    Piredda, Roberta ()
    Imperatori, F. ()
    Avishai, Michael ()
    Grimm, Guido W. ()
    Denk, Thomas
    Naturhistoriska riksmuseet, Enheten för paleobiologi.
    Comparative systematics and phylogeography of Quercus Section Cerris in western Eurasia: inferences from plastid and nuclear DNA variation2018Inngår i: PeerJ, E-ISSN 2167-8359, Vol. 6, nr e5793Artikkel i tidsskrift (Fagfellevurdert)
    Fulltekst (pdf)
    fulltext
  • 7. Simeone, Marco Cosimo
    et al.
    Grimm, Guido W.
    Papini, A.
    Vessella, F.
    Cardoni, S
    Tordoni, E.
    Piredda, R.
    Franc, A.
    Denk, Thomas
    Naturhistoriska riksmuseet, Enheten för paleobiologi.
    Plastome data reveal multiple geographic origins of Quercus Group Ilex.2016Inngår i: PeerJ, E-ISSN 2167-8359, Vol. 4:e, nr 1897, artikkel-id DOI 10.7717/peerj.1897Artikkel i tidsskrift (Fagfellevurdert)
  • 8.
    Stigenberg, Julia
    et al.
    Naturhistoriska riksmuseet, Enheten för zoologi.
    Zhang, Miles
    Sharanowski, Barbara
    Hope Meyer, Jacqueline
    Multilocus phylogeny of the parasitic wasps in the tribe Euphorini (Hymenoptera: Braconidae) with revised generic classifications2018Inngår i: PeerJ, E-ISSN 2167-8359, artikkel-id 6:e4783Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Background. Parasitic wasps in the family Braconidae are important regulators of

    insect pests, particularly in forest and agroecosystems. Within Braconidae, wasps in the

    tribe Euphorini (Euphorinae) attack economically damaging plant bugs (Miridae) that

    are major pests of field and vegetable crops. However, the evolutionary relationships

    of this tribe have been historically problematic. Most generic concepts have been

    based on ambiguous morphological characters which often leads to misidentification,

    complicating their use in biological control.

    Methods. Using a combination of three genes (COI, 28S, and CAD) and 80 taxa

    collected worldwide, we conducted Bayesian inference using MrBayes, and maximum

    likelihood analyses using RAxML and IQ-Tree on individual gene trees as well as the

    concatenated dataset.

    Results. The monophyly of the tribe Euphorini and the two genera Peristenus and

    Leiophron were confirmed using maximum likelihood and Bayesian inference. The subgeneric

    classifications of Leiophron sensu lato were not supported, and the monotypic

    genus Mama was also not supported.

    Discussion. Euphoriella, Euphoriana, Euphorus, and Mama syn. n, have been synonymized

    under Leiophron. Mama mariae syn. n was placed as a junior synonym of

    Leiophron reclinator. The generic concepts of Peristenus and Leiophron were refined to

    reflect the updated phylogeny. Further we discuss the need for revising Euphorini given

    the number of undescribed species within the tribe.

    Fulltekst (pdf)
    Euphorini
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